mtDNA heteroplasmy gives rise to a new maternal lineage in North Pacific humpback whales (Megaptera novaeangliae)Pierszalowski, Sophie P; Steel, Debbie J; Gabriele, Christine M; Neilson, Janet L; Vanselow, Phoebe B S; Cedarleaf, Jennifer A; Straley, Janice M; Baker, C Scott
doi: 10.1093/jhered/esac042pmid: 36146890
Heteroplasmy in the mitochondrial genome offers a rare opportunity to track the evolution of a newly arising maternal lineage in populations of non-model species. Here, we identified a previously unreported mitochondrial DNA haplotype while assembling an integrated database of DNA profiles and photo-identification records from humpback whales in southeastern Alaska (SEAK). The haplotype, referred to as A8, was shared by only 2 individuals, a mature female with her female calf, and differed by only a single base pair from a common haplotype in the North Pacific, referred to as A−. To investigate the origins of the A8 haplotype, we reviewed n = 1,089 electropherograms (including replicate samples) of n = 710 individuals with A− haplotypes from an existing collection. From this review, we found 20 individuals with clear evidence of heteroplasmy for A−/A8 (parental/derived) haplotypes. Of these, 15 were encountered in SEAK, 4 were encountered on the Hawaiian breeding ground (the primary migratory destination for whales in SEAK), and 1 was encountered in the northern Gulf of Alaska. We used genotype exclusion and likelihood to identify one of the heteroplasmic females as the likely mother of the A8 cow and grandmother of the A8 calf, establishing the inheritance and germ-line fixation of the new haplotype from the parental heteroplasmy. The mutation leading to this heteroplasmy and the fixation of the A8 haplotype provide an opportunity to document the population dynamics and regional fidelity of a newly arising maternal lineage in a population recovering from exploitation.
The impact of habitat loss on molecular signatures of coevolution between an iconic butterfly (Alcon blue) and its host plant (Marsh gentian)Warson, Jonas; Baguette, Michel; Stevens, Virginie M; Honnay, Olivier; De Kort, Hanne
doi: 10.1093/jhered/esac059pmid: 36749638
Habitat loss is threatening natural communities worldwide. Small and isolated populations suffer from inbreeding and genetic drift, which jeopardize their long-term survival and adaptive capacities. However, the consequences of habitat loss for reciprocal coevolutionary interactions remain poorly studied. In this study, we investigated the effects of decreasing habitat patch size and connectivity associated with habitat loss on molecular signatures of coevolution in the Alcon blue butterfly (Phengaris alcon) and its most limited host, the marsh gentian (Gentiana pneumonanthe). Because reciprocal coevolution is characterized by negative frequency-dependent selection as a particular type of balancing selection, we investigated how signatures of balancing selection vary along a gradient of patch size and connectivity, using single nucleotide polymorphisms (SNPs). We found that signatures of coevolution were unaffected by patch characteristics in the host plants. On the other hand, more pronounced signatures of coevolution were observed in both spatially isolated and in large Alcon populations, together with pronounced spatial variation in SNPs that are putatively involved in coevolution. These findings suggest that habitat loss can facilitate coevolution in large butterfly populations through limiting swamping of locally beneficial alleles by maladaptive ones. We also found that allelic richness (Ar) of the coevolutionary SNPs is decoupled from neutral Ar in the butterfly, indicating that habitat loss has different effects on coevolutionary as compared with neutral processes. We conclude that this specialized coevolutionary system requires particular conservation interventions aiming at generating a spatial mosaic of both connected and of isolated habitat to maintain coevolutionary dynamics.
A reference genome assembly of the declining tricolored blackbird, Agelaius tricolorBallare, Kimberly M; Escalona, Merly; Barr, Kelly; Seligmann, William; Sacco, Samuel; Sahasrabudhe, Ruta Madhusudan; Nguyen, Oanh; Wyckoff, Christy; Smith, Thomas B; Shapiro, Beth
doi: 10.1093/jhered/esac053pmid: 36099176
The tricolored blackbird, Agelaius tricolor, is a gregarious species that forms enormous breeding and foraging colonies in wetland and agricultural habitats, primarily in California, USA. Once extremely abundant, species numbers have declined dramatically in the past century, largely due to losses of breeding and foraging habitats. Tricolored blackbirds are currently listed as Endangered by the IUCN, and Threatened under the California Endangered Species Act. Increased genetic information is needed to detail the evolutionary consequences of a species-wide bottleneck and inform conservation management. Here, we present a contiguous tricolored blackbird reference genome, assembled with PacBio HiFi long reads and Dovetail Omni-C data to generate a scaffold-level assembly containing multiple chromosome-length scaffolds. This genome adds a valuable resource for important evolutionary and conservation research on tricolored blackbirds and related species.
Reference genome of the Monkeyface Prickleback, Cebidichthys violaceusWright, Daniel B; Escalona, Merly; Marimuthu, Mohan P A; Sahasrabudhe, Ruta; Nguyen, Oanh; Sacco, Samuel; Beraut, Eric; Toffelmier, Erin; Miller, Courtney; Shaffer, H Bradley; Bernardi, Giacomo; German, Donovan P
doi: 10.1093/jhered/esac054pmid: 36321765
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.
A high-quality genome assembly of the Laotian shad (Tenualosa thibaudeaui), an endemic species of the Mekong River BasinWang, Li; Lu, Liang; Sarker, Kishor Kumar; Li, Chenhong
doi: 10.1093/jhered/esac058pmid: 36223282
The Laotian shad (Tenualosa thibaudeaui) belongs to the family Clupeidae and is mainly distributed across Lao PRD, Cambodia, and northern Thailand. Due to overfishing and dam reconstruction, the Laotian shad is on the verge of extinction and currently listed as vulnerable by the IUCN. Nanopore and Illumina sequencing data were integrated to generate the first high-quality genome assembly for T. thibaudeaui. The assembled genome was 638 Mb in size, including 228 scaffolds with a N50 value of 16.6 Mb. BUSCO analysis revealed the completeness of the assembly to be more than 96%. A total of 24,810 protein-coding genes were predicted. According to the pairwise sequentially Markovian coalescent analysis, the effective population size of the Laotian shad sharply declined from 3 Mya to 20 Kya. We found a significant ratio in contraction of gene families that may reflect secondary gene loss. Our high-quality genome assembly of the Laotian shad will provide a valuable resource for future research in conservation genetics, as well as for investigating the phylogenetics and comparative genomics of shads.
A chromosome-level reference genome for the Versatile Fairy Shrimp, Branchinecta lindahliKieran Blair, Shannon Rose; Schreier, Andrea; Escalona, Merly; Finger, Amanda J; Joslin, Shannon E K; Sahasrabudhe, Ruta; Marimuthu, Mohan P A; Nguyen, Oanh; Chumchim, Noravit; Morris, Emily Reister; Mangelson, Hayley; Hull, Joshua
doi: 10.1093/jhered/esac057pmid: 36223244
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.
A draft reference genome of the Vernal Pool Fairy Shrimp, Branchinecta lynchiKieran Blair, Shannon Rose; Schreier, Andrea; Escalona, Merly; Finger, Amanda J; Joslin, Shannon E K; Sahasrabudhe, Ruta; Marimuthu, Mohan P A; Nguyen, Oanh; Chumchim, Noravit; Morris, Emily Reister; Mangelson, Hayley; Hull, Joshua
doi: 10.1093/jhered/esac056pmid: 36222891
We present the reference genome of the Vernal Pool Fairy Shrimp Branchinecta lynchi. This branchiopod crustacean is endemic to California’s freshwater ephemeral ponds. It faces enormous habitat loss and fragmentation as urbanization and agriculture have fundamentally changed the vernal pool landscape over the past 3 centuries. The assembled genome consists of 22 chromosome-length scaffolds that account for 96.85% of the total sequence. One hundred and ninety-five unscaffolded contigs comprise the rest of the genome’s 575.6 Mb length. The genome is substantially complete with a BUSCO score of 90.0%. There is no immediately identifiable sex chromosome, typical for this class of organism. This new resource will permit researchers to better understand the adaptive capacity of this imperiled species, as well as answer lingering questions about anostracan physiology, sex determination, and development.