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Understanding population connectivity helps inform resource and conservation managers about appropriate boundaries for management units. However, for many species facing recent increases in fishing or environmental pressure, accurate information on population structure is lacking. Reef Bugs (Thenus australiensis), commonly known as Moreton Bay Bugs, are iconic shovel-nosed lobsters in northern Australia and an increasingly important fisheries resource. Around 80% of landings occur in the Queensland East Coast Otter Trawl Fishery (ECOTF) where the first stock assessment of the species is underway. However, knowledge about population structure to inform stock assessment is lacking. We used genome complexity reduction-based sequencing to characterise high-quality Single Nucleotide Polymorphisms (SNPs) used to evaluate population structure among three management zones of the ECOTF. Post-filtering, a total of 3,031 SNPs were used to infer no genetic differences among locations indicating strong genetic population connectivity. The presence of a single panmictic population was further supported by cluster and kinship analyses. Broad-scale genetic connectivity likely results from pelagic larval dispersal due to limited adult movements. Findings of high gene flow among connected populations indicate a single biological stock of T. australiensis on Australia's east coast and will inform future fisheries management initiatives. [ABSTRACT FROM AUTHOR]

In the westernmost Canadian province of British Columbia, fishers (Pekania pennanti) occur in low-elevation forested ecosystems in the central and northern portions of the province, with several substantial mountain ranges and rivers bisecting this distribution. The effect of these geographic features on gene flow and population structuring is unknown and may contribute to fishers differentiating into 2 or more populations within the province. To better understand population structuring within the range of fishers in British Columbia, we collected tissue samples from 491 fishers from throughout the province and evaluated variation of neutral genetic markers using a 385-base pair section of the mitochondrial DNA control region and 13 microsatellite loci. Fishers appeared to be genetically structured as hierarchical stepping-stone populations where an upper hierarchical level of genetic partitioning resulted in 2 populations at the provincial scale, with 3 subpopulations occurring in the central interior region. We observed gene flow of 2 to 5 migrants per generation between the 2 upper populations, which was substantially less than the 90 migrants per generation estimated as needed to maintain genetic homogeneity. This resulted in differentiated upper populations (haplotype F ST = 0.272, microsatellite F ST = 0.049) characterized by relatively low N e (Columbian population = 252, 95% CI = 185 to 332; Boreal population [British Columbia only] = 136, 95% CI = 92 to 234). The consequence of low gene flow and resultant population structuring is that the Columbian population likely receives relatively little genetic and demographic support from other populations and, combined with precipitous recent declines in its numbers, puts this population at heightened conservation risk. As a result, swift and effective actions are needed to conserve this vulnerable population of fishers. [ABSTRACT FROM AUTHOR]

The Cumberland Plateau Salamander, Plethodon kentucki, is a cryptic species with respect to the sympatric Northern Slimy Salamander, Plethodon glutinosus. It was first described by Highton and MacGregor (1983) by using allozyme data. In that description, the authors reported extreme levels of genetic differentiation for a single species with a narrow distribution; however, follow-up studies found patterns of genetic variation that were discordant with the allozyme data. In this paper, we describe patterns of genetic variation within P. kentucki by using an anchored hybrid enrichment dataset of 21 individuals sampled from across its known range. We identified four genetic groups with extensive admixture and isolation by distance. We constructed a population tree by using TreeMix and inferred gene flow between two of the four genetic groups. Finally, we used Bayesian phylogenetics and phylogeography (BPP) in conjunction with the genealogical divergence index (gdi) to test species boundaries within P. kentucki. Although BPP suggested that P. kentucki could be four species, gdi indicated that none of the groups were sufficiently independent to constitute separate species. We conclude that P. kentucki is best recognized as a single species with substantial genetic structure within its limited distribution. [ABSTRACT FROM AUTHOR]

Species are the fundamental unit of biodiversity studies. However, many species complexes are difficult to delimit, especially those characterized by complicated patterns of population structure. Salamanders in the family Plethodontidae often form species by slowly fragmenting across a landscape over space and time. They thus provide many examples of species complexes in which gradual Darwinian evolution has resulted in multiple units of varying degrees of differentiation, including incompletely separated lineages. Herein, we report on a molecular systematic investigation of woodland salamanders in the Plethodon wehrlei group, a group that has recently been split from two species into five species. To quantify patterns of genetic variation, we collected genetic samples from 24 individuals from 20 populations, including all species and representing a carefully selected subset of previous work. From these samples, we obtained genomic data by using anchored hybrid enrichment, resulting in 319 loci averaging 1300 bp in length. Biallelic single-nucleotide polymorphisms were randomly selected from 316 of these loci for some analyses. We examined patterns of genetic structure by using a combination of multivariate statistics and methods based on evolutionary models (such as the Bayesian program STRUCTURE) and found that all of the recognized species formed genetic clusters; however, P. wehrlei and P. punctatus were relatively weakly differentiated and STRUCTURE identified three separate clusters within P. jacksoni. Species trees inferred using the weighted accurate species tree algorithm (wASTRAL), Bayesian phylogenetics and phylogeography (BPP), and TreeMix all recovered the same topology, with P. dixi sister to the other taxa, which included a northern clade (P. wehrlei, P. punctatus, P. pauleyi) and a southern clade (P. jacksoni, with three separate groups). TreeMix only inferred one gene flow event. We evaluated the candidate species by using BPP and the genealogical divergence index (gdi). Although BPP delimited all candidate species with strong support (all posterior probabilities = 1.0), the gdi only strongly supported P. dixi and P. pauleyi, both of which have only been recently described. We discuss the difficult problem of species delimitation in groups that form species via range fragmentation. We also provide a vision for future research, with the aim of better testing and diagnosing the species diversity within the P. wehrlei group. [ABSTRACT FROM AUTHOR]

Geographical barriers like mountain ranges impede genetic exchange among populations, promoting diversification. The effectiveness of these barriers in limiting gene flow varies between lineages due to each species' dispersal modes and capacities. Our understanding of how the Andes orogeny contributes to species diversification comes from well‐studied vertebrates and a few arthropods and plants, neglecting organisms unable to fly or walk long distances. Some arachnids, such as Gasteracantha cancriformis, have been hypothesized to disperse long distances via ballooning (i.e. using their silk to interact with the wind). Yet, we do not know how the environment and geography shape its genetic diversity. Therefore, we tested whether the Andes contributed to the diversification of G. cancriformis acting as an absolute or semi‐permeable barrier to genetic connectivity between populations of this spider at opposite sides of the mountain range. We sampled thousands of loci across the distribution of the species and implemented population genetics, phylogenetic, and landscape genetic analyses. We identified two genetically distinct groups structured by the Central Andes, and a third less structured group in the Northern Andes that shares ancestry with the previous two. This structure is largely explained by the altitude along the Andes, which decreases in some regions, possibly facilitating cross‐Andean dispersal and gene flow. Our findings support that altitude in the Andes plays a major role in structuring populations in South America, but the strength of this barrier can be overcome by organisms with long‐distance dispersal modes together with altitudinal depressions. [ABSTRACT FROM AUTHOR]

Effective dispersal among plant populations is dependent on vector behaviour, landscape features and availability of adequate habitats. To capture landscape feature effects on dispersal, studies must be conducted at scales reflecting single‐generation dispersal events (mesoscale). Many studies are conducted at large scales where genetic differentiation is due to dispersal occurring over multiple generations, making it difficult to interpret the effects of specific landscape features on vector behaviour. Genetic structure at the mesoscale may be determined by ecological and evolutionary processes, such as the consequences of vector behaviour on patterns of gene flow. We used chloroplast haplotypes and nuclear genome SNP surveys to identify landscape features influencing seed and pollen dispersal at a mesoscale within the Rogue River Valley in southern Oregon. We evaluated biotic and abiotic vector behaviour by contrasting two annual species with differing dispersal mechanisms; Achyrachaena mollis (Asteraceae) is a self‐pollinating and anemochoric species, and Plectritis congesta (Caprifoliaceae) is biotically pollinated with barochoric seeds. Using landscape genetics methods, we identified features of the study region that conduct or restrict dispersal. We found chloroplast haplotypes were indicative of historic patterns of gene flow prior to human modification of landscapes. Seed dispersal of A. mollis was best supported by models of isolation by distance, while seed‐driven gene flow of P. congesta was determined by the distribution of preserved natural spaces and quality habitat. Nuclear genetic structure was driven by both pollen and seed dispersal, and both species responded to contemporary landscape changes, such as urban and agricultural conversion, and habitat availability. [ABSTRACT FROM AUTHOR]

Effective population size (Ne) is a particularly useful metric for conservation as it affects genetic drift, inbreeding and adaptive potential within populations. Current guidelines recommend a minimum Ne of 50 and 500 to avoid short‐term inbreeding and to preserve long‐term adaptive potential respectively. However, the extent to which wild populations reach these thresholds globally has not been investigated, nor has the relationship between Ne and human activities. Through a quantitative review, we generated a dataset with 4610 georeferenced Ne estimates from 3829 populations, extracted from 723 articles. These data show that certain taxonomic groups are less likely to meet 50/500 thresholds and are disproportionately impacted by human activities; plant, mammal and amphibian populations had a <54% probability of reaching N̂e = 50 and a <9% probability of reaching N̂e = 500. Populations listed as being of conservation concern according to the IUCN Red List had a smaller median N̂e than unlisted populations, and this was consistent across all taxonomic groups. N̂e was reduced in areas with a greater Global Human Footprint, especially for amphibians, birds and mammals, however relationships varied between taxa. We also highlight several considerations for future works, including the role that gene flow and subpopulation structure plays in the estimation of N̂e in wild populations, and the need for finer‐scale taxonomic analyses. Our findings provide guidance for more specific thresholds based on Ne and help prioritise assessment of populations from taxa most at risk of failing to meet conservation thresholds. [ABSTRACT FROM AUTHOR]

Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which triggered the adaptive radiation of the clade. Within clownfishes, the "skunk complex" is particularly interesting. Besides ecological speciation, interspecific gene flow and hybrid speciation are thought to have shaped the evolution of the group. We investigated the mechanisms characterizing the diversification of this complex. By taking advantage of their disjunct geographical distribution, we obtained whole‐genome data of sympatric and allopatric populations of the three main species of the complex (Amphiprion akallopisos, A. perideraion and A. sandaracinos). We examined population structure, genomic divergence and introgression signals and performed demographic modelling to identify the most realistic diversification scenario. We excluded scenarios of strict isolation or hybrid origin of A. sandaracinos. We discovered moderate gene flow from A. perideraion to the ancestor of A. akallopisos + A. sandaracinos and weak gene flow between the species in the Indo‐Australian Archipelago throughout the diversification of the group. We identified introgressed regions in A. sandaracinos and detected in A. perideraion two large regions of high divergence from the two other species. While we found that gene flow has occurred throughout the species' diversification, we also observed that recent admixture was less pervasive than initially thought, suggesting a role of host repartition or behavioural barriers in maintaining the genetic identity of the species in sympatry. [ABSTRACT FROM AUTHOR]

Animal personality should be highly relevant to recovery of species following habitat restoration, but empirical evaluations remain scarce. In the Chihuahuan Desert of the southwestern United States and globally, grasslands are threatened with shrub encroachment, prompting landscape-scale restoration efforts to remove shrubs and improve habitat for grassland species. We examined the behavioural response of a keystone rodent of grasslands, banner-tailed kangaroo rats, Dipodomys spectabilis , to extensive shrub removal efforts in New Mexico, U.S.A. We captured individuals from replicated restoration and remnant grassland habitats and used standardized behavioural assays to determine whether D. spectabilis exhibits personality and whether it varies between restoration and remnant habitats. We also conducted a movement experiment using artificial shrubs to test whether personality mediates movement choices through shrub cover, which could be a mechanism contributing to the colonization dynamics of restoration sites. We found repeatable differences among individuals for multiple behaviours, including movements, providing evidence of personality. We also documented a syndrome in which bolder and more active individuals moved through movement trials quicker, indicating personality-dependent movement. Dipodomys spectabilis also exhibited personality-dependent movement through artificial shrub cover, suggesting the choice to move through shrublands may depend on personality. This result could have consequences for colonization dynamics of restoration sites if a subset of individuals is more likely to traverse low-quality shrublands and settle in habitats treated for shrub removal. Surprisingly, there was weak divergence in behavioural traits at the population level between restoration sites and remnant grasslands. This outcome could reflect personality-dependent colonization early in the restoration trajectory being eroded by subsequent gene flow and facilitation of alternative behavioural types. We hope our study will stimulate future research integrating animal personality with habitat restoration to benefit biodiversity in degraded ecosystems. • Multiple behaviours, including movements, were repeatable in kangaroo rats. • Kangaroo rats displayed a syndrome between personality and movement behaviour. • Behavioural traits only weakly diverged between remnant and restoration sites. • Links between animal personality and habitat restoration remain understudied. [ABSTRACT FROM AUTHOR]

Background and Aims Plant breeders are increasingly turning to crop wild relatives (CWRs) to ensure food security in a rapidly changing environment. However, CWR populations are confronted with various human-induced threats, including hybridization with their nearby cultivated crops. This might be a particular problem for wild coffee species, which often occur near coffee cultivation areas. Here, we briefly review the evidence for wild Coffea arabica (cultivated as Arabica coffee) and Coffea canephora (cultivated as Robusta coffee) and then focused on C. canephora in the Yangambi region in the Democratic Republic of the Congo. There, we examined the geographical distribution of cultivated C. canephora and the incidence of hybridization between cultivated and wild individuals within the rainforest. Methods We collected 71 C. canephora individuals from home gardens and 12 C. canephora individuals from the tropical rainforest in the Yangambi region and genotyped them using genotyping-by-sequencing (GBS). We compared the fingerprints with existing GBS data from 388 C. canephora individuals from natural tropical rainforests and the INERA Coffee Collection, a Robusta coffee field gene bank and the most probable source of cultivated genotypes in the area. We then established robust diagnostic fingerprints that genetically differentiate cultivated from wild coffee, identified cultivated–wild hybrids and mapped their geographical position in the rainforest. Key Results We identified cultivated genotypes and cultivated–wild hybrids in zones with clear anthropogenic activity, and where cultivated C. canephora in home gardens may serve as a source for crop-to-wild gene flow. We found relatively few hybrids and backcrosses in the rainforests. Conclusions The cultivation of C. canephora in close proximity to its wild gene pool has led to cultivated genotypes and cultivated–wild hybrids appearing within the natural habitats of C. canephora. Yet, given the high genetic similarity between the cultivated and wild gene pool, together with the relatively low incidence of hybridization, our results indicate that the overall impact in terms of risk of introgression remains limited so far. [ABSTRACT FROM AUTHOR]

Summary: Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers with c. 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited.Using exome capture sequencing and a fossil‐calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic.We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species.Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages. [ABSTRACT FROM AUTHOR]

In biogeography, vicariance and long‐distance dispersal are often characterised as competing scenarios. However, they are related concepts, both relying on collective geological, ecological, and phylogenetic evidence. This is illustrated by freshwater fishes, which may immigrate to islands either when freshwater connections are temporarily present and later severed (vicariance), or by unusual means when ocean gaps are crossed (long‐distance dispersal). Marine barriers have a strong filtering effect on freshwater fishes, limiting immigrants to those most capable of oceanic dispersal. The roles of vicariance and dispersal are debated for freshwater fishes of the Greater Antilles. We review three active hypotheses [Cretaceous vicariance, Greater Antilles–Aves Ridge (GAARlandia), long‐distance dispersal] and propose long‐distance dispersal to be an appropriate model due to limited support for freshwater fish use of landspans. Greater Antillean freshwater fishes have six potential source bioregions (defined from faunal similarity): Northern Gulf of México, Western Gulf of México, Maya Terrane, Chortís Block, Eastern Panamá, and Northern South America. Faunas of the Greater Antilles are composed of taxa immigrating from many of these bioregions, but there is strong compositional disharmony between island and mainland fish faunas (>90% of Antillean species are cyprinodontiforms, compared to <10% in Northern Gulf of México and Northern South America, and ≤50% elsewhere), consistent with a hypothesis of long‐distance dispersal. Ancestral‐area reconstruction analysis indicates there were 16 or 17 immigration events over the last 51 million years, 14 or 15 of these by cyprinodontiforms. Published divergence estimates and evidence available for each immigration event suggests they occurred at different times and by different pathways, possibly with rafts of vegetation discharged from rivers or washed to sea during storms. If so, ocean currents likely provide critical pathways for immigration when flowing from one landmass to another. On the other hand, currents create dispersal barriers when flowing perpendicularly between landmasses. In addition to high salinity tolerance, cyprinodontiforms collectively display a variety of adaptations that could enhance their ability to live with rafts (small body size, viviparity, low metabolism, amphibiousness, diapause, self‐fertilisation). These adaptations likely also helped immigrants establish island populations after arrival and to persist long term thereafter. Cichlids may have used a pseudo bridge (Nicaragua Rise) to reach the Greater Antilles. Gars (Lepisosteidae) may have crossed the Straits of Florida to Cuba, a relatively short crossing that is not a barrier to gene flow for several cyprinodontiform immigrants. Indeed, widespread distributions of Quaternary migrants (Cyprinodon, Gambusia, Kryptolebias), within the Greater Antilles and among neighbouring bioregions, imply that long‐distance dispersal is not necessarily inhibitory for well‐adapted species, even though it appears to be virtually impossible for all other freshwater fishes. [ABSTRACT FROM AUTHOR]

The Bagrid catfish, Bagrus orientalis, historically sustained communities in the Rufiji River basin (RRB), Tanzania, but has rapidly declined due to high consumer demand and unsustainable fishing. Consequently, a Ramsar site was designated within the RRB, although its potential to revitalize overexploited populations beyond its boundaries is uncertain because of limited information on genetic connectivity. To address this uncertainty, 158 partial cytochrome oxidase subunit I sequences of B. orientalis were analyzed to quantify genetic connectivity in the RRB. We observed significant genetic differentiation, indicating limited connectivity among populations. Populations in the Ramsar site were genetically connected to those in the Kilombero Valley Floodplain (KVFP), but were distinct from those in Ruaha and Rufiji, which clustered separately. Our findings suggested the Ramsar site could revitalize overexploited KVFP populations, and emphasized the need for sustained efforts against its encroachment. However, limited genetic connectivity with Ruaha and Rufiji implied that conservation measures in the site might have restricted effect in these areas. Conservation efforts should extend beyond the Ramsar site, by promoting sustainable fishing and enhancing habitat connectivity in Ruaha and Rufiji. [ABSTRACT FROM AUTHOR]

The taxonomic classification of Picea meyeri and P. mongolica has long been controversial. To investigate the genetic relatedness, evolutionary history, and population history dynamics of these species, genotyping-by-sequencing (GBS) technology was utilized to acquire whole-genome single nucleotide polymorphism (SNP) markers, which were subsequently used to assess population structure, population dynamics, and adaptive differentiation. Phylogenetic and population structural analyses at the genomic level indicated that although the ancestor of P. mongolica was a hybrid of P. meyeri and P. koraiensis, P. mongolica is an independent Picea species. Additionally, P. mongolica is more closely related to P. meyeri than to P. koraiensis, which is consistent with its geographic distribution. There were up to eight instances of interspecific and intraspecific gene flow between P. meyeri and P. mongolica. The P. meyeri and P. mongolica effective population sizes generally decreased, and Maxent modeling revealed that from the Last Glacial Maximum (LGM) to the present, their habitat areas decreased initially and then increased. However, under future climate scenarios, the habitat areas of both species were projected to decrease, especially under high-emission scenarios, which would place P. mongolica at risk of extinction and in urgent need of protection. Local adaptation has promoted differentiation between P. meyeri and P. mongolica. Genotype‒environment association analysis revealed 96,543 SNPs associated with environmental factors, mainly related to plant adaptations to moisture and temperature. Selective sweeps revealed that the selected genes among P. meyeri, P. mongolica and P. koraiensis are primarily associated in vascular plants with flowering, fruit development, and stress resistance. This research enhances our understanding of Picea species classification and provides a basis for future genetic improvement and species conservation efforts. [ABSTRACT FROM AUTHOR]

Elucidating the evolutionary processes that drive population divergence can enhance our understanding of the early stages of speciation and inform conservation management decisions. The honeybee Apis cerana displays extensive population divergence, providing an informative natural system for exploring these processes. The mainland lineage A. cerana includes several peripheral subspecies with disparate ecological and geographical settings radiated from a central ancestor. Under this evolutionary framework, we can explore the patterns of genome differentiation and the evolutionary models that explain them. We can also elucidate the contribution of non‐genomic spatiotemporal mechanisms (extrinsic features) and genomic mechanisms (intrinsic features) that influence these genomic differentiation landscapes. Based on 293 whole genomes, a small part of the genome is highly differentiated between central–peripheral subspecies pairs, while low and partial parallelism partly reflects idiosyncratic responses to environmental differences. Combined elements of recurrent selection and speciation‐with‐gene‐flow models generate the heterogeneous genome landscapes. These elements weight differently between central‐island and other central–peripheral subspecies pairs, influenced by glacial cycles superimposed on different geomorphologies. Although local recombination rates exert a significant influence on patterns of genomic differentiation, it is unlikely that low‐recombination rates regions were generated by structural variation. In conclusion, complex factors including geographical isolation, divergent ecological selection and non‐uniform genome features have acted concertedly in the evolution of reproductive barriers that could reduce gene flow in part of the genome and facilitate the persistence of distinct populations within mainland lineage of A. cerana. [ABSTRACT FROM AUTHOR]

The Splendid Fairywren Malurus splendens has four distinct phenotypic forms currently recognised as subspecies, although three species have been recognised within the group in the past. Here, we use multilocus nuclear DNA to test the recent hypothesis that the Splendid Fairywren represents three allopatric taxa with little to no modern-day contact, despite phenotypic evidence of periods of past contact and gene flow. Our nuclear dataset is concordant with earlier mtDNA-based data in supporting three distinct genetic groups within M. splendens. These genetic groups align with the three phenotypically distinct forms recently hypothesised to be allopatric and previously described at species-level – western M. splendens, central M. callainus and eastern M. melanotus. Nuclear gene flow does not appear to be rampant between the three forms; however, several individuals show signals of admixed nuclear ancestry, which we cannot distinguish as having resulted from incomplete lineage sorting, poor phylogenetic signal, or gene flow. Given changing modern taxonomic interpretations of the significance of gene flow in speciation, we argue that recognising three distinct species within the M. splendens complex might better represent their evolutionary distinctiveness, rather than continuing to treat these genetically and morphologically distinct forms as subspecies of a widespread polytypic species. Our study highlights the interesting complexity of determining species status when taxa are in the ‘grey zone’ near the subspecies/species continuum, and the value gained from adding perspectives from nuclear DNA. [ABSTRACT FROM AUTHOR]

Aim Location Taxon Methods Results Conclusions Arctic plants survived the Pleistocene glaciations in unglaciated refugia. The number, ages, and locations of these refugia are often unclear. We use high‐resolution genomic data from present‐day and Little‐Ice‐Age populations of Arctic Bell‐Heather to re‐evaluate the biogeography of this species and determine whether it had multiple independent refugia or a single refugium in Beringia.Circumpolar Arctic and Coastal British Columbia (BC) alpine.Cassiope tetragona L., subspecies saximontana and tetragona, outgroup C. mertensiana (Ericaceae).We built genotyping‐by‐sequencing (GBS) libraries using Cassiope tetragona tissue from 36 Arctic locations, including two ~250‐ to 500‐year‐old populations collected under glacial ice on Ellesmere Island, Canada. We assembled a de novo GBS reference to call variants. Population structure, genetic diversity and demography were inferred from PCA, ADMIXTURE, fastsimcoal2, SplitsTree, and several population genomics statistics.Population structure analyses identified 4–5 clusters that align with geographic locations. Nucleotide diversity was highest in Beringia and decreased eastwards across Canada. Demographic coalescent analyses dated the following splits with Alaska: BC subspecies saximontana (5 mya), Russia (~1.4 mya), Europe (>200–600 kya), and Greenland (~60 kya). Northern Canada populations appear to have formed during the current interglacial (7–9 kya). Admixture analyses show genetic variants from Alaska appear more frequently in present‐day than historic plants on Ellesmere Island.Population and demographic analyses support BC, Alaska, Russia, Europe and Greenland as all having had independent Pleistocene refugia. Northern Canadian populations appear to be founded during the current interglacial with genetic contributions from Alaska, Europe and Greenland. We found evidence, on Ellesmere Island, for continued recent gene flow in the last 250–500 years. These results suggest that a re‐analysis of other Arctic species with shallow population structure using higher resolution genomic markers and demographic analyses may help reveal deeper structure and other circumpolar glacial refugia. [ABSTRACT FROM AUTHOR]

Summary The tree of life is riddled with reticulate evolutionary histories, and some clades, such as the eastern standing Phlox, appear to be hotspots of hybridization. In this group, there are two cases of reinforcement and nine hypothesized hybrid species. Given their historical importance in our understanding of plant speciation, the relationships between these taxa and the role of hybridization in their diversification require genomic validation. Using phylogenomic analyses, we resolve the evolutionary relationships of the eastern standing Phlox and evaluate hypotheses about whether and how hybridization and gene flow played a role in their diversification. Our results provide novel resolution of the phylogenetic relationships in this group, including paraphyly across some taxa. We identify gene flow during one case of reinforcement and find genomic support for a hybrid lineage underlying one of the five hypothesized homoploid hybrid speciation events. Additionally, we estimate the ancestries of four allotetraploid hybrid species. Our results are consistent with hybridization contributing to diverse evolutionary outcomes within this group; although, not as extensively as previously hypothesized. This study demonstrates the importance of phylogenomics in evaluating hypothesized evolutionary histories of non‐model systems and adds to the growing support of interspecific genetic exchange in the generation of biodiversity. [ABSTRACT FROM AUTHOR]

In North America, a comparatively small number of Fraxinus (ash) cultivars were planted in large numbers in both urban and rural environments across the entire range of Fraxinus pennsylvanica Marsh (green ash) over the last 80 years. Undetected cultivar gene flow, if extensive, could significantly lower genetic diversity within populations, suppress differentiation between populations, generate interspecific admixture not driven by long-standing natural processes, and affect the impact of abiotic and biotic threats. In this investigation we generated the first range-wide genetic assessment of F. pennsylvanica to detect the extent of cultivar gene flow into natural stands. We used 16 EST-SSR markers to genotype 48 naturally regenerated populations of F. pennsylvanica distributed across the native range (1291 trees), 19 F. pennsylvanica cultivars, and one F. americana L. (white ash) cultivar to detect cultivar propagule dispersal into these populations. We detected first generation cultivar parentage with high confidence in 171 individuals in 34 of the 48 populations and extensive cultivar parentage (23–50%) in eight populations. The incidence of cultivar parentage was negatively associated with allele richness (R2 = 0.151, p = 0.006). The evidence for a locally high frequency of cultivar propagule dispersal and the interspecific admixture in eastern populations will inform Fraxinus gene pool conservation strategies and guide the selection of individuals for breeding programs focused on increasing resistance to the emerald ash borer (Agrilus planipennis Fairmaire), an existential threat to the Fraxinus species of North America. [ABSTRACT FROM AUTHOR]

Aim Location Time period Major taxa studied Methods Results Main conclusions Genetic diversity of marine forests results from complex interactions of eco‐evolutionary processes. Among them, oceanographic connectivity driven by dispersal through water transport is hypothesized to play a pivotal role, yet its relative contribution has not been addressed at the global scale. Here, we test how present‐day oceanographic connectivity is correlated with the distribution of genetic diversity of marine forests across the ocean.Global.Contemporary.Marine forests of brown macroalgae (order: Fucales, Ishigeales, Laminariales and Tilopteridales).Through literature review, we compiled a comprehensive dataset of genetic differentiation, encompassing 699 populations of 30 species. A biophysical model coupled with network analyses estimated multigenerational oceanographic connectivity and centrality across the marine forest global distribution. This approach integrated propagule dispersive capacity and long‐distance dispersal events. Linear mixed models tested the relative contribution of site‐specific processes, connectivity and centrality in explaining genetic differentiation.We show that spatiality‐dependent eco‐evolutionary processes, as described by our models, are prominent drivers of genetic differentiation in marine forests (significant models in 91.43% of the cases with an average R2 of 0.50 ± 0.07). Specifically, we reveal that 18.7% of genetic differentiation variance is explicitly induced by predicted contemporary connectivity and centrality. Moreover, we demonstrate that long‐distance dispersal is key in connecting populations of species distributed across large water masses and continents.Our findings highlight the role of present‐day oceanographic connectivity in shaping the extant distribution of genetic diversity of marine forests on a global scale, with significant implications for biogeography and evolution. This understanding can pave the way for future research aimed at guiding conservation efforts, including the designation of well‐connected marine protected areas, which is particularly relevant for sessile ecosystems structuring species such as brown macroalgae. [ABSTRACT FROM AUTHOR]

Aim Location Methods Results Main Conclusions The development of natural habitats into urban land uses has greatly accelerated in the recent past due to human activities. This habitat development disrupts species' natural dispersal processes and can lead to both direct and indirect impacts on dispersal. Whether human activities result in restricted or facilitated dispersal may depend on a species' development tolerance; however, this premise has not been tested. We examined the impact of urbanization and road networks on the dispersal of three lizard species in the context of their development tolerance.Curaçao.To quantify species' development tolerance, we modelled three lizard species abundances at sites based on surrounding landscape development. Using microsatellite genotypes, we conducted individual‐based resistance surface analyses and modelled the effect of habitat development on genetic admixture to assess indirect dispersal restriction and facilitation. We explored direct facilitation of dispersal using network analysis of mitochondrial haplotypes.Phyllodactylus martini, a native gecko species, was the least tolerant of development and experienced indirect dispersal restriction due to roads, according to resistance surface analyses. Anolis lineatus, a native anole species, exhibited a neutral relationship with development. Resistance surfaces and Structure analyses showed that A. lineatus faced indirect dispersal restrictions from roads and developed areas, while mitochondrial haplotype networks suggested they benefited from occasional human‐facilitated long‐distance dispersal events. Hemidactylus mabouia, an introduced gecko species, was the most tolerant of development, and experienced no dispersal restriction, but mitochondrial haplotypes suggest direct long‐distance dispersal facilitation.Our findings highlight development tolerance as a key predictor of dispersal impact for these species and future work should test whether these patterns are upheld in other systems. Understanding how human activities affect species' dispersal will aid in managing introduced species while promoting connectivity for native species navigating dispersal challenges in dynamic landscapes. [ABSTRACT FROM AUTHOR]

Pollinator losses threaten ecosystems and food security, diminishing gene flow and reproductive output for ecological communities and impacting ecosystem services broadly. For four focal families of bees and butterflies, we constructed over 1400 ensemble species distribution models over two time periods for North America. Models indicated disproportionally increased richness in eastern North America over time, with decreases in richness over time in the western US and southern Mexico. To further pinpoint geographic areas of vulnerability, we mapped records of potential pollinator species of conservation concern and found high concentrations of detections in the Great Lakes region, US East Coast, and southern Canada. Finally, we estimated asymptotic diversity indices for genera known to include species that visit flowers and may carry pollen for ecoregions across two time periods. Patterns of generic diversity through time mirrored those of species-level analyses, again indicating a decline in pollinators in the western U.S. Increases in generic diversity were observed in cooler and wetter ecoregions. Overall, changes in pollinator diversity appear to reflect changes in climate, though other factors such as land use change may also explain regional shifts. While statistical methods were employed to account for unequal sampling effort across regions and time, improved monitoring efforts with rigorous sampling designs would provide a deeper understanding of pollinator communities and their responses to ongoing environmental change. [ABSTRACT FROM AUTHOR]

Astyanax caucanus is an endemic fish species to the Magdalena-Cauca basin in Colombia. It is considered a Least Concern species by the International Union for Conservation of Nature, and currently, it is not a fishery resource. Its fertilized eggs may drift up to 4–5 days before hatching and can be carried up to 340 km given the water velocity of the river. Although A. caucanus is listed as short -migratory species (< 50 km), this study hypothesized that it exhibits gene flow along the middle and lower section of the Cauca River due to the great potential for larval dispersal. To test this hypothesis, we developed a set of species-specific microsatellite primers suitable for population genetic studies. Genetic structure analyses with 193 samples evidenced two genetic stocks that coexist, comigrate, and exhibit gene flow along the study area. Both stocks show high genetic diversity indices (Na and HE) and effective population sizes (Ne > 1000), but also show evidence of bottlenecked populations and high values of the inbreeding coefficient (FIS). Finally, these results are useful to understand the effects of other anthropic activities, besides fishing pressure on population bottlenecks found for other fish species cohabiting the area. [ABSTRACT FROM AUTHOR]

Octopus insularis is a shallow‐water octopus distributed throughout the western Atlantic, the Gulf of Mexico and the Caribbean. To evaluate its phylogeographic pattern, mitochondrial markers (16S rRNA and COIII) and genome‐wide nuclear markers (SNP's) were analyzed in individuals from artisanal fishing in different locations of the Colombian Caribbean coast. Mitochondrial analyzes displayed novel haplotypes (16S = H2, H3 and H4; COIII = H2–H7) and haplotypes shared with distant geographic areas (16S = H1 COIII = H1). The COIII gene did not show genetic differentiation between the analyzed localities, while the 16S gene showed significant differences between Santa Marta and Isla Fuerte. COIII's demographic analysis indicated that the species' effective population size has remained constant. Inferences were made from next‐generation genomic data with restriction site‐associated DNA (ddRAD‐seq) and 6769 polymorphic loci. The pairwise FST test indicated that there are low but significant differences between localities; however, the general molecular analysis of variance (AMOVA) and the principal coordinate analysis showed a lack of spatial structure in the populations analyzed. The Mantel test found no correlation between genetic distance and geographic distance, and the genetic structure analyses showed the presence of one genetic stock. The information obtained in this study indicates the genetic connectivity of O. insularis in the southwestern Caribbean, the absence of putative biogeographic barriers that affect its gene flow, and the crucial role played by life history strategies (planktonic paralarvae) and oceanographic factors to define the current distribution of its genetic diversity in this region. [ABSTRACT FROM AUTHOR]

Understanding the adaptability of small populations in the face of environmental change is a central problem in evolutionary biology. Solving this problem is challenging because neutral evolutionary processes that operate on historical and contemporary timescales can override the effects of selection in small populations. We assessed the effects of isolation by colonization (IBC), isolation by dispersal limitation (IBDL) as reflected by a pattern of isolation by distance (IBD), and isolation by adaptation (IBA) and the roles of genetic drift and gene flow on patterns of genetic differentiation among 19 cave‐dwelling populations of Icelandic Arctic charr (Salvelinus alpinus). We detected evidence of IBC based on the genetic affinity of nearby cave populations and the genetic relationships between the cave populations and the presumed ancestral population in the lake. A pattern of IBD was evident regardless of whether high‐level genetic structuring (IBC) was taken into account. Genetic signatures of bottlenecks and lower genetic diversity in smaller populations indicate the effect of drift. Estimates of gene flow and fish movement suggest that gene flow is limited to nearby populations. In contrast, we found little evidence of IBA as patterns of local ecological and phenotypic variation showed little association with genetic differentiation among populations. Thus, patterns of genetic variation in these small populations likely reflect localized gene flow and genetic drift superimposed onto a larger‐scale structure that is largely a result of colonization history. Our simultaneous assessment of the effects of neutral and adaptive processes in a tractable and replicated system has yielded novel insights into the evolution of small populations on both historical and contemporary timescales and over a smaller spatial scale than is typically studied. [ABSTRACT FROM AUTHOR]

Identification of taxonomically cryptic species is essential for the effective conservation of biodiversity. Freshwater‐limited organisms tend to be genetically isolated by drainage boundaries, and thus may be expected to show substantial cryptic phylogenetic and taxonomic diversity. By comparison, populations of diadromous taxa, that migrate between freshwater and marine environments, are expected to show less genetic differentiation. Here we test for cryptic diversity in Australasian populations (both diadromous and non‐diadromous) of two widespread Southern Hemisphere fish species, Galaxias brevipinnis and Galaxias maculatus. Both mtDNA and nuclear markers reveal putative cryptic species within these taxa. The substantial diversity detected within G. brevipinnis may be explained by its strong climbing ability which allows it to form isolated inland populations. In island populations, G. brevipinnis similarly show deeper genetic divergence than those of G. maculatus, which may be explained by the greater abundance of G. maculatus larvae in the sea allowing more ongoing dispersal. Our study highlights that even widespread, 'high‐dispersal' species can harbour substantial cryptic diversity and therefore warrant increased taxonomic and conservation attention. [ABSTRACT FROM AUTHOR]

Nilaparvata lugens, the brown planthopper (BPH), is a serious pest species. BPHs cause significant damage to rice plants in Korea as well as other countries in East and Southeast Asia. As BPHs cannot survive winter in Korea, they annually migrate into Korea from foreign countries. The BPHs found in Korea are believed to originate from China, but most BPHs in China are also known to originate from Southeast Asia. To understand the origin of Korean BPHs, we conducted a genotyping‐by‐sequencing (GBS) study. We sampled BPHs from five locations in Korea and five countries in Southeast Asia and analyzed the GBS and sequencing results using various methods based on the f statistics and admixture graph analyses. We confirmed that the domestic BPHs shared a greater genetic drift than the BPHs from Southeast Asian populations over several years, implying that a continuous genetic substratum of Korea exists. This genetic substratum is genetically closer to BPHs from the southern part (Thailand and Cambodia) of Southeast Asia than to BPHs from the northern part (Bhutan, Myanmar and Laos) of Southeast Asia. In addition, direct gene flows from Southeast Asia seem possible, so Korea is considered a hotspot where diverse BPH populations mix. Therefore, the origin of Korean BPHs extends beyond China and as far as southern Southeast Asia. This result will help to understand and control the population dynamics of the Korean BPH population. [ABSTRACT FROM AUTHOR]

Conservation is prioritized based on accepted taxa. As a consequence, a conservation incentive exists to emphasize inter‐population differences to define taxa, potentially leading to taxonomic inflation. But stressing the uniqueness of threatened populations has the side effect of hindering conservation actions that promote inter‐population gene flow, such as genetic rescue. These actions may be of critical importance for severely inbred populations involved in extinction vortices, for which an inflated taxonomy can become a conservation trap. Here, we exemplify this scenario with the western capercaillie (Tetrao urogallus, Phasianidae) population in the Cantabrian Mountains, described and legally listed as a subspecies not supported by recent molecular data. The Cantabrian capercaillie population is Critically Endangered after a long‐lasting decline and a recent demographic collapse. It shows clear signs of inbreeding depression, including striking clutch size decreases as well as reduced hatchability and chick survival. This critical situation could be alleviated through a genetic rescue, but this possibility is hindered by inertias rooted in the putative uniqueness of the Cantabrian capercaillie. It had been previously argued that poor taxonomy could hamper conservation, through the oblivion of populations deserving, but not having, a taxonomic status. We show that taxonomic inflation can also become an obstacle for effective conservation. [ABSTRACT FROM AUTHOR]

The two‐spotted spider mite, Tetranychus urticae Koch (Acarina, Tetranychidae), is a notorious agricultural pest known for its high dispersal ability. Understanding the dispersal patterns of T. urticae is crucial for studying its population dynamics and assessing the risk of gene dispersal related to acaricide resistance. We investigated the impact of surrounding landscapes on T. urticae occurrence and detected gene flow between nearby apple orchards. Land use data within 0.2–2 km radius buffers of the orchards were extracted and summarized using principal component analysis. The effects of landscape composition on the occurrence of T. urticae in apple orchards were analyzed using a hierarchical Bayesian model that considers spatial autocorrelation. In addition, we conducted a population genetic analysis on samples collected from five orchards. The results indicate that the best model was one at a 200‐m scale, revealing a positive correlation between forest area ratio and T. urticae occurrence. The population genetic analysis demonstrated distinct genetic structures within T. urticae populations across different orchards. However, we estimated gene flow among some orchards that were geographically close. These findings suggest that T. urticae may migrate from surrounding landscapes, particularly forests, and nearby orchards to apple orchards. These findings have substantial implications for developing control units based on the gene flow range of the two‐spotted spider mite, as well as for assessing the risk of infestation in each orchard. [ABSTRACT FROM AUTHOR]

Scots pine (Pinus sylvestris L.) is one of the most important tree species of the temperate and boreal zones in Eurasia. Its wide distribution range and current patterns of genetic variation have been influenced by Quaternary climatic oscillations and the demographic processes connected to them. In order to better understand the relationship between evolutionary history and demographic factors in a widespread species with a large genome, we used the single‐nucleotide polymorphism (SNP) array to genotype thousands of SNP markers across 62 natural populations (N = 686 trees) of Scots pine in Eurasia. This provides the largest range‐wide SNPs' genetic diversity assessment of Scots pine to date. Our findings show evidence of past admixture events between genetic clusters that were retained despite the potential for effective pollen‐mediated gene flow across the species' distribution range. We also examined the contemporary population structure of the species and analyzed the range‐wide genetic diversity patterns. Phylogenetic analyses and demographic modeling suggest that the observed divergence patterns between genetic lineages likely predate the last glaciation events. Two of the most distinctive groups are represented by trees from the eastern parts of Fennoscandia and Eastern Russia, which have remained separated since the mid‐Pleistocene. The patterns of genetic variation also confirm the dual colonization of Fennoscandia and the existence of an admixture zone in Central Europe that was formed during multiple waves of postglacial recolonization. This study provides insights into the genetic relationships of Scots pine populations from Europe and Asia and offers a more comprehensive understanding of the species' history. Highlights: •A range‐wide population genomic study of important highly outcrossing and wind‐dispersed Eurasian conifer (Pinus sylvestris) was carried out.•The signature of distinct genetic lineages was maintained across populations despite putative efficient gene flow.•Patterns of spatial genetic variation were shaped long before the Last Glacial Maximum. [ABSTRACT FROM AUTHOR]

A fundamental question in speciation genomics is how evolutionary processes shape the genomic landscape of differentiation between species. Regions of elevated differentiation, referred to as genomic islands, could be shared among closely related species (shared islands) or specific to a lineage (lineage‐specific islands). Shared islands are typically assumed to result from background selection. However, simulations and empirical studies have suggested that positive selection contributes to both shared and lineage‐specific islands. Here, we utilized comparative population genomics to examine the contributions of different evolutionary processes to patterns of genetic differentiation when gene flow and incomplete lineage sorting are minimal. We used whole‐genome resequencing data for 135 individuals from four oak species, including two independent species pairs, Quercus variabilis Blume and Quercus acutissima Carruth. in the subgenus Cerris, and Quercus dentata Thunb. and Quercus griffithii Hook.f. & Thomson ex Miq. in the subgenus Quercus. We found that both shared and subgenus‐specific islands were caused by positive selection, including selective sweeps in current populations and in their most recent common ancestors. Moreover, the recombination rate was a better predictor of genomic differentiation than gene density. Overall, our results reveal that recombination and positive selection impacted genomic differentiation considerably and provide a more precise grasp of how genomic islands formed in Quercus. [ABSTRACT FROM AUTHOR]

Interspecific trait divergence may reflect adaptation and reproductive isolation, particularly after the rapid differentiation that may follow the colonization of new environments. Although new lineages are generally expected to be morphologically and ecologically similar to their ancestors, environmental forces can also drive adaptive differentiation along specific phenotypic axes. We used climate niche models and comparative analyses based on a previously inferred phylogeny to examine the history of ecological and morphological divergence of Neotropical firs (Abies Mill., Pinaceae), a group of conifers that have recently colonized and diversified in the mountains of Mexico and northern Central America. We inferred past secondary contact zones by comparing current and past climate niche projections and looked for evidence of recent interspecific gene flow using genomic data. Neotropical firs have similar niches to each other and show a strong phylogenetic signal for most evaluated morphological traits. Analyses based on individual variables suggested a random walk model of differentiation. However, early adaptation to tropical conditions is inferred in the ancestor of the southernmost firs, as all modern southern taxa are differentiated climatically from Abies concolor, the northernmost species. In addition, observed autapomorphic traits for soil properties and the number of resin ducts in needles are consistent with possible species‐specific adaptations. Thus, a combination of nonadaptive and adaptive processes along different phenotypic axes, some related to the environment, likely operated after the southward migration of this plant lineage from North America and its subsequent radiation in the Neotropics. [ABSTRACT FROM AUTHOR]

Despite increasing recognition of the importance of the multiple dimensions of biodiversity, including functional or genetic diversity as well as species diversity, most conservation studies on ecosystem service‐providing insects focus on simple diversity measures such as species richness and abundance. In contrast, relatively little is known about the genetic diversity and resilience of pollinators or natural enemies of crop pests to population fragmentation and local extinction. The genetic diversity and demographic dynamics of remnant populations of beneficial insects in agricultural areas can be a useful indicator proving additional insights into their conservation status, but this is rarely evaluated. Although gene flow between agricultural and seminatural areas is key to maintaining genetic diversity, its extent and directionality remain largely unexplored. Here, we apply a pan‐European sampling protocol to quantify genetic diversity and structure and assess gene flow between agricultural and nearby seminatural landscapes in populations of two key ecosystem service‐providing insect species, the lady beetle Coccinella septempunctata, an important predator of aphids and other crop pests, and the bee pollinator Andrena flavipes. We show that A. flavipes populations are genetically structured at the European level, whereas populations of C. septempunctata experience widespread gene flow across the continent and lack any defined genetic structure. In both species, we found that there is high genetic connectivity between populations established in croplands and nearby seminatural areas and, as a consequence, they harbor similar levels of genetic diversity. Interestingly, demographic models for some regions support asymmetric gene flow from seminatural areas to nearby agricultural landscapes. Collectively, our study demonstrates how seminatural areas can serve as genetic reservoirs of both pollinators and natural enemies for nearby agricultural landscapes, acting as sources for recurrent recolonization and, potentially, contributing to enhancing ecosystem service and crop production resilience in the longer term. [ABSTRACT FROM AUTHOR]

The Zagros Mountains, characterized by complex topography and three large drainage systems, harbor the endemic freshwater crab Potamon persicum in Iran. Our study delves into the evolutionary history of P. persicum , utilizing two mitochondrial and one nuclear marker. We collected 214 specimens from 24 localities, identifying 21 haplotypes grouped into two major evolutionary lineages. Substantial differentiation exists between drainage systems and lineages. Historical demographic analysis revealed a significant decrease in population size during the late Holocene, accompanied by a recent population bottleneck. Species distribution modeling has revealed eastward shifts in suitable habitats between the last glacial maximum and the present day. Following the last glacial maximum, habitat fragmentation occurred, resulting in the establishment of small populations. These smaller populations are more vulnerable to climatic and geological events, thereby limiting gene flow and accelerating genetic differentiation within species. Historical biogeographic analysis traced the origin of P. persicum to the western Zagros Mountains, with major genetic divergence occurring during the Pleistocene. Our genetic analyses suggest that P. persicum may have shown a genetic pattern similar to a classical ring species before the Pleistocene. The Namak Lake sub-basin could have served as a contact zone where populations did not interbreed but were connected through gene flow in a geographic ring. Currently, genetic separation is evident between basins, indicating that P. persicum in the Zagros Mountains is not a contemporary ring species. Also, our biogeographical analysis estimated that range evolution may have been driven initially by dispersal, and only during the late Pleistocene by vicariance. [ABSTRACT FROM AUTHOR]

The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species. [ABSTRACT FROM AUTHOR]

Biodiversity conservation is a top priority in the face of global environmental change, and the practical restoration of biodiversity has emerged as a key objective. Nevertheless, the question of how to effectively contribute to biodiversity restoration and identify suitable systems for such efforts continues to present major challenges. By using genome-wide SNP data, our study revealed that populations from different mountain ranges of the Formosan Long-Arm Scarab beetle, a flagship species that receives strict protection, exhibited a single genetic cluster with no subdivision. Additionally, our result implied an association between the demographic history and historical fluctuations in climate and environmental conditions. Furthermore, we showed that, despite a stable and moderately sized effective population over recent history, all the individuals we studied exhibited signs of genetic inbreeding. We argued that the current practice of protecting the species as one evolutionarily significant unit remains the best conservation plan and that recent habitat change may have led to the pattern of significant inbreeding. We closed by emphasizing the importance of conservation genetic studies in guiding policy decisions and highlighting the potential of genomic data for identifying ideal empirical systems for genetic rescue, or assisted gene flow studies. [ABSTRACT FROM AUTHOR]

Habitat fragmentation can facilitate local adaptation of species to heterogeneous environments and affect population demographic history. To understand the factors influencing evolutionary dynamics, such as climatic fluctuations and complex geomorphological features, we used 18 chloroplast microsatellites, 15 nuclear microsatellites, three chloroplast fragments, and two nuclear regions to explore the genetic structure and phylogeographical history of Pseudotaxus chienii. Furthermore, its current and past distributions were constructed based on ecological niche modelling. Moderate to high levels of genetic diversity were found at the species level. Precipitation was a decisive factor influencing the genetic structure of P. chienii. In addition, local adaptation to heterogeneous environments also contributed to maintain the fragmented distribution. Finally, incomplete lineage sorting led to the cyto-nuclear discordance. Overall, we show that pre-Quaternary and Quaternary climatic fluctuations and restricted gene flow exerted significant effects on the formation and maintenance of the fragmented distribution of P. chienii. The study provides new insights into the evolutionary history of plants in subtropical China. [ABSTRACT FROM AUTHOR]

Population genetic structure is influenced by a combination of contemporary and historical events; however, this structure can be complicated by ongoing gene flow. While it is well known that contemporary hybridization occurs frequently among many closely related species, it often remains uncertain as to which populations are involved in introgression events, and this can be even more difficult to infer when introgression is historical. Here we use restriction-site associated DNA sequencing to look at the level of introgression among four species of songbirds in North America: the black-capped, mountain, boreal, and chestnut-backed chickadee. Samples from both sympatric and allopatric sites across the species' ranges supported limited ongoing mixing among the four species with Bayesian clustering and principal component analyses. In contrast, f4-statistics and admixture graphs revealed extensive historical introgression among geographically structured populations. Almost all historical admixture events were among populations west of the Rocky Mountains, and almost all populations west of the Rocky Mountains, excluding island and coastal populations, showed evidence of historical admixture. The inclusion of all four chickadee species proved crucial in differentiating which species were involved in hybridization events to avoid erroneous conclusions. Taken together, the results suggest a complex pattern of divergence with gene flow. [ABSTRACT FROM AUTHOR]

Knowing the location and movements of individuals at various temporal and spatial scales is an important facet of behavior and ecology. In threatened populations, movements that would ensure gene flow and population viability are often challenged by habitat fragmentation. Also in those endangered populations capturing and handling individuals to tag them, or to obtain tissue samples, can present additional challenges. DNA tagging, i.e. non‐invasive individual identification of samples, can reveal movement patterns. We used fecal material genetically assigned to individuals to indirectly track movements of a large‐bodied, endangered forest bird, Cantabrian capercaillie (Tetrao urogallus cantabricus). We wanted to know how the birds were using the fragmented forest landscape, and whether they showed fidelity to display areas. We used multi‐event capture−recapture models to estimate fidelity to display areas among three consecutive mating seasons. We identified 127 individuals, and registered movements of 22 females and 48 males. Most observed movements were as expected relatively short, concentrated around display areas. We did not find differences in movement distances between females and males within mating seasons, or between them. Fidelity to display areas among seasons was 0.62 (± 0.12 SE) for females and 0.77 (± 0.07 SE) for males. The best CR model suggested no sex or season effects. Several longer movements, up to 9.9 km, linked distant display areas, demonstrating that Cantabrian capercaillies were able to move between different parts of the study area, complementing previous studies on gene flow. Those longer movements may be taking birds out of the study area, and into historical capercaillie territories, which still include substantial forest cover. The non‐invasive DNA tagging approach provided a much larger sample size than would have been feasible with direct tracking. Lack of information on the social status of individuals, and timing of movements, are some disadvantages of DNA tagging. [ABSTRACT FROM AUTHOR]

Interspecific hybridization has long been of interest to biologists due to its implications for species concepts, gene flow, and conservation. We found a putative hybrid between the endangered brown shrike (Lanius cristatus superciliosus) and the common bull-headed shrike (Lanius bucephalus) at the foot of Mt. Fuji, central Japan, where the adult sex ratio of brown shrikes is biased towards the male. Brown and bull-headed shrikes are closely related, and their hybridization is critical for the survival and conservation of the brown shrike. We tried to identify this individual based on genetic, morphological, plumage, and acoustic analysis. The hybrid had intermediate genetic, morphological, and plumage features between the two parental species. The maternal lineage of the hybrid was suggested to be the bull-headed shrike by COI analysis. We thus conclude that the hybrid resulted from interbreeding between a male brown shrike and a female bull-headed shrike, and a skewed sex ratio in the brown shrike may have contributed to this hybridization. Skewed sex ratio is a useful indicator of population viability and knowledge of this is helpful in rare species conservation. Genetic introgression between brown and bull-headed shrikes cannot be denied because the hybrid individual was fertile and backcrossing occurred. Exploring past and ongoing genetic relationships of the shrikes has led to insights into the evolutionary background and the potential of hybridization in an evolutionary context. [ABSTRACT FROM AUTHOR]

Dispersal is one of the major processes controlling both genetic diversity and species diversity and is frequently studied in both phylogeography and community ecology. As such, integrating these fields to uncover how both historical and contemporary dispersal have affected local community structure can provide greater insights into community assembly. We used comparative phylogeography to determine if freshwater fish species in the Bonneville Basin show evidence of geologically recent dispersal and gene flow, which would probably have occurred when the basin was inundated by Lake Bonneville in the late Pleistocene. We then used museum records to uncover patterns of contemporary community structure and relate them to the results of the phylogeographical analyses. We found evidence for late Pleistocene dispersal throughout the Bonneville Basin in most of the fish species studied, which would have homogenized ancient communities. However, modern communities show evidence of non-random community structure and dispersal limitation between major sub-basins and habitats. Together, these results suggest that the Bonneville Basin fish fauna assembled due to a combination of historical dispersal and contemporary habitat filtering and extinction dynamics following isolation. Further work should continue to combine different data types to achieve more accurate inferences regarding contemporary community assembly. [ABSTRACT FROM AUTHOR]

Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco‐evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability. [ABSTRACT FROM AUTHOR]

The maintenance of polymorphisms often depends on multiple selective forces, but less is known on the role of stochastic or historical processes in maintaining variation. The common wall lizard (Podarcis muralis) is a colour polymorphic species in which local colour morph frequencies are thought to be modulated by natural and sexual selection. Here, we used genome‐wide single‐nucleotide polymorphism data to investigate the relationships between morph composition and population biogeography at a regional scale, by comparing morph composition with patterns of genetic variation of 54 populations sampled across the Pyrenees. We found that genetic divergence was explained by geographic distance but not by environmental features. Differences in morph composition were associated with genetic and environmental differentiation, as well as differences in sex ratio. Thus, variation in colour morph frequencies could have arisen via historical events and/or differences in the permeability to gene flow, possibly shaped by the complex topography and environment. In agreement with this hypothesis, colour morph diversity was positively correlated with genetic diversity and rates of gene flow and inversely correlated with the likelihood of the occurrence of bottlenecks. Concurrently, we did not find conclusive evidence for selection in the two colour loci. As an illustration of these effects, we observed that populations with higher proportions of the rarer yellow and yellow‐orange morphs had higher genetic diversity. Our results suggest that processes involving a decay in overall genetic diversity, such as reduced gene flow and/or bottleneck events have an important role in shaping population‐specific morph composition via non‐selective processes. [ABSTRACT FROM AUTHOR]

The Nanling Mountains, an important mountain range and watershed in south China, harbor a wealth of relictual plant species, and are considered a 'museum' of subtropical biodiversity. With respect to birds, however, the roles of the Nanling Mountains in impeding the dispersal of the subtropical birds and, as a result, shaping their population and community structures have received little consideration. To examine these roles, we compiled and analyzed two datasets. 1) To test the mountains' influence on gene flow, we undertook a comparative phylogeographic study comparing mitochondrial COI and Cytb DNA sequences of five sylvioid resident bird species of the mountains (Huet's fulvetta Alcippe hueti, red‐billed leiothrix Leiothrix lutea, greater necklaced laughingthrush Pterorhinus pectoralis, Indochinese yuhina Staphida torqueola and mountain bulbul Ixos mcclellandii). 2) To examine differential community development over the history of modern birds, we examined distributional data of all species of the Nanling region using public species occurrence records. For part 1), we sampled 327 individuals from 36 sites and conducted correlation analysis of genetic and geographic distances, taking into account the landscape of the mountains. We found that the mountains do not seriously impede gene flow among populations but influenced species differently. For part 2), comparative analysis of 446 species in 81 families indicated that family membership influenced the community composition of birds in Nanling region. Variation in family distributions is attributable to both environmental and evolutionary factors. Overall, we found that the Nanling Mountains are not currently a substantial barrier to gene flow among the species we studied but act as a corridor and refuge for these birds. However, analyses on higher ranked community data suggest the mountains acted as a barrier in older times, corresponding to the known diversification events in southeast Asian avifauna. [ABSTRACT FROM AUTHOR]

Aim: High‐elevation specialist species are threatened by climate change and habitat loss, and their distributions are becoming increasingly reduced and fragmented. In such a context, dispersal ability is crucial to maintain gene flow among patches of suitable habitat. However, information about dispersal is often lacking for these species, especially for those taxa that are usually considered as good dispersers such as birds. We adopted a landscape genomics approach to investigate dispersal in a climate‐sensitive high‐elevation specialist bird. Our aims were to assess the levels of gene flow within a wide mountain area, and to assess the effects of geographic distance and landscape characteristics on dispersal, by testing the isolation by distance (IBD) hypothesis against the isolation by resistance (IBR) hypothesis. Location: European Alps. Taxon: Montifringilla nivalis. Methods: We sampled individuals from several breeding areas and obtained single nucleotide polymorphism (SNP) data by ddRAD sequencing. We then calculated site‐ and individual level genetic distances and individual inbreeding coefficients. To test IBD versus IBR, we related genetic distances to both geographic distances and different measures of landscape resistance by using maximum likelihood population effects models. Results: Gene flow among breeding areas was partly restricted, and we found support for IBD, indicating that geographic distance limits snowfinch dispersal. Spatial patterns of genetic distances suggested that philopatry strongly contributed to determine the observed IBD. High inbreeding coefficients in several individuals indicated frequent mating among relatives. Main Conclusions: Restricted dispersal and frequent inbreeding within 'sky island' systems can also occur in highly mobile species, because their potential ability to cover very large distances can be counteracted by high philopatry levels that are likely related to high dispersal costs. IBD and philopatry will increasingly hinder snowfinch dispersal among suitable areas within the future more restricted and fragmented breeding range, increasing the risks of local extinctions. [ABSTRACT FROM AUTHOR]

Tomicus piniperda is a common pest of pine trees responsible for significant economic damage. Although the impact of T. piniperda on forestry is likely to increase in the future due to climate change, little is known about its dispersal within the United Kingdom (UK) or between continental Europe and the UK.This study addressed these knowledge gaps using mitochondrial and microsatellite DNA markers.Mitochondrial DNA revealed high levels of genetic diversity as previously reported for this species across Europe. Nuclear DNA diversity revealed two geographically incoherent groups (Scotland, Wales, Belgium and the Netherlands vs. England and Switzerland). These genetic patterns likely reflect a combination of historical gene flow, anthropogenic introduction and restricted contemporary gene flow between the UK and Europe.Significant structure was found among UK samples suggesting T. piniperda might not disperse extensively between pine stands. This differs from widespread gene flow across continental Europe and may be due to the low percentage of land covered by forests in the UK in addition to the high fragmentation of its forest cover.Genetic variation was higher among the Scottish samples compared to those from more southern clines, suggesting the potential proximity of Scotland to a Pleistocene glacial refuge for T. piniperda. [ABSTRACT FROM AUTHOR]

Characterizing the processes underlying reproductive isolation between diverging lineages is central to understanding speciation. Here, we present RIDGE—Reproductive Isolation Detection using Genomic polymorphisms—a tool tailored for quantifying gene flow barrier proportion and identifying the relevant genomic regions. RIDGE relies on an Approximate Bayesian Computation with a model‐averaging approach to accommodate diverse scenarios of lineage divergence. It captures heterogeneity in effective migration rate along the genome while accounting for variation in linked selection and recombination. The barrier detection test relies on numerous summary statistics to compute a Bayes factor, offering a robust statistical framework that facilitates cross‐species comparisons. Simulations revealed RIDGE's efficiency in capturing signals of ongoing migration. Model averaging proved particularly valuable in scenarios of high model uncertainty where no migration or migration homogeneity can be wrongly assumed, typically for recent divergence times <0.1 2Ne generations. Applying RIDGE to four published crow data sets, we first validated our tool by identifying a well‐known large genomic region associated with mate choice patterns. Second, while we identified a significant overlap of outlier loci using RIDGE and traditional genomic scans, our results suggest that a substantial portion of previously identified outliers are likely false positives. Outlier detection relies on allele differentiation, relative measures of divergence and the count of shared polymorphisms and fixed differences. Our analyses also highlight the value of incorporating multiple summary statistics including our newly developed outlier ones that can be useful in challenging detection conditions. [ABSTRACT FROM AUTHOR]

Wild-type sporophytes of Saccharina japonica have been recurrently observed on the infrastructures of kelp farming rafts in China’s northern production region (Liaoning and Shandong provinces). However, there are few detailed reports delineating their origin, genetic attributes and affiliations with farmed populations. Using microsatellite molecular analyses, we furnish a comparative analysis of the populations sampled from these rafts at one of the historical kelp farming regions Rongcheng city (Shandong province), both before and after the “2021–2022 kelp farming disaster”, in conjunction with two field populations from nearby intertidal zones where natural populations prevail. The results show that the wild kelp populations on the kelp farming rafts in 2023 had originated from the wild populations dwelling in intertidal zones several kilometers away, rather than from the artificially cultivated kelp cultivars. [ABSTRACT FROM AUTHOR]

We generated Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL), a high-depth whole-genome sequencing dataset comprising 3256 individuals from across Japan. Analysis of JEWEL revealed genetic characteristics of the Japanese population that were not discernible using microarray data. First, rare variant-based analysis revealed an unprecedented fine-scale genetic structure. Together with population genetics analysis, the present-day Japanese can be decomposed into three ancestral components. Second, we identified unreported loss-of-function (LoF) variants and observed that for specific genes, LoF variants appeared to be restricted to a more limited set of transcripts than would be expected by chance, with PTPRD as a notable example. Third, we identified 44 archaic segments linked to complex traits, including a Denisovan-derived segment at NKX6-1 associated with type 2 diabetes. Most of these segments are specific to East Asians. Fourth, we identified candidate genetic loci under recent natural selection. Overall, our work provided insights into genetic characteristics of the Japanese population. [ABSTRACT FROM AUTHOR]

Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigate the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses reveal a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets reveals only a partial habitat separation of the clusters. Globally, two clusters only show a separate gene composition coherent with ecological adaptations. These results suggest that genetic isolation has preceded ecological adaptations in the shaping of the species diversity, an evolutionary scenario coherent with the Evolutionary Extended Synthesis. A large comparative genomics study reveals that Serratia marcescens is composed of five main phylogenetic clusters, isolated by genetic barriers but not clearly separated by ecological specialisations. This results provides insights into the bacterial diversification process. [ABSTRACT FROM AUTHOR]