Samuel Sacco

Allegations that Thomas Jefferson fathered the children of the enslaved Sally Hemings emerged in the context of U.S. presidential politics in the late 1700s and early 1800s and entailed strongly contested denials and affirmations by family members, biographers, and historians ever since. Previous analysis of Y chromosome markers in contemporary members of the Jefferson and Hemings patrilines was consistent with the paternity hypothesis but rejected by those who pointed out that, absent Jefferson’s DNA and its direct comparison to the DNA of possible descendants, other Jefferson males could have fathered Sally Hemings’ children. In this study, we developed an innovative technique to recover DNA from multiple rootless hair samples in a museum collection whose provenance, mitochondrial genomes, Y chromosome markers, and identity to each other indicate that these hairs and the DNA from them are from Thomas Jefferson. Using these DNA data, we find clear evidence of Thomas Jefferson ancestry in descendants of both his wife Martha Wayles Jefferson and Sally Hemings. We measured the amount of identical-by-descent DNA shared between Thomas Jefferson and his known and putative descendants. We find that the amount of shared Jefferson DNA is more likely under the model of direct Thomas Jefferson paternity than other proposed scenarios.

We present a reference genome assembly for the trapdoor spider Aptostichus stephencolberti. This species, described in 2008, is endemic to the highly fragmented coastal dune habitats of Northern California from Monterey to the San Francisco Bay Area. Trapdoor spiders are ideal taxa for landscape scale genomic studies owing to their extreme site fidelity and limited dispersal capabilities; these same characteristics make them prone to extinction. Genomic studies of species like A. stephencolberti can reveal novel areas of endemism and high conservation value that may not be evident in species with wider ranges and greater dispersal capabilities. As part of the California Conservation Genomics Project, we constructed the A. stephencolberti reference genome from high quality long-read sequences, scaffolded with proximity ligation Omni-C data. The primary assembly comprises 551 scaffolds spanning 3.63 Gbp, a scaffold N50 of 62.2 Mbp and BUSCO completeness of 95.6%. We estimate 52 chromosomes yet find no (TTAGG)n telomere repeats. Expanding the telomeric repeat search finds an ancestral loss of the repeat from all spiders. Automated annotation using the NCBI refseq pipeline and RNAseq data from whole adults finds 14,067 genes with a BUSCO annotation completeness of 95.56%. Repeat annotation identified 77% of the genome to be interspersed repeats. This resource, the first for family Euctenizidae will facilitate future study and resulting conservation actions of A. stephencolberti and other Aptostichus sp. populations associated with the rapidly changing California coastal dune ecosystem.

American bison ( Bison bison ) were nearly hunted to extinction by the 20th century. This rapid decline and the fragmented nature of remnant populations pose challenges to their recovery and resilience, as does human-facilitated admixture between bison subspecies and cattle ( Bos taurus ). To contextualize current diversity, we sequenced 115 ancient and 45 modern bison genomes from the past ~20,000 years. Our results show that past bison populations were connected, in contrast to structured modern herds. Modern wood bison ( B. b. athabascae ), a northerly distributed subspecies, carry plains bison ( B. b. bison ) ancestry from 1920s translocations, and many sampled bison lack cattle ancestry. Our findings reveal the legacy of human impacts on bison and highlight the applicability of ancient DNA for guiding wildlife restoration.

The speckled dace, Rhinichthys osculus, is a cyprinoid fish species complex (family: Leuciscidae) with one of the widest native ranges of any freshwater fish in western North America. It occupies a variety of freshwater habitats and exhibits considerable morphological and genetic variation across its range. Several endemic taxa within the species complex are imperiled, four of which are protected under the US Endangered Species Act, with two more proposed for listing. Here, we present an annotated, scaffold-level assembly of the speckled dace genome as part of the California Conservation Genomics Project (CCGP). Consistent with the CCGP genome assembly strategy, we used Pacific Biosciences HiFi long reads and Omni-C data for our de novo genome assembly and performed genome annotations on National Center for Biotechnology Information (NCBI) Eukaryotic Genome Annotation Pipeline using novel, species-specific RNA-Seq reads generated from five tissue types. The assembly consists of 490 scaffolds totaling approximately 1.15 Gb, with a contig N50 of 10.9 Mb and a scaffold N50 of 44.5 Mb. A BUSCO score of 97.7% reflects the assembly’s strong completeness. The genome of R. osculus is estimated to consist of 25 chromosomes. This is the first scaffold-level genome assembly within the genus Rhinichthys. We annotated a total of 39,919 genes with a BUSCO completeness score of 98.3%. This reference genome will be a valuable resource for understanding the phylogeography and evolution of speckled dace and informing its conservation.

We assembled and annotated a chromosome-level genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (quality value [QV] = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This genome assembly, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

We present genome assemblies for two cyprinoid fishes, the tui chub (Siphateles bicolor) and the arroyo chub (Gila orcuttii). These fishes are ecologically important representatives of native fish assemblages in the western United States and are both species of conservation concern. The two species hybridize where introductions bring them into contact, with potentially important ecological and evolutionary implications that have not yet been thoroughly examined from a genomic perspective. We present de novo assemblies for both species, representing the first scaffold-level genomes within their respective genera, which were developed as part of the California Conservation Genomics Project using Pacific Biosciences HiFi and Omni-C data. Our tui chub assembly consists of 258 scaffolds spanning 1,148,084,093 base pairs, has a scaffold N50 of 45.9 mb, a contig N50 of 23.7 mb, and a BUSCO completeness score of 98.1%. Our arroyo chub assembly consists of 179 scaffolds spanning 1,263,410,250 base pairs, has a scaffold N50 of 50.5 mb, a contig N50 of 13.1 mb, and a BUSCO completeness score of 97.8%. A comparative analysis of the two species revealed relatively conserved genomes, with the exception of two inversions at chromosome 20. We annotated a total of 34,090 genes with a BUSCO completeness score of 98.1% for the tui chub, and 28,193 genes with a score of 97.4% for the arroyo chub. These assemblies will be valuable resources for characterizing the species’ phylogeographic histories and delineating the role of hybridization in their evolution.

Reconstructions of evolutionary history can be restricted by a lack of high-quality reference genomes. To date, only four of the eight species of bears (family Ursidae) have chromosome-level genome assemblies. Here, we present assemblies for three additional species—the sun, sloth, and Andean bears—and use a whole-genome alignment of all bear species and other carnivores to reconstruct the evolution of Ursidae. Multiple divergence dating approaches suggest that the six Ursine bears likely diversified in the last 5 Ma, but that divergence times within Ursinae are significantly impacted by gene tree heterogeneity. Consistent with this, we observe that nearly 50% of gene trees conflict with our highly supported species tree, a pattern driven by a significant early hybridization event within Ursinae. We also find that the karyotype of Ursinae is largely similar to the ancestral karyotype of all bears twenty million years prior. In contrast to this conservation of structure, dozens of chromosomal fissions and fusions associated with LINE/L1 retrotransposons dramatically restructured the genomes of the giant panda and Andean bear. Finally, we leverage these genomes to identify species-specific evidence for positive selection on genes associated with color, diet, and metabolism. One of these genes, TCPN2, has a role in pigmentation and shows a series of amino acid mutations in the polar bear over the last 0.5 Ma. Collectively, these new genomic resources enable improved reconstruction of the complex evolutionary history of bears and clarify how this enigmatic group diversified.

Mule deer (Odocoileus hemionus) is an ecologically and economically important cervid species which is widely distributed across western North America. Their broad range and use of diverse habitats, including those linked to historical glacial refugia, have made them an ideal model for studying the effects of climatic fluctuations and environmental heterogeneity on lineage diversification. The effects of this complex evolutionary history on the genome are further complicated by evidence of hybridization with other members of the genus, leading to extreme cases of mito-nuclear discordance. More recently, the influence of specific gene variants on disease dynamics, particularly the progression and morbidity of chronic wasting disease, has become an important topic of genomic research for this taxon. Here, we present and evaluate a new chromosome-level genome assembly of a representative mule deer from across the species’ diverse range as part of the California Conservation Genomics Project. We assembled a genome de novo utilizing Pacific Biosciences HiFi long-read and Omni-C chromatin-proximity sequencing data. The assembly consisted of 814 scaffolds and 901 contigs representing a contig N50 of 46.68 Mb and a scaffold N50 of 63.29 Mb. Lastly, our benchmarking universal single-copy ortholog completeness score was 96.3%. This genome represents one of the most complete Odocoileus assemblies and will further our understanding of the comparative genomic architecture of cervids.

Advances in genomic studies are revealing that gene flow between species is more frequent than previously understood, although the ways in which hybridization can bias gene flow across species boundaries or the extent to which introgression might be adaptive remain unexplored in most systems. We report on an annotated chromosome-level genome assembly for the Gilbert’s skink, Plestiodon gilberti, one of 18 clades of reptiles and amphibians selected for reference genome sequencing in the California Conservation Genomics Project. This assembly was produced using Pacific Biosciences HiFi long reads and Omni-C proximity ligation data. Although members of the Scincidae comprise nearly one-quarter of all lizard species (1785 described species), this de novo assembly represents one of only 10 skink species globally and the first North American skink with a reference genome. The assembly has a total length of ~ 1.57 Gb, a scaffold N50 length of ~ 231.32 Mb, read coverage of ~56X, and BUSCO completeness score of 97.2% based on the Tetrapoda ortholog database. Plestiodon gilberti is a member of the Plestiodon skiltonianus species complex, a group with many of the characteristics of ecological speciation but where ancient hybridization and biased introgression present challenges to retracing the initial patterns of lineage divergence. Combined with dense sampling of resequenced genomes in the California Conservation Genomics Project, including other members of the P. skiltonianus complex, this reference genome will enable future analyses of the links between divergent selection and the genes underlying speciation, as well as the potential for introgression to enable adaptation to new or changing environments.

The flowering plant genus Aquilegia (columbine) is an important contributor to biodiversity and an example of both biotic and abiotic niche adaptation across much of the Northern Hemisphere, especially in California. Here we report a near-chromosome level draft genome assembly for A. eximia, a California endemic species. A. eximia is a serpentine-soil specialist and is very closely related to 2 columbine species also being studied for the California Conservation Genomics Project (CCGP), A. formosa (widespread) and A. pubescens (high alpine). Utilizing high throughput, long reads (PacBio) and chromatin capture (Omni-C), the A. eximia genome makes marked contiguity improvements compared to the existing reference genome for another North American columbine, A. coerulea “Goldsmith.” The A. eximia genome will also be more useful for aligning whole genome resequencing data from California columbines than the genomes for more distantly related columbine species, the Asian A. oxysepala var. kansuensis and the European A. vulgaris. Notably, we found evidence that A. eximia, A. coerulea “Goldsmith,” and A. vulgaris all share the same overall genome structure and differ from A. oxysepala var. kansuensis by the same reciprocal translocation. The A. eximia reference genome will be a valuable tool for identifying patterns of plant biodiversity across California for the CCGP, as well as for future population genomic and trait mapping studies.