Genetic evidence of range-wide population declines in an Australian marsupial prior to European settlement

Brüniche‐Olsen, Anna; Hazlitt, Stephanie L.; Eldridge, Mark D. B.

doi:10.1007/s10592-017-0960-8

Cited by 3 publications

(5 citation statements)

References 78 publications

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“…Unfortunately, no historical genetic material was available to establish baseline genetic variability and cross-validate modeled estimates of temporal changes in the effective population sizes and contemporary genetic diversity values of Nassau grouper. However, previous studies have shown that the demography, distribution and genetic composition of species can be strongly influenced by geological processes and associated eustatic sea level changes (e.g., Hewitt, 2000;Pellissier et al, 2014;Brüniche-Olsen et al, 2017). For example, an analysis of >6,000 fish species showed strong correlations between current species richness and distribution patterns with historic climatic events that negatively impacted reef habitats (Pellissier et al, 2014).…”

Section: Effective Population Size and Population Bottlenecksmentioning

confidence: 99%

Historical Processes and Contemporary Anthropogenic Activities Influence Genetic Population Dynamics of Nassau Grouper (Epinephelus striatus) within The Bahamas

et al. 2017

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Severe declines of endangered Nassau grouper (Epinephelus striatus) across The Bahamas and Caribbean have spurred efforts to improve their fisheries management and population conservation. The Bahamas is reported to hold the majority of fish spawning aggregations for Nassau grouper, however, the status and genetic population structure of fish within the country is largely unknown, presenting a major knowledge gap for their sustainable management. Between August 2014-February 2017, 464 individual Nassau grouper sampled from The Bahamas were genotyped using 15 polymorphic microsatellite loci to establish measures of population structure, genetic diversity and effective population size (N e ). Nassau grouper were characterized by mostly high levels of genetic diversity, but we found no evidence for geographic population structure. Microsatellite analyses revealed weak, but significant genetic differentiation of Nassau grouper throughout the Bahamian archipelago (Global F ST 0.00236, p = 0.0001). Temporal analyses of changes in N e over the last 1,000 generations provide evidence in support of a pronounced historic decline in Bahamian Nassau grouper that appears to pre-date anthropogenic fishing activities. M-ratio results corroborate significant reductions in N e throughout The Bahamas, with evidence for population bottlenecks in three islands and an active fish spawning aggregation along with apparent signs of inbreeding at two islands. Current estimates of N e for Nassau grouper are considerably lower compared with historic levels. These findings represent important new contributions to our understanding of the evolutionary history, demographics and genetic connectivity of this endangered species, which are of critical importance for advancing their sustainable management.

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Section: Effective Population Size and Population Bottlenecksmentioning

confidence: 99%

Historical Processes and Contemporary Anthropogenic Activities Influence Genetic Population Dynamics of Nassau Grouper (Epinephelus striatus) within The Bahamas

et al. 2017

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“…Specieslevel relative faunal stability since the Middle Pliocene shown in Figure 3B is surprising, given that subsequent extreme climatic cycling is often suggested to have driven Pleistocene extinctions and massive (molecular-inferred) demographic shifts (e.g. Brüniche-Olsen et al, 2017;Loskutov et al, 2017). However, it is increasingly recognized that we need to understand better the extent to which molecular demographics confuse the population component of 'effective population size' with strong, short-term variation in selection and population structure (Mazet et al, 2016;Loskutov et al, 2017).…”

Section: Table 1 List Of Kangaroo Wallaroo and Wallaby Species In Fou...mentioning

confidence: 99%

A molecular and morphometric assessment of the systematics of the Macropus complex clarifies the tempo and mode of kangaroo evolution

Celik

Cascini

Haouchar

et al. 2019

Zoological Journal of the Linnean Society

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Kangaroos and wallabies of the Macropus complex include the largest extant marsupials and hopping mammals. They have traditionally been divided among the genus Macropus (with three subgenera: Macropus, Osphranter and Notamacropus) and the monotypic swamp wallaby, Wallabia bicolor. Recent retrotransposon and genome-scale phylogenetic analyses clarify the placement of Wallabia as sister to Notamacropus, with Osphranter and Macropus branching successively deeper. In view of the traditional Macropus concept being paraphyletic, we undertake to resolve the species-level phylogeny and genus-level taxonomy of the Macropus complex. For the first time, we include nuclear and mitochondrial DNA covering all extant species, and the first DNA sequences from the extinct Toolache wallaby (Notamacropus greyi), which we find groups with the black-gloved wallaby (Notamacropus irma). Morphological variation was examined using geometric morphometric methods on three-dimensional surface-scanned skulls. Wallabia skull shape fell close to Notamacropus (or Thylogale when controlling for allometry). We recommend the subgenera Macropus, Osphranter and Notamacropus be elevated to genera, alongside Wallabia, based on comparisons with other established macropodine genera for cranial disparity, ecology and molecular divergence. Our time tree estimates that all four 'Macropus' genera diverged close to the Miocene-Pliocene boundary (~6-5 Mya), then diversified coincident with Pliocene expansion of grasslands in Australia.

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“…Our limited sample size and the lack of phylogeographic structure in devils across southern Australia may have limited our ability to detect a gradual population decline. However, the congruent mainland extinction of the Tasmanian devil and thylacine (White, Saltre, et al, ), and decline in the brush‐tailed rock wallaby across its entire range in south‐eastern Australia (Brüniche‐Olsen et al., ) suggest that the factor(s) were wide ranging and affected both predators and prey species. If human intensification or dingo introduction was predominant drivers of the mainland devil extinction, we would not expect a coincident decline in the Tasmanian population given the absence of these factors in Tasmania.…”

Section: Discussionmentioning

confidence: 99%

“…(Figure 4). This could suggest that major shifts in climate likely influenced the devil populations, a common pattern for other species (Br€ uniche-Olsen, Hazlitt, & Eldridge, 2017;Kearns, Joseph, Toon, & Cook, 2014;Neaves, Zenger, Prince, & Eldridge, 2012;White, Mitchell, et al, 2018). While the island population was shielded from introduced dingoes and human intensification, the mainland population was exposed to all three impacts, suggesting a multi-causal role for the mainland extinction.…”

Section: Southern Mainland Extinction and Island Survival Of The Tamentioning

confidence: 98%

“…ENSO events result, critically, in greater variability in rainfall and increased intensity and duration of severe climate events, such as drought, rather than sustained aridity (Brown, 2006). During the period of increased ENSO activity both thylacines and rock wallabies declined (Br€ uniche-Olsen et al, 2017;White, Mitchell, et al, 2018). Unstable climate is associated with loss of species (Blois et al, 2010;Cooper et al, 2015), and the changes in vegetation are likely to have caused fluctuations in the abundance of herbivores, leading to reduced populations of predators (Carbone et al, 2011;Letnic & Dickman, 2006 (Petherick et al, 2013;Sandel et al, 2011).…”

Section: Potential Factors Impacting Tasmanian Devil Populationsmentioning

confidence: 99%

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Ancient DNA tracks the mainland extinction and island survival of the Tasmanian devil

Brüniche‐Olsen

Jones

Burridge

et al. 2018

Journal of Biogeography

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Aim The Tasmanian devil (Sarcophilus harrisii), currently restricted to the island of Tasmania, was found over most of the Australian mainland prior to its extinction ~3,000 years ago. Recent debate has focused on the roles of humans, climate change and dingoes as drivers of the mainland extinction. Determining past genetic diversity and population dynamics of both populations is a fundamental component to understand why the species went extinct on mainland Australia, but survived in Tasmania. Here, we investigate the phylogeography and demographic history of the Tasmanian devil across southern Australia over the last ~30k years. Location Australia. Taxon Tasmanian devil (Sarcophilus harrisii). Methods We used complete and partial mitochondrial DNA (mtDNA) genomes from 202 devils representing the extinct mainland (n = 17) and the extant Tasmanian (n = 185) populations to investigate the population dynamics of southern mainland and Tasmanian devils. The samples were sub‐fossil bones, historical museum specimens and modern tissue samples, dating from the present to 17k years before present. Using summary statistics, frequentist inference and Bayesian phylogenetic analysis we explored whether levels of genetic diversity were similar, and if the southern mainland experienced a gradual rather than an abrupt decline prior to its extinction. Results MtDNA genomes from mainland devils suggest that this population was larger and had more genetic diversity than the Tasmanian population. Directly dated samples indicates that the southern mainland population expanded after the last glacial maximum and remained stable until its extinction. The Tasmanian population has much lower diversity and descends from a single mtDNA lineage ~3,000 years ago. The recent origin for all Tasmanian mtDNA diversity is concordant with a previously documented late‐Holocene population bottleneck and is broadly contemporaneous with the extinction of the southern mainland population. Main conclusions This pattern shows striking similarity to the demographic history of thylacines, suggesting that a shared factor initiated population declines in both species on the southern mainland and in Tasmania. El Niño Southern Oscillation (ENSO)‐related climate change is the only factor common to both mainland Australia and Tasmania. Additional, direct or indirect, pressures from humans and/or dingoes on the mainland may have ultimately resulted in their extinction.

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Genetic evidence of range-wide population declines in an Australian marsupial prior to European settlement

Cited by 3 publications

References 78 publications

Historical Processes and Contemporary Anthropogenic Activities Influence Genetic Population Dynamics of Nassau Grouper (Epinephelus striatus) within The Bahamas

Historical Processes and Contemporary Anthropogenic Activities Influence Genetic Population Dynamics of Nassau Grouper (Epinephelus striatus) within The Bahamas

A molecular and morphometric assessment of the systematics of the Macropus complex clarifies the tempo and mode of kangaroo evolution

Ancient DNA tracks the mainland extinction and island survival of the Tasmanian devil

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