Biology subjects

Beyer, R.

Publications and source records attributed to Beyer, R..

8 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↗

bioRxiv2019

mtDNA-based reconstructions of change in effective population sizes of Holarctic birds do not agree with their reconstructed range sizes based on paleoclimates

During the Quaternary, large climate oscillations had profound impacts on the distribution, demography and diversity of species globally. Birds offer a special opportunity for studying these impacts because surveys of geographical distributions, publicly-available genetic sequence data, and the existence of species with adaptations to life in structurally different habitats, permit large-scale comparative analyses. We use Bayesian Skyline Plot (BSP) analysis of mitochondrial DNA to reconstruct profiles depicting how effective population size (Ne) may have changed over time, focussing on variation in the effect of the last deglaciation among 102 Holarctic species. Only 3 species showed a decline in Ne since the Last Glacial Maximum (LGM) and 7 showed no sizeable change, whilst 92 profiles revealed an increase in Ne. Using bioclimatic Species Distribution Models (SDMs), we also estimated changes in species potential range extent since the LGM. Whilst most modelled ranges also increased, we found no correlation across species between the magnitude of change in range size and change in Ne. The lack of correlation between SDM and BSP reconstructions could not be reconciled even when range shifts were considered. We suggest the lack of agreement between these measures might be linked to changes in population densities which can be independent of range changes. We caution that interpreting either SDM or BSPs independently is problematic and potentially misleading. Additionally, we found that Ne of wetland species tended to increase later than species from terrestrial habitats, possibly reflecting a delayed increase in the extent of this habitat type after the LGM.

evolutionary biology↗

bioRxiv2019

Global range contractions of mammals, birds and amphibians from 10,000 BC to 2100 AD.

Species vulnerability to extinction is strongly impacted by their geographical range size. Formulating effective conservation strategies therefore requires a better understanding of how the ranges of the worlds species have changed in the past, and how they will change under alternative future scenarios. Here, we used reconstructions of global land use and biomes of the past 7,000 years, and 16 possible climatic and socio-economic scenarios until the year 2100, to map the habitat ranges of 16,511 individual mammal, bird, and amphibian species through time. We estimate that extant species have lost an average of 19% of their natural range sizes thus far, and may lose up to 32% by 2100. Changes in range size vary greatly between species, with tropical, small-ranged, and threatened species being especially impacted. Our data reveal that range losses have been increasing disproportionately in relation to the size of destroyed habitat, driven by a long-term increase of land use in tropical biodiversity hotspots. The outcomes of different future land use and climate trajectories for global habitat ranges vary considerably, providing important quantitative evidence for conservation planners and policy makers of the costs and benefits of alternative pathways for the future of global biodiversity.

ecology↗

bioRxiv2019

History biases reveal novel dissociations between perceptual and metacognitive decision-making

Human decision-making and self-reflection often depend on context and internal biases. For instance, decisions are often influenced by preceding choices, regardless of their relevance. It remains unclear how choice history influences different levels of the decision-making hierarchy. We employed analyses grounded in information and detection theories to estimate the relative strength of perceptual and metacognitive history biases, and to investigate whether they emerge from common/unique mechanisms. Though both perception and metacognition tended to be biased towards previous responses, we observed novel dissociations which challenge normative theories of confidence. Different evidence levels often informed perceptual and metacognitive decisions within observers, and response history distinctly influenced 1st (perceptual) and 2nd (metacognitive) order decision-parameters, with the metacognitive bias likely to be strongest and most prevalent in the general population. We propose that recent choices and subjective confidence represent heuristics which inform 1st and 2nd order decisions in the absence of more relevant evidence.

neuroscience↗

bioRxiv2017

The co-regulatory interaction of transpiration and water potential: Implications for stomatal conductance models and height growth in trees

Leaf water potential decreases with increasing transpiration rate according to an analogue of Ohms law, while transpiration rate decreases with decreasing leaf water potential in the framework of stomatal control. This interaction is not accommodated in present-day models of stomatal conductance. We formally derive the equilibrium between these two counteracting processes for steady-state water conditions. We show that the mechanism considered causes an attenuation of the immediate effect of atmospheric variables on transpiration, which can improve existing models of stomatal conductance that presume noninterdependent variables. Parameters from European beech (Fagus sylvatica L.) are used to illustrate the results.

plant biology↗