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The relationships of the extinct New Zealand ravens (Corvus spp.) are poorly understood. We sequenced the mitogenomes of the two currently recognised species and found they were sister-taxa to a clade comprising the Australian raven, little raven, and forest raven (C.coronoides, C. mellori and C. tasmanicus respectively). The divergence between the New Zealand ravens and Australian raven clade occurred in the latest Pliocene, which coincides with the onset of glacial deforestation. We also found that the divergence between the two putative New Zealand species C. antipodum and C. moriorum probably occurred in the late Pleistocene making their separation as species untenable. Consequently, we consider Corax antipodum (Forbes, 1893) to be a subspecies of Corvus moriorum Forbes, 1892. We re-examine the osteological evidence that led 19th century researchers to assign the New Zealand taxa to a separate genus, and re-assess these features in light of our new phylogenetic hypotheses. Like previous researchers, we conclude that the morphology of the palate of C. moriorum is unique among the genus Corvus, and suggest this may be an adaptation for a specialist diet.

The New Zealand acanthisittid wrens are the sister-taxon to all other "perching birds" (Passeriformes) and - including recently extinct species - represent the most diverse endemic passerine family in New Zealand. Consequently, they are important for understanding both the early evolution of Passeriformes and the New Zealand biota. However, five of the seven species have become extinct since the arrival of humans in New Zealand, complicating evolutionary analyses. The results of morphological analyses have been largely equivocal, and no comprehensive genetic analysis of Acanthisittidae has been undertaken. We present novel mitochondrial genome sequences from four acanthisittid species (three extinct, one extant), allowing us to resolve the phylogeny and revise the taxonomy of acanthisittids. Reanalysis of morphological data in light of our genetic results confirms a close relationship between the extant rifleman (Acanthisitta chloris) and an extinct Miocene wren (Kuiornis indicator), making Kuiornis a useful calibration point for molecular dating of passerines. Our molecular dating analyses reveal that the stout-legged wrens (Pachyplichas) diverged relatively recently from a more gracile (Xenicus-like) ancestor. Further, our results suggest a possible Early Oligocene origin of the basal Lyall's wren (Traversia) lineage, which would imply that Acanthisittidae survived the Oligocene marine inundation of New Zealand and therefore that the inundation was not complete.

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. In the present study, we sequenced mitochondrial genomes from seven subfossil musk ox specimens (originally identified as Bootherium and/or Symbos), allowing us to evaluate the identity of these muskoxen, explore their phylogeography, and estimate the timeline for their evolution. We also used nuclear genomic data to determine the sex of six of our seven samples. Ultimately, our molecular data support the synonymisation of the North American muskoxen Bootherium and Symbos.

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. We obtained a near complete mitochondrial genome of N. hidalgo, allowing the first molecular phylogenetic analysis of this species. Analyses based on 15,167 bp of the mitochondrial genome placed N. hidalgo as close relative to the extant Himalayan shrew (Soriculus nigrescens), and a combined analysis using molecular and morphological data confirm that N. hidalgo and Asoriculus gibberodon are sister-taxa with S. nigrescens as the immediate outgroup. Molecular clock and divergence estimates suggest that the split between N. hidalgo and its closest living relative occurred around 6.44 Ma, which is in agreement with the previously proposed colonisation of the Balearic Islands from mainland Europe by nectogaline shrews during the Messinian Salinity Crisis (5.97–5.33 My ago). Our results highlight that it is possible to retrieve genetic data from extinct small mammals from marginal environments for DNA preservation. Additional finds from the fossil record of Soricinae from the Eurasian Late Miocene/Early Pliocene are needed to shed further light on the still confusing taxonomy and paleobiogeography of this clade.

The Chatham duck (Pachyanas chathamica) represented one of just three modern bird genera endemic to the Chatham archipelago (situated ∼850 km east of New Zealand) but became extinct soon after humans first settled the islands (c. 13th–15th centuries AD). The taxonomic affinity of the Chatham duck remains largely unresolved; previous studies have tentatively suggested placements within both Tadornini (shelducks) and Anatini (dabbling ducks). Herein, we sequence a partial mitochondrial genome (excluding the D-loop) from the Chatham duck and discover that it was a phenotypically-divergent species within the genus Anas (Anatini). This conclusion is further supported by a re-examination of osteological characters. Our molecular analyses convincingly demonstrate that the Chatham duck is the most basal member of a sub-clade comprising the New Zealand and sub-Antarctic brown teals (the brown teal [A. chlorotis], Auckland Island teal [A. aucklandica] and Campbell Island teal [A. nesiotis]). Molecular clock calculations based on an ingroup fossil calibration support a divergence between the Chatham duck and its sister-taxa that is consistent with the estimated time of emergence of the Chatham Islands. Additionally, we find that mtDNA divergence between the two sub-Antarctic teal species (A. aucklandica and A. nesiotis) significantly pre-dates the last few glacial cycles, raising interesting questions about the timing of their dispersal to these islands, and the recent phylogeographic history of brown teal lineages in the region.

The geographical range of extant peccaries extends from the southwestern United States through Central America and into northern Argentina. However, from the Miocene until the Pleistocene now-extinct peccary species inhabited the entirety of North America. Relationships among the living and extinct species have long been contentious. Similarly, how and when peccaries moved from North to South America is unclear. The North American flat-headed peccary (Platygonus compressus) became extinct at the end of the Pleistocene and is one of the most abundant subfossil taxa found in North America, yet despite this extensive fossil record its phylogenetic position has not been resolved. This study is the first to present DNA data from the flat-headed peccary and full mitochondrial genome sequences of all the extant peccary species. We performed a molecular phylogenetic analysis to determine the relationships among ancient and extant peccary species. Our results suggested that the flat-headed peccary is sister-taxon to a clade comprising the extant peccary species. Divergence date estimates from our molecular dating analyses suggest that if extant peccary diversification occurred in South America then their common ancestor must have dispersed from North America to South America well before the establishment of the Isthmus of Panama. We also investigated the genetic diversity of the flat-headed peccary by performing a preliminary population study on specimens from Sheriden Cave, Ohio. Flat-headed peccaries from Sheriden Cave appear to be genetically diverse and show no signature of population decline prior to extinction. Including additional extinct Pleistocene peccary species in future phylogenetic analyses will further clarify peccary evolution.