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Verry AJF, Mas-Carrió E, Gibb GC, Dutoit L, Robertson BC, Waters JM, Rawlence NJ. Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahē and moho. Mol Ecol 2024; 33:e17227. [PMID: 38018770 DOI: 10.1111/mec.17227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/05/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
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.
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Affiliation(s)
- Alexander J F Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Eduard Mas-Carrió
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Gillian C Gibb
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Jonathan M Waters
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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Lubbe P, Rawlence NJ, Kardailsky O, Robertson BC, Day R, Knapp M, Dussex N. Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The biogeographical origins of the endemic birds of New Zealand (Aotearoa) are of great interest, particularly Palaeogene lineages such as Callaeidae, a passerine family characterized by brightly coloured wattles behind the beak and, in some cases, extreme sexual dimorphism in bill size and shape. Ancestral representatives of Callaeidae are thought to have split from their closest relatives outside New Zealand in the Oligocene, but little is known about the timing of divergences within the family. We present a fully dated molecular phylogeny of Callaeidae mitogenomes and discuss the biogeographical implications. Our results suggest that formation of Pliocene marine seaways, such as the Manawatu Strait, are likely to have played a significant role in the differentiation of North Island and South Island kōkako (Callaeas spp.) and saddlebacks/tīeke (Philesturnus spp.).
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Affiliation(s)
- Pascale Lubbe
- Department of Anatomy, University of Otago , Dunedin , New Zealand
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago , Dunedin , New Zealand
| | - Olga Kardailsky
- Department of Anatomy, University of Otago , Dunedin , New Zealand
| | - Bruce C Robertson
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago , Dunedin , New Zealand
| | - Robert Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago , Dunedin , New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago , Dunedin , New Zealand
- Coastal People, Southern Skies Centre of Research Excellence, University of Otago , Dunedin , New Zealand
| | - Nicolas Dussex
- Swedish Museum of Natural History, Centre for Palaeogenetics (CPG) , Svante Arrhenius väg, Stockholm , Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History , Stockholm , Sweden
- Department of Zoology, Stockholm University , Stockholm , Sweden
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3
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Verry AJF, Lubbe P, Mitchell KJ, Rawlence NJ. Thirty years of ancient DNA and the faunal biogeography of Aotearoa New Zealand: lessons and future directions. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2093227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Alexander J. F. Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
- Centre for Anthropobiology and Genomics of Toulouse, Faculté de Médecine Purpan, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Pascale Lubbe
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Kieren J. Mitchell
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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4
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Marske KA, Boyer SL. Phylogeography reveals the complex impact of the Last Glacial Maximum on New Zealand’s terrestrial biota. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2079682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | - Sarah L. Boyer
- Biology Department, Macalester College, St. Paul, MN, USA
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5
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Shepherd L, Simon C, Langton-Myers S, Morgan-Richards M. Insights into Aotearoa New Zealand’s biogeographic history provided by the study of natural hybrid zones. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2061020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Lara Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
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Scarsbrook L, Verry AJF, Walton K, Hitchmough RA, Rawlence NJ. Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: phylogeography of the New Zealand gecko genus
Hoplodactylus. Mol Ecol 2022; 32:2964-2984. [DOI: 10.1111/mec.16434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Lachie Scarsbrook
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | - Alexander J. F. Verry
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | - Kerry Walton
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | | | - Nicolas J. Rawlence
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
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7
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Withers SJ, Parsons S, Hauber ME, Kendrick A, Lavery SD. Genetic divergence between isolated populations of the North Island New Zealand Rifleman ( Acanthisitta chloris granti) implicates ancient biogeographic impacts rather than recent habitat fragmentation. Ecol Evol 2021; 11:5998-6014. [PMID: 34141198 PMCID: PMC8207446 DOI: 10.1002/ece3.7358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 12/26/2020] [Accepted: 01/04/2021] [Indexed: 11/25/2022] Open
Abstract
This research investigates the extent and causal mechanisms of genetic population divergence in a poorly flighted passerine, the North Island Rifleman or Titipounamu (Acanthisitta chloris granti). While this species has a historically widespread distribution, anthropogenic forest clearance has resulted in a highly fragmented current distribution. We conducted analyses of mitochondrial DNA (COI and Control Region) and 12 nuclear DNA microsatellites to test for population divergence and estimate times of divergence. diyabc and biogeobears were then used to assess likely past dispersal scenarios based on both mtDNA and nDNA. The results reveal several significantly divergent lineages across the North Island of New Zealand and indicate that some populations have been isolated for extensive periods of time (0.7-4.9 mya). Modeling indicated a dynamic history of population connectivity, with a drastic restriction in gene flow between three geographic regions, followed by a more recent re-establishment of connectivity. Our analyses indicate the dynamic influence of key geological and climatological events on the distribution of genetic diversity in this species, including support for the genetic impact of old biogeographic boundaries such as the Taupo Line and Cockayne's Line, rather than recent anthropogenic habitat fragmentation. These findings present a rare example of an avian species with a genetic history more like that of flightless taxa and so provide new general insights into vicariant processes affecting populations of passerines with limited dispersal.
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Affiliation(s)
- Sarah J. Withers
- School of Biological SciencesPrivate Bag 92019Auckland Mail CentreThe University of AucklandAucklandNew Zealand
| | - Stuart Parsons
- School of Biological SciencesPrivate Bag 92019Auckland Mail CentreThe University of AucklandAucklandNew Zealand
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQLDAustralia
| | - Mark E. Hauber
- Department of Evolution, Ecology, and BehaviorSchool of Integrative BiologyUniversity of IllinoisUrbana‐ChampaignILUSA
| | - Alistair Kendrick
- School of Biological SciencesPrivate Bag 92019Auckland Mail CentreThe University of AucklandAucklandNew Zealand
| | - Shane D. Lavery
- Institute of Marine SciencePrivate Bag 92019Auckland Mail CentreThe University of AucklandAucklandNew Zealand
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Zhang Y, Chen J, Sun H. Alpine speciation and morphological innovations: revelations from a species-rich genus in the northern hemisphere. AOB PLANTS 2021; 13:plab018. [PMID: 34025962 PMCID: PMC8129467 DOI: 10.1093/aobpla/plab018] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 04/14/2021] [Indexed: 06/06/2023]
Abstract
A large number of studies have attempted to determine the mechanisms driving plant diversity and distribution on a global scale, but the diverse and endemic alpine herbs found in harsh environments, showing adaptive evolution, require more studies. Here, we selected 466 species from the genus Saussurea, one of the northern hemisphere's highest-altitude plant genera with high species richness and striking morphological traits, to explore the mechanisms driving speciation and adaptative evolution. We conducted phylogenetic signals analysis and ancestral character estimation to explore the phylogenetic significance of ecological factors. Moreover, we used spatial simultaneous autoregressive (SAR) error models, modified t-tests and partial regression models to quantify the relative effects of ecological factors and morphological diversity upon diversity and endemism of Saussurea. Phylogenetic analyses reveal that geological influences and climate stability exhibit significant phylogenetic signals and that Saussurea originated at a relatively high elevation. Regression models indicate that geological influences and climatic stability significantly affect the diversity and endemism patterns of Saussurea and its morphological innovations. Moreover, morphological innovations in an area show significant contributions to the local diversity and endemism of Saussurea. We conclude that geological influences (mean altitude and topographic heterogeneity), glacial-interglacial climate stability and phylogenetic conservatism have together promoted the speciation and adaptive evolution of the genus Saussurea. In addition, adaptively morphological innovations of alpine species also promote diversification in local regions. Our findings improve the understanding of the distribution pattern of diversity/endemism and adaptive evolution of alpine specie in the whole northern hemisphere.
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Affiliation(s)
- Yazhou Zhang
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132, Lanhei Road, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianguo Chen
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132, Lanhei Road, Kunming 650201, Yunnan, China
| | - Hang Sun
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132, Lanhei Road, Kunming 650201, Yunnan, China
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9
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Martini D, Dussex N, Robertson BC, Gemmell NJ, Knapp M. Evolution of the "world's only alpine parrot": Genomic adaptation or phenotypic plasticity, behaviour and ecology? Mol Ecol 2021; 30:6370-6386. [PMID: 33973288 DOI: 10.1111/mec.15978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023]
Abstract
Climate warming, in particular in island environments, where opportunities for species to disperse are limited, may become a serious threat to cold adapted alpine species. In order to understand how alpine species may respond to a warming world, we need to understand the drivers that have shaped their habitat specialisation and the evolutionary adaptations that allow them to utilize alpine habitats. The endemic, endangered New Zealand kea (Nestor notabilis) is considered the only alpine parrot in the world. As a species commonly found in the alpine zone it may be highly susceptible to climate warming. But is it a true alpine specialist? Is its evolution driven by adaptation to the alpine zone, or is the kea an open habitat generalist that simply uses the alpine zone to, for example, avoid lower lying anthropogenic landscapes? We use whole genome data of the kea and its close, forest adapted sister species, the kākā (Nestor meridionalis) to reconstruct the evolutionary history of both species and identify the functional genomic differences that underlie their habitat specialisations. Our analyses do not identify major functional genomic differences between kea and kākā in pathways associated with high-altitude. Rather, we found evidence that selective pressures on adaptations commonly found in alpine species are present in both Nestor species, suggesting that selection for alpine adaptations has not driven their divergence. Strongly divergent demographic responses to past climate warming between the species nevertheless highlight potential future threats to kea survival in a warming world.
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Affiliation(s)
- Denise Martini
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Nicolas Dussex
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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10
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Monks JM, O’Donnell CFJ, Greene TC, Weston KA. Evaluation of counting methods for monitoring populations of a cryptic alpine passerine, the rock wren (Passeriformes, Acanthisittidae, Xenicus gilviventris). PLoS One 2021; 16:e0247873. [PMID: 33661972 PMCID: PMC7932173 DOI: 10.1371/journal.pone.0247873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/16/2021] [Indexed: 11/19/2022] Open
Abstract
Developing and validating methods to determine trends in populations of threatened species is essential for evaluating the effectiveness of conservation interventions. For cryptic species inhabiting remote environments, this can be particularly challenging. Rock wrens, Xenicus gilviventris, are small passerines endemic to the alpine zone of southern New Zealand. They are highly vulnerable to predation by introduced mammalian predators. Establishing a robust, cost-effective monitoring tool to evaluate population trends in rock wrens is a priority for conservation of both the species and, more broadly, as part of a suite of indicators for evaluating effectiveness of management in New Zealand’s alpine ecosystems. We assessed the relative accuracy and precision of three population estimation techniques (mark-resight, distance sampling and simple counts on line transects) for two populations of rock wrens in the Southern Alps over six breeding seasons (2012–2018). The performance of these population estimators was compared to known rock wren population size derived from simultaneous territory mapping. Indices of abundance derived from counts on transects were correlated with territory mapping at both study areas, and performed better than either mark-resight methods or distance sampling. Simple counts on standardised line transects are a highly cost-effective method of monitoring birds because they do not require banding a population. As such, we recommend that line transect counts using the design outlined in this paper be adopted as a standard method for long-term monitoring of rock wren populations. Although species-specific testing is required to validate use of low-cost population indices, our results may have utility for the monitoring of other cryptic passerines in relatively open habitats.
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Affiliation(s)
- Joanne M. Monks
- Biodiversity Group, Department of Conservation, Dunedin, New Zealand
- * E-mail:
| | | | - Terry C. Greene
- Biodiversity Group, Department of Conservation, Christchurch, New Zealand
| | - Kerry A. Weston
- Biodiversity Group, Department of Conservation, Christchurch, New Zealand
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11
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Waters J, Emerson B, Arribas P, McCulloch G. Dispersal Reduction: Causes, Genomic Mechanisms, and Evolutionary Consequences. Trends Ecol Evol 2020; 35:512-522. [DOI: 10.1016/j.tree.2020.01.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 12/23/2022]
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12
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Verry AJF, Scarsbrook L, Scofield RP, Tennyson AJD, Weston KA, Robertson BC, Rawlence NJ. Who, Where, What, Wren? Using Ancient DNA to Examine the Veracity of Museum Specimen Data: A Case Study of the New Zealand Rock Wren (Xenicus gilviventris). Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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13
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Affiliation(s)
- Graham P. Wallis
- Department of Zoology, University of Otago, Dunedin, New Zealand
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14
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Dussex N, Taylor HR, Stovall WR, Rutherford K, Dodds KG, Clarke SM, Gemmell NJ. Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species. Ecol Evol 2018; 8:8736-8749. [PMID: 30271541 PMCID: PMC6157699 DOI: 10.1002/ece3.4411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/17/2018] [Accepted: 05/29/2018] [Indexed: 12/20/2022] Open
Abstract
Next-generation reduced representation sequencing (RRS) approaches show great potential for resolving the structure of wild populations. However, the population structure of species that have shown rapid demographic recovery following severe population bottlenecks may still prove difficult to resolve due to high gene flow between subpopulations. Here, we tested the effectiveness of the RRS method Genotyping-By-Sequencing (GBS) for describing the population structure of the New Zealand fur seal (NZFS, Arctocephalus forsteri), a species that was heavily exploited by the 19th century commercial sealing industry and has since rapidly recolonized most of its former range from a few isolated colonies. Using 26,026 neutral single nucleotide polymorphisms (SNPs), we assessed genetic variation within and between NZFS colonies. We identified low levels of population differentiation across the species range (<1% of variation explained by regional differences) suggesting a state of near panmixia. Nonetheless, we observed subtle population substructure between West Coast and Southern East Coast colonies and a weak, but significant (p = 0.01), isolation-by-distance pattern among the eight colonies studied. Furthermore, our demographic reconstructions supported severe bottlenecks with potential 10-fold and 250-fold declines in response to Polynesian and European hunting, respectively. Finally, we were able to assign individuals treated as unknowns to their regions of origin with high confidence (96%) using our SNP data. Our results indicate that while it may be difficult to detect population structure in species that have experienced rapid recovery, next-generation markers and methods are powerful tools for resolving fine-scale structure and informing conservation and management efforts.
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Affiliation(s)
- Nicolas Dussex
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | | | | | - Kim Rutherford
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
| | - Ken G. Dodds
- Invermay Agricultural CentreAgResearchPuddle AlleyMosgielNew Zealand
| | - Shannon M. Clarke
- Invermay Agricultural CentreAgResearchPuddle AlleyMosgielNew Zealand
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Full Mitogenomes in the Critically Endangered Kākāpō Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity. Genes (Basel) 2018; 9:genes9040220. [PMID: 29671759 PMCID: PMC5924562 DOI: 10.3390/genes9040220] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 12/02/2022] Open
Abstract
Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute to extinction. Using temporal approaches can help us understand the effects of population declines on genetic diversity in real time. Sequencing pre-decline as well as post-decline mitogenomes representing all the remaining mitochondrial diversity, we estimated the loss of genetic diversity in the critically endangered kākāpō (Strigops habroptilus). We detected a signal of population expansion coinciding with the end of the Pleistocene last glacial maximum (LGM). Also, we found some evidence for northern and southern lineages, supporting the hypothesis that the species may have been restricted to isolated northern and southern refugia during the LGM. We observed an important loss of neutral genetic diversity associated with European settlement in New Zealand but we could not exclude a population decline associated with Polynesian settlement in New Zealand. However, we did not find evidence for fixation of deleterious mutations. We argue that despite high pre-decline genetic diversity, a rapid and range-wide decline combined with the lek mating system, and life-history traits of kākāpō contributed to a rapid loss of genetic diversity following severe population declines.
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16
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Trewick SA, Pilkington S, Shepherd LD, Gibb GC, Morgan-Richards M. Closing the gap: Avian lineage splits at a young, narrow seaway imply a protracted history of mixed population response. Mol Ecol 2017; 26:5752-5772. [PMID: 28805283 DOI: 10.1111/mec.14323] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/01/2017] [Accepted: 08/07/2017] [Indexed: 12/01/2022]
Abstract
The evolutionary significance of spatial habitat gaps has been well recognized since Alfred Russel Wallace compared the faunas of Bali and Lombok. Gaps between islands influence population structuring of some species, and flightless birds are expected to show strong partitioning even where habitat gaps are narrow. We examined the population structure of the most numerous living flightless land bird in New Zealand, Weka (Gallirallus australis). We surveyed Weka and their feather lice in native and introduced populations using genetic data gathered from DNA sequences of mitochondrial genes and nuclear β-fibrinogen and five microsatellite loci. We found low genetic diversity among extant Weka population samples. Two genetic clusters were evident in the mtDNA from Weka and their lice, but partitioning at nuclear loci was less abrupt. Many formerly recognized subspecies/species were not supported; instead, we infer one subspecies for each of the two main New Zealand islands. Although currently range restricted, North Island Weka have higher mtDNA diversity than the more wide-ranging southern Weka. Mismatch and neutrality statistics indicate North Island Weka experienced rapid and recent population reduction, while South Island Weka display the signature of recent expansion. Similar haplotype data from a widespread flying relative of Weka and other New Zealand birds revealed instances of North Island-South Island partitioning associated with a narrow habitat gap (Cook Strait). However, contrasting patterns indicate priority effects and other ecological factors have a strong influence on spatial exchange at this scale.
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Affiliation(s)
- Steve A Trewick
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Stephen Pilkington
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Lara D Shepherd
- Te Papa Tongarewa Museum of New Zealand, Wellington, New Zealand
| | - Gillian C Gibb
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Mary Morgan-Richards
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
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17
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Painting CJ, Myers S, Holwell GI, Buckley TR. Phylogeography of the New Zealand giraffe weevil Lasiorhynchus barbicornis (Coleoptera: Brentidae): A comparison of biogeographic boundaries. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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18
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Transverse Alpine Speciation Driven by Glaciation. Trends Ecol Evol 2016; 31:916-926. [DOI: 10.1016/j.tree.2016.08.009] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/26/2016] [Accepted: 08/26/2016] [Indexed: 01/19/2023]
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19
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Grosser S, Abdelkrim J, Wing J, Robertson BC, Gemmell NJ. Strong isolation by distance argues for separate population management of endangered blue duck (Hymenolaimus malacorhynchos). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0908-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Genetic diversity and population differentiation within and between island populations of two sympatric Petroica robins, the Chatham Island black robin and tomtit. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0899-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Bergner LM, Dussex N, Jamieson IG, Robertson BC. European Colonization, Not Polynesian Arrival, Impacted Population Size and Genetic Diversity in the Critically Endangered New Zealand Kākāpō. J Hered 2016; 107:593-602. [DOI: 10.1093/jhered/esw065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 09/14/2016] [Indexed: 11/13/2022] Open
Abstract
Abstract
Island endemic species are often vulnerable to decline and extinction following human settlement, and the genetic study of historical museum specimens can be useful in understanding these processes. The kākāpō (Strigops habroptilus) is a critically endangered New Zealand parrot that was formerly widespread and abundant. It is well established that both Polynesian and European colonization of New Zealand impacted the native avifauna, but the timeframe and severity of impacts have differed depending on species. Here, we investigated the relative importance of the 2 waves of human settlement on kākāpō decline, using microsatellites and mitochondrial DNA (mtDNA) to characterize recent kākāpō genetic and demographic history. We analyzed samples from 49 contemporary individuals and 54 museum specimens dating from 1884 to 1985. Genetic diversity decreased significantly between historical and contemporary kākāpō, with a decline in mean number of microsatellite alleles from 6.15 to 3.08 and in number of mtDNA haplotypes from 17 to 3. Modeling of demographic history indicated a recent population bottleneck linked to the period of European colonization (approximately 5 generations ago) but did not support a major decline linked to Polynesian settlement. Effective population size estimates were also larger for historical than contemporary kākāpō. Our findings inform contemporary kākāpō management by indicating the timeframe and possible cause of the bottleneck, which has implications for the management of extant genetic diversity. We demonstrate the broader utility of a historical perspective in understanding causes of decline and managing extinction risk in contemporary endangered species.
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Affiliation(s)
- Laura M. Bergner
- From the Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand (Bergner, Dussex, Jamieson, and Robertson) and Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK (Bergner)
| | - Nicolas Dussex
- From the Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand (Bergner, Dussex, Jamieson, and Robertson) and Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK (Bergner)
| | - Ian G. Jamieson
- From the Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand (Bergner, Dussex, Jamieson, and Robertson) and Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK (Bergner)
| | - Bruce C. Robertson
- From the Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand (Bergner, Dussex, Jamieson, and Robertson) and Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK (Bergner)
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22
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Abstract
Molecular dating largely overturned the paradigm that global cooling during recent Pleistocene glacial cycles resulted in a burst of species diversification although some evidence exists that speciation was commonly promoted in habitats near the expanding and retracting ice sheets. Here, we used a genome-wide dataset of more than half a million base pairs of DNA to test for a glacially induced burst of diversification in kiwi, an avian family distributed within several hundred kilometers of the expanding and retracting glaciers of the Southern Alps of New Zealand. By sampling across the geographic range of the five kiwi species, we discovered many cryptic lineages, bringing the total number of kiwi taxa that currently exist to 11 and the number that existed just before human arrival to 16 or 17. We found that 80% of kiwi diversification events date to the major glacial advances of the Middle and Late Pleistocene. During this period, New Zealand was repeatedly fragmented by glaciers into a series of refugia, with the tiny geographic ranges of many kiwi lineages currently distributed in areas adjacent to these refugia. Estimates of effective population size through time show a dramatic bottleneck during the last glacial cycle in all but one kiwi lineage, as expected if kiwi were isolated in glacially induced refugia. Our results support a fivefold increase in diversification rates during key glacial periods, comparable with levels observed in classic adaptive radiations, and confirm that at least some lineages distributed near glaciated regions underwent rapid ice age diversification.
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23
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Mitchell KJ, Wood JR, Llamas B, McLenachan PA, Kardailsky O, Scofield RP, Worthy TH, Cooper A. Ancient mitochondrial genomes clarify the evolutionary history of New Zealand's enigmatic acanthisittid wrens. Mol Phylogenet Evol 2016; 102:295-304. [PMID: 27261250 DOI: 10.1016/j.ympev.2016.05.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 05/27/2016] [Accepted: 05/30/2016] [Indexed: 10/21/2022]
Abstract
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.
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Affiliation(s)
- Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia.
| | - Jamie R Wood
- Landcare Research, Post Office Box 69040, Lincoln 7640, New Zealand
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Patricia A McLenachan
- Institute of Fundamental Sciences, Massey University, Palmerston North 4474, New Zealand
| | - Olga Kardailsky
- Department of Anatomy, Otago University, Dunedin 9054, New Zealand
| | - R Paul Scofield
- Canterbury Museum, Rolleston Avenue, Christchurch 8013, New Zealand
| | - Trevor H Worthy
- School of Biological Sciences, Flinders University, South Australia 5001, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
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24
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Identifying populations for management: fine-scale population structure in the New Zealand alpine rock wren (Xenicus gilviventris). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0815-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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