Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal placental mammals

Mitogenome of Endemic Species of Flying Squirrel, Trogopterus xanthipes (Rodentia, Mammalia) and Phylogeny of the Sciuridae

Trogopterus xanthipes (Sciuridae, Rodentia) is a medium-sized flying squirrel species in the monotypic genus Trogopterus, and is endemic to China. It is distinguishable from other squirrels by the long black hairs on the inner and outer sides at the base of the ears and numerous ridges on the crowns of the upper and lower cheek teeth. Mitogenomes have been widely used in phylogenetic studies. We described T. xanthipes morphological features and successfully sequenced its mitogenome for the first time. The T. xanthipes mitogenome was conserved in number and order of genes. We analyzed codon usage patterns, evolutionary mutation rates, K2P distance, and genetic diversity of protein-coding genes. We reconstructed the phylogeny of Sciuridae (94 species and 21 genera in 4 subfamilies). All phylogenetic trees shared the same topologies and consistently supported the monophyly of Sciuridae, and the supported subfamilies relationship as follows: ((Xerinae + Callosciurinae) + Sciurinae) + Ratufinae. The relationship within the Sciurinae clade was ((Glaucomys + Hylopetes) + ((Trogopterus+Pteromys) + Petaurista) + Sciurus). The relationship within the Callosciurinae clade was Exilisciurus + ((Tamiops + Dremomys) + ((Lariscus+Sundasciurus) + Callosciurus)). The relationship within the Xerinae clade was Sciurotamias + (Tamias + (Callospermophilus + (Marmota + (Spermophilus + (Urocitellus + (Ictidomys + Cynomys)))))). The phylogenetic position among different subfamilies of Sciuridae was consistently recovered with high support across different datasets (PCGRNA and PCG12RNA) and supported the monophyletic lineage of each genus of Sciuridae. Trogopterus xanthipes was sister species to Pteromys volans. Species within the genus formed different minor clades, suggesting relatively high interspecific divergences. The tribe Pteromyini was sister taxon of the tribe Sciurini, which was not supported by the traditional division of Sciuridae into subfamilies Pteromyinae and Sciurinae. Hence, our data supported a division of the Sciuridae into five subfamilies.

Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahē and moho

Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahē (Porphyrio hochstetteri) and the moho (North Island takahē; P. mantelli), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahē and moho subfossils (12 takahē and 4 moho) and retrieved comparable sequence data from takahē museum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahē populations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahē have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time-calibrated phylogenetic analyses strongly support a sister species relationship between takahē and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted Porphyrio ancestor approximately 4 million years ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts.

Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone

Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near-complete mitogenomes from 22 specimens including 12 dry-preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra-short fragments and hybridization-capture of single-stranded DNA libraries. Phylogenetic analyses revealed three major, well-supported clades comprising samples from: 1) the Three Kings Islands; 2) the Auckland, Chatham and Antipodes Islands; and 3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our non-reliance on freshly collected or ethanol-preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult-to-sample populations. Broader application of these comparatively cost-effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research.

Revised phylogeny from complete mitochondrial genomes of phyllostomid bats resolves subfamilial classification

Classically, molecular phylogenetic trees of Phyllostomidae have been inferred using a combination of a few mitochondrial and nuclear markers. However, there is still uncertainty in the relationships, especially among deep clades within the family. In this study, we provide newly sequenced complete mitochondrial genomes from 26 bat species, including genomes of 23 species reported here for the first time. By carefully analysing these genomes using maximum likelihood and Bayesian methods and different ingroup and outgroup samples, partition schemes and data types, we investigated the robustness and sensitivity of our phylogenetic results. The optimal topologies were those inferred from the complete data matrix of nucleotides, with complex and highly parameterized substitution models and partition schemes. Our results show a statistically robust picture of the evolutionary relationships between phyllostomid subfamilies and clarify hitherto uncertain relationships of Lonchorhininae and Macrotinae.

Thirty years of ancient DNA and the faunal biogeography of Aotearoa New Zealand: lessons and future directions

Thirty years ago, DNA sequences were obtained from an extinct Aotearoa New Zealand animal for the first time. Since then, ancient DNA research has provided many - often unexpected - insights into the origins of New Zealand's terrestrial and marine vertebrate fauna. Because recent human activities in New Zealand have caused the decline or extinction of many endemic plant, bird, reptile, and marine mammal species, ancient DNA has been instrumental in reconstructing their identities and origins. However, most ancient DNA studies focusing on New Zealand species have been restricted to vertebrates, with small sample sizes, and/or relatively few genetic markers. This has limited their power to infer fine-scale biogeographic patterns, including (pre)historic distributions and range-shifts driven by past climate and environmental change. Recently, 'next-generation' methodological and technological advances have broadened the range of hypotheses that can feasibly be tested with ancient DNA. These advances represent an exciting opportunity for further exploring New Zealand biogeography using ancient DNA, but their promise has not yet been fully realised. In this review, we summarise the last 30 years of ancient DNA research into New Zealand faunal biogeography and highlight key objectives, challenges, and possibilities for the next 30 years and beyond.

Complete mitogenomes of four Trichiurus species: A taxonomic review of the T.lepturus species complex

Four Trichiurus species, T.japonicus, T.lepturus, T.nanhaiensis, and T.brevis, from the coasts of the China Seas, have been identified and their entire mitochondrial genomes (mitogenomes) have been sequenced by next-generation sequencing technology. A comparative analysis of five mitogenomes was conducted, including the mitogenome of T.gangeticus. The mitogenomes contained 16.568-16.840 bp and encoded 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding, and 21 transfer RNA-coding genes) and two typical noncoding control regions. Although tRNAPro is absent from Trichiurus mitogenomes, when compared with the 22 tRNAs reported in other vertebrates, the gene arrangements in the mitogenomes of the studied species are consistent with those in most teleost mitogenomes. The full-length sequences and protein-coding genes (PCGs) in the mitogenomes of the five species had obvious AT biases and negative GC skew values. Our study indicate that the specimens in the Indian Ocean are neither T.lepturus nor T.nanhaiensis but they are T.gangeticus; the Trichiurus species composition in the Indian Ocean is totally different from that in Pacific and Atlantic oceans; there are at least two Trichiurus species in Indian Ocean; and the worldwide systematics and diversity of the genus Trichiurus need to be reviewed.

The value of updating GenBank accessions for supermatrix phylogeny: The case of the New Guinean marsupial carnivore genus Myoictis

Erroneous taxonomic attributions in GenBank accessions can mislead phylogenetic inference and appear to be widespread within genera. We investigate the influence of taxonomic misattributions for reconstructing the phylogeny of three-striped dasyures, which include four recognized Myoictis species (Marsupialia: Dasyuridae) that are distributed across New Guinea and nearby islands. Molecular phylogenetic studies that have focused on dasyurids consistently resolve the interrelationships of these small carnivores, grouping M. leucura with M. wavicus, and placing M. wallacei and M. melas as successively deeper divergences from these. Two recent marsupial and mammalian supermatrix phylogenies instead favour an alternative Myoictis topology that is discordant with each of these relationships. We add new nuclear and mitochondrial sequences and employ randomized accession resampling that shows the supermatrix topologies are an artefact of several outdated taxonomic attributions in GenBank. Updating these accessions brings agreement across Myoictis phylogenies with randomly resampled accessions. We encourage authors to update GenBank taxonomic attributions and we argue that an option is needed for flagging accessions that are not demonstrably incorrect, but that provide anomalous results. This would serve both as a caution for future supermatrix construction and to highlight accessions of potentially significant biological interest for further study.