A targeted capture approach to generating reference sequence databases for chloroplast gene regions.

Metabarcoding has improved the way we understand plants within our environment, from their ecology and conservation to invasive species management. The notion of identifying plant taxa within environmental samples relies on the ability to match unknown sequences to known reference libraries. Without comprehensive reference databases, species can go undetected or be incorrectly assigned, leading to false-positive and false-negative detections.

Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes.

Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs.

Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow.

Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant 'islands'. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia.

A new species of turtle-headed sea Snake (Emydocephalus: Elapidae) endemic to Western Australia.

We describe a new species of turtle-headed sea snake Emydocephalus orarius sp. nov. (Elapidae) from Western Australia's Coral Coast, Pilbara and Kimberley regions.

Molecular resolution to a morphological controversy: The case of North American fossil muskoxen Bootherium and Symbos.

The musk ox (Ovibos moschatus) is the only surviving member of a group of Pleistocene North American musk ox genera (Praeovibos, Ovibos, Bootherium, Euceratherium, and Soergelia) whose taxonomy is uncertain. The helmeted musk ox (Bootherium bombifrons) and the woodland musk ox (Symbos cavifrons) have been synonymised as male and female forms of a single Nearctic species found from Alaska, in the north, to Texas, in the south. However, this reclassification has not been tested using molecular data, despite the potential to use ancient DNA to examine these late Pleistocene taxa.

Genetic diversity and drivers of dwarfism in extinct island emu populations.

Australia's iconic emu () is the only living representative of its genus, but fossil evidence and reports from early European explorers suggest that three island forms (at least two of which were dwarfs) became extinct during the nineteenth century. While one of these-the King Island emu-has been found to be conspecific with Australian mainland emus, little is known about how the other two forms-Kangaroo Island and Tasmanian emus-relate to the others, or even the size of Tasmanian emus. We present a comprehensive genetic and morphological analysis of diversity, including data from one of the few definitively genuine Tasmanian emu specimens known.

Molecular phylogenetics supports the origin of an endemic Balearic shrew lineage (Nesiotites) coincident with the Messinian Salinity Crisis.

The red-toothed shrews (Soricinae) are the most widespread subfamily of shrews, distributed from northern South America to North America and Eurasia. Within this subfamily, the tribe Nectogalini includes the fossil species Nesiotites hidalgo recorded from the Late Pleistocene to Holocene of the Balearic Islands (Western Mediterranean). Although there is a consensus about the close relationship between the extinct red-toothed shrew genera Nesiotites and Asoriculus based on morphology, molecular data are necessary to further evaluate the phylogenetic relationships of the Balearic fossils.

Potential Causative Mutation for Melanism in Rats Identified in the Agouti Signaling Protein Gene (Asip) of the Rattus rattus Species Complex on Okinawa Island, Japan.

The occurrence of black fur, or melanism, in many mammalian species is known to be linked to DNA sequence variation in the agouti signaling protein (Asip) gene, which is a major determinant of eumelanin and pheomelanin pigments in coat color. We investigated 38 agouti (i.e.

East African origins for Madagascan chickens as indicated by mitochondrial DNA.

The colonization of Madagascar by Austronesian-speaking people during AD 50-500 represents the most westerly point of the greatest diaspora in prehistory. A range of economically important plants and animals may have accompanied the Austronesians. Domestic chickens () are found in Madagascar, but it is unclear how they arrived there.

Phylogeography of the antilopine wallaroo () across tropical northern Australia.

The distribution of antilopine wallaroo, , is marked by a break in the species' range between Queensland and the Northern Territory, coinciding with the Carpentarian barrier. Previous work on revealed limited genetic differentiation between the Northern Territory and Queensland populations across this barrier. The study also identified a number of divergent lineages in the Northern Territory, but was unable to elucidate any geographic structure.

Phylogeography of Eastern Grey Kangaroos, Macropus giganteus, Suggests a Mesic Refugium in Eastern Australia.

Phylogeographic studies around the world have identified refugia where fauna were able to persist during unsuitable climatic periods, particularly during times of glaciation. In Australia the effects of Pleistocene climate oscillations on rainforest taxa have been well studied but less is known about the effects on mesic-habitat fauna, such as the eastern grey kangaroo (Macropus giganteus). The eastern grey kangaroo is a large mammal that is common and widespread throughout eastern Australia, preferring dry mesic habitat, rather than rainforest.

Late pleistocene Australian marsupial DNA clarifies the affinities of extinct megafaunal kangaroos and wallabies.

Understanding the evolution of Australia's extinct marsupial megafauna has been hindered by a relatively incomplete fossil record and convergent or highly specialized morphology, which confound phylogenetic analyses. Further, the harsh Australian climate and early date of most megafaunal extinctions (39-52 ka) means that the vast majority of fossil remains are unsuitable for ancient DNA analyses. Here, we apply cross-species DNA capture to fossils from relatively high latitude, high altitude caves in Tasmania.

Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific.

The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial control region DNA from 122 modern and 22 ancient chicken specimens from Polynesia and Island Southeast Asia and used these together with Bayesian modeling methods to examine the human dispersal of chickens across this area.

Pleistocene Chinese cave hyenas and the recent Eurasian history of the spotted hyena, Crocuta crocuta.

The living hyena species (spotted, brown, striped and aardwolf) are remnants of a formerly diverse group of more than 80 fossil species, which peaked in diversity in the Late Miocene (about 7-8 Ma). The fossil history indicates an African origin, and morphological and ancient DNA data have confirmed that living spotted hyenas (Crocuta crocuta) of Africa were closely related to extinct Late Pleistocene cave hyenas from Europe and Asia. The current model used to explain the origins of Eurasian cave hyena populations invokes multiple migrations out of Africa between 3.