1
|
Grzegorczyk E, Caizergues A, Eraud C, Francesiaz C, Le Rest K, Guillemain M. Demographic and evolutionary consequences of hunting of wild birds. Biol Rev Camb Philos Soc 2024; 99:1298-1313. [PMID: 38409953 DOI: 10.1111/brv.13069] [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: 10/27/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 02/28/2024]
Abstract
Hunting has a long tradition in human evolutionary history and remains a common leisure activity or an important source of food. Herein, we first briefly review the literature on the demographic consequences of hunting and associated analytical methods. We then address the question of potential selective hunting and its possible genetic/evolutionary consequences. Birds have historically been popular models for demographic studies, and the huge amount of census and ringing data accumulated over the last century has paved the way for research about the demographic effects of harvesting. By contrast, the literature on the evolutionary consequences of harvesting is dominated by studies on mammals (especially ungulates) and fish. In these taxa, individuals selected for harvest often have particular traits such as large body size or extravagant secondary sexual characters (e.g. antlers, horns, etc.). Our review shows that targeting individuals according to such genetically heritable traits can exert strong selective pressures and alter the evolutionary trajectory of populations for these or correlated traits. Studies focusing on the evolutionary consequences of hunting in birds are extremely rare, likely because birds within populations appear much more similar, and do not display individual differences to the same extent as many mammals and fishes. Nevertheless, even without conscious choice by hunters, there remains the potential for selection through hunting in birds, for example by genetically inherited traits such as personality or pace-of-life. We emphasise that because so many bird species experience high hunting pressure, the possible selective effect of harvest in birds and its evolutionary consequences deserves far more attention, and that hunting may be one major driver of bird evolutionary trajectories that should be carefully considered in wildlife management schemes.
Collapse
Affiliation(s)
- Emilienne Grzegorczyk
- Office Français de la Biodiversité, Service Conservation et Gestion Durable des Espèces Exploitées, 405 Route de Prissé-la-Charrière, Villiers-en-Bois, 79360, France
| | - Alain Caizergues
- Office Français de la Biodiversité, Service Conservation et Gestion Durable des Espèces Exploitées, 08 Bd A. Einstein, CS42355, Nantes Cedex 3, 44323, France
| | - Cyril Eraud
- Office Français de la Biodiversité, Service Conservation et Gestion des Espèces à Enjeux, 405 Route de Prissé-la-Charrière, Villiers-en-Bois, 79360, France
| | - Charlotte Francesiaz
- Office Français de la Biodiversité, Service Conservation et Gestion Durable des Espèces Exploitées, 147 Avenue de Lodève, Juvignac, 34990, France
| | - Kévin Le Rest
- Office Français de la Biodiversité, Service Conservation et Gestion Durable des Espèces Exploitées, 08 Bd A. Einstein, CS42355, Nantes Cedex 3, 44323, France
| | - Matthieu Guillemain
- Office Français de la Biodiversité, Service Conservation et Gestion Durable des Espèces Exploitées, La Tour du Valat, Le Sambuc, Arles, 13200, France
| |
Collapse
|
2
|
Edwards SV, Cloutier A, Cockburn G, Driver R, Grayson P, Katoh K, Baldwin MW, Sackton TB, Baker AJ. A nuclear genome assembly of an extinct flightless bird, the little bush moa. SCIENCE ADVANCES 2024; 10:eadj6823. [PMID: 38781323 DOI: 10.1126/sciadv.adj6823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.
Collapse
Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Glenn Cockburn
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Robert Driver
- Department of Biology, East Carolina University, E 5th Street, Greenville, NC 27605, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Kazutaka Katoh
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Timothy B Sackton
- Informatics Group, Harvard University, 38 Oxford Street, Cambridge, MA 02138, USA
| | - Allan J Baker
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, ON M5S 3B2, Canada
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON M5S 2C6, Canada
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Algeo TJ, Shen J. Theory and classification of mass extinction causation. Natl Sci Rev 2024; 11:nwad237. [PMID: 38116094 PMCID: PMC10727847 DOI: 10.1093/nsr/nwad237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 12/21/2023] Open
Abstract
Theory regarding the causation of mass extinctions is in need of systematization, which is the focus of this contribution. Every mass extinction has both an ultimate cause, i.e. the trigger that leads to various climato-environmental changes, and one or more proximate cause(s), i.e. the specific climato-environmental changes that result in elevated biotic mortality. With regard to ultimate causes, strong cases can be made that bolide (i.e. meteor) impacts, large igneous province (LIP) eruptions and bioevolutionary events have each triggered one or more of the Phanerozoic Big Five mass extinctions, and that tectono-oceanic changes have triggered some second-order extinction events. Apart from bolide impacts, other astronomical triggers (e.g. solar flares, gamma bursts and supernova explosions) remain entirely in the realm of speculation. With regard to proximate mechanisms, most extinctions are related to either carbon-release or carbon-burial processes, the former being associated with climatic warming, ocean acidification, reduced marine productivity and lower carbonate δ13C values, and the latter with climatic cooling, increased marine productivity and higher carbonate δ13C values. Environmental parameters such as marine redox conditions and terrestrial weathering intensity do not show consistent relationships with carbon-cycle changes. In this context, mass extinction causation can be usefully classified using a matrix of ultimate and proximate factors. Among the Big Five mass extinctions, the end-Cretaceous biocrisis is an example of a bolide-triggered carbon-release event, the end-Permian and end-Triassic biocrises are examples of LIP-triggered carbon-release events, and the Late Ordovician and Late Devonian biocrises are examples of bioevolution-triggered carbon-burial events. Whereas the bolide-impact and LIP-eruption mechanisms appear to invariably cause carbon release, bioevolutionary triggers can result in variable carbon-cycle changes, e.g. carbon burial during the Late Ordovician and Late Devonian events, carbon release associated with modern anthropogenic climate warming, and little to no carbon-cycle impact due to certain types of ecosystem change (e.g. the advent of the first predators around the end-Ediacaran; the appearance of Paleolithic human hunters in Australasia and the Americas). Broadly speaking, studies of mass extinction causation have suffered from insufficiently critical thinking-an impartial survey of the extant evidence shows that (i) hypotheses of a common ultimate cause (e.g. bolide impacts or LIP eruptions) for all Big Five mass extinctions are suspect given manifest differences in patterns of environmental and biotic change among them; (ii) the Late Ordovician and Late Devonian events were associated with carbon burial and long-term climatic cooling, i.e. changes that are inconsistent with a bolide-impact or LIP-eruption mechanism; and (iii) claims of periodicity in Phanerozoic mass extinctions depended critically on the now-disproven idea that they shared a common extrinsic trigger (i.e. bolide impacts).
Collapse
Affiliation(s)
- Thomas J Algeo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences—Wuhan, Wuhan430074, China
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences—Wuhan, Wuhan430074, China
- Department of Geosciences, University of Cincinnati, Cincinnati, OH45221, USA
| | - Jun Shen
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences—Wuhan, Wuhan430074, China
| |
Collapse
|
5
|
Basal Anseriformes from the Early Paleogene of North America and Europe. DIVERSITY 2023. [DOI: 10.3390/d15020233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
We describe nearly complete skeletons of basal Anseriformes from the Latest Paleocene to the early Eocene of North America and Europe. Collectively, these birds appear to be representative of anseriforms near the divergence of Anhimae and Anseres, but their exact positions relative to these clades remains uncertain. A new family, Anachronornithidae nov. fam., is erected on the basis of one of these, Anachronornis anhimops nov. gen., nov. gen. et sp., to which the others cannot be confidently assigned. The new fossils augment a growing collection of early Pan-Anseriformes, which in their diversity do not paint an unambiguous picture of phylogeny or character state evolution on the path to or within crown-Anseriformes. Anachronornis nov. gen. is similar in some aspects of both cranial and postcranial anatomy to other well-represented early Paleogene Anseriformes and members of Anseres, such as Presbyornis Wetmore, 1926. However, it exhibits a more landfowl-like bill, like that of Anhimae and unlike the spatulate bill of Anseres. Additional specimens of similar basal Anseriformes of uncertain affinities from the early Eocene of North America and Europe further complicate interpretation of character state polarity due to the mosaicism of primitive and derived characters they exhibit.
Collapse
|
6
|
Wehi PM, Rogers KM, Jowett T, Sabadel AJM. Interpreting past trophic ecology of a threatened alpine parrot, kea Nestor notabilis, from museum specimens. J Anim Ecol 2023; 92:273-284. [PMID: 35569094 PMCID: PMC10083992 DOI: 10.1111/1365-2656.13742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/26/2022] [Indexed: 11/28/2022]
Abstract
When ecosystems are under severe pressure or environments change, trophic position and intraspecific niche width may decrease or narrow, signalling that conservation action is required. In New Zealand, alpine and subalpine ecosystems have been extensively modified through farming since 19th-century European settlement, with consequences for indigenous species such as the kea Nestor notabilis. We investigated feather stable isotope values in the kea and predicted a lower trophic position in modern kea populations, to reflect reduced lowland habitat and a mixed diet with more plant material. We predicted that size and sex would influence trophic values in this sexually dimorphic species, with larger birds more likely to have a high protein diet. We examined potential dietary changes in 68 museum collected kea from 1880s to 2000s, first recording accession details including provenance and sex and measuring culmen length. We used bulk carbon and nitrogen stable isotope analyses (BSIAs) of feathers and a further feather subset using compound-specific stable isotope analyses of amino acids (CSIA-AA) to obtain isotopic values and estimate trophic position. BSIA showed δ15 N values in kea feathers declined through time and could indicate that early century kea were highly omnivorous, with δ15 N values on average higher than in modern kea. Variance in δ15 N values was greater after 1950, driven by a few individuals. Few differences between males and females were evident, although females in the south region had lower δ15 N values. There was a tendency for large male birds to have higher trophic values, perhaps reflecting dominant male bird behaviour noted in historical records. Nonetheless, CSIA-AA performed on a subset of the data suggested that variation in BSIA is likely due to baseline changes rather than relative trophic position which may be more homogenous than these data indicate. Although there was more variability in modern kea, we suggest caution in interpretation. Stable isotope data, particularly CSIA-AA, from museum specimens can reveal potential change in ecological networks as well as sexually dimorphic feeding patterns within species. The data can reveal temporal and regional variation in species trophic position and changes in ecosystem integrity to inform conservation decision-making.
Collapse
Affiliation(s)
- Priscilla M Wehi
- Centre for Sustainability (CSAFE), University of Otago, Dunedin, New Zealand.,Te Pūnaha Matatini Centre of Research Excellence in Complex Systems, University of Auckland, Auckland, New Zealand
| | - Karyne M Rogers
- National Isotope Centre, GNS Science, Lower Hutt, New Zealand.,Institute of Quality Safety and Nutrition of Agricultural Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tim Jowett
- Department of Maths and Statistics, University of Otago, Dunedin, New Zealand
| | | |
Collapse
|
7
|
Ancient proteins resolve controversy over the identity of Genyornis eggshell. Proc Natl Acad Sci U S A 2022; 119:e2109326119. [PMID: 35609205 PMCID: PMC9995833 DOI: 10.1073/pnas.2109326119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The realization that ancient biomolecules are preserved in "fossil" samples has revolutionized archaeological science. Protein sequences survive longer than DNA, but their phylogenetic resolution is inferior; therefore, careful assessment of the research questions is required. Here, we show the potential of ancient proteins preserved in Pleistocene eggshell in addressing a longstanding controversy in human and animal evolution: the identity of the extinct bird that laid large eggs which were exploited by Australia's indigenous people. The eggs had been originally attributed to the iconic extinct flightless bird Genyornis newtoni (†Dromornithidae, Galloanseres) and were subsequently dated to before 50 ± 5 ka by Miller et al. [Nat. Commun. 7, 10496 (2016)]. This was taken to represent the likely extinction date for this endemic megafaunal species and thus implied a role of humans in its demise. A contrasting hypothesis, according to which the eggs were laid by a large mound-builder megapode (Megapodiidae, Galliformes), would therefore acquit humans of their responsibility in the extinction of Genyornis. Ancient protein sequences were reconstructed and used to assess the evolutionary proximity of the undetermined eggshell to extant birds, rejecting the megapode hypothesis. Authentic ancient DNA could not be confirmed from these highly degraded samples, but morphometric data also support the attribution of the eggshell to Genyornis. When used in triangulation to address well-defined hypotheses, paleoproteomics is a powerful tool for reconstructing the evolutionary history in ancient samples. In addition to the clarification of phylogenetic placement, these data provide a more nuanced understanding of the modes of interactions between humans and their environment.
Collapse
|
8
|
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
| |
Collapse
|
9
|
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
| |
Collapse
|
10
|
Verry AJF, Mitchell KJ, Rawlence NJ. Genetic evidence for post-glacial expansion from a southern refugium in the eastern moa ( Emeus crassus). Biol Lett 2022; 18:20220013. [PMID: 35538842 PMCID: PMC9091836 DOI: 10.1098/rsbl.2022.0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/20/2022] [Indexed: 12/14/2022] Open
Abstract
Cycles of glacial expansion and contraction throughout the Pleistocene drove increases and decreases, respectively, in the geographical range and population size of many animal species. Genetic data have revealed that during glacial maxima the distribution of many Eurasian animals was restricted to small refugial areas, from which species expanded to reoccupy parts of their former range as the climate warmed. It has been suggested that the extinct eastern moa (Emeus crassus)-a large, flightless bird from New Zealand-behaved analogously during glacial maxima, possibly surviving only in a restricted area of lowland habitat in the southern South Island of New Zealand during the Last Glacial Maximum (LGM). However, previous studies have lacked the power and geographical sampling to explicitly test this hypothesis using genetic data. Here we analyse 46 ancient mitochondrial genomes from Late Pleistocene and Holocene bones of the eastern moa from across their post-LGM distribution. Our results are consistent with a post-LGM increase in the population size and genetic diversity of eastern moa. We also demonstrate that genetic diversity was higher in eastern moa from the southern extent of their range, supporting the hypothesis that they expanded from a single glacial refugium following the LGM.
Collapse
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, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - 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
| |
Collapse
|
11
|
Kimura Y, Fukui D, Yoshiyuki M, Higashi K. Conservation paleobiology on Minami-Daito Island, Okinawa, Japan: anthropogenic extinction of cave-dwelling bats on a tropical oceanic island. PeerJ 2022; 10:e12702. [PMID: 35127280 PMCID: PMC8801181 DOI: 10.7717/peerj.12702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/07/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND With strong environmental and geographic filtration, vertebrates incapable of flying and swimming are often extirpated from island ecosystems. Minami-Daito Island is an oceanic island in Okinawa, Japan that harbors the Daito flying fox (Pteropus dasymallus daitoensis), a subspecies of the fruit bat and the only extant mammal endemic to the island. However, the skeleton of a cave-dwelling bat Rhinolophus sp. and fossil guano were briefly reported in a previous study. METHODS Here, we present evidence for the anthropogenic extirpation of two species of cave-dwelling bats (Miniopterus sp. & Rhinolophus sp.) from Minami-Daito Island. Our goal is to reliably constrain the ages of the extirpated bat species by a multiproxy approach. Because skeletal materials did not preserve sufficient bone collagen for direct radiocarbon dating, we alternatively examined guano-like deposits based on SEM observation and Fourier-transform infrared spectroscopy (FTIR) along with stable carbon and nitrogen isotope analyses for possible indirect dating. We also examined stable carbon isotopes in bone apatite, assuming that an isotopic signal of C4 plants on the bat bones links to sugarcane plantation on the island based on the historical knowledge that early human settlers quickly replaced the island's native C3 forests with sugarcane (C4 perennial grass) plantation from 1900 onward. RESULTS Our cave survey documents the remains of Miniopterus sp. from the island for the first time. Based on the unique taphonomic conditions (unpermineralized bones, disarticulated skeletons closely scattered without sediment cover, various degrees of calcite crystal growth around bones) and a radiocarbon age of a humic sample, we suggest that the maximum age constraint of Miniopterus sp. and Rhinolophus sp. is 4,640 calBP. Based on a series of analyses, we conclude that the guano-like deposits are composed not of bat guano but mainly of humic substances; however, a hydroxyapatite crust associated with bat-lying stalagmites may be derived from bat feces. Stable carbon isotope analysis of bone apatite revealed C4 signals in various degrees, confirming that small populations of cave-dwelling bats persisted on Minami-Daito Island after 1900. CONCLUSIONS The results of this study indicate that these populations remained rather small and did not leave many generations and that the estimated ages can be bracketed from 4,640 calBP to the post-1900 (perhaps, until the 1950s). They likely faced a continuously high mortality risk due to severe anthropogenic stresses on the island, where most of the forests were turned into sugarcane plantations within a few decades in the early 20th century. A result of hearing surveys to local residents suggests the latest remnants most likely disappeared on the island concurrently with the introduction of chemical pesticides after World War II.
Collapse
Affiliation(s)
- Yuri Kimura
- Department of Geology and Paleontology, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan,Institut Català de Paleontologia Miquel Crusafont, ICTA-ICP, Barcelona, Spain
| | - Dai Fukui
- The University of Tokyo Hokkaido Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Furano, Hokkaido, Japan
| | - Mizuko Yoshiyuki
- Department of Agriculture, Tokyo University of Agriculture, Atsugi, Kanagawa, Japan
| | | |
Collapse
|
12
|
Zacho CM, Bager MA, Margaryan A, Gravlund P, Galatius A, Rasmussen AR, Allentoft ME. Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes. PLoS One 2021; 16:e0256353. [PMID: 34424926 PMCID: PMC8382189 DOI: 10.1371/journal.pone.0256353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/04/2021] [Indexed: 11/19/2022] Open
Abstract
Natural history museum collections worldwide represent a tremendous resource of information on past and present biodiversity. Fish, reptiles, amphibians and many invertebrate collections have often been preserved in ethanol for decades or centuries and our knowledge on the genomic and metagenomic research potential of such material is limited. Here, we use ancient DNA protocols, combined with shotgun sequencing to test the molecular preservation in liver, skin and bone tissue from five old (1842 to 1964) museum specimens of the common garter snake (Thamnophis sirtalis). When mapping reads to a T. sirtalis reference genome, we find that the DNA molecules are highly damaged with short average sequence lengths (38-64 bp) and high C-T deamination, ranging from 9% to 21% at the first position. Despite this, the samples displayed relatively high endogenous DNA content, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimens and tissues included here. Of the three tested types of tissue, bone shows marginally but significantly higher DNA quality in these metrics. Though at least one of the snakes had been exposed to formalin, neither the concentration nor the quality of the obtained DNA was affected. Lastly, we demonstrate that these specimens display a diverse and tissue-specific microbial genetic profile, thus offering authentic metagenomic data despite being submerged in ethanol for many years. Our results emphasize that historical museum collections continue to offer an invaluable source of information in the era of genomics.
Collapse
Affiliation(s)
- Claus M. Zacho
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Martina A. Bager
- Section for EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Section for EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Anders Galatius
- Department of Bioscience, Aarhus University, Roskilde, Denmark
| | - Arne R. Rasmussen
- Institute of Conservation, Royal Danish Academy—Architecture, Design, Conservation, Copenhagen, Denmark
| | - Morten E. Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| |
Collapse
|
13
|
Martínez-García L, Ferrari G, Oosting T, Ballantyne R, van der Jagt I, Ystgaard I, Harland J, Nicholson R, Hamilton-Dyer S, Baalsrud HT, Brieuc MSO, Atmore LM, Burns F, Schmölcke U, Jakobsen KS, Jentoft S, Orton D, Hufthammer AK, Barrett JH, Star B. Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.671281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.
Collapse
|
14
|
Seersholm FV, Hansen KL, Heydenrych M, Hansen AJ, Bunce M, Allentoft ME. Ancient DNA preserved in small bone fragments from the P.W. Lund collection. Ecol Evol 2021; 11:2064-2071. [PMID: 33717442 PMCID: PMC7920760 DOI: 10.1002/ece3.7162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/25/2020] [Accepted: 12/17/2020] [Indexed: 12/04/2022] Open
Abstract
The Lund collection is one of the oldest subfossil collections in the world. The vast assemblage of subfossils was collected in the 1830s and 1840s by Peter Wilhelm Lund in Lagoa Santa, Brazil, and was shipped to Copenhagen in 1848, where it was stored in various locations around the city with little attention for the future preservation of the collection. So far, successful genetic research on the material collected by Lund has been limited to two samples of human petrous bone. However, less is known about the preservation conditions of the vast amounts of small and fragmentary bones stored in the collection. To address this, we studied ancient DNA from bulk bone samples of approximately 100 bone fragments from the P.W. Lund collection from boxes with varying degrees of physical preservation conditions. Using bulk bone metabarcoding, we found a high species diversity in all samples. In total, we identified 17 species, representing 11 mammals, two birds, one fish, and three frogs. Of these, two species are new to the collection. Collectively, these results exhibit the potential of future genetic studies on the famous P.W. Lund collection and suggest that the effects of poor storage conditions are probably negligible compared with the long-term in situ degradation that specimens undergo before excavation.
Collapse
Affiliation(s)
- Frederik V. Seersholm
- Trace and Environmental DNA (TrEnD) LaboratorySchool of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
- Section for GeoGeneticsGLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Kasper Lykke Hansen
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Matthew Heydenrych
- Trace and Environmental DNA (TrEnD) LaboratorySchool of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
| | - Anders J. Hansen
- Section for GeoGeneticsGLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) LaboratorySchool of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
| | - Morten E. Allentoft
- Trace and Environmental DNA (TrEnD) LaboratorySchool of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
- Section for GeoGeneticsGLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
| |
Collapse
|
15
|
Smith BT, Gehara M, Harvey MG. The demography of extinction in eastern North American birds. Proc Biol Sci 2021; 288:20201945. [PMID: 33529556 DOI: 10.1098/rspb.2020.1945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Species are being lost at an unprecedented rate during the Anthropocene. Progress has been made in clarifying how species traits influence their propensity to go extinct, but the role historical demography plays in species loss or persistence is unclear. In eastern North America, five charismatic landbirds went extinct last century, and the causes of their extinctions have been heavily debated. Although these extinctions are most often attributed to post-colonial human activity, other factors such as declining ancestral populations prior to European colonization could have made these species particularly susceptible. We used population genomic data from these extinct birds and compared them with those from four codistributed extant species. We found extinct species harboured lower genetic diversity and effective population sizes than extant species, but both extinct and non-extinct birds had similar demographic histories of population expansion. These demographic patterns are consistent with population size changes associated with glacial-interglacial cycles. The lack of support for overall population declines during the Pleistocene corroborates the view that, although species that went extinct may have been vulnerable due to low diversity or small population size, their disappearance was driven by human activities in the Anthropocene.
Collapse
Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Avenue, Newark, NJ 07102, USA
| | - Michael G Harvey
- Department of Biological Sciences, The University of Texas at El Paso, 500 W University Avenue, El Paso, TX 79968, USA
| |
Collapse
|
16
|
Keighley X, Pálsson S, Einarsson BF, Petersen A, Fernández-Coll M, Jordan P, Olsen MT, Malmquist HJ. Disappearance of Icelandic Walruses Coincided with Norse Settlement. Mol Biol Evol 2020; 36:2656-2667. [PMID: 31513267 PMCID: PMC6878957 DOI: 10.1093/molbev/msz196] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
There is a growing body of evidence demonstrating the impacts of human arrival in new “pristine” environments, including terrestrial habitat alterations and species extinctions. However, the effects of marine resource utilization prior to industrialized whaling, sealing, and fishing have largely remained understudied. The expansion of the Norse across the North Atlantic offers a rare opportunity to study the effects of human arrival and early exploitation of marine resources. Today, there is no local population of walruses on Iceland, however, skeletal remains, place names, and written sources suggest that walruses existed, and were hunted by the Norse during the Settlement and Commonwealth periods (870–1262 AD). This study investigates the timing, geographic distribution, and genetic identity of walruses in Iceland by combining historical information, place names, radiocarbon dating, and genomic analyses. The results support a genetically distinct, local population of walruses that went extinct shortly after Norse settlement. The high value of walrus products such as ivory on international markets likely led to intense hunting pressure, which—potentially exacerbated by a warming climate and volcanism—resulted in the extinction of walrus on Iceland. We show that commercial hunting, economic incentives, and trade networks as early as the Viking Age were of sufficient scale and intensity to result in significant, irreversible ecological impacts on the marine environment. This is to one of the earliest examples of local extinction of a marine species following human arrival, during the very beginning of commercial marine exploitation.
Collapse
Affiliation(s)
- Xénia Keighley
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Arctic Centre and Groningen Institute of Archaeology, University of Groningen, Groningen, The Netherlands
| | - Snæbjörn Pálsson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Meritxell Fernández-Coll
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland.,Icelandic Museum of Natural History, Reykjavík, Iceland
| | - Peter Jordan
- Arctic Centre and Groningen Institute of Archaeology, University of Groningen, Groningen, The Netherlands
| | - Morten Tange Olsen
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | |
Collapse
|
17
|
Thomas JE, Carvalho GR, Haile J, Rawlence NJ, Martin MD, Ho SYW, Sigfússon AÞ, Jósefsson VA, Frederiksen M, Linnebjerg JF, Samaniego Castruita JA, Niemann J, Sinding MHS, Sandoval-Velasco M, Soares AER, Lacy R, Barilaro C, Best J, Brandis D, Cavallo C, Elorza M, Garrett KL, Groot M, Johansson F, Lifjeld JT, Nilson G, Serjeanston D, Sweet P, Fuller E, Hufthammer AK, Meldgaard M, Fjeldså J, Shapiro B, Hofreiter M, Stewart JR, Gilbert MTP, Knapp M. Demographic reconstruction from ancient DNA supports rapid extinction of the great auk. eLife 2019; 8:e47509. [PMID: 31767056 PMCID: PMC6879203 DOI: 10.7554/elife.47509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/22/2019] [Indexed: 01/23/2023] Open
Abstract
The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.
Collapse
Affiliation(s)
- Jessica E Thomas
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
| | - James Haile
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Michael D Martin
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Simon YW Ho
- School of Life and Environmental SciencesUniversity of SydneySydneyAustralia
| | | | | | | | | | | | - Jonas Niemann
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Mikkel-Holger S Sinding
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Greenland Institute of Natural ResourcesNuukGreenland
| | | | - André ER Soares
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Robert Lacy
- Department of Conservation ScienceChicago Zoological SocietyBrookfieldUnited States
| | | | - Juila Best
- Department of Archaeology, Anthropology and Forensic Science, Faculty of Science and TechnologyBournemouth UniversityPooleUnited Kingdom
- School of History, Archaeology and ReligionCardiff UniversityCardiffUnited Kingdom
| | | | - Chiara Cavallo
- Amsterdam Centre for Ancient Studies and ArchaeologyUniversity of AmsterdamAmsterdamNetherlands
| | - Mikelo Elorza
- Arqueología PrehistóricaSociedad de Ciencias AranzadiSan SebastiánSpain
| | - Kimball L Garrett
- Natural History Museum of Los Angeles CountyLos AngelesUnited States
| | - Maaike Groot
- Institut für Prähistorische ArchäologieFreie Universität BerlinBerlinGermany
| | | | | | - Göran Nilson
- Gothenburg Museum of Natural HistoryGothenburgSweden
| | - Dale Serjeanston
- Humanities ArchaeologyUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Paul Sweet
- Department of OrnithologyAmerican Museum of Natural HistoryNew YorkUnited States
| | | | | | | | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Beth Shapiro
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural SciencesUniversity of PotsdamPotsdamGermany
| | - John R Stewart
- Faculty of Science and TechnologyBournemouth UniversityDorsetUnited Kingdom
| | - M Thomas P Gilbert
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Michael Knapp
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
| |
Collapse
|
18
|
Unique parasite aDNA in moa coprolites from New Zealand suggests mass parasite extinctions followed human-induced megafauna extinctions. Proc Natl Acad Sci U S A 2018; 115:1411-1413. [PMID: 29440435 DOI: 10.1073/pnas.1722598115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
19
|
Wehi PM, Cox MP, Roa T, Whaanga H. Human Perceptions of Megafaunal Extinction Events Revealed by Linguistic Analysis of Indigenous Oral Traditions. HUMAN ECOLOGY: AN INTERDISCIPLINARY JOURNAL 2018; 46:461-470. [PMID: 30237652 PMCID: PMC6133014 DOI: 10.1007/s10745-018-0004-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Human settlement into new regions is typically accompanied by waves of animal extinctions, yet we have limited understanding of how human communities perceived and responded to such ecological crises. The first megafaunal extinctions in New Zealand began just 700 years ago, in contrast to the deep time of continental extinctions. Consequently, indigenous Māori oral tradition includes ancestral sayings that explicitly refer to extinct species. Our linguistic analysis of these sayings shows a strong bias towards critical food species such as moa, and emphasizes that Māori closely observed the fauna and environment. Temporal changes in form and content demonstrate that Māori recognized the loss of important animal resources, and that this loss reverberated culturally centuries later. The data provide evidence that extinction of keystone fauna was important for shaping ecological and social thought in Māori society, and suggest a similar role in other early societies that lived through megafaunal extinction events.
Collapse
Affiliation(s)
- Priscilla M. Wehi
- Centre for Sustainability, University of Otago, PO Box 56, Dunedin, 9054 New Zealand
- Te Pūnaha Matatini, Manaaki Whenua – Landcare Research, 764 Cumberland St, Private Bag 1930, Dunedin, 9054 New Zealand
| | - Murray P. Cox
- Te Pūnaha Matatini, Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442 New Zealand
| | - Tom Roa
- Faculty of Māori and Indigenous Studies, University of Waikato, Private Bag 3105, Hamilton, 3240 New Zealand
| | - Hēmi Whaanga
- Faculty of Māori and Indigenous Studies, University of Waikato, Private Bag 3105, Hamilton, 3240 New Zealand
| |
Collapse
|
20
|
Llamas B, Willerslev E, Orlando L. Human evolution: a tale from ancient genomes. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0484. [PMID: 27994125 DOI: 10.1098/rstb.2015.0484] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 12/21/2022] Open
Abstract
The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
Collapse
Affiliation(s)
- Bastien Llamas
- Australian Centre for ADNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Wellcome Genome Campus Hinxton, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark .,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, CNRS UMR 5288, 31000 Toulouse, France
| |
Collapse
|
21
|
Pujolar JM, Dalén L, Hansen MM, Madsen J. Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age. Mol Ecol 2017; 26:6270-6283. [PMID: 28980346 DOI: 10.1111/mec.14374] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 02/06/2023]
Abstract
We investigated how population changes and fluctuations in the pink-footed goose might have been affected by climatic and anthropogenic factors. First, genomic data confirmed the existence of two separate populations: western (Iceland) and eastern (Svalbard/Denmark). Second, demographic inference suggests that the species survived the last glacial period as a single ancestral population with a low population size (100-1,000 individuals) that split into the current populations at the end of the last glacial maximum with Iceland being the most plausible glacial refuge. While population changes during the last glaciation were clearly environmental, we hypothesize that more recent demographic changes are human-related: (1) the inferred population increase in the Neolithic is due to deforestation to establish new lands for agriculture, increasing available habitat for pink-footed geese, (2) the decline inferred during the Middle Ages is due to human persecution, and (3) improved protection explains the increasing demographic trends during the 20th century. Our results suggest both environmental (during glacial cycles) and anthropogenic effects (more recent) can be a threat to species survival.
Collapse
Affiliation(s)
- J M Pujolar
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | - L Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - M M Hansen
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | - J Madsen
- Department of Bioscience-Kalø, Aarhus University, Rønde, Denmark
| |
Collapse
|
22
|
Humans and climate change drove the Holocene decline of the brown bear. Sci Rep 2017; 7:10399. [PMID: 28871202 PMCID: PMC5583342 DOI: 10.1038/s41598-017-10772-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/14/2017] [Indexed: 12/03/2022] Open
Abstract
The current debate about megafaunal extinctions during the Quaternary focuses on the extent to which they were driven by humans, climate change, or both. These two factors may have interacted in a complex and unexpected manner, leaving the exact pathways to prehistoric extinctions unresolved. Here we quantify, with unprecedented detail, the contribution of humans and climate change to the Holocene decline of the largest living terrestrial carnivore, the brown bear (Ursus arctos), on a continental scale. We inform a spatially explicit metapopulation model for the species by combining life-history data and an extensive archaeofaunal record from excavations across Europe with reconstructed climate and land-use data reaching back 12,000 years. The model reveals that, despite the broad climatic niche of the brown bear, increasing winter temperatures contributed substantially to its Holocene decline — both directly by reducing the species’ reproductive rate and indirectly by facilitating human land use. The first local extinctions occurred during the Mid-Holocene warming period, but the rise of the Roman Empire 2,000 years ago marked the onset of large-scale extinctions, followed by increasingly rapid range loss and fragmentation. These findings strongly support the hypothesis that complex interactions between climate and humans may have accelerated megafaunal extinctions.
Collapse
|
23
|
Salmona J, Heller R, Quéméré E, Chikhi L. Climate change and human colonization triggered habitat loss and fragmentation in Madagascar. Mol Ecol 2017; 26:5203-5222. [DOI: 10.1111/mec.14173] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 04/24/2017] [Accepted: 05/02/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Jordi Salmona
- Instituto Gulbenkian de Ciênca; Oeiras Portugal
- Laboratoire Evolution & Diversité Biologique; UMR 5174 CNRS; Université Paul Sabatier; Toulouse France
- UMR 5174 EDB; Université de Toulouse; Toulouse France
| | - Rasmus Heller
- Department of Biology; University of Copenhagen; Copenhagen N Denmark
| | - Erwan Quéméré
- CEFS; Université de Toulouse; INRA; Castanet-Tolosan France
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciênca; Oeiras Portugal
- Laboratoire Evolution & Diversité Biologique; UMR 5174 CNRS; Université Paul Sabatier; Toulouse France
- UMR 5174 EDB; Université de Toulouse; Toulouse France
| |
Collapse
|
24
|
Brüniche-Olsen A, Hazlitt SL, Eldridge MDB. Genetic evidence of range-wide population declines in an Australian marsupial prior to European settlement. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0960-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
25
|
Sullivan AP, Bird DW, Perry GH. Human behaviour as a long-term ecological driver of non-human evolution. Nat Ecol Evol 2017; 1:65. [DOI: 10.1038/s41559-016-0065] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/20/2016] [Indexed: 12/26/2022]
|
26
|
Grosser S, Rawlence NJ, Anderson CNK, Smith IWG, Scofield RP, Waters JM. Invader or resident? Ancient-DNA reveals rapid species turnover in New Zealand little penguins. Proc Biol Sci 2017; 283:rspb.2015.2879. [PMID: 26842575 DOI: 10.1098/rspb.2015.2879] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The expansion of humans into previously unoccupied parts of the globe is thought to have driven the decline and extinction of numerous vertebrate species. In New Zealand, human settlement in the late thirteenth century AD led to the rapid demise of a distinctive vertebrate fauna, and also a number of 'turnover' events where extinct lineages were subsequently replaced by closely related taxa. The recent genetic detection of an Australian little penguin (Eudyptula novaehollandiae) in southeastern New Zealand may potentially represent an additional 'cryptic' invasion. Here we use ancient-DNA (aDNA) analysis and radiocarbon dating of pre-human, archaeological and historical Eudyptula remains to reveal that the arrival of E. novaehollandiae in New Zealand probably occurred between AD 1500 and 1900, following the anthropogenic decline of its sister taxon, the endemic Eudyptula minor. This rapid turnover event, revealed by aDNA, suggests that native species decline can be masked by invasive taxa, and highlights the potential for human-mediated biodiversity shifts.
Collapse
Affiliation(s)
- Stefanie Grosser
- Allan Wilson Centre, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nicolas J Rawlence
- Allan Wilson Centre, Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Ian W G Smith
- Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand
| | | | - Jonathan M Waters
- Allan Wilson Centre, Department of Zoology, University of Otago, Dunedin, New Zealand
| |
Collapse
|
27
|
Attard MRG, Wilson LAB, Worthy TH, Scofield P, Johnston P, Parr WCH, Wroe S. Moa diet fits the bill: virtual reconstruction incorporating mummified remains and prediction of biomechanical performance in avian giants. Proc Biol Sci 2016; 283:rspb.2015.2043. [PMID: 26763698 DOI: 10.1098/rspb.2015.2043] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The moa (Dinornithiformes) are large to gigantic extinct terrestrial birds of New Zealand. Knowledge about niche partitioning, feeding mode and preference among moa species is limited, hampering palaeoecological reconstruction and evaluation of the impacts of their extinction on remnant native biota, or the viability of exotic species as proposed ecological 'surrogates'. Here we apply three-dimensional finite-element analysis to compare the biomechanical performance of skulls from five of the six moa genera, and two extant ratites, to predict the range of moa feeding behaviours relative to each other and to living relatives. Mechanical performance during biting was compared using simulations of the birds clipping twigs based on muscle reconstruction of mummified moa remains. Other simulated food acquisition strategies included lateral shaking, pullback and dorsoventral movement of the skull. We found evidence for limited overlap in biomechanical performance between the extant emu (Dromaius novaehollandiae) and extinct upland moa (Megalapteryx didinus) based on similarities in mandibular stress distribution in two loading cases, but overall our findings suggest that moa species exploited their habitats in different ways, relative to both each other and extant ratites. The broad range of feeding strategies used by moa, as inferred from interspecific differences in biomechanical performance of the skull, provides insight into mechanisms that facilitated high diversities of these avian herbivores in prehistoric New Zealand.
Collapse
Affiliation(s)
- Marie R G Attard
- School of Environmental and Rural Science, Function, Evolution and Anatomy Research Laboratory, University of New England, Armidale, New South Wales 2351, Australia School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Laura A B Wilson
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Trevor H Worthy
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Paul Scofield
- Canterbury Museum, Rolleston Avenue, Christchurch 8013, New Zealand
| | - Peter Johnston
- Department of Anatomy, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - William C H Parr
- Surgical and Orthopaedic Research Laboratories, Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales 2031, Australia
| | - Stephen Wroe
- School of Environmental and Rural Science, Function, Evolution and Anatomy Research Laboratory, University of New England, Armidale, New South Wales 2351, Australia
| |
Collapse
|
28
|
Slow motion extinction: inbreeding, introgression, and loss in the critically endangered mangrove finch (Camarhynchus heliobates). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0890-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
29
|
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.
Collapse
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)
| |
Collapse
|
30
|
Genetic Diversity, Population Size, and Conservation of the Critically Endangered Perrier’s Sifaka (Propithecus perrieri). INT J PRIMATOL 2015. [DOI: 10.1007/s10764-015-9881-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
31
|
Pacioni C, Hunt H, Allentoft ME, Vaughan TG, Wayne AF, Baynes A, Haouchar D, Dortch J, Bunce M. Genetic diversity loss in a biodiversity hotspot: ancient
DNA
quantifies genetic decline and former connectivity in a critically endangered marsupial. Mol Ecol 2015; 24:5813-28. [DOI: 10.1111/mec.13430] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 10/07/2015] [Accepted: 10/13/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Carlo Pacioni
- Ancient DNA Laboratory School of Veterinary and Life Sciences Murdoch University Murdoch WA 6150 Australia
| | - Helen Hunt
- Ancient DNA Laboratory School of Veterinary and Life Sciences Murdoch University Murdoch WA 6150 Australia
| | - Morten E. Allentoft
- Ancient DNA Laboratory School of Veterinary and Life Sciences Murdoch University Murdoch WA 6150 Australia
- Centre for GeoGenetics Natural History Museum University of Copenhagen Øster Voldgade 5‐7 1350 Copenhagen K Denmark
| | - Timothy G. Vaughan
- Department of Computer Science University of Auckland Private Bag 92019 Auckland 1142 New Zealand
| | | | - Alexander Baynes
- Western Australian Museum Locked Bag 49 Welshpool DC WA 6986 Australia
| | - Dalal Haouchar
- Ancient DNA Laboratory School of Veterinary and Life Sciences Murdoch University Murdoch WA 6150 Australia
| | - Joe Dortch
- Archaeology M257 The University of Western Australia 35 Stirling Highway Nedlands WA 6009 Australia
| | - Michael Bunce
- Ancient DNA Laboratory School of Veterinary and Life Sciences Murdoch University Murdoch WA 6150 Australia
- Department of Environment and Agriculture Trace and Environmental DNA Laboratory Kent Street, Bentley Perth WA 6845 Australia
| |
Collapse
|
32
|
Rawlence NJ, Kennedy M, Anderson CNK, Prost S, Till CE, Smith IWG, Scofield RP, Tennyson AJD, Hamel J, Lalas C, Matisoo-Smith EA, Waters JM. Geographically contrasting biodiversity reductions in a widespread New Zealand seabird. Mol Ecol 2015; 24:4605-16. [DOI: 10.1111/mec.13338] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 07/22/2015] [Accepted: 07/27/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Nicolas J. Rawlence
- Allan Wilson Centre; Department of Zoology; University of Otago; Dunedin New Zealand
| | - Martyn Kennedy
- Allan Wilson Centre; Department of Zoology; University of Otago; Dunedin New Zealand
| | | | - Stefan Prost
- Department of Integrative Biology; University of California; Berkeley CA 94720-3140 USA
- Allan Wilson Centre; Department of Anatomy; University of Otago; Dunedin New Zealand
| | - Charlotte E. Till
- Allan Wilson Centre; Department of Zoology; University of Otago; Dunedin New Zealand
- School of Human Evolution and Social Change; Arizona State University; Tempe AZ USA
| | - Ian W. G. Smith
- Department of Anthropology and Archaeology; University of Otago; Dunedin New Zealand
| | | | | | | | - Chris Lalas
- Department of Marine Science; University of Otago; Dunedin New Zealand
| | | | - Jonathan M. Waters
- Allan Wilson Centre; Department of Zoology; University of Otago; Dunedin New Zealand
| |
Collapse
|
33
|
Allentoft ME, Heller R, Holdaway RN, Bunce M. Ancient DNA microsatellite analyses of the extinct New Zealand giant moa (Dinornis robustus) identify relatives within a single fossil site. Heredity (Edinb) 2015; 115:481-7. [PMID: 26039408 DOI: 10.1038/hdy.2015.48] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/27/2015] [Indexed: 12/26/2022] Open
Abstract
By analysing ancient DNA (aDNA) from 74 (14)C-dated individuals of the extinct South Island giant moa (Dinornis robustus) of New Zealand, we identified four dyads of closely related adult females. Although our total sample included bones from four fossil deposits located within a 10 km radius, these eight individuals had all been excavated from the same locality. Indications of kinship were based on high pairwise genetic relatedness (rXY) in six microsatellite markers genotyped from aDNA, coupled with overlapping radiocarbon ages. The observed rXY values in the four dyads exceeded a conservative cutoff value for potential relatives obtained from simulated data. In three of the four dyads, the kinship was further supported by observing shared and rare mitochondrial haplotypes. Simulations demonstrated that the proportion of observed dyads above the cutoff value was at least 20 times higher than expected in a randomly mating population with temporal sampling, also when introducing population structure in the simulations. We conclude that the results must reflect social structure in the moa population and we discuss the implications for future aDNA research.
Collapse
Affiliation(s)
- M E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - R Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - R N Holdaway
- Palaecol Research Ltd, Christchurch, New Zealand.,School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - M Bunce
- Trace and Environmental DNA (TrEnD) laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| |
Collapse
|
34
|
Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis). PLoS One 2015; 10:e0118522. [PMID: 25719752 PMCID: PMC4342260 DOI: 10.1371/journal.pone.0118522] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 11/19/2014] [Indexed: 12/02/2022] Open
Abstract
The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis). Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000–5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410), historical (n = 15) and fossil samples (n = 4) showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial) but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 – 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.
Collapse
|
35
|
Holdaway RN, Allentoft ME, Jacomb C, Oskam CL, Beavan NR, Bunce M. An extremely low-density human population exterminated New Zealand moa. Nat Commun 2014; 5:5436. [PMID: 25378020 DOI: 10.1038/ncomms6436] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 10/01/2014] [Indexed: 11/09/2022] Open
Abstract
New Zealand moa (Aves: Dinornithiformes) are the only late Quaternary megafauna whose extinction was clearly caused by humans. New Zealand offers the best opportunity to estimate the number of people involved in a megafaunal extinction event because, uniquely, both the Polynesian settlement of New Zealand and moa extinction are recent enough to be dated with a high degree of precision. In addition, the founding human population can be estimated from genetic evidence. Here we show that the Polynesian population of New Zealand would not have exceeded 2,000 individuals before extinction of moa populations in the habitable areas of the eastern South Island. During a brief (<150 years) period and at population densities that never exceeded ~0.01 km(-2), Polynesians exterminated viable populations of moa by hunting and removal of habitat. High human population densities are not required in models of megafaunal extinction.
Collapse
Affiliation(s)
- Richard N Holdaway
- 1] Palaecol Research Ltd, PO Box 16569, Christchurch 8042, New Zealand [2] School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Morten E Allentoft
- 1] School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand [2] Centre for Geogenetics, Natural History Museum, University of Copenhagen, Copenhagen DK-1350, Denmark
| | - Christopher Jacomb
- Southern Pacific Archaeological Research, Department of Anthropology and Archaeology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Charlotte L Oskam
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
| | - Nancy R Beavan
- School of Medical Sciences, University of Otago, PO Box 913, Dunedin 9054, New Zealand
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia
| |
Collapse
|
36
|
Fenner D. Fishing down the largest coral reef fish species. MARINE POLLUTION BULLETIN 2014; 84:9-16. [PMID: 24889317 DOI: 10.1016/j.marpolbul.2014.04.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 04/13/2014] [Indexed: 06/03/2023]
Abstract
Studies on remote, uninhabited, near-pristine reefs have revealed surprisingly large populations of large reef fish. Locations such as the northwestern Hawaiian Islands, northern Marianas Islands, Line Islands, U.S. remote Pacific Islands, Cocos-Keeling Atoll and Chagos archipelago have much higher reef fish biomass than islands and reefs near people. Much of the high biomass of most remote reef fish communities lies in the largest species, such as sharks, bumphead parrots, giant trevally, and humphead wrasse. Some, such as sharks and giant trevally, are apex predators, but others such as bumphead parrots and humphead wrasse, are not. At many locations, decreases in large reef fish species have been attributed to fishing. Fishing is well known to remove the largest fish first, and a quantitative measure of vulnerability to fishing indicates that large reef fish species are much more vulnerable to fishing than small fish. The removal of large reef fish by fishing parallels the extinction of terrestrial megafauna by early humans. However large reef fish have great value for various ecological roles and for reef tourism.
Collapse
Affiliation(s)
- Douglas Fenner
- Department of Marine & Wildlife Resources, American Samoa Government, PO Box 7390, Pago Pago, AS 96799, USA.
| |
Collapse
|