Journal of Heredity

Meschersky, Ilya G; Meschersky, Sergey I; Kryukova, Natalia V; Solovyeva, Maria A; Boltnev, Evgeniy A; Klimov, Fedor V; Rozhnov, Viatcheslav V

doi: 10.1093/jhered/esae064pmid: 39487738

The allelic diversity of exon 2 (DQB gene) and exon 3 (DRB gene) of major histocompatibility complex class II was studied for the first time in two species of the landlocked pinnipeds, Baikal (N = 79) and Caspian (N = 32) seals, and these were compared with the widespread Arctic species, the ringed seal (N = 13). The analysis of the second exon comprising the antigen-binding region revealed high allelic diversity in all three species, but the pattern of the diversity was the most specific for the Baikal seal. This species differs from the other two by the smallest number of alleles in the population, yet they have the largest number of alleles per individual and by the maximum similarity of individual genotypes. Presumably, this specificity is a consequence of the spatial and temporal homogeneity of the Lake Baikal environment. Analysis of the third exon encoding the conserved β2-domain showed that the Baikal seal differs by the greatest number of amino acid sequences per individual, while the Caspian seal has the lowest number of variants. A single variant of the β2-domain, the same as in the ringed seal, predominates in the Caspian seal, whereas in the Baikal seal the two other variants predominate. At the same time, three species-specific amino acid sequences were observed among minor variants in the Caspian seal, while only one was found in the Baikal seal. This fact may suggest a longer period of independent evolution in the Caspian seal compared to the Baikal seal.

Rodseth, Edmund; Amar, Arjun; Sumasgutner, Petra; Ingle, Robert A

doi: 10.1093/jhered/esae068pmid: 39552347

Melanin-based plumage polymorphisms in birds are often associated with mutations in the melanogenesis genes, notably the melanocortin-1 receptor (MC1R), but may also arise through changes in the expression of these genes. Here we investigate the molecular basis of plumage polymorphism in both adult and juvenile black sparrowhawks (Accipiter melanoleucus), an African raptor that occurs in two adult color morphs, light and dark, and also exhibits variation in juvenile plumage coloration. Our results confirmed that plumage differences in adult morphs were a result of differential deposition of eumelanin in their ventral contour feathers. No polymorphisms in the coding regions of the MC1R or the agouti signaling protein (ASIP) genes associated with adult color morph were identified. However, lack of pigmentation in the developing breast feathers of light morph birds was strongly associated with elevated ASIP expression, and concomitant downregulation of the downstream melanogenesis genes microphthalmia-associated transcription factor (MITF), tyrosinase (TYR), and tyrosinase-related protein 1 (TYRP1). Variation in the rufous colored plumage of juveniles was found to be due to covariation in eumelanin and pheomelanin levels in dorsal and ventral contour feathers. As in adult birds, an inverse relationship between melanin pigmentation and ASIP expression was observed. This covariation between eumelanin and pheomelanin levels is not consistent with the pigment type-switching model of melanogenesis, where increased ASIP expression results in a switch from eumelanin to pheomelanin production. This highlights the need for caution when extrapolating results from model systems to other animals and the value of conducting research in wild species.

Foy, Patrick D; Loetzerich, Sara R; Boxler, David; Burgess, Edwin R; Trout Fryxell, R T; Gerry, Alec C; Hinkle, Nancy C; Machtinger, Erika T; Olds, Cassandra; Tarone, Aaron M; Watson, Wes; Scott, Jeffrey G; Meisel, Richard P

Zayas, Gabriel A; Dikmen, Serdal; Mateescu, Raluca G; Hansen, Peter J

doi: 10.1093/jhered/esae057pmid: 39401185

This study evaluated the effectiveness of genetic introgression of the SLICK1 allele derived from Senepol cattle into the Holstein breed to enhance thermotolerance. The SLICK1 allele, located in the PRLR gene, confers a short and sleek coat that is inherited as a simple dominant phenotype. Approximately 40 years ago, the University of Florida initiated efforts to introgress this allele into the Holstein population. Here we tracked the introgression of the SLICK1 allele using a medium-density genotyping array and a reference population of both breeds (50 Holstein, 46 Senepol). Among the 31 SLICK1+ Holsteins, there was 15.25% ± 11.11% (mean ± SD) Senepol ancestry on BTA20. Holsteins at the University of Florida descended from slick matings that did not inherit the SLICK1 allele (n = 9) exhibited no Senepol ancestry. A secondary introgression of Senepol genetics in SLICK1+ animals was found on BTA4, spanning 54 markers and 15 genes, with 26.67% Senepol ancestry. This region, previously linked to heat stress adaptation, suggests that the introgression extends beyond the SLICK1 allele to incorporate additional beneficial genetics for thermal stress adaptation. These findings indicate that deliberate introgression of the SLICK1 allele enhances specific traits and potentially introduces other adaptive genetic variations. The study demonstrates the successful use of genetic interventions to improve livestock resilience against environmental challenges without significantly disrupting the recipient breed’s genetic structure. The introgression of the SLICK1 allele serves as a model for breeding programs aimed at optimizing animal welfare and productivity in the face of global climate change while maintaining breed integrity.

Lévêque, Agathe; Arnaud, Jean-François; Vignon, Vincent; Mazoyer, Clément; Godé, Cécile; Duputié, Anne

doi: 10.1093/jhered/esae073pmid: 39661399

Genomic markers are essential tools for studying species of conservation concern, yet nonmodel species often lack a reference genome. Here we describe a methodology for identifying and genotyping thousands of SNP loci in the southern damselfly (Coenagrion mercuriale), a bioindicator of freshwater stream quality classified as near-threatened, with locally declining populations. We used a hybrid approach combining reduced representation sequencing and target enrichment. First, we identified putative SNP loci using ddRADseq and de novo assembly. Then, single primer enrichment technology targeted 6000 of these SNPs across 1920 individuals. Challenges encountered included sequence recapture failure, coverage depth discrepancies, and aberrant FIS values. We provide recommendations to address such issues. After multiple filtering steps, 2092 SNPs were retained and used to analyze the genetic structure of 131 individuals belonging to 11 populations in France, comparing central and marginal populations. Genetic differentiation was lower among central populations, with no sign of inbreeding. As compared with microsatellite loci, SNPs exhibited greater resolution in detecting fine-scaled genetic structure, and identifying putative hybrids in adjacent populations. In this study, we emphasize the difficulties of large-scale SNP genotyping in nonmodel species via a hybrid method that ultimately did not offer the expected cost and time-saving compared with classical ddRAD approaches. However, SNPs showed greater power than previously available markers in identifying conservation units or admixture events, and the panel of reusable probes we describe here offers the potential to improve conservation efforts through future diachronic studies or finer estimations of key parameters like effective population size.

Kulkarni, Siddharth S; Klementz, Benjamin C; Sharma, Prashant P

doi: 10.1093/jhered/esae074pmid: 39679458

Within the arachnids, chromosome-level genome assemblies have greatly accelerated the understanding of gene family evolution and developmental genomics in key groups, such as spiders (Araneae), mites and ticks (Acariformes and Parasitiformes). Among other poorly studied arachnid orders that lack genome assemblies altogether are members of the clade Pedipalpi, which is comprised of three orders that form the sister group of spiders and diverged over 400 Mya. We close this gap by generating the first chromosome-level assembly from a single specimen of the vinegaroon Mastigoproctus giganteus (Uropygi). We show that this highly complete genome retains plesiomorphic conditions for many gene families that have undergone lineage-specific derivations within the more diverse spiders. Consistent with the phylogenetic position of Uropygi, macrosynteny in the M. giganteus genome substantiates the signature of an ancient whole genome duplication.

Cash, Elizabeth I; Escalona, Merly; Ward, Philip S; Sahasrabudhe, Ruta; Miller, Courtney; Toffelmier, Erin; Fairbairn, Colin; Seligmann, William; Shaffer, H Bradley; Tsutsui, Neil D

doi: 10.1093/jhered/esae047pmid: 39248324

Polyergus kidnapper ants are widely distributed, but relatively uncommon, throughout the Holarctic, spanning an elevational range from sea level to over 3,000 m. These species are well known for their obligate social parasitism with various Formica ant species, which they kidnap in dramatic, highly coordinated raids. Kidnapped Formica larvae and pupae become integrated into the Polyergus colony where they develop into adults and perform nearly all of the necessary colony tasks for the benefit of their captors. In California, Polyergus mexicanus is the most widely distributed Polyergus, but recent evidence has identified substantial genetic polymorphism within this species, including genetically divergent lineages associated with the use of different Formica host species. Given its unique behavior and genetic diversity, P. mexicanus plays a critical role in maintaining ecosystem balance by influencing the population dynamics and genetic diversity of its host ant species, Formica, highlighting its conservation value and importance in the context of biodiversity preservation. Here, we present a high-quality genome assembly of P. mexicanus from a sample collected in Plumas County, CA, United States, in the foothills of the central Sierra Nevada. This genome assembly consists of 364 scaffolds spanning 252.31 Mb, with contig N50 of 481,250 kb, scaffold N50 of 10.36 Mb, and Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 95.4%. We also assembled the genome of the Wolbachia endosymbiont of P. mexicanus—a single, circular contig spanning 1.23 Mb. These genome sequences provide essential resources for future studies of conservation genetics, population genetics, speciation, and behavioral ecology in this charismatic social insect.

Adams, Richard; Sylvester, Terrence; Mitchell, Robert F; Price, Mathew A; Shen, Rongrong; McKenna, Duane D

doi: 10.1093/jhered/esae049pmid: 39212260

Tetraopes are aposematic longhorn beetles (Cerambycidae) that feed primarily on toxic plants in the genus Asclepias (milkweeds). Studies of Tetraopes and their host plants have revealed compelling evidence for insect–plant coevolution and cospeciation. We sequenced, assembled, and annotated the genome of the common red milkweed beetle, Tetraopes tetrophthalmus, and explored gene content and evolution, focusing on annotated genes putatively involved in chemosensation, allelochemical detoxification, and phytophagy. Comparisons were made to the Asian longhorned beetle (Anoplophora glabripennis) genome. The genome assembly comprised 779 Mb distributed across 1,057 contigs, with an N50 of 2.21 Mb and 13,089 putative genes, including 97.3% of expected single-copy orthologs. Manual curation identified 122 putative odorant receptors (OR) and 162 gustatory receptors (GR), the former number similar to A. glabripennis but the latter only 69% of the A. glabripennis suite. We also documented a greater percentage of pseudogenic GRs and ORs compared to A. glabripennis, suggesting an ongoing reduction in chemosensory function, perhaps related to host specialization. We found lower diversity within certain well-studied gene families predicted to encode putative plant cell wall degrading enzymes in the T. tetrophthalmus genome, perhaps also due to host specialization. Exploring genes relevant to stress and allelochemical detoxification revealed evidence of an abundance of ABC-family genes in the T. tetrophthalmus genome, which may be related to sequestering toxic cardiac glycosides. Our studies further illuminate the genomic basis and evolution of chemosensation in longhorn beetles and provide a new vantage point from which to explore the ecology and evolution of specialized plant-feeding in Tetraopes and other phytophagous beetles.

Eichert, Anna; Sproul, John; Tolman, Ethan R; Birrell, Jackson; Meek, Jared; Heckenhauer, Jacqueline; Nelson, Charles Riley; Dudchenko, Olga; Jeong, Jiyun; Weisz, David; Aiden, Erez Lieberman; Hotaling, Scott; Ware, Jessica L; Frandsen, Paul B

doi: 10.1093/jhered/esae044pmid: 39171826

MacDonald, Zachary G; Schoville, Sean; Escalona, Merly; Marimuthu, Mohan P A; Nguyen, Oanh; Chumchim, Noravit; Fairbairn, Colin W; Seligmann, William; Toffelmier, Erin; Gillespie, Thomas; Shaffer, H Bradley

doi: 10.1093/jhered/esae051pmid: 39275847

We describe a highly contiguous and complete diploid genome assembly for the Chryxus Arctic, Oeneis chryxus (E. Doubleday, [1849]), a butterfly species complex spanning much of northern and western North America. One subspecies, the Ivallda Arctic (O. c. ivallda), is endemic to California’s Sierra Nevada and of particular biogeographic interest and conservation concern. Extreme alpine habitats occupied by this subspecies include the summit of Mt. Whitney, California, representing the highest elevation butterfly population in North America. The assembly presented here consists of two haplotypes, 738.92 and 770.85 Mb in length, with contig N50 values of 10.49 and 10.13 Mb, scaffold N50 values of 25.35 and 25.69 Mb, scaffold L50 values of 13 and 14, and BUSCO completeness scores of 96.5 and 98.3%, respectively. More than 97% of the assembly is organized into 29 scaffolds, which likely represent whole chromosomes. This assembly is the first major genomic resource for Oeneis, providing a foundational reference for future genomic studies on the taxonomy, evolutionary history, and conservation of the genus. As part of the California Conservation Genomics Project, we will use this assembly in conjunction with short-read resequencing to resolve patterns of evolutionary differentiation, adaptive genomic variation, and gene flow among remaining O. c. ivallda populations. These data can and will be used to inform the subspecies’ conservation as warming climatic conditions continue to lead to the loss and fragmentation of alpine habitats. We also provide genome assemblies for the O. chryxus mitochondrion and a Wolbachia endosymbiont.