Biology subjects

Krapp, M.

Publications and source records attributed to Krapp, M..

4 recordsLinked to original sources

bioRxiv2022

pastclim: an R package to easily access and use paleoclimatic reconstructions

The recent development of continuous paleoclimatic reconstructions covering hundreds of thousands of years paved the way to a large number of studies from disciplines ranging from paleoecology to linguistics, from archaeology to conservation and from population genetics to human evolution. Unfortunately, such climatic data can be challenging to extract and analyze for scholars unfamiliar with such specific climatic file formats. Here we present pastclim, an R package facilitating the access and use of two sets of paleoclimatic reconstructions covering respectively the last 120,000 and 800,000 years. The package contains a set of functions allowing to quickly and easily recover the climate for the whole world or specific areas for time periods of interest, extract data from locations scattered in space and/or time, retrieve time series from individual sites, and easily manage the ice or land coverage. The package can easily be adapted to paleoclimatic reconstructions different from the ones already included, offering a handy platform to include the climate of the past into existing analyses and pipelines.

evolutionary biology↗

bioRxiv2021

Climate and mountains shaped human ancestral genetic lineages

Extensive sequencing of modern and ancient human genomes has revealed that contemporary populations can be explained as the result of recent mixing of a few distinct ancestral genetic lineages1. But the small number of aDNA samples that predate the Last Glacial Maximum means that the origins of these lineages are not well understood. Here, we circumvent the limited sampling by modelling explicitly the effect of climatic changes and terrain on population demography and migrations through time and space, and show that these factors are sufficient to explain the divergence among ancestral lineages. Our reconstructions show that the sharp separation between African and Eurasian lineages is a consequence of only a few limited periods of connectivity through the arid Arabian peninsula, which acted as the gate out of the Arican continent. The subsequent spread across Eurasia was then mostly shaped by mountain ranges, and to a lesser extent deserts, leading to the split of European and Asians, and the further diversification of these two groups. A high tolerance to cold climates allowed the persistence at high latitudes even during the Last Glacial Maximum, maintaining a pocket in Beringia that led to the later, rapid colonisation of the Americas. The advent of food production was associated with an increase in movement2, but mountains and climate have been shown to still play a major role even in this latter period3,4, affecting the mixing of the ancestral lineages that we have shown to be shaped by those two factors in the first place.

genomics↗

bioRxiv2021

Post-glacial expansion dynamics, not refugial isolation, shaped the genetic structure of a migratory bird, the Yellow Warbler (Setophaga petechia)

During the glacial periods of the Pleistocene, swathes of the Northern Hemisphere were covered by ice sheets, tundra, and permafrost, leaving large areas uninhabitable for temperate and boreal species. The glacial refugia paradigm proposes that, during glaciations, species living in the Northern Hemisphere were forced southwards, forming isolated populations that persisted in disjunct regions known as refugia. According to this hypothesis, as ice sheets retreated, species recolonised the continent from these glacial refugia, and the mixing of these lineages is responsible for modern patterns of genetic diversity. An alternative hypothesis is that complex genetic patterns could also arise simply from heterogenous post-glacial expansion dynamics, without separate refugia. Both mitochondrial and genomic data from the North American yellow warbler (Setophaga petechia) shows the presence of an eastern and western clade, a pattern often ascribed to the presence of two refugia. However, species distribution modelling (SDM) of the past range of this species fails to identify obvious refugia during the Last Glacial Maximum. Using a climate-informed spatial genetic modelling (CISGeM) framework, which allows us to integrate knowledge of past geographic ranges based on SDM, we reconstructed past population sizes, range expansions, and likely recolonisation dynamics of this species, generating spatially and temporally explicit demographic reconstructions. The model captures the empirical genetic structure despite including only a single, large glacial refugium. The observed contemporary population structure was generated during the expansion dynamics after the glaciation and is due to unbalanced rates of northward advance to the east and west linked to the melting of the icesheets. Thus, modern population structure in this species is consistent with expansion dynamics, and refugial isolation is not required to explain it, highlighting the importance of explicitly testing drivers of geographic structure. Significance statementPatterns of population differentiation in many species have often been attributed to the mixing of isolates from distinct refugia that formed during periods of glaciation, when range fragmentation was likely. By formally bringing together multiple lines of evidence, we demonstrate that the patterns of genetic diversity seen across the range of the yellow warbler (Setophaga petechia) were not the result of multiple isolated refugia. Instead, asymmetric expansion from a single cohesive range generated the observed patterns; the expansions asymmetry was due to the uneven melting of the icesheets over time. Thus, we demonstrate the importance of reconstructing species range dynamics when trying to explain patterns of genetic differentiation.

evolutionary biology↗

bioRxiv2020

Windows out of Africa: A 300,000-year chronology of climatically plausible human contact with Eurasia

Whilst an African origin for Anatomically Modern Humans is well established 1, the timings of their expansions into Eurasia are the subject to heated debate, due to the scarcity of fossils and the lack of suitably old ancient DNA 2. Here, we estimate potential timings and routes out of Africa by deriving anthropologically and ecologically plausible precipitation requirements for human existence, and applying them to high-resolution palaeoclimate reconstructions for the past 300k years. We find that exit routes and timings previously suggested based on archaeological and genetic evidence coincide precisely with the presence of sufficiently wet corridors into Eurasia, while the gaps between the proposed exit timings co-occur with periods of insufficient rainfall. This demonstrates the key role that palaeoclimatic conditions played for out-of-Africa expansions. The challenging environmental conditions outside of Africa that occurred between windows of potential contact, coupled with the lack of a demographic rescue effect from migration and possible competition with other hominins, likely explain the demise of early colonists prior to the large-scale colonisation of the world beginning from [~]65kya.

evolutionary biology↗