A gradual change is more likely to have caused the Mid-Pleistocene Transition than an abrupt event

Legrain, Etienne; Parrenin, Frédéric; Capron, Émilie

doi:10.1038/s43247-023-00754-0

Cited by 12 publications

(2 citation statements)

References 59 publications

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“…We used our data set to explore the maternal evolutionary history of leopards on the African continent. The divergence of PAR-I and PAR-II from a common ancestor occurred during the mid-Pleistocene transition (1,250–700 Ka) ( Clark et al, 2006 ; Legrain, Parrenin & Capron, 2023 ), when glacial cycles increased from 40 to 100 ka, exposing sub-tropical regions to prolonged periods of aridity. As leopards are highly mobile and adaptable, it is unlikely that physical barriers such a mountains and rivers impede dispersal and gene flow over the long term.…”

Section: Discussionmentioning

confidence: 99%

Unravelling the maternal evolutionary history of the African leopard (Panthera pardus pardus)

Morris,

McWhorter,

Boardman

et al. 2024

PeerJ

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The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477–0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0–0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa.

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Section: Discussionmentioning

confidence: 99%

Unravelling the maternal evolutionary history of the African leopard (Panthera pardus pardus)

Morris,

McWhorter,

Boardman

et al. 2024

PeerJ

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“…This time span is constrained by the period for which there are sufficient data to establish a meaningful synthesis at a practical resolution. Conveniently this period covers the latter part of the Pleistocene dominated by 100 kyr glacial cycles after the MPT (Clark et al, 2006;Legrain et al, 2023), and allows comparison with the full duration of the EPICA Dome C (EDC) ice core record (Jouzel et al, 2007). Besides our original motivation, estimates of past CDW temperature variability are also useful for putting present-day changes into perspective.…”

Section: Introductionmentioning

confidence: 99%

Glacial-interglacial Circumpolar Deep Water temperatures during the last 800,000 years: estimates from a synthesis of bottom water temperature reconstructions

Chandler

Langebroek

2023

Preprint

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Abstract. Future climate and sea-level projections depend sensitively on the response of the Antarctic Ice Sheet to ocean-driven melting and the resulting freshwater fluxes into the Southern Ocean. Incursion of Circumpolar Deep Water (CDW) across the Antarctic continental shelf, and into cavities beneath ice shelves, is increasingly recognised as a crucial heat source for ice shelf melt. Quantifying past changes in the temperature of CDW is therefore of great benefit for modelling ice sheet response to past warm climates, for validating paleoclimate models, and for putting recent and projected changes in CDW temperature into context. Here we synthesise the few available bottom water temperature reconstructions representative of CDW and its principal source water mass (North Atlantic Deep Water) over the past 800 kyr. Estimated CDW temperature anomalies consistently reached ca. −2 °C during glacial periods, warming to +0.1 to +0.5 °C during the strongest interglacials (marine isotope stages MIS 11, 9, 5, and 1). The temperature anomaly in MIS 7 was comparatively cooler at ca. −0.6 °C. Despite high variance amongst a small number of records, and poor (4 kyr) temporal resolution, we find persistent and close relationships between our estimated CDW temperature and Southern Ocean sea-surface temperature, Antarctic surface air temperature, and global ocean temperature reconstructions at glacial cycle time scales. Given the important role that CDW plays in connecting the world's three main ocean basins, and in driving Antarctic Ice Sheet mass loss, additional temperature reconstructions targeting CDW are urgently needed to increase temporal resolution and to decrease uncertainty in past CDW temperatures – whether for use as a boundary condition, model validation or in their own right.

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High-Resolution Genome Assembly and Population Genetic Study of the Endangered MapleAcer pentaphyllum(Sapindaceae): Implications for Conservation Strategies

Li,

Jiang,

Deng

et al. 2024

Preprint

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SummaryAcer pentaphyllumDiels (Sapindaceae), a highly threatened maple endemic to dry-hot valleys of the Yalong River in western Sichuan, China, requires urgent conservation efforts due to its extremely rarity and restricted distribution. In this study, we present a high-quality chromosome-level reference genome ofA. pentaphyllum(626 Mb, 2n = 26), comprising 70.64% repetitive sequences and 38,540 protein-coding genes. Phylogenetic analysis shows thatA. pentaphyllumdiverged from a clade consisting ofA. yangbienseandA. saccharumin the late Eocene (∼37.83 Ma). In the genome ofA. pentaphyllum, genes involved in responding to external environmental change have undergone expansion and positive selection, potentially reflecting its adaptive strategies. While no recent independent whole-genome duplication events were detected, a recent rapid amplification of transposable elements was observed. Population genomic analysis of 227 individuals from 28 populations revealed low genetic diversity (1.04 ± 0.97 × 10−3) compared to other woody species. Phylogeographic patterns suggest an upstream colonization along the Yalong River, with two severe population bottlenecks correlating with major Pleistocene climatic transitions. In addition, most populations exhibit high inbreeding and genetic load, particularly those at range edges (TKX, CDG, TES). Based on these genomic insights, we propose targeted conservation strategies, including genetic rescue measures, to safeguard this unique maple species. These findings not only contribute to the preservation ofA. pentaphyllumbut also enhance our understanding of plant adaptation to extreme environments and the impacts of climate change on species with restricted distributions.

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A gradual change is more likely to have caused the Mid-Pleistocene Transition than an abrupt event

Cited by 12 publications

References 59 publications

Unravelling the maternal evolutionary history of the African leopard (Panthera pardus pardus)

Unravelling the maternal evolutionary history of the African leopard (Panthera pardus pardus)

Glacial-interglacial Circumpolar Deep Water temperatures during the last 800,000 years: estimates from a synthesis of bottom water temperature reconstructions

High-Resolution Genome Assembly and Population Genetic Study of the Endangered MapleAcer pentaphyllum(Sapindaceae): Implications for Conservation Strategies

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