Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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Item Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahē and moho(John Wiley and Sons, 2024-02) Verry AJF; Mas-Carrió E; Gibb GC; Dutoit L; Robertson BC; Waters JM; Rawlence NJ; Gillespie RMany 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.Item Ectoparasite and bacterial population genetics and community structure indicate extent of bat movement across an island chain.(Cambridge University Press, 2024-05-24) McKee CD; Peel AJ; Hayman DTS; Suu-Ire R; Ntiamoa-Baidu Y; Cunningham AA; Wood JLN; Webb CT; Kosoy MYFew studies have examined the genetic population structure of vector-borne microparasites in wildlife, making it unclear how much these systems can reveal about the movement of their associated hosts. This study examined the complex host-vector-microbe interactions in a system of bats, wingless ectoparasitic bat flies (Nycteribiidae), vector-borne microparasitic bacteria (Bartonella), and bacterial endosymbionts of flies (Enterobacterales) across an island chain in the Gulf of Guinea, West Africa. Limited population structure was found in bat flies and Enterobacterales symbionts compared to that of their hosts. Significant isolation by distance was observed in the dissimilarity of Bartonella communities detected in flies from sampled populations of Eidolon helvum bats. These patterns indicate that, while genetic dispersal of bats between islands is limited, some nonreproductive movements may lead to the dispersal of ectoparasites and associated microbes. This study deepens our knowledge of the phylogeography of African fruit bats, their ectoparasites, and associated bacteria. The results presented could inform models of pathogen transmission in these bat populations and increase our theoretical understanding of community ecology in host-microbe systems.Item High dispersal ability versus migratory traditions: Fine-scale population structure and post-glacial colonisation in bar-tailed godwits.(John Wiley and Sons Ltd, 2024-07-06) Conklin JR; Verkuil YI; Lefebvre MJM; Battley PF; Bom RA; Gill RE; Hassell CJ; Ten Horn J; Ruthrauff DR; Tibbitts TL; Tomkovich PS; Warnock N; Piersma T; Fontaine MC; Hansen MMIn migratory animals, high mobility may reduce population structure through increased dispersal and enable adaptive responses to environmental change, whereas rigid migratory routines predict low dispersal, increased structure, and limited flexibility to respond to change. We explore the global population structure and phylogeographic history of the bar-tailed godwit, Limosa lapponica, a migratory shorebird known for making the longest non-stop flights of any landbird. Using nextRAD sequencing of 14,318 single-nucleotide polymorphisms and scenario-testing in an Approximate Bayesian Computation framework, we infer that bar-tailed godwits existed in two main lineages at the last glacial maximum, when much of their present-day breeding range persisted in a vast, unglaciated Siberian-Beringian refugium, followed by admixture of these lineages in the eastern Palearctic. Subsequently, population structure developed at both longitudinal extremes: in the east, a genetic cline exists across latitude in the Alaska breeding range of subspecies L. l. baueri; in the west, one lineage diversified into three extant subspecies L. l. lapponica, taymyrensis, and yamalensis, the former two of which migrate through previously glaciated western Europe. In the global range of this long-distance migrant, we found evidence of both (1) fidelity to rigid behavioural routines promoting fine-scale geographic population structure (in the east) and (2) flexibility to colonise recently available migratory flyways and non-breeding areas (in the west). Our results suggest that cultural traditions in highly mobile vertebrates can override the expected effects of high dispersal ability on population structure, and provide insights for the evolution and flexibility of some of the world's longest migrations.Item Spatial Variation of Acanthophlebia cruentata (Ephemeroptera), a Mayfly Endemic to Te Ika-a-Māui-North Island of Aotearoa, New Zealand(MDPI (Basel, Switzerland), 2022-06-23) Trewick SA; Henderson IM; Pohe SR; Morgan-Richards M; Borges PAVThe mayfly Acanthophlebia cruentata of Aotearoa, New Zealand, is widespread in Te Ika-a-Māui North Island streams, but has never been collected from South Island despite land connection during the last glacial maximum. Population structure of this mayfly might reflect re-colonisation after volcanic eruptions in North Island c1800 years ago, climate cycling or conceal older, cryptic diversity. We collected population samples from 33 locations to estimate levels of population genetic diversity and to document phenotypic variation. Relatively low intraspecific haplotype divergence was recorded among mitochondrial cytb sequences from 492 individuals, but these resolved three geographic-haplotype regions (north, west, east). We detected a signature of isolation by distance at low latitudes (north) but evidence of recent population growth in the west and east. We did not detect an effect of volcanic eruptions but infer range expansion into higher latitudes from a common ancestor during the last glacial period. As judged from wing length, both sexes of adult mayflies were larger at higher elevation and we found that haplotype region was also a significant predictor of Acanthophlebia cruentata size. This suggests that our mitochondrial marker is concordant with nuclear genetic differences that might be explained by founder effect during range expansion.Item Regional patterns of mtDNA diversity in Styela plicata, an invasive ascidian, from Australian and New Zealand marinas(CSIRO PUBLISHING, 7/03/2013) Torkkola J; Riginos C; Liggins LThe ascidian Styela plicata is abundant in harbours and marinas worldwide and has likely reached this distribution via human-mediated dispersal. Previous worldwide surveys based on mitochondrial cytochrome oxidase one (COI) sequences have described two divergent clades, showing overlapping distributions and geographically widespread haplotypes. These patterns are consistent with recent mixing among genetically differentiated groups arising from multiple introductions from historically distinct sources. In contrast, a study of Australian S. plicata using nuclear markers found that population differentiation along the eastern coast related to geographic distance and no evidence for admixture between previously isolated genetic groups. We re-examined the genetic patterns of Australian S. plicata populations using mtDNA (CO1) to place their genetic patterns within a global context, and we examined New Zealand populations for the first time. We found that the haplotypic compositions of Australian and New Zealand populations are largely representative of other worldwide populations. The New Zealand populations, however, exhibited reduced diversity, being potentially indicative of a severely bottlenecked colonisation event. In contrast to results from nuclear markers, population differentiation of mtDNA among Australian S. plicata was unrelated to geographic distance. The discrepancy between markers is likely to be a consequence of non-equilibrium population genetic processes that typify non-indigenous species. © 2013 CSIRO.Item Evolutionary history of rat-borne Bartonella: the importance of commensal rats in the dissemination of bacterial infections globally(John Wiley & Sons, 2013) Hayman DTS; McDonald KD; Kosoy MYEmerging pathogens that originate from invasive species have caused numerous significant epidemics. Some bacteria of genus Bartonella are rodent-borne pathogens that can cause disease in humans and animals alike. We analyzed gltA sequences of 191 strains of rat-associated bartonellae from 29 rodent species from 17 countries to test the hypotheses that this bacterial complex evolved and diversified in Southeast Asia before being disseminated by commensal rats Rattus rattus (black rat) and Rattus norvegicus (Norway rat) to other parts of the globe. The analysis suggests that there have been numerous dispersal events within Asia and introductions from Asia to other regions, with six major clades containing Southeast Asian isolates that appear to have been dispersed globally. Phylogeographic analyses support the hypotheses that these bacteria originated in Southeast Asia and commensal rodents (R. rattus and R. norvegicus) play key roles in the evolution and dissemination of this Bartonella complex throughout the world.Item Origin and post-colonization evolution of the Chatham Islands skink (Oligosoma nigriplantare nigriplantare).(WILEY-BLACKWELL, 2008-07) Liggins L; Chapple DG; Daugherty CH; Ritchie PAIsland ecosystems provide an opportunity to examine a range of evolutionary and ecological processes. The Chatham Islands are an isolated archipelago situated approximately 800 km east of New Zealand. Geological evidence indicates that the Chatham Islands re-emerged within the last 1-4 million years, following a prolonged period of marine inundation, and therefore the resident flora and fauna is the result of long-distance overwater dispersal. We examine the origin and post-colonization evolution of the Chatham Islands skink, Oligosoma nigriplantare nigriplantare, the sole reptile species occurring on the archipelago. We sampled O. n. nigriplantare from across nine islands within the Chatham Islands group, and representative samples from across the range of its closest relative, the New Zealand mainland common skink (Oligosoma nigriplantare polychroma). Our mitochondrial sequence data indicate that O. n. nigriplantare diverged from O. n. polychroma 5.86-7.29 million years ago. This pre-dates the emergence date for the Chatham Islands, but indicates that O. n. nigriplantare colonized the Chatham Islands via overwater dispersal on a single occasion. Despite the substantial morphological variability evident in O. n. nigriplantare, only relatively shallow genetic divergences (maximum divergence approximately 2%) were found across the Chatham Islands. Our analyses (haplotypic diversity, Phi(ST), analysis of molecular variance, and nested clade phylogeographical analysis) indicated restricted gene flow in O. n. nigriplantare resulting in strong differentiation between islands. However, the restrictions to gene flow might have only arisen recently as there was also a significant pattern of isolation by distance, possibly from when the Chatham Islands were a single landmass during Pleistocene glacial maxima when sea levels were lower. The level of genetic and morphological divergence between O. n. nigriplantare and O. n. polychroma might warrant their recognition as distinct species.