Biology subjects

Dussex, N.

Publications and source records attributed to Dussex, N..

6 recordsLinked to original sources

bioRxiv2024

SNP panel for non-invasive genotyping of leopard (Panthera pardus)

Genetic resources for species monitoring should ideally be relevant for the species full distribution range, feasible economically and logistically, and validated for the range of sample types collected from the field. This is particularly important for large carnivores that are elusive and wide-ranging, where individual and population processes often traverse administrative borders, and where obtaining high-quality samples can be challenging. Here we present a small species-specific SNP panel for leopards. We used whole genome data from across the global range and RAD sequence data from Zambian leopards to select markers for assay development. These were ascertained for 590 individual leopards from eight African countries and final selection was based on marker variation and performance on non-invasive samples. The final 96 marker panel holds 5 mitochondrial markers for species recognition, 3 Y-markers for determination of individual sex, 3 X-markers and 85 somatic markers, with an associated genetic baseline holding nearly 900 individuals. The selected autosomal markers hold variation across the global range with high power to identify individuals (PID=2,45x10-35) and in most cases their provenance with high assignment probability (>95%). Markers were also selected based on their performance on samples with low target DNA content, with distinct genotype separation in the output marker plots. The genotypes from this panel are thus straightforward to analyze and do not require computationally challenging bioinformatic resources, making this a low cost and accessible resource for leopard monitoring and research.

genetics↗

bioRxiv2023

A paleogenomic investigation of overharvest implications in an endemic wild reindeer subspecies

Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-Arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17-20th century. Here we investigate changes in genetic diversity, population structure and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90), to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation and 400 years of genetic drift have altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 23%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long- term interplay of past, current, and future stressors in wildlife conservation.

genomics↗

bioRxiv2023

Population genomics reveals extensive inbreeding and purging of mutational load in wild Amur tigers

The inbreeding is a big threat for the persistence of genetic diversity in small and isolated populations of endangered species. The homozygous genome could exacerbate inbreeding depression by introducing homozygous deleterious alleles in the population. However, purging of inbreeding loads as they become homozygotes in small populations could alleviate the depression. The Amur tiger (Panthera tigris altaica) is typically exists in small population living in forests in Northeast Asia and is among the most endangered animals on the planet with great symbolic significance of conservation. By comparing with captive individuals, we revealed substantially higher and more extensive inbreeding in the wild Amur tiger population (FROH=0.51) than in captive Amur tigers (FROH=0.26). We further found much less mutational loads in wild populations when compared with captive Amur tigers. However, the frequency of loss of function and deleterious nonsynonymous mutations inside ROH regions are much lower than that in non-ROH regions in both wild and captive Amur tigers, indicating the purging may had occurred in both populations but much effective in the wild population. In addition, we found the average frequency of deleterious alleles was much lower than that of neutral alleles in the wild population, indicating that the purifying selection contributed to the purging of mutational loads in the wild Amur tigers. These findings provide valuable genome-wide evidence to support the making of future conservation plans of wild Amur tigers.

genomics↗

bioRxiv2022

Convergent evolution of skim feeding in baleen whales

The origin of pygmy right whales (Caperea marginata), the smallest and most enigmatic of the living baleen whales, remains contentious. Morphological analyses largely continue to ally Caperea with right whales (balaenids) based on shared cranial features like a tall braincase and a narrow, highly arched rostrum. By contrast, molecular data and some anatomical evidence suggest a closer relationship with rorquals (balaenopterids), but fail to explain "the substantial issue of convergence posed by the many balaenid features of Caperea" (Berta & Demere, 2017). To resolve this question, we sequenced the nuclear genome of C. marginata (812,269,251 paired reads; 47X average depth of coverage, with 89.33% of the genome covered at [≥]10X) and subjected it to a multispecies coalescent analysis including representatives of all baleen whale families. Our results confirm Caperea as sister to rorquals and, thus, the convergent origin of its right whale-like anatomy. Considering this overwhelming molecular evidence, we propose that the traditional taxonomic grouping of Caperea with right whales be abandoned.

evolutionary biology↗

bioRxiv2022

GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

BackgroundMany wild species have suffered drastic population size declines over the past centuries, which have led to genomic erosion processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses. ResultsHere, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode). ConclusionsGenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.

bioinformatics↗

bioRxiv2019

The tuatara genome: insights into vertebrate evolutionfrom the sole survivor of an ancient reptilian order

The tuatara (Sphenodon punctatus), the only living member of the archaic reptilian order Rhynchocephalia (Sphenodontia) once widespread across Gondwana, is an iconic and enigmatic terrestrial vertebrate endemic to New Zealand. A key link to the now extinct stem reptiles from which dinosaurs, modern reptiles, birds and mammals evolved, the tuatara provides exclusive insights into the ancestral amniotes. The tuatara genome, at [~]5 Gbp, is among the largest vertebrate genomes assembled. Analysis of this genome and comparisons to other vertebrates reinforces the uniqueness of the tuatara. Phylogenetic analyses indicate tuatara diverged from the snakes and lizards [~]250 MYA. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Genome sequence analysis identifies expansions of protein, non-protein-coding RNA families, and repeat elements, the latter of which show an extraordinary amalgam of reptilian and mammalian features. Sequencing of this genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. It also provides important insights into both the technical challenges and the cultural obligations associated with genome sequencing.

genomics↗