Journal of Heredity最新文献

Polyergus kidnapper ants are widely distributed, but relatively uncommon, throughout the Holarctic, spanning an elevational range from sea level to over 3000 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, Polyergus 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, USA, 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 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.

The common eider, Somateria mollissima mollissima (Chordata; Aves; Anseriformes; Anatidae), is a large sea duck with a circumpolar distribution. We here describe a chromosome-level genome assembly from an individual female. The haplotype-resolved assembly contains one pseudo-haplotype spanning 1205 megabases (with both Z and W sex chromosomes) and one pseudo-haplotype spanning 1080 megabases. Most of these two assemblies (91.13% and 93.18%, respectively) are scaffolded into 32 autosomal chromosomal pseudomolecules plus Z and W for pseudo-haplotype one. The BUSCO completeness scores are 94.0% and 89.9%, respectively, and gene annotations of the assemblies identified 17,479 and 16,315 protein coding genes. Annotation of repetitive sequences classify 17.84 % and 14.62 % of pseudo-haplotype one and two, respectively, as repeats. The genome of the common eider will be a useful resource for the widely distributed northern species in light of climate change and anthropogenic threats.

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 1057 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.

Botta's pocket gopher (Thomomys bottae) is a common and widespread subterranean rodent of the North American west. The species has been of long interest to evolutionary biologists due to the phenotypic diversity across its range and unusual levels of variation in chromosome number and composition. Here, we present a high-quality reference genome from a male T. b. bottae individual captured in the San Francisco Bay Area. The assembly is comprised of 2,792 scaffolds, with a scaffold N50 value of 23.6 Mb and a BUSCO score of 91.0%. This genome helps fill a significant taxonomic sampling gap in rodent genome resources. With this reference genome, we envision new opportunities to investigate questions regarding the genomics of adaptation to the belowground niche. Further, we can begin to explore the impact of associated life history traits, such as limited dispersal and low population connectivity, on intraspecific genetic and phenotypic variation, genome evolution, speciation, and phylogenetic relationships across the Geomyoidea.

Pteronarcys californica (Newport 1848) is commonly referred to as the giant salmonfly and is the largest species of stonefly (Insecta: Plecoptera) in the western United States. Historically, it was widespread and abundant in western rivers, but populations have experienced a substantial decline in the past few decades, becoming locally extirpated in numerous rivers in Utah, Colorado, and Montana. Although previous research has explored the ecological variables conducive to the survivability of populations of the giant salmonfly, a lack of genomic resources hampers exploration of how genetic variation is spread across extant populations. To accelerate research on this imperiled species, we present a de novo chromosomal-length genome assembly of P. californica generated from PacBio HiFi sequencing and Hi-C chromosome conformation capture. Our assembly includes 14 predicted pseudo chromosomes and 98.8% of Insecta universal core orthologs. At 2.40 gigabases, the P. californica assembly is the largest of available stonefly assemblies, highlighting at least 9.5-fold variation in assembly size across the order. Repetitive elements (REs) account for much of the genome size increase in P. californica relative to other stonefly species, with the content of Class I retroelements alone exceeding the entire assembly size of all but two other species studied. We also observed preliminary suborder-specific trends in genome size that merit testing with more robust taxon sampling.

We present genome assemblies for 18 snake species representing 18 families (Serpentes: Caenophidia): Acrochordus granulatus, Aparallactus werneri, Boaedon fuliginosus, Calamaria suluensis, Cerberus rynchops, Grayia smithii, Imantodes cenchoa, Mimophis mahfalensis, Oxyrhabdium leporinum, Pareas carinatus, Psammodynastes pulverulentus, Pseudoxenodon macrops, Pseudoxyrhopus heterurus, Sibynophis collaris, Stegonotus admiraltiensis, Toxicocalamus goodenoughensis, Trimeresurus albolabris, and Tropidonophis doriae. From these new genome assemblies, we extracted thousands of loci commonly used in systematic and phylogenomic studies on snakes, including target-capture datasets composed of ultraconserved elements (UCEs) and anchored hybrid enriched loci (AHEs), as well as traditional Sanger loci. Phylogenies inferred from the two target-capture loci datasets were identical with each other and strongly congruent with previously published snake phylogenies. To show the additional utility of these non-model genomes for investigative evolutionary research, we mined the genome assemblies of two New Guinea island endemics in our dataset (S. admiraltiensis and T. doriae) for the ATP1a3 gene, a thoroughly researched indicator of resistance to toad toxin ingestion by squamates. We find that both these snakes possess the genotype for toad toxin resistance despite their endemism to New Guinea, a region absent of any toads until the human-mediated introduction of Cane Toads in the 1930s. These species possess identical substitutions that suggest the same bufotoxin resistance as their Australian congenerics (Stegonotus australis and Tropidonophis mairii) which forage on invasive Cane Toads. Herein, we show the utility of short-read high-coverage genomes, as well as improving the deficit of available squamate genomes with associated voucher specimens.

Plastomes are used in phylogenetic reconstructions because of their relatively conserved nature. Nonetheless, some limitations arise, particularly at lower taxonomic levels due to reduced interspecific polymorphisms and frequent hybridization events that result in unsolved phylogenies including polytomies and reticulate evolutionary patterns. Next-generation sequencing technologies allow access to genomic data and strongly supported phylogenies, yet biased topologies may be obtained due to insufficient taxon sampling. We analyze the hypothesis that intraspecific plastome diversity reflects biogeographic history and hybridization cycles among taxa. We generated 12 new plastome sequences covering distinct latitudinal locations of all species of subgenus Nothofagus from North Patagonia. Chloroplast genomes were assembled, annotated, and searched for simple sequence repeats (SSRs). Phylogenetic reconstructions included species and sampled locations. The six Nothofagus species analyzed were of similar size and structure; only Nothofagus obliqua of subgenus Lophozonia, used as an outgroup, presented slight differences in size. We detected a variable number of SSRs in distinct species and locations. Phylogenetic analyses of plastomes confirmed that subgenus Nothofagus organizes into two monophyletic clades each consisting of individuals of different species. We detected a geographic structure within subgenus Nothofagus and found evidence of local chloroplast sharing due to past hybridization, followed by adaptive introgression and ecological divergence. These contributions enrich the comprehension of transversal evolutionary mechanisms such as chloroplast capture and its implications for phylogenetic and phylogenomic analyses.

Chromosome number is a fundamental genomic trait that is often the first recorded characteristic of a genome. Across large clades, a common pattern emerges: many or even most lineages exhibit relative stasis, while a handful of lineages or species exhibit striking variation. Despite recent developments in comparative methods, most of this heterogeneity is still poorly understood. It is essential to understand why some lineages have rapid rates of chromosome number evolution, as it can impact a variety of other traits. Previous research suggests that biased female meiotic drive may shape rates of karyotype evolution in some mammals. However, Carnivora exhibits variation that this female meiotic drive model cannot explain. We hypothesize that variation in effective population size may underlie rate variation in Carnivora. To test this hypothesis, we estimated rates of fusions and fissions while accounting for range size, which we use as a proxy for effective population size. We reason fusions and fissions are deleterious or underdominant and that only in lineages with small range sizes will these changes be able to fix due to genetic drift. In this study, we find that the rates of fusions and fissions are elevated in taxa with small range sizes relative to those with large range sizes. Based on these findings, we conclude that 1) naturally occurring structural mutations that change chromosome number are underdominant or mildly deleterious, and 2) when population sizes are small, structural rearrangements may play an important role in speciation and reduction in gene flow among populations.

Strong gene flow from outcrossing relatives tends to blur species boundaries, while divergent ecological selection can counteract gene flow. To better understand how these two forces affect the maintenance of species boundaries, we focused on a species complex including a rare species, maple-leaf oak (Quercus acerifolia), which is found in only four disjunct ridges in Arkansas. Its limited range and geographic proximity to co-occurring close relatives create the possibility for genetic swamping. In this study, we gathered genome-wide single nucleotide polymorphisms (SNPs) using restriction-site-associated DNA sequencing (RADseq) from 190 samples of Q. acerifolia and three of its close relatives, Q. shumardii, Q. buckleyi, and Q. rubra. We found that Q. shumardii and Q. acerifolia are reciprocally monophyletic with low support, suggesting incomplete lineage sorting, introgression between Q. shumardii and Q. acerifolia, or both. Analyses that model allele distributions demonstrate that admixture contributes strongly to this pattern. Populations of Q. acerifolia experience gene flow from Q. shumardii and Q. rubra, but we found evidence that divergent selection is likely maintaining species boundaries: 1) ex situ collections of Q. acerifolia have a higher proportion of hybrids compared to the mature trees of the wild populations, suggesting ecological selection against hybrids at the seed/seedling stage; 2) ecological traits co-vary with genomic composition; and 3) Q. acerifolia shows genetic differentiation at loci hypothesized to influence tolerance of radiation, drought, and high temperature. Our findings strongly suggest that in maple-leaf oak, selection results in higher divergence at regions of the genome despite gene flow from close relatives.