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ABSTRACT Aim Location Taxon Methods Results Main Conclusions Recent literature is unveiling more complex responses of biodiversity to Pleistocenic climatic oscillations than those derived from initial models based solely on southern glacial macrorefugia. Here, we zoom in to delve into the genetic diversity and population structure of Podarcis lusitanicus, a lizard species native to the north‐western Iberian Peninsula.North‐western Iberian Peninsula.Podarcis lusitanicus.Utilising a comprehensive multilocus approach, we explored the species' phylogeography and demographic history at a very fine spatial scale and timeframe. Concurrently, we evaluated both current and historical habitat suitability for the species, linking it to the observed demographic trends. We examined DNA sequences from two mitochondrial (cytb and ND4) and three nuclear genes (ACM4, MC1R and PDC) in 230 specimens collected from 21 populations spanning most of the species' distribution range.Our findings corroborate cytonuclear discordances in Podarcis, with nuclear genes failing to identify the mitochondrial clades in P. lusitanicus. Despite its separation from other Podarcis species approximately 4 million years ago, its diversification occurred much more recently, around 0.4 million years ago, resulting in three monophyletic lineages that are geographically coherent. This pattern suggests that some lineages of P. lusitanicus might have gone extinct after the split from the common ancestor. Pleistocene climatic oscillations profoundly influenced the demographic history of the species. During warmer periods, such as the Last Interglacial, populations expanded and came into secondary contact, whereas during the Last Glacial Maximum, populations contracted and became isolated in multiple micro‐refugia. The subsequent Mid‐Holocene warming facilitated population recovery, range expansion and lineage admixture.This study underscores the intricate interplay between isolation and dispersal at a microscale, driven by Pleistocene climatic fluctuations, which have profoundly shaped the genetic structure and diversity of Iberian terrestrial biodiversity and may remain overlooked by biogeographic studies at coarser scales. [ABSTRACT FROM AUTHOR]

Aim: In northern environments, periods of isolation during Pleistocene glaciations and subsequent recolonization and secondary contact have had a significant influence on contemporary diversity of many species. The recent advent of high‐resolution genomic analyses allows unprecedented power to resolve genomic signatures of such events in northern species. Here, we provide the highest resolution genomic characterization of Atlantic salmon in North America to date to infer glacial refugia and the geographic scales of post‐glacial secondary contact. Location: North America. Taxon: Atlantic salmon, Salmo salar. Methods: Samples were collected for 5455 individuals from 148 populations, encompassing the majority of the Atlantic salmon's native range in North America, from Labrador to Maine. Individuals were genotyped using a 220K single nucleotide polymorphism array aligned to the Atlantic salmon (Salmo salar) genome. Spatial genetic structure (principal component analysis, k‐means clustering, admixture) was evaluated in conjunction with genomic comparisons of these identified lineages to infer the refugia during the last glacial maximum and regions of secondary contact following recolonization. Results: Spatial genomic analyses identified three phylogeographic groups, consistent with the northward recolonization from two southern glacial refugia in North America (a western Maritime lineage and an eastern Newfoundland and Labrador lineage), with subsequent differentiation of the eastern lineage into two separate groups. Secondary contact among these North American groups was observed within the northern Gulf of St. Lawrence, and evidence of trans‐Atlantic secondary contact was detected within the eastern Newfoundland and Labrador lineage. Comparison of groups from insular Newfoundland with those from mainland Labrador suggests genomic regions displaying high differentiation were characterized by elevated European admixture, suggesting a possible role of European secondary contact in population divergence. Main Conclusions: These findings present the first evidence suggesting that genomic diversity in extant North American Atlantic salmon populations has resulted from allopatric isolation in two glacial refugia followed by both regional and trans‐Atlantic recolonization and secondary contact and demonstrate the power of genomic tools to resolve historical drivers of diversity in wild populations. [ABSTRACT FROM AUTHOR]

Aim: Reproductive systems strongly influence plants' evolution and adaption, and the biogeographic pattern of its variation has intrigued biologists and ecologists. Here, to test the impacts of paleoglaciation on plants' reproductive system variation, we compared the geographical pattern and environmental drivers in the proportions of different reproductive systems in Primula in regions affected and unaffected by paleoglaciation. Location: Global. Time Period: Since the Last Glacial Maximum (LGM). Major Taxa Studied: Primula. Methods: Using data on reproductive systems and distributions of 604 Primula taxa around the world and 221 along the elevational gradient of the Himalayas, we demonstrated the global pattern and the elevational pattern in the proportions of homostylous taxa. We employed general linear models to establish the relationship between the proportion of homostylous taxa and environmental variables and hierarchical partitioning to assess the relative contributions of these variables in both regions affected and unaffected by paleoglaciation, respectively. Results: We found a higher proportion of homostylous taxa in regions glaciated during the LGM than those unglaciated, with different latitudinal patterns and climate drivers. The proportion of homostylous taxa showed varying trends across different regions: increasing with latitude and temperature anomaly in glaciated regions while concentrating at lower latitudes with higher winter temperatures in unglaciated regions. Additionally, homostylous taxa were more prevalent at lower elevations in the Himalayas. Main Conclusions: Our study provides the first quantitative evidence for the hypothesis that selfers are more prevailing in regions affected by paleoglaciation facilitated by recolonization via comparing the geographic pattern and drivers in regions affected and unaffected by paleoglaciation. Our findings also reveal the concentrated distribution of homostylous taxa in Primula at low latitudes, which may be the result of population shrinkage caused by heat stress, facing a more severe survival crisis under the circumstances of global warming and increasing human activities. [ABSTRACT FROM AUTHOR]

Aim: Various species distributed in the Alps have their disjunct occurrences in the Carpathians. Fossil evidence for some woodland snails of Alpine distribution suggests that they colonized the Carpathians during the Holocene forest optimum or later. Here, we focus on disjunct Carpathian populations of the rock‐dwelling alpine snail Pyramidula saxatilis. As it occupies very stable habitats, that is, high‐elevation limestone rocks, one can assume its potential survival in Carpathian refugia over the glacial period(s). For comparison, the more widespread and warm‐climate P. pusilla is analysed. Location: Europe. Taxon: Pyramidula saxatilis and P. pusilla. Methods: We analysed the genetic diversity of P. saxatilis and P. pusilla populations across their entire ranges using mitochondrial DNA and nuclear DNA markers. Seven fossil mollusc successions from the area where P. saxatilis occurs in the Carpathians were analysed and dated using the radiocarbon method. Habitat suitability models of both species were calculated for selected time periods since the Last Glacial Maximum. Results: All Carpathian P. saxatilis populations were genetically homogeneous and similar to those from the Eastern Alps. In P. pusilla, we found a genetically distinct lineage in the southern Western Carpathians. Both species were found in three fossil profiles since the Middle Holocene, and in one already in the Late Glacial. Habitat suitability models suggested the fluctuations of suitable conditions in the Carpathians driven by summer precipitation, especially for P. saxatilis. Main Conclusions: Our results suggest that the Carpathian populations of P. saxatilis represent a post‐LGM colonization from the Eastern Alps triggered by climatic changes, mainly by the increase in summer precipitation during the Late Glacial interstadials and Middle Holocene. The evidence for P. pusilla is similar, but also suggests rare long‐term survival in the Carpathian microrefugia. The palaeoecological evidence indicates a possible threat to high‐elevation species from future fluctuations in precipitation regimes. [ABSTRACT FROM AUTHOR]

Aim: How the ability of plants to move towards newly favourable habitats (dispersal limitation) impacts the change of biome distribution and transition under fast climate warming is still debated. Analysing vegetation change in the past may help to clarify the relative importance of underlying ecological processes such as climate, biotic interactions, and dispersal. In this study, we investigated how dispersal limitation affected the distribution of European forests in the last 18,000 years. Location: Southern and Central Europe. Taxon: Spermatophyta. Methods: Using the LPJ‐GM 2.0 model (an extension of LPJ‐GUESS), we simulated European vegetation from the end of the Last Glacial Maximum (18.5 ka) to the current time (0 ka). Using biome reconstructions from pollen data as reference, we compared the performance of two dispersal modes: with no migration constraints or seed limitation (free dispersal mode), and with plant establishment depending on seed dynamics and dispersal (dispersal limitation mode). Results: The model run, including migration processes, was better at capturing the post‐glacial expansion of European temperate forests (and the longer persistence of boreal forests) than the setting assuming free dispersal, especially during periods of rapid warming. This suggests that a number of (temperate) tree taxa experienced delayed occupancy of climatically suitable habitats due to a limited dispersal capacity, i.e., post‐glacial migration lags. Main Conclusions: Our results show that including migration processes in model simulations allows for more realistic reconstructions of forest patterns under rapid climate change, with consequences for future projections of carbon sequestration and climate reconstructions with vegetation feedback, assisted migration and forest conservation. [ABSTRACT FROM AUTHOR]

Aim: Ecological niche‐based models (ENM) frequently rely on bioclimatic variables (BioV) to reconstruct biogeographic scenarios for species evolution, ignoring mechanistic relations. We tested if climatic predictors relevant to species hydric and thermal physiology better proximate distribution patterns and support location of Pleistocene refugia derived from phylogeographic studies. Location: The Western Palaearctic. Taxon: Vipera berus and Zootoca vivipara, two cold‐adapted species. Methods: We used two sets of variables, that is physiologically meaningful climatic variables (PMV) and BioV, in a multi‐algorithm ENM approach, to compare their ability to predict current and Last Glacial Maximum (LGM) species ranges. We estimated current and LGM permafrost extent to address spatially the cold hardiness dissimilarity between both species. Results: PMV explained more accurately the current distribution of these two cold‐adapted species and identified the importance of summer temperature and solar radiation that constrain activity in cold habitats. PMV also provide a better insight than BioV predictors on LGM distribution. By including notably, the permafrost extent, PMV‐based models gave parsimonious putative arrangement and validity of refugia for each clade and subclade in accordance with phylogeographic data. Northern refugia were also identified from 48 to 52° N for V. berus and from 50 to 54° N for Z. vivipara. Main Conclusions: Our hybrid approach based on PMV generated more realistic predictions for both current (biogeographical validation) and past distributions (phylogeographic validation). By combining constraints during the activity period (summer climatic niche) and those inherent to the wintering period (freeze tolerance), we managed to identify glacial refuges in agreement with phylogeographic hypotheses concerning post‐glacial routes and colonization scenarios. [ABSTRACT FROM AUTHOR]

Aim: The response of South American seasonally dry tropical forest (SDTF) and savanna species to the Quaternary climate changes is still poorly understood. Here we use multi‐model inference approach to compare the phylogeography and demographic history of five trumpet tree species (also known as pau‐d'arco) and draw general biogeographical patterns: Handroanthus impetiginosus, H. ochraceus, H. serratifolius, Tabebuia aurea and T. roseoalba. Location: Amazonia, Atlantic Forest, Cerrado and Caatinga ecoregions, South America and Brazil. Taxa: Bignoniaceae, Tabebuia Alliance, trees. Methods: We compiled genetic data, occurrence records and ecological niche modelling (ENM) from published articles. We used coalescent modelling to test patterns of co‐divergence, and analysed niche breadth and overlap and spatial patterns in genetic diversity using quantile regressions. Results: Species showed concordant lineage divergence times in the Pleistocene. Lineage diversification and phylogeographical patterns are more related to species niche breadth than to biome (savanna or SDTF). Differences in genetic diversity among species matches the expected for the demographic scenarios obtained with coalescent simulations and ENMs: species with wider range expansion during the Last Glacial Maximum had higher diversity than species with range retraction or multiple refugia. Main Conclusions: Diversification burst in the Pliocene, and major diversification of lineages during the Pleistocene seems to be a general pattern in SDTF and savannas in the South America. The high number of haplotypes at the Central Brazil, corresponding to the Cerrado ecoregion, highlights the importance of Protected Areas for SDTFs and savannas, highly threatened biomes in Brazil. [ABSTRACT FROM AUTHOR]

Aim: The evolutionary interactions between western spadefoot toads (genus Spea) represent a textbook example of character displacement, facilitated by dietary specialization of one Spea species on fairy shrimp (Anostraca) when all three co‐occur. The aim of this study is to understand the covariation between predator (Spea) and prey (Anostraca) range shifts in response to climate change oscillations, and whether biotic interactions can be used to project species distribution models on different time scales when studying species with dietary specialization. Taxon: Amphibia: Spea spp. and Crustacea: Anostraca. Location: North America. Methods: Using multiple modelling techniques, we first estimated the potential distribution of central and western North American fairy shrimp species (Crustacea: Anostraca) and two western spadefoot toad species (Spea bombifrons and Spea multiplicata). We then created a shrimp species richness map by aggregating individual species estimates. Third, we studied the relationship between the probability of spadefoot toad presence and fairy shrimp species richness during the present and Last Glacial Maximum conditions. Finally, we estimated the strength and direction of the co‐occurrence between spadefoot toads and fairy shrimp sampled at the level of entire predicted range and at the regional level (allopatric and sympatric). Results: First, the same abiotic environmental variables shape spadefoot toad and fairy shrimp species' distributions in central and western North America across time. Second, areas of sympatry of Spea bombifrons and Spea multiplicata correspond with dry conditions and higher shrimp richness. Finally, the spatial patterns of predator–prey co‐occurrence are highly variable across geography, forming a spatial mosaic over the species' ranges. Main Conclusion: Predator–prey relationships form a spatial mosaic across geography and species ranges. Including biotic interactions into species distribution estimates for organisms with dietary specialization is highly recommended. Biotic interactions can be projected across different time frames for organisms with dietary specialization as they are likely conserved. [ABSTRACT FROM AUTHOR]

Aims Location Taxon Methods Results Main Conclusions Glacial retreat at the end of the Pleistocene epoch opened vast expanses of emergent habitat in the northern hemisphere that were colonized by opportunistic taxa. However, species that undergo post‐glacial expansion may have originated from one or several glacial refugia. We inferred the post‐glacial expansion history of the Eastern Red‐backed Salamander (Plethodon cinereus), a fully terrestrial species with a vast distribution despite severe dispersal limitations. Previous studies indicated populations south of the glacial boundary at the eastern and western limits of the distribution were closely related, suggesting either multiple refugia or an extraordinary post‐glacial expansion event.Eastern North America.Plethodon cinereus (Green, 1818), Caudata: Plethodontidae.We collected ddRAD‐seq data from 106 individuals throughout the distribution of P. cinereus. We estimated phylogeographic structure, including finer‐scale structure among the post‐glacial populations. To test the origins and routes of colonization, we used ecological niche modelling, population trees and analyses of directional range expansion.Analyses supported our hypothesis of a southeastern glacial refugium, with northward expansion along the Eastern Seaboard prior to westward invasion into the Great Lakes region, including southwestern expansion into unglaciated areas at the western end of the distribution. However, a distinct subgroup in the northwestern portion of the range raises the possibility of a second refugium near the ice‐free Driftless Area.Based on our results, we hypothesize a southeastern refugium from which most of today's northern populations undertook extensive post‐glacial colonization. Our results indicate a geographically non‐linear colonization history for P. cinereus. [ABSTRACT FROM AUTHOR]

Aim: Patterns of individual variation are key to testing hypotheses about the mechanisms underlying biogeographic patterns. If species distributions are determined by environmental constraints, then populations near range margins may have reduced performance and be adapted to harsher environments. Model organisms are potentially important systems for biogeographical studies, given the available range‐wide natural history collections, and the importance of providing biogeographical context to their genetic and phenotypic diversity. Location: Global. Taxon: Arabidopsis thaliana ('Arabidopsis'). Methods: We fit occurrence records to climate data, and then projected the distribution of Arabidopsis under last glacial maximum, current and future climates. We confronted model predictions with individual performance measured on 2194 herbarium specimens, and we asked whether predicted suitability was associated with life history and genomic variation measured on ~900 natural accessions. Results: The most important climate variables constraining the Arabidopsis distribution were winter cold in northern and high elevation regions and summer heat in southern regions. Herbarium specimens from regions with lower habitat suitability in both northern and southern regions were smaller, supporting the hypothesis that the distribution of Arabidopsis is constrained by climate‐associated factors. Climate anomalies partly explained interannual variation in herbarium specimen size, but these did not closely correspond to local limiting factors identified in the distribution model. Late‐flowering genotypes were absent from the lowest suitability regions, suggesting slower life histories are only viable closer to the centre of the realized niche. We identified glacial refugia farther north than previously recognized, as well as refugia concordant with previous population genetic findings. Lower latitude populations, known to be genetically distinct, are most threatened by future climate change. The recently colonized range of Arabidopsis was well‐predicted by our native‐range model applied to certain regions but not others, suggesting it has colonized novel climates. Main Conclusions: Integration of distribution models with performance data from vast natural history collections is a route forward for testing biogeographical hypotheses about species distributions and their relationship with evolutionary fitness across large scales. [ABSTRACT FROM AUTHOR]

Aim: Contemporary environmental, historical and evolutionary factors are increasingly used to decipher the drivers of spatial patterns of species richness. Evidence of such correlations for Chinese reptiles is scarce and poorly understood. We therefore explored the validity of the environmental capacity, historical climatic stability and diversification rates hypotheses on Chinese lizard richness. Location: Mainland China. Taxon: Squamata: Sauria. Methods: We mapped the distribution ranges of all 237 lizards in mainland China using a combination of different datasets. We used current environmental conditions (ambient energy, environmental productivity, and habitat heterogeneity), historical climate stability indices (long term: since ~3.3 Ma and short term: since the last glacial maximum) and mean tip diversification rates, to test whether current environmental conditions, historical climate change and diversification rates drive contemporary richness patterns of lizards in China. We applied piecewise structural equation models (pSEM) to jointly evaluate our hypotheses, considering direct and indirect effects. Results: Chinese lizards showed strong latitudinal diversity gradients. We found consistent support for contemporary climatic and environmental factors relationships with richness. Richness was also positively correlated with short‐term climatic stability, but less so with long‐term stability. Diversification rates were seldom found to be positively correlated with lizard richness. Main Conclusions: Our results support the environmental capacity and historical climate hypotheses, which link high richness to highly productive warm and stable regions (and low richness to cold and unstable regions). We conclude that post‐speciation dispersal and short‐term climatic oscillations quickly swamp the long‐term signal of diversification rates and climatic fluctuations, creating strong current climate–richness associations. [ABSTRACT FROM AUTHOR]

Aim: Current distributions of widespread North American (NA) species have been shaped by Pleistocene glacial cycles, latitudinal temperature gradients, sharp longitudinal habitat transitions and the vicariant effects of major mountain and river systems that subdivide the continent. Within these transcontinental species, genetic diversity patterns might not conform to established biogeographic breaks compared to more spatially restricted taxa due to intrinsic differences or spatiotemporal differences. In this study, we highlight the effects of these extrinsic variables on genetic structuring by investigating the phylogeographic history of a widespread generalist squamate found throughout NA. Location: North America. Taxon: Common gartersnake, Thamnophis sirtalis. Methods: We evaluate the effects of major river basins and the forest‐grassland transition into the Interior Plains on genetic structure patterns using phylogenetic, spatially informed population structure and demographic analyses of single nucleotide polymorphism data and address range expansion history with ecological niche modelling using locality and historic climate data. Results: We identify four phylogeographic lineages with varying degrees of connectivity between them. We find discordant population structure patterns between sex‐linked and autosomal loci with respect to the relationship between the central NA lineage relative to coastal lineages. We find support for southeast Pleistocene refugia where recent secondary contact occurred during the Last Glacial Maximum and evidence for both northern and southern refugia in western NA. Main Conclusion: Our results provide strong evidence for a Pliocene origin for T. sirtalis in central‐southeastern NA preceding its rapid expansion across the continent prior to middle Pleistocene climate‐mediated lineage formation. We implicate major riverine networks within the Mississippi watershed in likely repeated westward expansion events across the Interior Plains. Finally, we corroborate prior conclusions that phenotypic differences between subspecies do not reflect shared evolutionary history and note that the degree of separation between inferred lineages warrants further investigation before any taxonomic revisions are proposed. [ABSTRACT FROM AUTHOR]

Aim: Knowing a species' response to historical climate shifts helps understanding its perspectives under global warming. We infer the hitherto unresolved postglacial history of Pinus cembra. Using independent evidence from genetic structure and demographic inference of extant populations, and from palaeoecological findings, we derive putative refugia and re‐colonisation routes. Location: European Alps and Carpathians. Taxa: Pinus cembra. Methods: We genotyped nuclear and chloroplast microsatellite markers in nearly 3000 individuals from 147 locations across the entire natural range of P. cembra. Spatial genetic structure (Bayesian modelling) and demographic history (approximate Bayesian computation) were combined with palaeobotanical records (pollen, macrofossils) to infer putative refugial areas during the Last Glacial Maximum (LGM) and re‐colonisation of the current range. Results: We found distinct spatial genetic structure, despite low genetic differentiation even between the two disjunct mountain ranges. Nuclear markers revealed five genetic clusters aligned East–West across the range, while chloroplast haplotype distribution suggested nine clusters. Spatially congruent separation at both marker types highlighted two main genetic lineages in the East and West of the range. Demographic inference supported early separation of these lineages dating back to a previous interstadial or interglacial c. 210,000 years ago. Differentiation into five biologically meaningful genetic clusters likely established during postglacial re‐colonisation. Main Conclusions: Combining genetic and palaeoecological evidence suggests that P. cembra primarily survived the LGM in 'cold period' refugia south of the Central European Alps and near the Carpathians, from where it expanded during the Late Glacial into its current Holocene 'warm period' refugia. This colonisation history has led to the distinct East–West structure of five genetic clusters. The two main genetic lineages likely derived from ancient divergence during an interglacial or interstadial. The respective contact zone (Brenner line) matches a main biogeographical break in the European Alps also found in herbaceous alpine plant species. [ABSTRACT FROM AUTHOR]

Aim: Periodic lowering of sea levels and formation of land bridges can reshape phylogeographic patterns of insular biotas. Using archipelago‐wide sampling, we aimed to test if phylogeography of an old‐endemic bat lineage reflected Pleistocene land bridges. Location: Solomon Islands and Papua New Guinea. Taxon: Melonycteris and Nesonycteris bats (Pteropodidae). Methods: We sequenced genome‐wide RADseq data for 49 specimens from 15 islands. We assessed phylogenetic relationships using maximum likelihood in RAxML and quartet‐based methods in SVDquartets, population structure using Structure, and admixture using maximum likelihood methods in TreeMix. We tested for genetic and geographic distance correlations using distance‐based redundancy analyses (dbRDA), identifying best‐fit models using stepwise model selection. Results: Phylogenetic analyses identified five Nesonycteris clades corresponding to Greater Bukida, Guadalcanal, Makira, Malaita and New Georgia group. Makira samples were sister to remaining Nesonycteris. Structure identified four populations: New Ireland Melonycteris melanops; and Nesonycteris from Greater Bukida (including Guadalcanal); Malaita and Makira; and New Georgia group. Genetic backgrounds of Mono, Ngella and Guadalcanal separated from remaining Greater Bukida islands. Makira and Malaita separated into two populations. New Georgia group lacked structure, and genetic and geographic distances were not correlated. The best‐fit geographic distance models for Nesonycteris and a Greater Bukida subset were least shore‐to‐shore distance; and Euclidean and least‐cost distances respectively. Main Conclusions: Influences of modern and Pleistocene island isolation and connectivity were evident in the overall Phylogeography of Nesonycteris. The lack of structure or geographic distance correlations within the New Georgia group indicated all islands were interconnected during the Last Glacial Maximum or contemporary oceanic divides are ineffective barriers. Conversely, genetic divergence across Greater Bukida islands reflected land‐bridge constrained dispersal. A Makira clade sister to all Nesonycteris possibly indicates an origin on Makira. Alternately it reflects Makira's long‐isolated geographic status, as similar results exist for a range of taxa. [ABSTRACT FROM AUTHOR]

Aim: Understanding how past geological and climatic events could have generated intraspecific genetic variation at different temporal and spatial scales in the Neotropics requires a model encompassing distinct ecoregions. Because Anura species have their evolutionary history affected by climate and environmental changing, it is a suitable model to investigate the signatures of Neotropical historical events in species populations. Here we used a treefrog species to test hypotheses associated with tectonic, eustatic and climatic events along with isolation‐by‐environment and isolation‐by‐distance spatial patterns in genetic diversity. Taxon: Scinax squalirostris (Lutz, 1925), Anura: Hylidae. Location: Atlantic Forest, Cerrado, Chaco, Uruguayan Savanna and Pampas ecoregions in South America. Methods: We sequenced nuclear and mitochondrial data from 219 individuals of S. squalirostris sampled at 26 locations in South America. We performed statistical phylogeographic analyses and reconstruction of spatiotemporal dispersal dynamics. Ecological niche modelling was conducted to predict spatial changes in environmental suitability from the Last Glacial Maximum to the Holocene and present day. Results: We recovered a significant phylogeographic break roughly dated back to the Miocene (~7.6 Ma), coinciding with the retraction of marine incursions in the Paraná basin. Most dispersal events occurred in cooler periods of the Pliocene–Pleistocene transition. The spatial pattern in genetic diversity was not correlated with geographical distance or environmental variables. Main Conclusions Scinax squalirostris had a quasi‐stable distribution through time. Neogene–Quaternary tectonic, eustatic and climatic events drove the demographic history and dispersal dynamics of species, with a phylogeographical break dated to the Miocene coinciding with retractions of marine incursions in the Paraná basin. Lineage dispersal spread from the southern Atlantic Forest and retrieved gene flow signals congruent with the cold periods of the Pliocene and Pleistocene. [ABSTRACT FROM AUTHOR]

Aims: Quaternary climate changes dramatically affected species' distributions and thus impacted genetic diversity patterns, particularly for rear‐edge populations. Empirical studies have shown the southernmost (rear‐edge), fragmented populations of Japanese woody plants can harbour high genetic diversity owing to their origin in southern glacial refugia. The effect of Holocene climate warming on rear‐edge populations has, however, rarely been demonstrated. We assessed whether the genetic structure of populations of temperate plants in Japan can be interpreted to show legacies of both icy (Last Glacial Maximum, LGM) and warm (Holocene) climates. Location: Japanese Archipelago. Taxon: Hemerocallis middendorffii (Asphodelaceae). Methods: Population genetic profiles of 737 individuals from 41 populations were analysed to examine population structure and past population demography, using 12 EST‐SSR markers. Present and past suitable habitat areas during the LGM and the Holocene climatic optimum were estimated by ecological niche modelling (ENM). Reconstructed palaeodistribution was combined with population genetics to statistically predict population demographics in relation to past climate changes. Results: Genetic analysis of the 41 populations revealed 6 regional population groups. Four groups widely dominating the northern–central ranges harboured high genetic diversity, whereas genetic divergence within the groups was low. In contrast, the two groups at the southwestern edge were geographically and genetically isolated, and they showed the lowest genetic diversity. The estimated palaeodistributions showed a decrease in the suitable range during the Holocene in comparison with that at the LGM, and only habitat suitability in the Holocene was able to predict the genetic diversity across the range. Main conclusions Populations at the centre of the current distribution harbour high genetic diversity because they remained stable during both cold and warm periods. However, habitat fragmentation and population decline in relation to climate warming during the Holocene resulted in genetic isolation and impoverishment of the rear‐edge populations. [ABSTRACT FROM AUTHOR]

Aim: Environmental drivers and host richness play key roles in affecting herbivore diversity. However, the relative effects of these factors and their effects on lineages characterized by high host specificity are not well known. In this study, we explored the extent to which contemporary climate, Quaternary climate change, habitat heterogeneity and host plants determine the species richness and endemism patterns of herbivorous eriophyoid mites. Location: Global. Taxon: Eriophyoid mites (Acari: Eriophyoidea). Methods: We compiled a dataset comprising 4278 eriophyoid mite species from 22,973 occurrence sites based on a comprehensive search of the published literature and the Global Biodiversity Information Facility (GBIF) as a basis for predicting their global distribution patterns. We measured the association of environmental variables and host plant richness with species richness and endemism of eriophyoid mites through multiple regression analyses using a simultaneous autoregressive (SAR) model, an ordinary least squares (OLS) model and a random forest model. We examined the direct and indirect effects of these environmental variables and the host plant richness on eriophyoid mite diversity using structural equation models (SEMs). Results: The species richness and endemism patterns of eriophyoid mites are concentrated in temperate regions. Contemporary climate, Quaternary climate change, habitat heterogeneity and host plants all significantly affected eriophyoid mite richness, while Quaternary climate change, habitat heterogeneity and host plants contributed to the eriophyoid mite endemism. Abiotic factors indirectly influenced the species richness and endemism of eriophyoid mites, via biotic factors—host plants. Main Conclusions: The species richness and endemism of eriophyoid mites peak in temperate regions, opposite to the patterns of plants and some other organisms. Complex interactions among biotic and abiotic factors shape the current eriophyoid mite species diversity. [ABSTRACT FROM AUTHOR]

Aim: Many species experienced population turnover and local extinction during the Late Pleistocene. In the case of megafauna, it remains challenging to disentangle climate change and the activities of Palaeolithic hunter‐gatherers as the main cause. In contrast, the impact of humans on rodent populations is likely to be negligible. This study investigated which climatic and/or environmental factors affect the population dynamics of the common vole. This temperate rodent is widespread across Europe and was one of the most abundant small mammal species throughout the Late Pleistocene. Location: Europe. Taxon: Common vole (Microtus arvalis). Methods: We generated a dataset comprised of 4.2 kb long fragment of mitochondrial DNA (mtDNA) from 148 ancient and 51 modern specimens sampled from multiple localities across Europe and covering the last 60 thousand years (ka). We used Bayesian inference to reconstruct their phylogenetic relationships and to estimate the age of the specimens that were not directly dated. Results: We estimated the time to the most recent common ancestor of all last glacial and extant common vole lineages to be 90 ka ago and the divergence of the main mtDNA lineages present in extant populations to between 55 and 40 ka ago, which is earlier than most previous estimates. We detected several lineage turnovers in Europe during the period of high climate variability at the end of Marine Isotope Stage 3 (MIS 3; 57–29 ka ago) in addition to those found previously around the Pleistocene/Holocene transition. In contrast, data from the Western Carpathians suggest continuity throughout the Last Glacial Maximum (LGM) even at high latitudes. Main Conclusions: The main factor affecting the common vole populations during the last glacial period was the decrease in open habitat during the interstadials, whereas climate deterioration during the LGM had little impact on population dynamics. This suggests that the rapid environmental change rather than other factors was the major force shaping the histories of the Late Pleistocene faunas. [ABSTRACT FROM AUTHOR]

Aim: Discerning the relative role of geographical and ecological factors in promoting diversification is central to our understanding of the origin and maintenance of biodiversity. We explore the roles of geology and ecological tolerance in the diversification of a group of wingless beetles with low dispersal potential. Location: Western Mediterranean (Iberian Peninsula and North Africa). Taxon: Darkling beetles (Tenebrionidae: Misolampus). Methods: We sequenced nine gene fragments from the mitochondrial and nuclear genomes in all extant Misolampus species to reconstruct their phylogeny, evaluate species boundaries and potential contact zones and estimate divergence times. We modelled species distributions for different time periods to infer ecological preferences and assess the effects of climatic changes since the last interglacial. We used a time‐stratified process‐based biogeographical model to estimate ancestral areas of origin and the evolution of geographical ranges. Results: The palaeoclimatic model projections show contractions of favourable areas during the last interglacial period and mid‐Holocene, and wide stretches of suitable areas during the last glacial maximum. Analyses of ancestral bioclimatic preferences reveal ecological adaptations in isolated lineages within three species. The phylogeny of Misolampus is strongly supported and unveils deep divergences within the six species. Two well‐supported clades were recovered, one distributed in North Africa‐Balearic Islands and another in the Iberian Peninsula. The divergence between the North African and Iberian clades occurred during the early Miocene. Biogeographical analyses infer an ancestral range including the Iberian, Betic and Rifean Plates, with subsequent splits followed by dispersal events. Main conclusions Our results favour a dual role of vicariance and dispersal in driving the historical biogeography and diversification of Misolampus since the early Miocene. We also found evidence for incipient speciation events, underscoring the role of tectonic events and adaptation to local climatic conditions in the diversification of the group. [ABSTRACT FROM AUTHOR]

Aim: Seascape genomic studies aim to understand how environmental variables shape species diversity through genotype–environment associations. Identifying these effects on lecithotrophic larval species that live in intertidal zones is particularly challenging because they are subject to environmental heterogeneity and anthropogenic events. Here, we evaluate how biotic and abiotic features in the Southwest Atlantic littoral zone can affect a high dispersal species' present and historical demography. Location: Brazilian coast, covering more than 3000 km. Taxon: Perinereis ponteni. Methods: We investigated population genetic diversity, connectivity and past dynamics using 23,300 single‐nucleotide polymorphisms (SNPs) generated using genotyping by sequencing. We tested whether environmental abiotic variables could explain the variance found in genotype frequencies using isolation‐by‐environment (IBE) and landscape association approaches. These data, combined with palaeodistribution simulations and oceanic circulation modelling, were used to infer species demographic history and connectivity patterns. Results: Along with high levels of connectivity detected, we found a genetic boundary in the southeastern region of Brazil around Cabo Frio (Rio de Janeiro), and a cline trend for some loci. The palaeodistribution simulations reveal a spatial refuge in the southeast during the Last Glacial Maximum (21 kya), with the expansion of the northern region. We identified 1421 SNPs with frequencies associated with eight environmental variables, most of which were related to temperature—the main environmental factor determining IBE. Main Conclusions: Perinereis ponteni, a polychaete with high gene flow capability responds to biogeographic barriers, highlighting the importance of biotic and abiotic factors in shaping population connectivity. Furthermore, the effect of temperature indicates that future climate change and ocean warming can hugely impact this species. [ABSTRACT FROM AUTHOR]

Aim: Reconstructing species' glacial refugial history and demographic changes over time has greatly relied on comparing inferences from multiple methods while not sufficiently acknowledging their limitations. Here, we aim to integrate as fully as possible complementary methods in ecology, genomics and palaeobiology to improve the reconstruction of species biogeographical history. Location: South‐western Europe. Taxon: Cabrera vole (Microtus cabrerae). Methods: We compiled and mapped the raw fossil data of the Cabrera vole for the Last Glacial Maximum (LGM) and Mid‐Holocene (MH). Alongside, we projected the calibrated ecological niche model (ENM) of the species' current distribution for the LGM, the Younger Dryas and the MH. Complementarily, we used previously obtained Genotyping‐by‐Sequencing data to evaluate the demographic history and range expansion patterns of all four Evolutionarily Significant Units of the species, in an integrative framework. Results: ENM‐inferred refugial areas and genomic modelling consistently supported northern Iberian glacial refugia for the Cabrera vole. This contrasted with the higher fossil abundance of the species in southern and eastern Iberia and southern France from the LGM to the MH. Our results suggest that populations in areas with high fossil abundance went extinct, and were later replaced by northern Iberian populations such that they did not contribute significantly to the current gene pool. Main conclusions Our integrative approach indicates how the range of the Cabrera vole fluctuated in response to environmental change during and following the LGM. Despite methodological limitations, the ENM and genomic approaches produced generally congruent results. Instead, the fossil record may misrepresent the ancestral distribution of this species and should be considered cautiously for ancestral distribution reconstruction, considering that it also reflects the fossilization conditions. Overall, our study supports the idea that integrative approaches are essential to provide an accurate and well‐supported picture of historical refugial areas and range dynamics. [ABSTRACT FROM AUTHOR]

Aim: The proximate ecological and evolutionary processes underlying the high biodiversity of neotropical montane cloud forests are still very poorly understood. Climatic oscillations may have contributed to vicariance and cladogenesis, but also promoted secondary contact and erosion of genetic divergence. Here we tested whether geographical diversification – or its lack thereof – in a complex of arboreal alligator lizards is explained by range shifts during Quaternary climatic oscillations. Location: Pine–oak and cloud forests, central Mexico. Taxon: Abronia taeniata–graminea species complex (Squamata: Anguidae: Gerrhonotinae). Methods: We generated genomic data (ddRADseq) to infer patterns of geographical diversification in the complex, reconstruct its demographic history, estimate the timing of lineage split, and test for the presence of contemporary and/or historical hybridization. We evaluated whether the tempo and mode of diversification (i.e. strict isolation vs. secondary contact with introgression) are explained by the contemporary distribution of suitable habitats and/or range shifts experienced by the complex since the Last Glacial Maximum (LGM), as inferred from environmental niche modelling (ENM). Results: Genomic data supported a marked genetic structure within the complex, and phylogenomic and dating analyses revealed cryptic lineage diversification starting at the onset of the Pleistocene followed by secondary contact with limited introgression. ENM pointed to considerable range expansions of the complex during the LGM and a marked fragmentation and scarce connectivity among contemporary populations, which was supported by genomic‐based demographic reconstructions. Main Conclusions: The geographical diversification of the complex has been moulded by vicariant events promoted by Pleistocene geologic and climatic changes impacting the distribution of their pine–oak and cloud forest habitats. Our data supported a model of divergence with introgression, indicating that pulses of population fragmentation and expansion during the Quaternary have led to multiple opportunities for both allopatric isolation and secondary contact. [ABSTRACT FROM AUTHOR]

Aim: Species' ecological traits influence their spatial genetic patterns. Bedrock preference strongly shapes the phylogeography of alpine plants, but its interactions with other ecological traits have rarely been disentangled. Here, we explore whether dispersal ability and degree of habitat specialization account for divergent postglacial expansion patterns of high‐elevation plants in spite of similar bedrock preference. Location: The Pyrenees, southwestern Europe. Taxon: Cirsium glabrum (Asteraceae), Salix pyrenaica (Salicaceae) and Silene borderei (Caryophyllaceae). Methods: Phylogenetic, genetic structure and demographic modelling analyses based on restriction‐site‐associated DNA sequencing (RADseq) data from a range‐wide populational sampling were conducted. Occurrence data and environmental variables were used to construct species distribution models, which were projected under current and Last Glacial Maximum conditions, and were combined with RADseq data to reconstruct the postglacial history of the study species. The degree of habitat specialization of each species was estimated based on the plant communities within which they occur, and their climatic niche breadth. Results: Salix pyrenaica, which occupies a broad range of habitats, shows a high level of range filling, a blurred genetic structure and an admixture cline between the two main genetic groups, congruent with rapid postglacial expansion. The microsite specialists C. glabrum and S. borderei exhibit a strong genetic structure and low levels of range filling, indicative of slow postglacial expansion. The good disperser C. glabrum shows higher levels of admixture between genetic groups and weaker population differentiation than the poor disperser S. borderei. Main Conclusions: Factors other than bedrock preference have a strong impact on the postglacial range dynamics of high‐elevation species. Habitat specialization plays an important role, allowing species occupying a broad range of habitats to more rapidly expand their ranges after environmental change. The effect of dispersal ability is lower than expected for the study species. [ABSTRACT FROM AUTHOR]

Aim: Major knowledge gaps exist regarding the evolution of arid zone organisms. For freshwater species with high dispersal potential, little is known if historical aridification influenced connectivity across drainage divides and impacted on their divergence and diversification. We tested the hypothesis that the historical aridification of Australia promoted the isolation and influenced the demographic histories and evolutionary divergence of a migratory group of freshwater obligates. Location: Central and eastern Australia; Murray–Darling Basin (MDB), Lake Eyre Basin (LEB), Fitzroy Basin (FIT). Taxon Three lineages of golden perch (Macquaria ambigua), a widespread fishery resource from inland Australia. Methods: We obtained genome‐wide data for golden perch sampled throughout their range. Phylogenetic relationships were reconstructed using maximum likelihood. Species distribution modelling was used to predict contemporary and past distributions for the three lineages and to develop hypotheses regarding their biogeographic and demographic histories. Hypotheses were independently tested using coalescent simulations in fastsimcoal and DIYABC with the genomic dataset. Results: We found evidence for three reciprocally monophyletic lineages that have experienced little to nil genetic connectivity since divergence. Coalescent models suggest that the coastal (FIT) and inland (MDB and LEB) lineages diverged ~103 thousand years ago (ka), followed by the split of MDB and LEB lineages ~58 ka. These timings agree with reductions of large freshwater environments in Australia during the late Pleistocene. Species distribution models show an extreme decrease in habitat during the Last Glacial Maximum ~21 ka, consistent with inferred demographic contractions in coalescent tests. Main conclusions We reveal that aridification of Australia during the late Pleistocene has driven and reinforced the divergence of a migratory freshwater obligate. Our findings are important for informing the conservation management of aquatic organisms under climate change. This work further demonstrates the value of using species distribution modelling to formulate diversification hypotheses and to improve interpretation of coalescent analyses. [ABSTRACT FROM AUTHOR]

Aim: Identifying appropriate conservation measures requires a reasonable understanding of a species' population status, distribution and vulnerability. However, for many species, these variables may not be understood under the context of current conditions alone. Here, we assess the potential role historical changes in climate, sea level and anthropogenic activity may have had on the distribution of one of the world's least‐understood wild cats and identify broader implications for conservation efforts that may not be apparent from just an examination of the species' current distribution. Location: Tropical Asia. Taxon: Fishing cat (Prionailurus viverrinus). Methods: We used a presence‐only ecological niche model and a least‐cost graph‐based connectivity model to characterize the species' bio‐climatic niche and predict changes in suitability and connectivity under current and paleoenvironmental conditions. Results: Fishing cat occurrence was associated with landscapes that were low in elevation and high in topographic wetness and climates that were warm with moderate annual precipitation and moderate seasonal variation in both temperature and precipitation. Since the Last Interglacial, the area predicted to be climatically suitable has ranged from 5.9 million km2 during the Last Glacial Maximum to 2.2 million km2 during the Current Era. Changes in regional connectivity correlated with changes in suitable area for all periods except the Current Era. Relative connectivity of areas affected by past sea level rise was highest in areas with large alluvial plains, emergent coastal areas and deltas. Main conclusions: Our findings suggest that the fishing cat's current distribution and vulnerability can be explained by a synergistic combination of historical climate change, sea level rise, and anthropogenic land‐use change. Changes in suitability and connectivity over time highlight potential core areas that are underrepresented by historical survey efforts. Future survey efforts should include these areas, with an emphasis on quantifying tolerances to anthropogenic disturbances. [ABSTRACT FROM AUTHOR]

Aim: Pleistocene climate shifts were influential in shaping biodiversity patterns for forest‐dependent species. Within southern Africa, palaeoclimatic shifts possibly homogenised subtropical Afromontane forest biodiversity, yet these forests continue to harbour unique diversity. For the three songbird species with different natural histories, we investigated the refugial role of subtropical Afromontane and scarp forests and explored specifically how palaeoclimatic events impacted genetic connectivity among forest patches. Location: Maputaland‐Pondoland‐Albany Biodiversity Hotspot, south‐eastern South Africa. Taxon: Batis capensis, Phylloscopus ruficapilla and Pogonocichla stellata. Methods: Mitochondrial control region sequences and microsatellite data were used to assess genetic diversity and population structure among 406 birds. Demographic change was inferred using Bayesian skyline plots (BSPs), and approximate Bayesian computations (ABCs) were used to identify gene flow trends among putative refugia. Environmental niche models (ENMs) were used to infer past occurrence probabilities. Results: Species BSPs supported regional presence predating the Last Glacial Maximum (21 kya) and indicated post‐glacial population expansions. ABC modelling revealed that present‐day gene flow trends emerged largely during the current interglacial (<12 kya), suggesting that thermal maxima promote regional forest expansion. The north‐eastern source of gene flow in all the three species suggested a post‐glacial influx from refugia further north, while southern scarp forests sustained secondary source populations for B. capensis and P. ruficapilla. High gene flow signatures from south‐western forests in B. capensis and especially P. stellata alluded to hidden source populations in the under‐surveyed southern Afrotemperate forests—the southernmost Afromontane forest bloc. ENMs corroborated both scarp and southern Afrotemperate forests as glacial refugia and demonstrated persistent regional population presence over the past 120 kya. Main Conclusions: The population genetics and palaeodistribution of the three bird species indicate their regional persistence throughout the late Pleistocene, suggesting that Afromontane and scarp forests of south‐eastern South Africa served as refugia for subtropical African avian forest biota. [ABSTRACT FROM AUTHOR]

Aims: In many taxa, the latitudinal span of species' geographic ranges are positively correlated with median latitude (the Rapoport effect). This correlation is frequently explained as adaptation to contemporary climate; however, variability in post‐glacial range expansion among species could also explain this observation. We analyse geographic data for North American salamanders to test the potential causes of Rapoport effects. Location: Temperate North America. Taxon: Salamanders (order Caudata). Methods: We tested for a Rapoport effect by estimating correlations between the latitudinal midpoint and latitudinal range among species. Next, we manipulated species' latitudinal ranges by removing post‐glacial habitat and assessing the impact of species demonstrating post‐glacial range expansion in forming a Rapoport effect. We built ecological niche models for species found south of the Wisconsin Ice Sheet during the Last Glacial Maximum and transferred these models to post‐glacial areas. If dispersal is important in forming a Rapoport effect, then some species may tolerate northern climates but have not expanded northward as a result of variation in geographic access to post‐glacial habitats. We created binary ecological niche models by thresholding using the equal sensitivity and specificity value. Results: We recovered a Rapoport effect that was robust to the null models we tested. Analyses that manipulated ranges and species pools supported a role for variation in post‐glacial range expansion among species, especially for eastern North America. Results from transferring ecological niche models indicated that species have suitable habitat north of their range limit. Main conclusions: Variation in post‐glacial range expansion is important in shaping geographic range size clines among species in areas where climates changed rapidly, though we also found support for the climatic variability hypothesis. Post‐glacial colonization and range expansion likely plays an important role in forming latitudinal biodiversity gradients in northern taxa. While ecophysiology and biotic interactions have been emphasized as important contributors to diversity gradients, our study indicates that post‐glacial colonization also plays a key role in forming latitudinal gradients. [ABSTRACT FROM AUTHOR]

Aim: Understanding how natural populations respond to climatic shifts is a fundamental goal of biological research in a fast‐changing world. The Southern Ocean represents a fascinating system for assessing large‐scale climate‐driven biological change, as it contains extremely isolated island groups within a predominantly westerly, circumpolar wind and current system. Blue‐eyed shags represent a paradoxical seabird radiation—a circumpolar distribution implies strong dispersal capacity yet their species‐rich nature suggests local adaptation and isolation. Here we attempt to resolve this paradox in light of the history of repeated cycles of climate change in the Southern Ocean. Location: Southern Ocean. Taxa: 16 species and subspecies of blue‐eyed shags (Phalacrocoracidae; Leucocarbo spp.). Methods: We use mitochondrial and nuclear sequence data from individuals across the geographical range of the genus to conduct the first comprehensive, time‐calibrated phylogenetic analyses and ancestral‐range biogeographical reconstructions of the blue‐eyed shags. Results: The origins of many island‐endemic lineages are remarkably recent, consistent with a recent high‐latitude circumpolar radiation in the Pliocene or Early Pleistocene. This recent sub‐Antarctic expansion contrasts with significantly deeper lineages detected in South America and, to a lesser extent, New Zealand. These regions, particularly South America, acted as glacial refugia and sources for multiple waves of post‐glacial dispersal. Main conclusions: The blue‐eyed shag paradox is resolved, with at least two waves of dispersal, linked to interglacial cycles, explaining the current distribution and diversity. Descendants of a Pliocene or Early Pleistocene wave of dispersal out of South America survive in the New Zealand region. In contrast, taxa distributed on sub‐Antarctic islands originated much later, possibly since the Last Glacial Maximum. Blue‐eyed shags therefore represent a powerful model system—comprising several natural replicates—for studying the early stages of founder‐event speciation and adaptation in a Southern‐Ocean bird group. [ABSTRACT FROM AUTHOR]

Aim: Range shifts are a key process that determine species distributions and genetic patterns. A previous investigation reported that Juglans cinerea (butternut) has lower genetic diversity at higher latitudes, hypothesized to be the result of range shifts following the last glacial period. However, genetic patterns can also be impacted by modern ecogeographical conditions. Therefore, we re‐investigate the genetic patterns of butternut with additional northern population sampling, hindcasted species distribution models and fossil pollen records to clarify the impact of glaciation on butternut. Location: Eastern North America. Taxon: Juglans cinerea (L., Juglandaceae) (butternut). Methods: Using 11 microsatellites, we examined range‐wide spatial patterns of genetic diversity (allelic richness, heterozygosity, FST) for 1004 previously studied butternut individuals and an additional 757 samples. We constructed hindcast species distribution models and mapped fossil pollen records to evaluate habitat suitability and evidence of species' presence throughout space and time. Results: Contrary to previous work on butternut, we found that genetic diversity increased with distance to range edge, and previously observed latitudinal clines in diversity were likely due to a few outlier populations. Populations in New Brunswick, Canada were genetically distinct from other populations. At the Last Glacial Maximum, pollen records demonstrate butternut likely persisted near the glacial margin, and hindcast species distribution models identified suitable habitat in the southern United States and near Nova Scotia. Main conclusions: Genetic patterns in butternut may be shaped by both glaciation and modern environmental conditions. Pollen records and hindcast species distribution models combined with genetic distinctiveness in New Brunswick suggest that butternut may have persisted in cryptic northern refugia. We suggest that thorough sampling across a species range and evaluating multiple lines of evidence are essential to understanding past species movements. [ABSTRACT FROM AUTHOR]

Aim: Drivers of extant population genetic structure include past climate‐driven range shifts and vicariant events, as well as gene flow mediated by dispersal and habitat continuity. Their integration as alternative or complementary drivers is often missing or incomplete, potentially overlooking relevant processes and time scales. Here we ask whether it is the imprint of past range shifts or habitat connectivity driven by oceanographic transport that best explain genetic structure in a poorly understood model, a forest‐forming African kelp. Location: Southwestern coast of Africa (Benguela current region). Taxon Laminaria pallida. Methods: We estimated genetic variability along the species distributional range using 14 microsatellite markers. This genetic variability was compared to estimates of past range shifts derived from species distribution modelling for the Last Glacial Maximum (LGM), the mid‐Holocene (MH) and the present, and estimates of habitat connectivity derived from oceanographic biophysical modelling. Results: The species is structured in two clusters, a southern cluster with much richer (allelic richness A: 10.40 ± 0.33) and unique (private alleles PA: 56.69 ± 4.05) genetic diversity, and a northern cluster (A: 4.75 ± 0.17; PA: 6.70 ± 1.45). These clusters matched well‐known biogeographical regions and their transition coincided with a dispersal barrier formed by upwelled offshore transport. No major range shifts or vicariant events were hindcasted along the present range, suggesting population stability from the LGM to the present. Main conclusions: Habitat connectivity, rather than past range shifts, explains the extant population structure. Future environmental requirements of the species along the Benguela upwelling system are projected to persist or even intensify, likely preserving the observed genetic patterns for the years to come. Yet, the differentiation and endemicity between clusters, and the isolation structured by the regional oceanography, implies high conservation value for genetic biodiversity, and even more if considering the ecological, social and economic services provided by kelp forests. [ABSTRACT FROM AUTHOR]

Aim: Mammalian carnivores are among the best studied groups in terms of evolutionary history. However, the effects of species interactions in shaping community assemblages remain poorly understood. We hypothesize that indirect interactions via ecological trait filtering play a key role in structuring carnivoran assemblages, mediate coexistence and thus should show high functional diversity (FD) in space and time at continental scales. Location: The Americas. Taxon Mammalian carnivores (Mammalia: Carnivora). Methods: We followed a macroecological perspective via ecological network analyses for indirect interactions and assessed the underlying FD across space and from the last interglacial to the present in the Americas. We analysed the potential distributions and six ecological traits of 88 species to establish possible mechanisms that enables species to coexist and the underlying diversity patterns. We compared the empirical results with two null models and two sensitivity analyses. Results: Co‐occurring carnivore species presented ecological segregation driven mainly by a size ratio (SR) relationship, called here the body size spatial anti‐clustering effect. The underlying FD patterns showed low redundancy towards the tropics and the poles during the times evaluated. However, during the last glacial maximum, shifts occurred primarily at high latitudes in North America. This shift affected the SR relationship and therefore changed FD patterns. These local‐to‐continental interactions mediated by the SR are significant from an ecological and biogeographic perspective, suggesting a robust and consistent trend in which carnivore species of similar size have a lower probability of occupying the same area unless they differentiate in other ecological trait spaces. Main conclusions: The SR relationship is potentially a primary mechanism limiting carnivore coexistence, reflecting functional filtering. The SR tends to be conservative across different ecological trait groups and through time and space. We propose that the body‐size spatial anti‐clustering effect can directly measure species' coexistence and mediate FD patterns in the Americas. [ABSTRACT FROM AUTHOR]

Aim: Research in island biogeography has long focused mainly on present‐day island configurations. Recently, there has been an increasing focus on islands' past histories of land connection, shape and size. Moreover, continental islands (=shelf islands) have received less attention than oceanic islands, and species inventories from extremely small islands are lacking in many datasets. We examine the effects of sea‐level rise since the Last Glacial Maximum (LGM) on bird species diversity and composition of tropical shelf islands in Southeast Asia. Location: Sundaland. Taxon: Birds. Methods: We compiled avifaunal island inventories for 94 islands using an exhaustive literature review of historic surveys of larger islands combined with our own comprehensive island surveys from both small and large islands. Using generalised least‐squares models with spatial autocorrelation, we assessed the importance of traditional biogeographical parameters including area, maximum elevation, distance from mainland and geographical isolation, along with post‐LGM effects of change in island area and duration since isolation. We also compared the species composition on similar‐sized shelf islands from two categories—recently submerged and unsubmerged—using non‐metric multidimensional scaling. Results: Post‐LGM effects on species diversity are minimal and insular diversity is instead well explained by present‐day island characteristics, such as area, distance to mainland and proportion of land surrounding an island within a 10 km radius (Cox and Snell Pseudo‐R2 = 0.803). Avifaunal diversity is similar across recently submerged and unsubmerged small shelf islands. Main conclusion: Avifaunal diversity on tropical shelf islands equilibrates rapidly after isolation, indicating that both extinction and immigration rates are high. In particular, a high immigration rate of dispersive species maintains diversity, especially on small islands. Over‐water dispersal is generally restricted to short distances among Sundaic birds. Consequently, the diversity of an island can be maintained by the presence of large or stepping‐stone islands near it. [ABSTRACT FROM AUTHOR]

Aim: To analyse the biogeographic patterns of Temperate Deciduous Forests (TDFs) in Western Eurasia based on different life‐forms and forests layers and explore their relationships with the current climate, Last Glacial Maximum (LGM) climate and topography. Location: Western Eurasia. Taxon: Vascular plants. Methods: We delimited nine regions encompassing the variability of TDFs in Western Eurasia and collected 1000 vegetation plots from each. We deconstructed the plant communities into three layers, tree, shrub and floor. We used (i) generalized linear mixed models (GLMM) to analyse the influence of current climate, historical climate and topography on species richness by accounting for regional effects and (ii) redundancy analysis (RDA) with variance partitioning to describe the variation in life forms along abiotic gradients. The three forest layers were analysed jointly and separately. Results: The Balkans, Alps and Carpathians appeared to be the richest in plant species, whereas the British Isles and the Hyrcanian region were the poorest. Annual temperature range and annual mean temperature were the best predictors of species richness for the whole dataset and for the shrub layer. The tree layer richness was mainly explained by the annual temperature range and by elevation, whereas the forest floor richness was more related to the annual temperature range and the annual mean temperature differences between the LGM and current climate. The current climate was the main predictor of the composition of the whole community, the tree layer and the floor layer, while the shrub layer was also influenced by historical climate. Main conclusions: Our overview of the diversity of temperate deciduous forests in Western Eurasia demonstrates different patterns and drivers across life‐forms and forest layers. While the diversity of trees is mainly linked to current climatic conditions, the shrub layer is also driven by postglacial‐glacial climatic stability, suggesting a different origin from forest trees. [ABSTRACT FROM AUTHOR]

Aim: The Last Glacial Maximum (LGM) remains an enigmatic period in southeast Australia due to the limited spatial and temporal resolution of its palaeoclimatic records. A major feature of the LGM landscape was the existence of the Bassian Land Bridge, joining Tasmania with the mainland of Australia during periods of low sea level, and potentially facilitating increased biotic movement between these regions. To better understand biogeographical changes on the land bridge and in southeast Australia generally during the LGM, we present a 35 ka‐year palaeoecological record from one of the larger islands of Bass Strait. Location: Bass Strait, southeast Australia. Taxon: Eucalyptus, Poaceae, Monotoca, Myriophyllum, Zygnemataceae, Botryococcus, Pediastrum. Methods: Pollen, charcoal, and non‐pollen palynomorphs were analysed in a 1.75‐m sediment core from truwana/Cape Barren Island, Bass Strait, to reconstruct changes in vegetation, fire regimes and lake levels on the Bassian Land Bridge. Results were then compared to existing palaeoenvironmental studies in the region to develop a broader context of the prevailing land bridge environment and the potential influence on biotic dispersals in Australia during the last glacial period. Results: Results suggest a major vegetation shift on the Bassian Land Bridge in response to the establishment of the LGM climate, with grassland expansion at the expense of woodland from ~29–11 ka. Floristic richness, biomass burned and lake levels also markedly decreased through this period, with the driest interval being ~25–18 ka. Dryland herbaceous taxa dispersed between the mainland and Tasmania when the landbridge was fully exposed. Main conclusions: In agreement with previous studies, our results show that the dry grassland that dominated southeast Australia (and Southern Hemisphere mid‐latitude areas) during the LGM also extended across the Bassian Land Bridge. The prevailing environment on the land bridge is likely to have exerted a selective influence on biotic dispersals in Australia during glacial periods. [ABSTRACT FROM AUTHOR]

Aim: During the glacial phases, the Andean slopes of southern South America were covered by ice sheets, causing the isolation of many species in glacial refugia. This work aimed to test the number and putative location of glacial refugia in southern South America and establish the sources, timing and direction of post‐glacial colonization events. Location: Southern South America, Patagonia. Taxon: Olive mouse (Abrothrix olivacea). Methods: Using exome capture, we genotyped 7339 SNPs in 172 specimens of A. olivacea collected at 21 localities distributed across the steppe, grasslands, and forests in the Patagonian‐Fuegian region and seven specimens from two other species of Abrothrix. Based on the effective migration rate, principal component analysis, and admixture composition, we first study the population structure of A. olivacea. The source and direction of colonization events were inferred using the directionality index and standard population genetic analyses. To study the role of the glacial phases, we performed a bayesian demographic analysis to infer divergences times and ancestral population sizes. Results: Population genomic analyses based on SNPs of more than 7000 exons identified three Patagonian genetic clusters: Valdivian forests, continental Magellan forests, and a combination of continental open biomes and Tierra del Fuego. The directionality index supports a single source in northwestern forests, in line with a Valdivian forest refugium, from which the post‐glacial colonization may have started. The effective diversity rate, the onset of population expansions and divergence times also support a Valdivian forest refugium and rule out a separate southern refugium in Tierra del Fuego. Main conclusions: Our results support a coastal refugium located in or near the previously proposed Valdivian refugium and reject in situ differentiation in Tierra del Fuego. More in general, our demographical analysis reveals the role of the Last Glacial Maximum in affecting the population dynamics (i.e., contraction and expansion) of A. olivacea and in fostering the geographical diversification of populations. [ABSTRACT FROM AUTHOR]

Aim: Intraspecific diversity is a significant component of adaptive potential, and thus, it is important to identify the evolutionary processes that have and will continue to shape the molecular diversity of natural populations. This study aims to untangle the possible drivers of intraspecific molecular diversity by testing whether patterns of historical climatic stability or contemporary range position correlate with molecular diversity. Location: South African coastline. Taxa: The cape urchin (Parechinus angulosus), common shore crab (Cyclograpsus punctatus) and granular limpet (Scutellastra granularis). Methods: Species distributions were hindcasted to the Last Glacial Maximum to assess the biogeography of the study species. Linear models were built to compare the relationships between historical climatic stability or contemporary distributional ranges with extant genetic (mtDNA) and genomic (SNP) diversity. Results: We found large differences in the historical ranges among species and time periods. Regions of higher habitat stability corresponded to regions of higher molecular diversity, but historical climatic variability was not a predictor of molecular diversity within linear models. Lower genetic diversity values, and higher genetic differentiation, were detected in edge populations, but this was not consistent across marker type or species. Main conclusions: Both historical and contemporary processes are potentially driving patterns of diversity, but a large portion of the variation in molecular diversity remains unexplained. Our findings suggest that marine species within cool‐temperate bioregions in the Southern Hemisphere may have more complex biogeographic and evolutionary histories than terrestrial taxa and/or coastal species within northern, formerly glaciated regions. [ABSTRACT FROM AUTHOR]

Aim: The effect of eustasy driven by climatic oscillations on species diversification across the East China Sea (ECS) remains unclear. In this study, Machilus thunbergii (红楠, red nanmu in Chinese) was used as a model species to determine whether the ECS acted as either a "species pump" or "species vacuum" during the Pleistocene. Locations: Eastern China, and southern and central Japan. Taxon: Lauraceae. Methods: Ecological niche modelling was employed to predict the potential distribution of M. thunbergii during the Last Glacial Maximum (LGM) and the last interglacial period. Nuclear microsatellite and chloroplast markers were used to reveal the phylogeographic pattern and infer the population history of 33 M. thunbergii populations. Results: The ecological niche models suggested that the ECS provided potentially suitable habitats for M. thunbergii during the LGM. A sharp change in cpDNA haplotypes was found along the eastern China coasts, while microsatellites revealed a clinal pattern for genetic composition from eastern China to central Japan. The divergent lineages formed an admixture on the Zhoushan Archipelago of China and Kyushu Island of Japan. The estimated divergent and admixture times were c. 68 kyr and c. 15 kyr, corresponding to the periods where there were rising sea levels after the MIS4 glaciation and falling sea levels during the LGM, respectively. Main conclusions: Machilus thunbergii probably underwent alternating population isolation during interglacial periods and connection during glacial maxima across the ECS, but such periodicity of isolation and connection seems not to have promoted diversification as suggested by the species pump hypothesis. Incipient divergence has been periodically wiped out due to frequent coalescence, rendering the ECS more like a "species vacuum", particularly for species with relatively long generation lengths. [ABSTRACT FROM AUTHOR]

Aim: The afroalpine sky‐islands present one of the most interesting models to study discrete biogeographic patterns in a terrestrial island system. Here, we performed range‐wide sampling of the afroalpine clade of fine‐leaved Festuca grasses and address a set of hypotheses on its origin and dispersal. We focus on the widespread species F. abyssinica and explore the role of the eastern and western African sky‐islands. Location: Tropical Africa. Taxon: Afroalpine Festuca. Methods: We combine data from field surveys, phylogeography, coalescence‐based dispersal modelling, and environmental niche and dispersal costs analyses to infer patterns of genetic diversity, genealogical relationships, colonization routes and range shifts under two Quaternary climates (current – to represent warm periods; and Last Glacial Maximum (LGM) – to represent cold periods). Results: The westernmost populations in East Africa show higher genetic diversity and higher similarities with the West African populations and the Ethiopian Simen Mountains than with the more closely situated East African populations. Dispersal models and ecological niche predictions of F. abyssinica supported multiple long‐distance dispersals (LDD) among the eastern African sky‐islands, and at least two dispersal events between the two sides of Africa (0.86 Ma and 0.52 Ma), probably facilitated by bridging suitable habitats during the coldest periods of the Pleistocene. Main conclusions: We reconstruct an afroalpine mountain‐hopping dispersal model, with migrations occurring between adjacent sky‐islands in eastern Africa, and through a Central Africa–Sudan pathway connecting afroalpine patches on the two sides of the continent. [ABSTRACT FROM AUTHOR]

Aim: Species with widespread distributions offer excellent opportunities for investigating recent biogeographical patterns across broad scales. Here, we tested the hypothesis that, due to its intermediate geographical location, NW Africa is pivotal in explaining the phylogeographical patterns of taxa with Mediterranean–Macaronesian distributions using a legume species with short generation times. Location: Mediterranean, with a focus on NW Africa and the Canary Islands. Taxon: Pitch trefoil (Bituminaria bituminosa). Methods: We generated genetic data and performed phylogeographical and demographic analyses at two geographical scales: Mediterranean Basin (MB), using plastid sequences (115 individuals), and Macaronesia, using plastid sequences (182 individuals) and 10 nuclear microsatellite loci (220 individuals). We also performed a literature survey focusing on phylogeographical studies of other circum‐Mediterranean taxa. Results: Northwest Africa was identified as a centre of genetic diversity (19 out of 38 haplotypes) and demographic expansion of B. bituminosa in the MB during the Pleistocene. Our literature review revealed two main phylogeographical patterns in widespread species: pre‐Mediterranean evergreen sclerophylls versus Pleistocene facultative‐deciduous (including Bituminaria) taxa, but on average, both functional groups show a similar, large genetic diversity (~40% of haplotypes) in NW Africa. At the Macaronesian scale, we found that Canarian Bituminaria is composed of two genetic sublineages that coexist and hybridize on the central islands and in the mainland Macaronesian enclave (Anti‐Atlas region). Demographic analyses rejected the progression rule as the model of island colonization but strongly suggested that Anti‐Atlas populations are the result of back‐colonization from the easternmost islands before the Last Glacial Maximum (LGM). Conclusions: Bituminaria displays a pattern of Quaternary eastward expansion in the MB that appears to be paralleled by several members of its functional plant group. Thus, our study reveals a previously undescribed dual role of NW Africa in plant biogeography, acting both as a source of species expansion to the rest of the MB and a LGM refugium of plant populations with a Macaronesian island origin. [ABSTRACT FROM AUTHOR]

Aim: The homogenisation of historically isolated gene pools has been recognised as one of the most serious conservation problems in the Antarctic. Lichens are the dominant components of terrestrial biotas in the Antarctic and in high mountain ranges of southern South America. We study the effects of dispersal strategy and migration history on their genetic structure to better understand the importance of these processes and their interplay in shaping population structure as well as their relevance for conservation. Location: Maritime Antarctic and southern South America. Methods: Populations of three fruticose lichen species, Usnea aurantiacoatra, U. antarctica and Cetraria aculeata, were collected in different localities in the Maritime Antarctic and southern South America. Usnea aurantiacoatra reproduces sexually by ascospores, whereas the other two species mostly disperse asexually by symbiotic diaspores. Samples were genotyped at 8–22 microsatellite loci. Different diversity and variance metrics, Bayesian cluster analyses and Discriminant Analysis of Principal Components (DAPC) were used to study population genetic structure. Historical migration patterns between southern South America and the Antarctic were investigated for U. aurantiacoatra and C. aculeata by approximate Bayesian computation (ABC). Results: The two vegetative species display lower levels of genetic diversity than U. aurantiacoatra. Antarctic populations of C. aculeata and South American populations of U. aurantiacoatra display much stronger genetic differentiation than their respective counterparts on the opposite side of the Drake Passage. Usnea antarctica was not found in South America but shows comparably low levels of genetic differentiation in Antarctica as those revealed for U. aurantiacoatra. Phylogeographic histories of lichens in the region differ strongly with recent colonisation in some instances and potential in situ persistence during Last Glacial Maximum (LGM) in others. Patterns of genetic diversity indicate the presence of glacial refugia near Navarino Island (South America) and in the South Shetland Islands. ABC analyses suggest that C. aculeata colonised the Antarctic from Patagonia after the LGM. Results for U. aurantiacoatra are ambiguous, indicating a more complex population history than expressed in the simplified scenarios. Main Conclusions: Mode of propagation affects levels of genetic diversity, but the location of glacial refugia and postglacial colonisation better explains the diversity patterns displayed by each species. We found evidence for glacial in situ survival of U. aurantiacoatra on both sides of the Drake Passage and postglacial colonisation of Antarctica from South America by C. aculeata. Maintaining the strong genetic differentiation of Antarctic populations of C. aculeata requires strict conservation measures, whereas populations of U. aurantiacoatra are exposed to a much lower risk due to their higher diversity and connectivity. [ABSTRACT FROM AUTHOR]

Aim: Although many phylogeographic studies have focused on continental refugia, the roles of islands as refugia have long been overlooked. In this study, we conducted phylogeographic studies of a plant with insular distribution, Microtropis japonica, to elucidate the potential roles of islands as refugia during recent glacial periods. Specifically, we test the hypothesis that two remote groups of Japanese islands (the Izu and Ryukyu Islands) were refugia for M japonica. Location: The Izu and Ryukyu Islands of Japan and their adjacent areas including the Japanese mainland and Taiwan. Taxon: Microtropis japonica (Celastraceae). Methods: A total of 363 individuals were sampled from 44 populations of M japonica. To elucidate population genetic differentiation and demographic change in M japonica, we performed molecular variance and mismatch distribution analyses based on chloroplast DNA (cpDNA) sequence variations and Bayesian clustering and gene flow estimates based on nuclear single‐nucleotide polymorphism (SNP) data. In addition, to examine distribution changes, ecological niche modelling using the maximum entropy method was used to determine suitable habitats existing currently or during the last glacial maximum, using occurrence data and six bioclimatic variables. Results: Both cpDNA and nuclear SNP data showed genetic differentiation between two disjunct regions. However, cpDNA data indicated genetic differentiation within the Ryukyu Islands but not within the Izu Islands, while nuclear SNP data indicated genetic differentiation within both island groups. Ecological niche modelling showed that both the Izu and Ryukyu archipelagos had contained some islands with a climate compatible with modern M japonica climate envelopes despite climate oscillations. Main conclusions: Islands within both the Izu and Ryukyu archipelagos may have supported M japonica populations throughout historical climate oscillations. The current disjunct distribution of M japonica strongly reflects its refugial locations during the last glacial period and the subsequent range expansion. Islands were important refuges, contributing to the modern disjunct distribution of M japonica. [ABSTRACT FROM AUTHOR]

Aim: Understanding patterns and processes of geographic genetic variation within and among closely related species is the essence of phylogeography. Japanese macaques, also called snow monkeys, have been extensively studied, particularly in the fields of sociobiology, ecology and experimental biology; however, our knowledge of their evolutionary history is relatively limited. In this study we aimed to elucidate the geographic patterns of genetic variation in Japanese macaques and the processes that underlie them. Location: Japan. Taxa: Japanese macaque, Macaca fuscata; rhesus macaque, M. mulatta; Taiwanese macaque, M. cyclopis. Methods: Double‐digest restriction site‐associated DNA (RAD) sequencing was used to identify genome‐wide single nucleotide variants. We used fineRADstructure, ADMIXTURE and principal component analyses to estimate the genetic population structure. Phylogenetic relationships were then inferred based on neighbour‐net, neighbour‐joining, maximum likelihood and SVDquartets algorithms. We assessed gene flow using demographic inference and ABBA‐BABA tests, and estimated past distributions during the Last Glacial Maximum (LGM) using ecological niche modelling. Results: Japanese macaques show a sister group relationship with a clade comprising Chinese rhesus, Indian rhesus and Taiwanese macaques. Japanese macaques comprise major north‐eastern and south‐western clades, with a boundary located near central Japan, and gene flow between the north‐eastern and south‐western lineages was detected. Refugia during the LGM were estimated to be distributed in limited areas along the south coasts of the Japanese archipelago. Main conclusions: Phylogeographic variation of Japanese macaques is likely due mainly to northeast–southwest divergence, which resulted from withdrawal into refugia during the glacial period, and subsequent gene flow. [ABSTRACT FROM AUTHOR]

Aim: The evolutionary importance of paleoclimate regimes has been noted in biogeographic studies. However, little is known about how paleoclimate differences shaped the biogeographic pattern and diversification history of the freshwater fauna in important zoogeographical boundary regions. Here, we aim to investigate how past regional climatic differences have shaped the biogeographic history of the inland aquatic fauna in China using an endemic freshwater crab species complex found on both sides of the Qinling Mountains–Huaihe River Line (QHL), a critical ecological boundary in eastern China, as a model system. Location: Eastern China, the Qinling Mountains–Huaihe River Line. Taxon: The Sinopotamonyangtsekiense species complex. Methods: A total of 482 individuals of Sinopotamonyangtsekiense sensu lato were collected from 34 localities throughout its entire distributional range. The phylogeographic analyses of population structure, morphological and genetic variations, and demographic dynamics were made based on multiple mtDNA and nuDNA loci and on morphological traits. Fine‐tuned ecological niche modeling was used to reconstruct the location of climatically suitable areas that existed during the Last Glacial Maximum. Results: The divergence of two freshwater crab lineages across the QHL correlated with significant past variations in monsoon intensity and with the location of multiple refuges. The divergence time was broadly consistent with the timing of the critical paleoclimate transition event in the mid‐Pleistocene (95% HPD, 0.48–1.06 Ma). Each freshwater crab lineage has evolved distinct male genital traits associated with their isolation in areas with different precipitation rates and temperatures in the past. The patterns of crab distribution observed today reflect past contractions of the two lineages in response to glacial and interglacial cycles during the Pleistocene, followed by their subsequent rapid expansion after the Last Glacial Maximum (~15 kya). Main conclusions: Populations of the widespread species Sinopotamonyangtsekiense s.l. experienced a deep division in the past that led to the phylogeographical isolation observed today. The two main drivers of genetic isolation in this taxon were (a) differences in the intensity of the monsoons on each side of the QHL boundary during the mid‐Pleistocene, and (b) isolation of different populations of S. yangtsekiense s.l. in a number of separate refuges during the LGM. [ABSTRACT FROM AUTHOR]

Aim: Exchange of plant lineages between Australia and Southeast Asia has had a substantial impact on the evolution of Australia's northern, tropical flora, with important ramifications for its conservation and biosecurity. Despite this, floristic exchange tracks between northern Australia and Southeast Asia remain poorly understood. To address this, we conducted a molecular phylogeographic case study to identify exchange tracks between Australia and Southeast Asia. Location: India, Southeast Asia, Australia and Pacific islands. Taxon: The widespread tropical monsoonal tree species Aglaia elaeagnoidea (Meliaceae). Methods: We conducted a DArTseq phylogeographic study of 141 herbarium and silica‐dried samples sourced from across the range of A. elaeagnoidea. We analysed 176,331 single nucleotide polymorphisms (SNPs) across 90,456 loci using multivariate, admixture, genetic differentiation and coalescent methods to characterise phylogeographic and phylogenetic patterns. These analyses were considered in the context of an environmental niche model for the last glacial maximum. Results: Two exchange tracks were identified: one from New Guinea to Cape York Peninsula in north‐east Australia, and a second from Timor‐Leste to the Kimberley Plateau of north‐west Australia. The Cape York Peninsula track is contemporary, characterised by ongoing genetic exchange, whereas the Kimberley Plateau track is historic, facilitated by multiple past exposures of the Arafura Shelf during the Pleistocene. Overall, we suggest that phylogeographic patterns of A. elaeagnoidea have resulted from a combination of repeated range expansion and contraction cycles concurrent with Quaternary climate fluctuations and stochastic dispersal events. Main conclusions: This study provides the first molecular phylogeographic evidence for two floristic exchange tracks between northern Australia and Southeast Asia. It also highlights the influence of Quaternary climate fluctuations on the complex biogeography of the region, and supports the idea that the Kimberley Plateau and Cape York Peninsula in northern Australia have separate biogeographic histories. [ABSTRACT FROM AUTHOR]

Aim: Forest fragmentation is a major driver of biodiversity loss causing declines in species richness and functional diversity of biotic communities. Bats are essential components of ecosystems and are useful bio‐indicators of habitat disturbance, yet the response and vulnerability of bats to fragmentation have been poorly studied in Africa. We aim to assess the effects of forest biogeographical history and fragmentation on functional diversity of bats and their functional traits. Location: Eastern Cape and southern KwaZulu‐Natal, South Africa. Taxon: Insectivorous bats. Methods: We surveyed forest‐utilizing bats to derive four functional diversity indices. Generalized linear models were used to assess the response of diversity indices to biogeographical history and fragmentation, represented by forest type and five landscape fragmentation metrics. RLQ and fourth‐corner analysis were used to investigate the interaction of traits with fragmentation metrics and forest type. Results: Pondoland Scarp forests displayed high functional richness, while Eastern Cape Dune forests exhibited high functional divergence yet low functional richness and dispersion. Two fragmentation metrics affected functional diversity dynamically: edge density had a positive effect on functional evenness; and dispersion was negatively affected by river length through forests. Results showed stronger interactions of functional traits with forest type than fragmentation metrics, with filtering effects on body size and wing morphology. Main conclusions: The large‐scale processes related to biogeographical history, and associated forest structure, are important determinants of functional richness, divergence and dispersion of insectivorous bat communities. Scarp forests showed the highest species and functional richness as they experienced less extreme climatic extinction filtering than Mistbelt forests during the Last Glacial Maximum, whereas the low diversity of Eastern Cape Dune forests results from their younger evolutionary history and homogenous vegetation structure. Little is known of the sensitivity of bats to habitat fragmentation in Africa: here, we show larger‐sized insectivorous species; and species exhibiting low wing loading may be more vulnerable to fragmentation. [ABSTRACT FROM AUTHOR]

Aim: Numerous glacial refugia have been hypothesized along North America's North Pacific Coast that may have increased divergence of refugial taxa, leading to elevated endemism and subsequently clustered hybrid zones following deglaciation. The locations and community composition of these ice‐free areas remains controversial, but whole‐genome sequences now enable detailed analysis of the demographic and evolutionary histories of refugial taxa. Here, we use genomic data to test spatial and temporal processes of diversification among martens with respect to the Coastal Refugium Hypothesis, to understand the role of climate cycling in shaping diversity across complex landscapes. Location: North America and North Pacific Coast archipelagos. Taxon: North American martens (Martes). Methods: Short‐read whole‐genome resequencing data were generated for 11 martens: four M. americana, four M. caurina, two hybrids, and one outgroup (Martes zibellina). Sampling was representative of known genetic clades within New World martens, including sampling within insular and continental hybrid zones and along the North Pacific Coast (five island populations). ADMIXTURE, F‐statistics, and D‐statistics (ABBA‐BABA) were used to identify introgression and infer directionality. Heterozygosity densities, estimated via PSMC, were used to characterize historical demography at and below the species level to infer refugial and colonization processes. Results: Forest‐associated Pacific martens (M. caurina) are divided into distinct insular and continental clades consistent with the Coastal Refugium Hypothesis. There was no evidence of introgression on islands that received historical translocations of American pine martens (M. americana), but introgression was detected in two active zones of secondary contact: one insular and one continental. Only early‐generational hybrids were identified across multiple hybrid zones, a pattern consistent with potential genetic swamping of M. caurina by M. americana. Main conclusions: Despite an incomplete fossil record, genomic evidence supports the persistence of forest‐associated martens, likely the insular Pacific marten lineage, along the western edges of the Alexander Archipelago during the Last Glacial Maximum. This discovery informs our understanding of refugial paleoenvironments, critical to interpreting refugial timing, duration, and community composition. Genomic reevaluations of other taxa along North America's North Pacific Coast may yield new and deeper perspectives on the history of refugial forest communities and the role of dynamic climate shifts in shaping high‐latitude diversity across complex insular landscapes. [ABSTRACT FROM AUTHOR]

Aim: Pleistocene (2.58 Ma–11.7 ka) climatic fluctuations have shaped intraspecific genetic patterns worldwide; however, their impact on species in many regions remains unknown. In order to determine the impact of Pleistocene climatic fluctuations on the tropical rain forests of western Ecuador, we explored the evolutionary history of the endemic palm Phytelephas aequatorialis. Location: Western Ecuador, north‐western South America. Taxon: Phytelephas aequatorialis (Arecaceae). Methods: One hundred and seventy‐six nuclear genes were sequenced in 91 individuals for phylogenomic and population structure analyses. The time of divergence between identified genetic lineages was estimated using a coalescent phylogenomic analysis. Palaeoecological niche modelling analyses were performed to determine areas of historical climatic suitability since the Last Glacial Maximum (LGM; 22 ka) that potentially acted as forest refugia during the Pleistocene. A Wilcoxon test and Pearson correlations were used to explore how current levels of genetic diversity, in terms of expected heterozygosity (Hs), have been shaped by several palaeoclimatic and geographic factors. Results: Phylogenomic and population structure analyses revealed two main genetic lineages with a north–south distribution, which diverged 1.14 Ma during the Pleistocene. Two potential Pleistocene refugia were identified, one along the Pacific coast of Ecuador and one in the Andean foothills of south‐western Ecuador. The location of these refugia agrees with the spatial location of the two genetic lineages. Within the Andean foothills, Hs was lower for the southern lineage than for the northern lineage. Hs significantly increased with decreasing latitude across the species as a whole. Main conclusions: Pleistocene climatic fluctuations promoted intraspecific divergence in P. aequatorialis within the rain forests of western Ecuador. The Andean foothills of south‐western Ecuador could be an important area for rain forest evolution because they potentially remained climatically suitable throughout the Pleistocene. Lower genetic diversity in the southern lineage, which apparently remained isolated in the Andean foothills during glacial cycles, adds evidence to the presence of a forest refugium in south‐western Ecuador. The geographic pattern in genetic diversity suggests that P. aequatorialis colonized western Ecuador from the north. This study supports the role of Pleistocene climatic fluctuations in promoting intraspecific divergence, and for the first time, we show their impact west of the Andes. [ABSTRACT FROM AUTHOR]

Aim: Predictions of species' responses to accelerating global climate change require an understanding of historical range shifts. However, large‐scale phylogeographical studies of Eastern North American understorey plant taxa are relatively scarce. Here we employ ecological niche modelling and genetic analyses for inference of optimal pawpaw habitat in the past and future. Location: In all, 26 states in the eastern United States. Taxon: Asimina triloba (L.) Dunal (Annonaceae). Methods: The present‐day niche of Asimina triloba was modelled in Maxent using seven bioclimatic variables, elevation and location data from field samples and herbarium specimens. To model historically optimal habitats, the present‐day model was projected onto rasters of seven bioclimatic variables and elevation representing the last glacial maximum (~22,000 years before present [YBP]) and the mid‐Holocene (~6,000 YBP). Predicted habitat suitability for 2070 was also modelled. Additionally, 62 populations were genotyped with nine nuclear microsatellite loci and statistically analysed. Levels and partitioning of genetic variation within and among populations were estimated within a geographical context. Results: Models indicate that optimal habitat 22,000 YBP was severely restricted to mostly now‐submerged Gulf of Mexico and southeastern US coastlines. By 2070, models suggest that optimal habitat will expand substantially northward relative to the present. Species‐level genetic diversity (HE = 0.765) is high and genetic structure among populations is moderate (GST = 0.202). Structure indicates that there are two population clusters straddling the Appalachian Mountains. Main conclusions: Models suggest that 22,000 YBP A. triloba was restricted to two major refugia in narrow bands of mostly now‐submerged habitat and possibly several small inland refugia. Molecular data are consistent suggesting that the eastern refugia expanded to give rise to the eastern cluster which is characterized by higher genetic diversity. The Gulf of Mexico refugium likely gave rise to populations in the western cluster, which is characterized by lower genetic diversity. [ABSTRACT FROM AUTHOR]

Aim: Phylogeographic studies show how historical and current changes in landscapes shape the geographic distribution of genetic diversity in species of animals and plants. In particular, for the species of the Diagonal of Open Formations (DOF), the compartmentalization of the Central Brazilian Plateau (CBP) during the Tertiary and climatic oscillations during the Quaternary have often been invoked to explain the origin and current patterns of biodiversity. We investigated how landscape changes and climatic oscillations shaped the distribution and diversification history of a widespread South American treefrog. Location: South American Diagonal of Open Formations (DOF) including Caatinga, Cerrado, and Chaco biomes. Taxon: Treefrog Boana raniceps. Methods: We used a multi‐locus dataset from 288 individual frogs collected at 115 localities throughout most of the species' distribution. We used population assignment analysis, species distribution models, historical demography models, approximate Bayesian computation and landscape genetic analyses to test alternative hypotheses of diversification. Results: We found two genetic lineages that diverged during the mid‐Pleistocene with continued gene flow. Approximate Bayesian computation supported a scenario of isolation with migration until the Last Glacial Maximum, followed by more recent population expansion in north‐eastern Brazil and stability at the southwest in South America. Isolation by environment was the best predictor of genetic distance between populations, which is in accordance with their different environmental niches. As Boana raniceps is a lowland species, steep slopes in the CBP likely restrained gene flow enough to sustain population divergence. We found evidence for major range contraction during the Last Glacial Maximum, raising the possibility of synergic action of climate change and the CBP compartmentalization in regulating migration. Main conclusions: Our findings highlight how landscape and climatic changes can shape the diversification of DOF biota. Past climatic fluctuations and environmental resistance due to topography acted in concert, forming a semipermeable barrier to gene flow, promoting intraspecific differentiation in a continentally distributed species. [ABSTRACT FROM AUTHOR]

Aim: Spatio‐temporal changes have likely caused range fragmentation and population isolation, which could have given rise to the observed current intraspecific differentiation in some species. Here, we test several hypotheses on the potential effect of Pleistocene glacial cycles in the diversification of Arctic shorebird species, comparing between different scenarios of fragmentation of the breeding distribution during glacial and interglacial periods. Location: Global. Taxon: Arctic migratory shorebirds. Methods: We performed species distribution models (SDMs) to explore the changes in the breeding and non‐breeding ranges of 69 species between the last glacial maximum (c. 21,000 years ago) and the present. We also included independent evidence from the fossil record and estimations on the potential extension of the tundra during glacial periods to validate the results from the SDMs. We assigned each species to one of four potential scenarios based on fragmentation and potential recolonization patterns of their breeding ranges during glaciations. Results: Our findings show that most of the species with subspecies experienced fragmentation of their ranges during the glacial, the interglacial or both periods. Meanwhile, the majority of the monotypic species maintained their ranges as a continuum. Moreover, the impacts of glacial cycles in the distribution were not homogeneous across the Arctic, and some regions were more prone to the fragmentation of breeding ranges than others. Main conclusions: Our work suggests that Pleistocene climatic cycles drove the diversification of Arctic shorebirds by creating allopatric breeding distributions. While the fragmentation of the breeding ranges occurred mainly during glacial periods, interglacials also played a part in maintaining or establishing newly isolated breeding populations for many species. Furthermore, species' distribution changes varied between different regions and habitats, which determined current shorebird diversity patterns. [ABSTRACT FROM AUTHOR]