Genome-wide diversity in the California condor tracks its prehistoric abundance and decline

Abstract

Highlights d The de novo California condor genome assembly is complete and contiguous d Runs of homozygosity in California condor genomes reveal inbreeding in the wild d Genome-wide diversity suggests California condors were historically abundant d Andean condor and turkey vulture genomes also reveal historic declines

Facultative Parthenogenesis in California Condors

“… Card et al (2021) provided evidence for terminal automixis fusion in the king cobra utilizing genome-wide data from reduced representation sequencing. The use of the recently published chromosome-level reference genome of the California condor ( Robinson et al 2021 ) and genome re-sequencing efforts can map genetic variation genome-wide to evaluate the mechanism of parthenogenesis in this species.…”

“…Genetic analysis of museum specimens could also shed light on this question and assist in understanding the evolution of facultative parthenogenesis, its genetic basis, and contribute to comprehending the levels of genetic variation in the recovering California condor population. Additionally, the use of the high-quality reference genome for the California condor ( Robinson et al 2021 ) and generation of genomic sequence data at the population level will allow validating the parthenogenetic observations made based on microsatellite data.…”

New developments in the field of genomic technologies and their relevance to conservation management

“…For many species of conservation concern, such information is either missing or incomplete, and genomics has proven key in filling knowledge gaps (e.g. Frandsen et al 2020;Robinson et al 2021a) and delineating management units (Barbosa et al 2018) starting from almost any type of sample (e.g. museum collections and biobanks; Baveja et al 2020).…”

The relevance of pedigrees in the conservation genomics era.

“…Pedigree data is also an invaluable resource for selecting individuals for resequencing (i.e., whole genome resequencing, or WGS). For example, a pedigree can inform the choice of closely related family groups for genomic inquiry (e.g., Galla et al, 2020), understanding characterized phenotypes of interest (Nersisyan, Nikoghosyan, & Arakelyan, 2019), or when maximizing representative genomic diversity across a species (Robinson et al, 2021). In the case of sable antelope (Hippotragus niger ; Gooley et al, 2020) the software program PedSam (https://sites.uwm.edu/latch/software-2/) was used to streamline the selection of individuals representative of founder diversity across many managed populations for downstream diversity comparisons.…”

“…In the case of sable antelope (Hippotragus niger ; Gooley et al, 2020) the software program PedSam (https://sites.uwm.edu/latch/software-2/) was used to streamline the selection of individuals representative of founder diversity across many managed populations for downstream diversity comparisons. In a recent study in California condors, individuals with low inbreeding and kinship coefficients were selected using the pedigree, and were compared in terms of runs of homozygosity using WGS (Robinson et al, 2021). When familial relationships are known via pedigrees, this information can also be used to validate whether molecular genetic and genomic approaches (e.g., extraction, amplification, library preparation, or sequencing) produce data that are consistent with biologically-relevant expectations or experienced error along the way (see Galla et al, 2020 for details).…”