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Anthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. These impacts are likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic to the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426 genomic (ddRAD-seq) markers and species distribution modelling, we explored the phylogeographic history of western (Nannoperca vittata) and little (Nannoperca pygmaea) pygmy perches, assessing population divergence and phylogenetic relationships, delimiting species and estimating changes in species distributions from the Pliocene to 2100. We identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability but with significant range contractions likely under future climate change. Our results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region., (© 2024. The Author(s).)

Climatic oscillations during the Pleistocene have greatly influenced the distribution and connectivity of many organisms, leading to extinctions but also generating biodiversity. While the effects of such changes have been extensively studied in the terrestrial environment, studies focusing on the marine realm are still scarce. Here we used sequence data from one mitochondrial and five nuclear loci to assess the potential influence of Pleistocene climatic changes on the phylogeography and demographic history of a cosmopolitan marine predator, the common dolphin (genus Delphinus). Population samples representing the three major morphotypes of Delphinus were obtained from 10 oceanic regions. Our results suggest that short-beaked common dolphins are likely to have originated in the eastern Indo-Pacific Ocean during the Pleistocene and expanded into the Atlantic Ocean through the Indian Ocean. On the other hand, long-beaked common dolphins appear to have evolved more recently and independently in several oceans. Our results also suggest that short-beaked common dolphins had recurrent demographic expansions concomitant with changes in sea surface temperature during the Pleistocene and its associated increases in resource availability, which differed between the North Atlantic and Pacific Ocean basins. By proposing how past environmental changes had an effect on the demography and speciation of a widely distributed marine mammal, we highlight the impacts that climate change may have on the distribution and abundance of marine predators and its ecological consequences for marine ecosystems., (© 2012 Blackwell Publishing Ltd.)

The unparalleled diversity of tropical ecosystems like the Amazon Basin has been traditionally explained using spatial models within the context of climatic and geological history. Yet, it is adaptive genetic diversity that defines how species evolve and interact within an ecosystem. Here, we combine genome scans, population genetics and sequence-based phylogeographic analyses to examine spatial and ecological arrangements of selected and neutrally evolving regions of the genome of an Amazonian fish, Triportheus albus. Using a sampling design encompassing five major Amazonian rivers, three hydrochemical settings, 352 nuclear markers and two mitochondrial DNA genes, we assess the influence of environmental gradients as biodiversity drivers in Amazonia. We identify strong divergent natural selection with gene flow and isolation by environment across craton (black and clear colour)- and Andean (white colour)-derived water types. Furthermore, we find that heightened selection and population genetic structure present at the interface of these water types appears more powerful in generating diversity than the spatial arrangement of river systems and vicariant biogeographic history. The results from our study challenge assumptions about the origin and distribution of adaptive and neutral genetic diversity in tropical ecosystems. In addition, they have important implications for measures of biodiversity and evolutionary potential in one of the world's most diverse and iconic ecosystems., (© 2012 Blackwell Publishing Ltd.)

Genetic divergence among populations of marine broadcast spawners in the absence of past geological barriers presents an intriguing challenge to understanding speciation in the sea. To determine how differences in life history affect genetic divergence and demographic histories across incomplete dispersal barriers, we conducted a comparative phylogeographic study of three intertidal limpets (Siphonaria spp.) represented on either side of a biogeographic disjunction separating tropical and subtropical marine provinces in southeastern Africa. Using a combination of mitochondrial and nuclear sequence data, we identified two distinct evolutionary lineages each in both Siphonaria concinna (a planktonic disperser) and S. nigerrima (a direct developer), and panmixia in a second planktonic disperser, S. capensis. Although phylogeographic breaks were present in two species, how these became established differed depending on their life histories. In the direct developer, lack of gene flow following divergence, and demographic expansion from a small initial size in the species' subtropical population, point to a single colonisation event. In contrast, the evolutionary lineages of the planktonic disperser split into two genetic lineages with much larger initial population sizes and southward gene flow continued at least periodically, indicating that divergence in this species may have been driven by a combination of reduced larval dispersal and divergent selection. These findings help explain why the presence or absence of phylogeographic breaks often appears to be independent of species' dispersal potential., (© 2011 Blackwell Publishing Ltd.)

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]

While the influence of Pleistocene climatic changes on divergence and speciation has been well‐documented across the globe, complex spatial interactions between hydrology and eustatics over longer timeframes may also determine species evolutionary trajectories. Within the Australian continent, glacial cycles were not associated with changes in ice cover and instead largely resulted in fluctuations from moist to arid conditions across the landscape. We investigated the role of hydrological and coastal topographic changes brought about by Plio‐Pleistocene climatic changes on the biogeographic history of a small Australian freshwater fish, the southern pygmy perch Nannoperca australis. Using 7958 ddRAD‐seq (double digest restriction‐site associated DNA) loci and 45,104 filtered SNPs, we combined phylogenetic, coalescent and species distribution analyses to assess the various roles of aridification, sea level and tectonics and associated biogeographic changes across southeast Australia. Sea‐level changes since the Pliocene and reduction or disappearance of large waterbodies throughout the Pleistocene were determining factors in strong divergence across the clade, including the initial formation and maintenance of a cryptic species, N. 'flindersi'. Isolated climatic refugia and fragmentation due to lack of connected waterways maintained the identity and divergence of inter‐ and intraspecific lineages. Our historical findings suggest that predicted increases in aridification and sea level due to anthropogenic climate change might result in markedly different demographic impacts, both spatially and across different landscape types. [ABSTRACT FROM AUTHOR]

Aim: During ecological speciation, reproductive isolation is predicted to evolve between populations adapted to different biotic or abiotic environments despite the absence of geographical isolation. Regions of oceanographic heterogeneity (e.g. current interfaces, habitat transition zones, ecological gradients) are strong candidates for the presence of ecologically divergent natural selection, but their role in the radiation of elasmobranch species is yet to be tested. We used an integrative framework to assess the relative influence of oceanographic heterogeneity and geological history on the diversification of an elasmobranch genus. Location: Gulf of California (GC) and Baja California Peninsula (BCP), Mexico. Taxon: Shovelnose guitarfish (genus Pseudobatos). Methods: We sampled 210 Pseudobatos specimens from four distinct but physically connected oceanographic regions within the GC and in the BCP. We used genetic (mtDNA sequences and AFLP genotypes) and environmental (six oceanographic variables) datasets to clarify phylogenetic relationships, demographic history and evolutionary divergence among populations, and to test for associations between ecologically driven selection and reproductive isolation. Results: Phylogenetic and population genetic evidence exposed five distinct lineages of Pseudobatos in the region, including four cryptic lineages in the GC. Phylogeographic analyses indicate a recent history of ecologically driven diversification associated with the Gulf's young oceanographic environment and its four ecologically discrete regions. This hypothesis was supported by seascape genetics, ecological niche modelling and by tests of selection. Main conclusions: We propose an adaptive radiation for the genus Pseudobatos linked with habitat heterogeneity of the GC. Our study likely represents the first assessment of an ecological radiation in the highly diverse elasmobranch group. It capitalizes on the environmental and biogeographic settings of the GC to offer a new perspective about the application of integrative approaches to study divergent natural selection and diversification in the sea. [ABSTRACT FROM AUTHOR]

Abstract: Dispersal and natural selection are key evolutionary processes shaping the distribution of phenotypic and genetic diversity. For species inhabiting complex spatial environments however, it is unclear how the balance between gene flow and selection may be influenced by landscape heterogeneity and environmental variation. Here, we evaluated the effects of dendritic landscape structure and the selective forces of hydroclimatic variation on population genomic parameters for the Murray River rainbowfish, Melanotaenia fluviatilis across the Murray–Darling Basin, Australia. We genotyped 249 rainbowfish at 17,503 high‐quality SNP loci and integrated these with models of network connectivity and high‐resolution environmental data within a riverscape genomics framework. We tested competing models of gene flow before using multivariate genotype–environment association (GEA) analysis to test for signals of adaptive divergence associated with hydroclimatic variation. Patterns of neutral genetic variation were consistent with expectations based on the stream hierarchy model and M. fluviatilis’ moderate dispersal ability. Models incorporating dendritic network structure suggested that landscape heterogeneity is a more important factor determining connectivity and gene flow than waterway distance. Extending these results, we also introduce a novel approach to controlling for the unique effects of dendritic network structure in GEA analyses of populations of aquatic species. We identified 146 candidate loci potentially underlying a polygenic adaptive response to seasonal fluctuations in stream flow and variation in the relative timing of temperature and precipitation extremes. Our findings underscore an emerging predominant role for seasonal variation in hydroclimatic conditions driving local adaptation and are relevant for informing proactive conservation management. [ABSTRACT FROM AUTHOR]

Little is known about the population ecology of the recently described bottlenose dolphin species Tursiops australis. The classification of this species is still under debate, but this putative species is thought to be comprised of small and genetically distinct populations (including sub-populations under increasing anthropogenic threats) and is likely endemic to coastal southern Australia. Mitochondrial DNA (mtDNA) control region sequences and microsatellite loci were used to assess genetic variation and hierarchical population structure of coastal T. cf. australis across a range of spatial scales and environmental discontinuities between southern Western Australia (WA) and central South Australia (SA). Overall, genetic diversity was similar to that typically found for bottlenose dolphins, although very low mtDNA diversity was found in Gulf St. Vincent (GSV) dolphins. We found historical genetic subdivision and likely differences in colonisation between GSV and Spencer Gulf, outer- and inner-gulf locations, and SA/WA and previously identified Victorian/Tasmanian populations. A hierarchical metapopulation structure was revealed along southern Australia, with at least six genetic populations occurring between Esperance, WA and southern Tasmania. In addition, fine-scale genetic subdivision was observed within each SA/WA population. In general, contemporary migration was limited throughout southern Australia, but an important gene flow pathway was identified eastward along the Great Australian Bight. Management strategies that promote gene flow among populations should be implemented to assist with the maintenance of the inferred metapopulation structure. Further research into the population ecology of this species is needed to facilitate well-informed management decisions. [ABSTRACT FROM AUTHOR]

Evolution creates and sustains biodiversity via adaptive changes in ecologically relevant traits. Ecologically mediated selection contributes to genetic divergence both in the presence or absence of geographic isolation between populations, and is considered an important driver of speciation. Indeed, the genetics of ecological speciation is becoming increasingly studied across a variety of taxa and environments. In this paper we review the literature of ecological speciation in the tropics. We report on low research productivity in tropical ecosystems and discuss reasons accounting for the rarity of studies. We argue for research programs that simultaneously address biogeographical and taxonomic questions in the tropics, while effectively assessing relationships between reproductive isolation and ecological divergence. To contribute toward this goal, we propose a new framework for ecological speciation that integrates information from phylogenetics, phylogeography, population genomics, and simulations in evolutionary landscape genetics (ELG). We introduce components of the framework, describe ELG simulations (a largely unexplored approach in ecological speciation), and discuss design and experimental feasibility within the context of tropical research. We then use published genetic datasets from populations of five codistributed Amazonian fish species to assess the performance of the framework in studies of tropical speciation. We suggest that these approaches can assist in distinguishing the relative contribution of natural selection from biogeographic history in the origin of biodiversity, even in complex ecosystems such as Amazonia. We also discuss on how to assess ecological speciation using ELG simulations that include selection. These integrative frameworks have considerable potential to enhance conservation management in biodiversity rich ecosystems and to complement historical biogeographic and evolutionary studies of tropical biotas. [ABSTRACT FROM AUTHOR]

Aim We propose a phylogenetic hypothesis for the marine-derived sciaenid genus Plagioscion in the context of geomorphology and adaptation to freshwaters of South America, and assess the extent to which contemporary freshwater hydrochemical gradients influence diversification within a widely distributed Plagioscion species, Plagioscion squamosissimus. Location Amazon Basin and South America. Methods Using nuclear and mitochondrial DNA sequence data, phylogenetic analyses were conducted on the five nominal Plagioscion species, together with representatives from Pachyurus and Pachypops, using character and model-based methods. Genealogical relationships and population genetic structure of 152 P. squamosissimus specimens sampled from the five major rivers and three hydrochemical settings/'colours' (i.e. white, black and clear water) of the Amazon Basin were assessed. Results Phylogenetic analyses support the monophyly of Plagioscion in South America and identify two putative cryptic species of Plagioscion. Divergence estimates suggest that the Plagioscion ancestor invaded South America via a northern route during the late Oligocene to early Miocene. Within P. squamosissimus a strong association of haplotype and water colour was observed, together with significant population structure detected between water colours. Main conclusions Our analyses of Plagioscion are consistent with a biogeographic scenario of early Miocene marine incursions into South America. Based on our phylogenetic results, the fossil record, geomorphological history and distributional data of extant Plagioscion species, we propose that marine incursions into western Venezuela between the late Oligocene and early Miocene were responsible for the adaptation to freshwaters in Plagioscion species. Following the termination of the marine incursions during the late Miocene and the establishment of the modern Amazon River, Plagioscion experienced a rapid diversification. Plagioscion squamosissimus arose during that time. The formation of the Amazon River probably facilitated population and range expansions for this species. Further, the large-scale hydrochemical gradients within the Amazon Basin appear to be acting as ecological barriers maintaining population discontinuities in P. squamosissimus even in the face of gene flow. Our results highlight the importance of divergent natural selection through time in the generation and maintenance of sciaenid diversity in Amazonia. [ABSTRACT FROM AUTHOR]

Rivers provide an excellent system to study interactions between patterns of biodiversity structure and ecological processes. In these environments, gene flow is restricted by the spatial hierarchy and temporal variation of connectivity within the drainage network. In the Australian arid zone, this variability is high and rivers often exist as isolated waterholes connected during unpredictable floods. These conditions cause boom/bust cycles in the population dynamics of taxa, but their influence on spatial genetic diversity is largely unknown. We used a landscape genetics approach to assess the effect of hydrological variability on gene flow, spatial population structure and genetic diversity in an Australian freshwater fish, Macquaria ambigua. Our analysis is based on microsatellite data of 590 samples from 26 locations across the species range. Despite temporal isolation of populations, the species showed surprisingly high rates of dispersal, with population genetic structure only evident among major drainage basins. Within drainages, hydrological variability was a strong predictor of genetic diversity, being positively correlated with spring-time flow volume. We propose that increases in flow volume during spring stimulate recruitment booms and dispersal, boosting population size and genetic diversity. Although it is uncertain how the hydrological regime in arid Australia may change under future climate scenarios, management strategies for arid-zone fishes should mitigate barriers to dispersal and alterations to the natural flow regime to maintain connectivity and the species' evolutionary potential. This study contributes to our understanding of the influence of spatial and temporal heterogeneity on population and landscape processes. [ABSTRACT FROM AUTHOR]

Aim We conducted a range-wide phylogeographic study of a common Australian freshwater fish, the golden perch ( Macquaria ambigua), to investigate the relationship between environmental processes and evolutionary history in drainage basins. Location Inland [Lake Eyre (LEB), Murray–Darling (MDB) and Bulloo (BULL)] and coastal basins [Fitzroy (FITZ)] of eastern Australia. Methods A total of 590 samples were collected from across the entire species’ distribution and a section of the mitochondrial DNA control region was sequenced. In order to reconstruct the evolutionary history of M. ambigua a comprehensive suite of phylogeographic analyses was conducted, including nested clade phylogeographic analysis, mismatch analysis and isolation-with-migration model simulations. Results Three major lineages corresponding to the major drainage basins, FITZ, MDB and LEB/BULL, were identified (ΦST = 0.92). Lineages from the coastal basin (FITZ) were highly divergent from those of the inland basins (up to 6%). Levels of genetic diversity in the inland basins were relatively low and our analyses indicate that these populations experienced both demographic and range expansions during the Pleistocene. Main conclusions Investigation of the range-wide phylogeography of M. ambigua has revealed new insights into the biogeography of the Australian arid zone, particularly with regard to evolutionary events chronologically associated with cyclical moist and dry conditions. We propose that M. ambigua originated on the east coast (FITZ) and crossed a major geographic barrier, the Great Dividing Range (GDR), to colonize the inland basins (MDB, LEB and BULL). We infer a series of demographic and range expansion events for M. ambigua consistent with a scenario of moister Pleistocene conditions and increased connectivity of freshwater environments, both within and among drainage basins. Major lineages then diversified following isolation of freshwater environments under increasingly arid climate conditions. We suggest that management priorities for M. ambigua should include the resolution of taxonomic uncertainties and the maintenance of genetic diversity of both stocked populations in the MDB and native populations of the LEB that may be at risk of further isolation and reduced gene flow due to increased aridification under future climate change scenarios. [ABSTRACT FROM AUTHOR]

Abstract: The elasmobranch fish are an ancient, evolutionarily successful, but under-researched vertebrate group, particularly in regard to their recent evolutionary history. Their lineage has survived four mass extinction events and most present day taxa are thought to be derived from Mesozoic forms. Here we present a molecular phylogenetic analysis of the family Orectolobidae that provides evidence for recent events of diversification in this shark group. Species interrelationships in Orectolobidae were reconstructed based on four mitochondrial and nuclear genes. In line with previous morphological work, our results do not support current taxonomic arrangements in Orectolobidae and indicate that a taxonomic revision of the family is warranted. We propose that the onset of diversification of orectolobid sharks is of Miocene age and occurred within the Indo-Australian region. Surprisingly, we also find evidence for a recent (∼last 2 million years) and rapid radiation of wobbegong sharks. Allopatric speciation followed by range expansion seems like the general most likely explanation to account for wobbegong relationships and distributions. We suggest that the evolution of this shark group was mostly influenced by two temporal scenarios of diversification. The oldest relates to major geological changes in the Indo-West Pacific associated with the Miocene collision of the Indo-Australian and Eurasian plates. The most recent scenario was influenced by changes in oceanography and the emergence of biogeographic barriers related to Pleistocene glacial cycles in Australian waters. [Copyright &y& Elsevier]

1. Historic and extant landscape structures and environmental conditions are known to influence phylogeographic patterns and population histories in organisms from Amazonia. Recent work suggests that events of the Tertiary Period have played a significant role in generating biodiversity in this exceptionally rich but understudied region. However, species distributions and population structures are also affected by recent environmental and physical changes, especially within highly dynamic ecosystems. 2. The cardinal tetra is a small luminous fish native to the dynamic flooded forest ecosystems of the Rio Negro and Orinoco basins of South America. This very popular aquarium fish represents the single most important species in the ornamental fishery of the Rio Negro, an activity of high socio-economic value for local riverine communities. Here we use a fine-scale sampling regime and sequence data from the second intron of the Ribosomal protein S7 (S7 2) to investigate population structure, colonisation history and genealogical relationships in cardinal tetras of the Rio Negro. 3. High levels of S7 2 polymorphisms revealed phylogeographic patterns across several temporal settings that appear associated with the complex dynamics of the region. Our results suggest a long history of isolation and persistence of cardinal tetra populations in the headwaters and upper regions of the Rio Negro and recent events of colonisation within the incipient Rio Negro floodplain. These colonisation events were followed by recent population expansions likely facilitated by the establishment of the extensive Rio Negro floodplain, an anabranching ecosystem of Holocene age. 4. Our reconstruction of the phylogeographic history of cardinal tetras based on S7 2 intron sequence data reflects the complex influence of both geomorphological and climatic events through time in the Rio Negro basin. Our findings also indicate that in order to maintain the cardinal tetra fishery as a sustainable activity for rural Amazonians, the fishery should be restricted to the middle Rio Negro, the region of the basin where population replenishment is more likely to occur. [ABSTRACT FROM AUTHOR]

Phylogeography is a young, vigorous and integrative field of study that uses genetic data to understand the history of populations. This field has recently expanded into many areas of biology and also into several historical disciplines of Earth sciences. In this review, I present a numerical synthesis of the phylogeography literature based on an examination of over 3000 articles published during the first 20 years of the field (i.e. from 1987 to 2006). Information from several topics needed to evaluate the progress, tendencies and deficiencies of the field is summarized for 10 major groups of organisms and at a global scale. The topics include the geography of phylogeographic surveys, comparative nature of studies, temporal scales and major environments investigated, and genetic markers used. I also identify disparities in research productivity between the developing and the developed world, and propose ways to reduce some of the challenges faced by phylogeographers from less affluent countries. Phylogeography has experienced explosive growth in recent years fuelled by developments in DNA technology, theory and statistical analysis. I argue that the intellectual maturation of the field will eventually depend not only on these recent developments, but also on syntheses of comparative information across different regions of the globe. For this to become a reality, many empirical phylogeographic surveys in regions of the Southern Hemisphere (and in developing countries of the Northern Hemisphere) are needed. I expect the information and views presented here will assist in promoting international collaborative work in phylogeography and in guiding research efforts at both regional and global levels. [ABSTRACT FROM AUTHOR]

Nine polymorphic microsatellite loci were characterized from an enrichment library of the Australian praying mantid Ciulfina rentzi, a group with a unique reproductive morphology and behaviour. The number of alleles per locus ranged from three to 16 and heterozygosity from 0.24 to 0.94. These markers are the first microsatellites developed for any praying mantid. They will be useful for paternity analysis and for population genetic studies in the Wet Tropics World Heritage Region of Australia. [ABSTRACT FROM AUTHOR]

Eleven polymorphic microsatellite loci were developed from an enrichment library of the roman, Chrysoblephus laticeps, and characterized for 40 individuals collected in Africa's largest and oldest Marine Protected Area (MPA), the Tsitsikamma National Park. The number of alleles per locus ranged from three to 19, and heterozygosities ranged from 0.20 to 0.85. A significant departure from Hardy–Weinberg equilibrium was detected for one locus, and linkage disequilibrium was identified among three pairs of loci. The markers will be useful to detect whether populations resident in MPAs along the South African coast are genetically connected, and whether there is spillover of recruits into adjacent exploited areas. [ABSTRACT FROM AUTHOR]

We describe polymerase chain reaction primers that amplify the low-copy nuclear adenine nucleotide transporter gene in decapod crustaceans. These were tested on 35 species from 14 decapod families, and a single polymerase chain reaction product amplified in 32 species. Of 49 sequences generated, only two did not contain an intron, and the longest intron identified was more than 834 nucleotides in length. The amplified fragment is likely to be useful at various taxonomic levels. While the intron is suitable for phylogeographical/population genetic studies and to identify cryptic speciation, the second exon region is sufficiently long to provide signal at both the phylogeographical and phylogenetic levels. [ABSTRACT FROM AUTHOR]

Volcanic islands represent excellent models with which to study the effect of vicariance on colonization and dispersal, particularly when the evolution of genetic diversity mirrors the sequence of geological events that led to island formation. Phylogeographic inference, however, can be particularly challenging for recent dispersal events within islands, where the antagonistic effects of land bridge formation and vicariance can affect movements of organisms with limited dispersal ability. We investigated levels of genetic divergence and recovered signatures of dispersal events for 631 Galapagos giant tortoises across the volcanoes of Sierra Negra and Cerro Azul on the island of Isabela. These volcanoes are among the most recent formations in the Galapagos (<0.7 million years), anti previous studies based on genetic and morphological data could not recover a consistent pattern of lineage sorting. We integrated nested clade analysis of mitochondrial DNA control region sequences, to infer historical patterns of colonization, and a novel Bayesian multilocus geno-typing method for recovering evidence of recent migration across volcanoes using eleven microsatellite loci. These genetic studies illuminate taxonomic distinctions as well as provide guidance to possible repatriation programs aimed at countering the rapid population declines of these spectacular animals. [ABSTRACT FROM AUTHOR]

The recognition of cryptic diversity within geographically widespread species is gradually becoming a trend in the highly speciose Neotropical biomes. The statistical methods to recognise such cryptic lineages are rapidly advancing, but have rarely been applied to genomic-scale datasets. Herein, we used phylogenomic data to investigate phylogenetic history and cryptic diversity within Tropidurus itambere , a lizard endemic to the Cerrado biodiversity hotspot. We applied a series of phylogenetic methods to reconstruct evolutionary relationships and a coalescent Bayesian species delimitation approach (BPP) to clarify species limits. The BPP results suggest that the widespread nominal taxon comprises a complex of 5 highly supported and geographically structured cryptic species. We highlight and discuss the different topological patterns recovered by concatenated and coalescent species tree methods for these closely related lineages. Finally, we suggest that the existence of cryptic lineages in the Cerrado is much more common than traditionally thought, highlighting the value of using NGS data and coalescent techniques to investigate patterns of species diversity. [ABSTRACT FROM AUTHOR]

Levels of biodiversity in the Neotropics are largely underestimated despite centuries of research interest in this region. This is particularly true for the Cerrado, the largest Neotropical savanna and a formally recognized biodiversity hotspot. Molecular species delimitation methods have become essential tools to uncover cryptic species and can be notably robust when coupled with morphological information. We present the first evaluation of the monophyly and cryptic speciation of a widespread Cerrado endemic lizard, Gymnodactylus amarali , using phylogenetic and species-trees methods, as well as a coalescent-based Bayesian species delimitation method. We tested whether lineages resulting from the analyses of molecular data are morphologically diagnosed by traditional meristic scale characters. We recovered eight deeply divergent molecular clades within G. amarali , and two additional ones from seasonally dry tropical forest enclaves between the Cerrado and the Caatinga biomes. Analysis of morphological data statistically corroborated the molecular delimitation for all groups, in a pioneering example of the use of support vector machines to investigate morphological differences in animals. The eight G. amarali clades appear monophyletic and endemic to the Cerrado. They display several different properties used by biologists to delineate species and are therefore considered here as candidates for formal taxonomic description. We also present a preliminary account of the biogeographic history of these lineages in the Cerrado, evidence for speciation of sister lineages in the Cerrado–Caatinga contact, and highlight the need for further morphological and genetic studies to assess cryptic diversity in this biodiversity hotspot. [ABSTRACT FROM AUTHOR]