Journal of Heredity最新文献

As climate variability continues to impact agricultural systems, identifying genetic factors that contribute to environmental adaptation will be essential for optimizing breeding strategies for the development of climate-resilient varieties. Through human cultivation and naturalization, Cannabis sativa has dispersed globally, adapting to a range of environmental conditions across various climates and latitudes. We combined raw data from multiple public sources to conduct an environmental genomic selection (EGS) analysis on 149 C. sativa samples to assess how different populations of Cannabis relate to their environmental conditions. Exploring genomic estimated adaptive values (GEAVs) across bioclimatic variables can facilitate the selection of parental material adapted for a specific condition. We further explore potential mechanisms of local adaptation by characterizing the individual marker effects that underlie these GEAV scores. To facilitate interpretation, we used previously described genetic groupings (basal, hemp-type, drug-type feral, and drug-type). Distinct patterns emerged across population groups with the drug-type (type I) group showing consistently narrow GEAV ranges, whereas the drug-type feral group showed a broader distribution, often having high GEAVs for precipitation variables. A key climate variable difference was seen in monthly average values, revealing a seasonal response to precipitation in drug-type feral samples. By examining monthly differences in marker effects associated with precipitation, we identify potential genomic mechanisms underlying seasonal environmental responses in drug-type feral samples. As these samples are sourced from geographic regions that have seasonal monsoons, they may have traits conferring flood tolerance (waterlogging) that could be introgressed into other backgrounds. The basal group also exhibited broad GEAV ranges across several bioclimatic traits, indicating they may be a valuable genetic resource for introgression to enhance environmental resilience. These findings underscore the importance of incorporating diverse germplasm into breeding programs to improve Cannabis resilience to changing environmental conditions. EGS provides a fast method to enable climate-conscious parental selection while gaining mechanistic information. Ultimately, we hope that such a strategy could support the development of climate-resilient Cannabis varieties tailored to both current and future environmental challenges.

The White-bellied Sholakili (Sholicola albiventris) is an endemic, elevationally restricted species occurring in the Shola Sky Islands of the Western Ghats of India. This unique understory bird, with a complex vocal repertoire, exhibits impacts of anthropogenic habitat fragmentation on gene flow. Here, we present the first genome assembly for S. albiventris, which was assembled using a combination of Nanopore and Illumina sequences. The final assembly is 1.083 Gbp, consisting of 975 scaffolds with an N50 of 68.64 Mbp and L50 of 6. Our genome assembly's completeness is supported by a number of metrics-high Benchmarking Universal Single-Copy Orthologs (99.9%), and a total of 4,887 ultra-conserved element loci retrieved. We also report the complete mitochondrial genome comprising 13 protein-coding genes, 22 tRNAs, and 2 rRNAs. We identified 11.82% of the nuclear genome as repetitive and 36,000 putative genes, with 12,017 genes functionally annotated. Our assembly showed a great synteny between Taeniopygia guttata and Gallus gallus chromosome level assemblies. This reference will be pivotal for investigating landscape connectivity, sub-population genetics, local adaptation, and conservation genetics of this high-elevation, range-restricted endemic bird species.

American plains bison (Bison bison bison, bison hereafter) experienced an extreme demographic bottleneck in the late 1800s. The species has since rebounded but is primarily managed as small and isolated herds due to habitat and sociopolitical limitations. Thus, reintroducing bison and allowing herds to achieve as much of their natural dynamics as possible is a major conservation goal. Concerns about genetic diversity loss in small, isolated herds and the persistence of cattle-origin variants from historical crossbreeding efforts have made genetic analysis an important part of bison conservation. The limitations of the current conservation genetic tools which are based on traditional markers such as microsatellites and mitochondrial DNA sequences, may be overcome with genome-wide genotyping panels commonly developed for agricultural species. Bison reintroduction in the grasslands at American Prairie began in 2005. Genetic analysis on these herds has yet to be conducted. We used the Illumina 777K Bovine genotyping panel to obtain data from 197 bison and 179 domestic cows to understand the current population genetic state of bison at American Prairie and gain insight on cattle (Bos taurus) introgression. Overall, bison at American Prairie currently have relatively high genetic diversity, low inbreeding, and no obvious signs of cattle introgression. A more comprehensive evaluation of introgression, likely including whole-genome sequence data, would clarify this finding. These results can serve as a baseline for future comparison as part of a genetic monitoring framework.

The diamondback terrapin (Malaclemys terrapin) is a mid-sized turtle that serves as a keystone predator in salt marsh ecosystems of eastern North America. The terrapin has historically faced population declines due to habitat loss and overharvesting, which has resulted in its listing under multiple jurisdictions across the northern part of its range. To characterize levels and partitioning of terrapin genetic variation throughout the northeast region, we used restriction site-associated DNA sequencing (RADseq). We analyzed genetic variation among 116 individuals sampled across 18 sites. Within-population genetic diversity was relatively low (He = 0.080 to 0.122), and we observed a strong negative correlation between diversity and latitude. Furthermore, levels of genetic differentiation were moderate (pairwise FST = 0.00 to 0.19), with the mean pairwise FST of each population exhibiting a strong positive correlation with latitude. Together, these results are consistent with a model of serial colonization from a Pleistocene refugium in the mid-Atlantic. Spatial genetic variation was best explained by a landscape model that considered migration to be limited to coastal habitats, where northern range-edge populations maintained comparatively low genetic diversity and were more genetically distinct than populations to the south-consistent with their greater geographic isolation. Admixture analyses revealed weak genetic clustering, with the distribution of genetic clusters reflecting the combined historical effects of isolation-by-distance and human-mediated translocations. Regional efforts to restore terrapin habitat or reintroduce captive individuals should consider patterns of historic gene flow, cognizant of the relatively distinct and isolated populations at the northeastern range edge.

The digger wasp genus Cerceris represents an important transition from predacious hymenopterans to the bees. Here, we present a refined genome assembly of Cerceris sabulosa. A drone specimen was sequenced using the Oxford Nanopore platform and polished by Illumina paired-end reads. The assembled genome size was 372.7 Mb, including 587 contigs (N50 = 6.6 Mb), with 99.4% of BUSCO genes present in the assembly. A total of 12,425 protein-coding genes were annotated. In addition, 140.3 Mb of repeat elements and 938 noncoding RNAs were identified. Genome evolution analysis showed that many genes related to binding had experienced significant expansion. Our new genome assembly builds the foundation for in-depth research on evolutionary adaptation and lifestyle transition in Cerceris species.

Understanding patterns of differentiation at microgeographic scales can enhance our understanding of evolutionary dynamics and lead to the development of effective conservation strategies. In particular, high levels of landscape heterogeneity can strongly influence species abundances, genetic structure, and demographic trends. The bearded anole, Anolis pogus, is endemic to the topographically complex island of St. Martin and of conservation concern. Here, we examined genetic diversity and inbreeding, assessed which features of the landscape influence population abundances, tested for population genetic structure across St. Martin, and inferred historical demographic trends. We found minimal inbreeding or low genetic diversity in A. pogus. We found that suitable habitat occurs broadly across the island and that population abundances were largely predicted by canopy cover. However, there was no signature of population genetic structure across the distribution, in contrast to the co-distributed anole species (Anolis gingivinus). Historical demographic trends in A. pogus were in sharp contrast to A. gingivinus, with effective population sizes of A. pogus increasing in the recent past, whereas A. gingivinus population sizes have declined. We posit that declines in a competitor species allowed for population size expansion in A. pogus. Overall, these analyses suggest that A. pogus is unlikely to be of immediate conservation concern. Further, we highlight the role of demographic history and ecological interactions in shaping population structure.

The genus Elaphe Fitzinger, a large species clade within Colubridae, comprises 18 non-venomous snake species. Among them, Elaphe taeniura serves as a representative species due to its wide distribution and strong adaptability. However, genomic studies on this group remain limited. Here, we present a chromosome-level, high-quality reference genome for this species. The genome is assembled by integrating high-accuracy PacBio HiFi long-read sequencing and Hi-C chromatin conformation capture technologies and comprehensively annotated with the aid of transcriptomic data. The genome of E. taeniura spans 1.62 Gb, with a scaffold N50 of 206.4 Mb and the longest scaffold reaching 344.4 Mb. The genome exhibits a BUSCO completeness score of 98.2% and contains 22,246 protein-coding genes. Comparative analysis between the assembled genome and three other colubrid species revealed high synteny. In addition, several chromosomal fusion and fission events were observed. This reference genome provides a valuable resource for studying the taxonomy, conservation, and evolutionary history of the widely distributed Elaphe species.

The flowering plant genus Aquilegia (columbine) is an important contributor to biodiversity and an example of both biotic and abiotic niche adaptation across much of the Northern Hemisphere, especially in California. Here we report a near-chromosome level draft genome assembly for A. eximia, a California endemic species. A. eximia is a serpentine-soil specialist and is very closely related to 2 columbine species also being studied for the California Conservation Genomics Project (CCGP), A. formosa (widespread) and A. pubescens (high alpine). Utilizing high throughput, long reads (PacBio) and chromatin capture (Omni-C), the A. eximia genome makes marked contiguity improvements compared to the existing reference genome for another North American columbine, A. coerulea "Goldsmith." The A. eximia genome will also be more useful for aligning whole genome resequencing data from California columbines than the genomes for more distantly related columbine species, the Asian A. oxysepala var. kansuensis and the European A. vulgaris. Notably, we found evidence that A. eximia, A. coerulea "Goldsmith," and A. vulgaris all share the same overall genome structure and differ from A. oxysepala var. kansuensis by the same reciprocal translocation. The A. eximia reference genome will be a valuable tool for identifying patterns of plant biodiversity across California for the CCGP, as well as for future population genomic and trait mapping studies.