The Tasmanian devil (Sarcophilus harrisii) was widespread in Australia during the Late Pleistocene but is now endemic to the island of Tasmania. Low genetic diversity combined with the spread of devil facial tumour disease have raised concerns for the species' long-term survival. Here, we investigate the origin of low genetic diversity by inferring the species' demographic history using temporal sampling with summary statistics, full-likelihood and approximate Bayesian computation methods. Our results show extensive population declines across Tasmania correlating with environmental changes around the last glacial maximum and following unstable climate related to increased 'El Niñ o-Southern Oscillation' activity.

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The increasing number of non-model organism scaffold-level genome assemblies provides new information on biodiversity and how evolutionary processes have shaped it (Ellegren, 2014). An essential part of genome assembly and annotation is the identification of autosomes and sex chromosomes. Vertebrate species are generally diploid with the majority of their genome represented by a variable number of autosomes and two sex chromosomes (Graves, 2008).In mammals, the homogametic sex is the female (XX) and the heterogametic sex is the male (XY). This is opposite in birds, where males are homogametic (ZZ) and females heterogametic (ZW). Due to their inheritance, sex chromosomes differ from autosomes in several aspects of their population genetics and molecular evolution,

Africa is unique among the continents in having maintained an extraordinarily diverse and prolific megafauna spanning the Pleistocene-Holocene epochs. Little is known about the historical dynamics of this community and even less about the reasons for its unique persistence to modern times. We sequenced complete mitochondrial genomes from 43 Cape buffalo (Syncerus caffer caffer) to infer the demographic history of this large mammal. A combination of Bayesian skyline plots, simulations and Approximate Bayesian Computation (ABC) were used to distinguish population size dynamics from the confounding effect of population structure and identify the most probable demographic scenario. Our analyses revealed a late Pleistocene expansion phase concurrent with the human expansion between 80 000 and 10 000 years ago, refuting an adverse ecological effect of Palaeolithic humans on this quarry species, but also showed that the buffalo subsequently declined during the Holocene. The distinct two-phased dynamic inferred here suggests that a major ecological transition occurred in the Holocene. The timing of this transition coincides with the onset of drier conditions throughout tropical Africa following the Holocene Optimum (∼9000-5000 years ago), but also with the explosive growth in human population size associated with the transition from the Palaeolithic to the Neolithic cultural stage. We evaluate each of these possible causal factors and their potential impact on the African megafauna, providing the first systematic assessment of megafauna dynamics on the only continent where large mammals remain abundant.

Genomic diversity is the evolutionary foundation for adaptation to environmental change and thus is essential to consider in conservation planning. Island species are ideal for investigating the evolutionary drivers of genomic diversity, in part because of the potential for biological replicates. Here, we use genome data from 180 individuals spread among 27 island populations from 17 avian species to study the effects of island area, body size, demographic history and conservation status on contemporary genomic diversity. Our study expands earlier work on a small number of neutral loci to the entire genome and from a few species to many. We find significant positive correlation between island size and genomic diversity, a significant negative correlation between body size and genomic diversity, and that historical population declines significantly reduced contemporary genomic diversity. Our study shows that island size is the key factor in determining genomic diversity, indicating that habitat conservation is key to maintaining adaptive potential in the face of global environmental change. We found that threatened species generally had a significantly smaller values of Watterson's theta (θW = 4Neμ) compared to nonthreatened species, suggesting that θW may be useful as a conservation indicator for at‐risk species. Overall, these findings (a) provide biological insights into how genomic diversity scales with ecological, morphological and demographic factors; and (b) illustrate how population genomic data can be leveraged to better inform conservation efforts.

Aim The Tasmanian devil (Sarcophilus harrisii), currently restricted to the island of Tasmania, was found over most of the Australian mainland prior to its extinction ~3,000 years ago. Recent debate has focused on the roles of humans, climate change and dingoes as drivers of the mainland extinction. Determining past genetic diversity and population dynamics of both populations is a fundamental component to understand why the species went extinct on mainland Australia, but survived in Tasmania. Here, we investigate the phylogeography and demographic history of the Tasmanian devil across southern Australia over the last ~30k years. Location Australia. Taxon Tasmanian devil (Sarcophilus harrisii). Methods We used complete and partial mitochondrial DNA (mtDNA) genomes from 202 devils representing the extinct mainland (n = 17) and the extant Tasmanian (n = 185) populations to investigate the population dynamics of southern mainland and Tasmanian devils. The samples were sub‐fossil bones, historical museum specimens and modern tissue samples, dating from the present to 17k years before present. Using summary statistics, frequentist inference and Bayesian phylogenetic analysis we explored whether levels of genetic diversity were similar, and if the southern mainland experienced a gradual rather than an abrupt decline prior to its extinction. Results MtDNA genomes from mainland devils suggest that this population was larger and had more genetic diversity than the Tasmanian population. Directly dated samples indicates that the southern mainland population expanded after the last glacial maximum and remained stable until its extinction. The Tasmanian population has much lower diversity and descends from a single mtDNA lineage ~3,000 years ago. The recent origin for all Tasmanian mtDNA diversity is concordant with a previously documented late‐Holocene population bottleneck and is broadly contemporaneous with the extinction of the southern mainland population. Main conclusions This pattern shows striking similarity to the demographic history of thylacines, suggesting that a shared factor initiated population declines in both species on the southern mainland and in Tasmania. El Niño Southern Oscillation (ENSO)‐related climate change is the only factor common to both mainland Australia and Tasmania. Additional, direct or indirect, pressures from humans and/or dingoes on the mainland may have ultimately resulted in their extinction.

More than 25% of species assessed by the International Union for Conservation of Nature (IUCN) are threatened with extinction. Understanding how environmental and biological processes have shaped genomic diversity may inform management practices. Using 68 extant avian species, we parsed the effects of habitat availability and life-history traits on genomic diversity over time to provide a baseline for conservation efforts. We used published whole-genome sequence data to estimate overall genomic diversity as indicated by historical long-term effective population sizes ( N e ) and current genomic variability ( H ), then used environmental niche modelling to estimate Pleistocene habitat dynamics for each species. We found that N e and H were positively correlated with habitat availability and related to key life-history traits (body mass and diet), suggesting the latter contribute to the overall genomic variation. We found that H decreased with increasing species extinction risk, suggesting that H may serve as a leading indicator of demographic trends related to formal IUCN conservation status in birds. Our analyses illustrate that genome-wide summary statistics estimated from sequence data reflect meaningful ecological attributes relevant to species conservation.