Biology subjects

Paijmans, J. L. A.

Publications and source records attributed to Paijmans, J. L. A..

5 recordsLinked to original sources

bioRxiv2025

Pan-African metapopulation model explains Homo sapiens genetic and morphological evolution

A growing body of evidence has challenged the traditional assumption of a single-region origin for Homo sapiens, suggesting instead that our species originated from multiple geographically distinct populations in Africa, which intermittently exchanged genes and culture. However, our understanding of how this Pan-African metapopulation would have evolved through time is still limited. Furthermore, the drivers of such changes are uncertain, and quantitative models of the respective contributions of different African regions are lacking. Here we provide a complete reconstruction of the meta-population dynamics over the last 200,000 years by quantitatively integrating an ecological niche model, informed by archaeological sites, within a spatially explicit population genetic framework. The inferred metapopulation dynamics account for the divergence among all available contemporary and ancient genomes of African hunter-gatherers used to calibrate the model. In addition, it also accurately predicts the patterns of craniometric diversification across the continent from the Late Middle Pleistocene to the present. Finally, we show how the climate-driven changes in population sizes and connectivity are congruent with major patterns of archaeological and phenotypic diversification over the last 200,000 years across the African continent.

evolutionary biology↗

bioRxiv2023

Niche conservatism in a generalist felid: low differentiation of the climatic niche among subspecies of the leopard (Panthera pardus)

AimSpecies distribution modelling can be used to reveal if the ecology of a species varies across its range, to investigate if range expansions entailed niche shifts, and to help assess ecological differentiation: the answers to such questions are vital for effective conservation. The leopard (Panthera pardus spp.) is a generalist species composed of one African and eight Asian subspecies, reflecting dispersal from an ancestral African range. This study uses species distribution models to compare the niches of leopard subspecies, to investigate if they conserved their niches when moving into new territories or adapted to local conditions and shifted niche. LocationAfrica and Eurasia MethodsWe assembled a database of P. pardus spp. presences. We then associated them with bioclimatic variables to identify which are relevant in predicting the distribution of the leopard. We then constructed a species distribution model and compared the distribution predicted from models based on presences from all subspecies versus the ones built only using African leopards. Finally, we used multivariate analysis to visualise the niche occupied by each subspecies in the climate space, and to compare niche overlaps to assess ecological differentiation. ResultsNiche comparisons and model predictions suggest a general lack of niche separation between all subspecies. Most Asian subspecies have overlapping niches and occupy subsets of the niche of the African leopard. Nevertheless, we found the Persian leopard Panthera pardus saxicolor to have the most distinct niche, giving some evidence for niche expansion in more Northern Asian subspecies. Main conclusionsThese results suggest little ecological differentiation among leopard subspecies and a lack of adaptation to novel climates after dispersal from Africa. This finding complements recent genetic studies in implying that the taxonomy of Asian leopards may not reflect biological differentiation, an issue that is important to resolve due to its relevance for the conservation of the species.

ecology↗

bioRxiv2018

Consensify: a method for generating pseudohaploid genome sequences from palaeogenomic datasets with reduced error rates

A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, typically by selecting a single high quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic analysis, we find that Consensify is less affected by branch length artefacts than methods based on standard pseudohaploidisation, and it performs similarly for population clustering analysis based on genetic distances. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other available methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consenify will be a useful tool for future studies of palaeogenomes.

genomics↗

bioRxiv2018

Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations

BackgroundResolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts?\n\nResultsIn this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages ([~]710 Ka), with the European ancient samples as sister to all Asian lineages ([~]483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor ([~]122 Ka), and we find one Javan sample nested within these.\n\nConclusionsThe phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.

evolutionary biology↗

bioRxiv2017

Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model species

Hybridization capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. A cross-species approach makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for non-model organisms, for which often no a priori knowledge exists regarding these loci. Here, we have adopted cross-species capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a non-model organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). In this manner, we were able to survey intraspecific variation at hundreds of nuclear loci across the European range of L. lynx. A large set of bi-allelic candidate SNPs was then tested in a high throughput SNP-genotyping platform (Fluidigm), which we reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with additional samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (incl. the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.

genetics↗