Improved reference genome for the domestic horse increases assembly contiguity and composition

Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of non-N bases in the incorporated chromosomes is improved from 2.33 Gb in EquCab2 to 2.41 Gb in EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5 Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold

Improved reference genome for the domestic horse increases assembly contiguity and composition

Theodore Kalbfleisch et al. present an improved genome assembly for the domestic horse by combining short- and long-read data, as well as proximity ligation data. They improve contiguity of the assembly by 40-fold, with a 10-fold reduction in gaps

Dire wolves were the last of an ancient New World canid lineage

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently

A genomic approach to studying the evolutionary consequences of population declines

Since the release of the human genome sequence in 2003, decreasing costs of DNA sequencing and advances in laboratory techniques have allowed scientists to study demography, admixture, and evolution for a growing diversity of taxa beyond humans. The work I present in this dissertation is part of the continued expansion of genomics. In particular, I present the assembly and analysis of whole genome data of extant and extinct species to study the evolutionary processes and consequences of population reduction. My first chapter looks at the effects of habitat loss in the puma, whose range is the largest of any felid in the Western Hemisphere. I present a genome assembly of a puma from the Santa Cruz Mountains, and resequencing data for a panel of pumas from across their current range. I learn about the genomic health of the species, uncover Central American ancestry in present-day Florida pumas, and present a new model for the demographic history of the species.In my second chapter, I present an assembly of the genome of the sole bear species to inhabit South America, the spectacled bear. The spectacled bear is the closest living relative to the extinct giant short-faced bears that roamed North America during the last Ice Age. I use the genome of the spectacled bear as a reference for mapping the genome of the extinct giant short-faced bear, and analyze both genomes to learn their population histories and relationships to extant ursids. In my third chapter, I focus on another extinct bear, the California grizzly bear. Having gone extinct in the early 1900s due to overhunting, the California grizzly bear is an example of the detrimental results humans impose on their environment. Using genomic data from two preserved California grizzly bears, as well as the genomes of several modern brown bears, I characterize the genetic diversity among extant brown bears and explore the diversity of California grizzly bears. Together, the research that comprises my dissertation presents a significant contribution to the growing body of literature for non-model organisms and provides resources relevant to the conservation of top predators

A genomic approach to studying the evolutionary consequences of population declines

Since the release of the human genome sequence in 2003, decreasing costs of DNA sequencing and advances in laboratory techniques have allowed scientists to study demography, admixture, and evolution for a growing diversity of taxa beyond humans. The work I present in this dissertation is part of the continued expansion of genomics. In particular, I present the assembly and analysis of whole genome data of extant and extinct species to study the evolutionary processes and consequences of population reduction. My first chapter looks at the effects of habitat loss in the puma, whose range is the largest of any felid in the Western Hemisphere. I present a genome assembly of a puma from the Santa Cruz Mountains, and resequencing data for a panel of pumas from across their current range. I learn about the genomic health of the species, uncover Central American ancestry in present-day Florida pumas, and present a new model for the demographic history of the species.In my second chapter, I present an assembly of the genome of the sole bear species to inhabit South America, the spectacled bear. The spectacled bear is the closest living relative to the extinct giant short-faced bears that roamed North America during the last Ice Age. I use the genome of the spectacled bear as a reference for mapping the genome of the extinct giant short-faced bear, and analyze both genomes to learn their population histories and relationships to extant ursids. In my third chapter, I focus on another extinct bear, the California grizzly bear. Having gone extinct in the early 1900s due to overhunting, the California grizzly bear is an example of the detrimental results humans impose on their environment. Using genomic data from two preserved California grizzly bears, as well as the genomes of several modern brown bears, I characterize the genetic diversity among extant brown bears and explore the diversity of California grizzly bears. Together, the research that comprises my dissertation presents a significant contribution to the growing body of literature for non-model organisms and provides resources relevant to the conservation of top predators

Environmental genomics of Late Pleistocene black bears and giant short-faced bears

Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1–3 by allowing for parallel sequencing of DNA from all trophic levels.4–8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14–16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16–14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22–50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics