Biology subjects

Kerdoncuff, E.

Publications and source records attributed to Kerdoncuff, E..

6 recordsLinked to original sources

bioRxiv2026

Estimate of the mutation rate in the endangered Devils Hole pupfish provides support for the drift-barrier hypothesis at an outlying extreme

Mutation rates vary by orders of magnitude across eukaryotes. The drift-barrier hypothesis proposes that drift overwhelms selection for lower mutation rates in small populations, leading to higher mutation rates over time due to the gradual accumulation of mutator alleles. Here, we test this hypothesis in one of the smallest long-term isolated populations in the world, the endangered Devils Hole pupfish (Cyprinodon diabolis). We estimated germline mutation rates in adults and embryos that died prematurely using autozygous segments due to recent inbreeding events. Our estimate of 8.09 x 10-9 per base pair per generation was higher than the mean rate for actinopterygian fishes of 5.97 x 10-9 (95% CI: 4.39 x 10-9 - 7.55 x 10-9) but was lower than predicted for such a low effective population size based on a recent meta-analysis of vertebrate mutation rates and similar to species with much larger effective population sizes, contradicting the drift barrier hypothesis. We also found that embryos which died during development had a higher mutation rate than mature adults, potentially reflecting a segregating lethal mutator allele. We analyzed the mutational spectra of germline mutations and found that spectra between embryonic lethal and mature adults were similar and comparable to other fishes, despite environmental differences in temperature, oxygen saturation, and UV exposure. Mutation rates in this endangered species provide new insights into the mechanisms driving mutation rate variation across vertebrates at one extreme of low effective population size in nature.

evolutionary biology↗

bioRxiv2025

Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes

Lactase persistence (LP), the ability to digest lactose from milk into adulthood, is a classic example of natural selection in humans. Multiple mutations upstream of the LCT gene are associated with LP and have been previously shown to be under selection in Europeans and Africans. South Asia is the worlds largest producer of dairy, and milk and dairy products are widely consumed throughout the subcontinent. However, the origin, evolutionary history and selective pressures associated with LP in South Asia remain elusive. We assembled genome-wide data from [~]8,000 present-day and ancient genomes from India, Pakistan, and Bangladesh, spanning diverse timescales ([~]3300 BCE-1650 CE), geographic regions, and ethnolinguistic and subsistence groups. We find that the Eurasian LP-associated variant,-13.910:C>T, is widespread across South Asia, exhibiting clinal variation along north-south and east-west gradients. Ancient DNA analysis reveals that this variant first appeared in South Asia during the historical and medieval periods through Steppe pastoralist-related gene flow. Interestingly, unlike in other worldwide populations, the LP prevalence is almost entirely explained by Steppe ancestry--not selection--in most contemporary South Asians. A notable exception is the only two pastoralist groups, Toda in South India and Gujjar in Pakistan, that have unexpectedly high frequencies of-13.910*T, comparable to estimates in Northern Europeans. By performing local ancestry inference, we find significant enrichment for Steppe pastoralist ancestry around the LCT locus in these two geographically-distant pastoralist groups, indicative of strong selection. Together, these findings highlight the complex role of ancestry and natural selection in shaping the prevalence of lactase persistence on the subcontinent.

evolutionary biology↗

bioRxiv2024

50,000 years of Evolutionary History of India: Insights from ~2,700 Whole Genome Sequences

India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from India--including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups--providing a comprehensive survey of genetic variation in India. With these data, we reconstruct the evolutionary history of India through space and time at fine scales. We show that most Indians derive ancestry from three ancestral groups related to ancient Iranian farmers, Eurasian Steppe pastoralists and South Asian hunter-gatherers. We uncover a common source of Iranian-related ancestry from early Neolithic cultures of Central Asia into the ancestors of Ancestral South Indians (ASI), Ancestral North Indians (ANI), Austro-asiatic-related and East Asian-related groups in India. Following these admixtures, India experienced a major demographic shift towards endogamy, resulting in extensive homozygosity and identity-by-descent sharing among individuals. At deep time scales, Indians derive around 1-2% of their ancestry through gene flow from archaic hominins, Neanderthals and Denisovans. By assembling the surviving fragments of archaic ancestry in modern Indians, we recover [~]1.5 Gb (or 50%) of the introgressing Neanderthal and [~]0.6 Gb (or 20%) of the introgressing Denisovan genomes, more than any other previous archaic ancestry study. Moreover, Indians have the largest variation in Neanderthal ancestry, as well as the highest amount of population-specific Neanderthal segments among worldwide groups. Finally, we demonstrate that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, with minimal contribution from earlier migration waves. Together, these analyses provide a detailed view of the population history of India and underscore the value of expanding genomic surveys to diverse groups outside Europe.

evolutionary biology↗

bioRxiv2023

How demography shapes linkage disequilibrium with or without recombination

Linkage Disequilibrium (LD) is a measure of the statistical association, within a population, between alleles present at different loci. Here, we produce detailed characterizations of LD statistics in different demographic scenarios, with simulations and with analytic results, focusing on several widely used measures of LD (D, |D'|, and r2), and introducing a fourth class of statistics: 2-site configuration probabilities, which correspond to the frequencies of different allelic association patterns. By studying these measures under no recombination, a single recombination event, and between fully independent loci, we are able to gain new insights to how these measures vary across recombination scales. We also classify recombination events into four types and rank them according to their respective frequencies and effects on LD measures. Using previously published human data, we show how tree-sequence information can be used to partition the genome and to analyze LD in relation to theoretical expectations. Finally, we provide recommendations for the use of the different statistics and suggest applications of LD measures in the absence of recombination.

evolutionary biology↗

bioRxiv2022

Interpreting the pervasive observation of U-shaped Site Frequency Spectra

The standard neutral model of molecular evolution has traditionally been used as the null model for population genomics. We gathered a collection of 45 genome-wide site frequency spectra from a diverse set of species, most of which display an excess of low and high frequency variants compared to the expectation of the standard neutral model, resulting in U-shaped spectra. We show that multiple merger coalescent models often provide a better fit to these observations than the standard Kingman coalescent. Hence, in many circumstances these under-utilized models may serve as the more appropriate reference for genomic analyses. We further discuss the underlying evolutionary processes that may result in the widespread U-shape of frequency spectra.

evolutionary biology↗

bioRxiv2019

Testing for population decline using maximal linkage disequilibrium blocks

Only 6% of known species have a conservation status. Methods that assess conservation statuses are often based on individual counts and are thus too laborious to be generalized to all species. Population genomics methods that infer past variations in population size are easy to use but limited to the relatively distant past. Here we propose a population genomics approach that tests for recent population decline and may be used to assess species conservation statuses. More specifically, we study Maximal Recombination Free (MRF) blocks, that are segments of a sequence alignment inherited from a common ancestor without recombination. MRF blocks are relatively longer in small than in large populations. We use the distribution of MRF block lengths rescaled by their mean to test for recent population decline. However, because MRF blocks are difficult to detect, we also consider Maximal Linkage Disequilibrium (MLD) blocks, which are runs of single nucleotide polymorphisms compatible with a single tree. We develop a new method capable of inferring a very recent decline (e.g. with a detection power of 50% for populations which size was halved to N, 0.05 xN generations ago) from rescaled MLD block lengths. Our framework could serve as a basis for quantitative tools to assess conservation status in a wide range of species.

evolutionary biology↗