Biology subjects

Grossen, C.

Publications and source records attributed to Grossen, C..

12 recordsLinked to original sources

bioRxiv2026

Paleogenomic time series reveal past population dynamics and their relevance for the conservation of the Alpine ibex

Endangered species often suffer from genetic threats such as inbreeding depression, the accumulation of mutation load and the general loss of genetic diversity, which may deprive them from future adaptation. Since the genetic make-up of a species is strongly affected by its evolutionary past, however, interspecific comparisons are difficult and absolute levels of genetic diversity may be a relatively poor predictor of extinction risk. To better interpret current levels of genetic diversity of actively managed species, the comparison of present-day genomic data to that of ancient material pre-dating recent anthropogenic population declines has been advocated, but remains rarely done at the evolutionary time scales necessary to understand past population dynamics. Here we demonstrate the usefulness of deep genomic time series through 40 high quality ancient genomes of the Alpine ibex, which faced near-extinction in the 19th century but has since been reintroduced across the Alps and recovered remarkably. The samples, which span the last 14,000 years, evidence strong and stable population structure at the continental scale, paired with frequent extinction and recolonization events at the local scale. These metapopulation dynamics resulted in small and largely isolated populations, with present-day, reintroduced populations only having 20% to 40% less neutral genetic diversity and 3% higher mutation load, likely due to efficient purging in the past. At the species level, however, the loss of genetic diversity was dramatic and reduced to the small fraction that segregated within the only surviving population in the Gran Paradiso area. Our analyses of ancient metapopulation dynamics in Alpine ibex underscore the importance of a healthy genetic pool for successful recolonization and long-term survival, as well as the real possibility of regional extinctions.

evolutionary biology↗

bioRxiv2025

Evolutionary dynamics of a lethal recessive allele in reintroduced fragmented lynx populations

Conservation programs worldwide use reintroductions and translocations as management tools to support endangered species. Such efforts often face genetic challenges, as small populations and restricted gene flow can lead to inbreeding and loss of genetic diversity. Inbreeding depression is a well-known risk in small, isolated populations, where reduced genetic diversity can compromise fitness and threaten population persistence. While correlations between inbreeding and reduced fitness are well documented, so far, no causal variant for a fitness-relevant phenotype has been described in a wild population. Here, we combine long-term health and population data with genomic analyses to identify a recessive lethal allele responsible for extensive organ mineralization in young Eurasian lynx (Lynx lynx) from a reintroduced population in Switzerland. The causal variant is located in FGF23 and predicted to impair secretion of fibroblast growth factor 23, an important regulator of phosphate homeostasis. The deleterious allele was likely introduced from one of the lynx source populations and subsequently increased in frequency through founder effects and inbreeding. All three Swiss lynx populations show high inbreeding levels (FROH > 0.4), reflecting substantial loss of genetic diversity. Our findings uniquely demonstrate how demographic history, founder effects, genetic drift, and inbreeding interact to shape the fate of a recessive deleterious allele, highlighting the importance of multiscale monitoring in wildlife conservation.

evolutionary biology↗

bioRxiv2024

A highly contiguous reference genome for the Alpine ibex (Capra ibex)

Species conservation efforts can be threatened by deleterious mutation accumulation following population contractions. In addition to de novo mutations, a significant source of genetic load could be deleterious variants introduced into a population through hybridization. Hence, even successfully restored species may face deleterious mutation swamping due to hybridization with an abundant and closely related species. The outcomes of such hybridization events are poorly understood given the complex interplay of introduced adaptive and maladaptive variation. Here, we analyze this potential risk for Alpine ibex (Capra ibex), a flagship species of large mammal restoration in the Alps. Near-extinction two centuries ago resulted in exceptionally low genome-wide diversity and increased inbreeding, which facilitated the purging of severe deleterious mutations but accumulation of less severe ones. We produced a highly contiguous chromosome-level genome assembly of the Alpine ibex capturing structural divergence from its closest domestic species, the domestic goat (Capra hircus) known to hybridize with Alpine ibex Genome sequencing of eight recent ibex-goat hybrids and backcrosses from two hybrid swarms in Northern Italy revealed highly diverse recombinants and an average of 30 masked, predicted loss-of-function (LOF) mutations per hybrid compared to 10 in non-hybrid Alpine ibex. This exposes Alpine ibex to further backcrosses, exposing their vulnerable gene pool to an influx of hybridization load. Individual-based genomic simulations suggest that such LOF load would return to pre- hybridization levels with a lag of over 100 generations after gene flow subsides. Hybridization could also disrupt local adaptation in the recipient species. Our work provides a direct estimate of hybridization load and, by this, informs on the complexity of managing endangered gene pools in the face of hybridization.

evolutionary biology↗

bioRxiv2024

Genotype likelihoods incorporated in non-linear dimensionality reduction techniques infer fine-scale population genetic structure

O_LIUnderstanding population structure is essential for conservation genetics, as it provides insights into population connectivity and supports the development of targeted strategies to preserve genetic diversity and adaptability. C_LIO_LIT-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) have proven effective for revealing population genetic structures in human and model organisms using hard-called genotypes, but their application in wild species using genotype likelihoods from low coverage sequencing (as a cost-saving measure) remains underexplored. C_LIO_LIHere, we present a Jupyter Notebook-based workflow that facilitates the use of UMAP and t-SNE on genotype likelihood-derived principal components. C_LIO_LIThis workflow is demonstrated using medium to low-coverage whole-genome sequencing data from scimitar-horned oryx, which has been reintroduced into the wild and faces multiple conservation challenges. C_LIO_LIDetailed guidance on hyperparameter tuning and practical implementation is also provided, enhancing the application of these methods in wildlife genetics to potentially support biodiversity conservation. C_LI

bioinformatics↗

bioRxiv2023

Genetic evidence of a hybrid swarm between Alpine ibex and domestic goat

Improving the understanding of the causes and effects of anthropogenic hybridization is fundamental to ensure the conservation of wild species, particularly in the case of hybridization between wild species and their domestic relatives. Knowledge is missing for many species also because of a lack of appropriate tools for hybrid identification. Here, coupling genotype and phenotype analysis, we carried out an extensive investigation of ongoing hybridization in Alpine ibex Capra ibex, a mountain ungulate of conservation concern from a genetic perspective. By genotyping at 63 diagnostic and 465 neutral SNPs 20 suspected hybrids and 126 Alpine ibex without suspicious phenotype, representing eight populations across a major part of the species distribution, we found evidence for ongoing hybridization between Alpine ibex and domestic goat. We identified different levels of hybridization including back crosses into both Alpine ibex and domestic goat. Our results suggest a lack of reproductive barriers between the two species and good survival and reproductive success of the hybrids. Hybridization was locally intense, alike a hybrid swarm, but not spread across the rest of the species distribution. Most of the hybrids were discovered in two locations in the North-West of Italy, while random sampling of individuals from different areas did not provide evidence of recent hybridization. Our method, based on Amplicon sequencing of 63 diagnostic SNPs specifically developed for this purpose, allowed us to identify hybrids and back crosses up to the 4th-5th generation and was suitable for genetic samples of different quality, although with varying levels of certainty regarding the exact number of generations passed since hybridization. Based on the paired analysis of genotype and phenotype we provide guidelines for a first identification of hybrids in the field and suggest a procedure for the reliable identification of hybrids.

evolutionary biology↗

bioRxiv2023

Facilitated introgression from domestic goat into Alpine ibex at immune loci

Introgression is expected to be adaptive at loci under balancing selection, for instance at loci relevant for the immune response, but these loci generally also contain ancient polymorphisms. Ancient genomics is a promising tool to detect recent introgression and disentangle it from ancient polymorphisms. Alpine ibex (Capra ibex), a wild goat species native to the European Alps, faced near-extinction two centuries ago, but has recovered thanks to successful restoration programs. Previously, signals of introgression from the domestic goat (Capra aegagrus hircus) into the Alpine ibex genome were found at the major histocompatibility complex. This introgression was suggested to potentially be adaptive since it introduced new diversity at a gene locus important for immunity. But no genome-wide analyses of introgression have been performed to confirm the potential relevance of immune loci. Here we take advantage of two ancient whole genomes of Alpine ibex combined with 29 modern Alpine ibex genomes and 31 genomes representing six related Capra species to investigate genome-wide patterns of introgression. Our complementary analysis of putatively introgressed haplotypes and demographic modelling suggests 2.3% recent domestic goat ancestry among wild Alpine ibex. The introgression was estimated to have happened during the last 300 years coinciding with the time when the species had very small population size. Further analysis suggested an enrichment of immune-related genes, where the adaptive value of alternative alleles may give individuals with otherwise depleted genetic diversity a selective advantage.

evolutionary biology↗

bioRxiv2022

Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two giant tortoise species left in the world. The species is endemic to Aldabra Atoll in Seychelles and is considered vulnerable due to its limited distribution and threats posed by climate change. Genomic resources for A. gigantea are lacking, hampering conservation efforts focused on both wild and ex-situ populations. A high-quality genome would also open avenues to investigate the genetic basis of the exceptionally long lifespan. Here, we produced the first chromosome-level de novo genome assembly of A. gigantea using PacBio High-Fidelity sequencing and high-throughput chromosome conformation capture (Hi-C). We produced a 2.37 Gbp assembly with a scaffold N50 of 148.6 Mbp and a resolution into 26 chromosomes. RNAseq-assisted gene model prediction identified 23,953 protein-coding genes and 1.1 Gbp of repetitive sequences. Synteny analyses among turtle genomes revealed high levels of chromosomal collinearity even among distantly related taxa. We also performed a low-coverage re-sequencing of 30 individuals from wild populations and two zoo individuals. Our genome-wide population structure analyses detected genetic population structure in the wild and identified the most likely origin of the zoo-housed individuals. The high-quality chromosome-level reference genome for A. gigantea is one of the most complete turtle genomes available. It is a powerful tool to assess the population structure in the wild population and reveal the geographic origins of ex-situ individuals relevant for genetic diversity management and rewilding efforts.

genomics↗

bioRxiv2021

Ancient mitogenomes unravel massive genetic diversity loss during near extinction of Alpine ibex

Population bottlenecks can have dramatic consequences for the health and long-term survival of a species. A recent bottleneck event can also largely obscure our understanding of standing variation prior to the contraction. Historic population sizes can be modeled based on extant genomics, however uncertainty increases with the severity of the bottleneck. Integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high-quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 {+/-} 33 BP to 1919 CE and combine these with 60 published modern genomes. Coalescent demography simulations based on modern genomes indicate population fluctuations matching major climatic change over the past millennia. Using ancient genomes, we show that mitochondrial haplotype diversity has been reduced to a fifth of the pre-bottleneck diversity with several highly differentiated mitochondrial lineages having co-existed historically. The main collapse of mitochondrial diversity coincided with human settlement expansions in the Middle Ages. The near extinction severely reduced the mitochondrial diversity. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Contrary to expectations, we show that a second ancestral mitochondrial lineage has survived in an isolated population further south. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long-term population fluctuations.

evolutionary biology↗

bioRxiv2021

Low-coverage reduced representation sequencing reveals subtle within-island genetic structure in Aldabra giant tortoises

Aldabrachelys gigantea (Aldabra giant tortoise) is one of only two giant tortoise species left in the world and survives as a single wild population of over 100,000 individuals on Aldabra Atoll, Seychelles. Despite this large current population size, the species faces an uncertain future because of its extremely restricted distribution range and high vulnerability to the projected consequences of climate change. Captive-bred A. gigantea are increasingly used in rewilding programs across the region, where they are introduced to replace extinct giant tortoises in an attempt to functionally resurrect degraded island ecosystems. However, there has been little consideration of the current levels of genetic variation and differentiation within and among the islands on Aldabra. As previous microsatellite studies were inconclusive, we combined low-coverage and double digest restriction associated DNA (ddRAD) sequencing to analyze samples from 33 tortoises (11 from each main island). Using 5,426 variant sites within the tortoise genome, we detected patterns of population structure within two of the three studied islands, but no differentiation between the islands. These unexpected results highlight the importance of using genome-wide genetic markers to capture higher-resolution genetic structure to inform future management plans, even in a seemingly panmictic population. We show that low-coverage ddRAD sequencing provides an affordable alternative approach to conservation genomic projects of non-model species with large genomes.

ecology↗

bioRxiv2021

Disentangling adaptation from drift in bottlenecked and reintroduced populations of Alpine ibex

Identifying local adaptation in bottlenecked species is essential for effective conservation management. Selection detection methods are often applied to bottlenecked species and have an important role in species management plans, assessments of the species adaptive capacity, and looking for responses to major threats like climate change. Yet, the allele frequency changes driven by selection and exploited in selection detection methods, are similar to those caused by the strong neutral genetic drift expected during a bottleneck. Consequently, it is often unclear what accuracy selection detection methods may offer within bottlenecked populations. In this study, we used simulations to explore if signals of selection could be confidently distinguished from genetic drift across 23 bottlenecked and reintroduced populations of Alpine ibex (Capra ibex). We used the meticulously recorded demographic history of the Alpine ibex to generate a comprehensive simulated SNP data. The simulated SNPs were then used to benchmark the confidence we could place in putative outliers identified through selection scans on empirical Alpine ibex SNP data. Within the simulated dataset, the false positive rates were high for all selection detection methods but fell substantially when two or more selection detection methods were combined. However, the true positive rates were consistently low and became essentially negligible after this increased stringency. Despite the detection of many putative outlier loci in the empirical Alpine ibex RADseq data, none met the threshold needed to distinguish them from genetic drift-driven false positives. Unfortunately, the low true positive rate also creates a paradox, by preventing the exclusion of recent local adaptation within the Alpine ibex.

evolutionary biology↗

bioRxiv2020

A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics

Genetic variation is a major factor determining susceptibility to diseases. Polymorphism at the major histocompatibility complex (MHC) and other immune function loci can underlie health and reproductive success of individuals. Endangered species of low population size could be severely compromised to evolve disease resistance due to reduced adaptive variation. A major impediment to screen adaptive genetic variation in wild species is the difficulty to comprehensively genotype immune-related loci based on low input material. Here, we design and validate a targeted amplicon sequencing assay to parallelize the analysis of a thousand loci of the MHC, other immunity-related genes, and genome-wide markers for the assessment of population structure. We apply the approach to Alpine ibex, one of the most successful examples of restoration of a large mammal in Europe. We used 51 whole genome sequenced individuals to select representative target SNPs. We integrated SNP call data from four related species for amplification robustness and genotyped 158 Alpine ibex individuals for validation. We show that the genome-wide markers perform equally well at resolving population structure as RAD-seq or low-coverage genome sequencing datasets with orders of magnitude more markers. The targeted amplicon sequencing assay is robust to >100-fold variation in input DNA quantity and generates useful genotype information from fecal samples. The amplicon marker set also identified recent species hybridization events with domestic goats. The immune loci show unexpectedly high degrees of differentiation within the species. Our assay strategy can realistically be implemented into population genetic surveys of a large range of species.

genomics↗

bioRxiv2019

Accumulation and purging of deleterious mutations through severe bottlenecks in ibex

Human activity caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of a species with unknown consequences for health. A key genetic factor for species survival is the evolution of deleterious mutation load, but how bottleneck strength and mutation load interact lacks empirical evidence. Here, we take advantage of the exceptionally well-characterized population bottlenecks of the once nearly extinct Alpine ibex. The species survived one of the most dramatic bottlenecks known for successfully restored species. We analyze 60 complete genomes of six ibex species and the domestic goat. We show that historic bottlenecks rather than the current conservation status predict levels of genome-wide variation. By retracing the recolonization of the Alps by Alpine ibex, we find genomic evidence of concurrent purging of highly deleterious mutations but accumulation of mildly deleterious mutations. This demonstrates how human-induced severe bottlenecks caused both relaxed selection and purging, thus reshaping the landscape of deleterious mutation load. Our findings also highlight that even populations of ~1000 individuals can accumulate mildly deleterious mutations. Hence, conservation efforts should focus on preventing population declines below such levels to ensure long-term survival of species.

evolutionary biology↗