Natural selection on feralization genes contributed to the invasive spread of wild pigs throughout the United States.

Despite a long presence in the contiguous United States (US), the distribution of invasive wild pigs (Sus scrofa × domesticus) has expanded rapidly since the 1980s, suggesting a more recent evolutionary shift towards greater invasiveness. Contemporary populations of wild pigs represent exoferal hybrid descendants of domestic pigs and European wild boar, with such hybridization expected to enrich genetic diversity and increase the adaptive potential of populations. Our objective was to characterize how genetic enrichment through hybridization increases the invasiveness of populations by identifying signals of selection and the ancestral origins of selected loci. Our study focused on invasive wild pigs within Great Smoky Mountains National Park, which represents a hybrid population descendent from the admixture of established populations of feral pigs and an introduction of European wild boar to North America. Accordingly, we genotyped 881 wild pigs with multiple high-density single-nucleotide polymorphism (SNP) arrays. We found 233 markers under putative selection spread over 79 regions across 16 out of 18 autosomes, which contained genes involved in traits affecting feralization. Among these, genes were found to be related to skull formation and neurogenesis, with two genes, TYRP1 and TYR, also encoding for crucial melanogenesis enzymes. The most common haplotypes associated with regions under selection for the Great Smoky Mountains population were also common among other populations throughout the region, indicating a key role of putatively selective variants in the fitness of invasive populations. Interestingly, many of these haplotypes were absent among European wild boar reference genotypes, indicating feralization through genetic adaptation.

Population genomics provide insight into ancestral relationships and diversity of the feral horses of Theodore Roosevelt National Park.

Theodore Roosevelt National Park (TRNP) manages a herd of feral horses (Equus caballus) which was present on the landscape prior to the establishment of the park. The population presents a unique scenario in that it has experienced fairly intensive and well-documented management since the park's establishment, including herd size reductions, intentional introduction of diversity, and subsequent attempts to remove introduced lineages. This provides an interesting case study on the genetic effects of diverse evolutionary forces on an isolated feral population. To explore the effects of these forces and clarify the relationship of this feral herd with other horses, we used genome-wide markers to examine the population structure of a combined dataset containing common established breeds. Using the Illumina Equine 70k BeadChip, we sampled SNPs across the genome for 118 TRNP horses and evaluated the inbreeding coefficient f and runs of homozygosity (RoH). To identify breed relationships, we compared 23 representative TRNP samples with 792 horses from 35 different breeds using genomic population structure analyses. Mean f of TRNP horses was 0.180, while the mean f for all other breeds in the dataset was 0.116 (SD 0.079). RoH analysis indicates that the TRNP population has experienced recent inbreeding in a timeframe consistent with their management. With Bayesian clustering, PCA, and maximum likelihood phylogeny, TRNP horses show genetic differentiation from other breeds, likely due to isolation, historical population bottlenecks, and genetic drift. However, maximum likelihood phylogeny places them with moderate confidence (76.8%) among draft breeds, which is consistent with the known history of breeds used on early North Dakota ranches and stallions subsequently introduced to the park herd. These findings will help resolve speculation about the origins of the herd and inform management decisions for the TRNP herd.

Chromosome-level reference genome for North American bison (Bison bison) and variant database aids in identifying albino mutation.

We developed a highly contiguous chromosome-level reference genome for North American bison to provide a platform to evaluate the conservation, ecological, evolutionary, and population genomics of this species. Generated from a F1 hybrid between a North American bison dam and a domestic cattle bull, completeness and contiguity exceed that of other published bison genome assemblies. To demonstrate the utility for genome-wide variant frequency estimation, we compiled a genomic variant database consisting of 3 true albino bison and 44 wild-type pelage color bison. Through the examination of genomic variants fixed in the albino cohort and absent in the controls, we identified a nonsynonymous single nucleotide polymorphism (SNP) mutation on chromosome 29 in exon 3 of the tyrosinase gene (c.1114C>T). A TaqMan SNP Genotyping Assay was developed to genotype this SNP in a total of 283 animals across 29 herds. This assay confirmed the absence of homozygous variants in all animals except 7 true albino bison included in this study. In addition, the only heterozygous animals identified were 2 wild-type pelage color dams of albino offspring. Therefore, we propose that this new high-quality bison genome assembly and incipient variant database provides a highly robust and informative resource for genomics investigations for this iconic North American species.

Mitogenomes revealed the history of bison colonization of Northern Plains after the Last Glacial Maximum.

American bison demonstrated differential patterns of extinction, survival, and expansion since the terminal Pleistocene. We determined population dynamics of the Northern Great Plains bison using 40 mitochondrial genomes from radiocarbon dated remains with the age ranging from 12,226 to 167 calibrated years before present. Population dynamics correlated with environmental and anthropogenic factors and was characterized by three primary periods: terminal Pleistocene population growth starting 14,000 years ago, mid Holocene demographic stability between 6700 and 2700 years ago, and late Holocene population decline in the last 2700 years. Most diversification of mtDNA haplotypes occurred in the early Holocene when bison colonized new territories opened by retreating ice sheets. Holocene mtDNA lineages were not found in modern bison and lacked association with archaeological sites and morphological forms.

Major locus on ECA18 influences effectiveness of GonaCon vaccine in feral horses.

Contraceptive vaccines are used to reduce birth rates in wild and feral animal populations. While the immunocontraceptive GonaCon-Equine has proven effective in reducing fertility among female feral horses, there is individual variation in the duration of infertility following treatment. To identify genetic factors influencing the effectiveness of GonaCon-Equine, we conducted a genome-wide association study of 88 mares from a feral population genotyped using the Illumina GGP Equine 70k SNP array. Contraceptive treatment schedules and long-term foaling rates have been recorded for each individual. We used mixed linear models to control for relatedness among mares. We found a significant association (p < 5 ×10-8) with a locus on equine chromosome 18. The most likely candidate genes in this region are STAT1 and STAT4, which are both involved in immune system function. Variation in STAT function could affect the immune response to the vaccine, leading to variation in contraceptive efficacy. Additional SNPs reaching a less stringent threshold of significance (p < 5 ×10-6) were located on other chromosomes near known immune system genes, supporting the hypothesis that variation in immunocontraceptive efficacy can be attributed to genetic variation in immune response rather than fertility genes.

Genetic variation of the mitochondrial DNA control region across plains bison herds in USA and Canada.

Once numbering in the tens of millions, bison (Bison bison) have faced a broad range of challenges over the past century, including genetic impacts from the population bottleneck in the 1800s, and significant loss and fragmentation of habitat resulting in little opportunity for population growth on remaining small, geographically isolated reserves. To identify best practices for bison stewardship against this backdrop, managers must understand the genetic composition of existing conservation herds. This study characterized 14 plains bison (Bison bison bison) herds managed by the U.S. Department of Interior and Parks Canada Agency based on complete mtDNA control region sequences. Among 209 bison, we detected 11 major mtDNA control region haplotypes based on nucleotide substitutions and 23 sub-haplotypes where indels are considered. We determined matrilineal relationships between the herds and compared our genetic findings to historic records. The recent common ancestry of modern bison deriving from small, scattered groups combined with gene flow through foundation and translocation events between herds during the last 100 years, is reflected in Fst value (0.21), haplotype (0.48 ± 0.04) and nucleotide (0.004 ± 0.002) diversities, and mean number of pairwise differences (3.38 ± 1.74). Genetic diversity was distributed unevenly among herds, with 21.41% of genetic variation observed between herds. Median joining network, together with trends in the Tajima's D and Fs tests, revealed two patterns in the recent evolution of mtDNA sequences in bison: mutational process has generated diversity with a Hap 1 haplotype epicenter, and missed mtDNA haplotypes exist in the network due to bottleneck, loss through management practices, or incomplete sampling of specimens across conservation herds. This work significantly expands characterization of the genetic diversity among bison conservation herds, providing additional decision support for managers considering restoring gene flow to achieve long-term species viability.

Isotopic paleoecology of Northern Great Plains bison during the Holocene.

Bison (Bison bison) are one of the few terrestrial megafauna to survive the transition into the Holocene and provide a unique opportunity to study a species on a broad spatiotemporal scale. Today, bison are primarily managed in small and isolated herds with little known about their ancestral ecology. We studied the carbon and nitrogen isotopes of Northern Great Plains bison from the terminal Pleistocene and throughout the Holocene to gain insight into their paleoecology. This time span is contemporary with the first population bottleneck experienced by bison at the end of the Pleistocene and includes the second bottleneck which occurred in the late 19th century. Results were compared with modern bison herd isotopic values from Theodore Roosevelt National Park (TRNP). Patterns of isotopic variation found in bison over time indicate significant (δ13C p = 0.0008, δ15N p = 0.002) differences in diet composition and correlate with climate throughout the Holocene. Isotopic relationships described here reveal the plasticity of ancient bison in unrestricted rangelands during periods of climatic fluctuations. Managers at TRNP and elsewhere should pursue opportunities to expand bison range to maximize forage opportunities for the species in the face of future environmental change.

Genetic diversity and origin of the feral horses in Theodore Roosevelt National Park.

Feral horses in Theodore Roosevelt National Park (TRNP) represent an iconic era of the North Dakota Badlands. Their uncertain history raises management questions regarding origins, genetic diversity, and long-term genetic viability. Hair samples with follicles were collected from 196 horses in the Park and used to sequence the control region of mitochondrial DNA (mtDNA) and to profile 12 autosomal short tandem repeat (STR) markers. Three mtDNA haplotypes found in the TRNP horses belonged to haplogroups L and B. The control region variation was low with haplotype diversity of 0.5271, nucleotide diversity of 0.0077 and mean pairwise difference of 2.93. We sequenced one mitochondrial genome from each haplotype determined by the control region. Two complete mtDNA sequences of haplogroup L were closely related to the mtDNA of American Paint horse. The TRNP haplotype B did not have close matches in GenBank. The phylogenetic test placed this sequence in a group consisting of two horses from China, one from Yakutia, and one from Italy raising a possibility of historical transportation of horses from Siberia and East Asia to North America. Autosomal STR loci were polymorphic and indicated that the TRNP horses were distinctly different from 48 major horse breeds. Heterozygosity, mean number of alleles, and other measures of diversity indicated that TRNP herd diversity was below that observed for most other feral herds and domestic breeds. Both mtDNA and STRs demonstrated that the existing genetic data sets of horses are insufficient to determine the exact origins of the TRNP horses. However, measures of nuclear and mitochondrial diversity have elucidated management needs. It is recommended that new genetic stock be introduced and that adaptive management principles are employed to ensure that unique mitochondrial lineages are preserved and genetic diversity is increased and maintained over time.

Reimmunization increases contraceptive effectiveness of gonadotropin-releasing hormone vaccine (GonaCon-Equine) in free-ranging horses (Equus caballus): Limitations and side effects.

Wildlife and humans are increasingly competing for resources worldwide, and a diverse, innovative, and effective set of management tools is needed. Controlling abundance of wildlife species that are simultaneously protected, abundant, competitive for resources, and in conflict with some stakeholders but beloved by others, is a daunting challenge. Free-ranging horses (Equus caballus) present such a conundrum and managers struggle for effective tools for regulating their abundance. Controlling reproduction of female horses presents a potential alternative. During 2009-2017, we determined the long-term effectiveness of GnRH vaccine (GonaCon-Equine) both as a single immunization and subsequent reimmunization on reproduction and side effects in free-ranging horses. At a scheduled management roundup in 2009, we randomly assigned 57 adult mares to either a GonaCon-Equine treatment group (n = 29) or a saline control group (n = 28). In a second roundup in 2013, we administered a booster vaccination to these same mares. We used annual ground observations to estimate foaling proportions, social behaviors, body condition, and injection site reactions. We found this vaccine to be safe for pregnant females and neonates, with no overt deleterious behavioral side effects during the breeding season. The proportion of treated mares that foaled following a single vaccination was lower than that for control mares for the second (P = 0.03) and third (P = 0.08) post-treatment foaling seasons but was similar (P = 0.67) to untreated mares for the fourth season, demonstrating reversibility of the primary vaccine treatment. After two vaccinations, however, the proportion of females giving birth was lower (P <0.001) than that for control mares for three consecutive years and ranged from 0.0-0.16. The only detectable adverse side effect of vaccination was intramuscular swelling at the vaccination site. Regardless of vaccine treatment (primary/secondary), approximately 62% (34/55) of immunized mares revealed a visible reaction at the vaccine injection site. However, none of these mares displayed any evidence of lameness, altered gait or abnormal range of movement throughout the 8 years they were observed in this study. Our research suggests that practical application of this vaccine in feral horses will require an initial inoculation that may provide only modest suppression of fertility followed by reimmunization that together could result in greater reduction in population growth rates over time.