Biology subjects

Bruniche-Olsen, A.

Publications and source records attributed to Bruniche-Olsen, A..

5 recordsLinked to original sources

bioRxiv2026

The contemporary Pacific gray whale (Eschrichtius robustus) gene pool includes ancestry from a potential ghost population: inferences from population genomics

Local extirpations and extreme bottlenecks can deplete genetic variation and obscure population dynamics, especially in highly mobile species. The gray whale (Eschrichtius robustus) undertakes some of the longest known migrations among mammals, and conventional wisdom acknowledges two stocks (eastern and western gray whales) in the Pacific. Commercial whaling depleted both stocks, and while the Eastern North Pacific (ENP) stock has rebounded, the western stock was feared extirpated. In the post-whaling era, the origin of a small summer aggregation near Sakhalin Island, Russia (which we refer to as the Western North Pacific (WNP) stock) is unclear; this group may include descendants from the original western stock, founders from the eastern stock, or some combination of the two. To clarify the genetic affinities of WNP gray whales, we generated whole genome resequencing data for 74 individuals sampled from both geographic regions to assess their origins. Surprisingly, WNP whales are more genetically varied than ENP whales according to principal components and admixture analyses. We present evidence that this structure is due to mixed ancestry in WNP, with admixture occurring between historical eastern and western stocks. Genomic signals based on both single nucleotide polymorphisms and on copy number variants indicate that despite mixed ancestry, the influx of eastern gene flow has largely homogenized genomic diversity across the Pacific. These findings highlight the ability of whole-genome data to help resolve questions of extirpation and to clarify complex gene flow dynamics in highly mobile species.

genomics↗

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

An improved gray whale assembly highlights how allospecific reference-genome choice can affect genomic diversity estimates

Gray whales (Eschrichtius robustus) are unique as bottom feeding baleen whales and they have long been a conservation concern on both sides of the Pacific, in part because they migrate and disperse farther than any other species on earth. They experienced drastic population size declines due to environmental changes and commercial whaling. Here, we present an improved genome assembly for the gray whale. This genome assembly covers 2.4 Gb divided across 2689 contigs with an N50 of 15Mb. From the new assembly, we identify 75Mb sex-linked contigs and a identify 94.6% of searched genes based on Benchmarking Universal Single-Copy Ortholog score. We use the gray whale assembly to explore the effects of mapping to conspecific vs allospecific reference genomes when estimating genome-wide heterozygosity (H) and runs of homozygosity (ROH). The use of allospecific genomes significantly underestimate both H and ROH burden regardless of genomic distance and assembly quality. Our analyses highlight the importance of using contiguous conspecific assemblies in whale genomics and conservation. SignificanceGray whales are unique in their behavior, morphology and ecology. The novel and contiguous genome assembly presented here will serve as a valuable resource for studies of their population and comparative genomics, as well as for identifying key adaptations that have evolved in this clade. Finally, our results demonstrate that biases can arise when using allopatric assemblies to evaluate diversity metrics, so they should be used and interpreted with caution.

evolutionary biology↗

bioRxiv2023

African bush pigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival

Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1,000-5,000 years ago, concurrent with human arrival in Madagascar. These results shed new light on the evolutionary history of an iconic and widespread African genus and provide insight into the longstanding biogeographic puzzle surrounding the bushpigs presence in Madagascar.

evolutionary biology↗

bioRxiv2021

Joint identification of sex and sex-linked scaffolds in non-model organisms using low depth sequencing data

Being able to assign sex to individuals and identify autosomal and sex-linked scaffolds are essential in most population genomic analyses. Non-model organisms often have genome assemblies at scaffold level and lack characterization of sex-linked scaffolds. Previous methods to identify sex and sex-linked scaffolds have relied on e.g. sequence similarity between the non-model organism and a closely related species or prior knowledge about the sex of the samples to identify sex-linked scaffolds. In the latter case, the difference in depth of coverage between the autosomes and the sex chromosomes are used. Here we present Sex Assignment Through Coverage (SATC), a method to identify sample sex and sex-linked scaffolds from NGS data. The method only requires a scaffold level reference assembly and sampling of both sexes with whole genome sequencing (WGS) data. We use the sequencing depth distribution across scaffolds to jointly identify: i) male and female individuals and ii) sex-linked scaffolds. This is achieved through projecting the scaffold depths into a low-dimensional space using principal component analysis (PCA) and subsequent Gaussian mixture clustering. We demonstrate the applicability of our method using data from five mammal species and a bird species complex. The method is open source and freely available at https://github.com/popgenDK/SATC

evolutionary biology↗