Organisms living in arid environments are predicted to be at increased risk of extinction under climatic and anthropogenic change. Response to past climate change can provide some insights into these risks; however, our understanding of the diversification and evolutionary history of many arid‐adapted species is still limited, particularly in Australia. Here, we evaluate the demographic and evolutionary history of a widespread...

Parthenogenesis, or all‐female clonal reproduction, is rare among vertebrates. This is often attributed to the selective disadvantages of assumed reduction of genetic diversity in the absence of sex. However, parthenogenetic vertebrates have highly complex evolutionary histories, with most arising through hybridisation and many being polyploid. Here, we show that geographically widespread triploid parthenogenetic forms of the...

Translocation programmes are increasingly being informed by genetic data to monitor and enhance conservation outcomes for both natural and established populations. These data provide a window into contemporary patterns of genetic diversity, structure and relatedness that can guide managers in how to best source animals for their translocation programmes. The inclusion of historical samples, where possible, strengthens monitori...

Mitochondrial introgression is common among animals and is often first identified through mitonuclear discordance—discrepancies between evolutionary relationships inferred from mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA). Over recent decades, genomic data have also revealed extensive nuclear introgression in many animal groups, with implications for genetic and phenotypic diversity. However, the extent to which mtDNA int...

Genomic‐scale datasets, sophisticated analytical techniques, and conceptual advances have disproportionately failed to resolve species boundaries in some groups relative to others. To understand the processes that underlie taxonomic intractability, we dissect the speciation history of an Australian lizard clade that arguably represents a “worst‐case” scenario for species delimitation within vertebrates: the Ctenotus inornatus...

Phylogeographic studies of continental clades, especially when combined with palaeoclimate modelling, provide powerful insight into how environment drives speciation across climatic contexts. Australia, a continent characterized by disparate modern biomes and dynamic climate change, provides diverse opportunity to reconstruct the impact of past and present environments on diversification. Here, we use genomic‐scale data (1310...

Population isolation and concomitant genetic divergence, resulting in strong phylogeographical structure, is a core aspect of speciation initiation. If and how speciation then proceeds and ultimately completes depends on multiple factors that mediate reproductive isolation, including divergence in genomes, ecology and mating traits. Here we explored these multiple dimensions in two young (Plio‐Pleistocene) species complexes of...

Landscape‐scale conservation that considers metapopulation dynamics will be essential for preventing declines of species facing multiple threats to their survival. Toward this end, we developed a novel approach that combines occurrence records, spatial–environmental data, and genetic information to model habitat, connectivity, and patterns of genetic structure and link spatial attributes to underlying ecological mechanisms. Us...

Aim We consider the opportunities and challenges comparative phylogeography (CP) faces in the genomic age to determine: (1) how we can maximise the potential of big CP analyses to advance biogeographic and macroevolutionary theory; and (2) what we can, and will struggle, to achieve using CP approaches in this era of genomics. Location World‐wide. Taxon All. Methods We review the literature to discuss the future of CP ‐ particu...

When closely related species come into contact via range expansion, both may experience reduced fitness as a result of the interaction. Selection is expected to favour traits that minimize costly interspecies reproductive interactions (such as mismating) via a phenomenon called reproductive character displacement (RCD). Research on RCD frequently assumes secondary contact between species, but the geographical history of specie...

Landscape genetics commonly focuses on the effects of environmental resistance on animal dispersal patterns, but there is an emerging focus on testing environmental effects on emigration and settlement choices. In this study, we used landscape genetics approaches to quantify dispersal patterns in the world's largest crocodilian, the saltwater crocodile ( Crocodylus porosus ), and demonstrated environmental influences on three...

Differences in the geographic scale and depth of phylogeographic structure across codistributed taxa can reveal how microevolutionary processes such as population isolation and persistence drive diversification. In turn, environmental heterogeneity, species’ traits, and historical biogeographic barriers may influence the potential for isolation and persistence. Using extensive SNP data and a combination of population genetic s...

Aim Understanding where and why species diversity is geographically concentrated remains a challenge in biogeography and macroevolution. This is true for the Cerrado, the most biodiverse tropical savanna in the world, which has experienced profound biodiversity loss. Previous studies have focused on a single metric (species composition), neglecting the fact that ‘species’ within the biome are often composed of cryptic species....

Aim Focussing on pairs of sister species across three genera of scincid lizards, we use genomic evidence to test for larger‐scale, late‐Pleistocene changes in distributions of lizards in the Australian arid zone (AZ) than in the adjacent monsoonal tropics (MT). Location Northern and central Australia. Taxon Scincidae: Squamata. Methods We sequenced ~2000 nuclear exons and one mitochondrial gene across the distributions of spec...

The Arctic Mediterranean (AM) is the collective name for the Arctic Ocean, the Nordic Seas, and their adjacent shelf seas. Water enters into this region through the Bering Strait (Pacific inflow) and through the passages across the Greenland–Scotland Ridge (Atlantic inflow) and is modified within the AM. The modified waters leave the AM in several flow branches which are grouped into two different categories: (1) overflow of d...

Genome divergence is greatly influenced by gene flow during early stages of speciation. As populations differentiate, geographic barriers can constrain gene flow and so affect the dynamics of divergence and speciation. Current geography, specifically disjunction and continuity of ranges, is often used to predict the historical gene flow during the divergence process. We test this prediction in eight meliphagoid bird species co...

Aim The aim was to examine the links between past biome stability, vegetation dynamics and biodiversity patterns. Location South America. Time period Last 30,000 years. Major taxa studied Plants. Methods We classified South America into major biomes according to their dominant plant functional groups (grasses, trees and shrubs) and ran a random forest (RF) classification with data on current climate. We then fitted the algorit...

Spatial responses of species to past climate change depend on both intrinsic traits (climatic niche breadth, dispersal rates) and the scale of climatic fluctuations across the landscape. New capabilities in generating and analysing population genomic data, along with spatial modelling, have unleashed our capacity to infer how past climate changes have shaped populations, and by extension, complex communities. Combining these a...

Aim The diversification of the Australian avifauna has been greatly influenced by prominent historical and modern barriers to dispersal. The aims of this study were to characterize the patterns of divergence in population pairs of meliphagoid birds across adjacent transition zones and characterize how well morphometric divergence, habitat association and taxonomic or species ranking can predict genetic divergence. Location Nor...

The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture data set and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in...

Species endemic to the tropical regions are expected to be vulnerable to future climate change due in part to their relatively narrow climatic niches. In addition, these species are more likely to have responded strongly to past climatic change, and this can be explored through phylogeographic analyses. To test the hypothesis that tropical specialists are more sensitive to climate change than climate generalists, we generated...