Biology subjects

Hvilsom, C.

Publications and source records attributed to Hvilsom, C..

12 recordsLinked to original sources

bioRxiv2026

Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River

Bonobos (Pan paniscus), an endangered species, have for decades been genetically understudied, partly due to difficulties in obtaining high-quality samples. The study of their genome is important not only for understanding their evolution, but also for improving conservation efforts, including population management, diversity and inbreeding assessment, and tracking rescued individuals to combat illegal wildlife trafficking. Here, we use chromosome 21 target capture data from 156 non-invasively collected faecal samples from wild bonobos to perform a comprehensive analysis of their population structure. We confirm the existence of three previously suggested subpopulations identified here as Western, Central and Eastern bonobos which are defined by natural barriers of gene flow such as the Lomami River. By estimating levels of inbreeding, diversity and differentiation, we find support for isolation of mainly Western and Eastern populations and add information on the dispersal routes of their ancestors. We infer split times and separation of these populations and apply a genetic framework to geolocalize samples of unknown origin, showing that locations of their potential origin can be estimated with a precision of up to a median of [~]50 km. Our study provides valuable insight into the evolution and population structure of bonobos and reveals how rivers act as strong barriers between populations. It also offers resources for conservation efforts and highlights the need to monitor bonobo populations more closely, in particular isolated ones. ImpactBonobos have been difficult to study genetically due to their remote forest habitat and endangered status. Here we used non-invasive sampling and chromosome 21 target capture sequencing to perform the most detailed analysis to date of their population structure. We find three main subpopulations and genetic differentiation influenced by river barriers, especially with populations found on the Eastern side of the Lomami river. This data will be useful for identifying the geographic origin of confiscated samples and thus aid bonobo conservation efforts.

bioinformatics↗

bioRxiv2025

New high accuracy diagnostics for avian Aspergillus fumigatus infection using Nanopore methylation sequencing of host cell-free DNA and machine learning prediction

Avian aspergillosis is a detrimental fungal infection affecting wild and domestic birds yet sensitive antemortem diagnostics for early clinical infections are lacking. Here we present new diagnostics for Aspergillus fumigatus (Af) infection developed from cell-free DNA (cfDNA) methylation markers. Broiler chickens were experimentally infected with either Af, a non-Af agent (Escherichia coli or Gallibacterium anatis) or assigned as controls. Oxford Nanopore (ONT) sequencing was performed on serum cfDNA (n = 124), and machine learning (ML) models were trained on infection-specific markers. Three tests were developed: A High Accuracy test for best performance (sensitivity: 100%, specificity: 89.2%) and robustness (ROC-AUC: 0.92) as well as Fast- and In situ tests for rapid turnaround and methylation PCR. Diagnostic accuracies were 92.3%, 82.7%, and 73.1%, respectively. In conclusion, new tests using on ML- and host cfDNA methylation markers demonstrated high diagnostic performance comparable to microbial cfDNA (mcfDNA) tests but without concern for environmental contamination. Key highlightsO_LIWe present three new high accuracy diagnostic tests for Aspergillus fumigatus infection in chickens that use methylation markers from serum cell-free DNA (cfDNA). C_LIO_LIDifferentially methylated cfDNA regions (DMRs) were detected by Oxford Nanopore sequencing (ONT) in experimentally infected chickens and used as markers to train machine learning (ML) models for development of three diagnostic tests. C_LIO_LIThe highest accuracy was found with 83 markers of 10 kilobases (KB) using the glmnet algorithm for the ML model, which classified 92.3% blinded samples correctly. C_LIO_LIA Fast test designed for cheap <1h sequencing using adaptive sampling could correctly classify 82.7% samples with 22 markers using a random forest (rf) model. C_LIO_LIAn In situ test with only four markers, envisioned for use in a simple methylation-specific PCR (MSP-PCR) assay, could correctly classify 73.1% blinded samples. C_LIO_LIReference values with associated probabilities of infection were calculated for each of the three tests and are presented for further evaluation. C_LI

microbiology↗

bioRxiv2025

Population structure and domestication history of the Javan banteng (Bos javanicus javanicus)

The domestication of the banteng in Southeast Asia is one of the Worlds least known livestock domestications, yet a vital component of the agricultural system in Indonesia and surrounding countries. Here we generated the first reference genome of the banteng and used it to analyze a set of 78 resequenced wild and domesticated bantengs, including 19 newly generated whole-genome sequenced samples of which three are historical samples. We found low heterozygosity and significant differentiation, the latter primarily driven by recent genetic drift and inbreeding in two populations, and clearly attributable to anthropogenically driven founder events or ex-situ breeding. Population structure when excluding these two populations was limited, and we found that the evolutionary divergence between wild and domestic banteng is moderate (FST = 0.14), relatively young (10,356 years), and with post-divergence gene flow. We found only weak signals of a domestication bottleneck between [~]6100-2900 years ago, and genetic diversity is on average higher in domestic than in wild banteng. Despite the soft domestication history, we found 56 candidate genes under selection during domestication, with the leptin receptor gene (LEPR) of particular interest due to the robust selection signal across methods, and its known association to metabolism, obesity and energy homeostasis. Finally, genetic load estimation revealed that Bali cattle in Australia have high realized load, while Bali cattle from Bali have high masked load. These findings provide the first genomic insights into an understudied bovine that is Critically Endangered in its wild form, and agriculturally important in its domesticated form.

evolutionary biology↗

bioRxiv2025

Unfolding admixed ancestry and genomic diversity in zoo giraffes

A giraffe nicknamed Marius attracted international media attention and world-wide notoriety when euthanized by Copenhagen Zoo in 2014, deemed surplus to the European breeding program. This incident highlights the challenges of managing zoo populations to best contribute to species conservation amid limited resources. Here, we investigated the degree of admixture, genetic diversity and inbreeding in ex situ giraffes using whole genome sequencing data from Marius and 12 other zoo giraffes, leveraging a reference data set from 71 wild giraffes. We found that most zoo giraffes show admixed ancestries. Marius, and zoo individuals assigned to Reticulated giraffes, exhibits mosaic ancestry with 85% Reticulated and 15% Nubian origin. We further detected recent inbreeding in some of the zoo individuals, consistent with their studbook data. Runs of homozygosity revealed that Marius and three other zoo giraffes were more inbred than their wild counterparts, although their admixed ancestry compensates for the reduction in genetic diversity caused by inbreeding. Our findings highlight the dual challenges of admixture and inbreeding in ex situ populations of giraffe, emphasizing the need for balanced genetic management to mitigate inbreeding and outbreeding degression while preserving diversity reflective of wild populations. This study also reinforces the importance of studbooks and genomic tools in guiding ex situ conservation strategies.

evolutionary biology↗

bioRxiv2025

The genomic landscape of spider monkeys and northern muriquis from a conservation perspective

BackgroundMost populations of spider monkeys (Ateles) and muriquis (Brachyteles), two Neotropical primate genera, are under severe anthropogenic threats. Yet, taxon-wide population-level studies leveraging their degree of endangerment linked to their genetic diversity patterns and demographic history are lacking. To properly address this, there is a need to expand from morphological and genetic marker-based studies. ResultsWe generated high-coverage genome sequencing for 58 individuals sampled across 8 Atelidae species, in the first population-wide study of all extant spider monkey species, in the wild and captivity, alongside northern muriquis (Brachyteles hypoxanthus). Additionally, we present a high-contiguity reference genome for Ateles hybridus. Here, we observe the overall levels of genetic diversity and genetic load of the analyzed populations do not align to their IUCN endangerment category. Moreover, we show that in the wild, genetic load is overall higher compared to the captive populations analyzed. Then, we depict two main trans and cis-Andean sister clades in Ateles, and further structure and dynamics outlined by the Madeira River in the latter clade. Lastly, we find that genes in highly divergent regions between Ateles and B. hypoxanthus are involved in central nervous system development and photorreception. ConclusionsOur study shows i) the lack of concordance between the genetic diversity levels and extinction risk of these populations, suggestive of recent and strong external drivers; ii) increased genetic load in the wild in contrast to effective captive management, indicating mostly past demographic events; iii) structure and dynamics in spider monkeys that agrees with common biogeographical patterns and iv) genetic divergence between Ateles and Brachyteles potentially linked to distinct environmental light levels.

genomics↗

bioRxiv2024

Insights into gene conversion and crossing-over processes from long-read sequencing of human, chimpanzee and gorilla testes and sperm

Homologous recombination rearranges genetic information during meiosis to generate new combinations of variants. Recombination also causes new mutations, affects the GC content of the genome and reduces selective interference. Here, we use HiFi long-read sequencing to directly detect crossover and gene conversion events from switches between the two haplotypes along single HiFi-reads from testis tissue of humans, chimpanzees and gorillas as well as human sperm samples. Furthermore, based on DNA methylation calls, we classify the cellular origin of reads to either somatic or germline cells in the testis tissue. We identify 1692 crossovers and 1032 gene conversions in nine samples and investigate their chromosomal distribution. Crossovers are more telomeric and correlate better with recombination maps than gene conversions. We show a strong concordance between a human double-strand break map and the human samples, but not for the other species, supporting different PRDM9-programmed double-strand break loci. We estimate the average gene conversion tract lengths to be similar and very short in all three species (means 40-100 bp, fitted well by a geometric distribution) and that 95-98% of non-crossover events do not involve tracts intersecting with polymorphism and are therefore not detectable. Finally, we detect a GC bias in the gene conversion of both single and multiple SNVs and show that the GC-biased gene conversion affects SNVs flanking crossover events. This implies that gene conversion events associated with crossover events are much longer (estimated above 500 bp) than those associated with non-crossover events. Highly accurate long-read sequencing combined with the classification of reads to specific cell types provides a new, powerful way to make individual, detailed maps of gene conversion and crossovers for any species.

evolutionary biology↗

bioRxiv2024

Deep genetic substructure within bonobos

Establishing the genetic and geographic structure of populations is fundamental both to understand their evolutionary past and preserve their future, especially for endangered species. Nevertheless, the patterns of genetic population structure are unknown for most endangered species, including some of our closest living relatives. This is the case of bonobos (Pan paniscus) which together with chimpanzees (Pan troglodytes) are humans closest living relatives. Chimpanzees live across equatorial Africa and are classified into four subspecies (Groves, 2001), with some genetic population substructure even within subspecies. Conversely, bonobos live exclusively in the Democratic Republic of Congo and are considered a homogeneous group with low genetic diversity (Fischer et al. 2011) despite some population structure inferred from mtDNA. Nevertheless, mtDNA aside, their genetic structure remains unknown, hampering our understanding of the species and conservation efforts. Placing bonobos genetics in space is however challenging because, being endangered, only non-invasive sampling is possible for wild individuals. Here, we jointly analyse the exomes and mtDNA from 20 wild-born bonobos, the whole-genomes of 10 captive bonobos and the mtDNA of 61 wild individuals. We identify three genetically distinct bonobo groups of inferred Central, Western and Far-Western geographic origin within the bonobo range. We estimate the split time between the central and western populations to [~]145,000 years ago, and genetic differentiation to be in the order of that of the closest chimpanzee subspecies. We identify putative signatures of differential genetic adaptation among populations for genes associated with homeostasis, metabolism and the nervous system. Furthermore, our estimated long-term Ne for Far-West ([~]3,000) is among the lowest estimated for any great ape lineage. Our results highlight the need of attention to bonobo substructure, both in terms of research and conservation. Highlights- We identified three genetically distinct populations of bonobos, inferred as having Central, Western and Far-Western geographic origin within the species range. The estimated split time is [~]145,000 years ago for the Central and Western populations, and [~]60,000 years ago for the two Western populations. - The genetic differentiation between the Central and Far-Western bonobo populations is in the order of that between Central and Eastern chimpanzee subspecies, while the genetic differentiation among Western bonobo populations is similar to that among human groups. - Once substructure is accounted for, we infer a long-term effective population size (Ne) of only [~]3,000 for Far-Western bonobos, genetic isolation and inbreeding.

evolutionary biology↗

bioRxiv2023

The landscape of tolerated genetic variation in humans and primates

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence SummaryDeep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.

genomics↗

bioRxiv2023

A global catalog of whole-genome diversity from 233 primate species

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology, and is urgent given severe threats these species are facing. Here, we present high coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human-specific. This study will open a wide range of research avenues for future primate genomic research. One-Sentence SummaryThe whole genome sequences of 233 primate species provide insight into the determinants of genetic diversity, phylogenomics, and human uniqueness.

genomics↗

bioRxiv2023

Conserving genetic diversity during climate change:Niche marginality and discrepant monitoring capacity in Europe

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. Genetic diversity has been largely neglected in biodiversity monitoring, and when addressed is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. Genetic monitoring supports the conservation and management of fisheries, game, and threatened populations. It also can contribute to the assessment of predicted and realized impacts of climate change, and their management. We report the first accounting of genetic monitoring efforts among countries in Europe (their genetic monitoring capacity, GMC) to determine where GMC suggests the combination of national infrastructure, political support and resources for continued and expanded monitoring. Overlaying GMC with areas where species ranges approach current and future climate niche limits (i.e., niche marginality) helps identify whether GMC coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area extent, financial resources, and conservation policy influence GMC, high values of which inconsistently match joint species patterns of climate niche marginality. Populations at niche margins likely hold genetic diversity that is important to adaptation to changing climate, and our results illuminate the need in Europe for expanded genetic monitoring across the climate gradients occupied by species, a need arguably greatest in southeastern European countries.

ecology↗

bioRxiv2021

The genetic impact of an Ebola outbreak on a wild gorilla population

BackgroundNumerous Ebola virus outbreaks have occurred in Equatorial Africa over the past decades. Besides human fatalities, gorillas and chimpanzees have also succumbed to the fatal virus. The 2004 outbreak at the Odzala-Kokoua National Park (Republic of Congo) alone caused a severe decline in the resident western lowland gorilla (Gorilla gorilla gorilla) population, with a 95% mortality rate. Here, we explore the immediate genetic impact of the Ebola outbreak in the western lowland gorilla population. ResultsAssociations with survivorship were evaluated by utilizing DNA obtained from fecal samples from 16 gorilla individuals declared missing after the outbreak (non-survivors) and 15 individuals observed before and after the epidemic (survivors). We used a target enrichment approach to capture the sequences of 123 genes previously associated with immunology and Ebola virus resistance and additionally analyzed the gut microbiome which could influence the survival after an infection. Our results indicate no changes in the population genetic diversity before and after the Ebola outbreak, and no significant differences in microbial community composition between survivors and non-survivors. However, and despite the low power for an association analysis, we do detect six nominally significant missense mutations in four genes that might be candidate variants associated with an increased chance of survival. ConclusionThis study offers the first insight to the genetics of a wild great ape population before and after an Ebola outbreak using target capture experiments from fecal samples, and presents a list of candidate loci that may have facilitated their survival.

genomics↗

bioRxiv2018

Direct estimation of mutations in great apes reveals significant recent human slowdown in the yearly mutation rate

The human mutation rate per generation estimated from trio sequencing has revealed an almost linear relationship with the age of the father and the age of the mother. The yearly trio-based mutation rate estimate of ~0.43x10-9 is markedly lower than prior indirect estimates of ~1x10-9 per year from phylogenetic comparisons of the great apes. This suggests either a slowdown over the past 10 million years or an inaccurate interpretation of the fossil record. Here we use sequencing of chimpanzee, gorilla and orangutan trios and find that each species has higher estimated mutation rates per year by factors of 1.67+/- 0.22, 1.54+/- 0.2 and 1.84+/- 0.19, respectively. These estimates suggest a very recent and appreciable slowdown in human mutation rate, and, if extrapolated over the great apes phylogeny, yields divergence estimates much more in line with the fossil record and the biogeography.

evolutionary biology↗