ORCID Profile
0000-0002-3921-0262
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Palaeoecology | Life Histories | Quaternary Environments | Archaeology | Ecology | Ecological Impacts of Climate Change | Archaeological Science | Aboriginal and Torres Strait Islander Archaeology | Anthropological Genetics
ANZSRC Socio-Economic Objective (SEO)
Understanding Australia's Past | Ecosystem Adaptation to Climate Change | Expanding Knowledge in the Earth Sciences | Dental Health | Flora, Fauna and Biodiversity at Regional or Larger Scales |
Related Links
Publications
Comment on “Whole-genome analyses resolve early branches in the tree of life of modern birds”
Publisher: American Association for the Advancement of Science (AAAS)
Date: 25-09-2015
Abstract: Jarvis et al . (Research Articles, 12 December 2014, p. 1320) presented molecular clock analyses that suggested that most modern bird orders erged just after the mass extinction event at the Cretaceous-Paleogene boundary (about 66 million years ago). We demonstrate that this conclusion results from the use of a single inappropriate maximum bound, which effectively precludes the Cretaceous ersification overwhelmingly supported by previous molecular studies.
Ancient and modern genomes unravel the evolutionary history of the rhinoceros family
Publisher: Elsevier BV
Date: 09-2021
DOI: 10.1016/J.CELL.2021.07.032
Abstract: Only five species of the once- erse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early ergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide ersity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic ersity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
Ancient mitochondrial genomes reveal the demographic history and phylogeography of the extinct, enigmatic thylacine (Thylacinus cynocephalus)
Publisher: Wiley
Date: 27-09-2018
DOI: 10.1111/JBI.13101
Unraveling the phylogenetic relationships of the extinct bovid Myotragus balearicus Bate 1909 from the Balearic Islands
Publisher: Elsevier BV
Date: 07-2019
Ancient mitochondrial genomes clarify the evolutionary history of New Zealand’s enigmatic acanthisittid wrens
Publisher: Elsevier BV
Date: 09-2016
DOI: 10.1016/J.YMPEV.2016.05.038
Abstract: The New Zealand acanthisittid wrens are the sister-taxon to all other "perching birds" (Passeriformes) and - including recently extinct species - represent the most erse 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) erged 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.
Ancient mitochondrial DNA reveals convergent evolution of giant short-faced bears (Tremarctinae) in North and South America
Publisher: The Royal Society
Date: 04-2016
Abstract: The Tremarctinae are a subfamily of bears endemic to the New World, including two of the largest terrestrial mammalian carnivores that have ever lived: the giant, short-faced bears Arctodus simus from North America and Arctotherium angustidens from South America (greater than or equal to 1000 kg). Arctotherium angustidens became extinct during the Early Pleistocene, whereas Arctodus simus went extinct at the very end of the Pleistocene. The only living tremarctine is the spectacled bear ( Tremarctos ornatus ), a largely herbivorous bear that is today only found in South America. The relationships among the spectacled bears ( Tremarctos ), South American short-faced bears ( Arctotherium ) and North American short-faced bears ( Arctodus ) remain uncertain. In this study, we sequenced a mitochondrial genome from an Arctotherium femur preserved in a Chilean cave. Our molecular phylogenetic analyses revealed that the South American short-faced bears were more closely related to the extant South American spectacled bear than to the North American short-faced bears. This result suggests striking convergent evolution of giant forms in the two groups of short-faced bears ( Arctodus and Arctotherium ), potentially as an adaptation to dominate competition for megafaunal carcasses.
Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution
Publisher: American Association for the Advancement of Science (AAAS)
Date: 23-05-2014
Abstract: The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant from the basal ratite lineage of ostriches. This unexpected result strongly contradicts continental vicariance and instead supports flighted dispersal in all major ratite lineages. We suggest that convergence toward gigantism and flightlessness was facilitated by early Tertiary expansion into the diurnal herbivory niche after the extinction of the dinosaurs.
Low-cost cross-taxon enrichment of mitochondrial DNA using in-house synthesised RNA probes
Publisher: Public Library of Science (PLoS)
Date: 04-02-2019
Phylogenetic relationships of the cuscuses (Diprotodontia: Phalangeridae) of island Southeast Asia and Melanesia based on the mitochondrial ND2 gene
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/AM18050
Abstract: The species-level systematics of the marsupial family Phalangeridae, particularly Phalanger, are poorly understood, due partly to the family’s wide distribution across Australia, New Guinea, eastern Indonesia, and surrounding islands. In order to refine the species-level systematics of Phalangeridae, and improve our understanding of their evolution, we generated 36 mitochondrial ND2 DNA sequences from multiple species and s le localities. We combined our new data with available sequences and produced the most comprehensive molecular phylogeny for Phalangeridae to date. Our analyses (1) strongly support the monophyly of the three phalangerid subfamilies (Trichosurinae, Ailuropinae, Phalangerinae) (2) reveal the need to re-examine all specimens currently identified as ‘Phalanger orientalis’ and (3) suggest the elevation of the Solomon Island P. orientalis subspecies to species level (P. breviceps Thomas, 1888). In addition, s les of P. orientalis from Timor formed a clade, consistent with an introduction by humans from a single source population. However, further research on east Indonesian P. orientalis populations will be required to test this hypothesis, resolve inconsistencies in ergence time estimates, and locate the source population and taxonomic status of the Timor P. orientalis.
Somatic Symptom Disorders in Adolescent Inpatients
Publisher: Elsevier BV
Date: 12-2018
DOI: 10.1016/J.JADOHEALTH.2018.06.026
Abstract: There are only a few reports of adolescents with somatic disorders (SDs) whose symptoms are sufficiently severe to require hospital admission. The aim of this study was to describe the symptom profile, health service utilization, and outcome of adolescents with SDs admitted to a tertiary children's hospital. A retrospective cohort study of all adolescents admitted to the Adolescent Medicine Unit of a tertiary children's hospital was undertaken from July 2013 to June 2014. In a two-stage process, medical records were examined to identify patients who met the diagnostic criteria for SD. Evidence of functional recovery was obtained for the period from 18 to 30 months after discharge and rated as completely recovered, partially recovered, or functionally disabled. A total of 60 admissions (53 patients, 79% female) were identified with SD, accounting for 12% of the unit's admissions and 2% of hospital admissions over 12 years old. Nearly half (45%) the presenting symptoms were neurological and 39% involved pain. In total, 20% of admissions were for complex symptoms involving multiple body systems. The majority (81%) of adolescents with follow-up documentation (n = 37) demonstrated complete or partial recovery. Patients whose families fully accepted the diagnosis were more likely to accept counseling following discharge (p < .001) and were almost 20 times more likely to have completely recovered compared to adolescents whose families partially accepted or rejected the diagnosis (odds ratio 17.36, p = .003). Hospitalized adolescents with SD utilize substantial resources due to the requirement for comprehensive assessment, including multidisciplinary communication. Recovery can be anticipated for the majority, especially if supported by parents.
Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact
Publisher: MDPI AG
Date: 24-06-2021
Abstract: The tropical archipelago of Wallacea contains thousands of in idual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul—i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level—by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been h ered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000–4000 years ago (3–4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new s les from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region.
Ancient DNA from an extinct Mediterranean micromammal-Hypnomys morpheus (Rodentia: Gliridae)-Provides insight into the biogeographic history of insular dormice
Publisher: Hindawi Limited
Date: 25-11-2020
DOI: 10.1111/JZS.12343
Early cave art and ancient DNA record the origin of European bison
Publisher: Springer Science and Business Media LLC
Date: 18-10-2016
DOI: 10.1038/NCOMMS13158
Abstract: The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus ) before the Holocene ( .7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison ( Bison priscus ) and ancestors of modern cattle (aurochs, Bos primigenius ) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21–18 kya).
Widespread male sex bias in mammal fossil and museum collections
Publisher: Proceedings of the National Academy of Sciences
Date: 03-09-2019
Abstract: The extent to which the fossil record provides an accurate picture of past life is an important issue that is often difficult to assess. We genetically sexed 277 mammalian subfossils using high-throughput sequencing of ancient DNA, and found a strong male bias (∼75%) in Pleistocene bison ( n = 186) and brown bears ( n = 91), matching signals previously reported for mammoth. Similarly, a male bias was also found in species of nearly all mammal orders in 4 large museum collections. For mammals, we suggest both male behavior and appearance can lead to increased chances of representation in fossil and museum collections, and this previously unrecognized sex bias could have substantial implications for views of past population and ecological processes.
Molecular Phylogeny, Biogeography, and Habitat Preference Evolution of Marsupials
Publisher: Oxford University Press (OUP)
Date: 30-05-2014
Abstract: Marsupials exhibit great ersity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.
Genetic diversity and drivers of dwarfism in extinct island emu populations
Publisher: The Royal Society
Date: 04-2018
Abstract: Australia's iconic emu ( Dromaius novaehollandiae novaehollandiae ) 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 Dromaius ersity, including data from one of the few definitively genuine Tasmanian emu specimens known. Our genetic analyses suggest that all the island populations represent sub-populations of mainland D . novaehollandiae . Further, the size of island emus and those on the mainland appears to scale linearly with island size but not time since isolation, suggesting that island size—and presumably concomitant limitations on resource availability—may be a more important driver of dwarfism in island emus, though its precise contribution to emu dwarfism remains to be confirmed.
Revision of the Litoria watjulumensis (Anura: Pelodryadidae) group from the Australian monsoonal tropics, including the resurrection of L. spaldingi
Publisher: Magnolia Press
Date: 19-02-2021
DOI: 10.11646/ZOOTAXA.4933.2.3
Abstract: We show that the Wotjulum frog, Litoria watjulumensis (Copland, 1957), comprises two deeply ergent mitochondrial DNA lineages that are also reciprocally monophyletic for a nuclear gene locus and have discrete distributions. The taxa are differentiated in multivariate analysis of shape but show no appreciable differences in colour and pattern. The two taxa differ substantially in the degree of female biased sexual size dimorphism, with the western taxon showing considerably more pronounced dimorphism. We subsequently resurrect Litoria (Hyla) spaldingi (Hosmer, 1964) for populations from east of the Daly River system in the Northern Territory through to western Queensland and restrict L. watjulumensis to populations from the Kimberley region of north-western Australia and the Victoria River system of the western Northern Territory. The complex advertisement call of L. spaldingi is described for the first time.
Ancient mitochondrial genome reveals unsuspected taxonomic affinity of the extinct Chatham duck (Pachyanas chathamica) and resolves divergence times for New Zealand and sub-Antarctic brown teals
Publisher: Elsevier BV
Date: 2014
DOI: 10.1016/J.YMPEV.2013.08.017
Abstract: 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- ergent 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 C bell Island teal [A. nesiotis]). Molecular clock calculations based on an ingroup fossil calibration support a ergence 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 ergence 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.
Phylogenetic relationships and terrestrial adaptations of the extinct laughing owl, Sceloglaux albifacies (Aves: Strigidae)
Publisher: Oxford University Press (OUP)
Date: 08-2017
DOI: 10.1111/ZOJ.12483
An extinct nestorid parrot (Aves, Psittaciformes, Nestoridae) from the Chatham Islands, New Zealand
Publisher: Oxford University Press (OUP)
Date: 28-08-2014
DOI: 10.1111/ZOJ.12164
Disparate origins for endemic bird taxa from the ‘Gondwana Rainforests’ of Central Eastern Australia
Publisher: Oxford University Press (OUP)
Date: 04-06-2021
DOI: 10.1093/BIOLINNEAN/BLAB031
Abstract: Subtropical and temperate rainforests of Central Eastern Australia are some of the largest remaining fragments of their kind globally. The biota of these rainforests appears to comprise two broad biogeographical elements: a more ancient (Miocene or older) and typically upland temperate (‘Gondwanan’) element and a younger (Plio-Pleistocene) lowland tropical element. We present the first phylogenetic synthesis of the spatiotemporal origins for the eight bird taxa endemic to Central Eastern Australian Rainforests. At least five of these eight focal taxa show Plio-Pleistocene ergences from their respective northern sister taxa, consistent with origins driven by recent expansion and contraction of lowland rainforest. In contrast, two more strictly upland species, the rufous scrub-bird (Atrichornis rufescens) and the logrunner (Orthonyx temminckii), erged from their nearest living relatives during the Miocene, suggesting potentially longer histories of persistence and more temperate origins. Finally, we did not recover reciprocal monophyly in mitogenomes from the two extant lyrebirds, Albert’s lyrebird (Menura alberti) and the superb lyrebird (Menura novaehollandiae). The disparate ergence ages recovered among all eight taxa are consistent with the biota of the Central Eastern Australian Rainforests comprising isolates either of younger age and tropical lowland origins or of older age and temperate upland origins.
The origin and phylogenetic relationships of the New Zealand ravens
Publisher: Elsevier BV
Date: 2017
DOI: 10.1016/J.YMPEV.2016.09.022
Abstract: 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 ergence 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 ergence 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.
Dire wolves were the last of an ancient New World canid lineage
Publisher: Springer Science and Business Media LLC
Date: 13-01-2021
An age-depth model and revised stratigraphy of vertebrate-bearing units in Natural Trap Cave, Wyoming
Publisher: Elsevier BV
Date: 02-2023
Mitochondrial Genomes from New Zealand’s Extinct Adzebills (Aves: Aptornithidae: Aptornis) Support a Sister-Taxon Relationship with the Afro-Madagascan Sarothruridae
Publisher: MDPI AG
Date: 15-02-2019
DOI: 10.3390/D11020024
Abstract: The recently extinct New Zealand adzebills (Aptornithidae, Aptornis spp.) were an enigmatic group of large flightless birds that have long eluded precise taxonomic assignment as they do not closely resemble any extant birds. Adzebills were nearly wingless, weighed approximately 16–19 kg, and possessed massive adze-like reinforced bills whose function remains unknown. Using hybridisation enrichment and high-throughput sequencing of DNA extracted from subfossil bone and eggshell, near-complete mitochondrial genomes were successfully assembled from the two Quaternary adzebill species: the North Island Adzebill (Aptornis otidiformis) and South Island Adzebill (A. defossor). Molecular phylogenetic analyses confirm that adzebills are members of the Ralloidea (rails and allies) and are sister-taxon to the Sarothruridae, which our results suggest comprises the Madagascan wood rails (Mentocrex, two likely sp.) in addition to the tiny ( gram) rail-like Afro-Madagascan flufftails (Sarothrura, 9 spp.). Node age estimates indicate that the split between adzebills and Sarothruridae occurred ~39.6 Ma, suggesting that the ancestors of the adzebills arrived in New Zealand by long-distance dispersal rather than continental vicariance. This newly identified biogeographic link between physically distant New Zealand and Afro-Madagascar, echoed by the relationship between the New Zealand kiwi (Apterygiformes) and Madagascan elephant-birds (Aepyornithiformes), suggests that the adzebill’s near relatives were formerly more widespread. In addition, our estimate for the ergence time between the two Quaternary adzebill species (0.2–2.3 Ma) coincides with the emergence of a land-bridge between the North and South islands of New Zealand (ca. 1.5–2 Ma). This relatively recent ergence suggests that North Island adzebills are the result of a relatively recent dispersal from the South Island, from which the earliest (Miocene) adzebill fossil has been described.
Ancient DNA from the extinct South American giant glyptodont Doedicurus sp. (Xenarthra: Glyptodontidae) reveals that glyptodonts evolved from Eocene armadillos
Publisher: Wiley
Date: 30-06-2016
DOI: 10.1111/MEC.13695
Abstract: Glyptodonts were giant (some of them up to ~2400 kg), heavily armoured relatives of living armadillos, which became extinct during the Late Pleistocene/early Holocene alongside much of the South American megafauna. Although glyptodonts were an important component of Cenozoic South American faunas, their early evolution and phylogenetic affinities within the order Cingulata (armoured New World placental mammals) remain controversial. In this study, we used hybridization enrichment and high-throughput sequencing to obtain a partial mitochondrial genome from Doedicurus sp., the largest (1.5 m tall, and 4 m long) and one of the last surviving glyptodonts. Our molecular phylogenetic analyses revealed that glyptodonts fall within the ersity of living armadillos. Reanalysis of morphological data using a molecular 'backbone constraint' revealed several morphological characters that supported a close relationship between glyptodonts and the tiny extant fairy armadillos (Chlamyphorinae). This is surprising as these taxa are among the most derived cingulates: glyptodonts were generally large-bodied and heavily armoured, while the fairy armadillos are tiny (~9-17 cm) and adapted for burrowing. Calibration of our phylogeny with the first appearance of glyptodonts in the Eocene resulted in a more precise timeline for xenarthran evolution. The osteological novelties of glyptodonts and their specialization for grazing appear to have evolved rapidly during the Late Eocene to Early Miocene, coincident with global temperature decreases and a shift from wet closed forest towards drier open woodland and grassland across much of South America. This environmental change may have driven the evolution of glyptodonts, culminating in the bizarre giant forms of the Pleistocene.
Pleistocene origins, western ghost lineages, and the emerging phylogeographic history of the red wolf and coyote
Publisher: Wiley
Date: 07-07-2021
DOI: 10.1111/MEC.16048
Abstract: The red wolf ( Canis rufus ) of the eastern US was driven to near‐extinction by colonial‐era persecution and habitat conversion, which facilitated coyote ( C . latrans ) range expansion and widespread hybridization with red wolves. The observation of some grey wolf ( C . lupus ) ancestry within red wolves sparked controversy over whether it was historically a subspecies of grey wolf with its predominant “coyote‐like” ancestry obtained from post‐colonial coyote hybridization (2‐species hypothesis) versus a distinct species closely related to the coyote that hybridized with grey wolf (3‐species hypothesis). We analysed mitogenomes sourced from before the 20th century bottleneck and coyote invasion, along with hundreds of modern licons, which led us to reject the 2‐species model and to investigate a broader phylogeographic 3‐species model suggested by the fossil record. Our findings broadly support this model, in which red wolves ranged the width of the American continent prior to arrival of the grey wolf to the mid‐continent 60–80 ka red wolves subsequently disappeared from the mid‐continent, relegated to California and the eastern forests, which ushered in emergence of the coyote in their place (50–30 ka) by the early Holocene (12–10 ka), coyotes had expanded into California, where they admixed with and phenotypically replaced western red wolves in a process analogous to the 20th century coyote invasion of the eastern forests. Findings indicate that the red wolf pre‐dated not only European colonization but human, and possibly coyote, presence in North America. These findings highlight the urgency of expanding conservation efforts for the red wolf.
Evolution and extinction of the giant rhinoceros Elasmotherium sibiricum sheds light on late Quaternary megafaunal extinctions
Publisher: Springer Science and Business Media LLC
Date: 26-11-2018
DOI: 10.1038/S41559-018-0722-0
Abstract: Understanding extinction events requires an unbiased record of the chronology and ecology of victims and survivors. The rhinoceros Elasmotherium sibiricum, known as the 'Siberian unicorn', was believed to have gone extinct around 200,000 years ago-well before the late Quaternary megafaunal extinction event. However, no absolute dating, genetic analysis or quantitative ecological assessment of this species has been undertaken. Here, we show, by accelerator mass spectrometry radiocarbon dating of 23 in iduals, including cross-validation by compound-specific analysis, that E. sibiricum survived in Eastern Europe and Central Asia until at least 39,000 years ago, corroborating a wave of megafaunal turnover before the Last Glacial Maximum in Eurasia, in addition to the better-known late-glacial event. Stable isotope data indicate a dry steppe niche for E. sibiricum and, together with morphology, a highly specialized diet that probably contributed to its extinction. We further demonstrate, with DNA sequencing data, a very deep phylogenetic split between the subfamilies Elasmotheriinae and Rhinocerotinae that includes all the living rhinoceroses, settling a debate based on fossil evidence and confirming that the two lineages had erged by the Eocene. As the last surviving member of the Elasmotheriinae, the demise of the 'Siberian unicorn' marked the extinction of this subfamily.
Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore.
Publisher: Springer Science and Business Media LLC
Date: 11-12-2018
DOI: 10.1038/S41559-017-0417-Y
Abstract: The Tasmanian tiger or thylacine ( Thylacinus cynocephalus ) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking ex le of convergent evolution in mammals. The last known thylacine died in captivity in 1936 and many aspects of the evolutionary history of this unique marsupial apex predator remain unknown. Here we have sequenced the genome of a preserved thylacine pouch young specimen to clarify the phylogenetic position of the thylacine within the carnivorous marsupials, reconstruct its historical demography and examine the genetic basis of its convergence with canids. Retroposon insertion patterns placed the thylacine as the basal lineage in Dasyuromorphia and suggest incomplete lineage sorting in early dasyuromorphs. Demographic analysis indicated a long-term decline in genetic ersity starting well before the arrival of humans in Australia. In spite of their extraordinary phenotypic convergence, comparative genomic analyses demonstrated that amino acid homoplasies between the thylacine and canids are largely consistent with neutral evolution. Furthermore, the genes and pathways targeted by positive selection differ markedly between these species. Together, these findings support models of adaptive convergence driven primarily by cis -regulatory evolution.
Ancient DNA analysis of the extinct North American flat-headed peccary (Platygonus compressus)
Publisher: Elsevier BV
Date: 07-2017
DOI: 10.1016/J.YMPEV.2017.03.024
Abstract: 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 ersification 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 ersity 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 erse 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.
Evidence for Pleistocene gene flow through the ice-free corridor from extinct horses and camels from Natural Trap Cave, Wyoming
Publisher: Elsevier BV
Date: 02-2023
The Dogma of Dingoes—Taxonomic status of the dingo: A reply to Smith et al.
Publisher: Magnolia Press
Date: 04-03-2019
DOI: 10.11646/ZOOTAXA.4564.1.7
Abstract: Adopting the name Canis dingo for the Dingo to explicitly denote a species-level taxon separate from other canids was suggested by Crowther et al. (2014) as a means to eliminate taxonomic instability and contention. However, Jackson et al. (2017), using standard taxonomic and nomenclatural approaches and principles, called instead for continued use of the nomen C. familiaris for all domestic dogs and their derivatives, including the Dingo. (This name, C. familiaris, is applied to all dogs that derive from the domesticated version of the Gray Wolf, Canis lupus, based on nomenclatural convention.) The primary reasons for this call by Jackson et al. (2017) were: (1) a lack of evidence to show that recognizing multiple species amongst the dog, including the Dingo and New Guinea Singing Dog, was necessary taxonomically, and (2) the principle of nomenclatural priority (the name familiaris Linnaeus, 1758, antedates dingo Meyer, 1793). Overwhelming current evidence from archaeology and genomics indicates that the Dingo is of recent origin in Australia and shares immediate ancestry with other domestic dogs as evidenced by patterns of genetic and morphological variation. Accordingly, for Smith et al. (2019) to recognise Canis dingo as a distinct species, the onus was on them to overturn current interpretations of available archaeological, genomic, and morphological datasets and instead show that Dingoes have a deeply ergent evolutionary history that distinguishes them from other named forms of Canis (including C. lupus and its domesticated version, C. familiaris). A recent paper by Koepfli et al. (2015) demonstrates exactly how this can be done in a compelling way within the genus Canis—by demonstrating deep evolutionary ergence between taxa, on the order of hundreds of thousands of years, using data from multiple genetic systems. Smith et al. (2019) have not done this instead they have misrepresented the content and conclusions of Jackson et al. (2017), and contributed extraneous arguments that are not relevant to taxonomic decisions. Here we dissect Smith et al. (2019), identifying misrepresentations, to show that ecological, behavioural and morphological evidence is insufficient to recognise Dingoes as a separate species from other domestic dogs. We reiterate: the correct binomial name for the taxon derived from Gray Wolves (C. lupus) by passive and active domestication, including Dingoes and other domestic dogs, is Canis familiaris. We are strongly sympathetic to arguments about the historical, ecological, cultural, or other significance of the Dingo, but these are issues that will have to be considered outside of the more narrow scope of taxonomy and nomenclature.
Molecular resolution to a morphological controversy: The case of North American fossil muskoxen Bootherium and Symbos.
Publisher: Elsevier BV
Date: 12-2018
DOI: 10.1016/J.YMPEV.2018.08.008
Abstract: 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 s les. Ultimately, our molecular data support the synonymisation of the North American muskoxen Bootherium and Symbos.
Molecular phylogenetics supports the origin of an endemic Balearic shrew lineage (Nesiotites) coincident with the Messinian Salinity Crisis
Publisher: Elsevier BV
Date: 08-2018
DOI: 10.1016/J.YMPEV.2018.03.028
Abstract: 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 ergence 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.
Mitogenomes Uncover Extinct Penguin Taxa and Reveal Island Formation as a Key Driver of Speciation
Publisher: Oxford University Press (OUP)
Date: 05-02-2019
Abstract: The emergence of islands has been linked to spectacular radiations of erse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary ersification of penguins. We test this hypothesis using a fossil-calibrated phylogeny of mitochondrial genomes (mitogenomes) from all extant and recently extinct penguin taxa. Our temporal analysis demonstrates that numerous recent island-endemic penguin taxa erged following the formation of their islands during the Plio-Pleistocene, including the Galápagos (Galápagos Islands), northern rockhopper (Gough Island), erect-crested (Antipodes Islands), Snares crested (Snares) and royal (Macquarie Island) penguins. Our analysis also reveals two new recently extinct island-endemic penguin taxa from New Zealand’s Chatham Islands: Eudyptes warhami sp. nov. and a dwarf subspecies of the yellow-eyed penguin, Megadyptes antipodes richdalei ssp. nov. Eudyptes warhami erged from the Antipodes Islands erect-crested penguin between 1.1 and 2.5 Ma, shortly after the emergence of the Chatham Islands (∼3 Ma). This new finding of recently evolved taxa on this young archipelago provides further evidence that the radiation of penguins over the last 5 Ma has been linked to island emergence. Mitogenomic analyses of all penguin species, and the discovery of two new extinct penguin taxa, highlight the importance of island formation in the ersification of penguins, as well as the extent to which anthropogenic extinctions have affected island-endemic taxa across the Southern Hemisphere’s isolated archipelagos.
Oligocene divergence of frogmouth birds (Podargidae) across Wallace's Line
Publisher: The Royal Society
Date: 05-2020
Abstract: Wallace's Line demarcates the transition between the differentiated regional faunas of Asia and Australia. However, while patterns of biotic differentiation across these two continental landmasses and the intervening island groups (Wallacea) have been extensively studied, patterns of long-term dispersal and ersification across this region are less well understood. Frogmouths (Aves: Podargidae) are a relictual family of large nocturnal birds represented by three extant genera occurring, respectively, in Asia, ‘Sahul’ (Australia and New Guinea) and the Solomon Islands, thus spanning Wallace's Line. We used new mitochondrial genomes from each of the extant frogmouth genera to estimate the timeline of frogmouth evolution and dispersal across Wallace's Line. Our results suggest that the three genera erged and dispersed during the mid-Cenozoic between approximately 30 and 40 Mya. These ergences are among the oldest inferred for any trans-Wallacean vertebrate lineage. In addition, our results reveal that the monotypic Solomons frogmouth ( Rigidipenna inexpectata ) is one of the most phylogenetically ergent endemic bird lineages in the southwest Pacific. We suggest that the contemporary distribution of exceptionally deep ergences among extant frogmouth lineages may be explained by colonization of, and subsequent long-term persistence on, island arcs in the southwest Pacific during the Oligocene. These island arcs may have provided a pathway for biotic dispersal out of both Asia and Australia that preceded the formation of extensive emergent landmasses in Wallacea by at least 10 million years.
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Unlocking The Past: A Novel Approach To Quantifying Biodiversity Loss In The Fossil Record
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View Funded ActivityAustralian Laureate Fellowships - Grant ID: FL140100260
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Amount: $2,775,898.00
Funder: Australian Research Council
View Funded ActivityARC Centres Of Excellence - Grant ID: CE170100015
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