Biology subjects

Cilingir, F. G.

Publications and source records attributed to Cilingir, F. G..

4 recordsLinked to original sources

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↗

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

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↗