Reduction of genetic diversity in 'Alala (Hawaiian crow; Corvus hawaiiensis) between the late 1800s and the late 1900s.

Genetic and genomic data are increasingly used to aid conservation management of endangered species by providing insights into evolutionary histories, factors associated with extinction risks, and potential for future adaptation. For the 'Alala, or Hawaiian crow (Corvus hawaiiensis), genetic concerns include negative correlations between inbreeding and hatching success. However, it is unclear if low genetic diversity and inbreeding depression are consequences of a historical population bottleneck, or if 'Alala had historically low genetic diversity that predated human influence, perhaps as a result of earlier declines or founding events. In this study, we applied a hybridization-based sequence capture to generate a genome-wide single nucleotide polymorphism (SNP) dataset for comparing historical specimens collected in the 1890s, when 'Alala were more numerous, to samples taken between 1973 and 1998, when 'Alala population densities were near the lowest documented levels in the wild, prior to all individuals being collected for captive rearing. We found low genome-wide diversity in both sample groups, however, the modern sample group (1973 to 1998 cohort) exhibited relatively fewer polymorphic alleles, a lower proportion of polymorphic loci, and lower observed heterozygosity, consistent with a population decline and potential bottleneck effects. These results combined with a current low population size highlight the importance of continued efforts by conservation managers to mitigate inbreeding and maintain founder representation to preserve what genetic diversity remains.

Conservation genomics and systematics of a near-extinct island radiation.

Conservation benefits from incorporating genomics to explore the impacts of population declines, inbreeding, loss of genetic variation and hybridization. Here we use the near-extinct Mariana Islands reedwarbler radiation to showcase how ancient DNA approaches can allow insights into the population dynamics of extinct species and threatened populations for which historical museum specimens or material with low DNA yield (e.g., scats, feathers) are the only sources for DNA. Despite their having paraphyletic mitochondrial DNA (mtDNA), nuclear single nucleotide polymorphisms (SNPs) support the distinctiveness of critically endangered Acrocephalus hiwae and the other three species in the radiation that went extinct between the 1960s and 1990s. Two extinct species, A. yamashinae and A. luscinius, were deeply divergent from each other and from a third less differentiated lineage containing A. hiwae and extinct A. nijoi. Both mtDNA and SNPs suggest that the two isolated populations of A. hiwae from Saipan and Alamagan Islands are sufficiently distinct to warrant subspecies recognition and separate conservation management. We detected no significant differences in genetic diversity or inbreeding between Saipan and Alamagan, nor strong signatures of geographical structuring within either island. However, the implications of possible signatures of inbreeding in both Saipan and Alamagan, and long-term population declines in A. hiwae that pre-date modern anthropogenic threats require further study with denser population sampling. Our study highlights the value that conservation genomics studies of island radiations have as windows onto the possible future for the world's biota as climate change and habitat destruction increasingly fragment their ranges and contribute to rapid declines in population abundances.

Nuclear introns help unravel the diversification history of the Australo-Pacific Petroica robins.

Australo-Pacific Petroica robins are known for their striking variability in sexual plumage coloration. Molecular studies in recent years have revised the taxonomy of species and subspecies boundaries across the southwest Pacific and New Guinea. However, these studies have not been able to resolve phylogenetic relationships within Petroica owing to limited sampling of the nuclear genome. Here, we sequence five nuclear introns across all species for which fresh tissue was available. Nuclear loci offer support for major geographic lineages that were first inferred from mtDNA. We find almost no shared nuclear alleles between currently recognized species within the New Zealand and Australian lineages, whereas the Pacific robin radiation has many shared alleles. Multilocus coalescent species trees based on nuclear loci support a sister relationship between the Australian lineage and the Pacific robin radiation-a node that is poorly supported by mtDNA. We also find discordance in support for a sister relationship between the similarly plumaged Rose Robin (P. rosea) and Pink Robin (P. rodinogaster). Our nuclear data complement previous mtDNA studies in suggesting that the phenotypically cryptic eastern and western populations of Australia's Scarlet Robin (P. boodang) are genetically distinct lineages at the early stages of divergence and speciation.

Genomic evidence of speciation reversal in ravens.

Many species, including humans, have emerged via complex reticulate processes involving hybridisation. Under certain circumstances, hybridisation can cause distinct lineages to collapse into a single lineage with an admixed mosaic genome. Most known cases of such 'speciation reversal' or 'lineage fusion' involve recently diverged lineages and anthropogenic perturbation. Here, we show that in western North America, Common Ravens (Corvus corax) have admixed mosaic genomes formed by the fusion of non-sister lineages ('California' and 'Holarctic') that diverged ~1.5 million years ago. Phylogenomic analyses and concordant patterns of geographic structuring in mtDNA, genome-wide SNPs and nuclear introns demonstrate long-term admixture and random interbreeding between the non-sister lineages. In contrast, our genomic data support reproductive isolation between Common Ravens and Chihuahuan Ravens (C. cryptoleucus) despite extensive geographic overlap and a sister relationship between Chihuahuan Ravens and the California lineage. These data suggest that the Common Raven genome was formed by secondary lineage fusion and most likely represents a case of ancient speciation reversal that occurred without anthropogenic causes.

Sequencing of the complete mitochondrial genome of the common raven Corvus corax (Aves: Corvidae) confirms mitogenome-wide deep lineages and a paraphyletic relationship with the Chihuahuan raven C. cryptoleucus.

Previous studies based on single mitochondrial markers have shown that the common raven (Corvus corax) consists of two highly diverged lineages that are hypothesised to have undergone speciation reversal upon secondary contact. Furthermore, common ravens are paraphyletic with respect to the Chihuahuan raven (C. cryptoleucus) based on mitochondrial DNA (mtDNA). Here we explore the causes of mtDNA paraphyly by sequencing whole mitochondrial genomes of 12 common ravens from across the Northern Hemisphere, in addition to three Chihuahuan ravens and one closely related brown-necked raven (C. ruficollis) using a long-range PCR protocol. Our raven mitogenomes ranged between 16925-16928 bp in length. GC content varied from 43.3% to 43.8% and the 13 protein coding genes, two rRNAs and 22 tRNAs followed a standard avian mitochondrial arrangement. The overall divergence between the two common raven clades was 3% (range 0.3-5.8% in 16 regions including the protein coding genes, rRNAs and the control region). Phylogenies constructed from whole mitogenomes recovered the previously found mitochondrial sister relationship between the common raven California clade and the Chihuahuan raven (overall divergence 1.1%), which strengthens the hypothesis that mtDNA paraphyly in the common raven results from speciation reversal of previously distinct Holarctic and California lineages.

Australia's arid-adapted butcherbirds experienced range expansions during Pleistocene glacial maxima.

A model of range expansions during glacial maxima (GM) for cold-adapted species is generally accepted for the Northern Hemisphere. Given that GM in Australia largely resulted in the expansion of arid zones, rather than glaciation, it could be expected that arid-adapted species might have had expanded ranges at GM, as cold-adapted species did in the Northern Hemisphere. For Australian biota, however, it remains paradigmatic that arid-adapted species contracted to refugia at GM. Here we use multilocus data and ecological niche models (ENMs) to test alternative GM models for butcherbirds. ENMs, mtDNA and estimates of nuclear introgression and past population sizes support a model of GM expansion in the arid-tolerant Grey Butcherbird that resulted in secondary contact with its close relative--the savanna-inhabiting Silver-backed Butcherbird--whose contemporary distribution is widely separated. Together, these data reject the universal use of a GM contraction model for Australia's dry woodland and arid biota.

A multilocus coalescent analysis of the speciational history of the Australo-Papuan butcherbirds and their allies.

Changes in geology, sea-level and climate are hypothesised to have been major driving processes of evolutionary diversification (speciation and extinction) in the Australo-Papuan region. Here we use complete species-level sampling and multilocus (one mitochondrial gene, five nuclear loci) coalescent analyses to estimate evolutionary relationships and test hypotheses about the role of changes in climate and landscape in the diversification of the Australo-Papuan butcherbirds and allies (Cracticinae: Cracticus, Strepera, Peltops). Multilocus species trees supported the current classification of the morphologically, ecologically and behaviourally divergent Australian Magpie (Cracticus tibicen (previously Gymnorhina tibicen)) as a member of an expanded genus Cracticus, which includes seven other species with 'butcherbird' morphology and behaviour. Non-monophyly of currently recognised species within Peltops and the white-throated butcherbird species-group (C.argenteus, C.mentalis, C. torquatus) at both mtDNA and nuclear loci suggest that a comprehensive taxonomic revision is warranted for both of these groups. The time-calibrated multilocus species tree revealed an early divergence between the New Guinean rainforest-restricted Peltops lineage and the largely open-habitat inhabiting Cracticus (butcherbirds and magpies) plus Strepera (currawongs) lineage around 17-28Ma, as well as a relatively recent radiation of lineages within Cracticus over the past 8Ma. Overall, patterns and timings of speciation were consistent with the hypothesis that both the expansion of open sclerophyllous woodlands 25-30Ma and the formation of extensive grassland-dominated woodlands 6-8Ma allowed the radiation of lineages adapted to open woodland habitats.

Testing the effect of transient Plio-Pleistocene barriers in monsoonal Australo-Papua: did mangrove habitats maintain genetic connectivity in the Black Butcherbird?

Changes in climate and sea level are hypothesized to have promoted the diversification of biota in monsoonal Australia and New Guinea by causing repeated range disjunctions and restricting gene flow between isolated populations. Using a multilocus (one mtDNA locus, five nuclear introns) phylogeographic approach, we test whether populations of the mangrove and rainforest restricted Black Butcherbird (Cracticus quoyi) have diverged across several geographic barriers defined a priori for this region. Phylogeographic structure and estimates of divergence times revealed Plio-Pleistocene divergences and long-term restricted gene flow of populations on either side of four major geographic barriers between and within Australia and New Guinea. Overall, our data are consistent with the hypothesis that mesic-adapted species did not disperse across the open dry woodlands and grasslands that dominated the transient palaeo-landbridges during the Plio-Pleistocene despite the presence of mangrove forests that might have acted as dispersal corridors for mesic-adapted species. Our study offers one of the first multilocus perspectives on the impact of changes in climate and sea level on the population history of widespread species with disjunct ranges in Australia and New Guinea.