Mychajliw, A. M. | Search bioRxiv

bioRxiv2023

What does the fox (genome) say? A chromosome-level assembly for the gray fox (Urocyon cinereoargenteus)

Reference genome assemblies have been created from multiple lineages within the Canidae family, however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a contig N50 and scaffold N50 of 59.4 and 72.9 Megabases (Mb), respectively. Repeat analyses identified an increased number of simple repeats relative to other canids. Based on mitochondrial DNA, our Vermont sample clusters with other gray fox samples from the northeastern US and contains slightly lower levels of heterozygosity than gray foxes on the west coast of California. This new assembly lays the groundwork for future studies to describe past and present population dynamics, including the delineation of evolutionarily significant units of management relevance. Importantly, the phylogenetic position of Urocyon allows us to verify the loss of PRDM9 functionality in the basal canid lineage, confirming that pseudogenization occurred at least 10 million years ago.

genomics↗

bioRxiv2020

7,000 years of turnover: historical contingency and human niche construction shape the Caribbean's Anthropocene biota

The human-mediated movement of species across biogeographic boundaries--whether intentional or accidental--is dramatically reshaping the modern world. Yet, humans have been reshaping ecosystems and translocating species for millennia, and acknowledging the deeper roots of these phenomena is important for contextualizing present-day biodiversity loss, ecosystem functioning, and management needs. Here, we present the first database of terrestrial vertebrate species introductions spanning the entire anthropogenic history of a system: the Caribbean. We employ this ~7,000 year dataset to assess the roles of historical contingency and priority effects in shaping present-day community structure and conservation outcomes, finding that serial human colonization events contributed to habitat modifications and species extinctions that shaped the trajectories of subsequent species introductions by other human groups. We contextualized spatial and temporal patterns of species introductions within cultural practices and population histories of Indigenous, colonial, and modern human societies, and show that the taxonomic and biogeographic diversity of introduced species reflects diversifying reasons for species introductions through time. Recognition of the complex social and economic structures across the 7,000-year human history of the Caribbean provides the necessary context for interpreting the formation of an Anthropocene biota.

ecology↗