Conservation Genomics Research Articles

Diverse data sources and new statistical models offer prospects for improving the predictability of anthropogenic hybridization.

Human disturbance can theoretically influence the rates of hybridization, but few studies have convincingly identified a causal link. Grabenstein et al. (2022) used a genomic and phenotypic study of chickadees to associate hybridization with human disturbance. Additionally, this is consistent with citizen science reports of chickadee hybrids across the range. We highlight the exciting aspects of this work and make suggestions about a role for broad geographic and genomic sampling, and new statistical methods to better connect hybridization outcomes to anthropogenic disturbance in diverse study systems.

Towards a Genetic Linkage Map of the California Condor, an Endangered New World Vulture Species.

The development of a linkage map is an important component for promoting genetic and genomic studies in California condors, an endangered New World vulture species. Using a set of designed anonymous microsatellite markers, we genotyped a reference condor population involving 121 individuals. After marker validation and genotype filtering, the genetic linkage analysis was performed using 123 microsatellite loci. This resulted in the identification of 15 linkage groups/subgroups that formed a first-generation condor genetic map, while no markers linked to a lethal chondrodystrophy mutation were found. A panel of polymorphic markers that is instrumental in molecular parentage diagnostics and other genetic studies in the California condor was selected. Further condor conservation genomics research will be focused on updating the linkage map and integrating it with cytogenetic and BAC-based physical maps and ultimately with the genome sequence assembly.

Reference genome of the Monkeyface Prickleback, Cebidichthys violaceus.

Pricklebacks (Family Stichaeidae) are generally cold-temperate fishes most commonly found in the north Pacific. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Monkeyface Prickleback, Cebidichthys violaceus, to establish a genomic model for understanding phylogeographic patterns of marine organisms in California. These patterns, in turn, may inform the design of marine protected areas using dispersal models based on forthcoming population genomic data. The genome of C. violaceus is typical of many marine fishes at less than 1 Gb (genome size = 575.6 Mb), and our assembly is near-chromosome level (contig N50 = 1 Mb, scaffold N50 = 16.4 Mb, BUSCO completeness = 93.2%). Within the context of the CCGP, the genome will be used as a reference for future whole genome resequencing projects, enhancing our knowledge of the population structure of the species and more generally, the efficacy of marine protected areas as a primary conservation tool across California's marine ecosystems.

Conservation and the genomics of populations, 3rd edition, Allendorf F. W., Funk W. C., Aitken S. N., Byrne M., Luikart G.

Conservation and the genomics of populations, 3rd edition, Allendorf F. W., Funk W. C., Aitken S. N., Byrne M., Luikart G.

Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec.

The loss of genetic diversity is a challenge many species are facing, with genomics being a potential tool to inform and prioritize decision-making. Most caribou (Rangifer tarandus) populations have experienced significant recent declines throughout Québec, Canada, and are considered of concern, threatened or endangered. Here, we calculated the ancestral and contemporary patterns of genomic diversity of five representative caribou populations and applied a comparative population genomics framework to assess the interplay between demographic events and genomic diversity. We first calculated a caribou specific mutation rate, μ, by extracting orthologous genes from related ungulates and estimating the rate of synonymous mutations. Whole genome re-sequencing was then completed on 67 caribou: from these data we calculated nucleotide diversity, θ π and estimated the coalescent or ancestral effective population size (N e), which ranged from 12,030 to 15,513. When compared to the census size, N C, the endangered Gaspésie Mountain caribou population had the highest ancestral N e:N C ratio which is consistent with recent work suggesting high ancestral N e:N C is of conservation concern. In contrast, values of contemporary N e, estimated from linkage-disequilibrium, ranged from 11 to 162, with Gaspésie having among the highest contemporary N e:N C ratio. Importantly, classic conservation genetics theory would predict this population to be of less concern based on this ratio. Interestingly, F varied only slightly between populations, and despite evidence of bottlenecks across the province, runs of homozygosity were not abundant in the genome. Tajima's D estimates mirrored the demographic models and current conservation status. Our study highlights how genomic patterns are nuanced and potentially misleading if viewed only through a contemporary lens; we argue a holistic conservation genomics view should integrate ancestral N e and Tajima's D into management decisions.

Conservation Genomic Analysis of the Asian Honeybee in China Reveals Climate Factors Underlying Its Population Decline.

Simple SummaryThe Asian honeybee is an important pollinator in Asia that plays a vital role in maintaining biodiversity. Based on field surveys and personal observations, Asian honeybee populations in China were reported to be undergoing significant decline in 2005. However, a more recent survey revealed that its populations are stable and even slightly increased in some regions of China. Therefore, the status of declining Asian honeybee populations in China is still unclear. In this study, taking advantage of the abundant genomic data for Asian honeybees, we employed conservation genomics methods to understand the declining status of Asian honeybee populations in China and identify the causing factors. We found that most of the Asian honeybee populations of China showed a relatively stable population size during recent years, however, the population in Bomi, Tibet was in a serious decline and low temperatures and strong ultraviolet radiation should have synergistically led to this decline. Our study provides insights into the dynamic changes of Asian honeybee populations in China and identifies climate factors that underlie its population decline, which are valuable for the conservation of this important pollinator.The Asian honeybee, Apis cerana, is one of the most important native pollinators in Asia. Asian honeybees were believed to be under significant decline in China based on a report in 2005. On the contrary, a recent survey revealed that Asian honeybee populations in China are stable and even slightly increased in some regions. Therefore, the declining status of A. cerana populations in China is still unclear. Taking advantage of the abundant, publicly available genomic data for Asian honeybees in China, we employed conservation genomics methods to understand if Asian honeybee populations in China are declining and what the underlying climate factors are. We reconstructed the changes of effective population size (Ne) within the recent past for 6 population groups of Asian honeybees and found out that only one of them (population in Bomi, Tibet) showed a consistently declining Ne from the last 100 generations to 25 generations. Selective sweep analysis suggests that genes related to the tolerance of low temperatures and strong ultraviolet radiation are under selection in the declining population, indicating that these two climate factors most likely underlie the decline of BM populations during the recent past. Our study provides insights into the dynamic changes of Asian honeybee populations in China and identifies climate factors that underlie its population decline, which is valuable for the conservation of this important pollinator.

A chromosome-level reference genome for the Versatile Fairy Shrimp, Branchinecta lindahli.

We present the novel reference genome of the Versatile Fairy Shrimp, Branchinecta lindahli. The Versatile Fairy Shrimp is a freshwater anostracan crustacean found across the western United States from Iowa to Oregon and from Alberta to Baja California. It is an ephemeral pool specialist, living in prairie potholes, irrigation ditches, tire treads, vernal pools, and other temporary freshwater wetlands. Anostracan fairy shrimp are facing global declines with 3 species in California on the Endangered Species list. This species was included in the California Conservation Genomics Project to provide an easily accessible reference genome, and to provide whole-genome resources for a generalist species, which may lead to new insights into Anostracan resiliency in the face of climate change. The final gapped genome comprises 15 chromosome-length scaffolds covering 98.63% of the 384.8 Mb sequence length, and an additional 55 unscaffolded contigs.

Reference genome of the color polymorphic desert annual plant sandblossoms, Linanthus parryae.

Sandblossoms, Linanthus parryae is a widespread annual plant species found in washes and sandy open habitats across the Mojave Desert and Eastern Sierra Nevada of California. Studies in this species have played a central role in evolutionary biology, serving as the first test cases of the shifting balance theory of evolution, models of isolation by distance, and metrics to describe the genetic structure of natural populations. Despite the importance of L. parryae in the development of landscape genetics and phylogeography, there are no genomic resources available for the species. Through the California Conservation Genomics Project, we assembled the first genome in the genus Linanthus. Using PacBio HiFi long reads and Hi-C chromatin conformation capture, we assembled 123 scaffolds spanning 1.51 Gb of the 1.96 Gb estimated genome, with a contig N50 of 18.7 Mb and a scaffold N50 of 124.8 Mb. This assembly, with a BUSCO completeness score of 88.7%, will allow us to revisit foundational ideas central to our understanding of how evolutionary forces operate in a geographic landscape. In addition, it will be a new resource to uncover adaptations to arid environments in the fragile desert habitat threatened by urban and solar farm development, climate change, and off-road vehicles.

Reference genome of the Woolly Sculpin, Clinocottus analis.

Sculpins (Family Cottidae) are generally cold-temperate intertidal reef fishes most commonly found in the North Pacific. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Woolly Sculpin, Clinocottus analis, to establish a genomic model for understanding phylogeographic structure of inshore marine taxa along the California coast. These patterns, in turn, should further inform the design of marine protected areas using dispersal models based on genomic data. The small genome of C. analis is typical of marine fishes at less than 1 Gb (genome size = 538 Mb), and our assembly is near-chromosome level (contig N50 = 9.1 Mb, scaffold N50 = 21 Mb, BUSCO completeness = 97.9%). Within the context of the CCGP, the Woolly Sculpin genome will be used as a reference for future whole-genome resequencing projects aimed at enhancing our knowledge of the population structure of the species, and efficacy of marine protected areas across the state.

Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern.

The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California's coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae.

Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus).

We live in a world characterized by biodiversity loss and global environmental change. The extinction of large carnivores can have ramifying effects on ecosystems like an uncontrolled increase in wild herbivores, which in turn can have knock‐on impacts on vegetation regeneration and communities. Cheetahs (Acinonyx jubatus) serve important ecosystem functions as apex predators; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human‐wildlife conflict and illegal trafficking, there are only approximately 7100 individuals remaining in nature. We present the most comprehensive genome‐wide analysis of cheetah phylogeography and conservation genomics to date, assembling samples from nearly the entire current and past species' range. We show that their phylogeography is more complex than previously thought, and that East African cheetahs (A. j. raineyi) are genetically distinct from Southern African individuals (A. j. jubatus), warranting their recognition as a distinct subspecies. We found strong genetic differentiation between all classically recognized subspecies, thus refuting earlier findings that cheetahs show only little differentiation. The strongest differentiation was observed between the Asiatic and all the African subspecies. We detected high inbreeding in the Critically Endangered Iranian (A. j. venaticus) and North‐western (A. j. hecki) subspecies, and show that overall cheetahs, along with snow leopards, have the lowest genome‐wide heterozygosity of all the big cats. This further emphasizes the cheetah's perilous conservation status. Our results provide novel and important information on cheetah phylogeography that can support evidence‐based conservation policy decisions to help protect this species. This is especially relevant in light of ongoing and proposed translocations across subspecies boundaries, and the increasing threats of illegal trafficking.

Reference Genome of the Black Surfperch, Embiotoca jacksoni (Embiotocidae, Perciformes), a California Kelp Forest Fish That Lacks a Pelagic Larval Stage.

Surfperches (Family Embiotocidae) are viviparous temperate reef fishes that brood their young. This life history trait translates into limited dispersal, strong population structure, and an unusually strong potential for local adaptation in a marine fish. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Black Surfperch, Embiotoca jacksoni, to establish a genomic model for understanding phylogeographic patterns of marine organisms in California. These patterns, in turn, may inform the design of marine protected areas using dispersal models based on genomic data. The genome of E. jacksoni is typical of marine fishes at less than 1Gb (genome size = 635 Mb), and our assembly is near-chromosome level (contig N50 = 6.5Mb, scaffold N50 = 15.5 Mb, BUSCO = 98.1%). Within the context of the CCGP, the genome will be used as a reference for future whole genome resequencing projects aimed at enhancing our knowledge of the population structure of the species, and efficacy of Marine Protected Areas across the state.

Reference Genome of the California Sheephead, Semicossyphus pulcher (Labridae, Perciformes), A Keystone Fish Predator in Kelp Forest Ecosystems.

Keystone species are known to play a critical role in kelp forest health, including the well-known killer whales, sea otter, sea urchin, kelp trophic cascade in the Aleutian Islands, Alaska, USA. In California, a major player in the regulation of sea urchin abundance, and in turn, the health of kelp forests ecosystems, is a large wrasse, the California Sheephead, Semicossyphus pulcher. We present a reference genome for this ecologically important species that will serve as a key resource for future conservation research of California's inshore marine environment utilizing genomic tools to address changes in life-history traits, dispersal, range shifts, and ecological interactions among members of the kelp forest ecological assemblages. Our genome assembly of S. pulcher has a total length of 0.794 Gb, which is similar to many other marine fishes. The assembly is largely contiguous (N50 = 31.9 Mb) and nearly complete (BUSCO single-copy core gene content = 98.1%). Within the context of the California Conservation Genomics Project (CCGP), the genome of S. pulcher will be used as an important reference resource for ongoing whole genome resequencing efforts of the species.

The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation

Microsatellites are one of the important genome characterizations that can be a valuable resource for variety identification, genetic diversity, phylogenetic analysis, as well as comparative and conservation genomics research. Here, we developed comprehensive microsatellites through genome-wide mining for the threatened cetacean Indo-Pacific humpback dolphin (Sousa chinensis). We found 87,757 microsatellites with 2–6 bp nucleotide motifs, showing that about 32.5 microsatellites per megabase comprises microsatellites sequences. Approximately 97.8% of the markers developed in this study were consistent with the published identified markers. About 75.3% microsatellites were with dinucleotide motifs, followed by tetranucleotide motifs (17.4%), sharing the same composition pattern as other cetaceans. The microsatellites were not evenly distributed in the S. chinensis genome, mainly in non-coding regions, with only about 0.5% of the markers located in coding regions. The microsatellite-containing genes were mainly functionally enriched in the methylation process, probably demonstrating the potential impacts of microsatellites on biological functions. Polymorphic microsatellites were developed between different genders of S. chinensis, which was expected to lay the foundation for genetic diversity investigation in cetaceans. The specific markers for a male Indo-Pacific humpback dolphin will provide comprehensive and representative male candidate markers for sex identification, providing a potential biomolecular tool for further analysis of population structure and social behavior of wild populations, population trend evaluation, and species conservation management.

A Reference Genome Assembly of the Bobcat, Lynx rufus.

The bobcat (Lynx rufus) is a medium-sized carnivore well adapted to various environments and an indicator species for landscape connectivity. It is one of the 4 species within the extant Lynx genus in the family Felidae. Because of its broad geographic distribution and central role in food webs, the bobcat is important for conservation. Here we present a high-quality de novo genome assembly of a male bobcat located in Mendocino County, CA, as part of the California Conservation Genomics Project (CCGP). The assembly was generated using the standard CCGP pipeline from a combination of Omni-C and HiFi technologies. The primary assembly comprises 76 scaffolds spanning 2.4 Gb, represented by a scaffold N50 of 142 Mb, a contig N50 of 66.2 Mb, and a BUSCO completeness score of 95.90%. The bobcat genome will be an important resource for the effective management and conservation of this species and comparative genomics exploration.

Reference Genome of the Northwestern Pond Turtle, Actinemys marmorata.

The northwestern pond turtle, Actinemys marmorata, and its recently recognized sister species, the southwestern pond turtle, A. pallida, are the sole aquatic testudines occurring over most of western North America and the only living representatives of the genus Actinemys. Although it historically ranged from Washington state through central California, USA, populations of the northwestern pond turtle have been in decline for decades and the species is afforded state-level protection across its range; it is currently being considered for protection under the US Endangered Species Act. Here, we report a new, chromosome-level assembly of A. marmorata as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 198 scaffolds spanning 2,319,339,408 base pairs, has a contig N50 of 75 Mb, a scaffold N50 of 146Mb, and BUSCO complete score of 96.7%, making it the most complete testudine assembly of the 24 species from 13 families that are currently available. In combination with the A. pallida reference genome that is currently under construction through the CCGP, the A. marmorata genome will be a powerful tool for documenting landscape genomic diversity, the basis of adaptations to salt tolerance and thermal capacity, and hybridization dynamics between these recently diverged species.

Evolutionary Conservation Genomics Reveals Recent Speciation and Local Adaptation in Threatened Takins.

Incorrect species delimitation will lead to inappropriate conservation decisions, especially for threatened species. The takin (Budorcas taxicolor) is a large artiodactyl endemic to the Himalayan–Hengduan–Qinling Mountains and is well known for its threatened status and peculiar appearance. However, the speciation, intraspecies taxonomy, evolutionary history, and adaptive evolution of this species still remain unclear, which greatly hampers its scientific conservation. Here, we de novo assembled a high-quality chromosome-level genome of takin and resequenced the genomes of 75 wild takins. Phylogenomics revealed that takin was positioned at the root of Caprinae. Population genomics based on the autosome, X chromosome, and Y chromosome SNPs and mitochondrial genomes consistently revealed the existence of two phylogenetic species and recent speciation in takins: the Himalayan takin (B. taxicolor) and the Chinese takin (B. tibetana), with the support of morphological evidence. Two genetically divergent subspecies were identified in both takin species, rejecting three previously proposed taxonomical viewpoints. Furthermore, their distribution boundaries were determined, suggesting that large rivers play important roles in shaping the genetic partition. Compared with the other subspecies, the Qinling subspecies presented the lowest genomic diversity, higher linkage disequilibrium, inbreeding, and genetic load, thus is in urgent need of genetic management and protection. Moreover, coat color gene (PMEL) variation may be responsible for the adaptive coat color difference between the two species following Gloger’s rule. Our findings provide novel insights into the recent speciation, local adaptation, scientific conservation of takins, and biogeography of the Himalaya–Hengduan biodiversity hotspot.

The First Genome of the Balearic Shearwater (Puffinus mauretanicus) Provides a Valuable Resource for Conservation Genomics and Sheds Light on Adaptation to a Pelagic lifestyle.

The Balearic shearwater (Puffinus mauretanicus) is the most threatened seabird in Europe and a member of the most speciose group of pelagic seabirds, the order Procellariiformes, which exhibit extreme adaptations to a pelagic lifestyle. The fossil record suggests that human colonisation of the Balearic Islands resulted in a sharp decrease of the Balearic shearwater population size. Currently, populations of the species continue to be decimated mainly due to predation by introduced mammals and bycatch in longline fisheries, with some studies predicting its extinction by 2070. Here, using a combination of short and long reads, we generate the first high-quality reference genome for the Balearic shearwater, with a completeness amongst the highest across available avian species. We used this reference genome to study critical aspects relevant to the conservation status of the species and to gain insights into the adaptation to a pelagic lifestyle of the order Procellariiformes. We detected relatively high levels of genome-wide heterozygosity in the Balearic shearwater despite its reduced population size. However, the reconstruction of its historical demography uncovered an abrupt population decline potentially linked to a reduction of the neritic zone during the Penultimate Glacial Period (∼194–135 ka). Comparative genomics analyses uncover a set of candidate genes that may have played an important role into the adaptation to a pelagic lifestyle of Procellariiformes, including those for the enhancement of fishing capabilities, night vision, and the development of natriuresis. The reference genome obtained will be the crucial in the future development of genetic tools in conservation efforts for this Critically Endangered species.

Conservation genomics in practice.

Securing biodiversity takes many measures, including the involvement of Indigenous peoples.

Combining citizen science and conservation genomics to reveal the causes of rapid population decline in the Garden Dormouse (Eliomys quercinus)

The Garden Dormouse (Eliomys quercinus) is a native European rodent species that has suffered extensive range contraction and severe population decline across large parts of its distribution in Central and Eastern Europe and is now considered extinct in several countries. At the same time, contrasting population dynamics are observed in its western distribution, where Garden Dormice are regionally abundant and even occupy habitats in the built environment. Reasons for these opposing range dynamics and drastic declines remain unknown. We therefore started a long-term cooperation project, joining the efforts of different research institutions, conservation NGOs and citizen scientists to investigate the underlying causes. Here, we present the results of a RADseq analysis of 103 samples collected from several parts of the European species range to infer regional phylogeography and delineate different conservation units. Preliminary genomic data show the existence of highly divergent genetic lineages, even on a local scale. Based on these findings, we have developed a reduced SNP panel, which allows for lineage discrimination, assessment of population structure and identification of individuals from non-invasively collected samples. The panel is now routinely applied in Garden Dormouse conservation, e.g., when selecting appropriate locations to release displaced Garden Dormice found accidentally or to identify isolated Garden Dormouse populations in need of improved habitat connectivity.