Journal of Heredity最新文献

Understanding the processes that shape spatial genetic differentiation is essential for understanding how populations adapt to environmental change. By evaluating the influence of these processes, we can gain insights into evolutionary dynamics and the potential for species to respond to shifting landscapes. Three well-accepted processes that create spatial patterns in genetic variation are isolation-by-distance (IBD), where individuals are more genetically similar the closer they are geographically; isolation-by-environment (IBE), where gene flow is reduced due to selection against migrants in unsuitable ecological conditions; and isolation-by-resistance (IBR), where landscape features limit dispersal. We conducted a macrogenetic meta-analysis of single-nucleotide-polymorphism data to identify patterns shaping spatial genetic differentiation in 40 mammalian datasets globally. For each species, we built a species-distribution model and combined it with the global Human Footprint layer to create a composite resistance surface, revealing that habitat suitability and anthropogenic impact contribute roughly equally to resistance. Model selection tests found IBR was the mechanism most frequently retained in the best models and had the highest variable importance. IBD and IBE alone had little effect but were often selected alongside IBR, suggesting they may have secondary, context-dependent effects. However, the probability of finding IBD in the best model of divergence significantly increased as the number of populations sampled increased. Similarly, the probability of finding IBE increased with the spatial scale of the study. Our findings suggest that resistance is pervasive in shaping genetic variation in mammals worldwide, but that study design affects our ability to detect the presence of IBD and IBE.

Ecological and genetic interactions of species at the far end of the speciation continuum can often be studied in sympatry. Triturus cristatus (C) and T. marmoratus (M) are two deeply differentiated yet hybridizing salamander species that engage in a mosaic distribution over a wide zone of range overlap in the west of France. Interspecies hybrids are easy to distinguish from both parentals and occur at ca. 3% of the total breeding population. Most hybrids are thought to be F1 diploids (CM). We aim to identify triploid F1 hybrids with single nucleotide polymorphism (SNP) data and determine their frequency. Special attention to the genus Triturus is warranted because triploidy might in principle constitute an escape route to the enigmatic chromosome-1 syndrome that constitutes a long-term 50% genetic load. Species-specific signals for a panel of 30 SNPs, analysed with metric multidimensional scaling, suggest that triploid frequency is one out of 26 (3.8%), although a frequence of 18% was found in a larger sampling (N=100) that paid particular attention to aberrant hybrid phenotypes. Triploids with a CMM genetic configuration appear more frequent than the CCM counterpart. The triploid status could be confirmed for two CMM females, either by target capture or cellular morphometric data. One triploid individual relocated in the field showed a hybrid phenotype leaning towards T. marmoratus, an exceptional life span (17+ yrs), length (187 mm) and the frequent skipping of annual breeding opportunities. Future research on the T. cristatus - T. marmoratus system should consider the different classes of interspecies hybrids.

We present genome assemblies for two cyprinoid fishes, the tui chub (Siphateles bicolor) and the arroyo chub (Gila orcuttii). These fishes are ecologically important representatives of native fish assemblages in the western United States and are both species of conservation concern. The two species hybridize where introductions bring them into contact, with potentially important ecological and evolutionary implications that have not yet been thoroughly examined from a genomic perspective. We present de novo assemblies for both species, representing the first scaffold-level genomes within their respective genera, which were developed as part of the California Conservation Genomics Project (CCGP) using Pacific Biosciences HiFi and Omni-C data. Our tui chub assembly consists of 258 scaffolds spanning 1 148 084 093 base pairs, has a scaffold N50 of 45.9 Mb, a contig N50 of 23.7 Mb, and a BUSCO completeness score of 98.1%. Our arroyo chub assembly consists of 179 scaffolds spanning 1 263 410 250 base pairs, has a scaffold N50 of 50.5 Mb, a contig N50 of 13.1 Mb, and a BUSCO completeness score of 97.8%. A comparative analysis of the two species revealed relatively conserved genomes, with the exception of two inversions at chromosome 20. We annotated a total of 34 090 genes with a BUSCO completeness score of 98.1% for the tui chub, and 28 193 genes with a score of 97.4% for the arroyo chub. These assemblies will be valuable resources for characterizing the species' phylogeographic histories and delineating the role of hybridization in their evolution.

Natural history museum collections are invaluable repositories of biodiversity, offering insights into life on Earth. Genomic approaches provide powerful tools to characterize biodiversity in these collections. However using these collections for genomics without damaging specimens is a challenge. Here, we develop and test non-destructive DNA metabarcoding methods to capture biodiversity from the preservative fluids of archived insect collections ('Bycatch'). We optimized workflows for extracting and amplifying the partial CO1 locus (CO1) and fungal ITS1 locus (FITS) from ethanol-based preservative fluids, validating ethanol preparation methods, comparing DNA extraction kits, and refining PCR protocols. Our results demonstrate that from museum collections with low DNA yields, CO1 and FITS loci can often be recovered from preservative fluids, and we present detailed methodology and workflows. We test metabarcoding success to recover taxa in several museum collections ranging in age and storage condition. This is to support the State of California's effort to catalog and sequence all insects and fungi, building baselines of California biodiversity with help from museum collections. And lastly we investigate the complementarity of metabarcoding water versus ethanol and morphological identifications aimed to capture benthic macroinvertebrate biodiversity in streams. Our findings highlight that DNA metabarcoding of the preservative fluid is a non-destructive tool for capturing biodiversity in historical specimens, but there are limitations on the overlaps between DNA results and physical contents, where morphological identification still reigns in taxon counts, but metabarcoding sometimes provides more taxonomic resolution, and can be used to track DNA from other organisms beyond the directly surveyed specimens.

Sparganum proliferum is an enigmatic, highly proliferative cestode that causes fatal sparganosis. We present a 681 Mb chromosome-level genome assembled from Oxford Nanopore, PacBio HiFi, Illumina, and Hi-C data, yielding nine chromosome-length scaffolds consistent with 2n = 18. The assembly exhibits strong intra-chromosomal Hi-C contact signals and a repeat content of 55.8%, dominated by LINEs. We annotated 29 231 protein-coding genes, including 6316 transposable element-associated loci, with BUSCO completeness scores of 91% (eukaryote_odb10) and 73% (metazoa_odb10). Macrosynteny is well conserved with Echinococcus granulosus and Hymenolepis microstoma, moderately conserved with the trematode Schistosoma mansoni, but largely disrupted in the free-living flatworm Schmidtea mediterranea, revealing lineage-specific genome reorganization among flatworms. To enable functional genetics, we identified candidate genomic safe harbours (GSHs)-intergenic loci within transcriptionally active neighborhoods, separated from adjacent genes by 2-10 kb gene-free buffers, flanked by convergently oriented genes, and containing CRISPR/Cas9 PAM motifs (NGG)-and compiled housekeeping promoters for stable transgene expression. Together, these resources provide a reference framework for chromosome evolution and parasitic adaptation in Diphyllobothriidea and establish practical entry points for CRISPR-based functional studies in cestodes.

Despite the unprecedented rate of global urbanization, diverse array of taxa are supported in urban areas. However, the long-term persistence of urban wildlife cannot be guaranteed due to the various adverse effects that come with urbanization, such as resource depletion and reduced gene flow. Accordingly, it is imperative to evaluate the health and viability of urban wildlife, particularly of species that are underrepresented in the existing literature, like herpetofauna. Genomic techniques can provide critical insights into urban wildlife health and population viability. Here, we generated a ddRADseq dataset of 162 Dekay's brown snakes (Storeria dekayi) among 11 locations with different urbanization magnitudes across New Jersey, United States of America, and examined the population genetic patterns of this common urban reptile. While genetic diversity was not severely reduced within those populations, we uncovered the presence of genetic differentiation and structuring across them, especially for those from the most urbanized areas. Deviations of interpopulation structure from their geographic distributions might reflect either habitat alteration or human intervention in recent history. Landscape genetic analyses revealed the presence of an isolation-by-distance relationship that was only significant within a short spatial distance of 1,500 m. Most urban populations also displayed lower-than-expected historic migration and diversity rates, but some remained genetically connected and diverse. To conclude, our study can serve as a useful guide for population genomic studies on urban herpetofauna. Based on our results, urbanization is likely to impact interpopulation genetic connectivity, but to have limited effects on intrapopulation genetic diversity of small-bodied, terrestrial urban dwellers.

Squirrels (Rodentia; Sciuridae) are a well-known and diverse group of rodents, including the charismatic ground-dwelling members of the Tribe Marmotini. In particular, the California ground squirrel (Otospermophilus beecheyi) is an emerging model system for the study of social and risk-sensitive behaviors in a rapidly changing world, as well as the physiology of resistance to snake venoms. To complement extensive natural history information for O. beecheyi, we provide a chromosome-scale genome to facilitate molecular studies focused on the genetic basis of ecologically important traits, population genetics, comparative genomics, and social evolution. The final scaffolded genome was 2.27 Gb contained in 9,960 contigs and placed into 1,383 scaffolds. The scaffold N50 was just more than 125 Mb. We used the presence of 10,248 complete genes detected by BUSCO v5 specifically to compare broad patterns of chromosomal synteny between chromosomal scaffolds for O. beecheyi and two other sciurid rodents. The recovered pattern of synteny suggests several fusion and fission events for O. beecheyi in relation to the other two species. Taken together, this new information should advance our understanding of O. beecheyi and comparative studies of mammalian genomic biology and evolution.

The pink volcano barnacle, Tetraclita rubescens, has experienced a poleward range expansion along the eastern Pacific coastline amidst recent climate changes, likely facilitated by high gene flow and high genetic diversity in a large population. A high-quality reference genome provides the next step to investigate these patterns in more detail. We present a highly contiguous, chromosome-level genome assembly for T. rubescens using long-read sequencing and short-read proximity ligation data. The genome assembly is 2.44 Gb, contains 92.5% complete ortholog genes based on the known Arthropoda gene list, the largest N50 compared with other high-quality barnacle genomes (~107 Mb), and a low L50 score (10 scaffolds). With this chromosome-level assembly, we will be better able to contrast the roles of drift, migration, and selection in population and spatial expansion dynamics and the roles of dispersal and adaptation within the range and to investigate the genomic diversity of the species, including the roles of transposable elements in the genome. T. rubescens is an iconic barnacle on central and southern Californian rocky intertidal shores, and understanding its dynamics can help inform and support the conservation of intertidal communities along the northeastern Pacific coastline.

Advances in genomic studies are revealing that gene flow between species is more frequent than previously understood, although the ways in which hybridization can bias gene flow across species boundaries or the extent to which introgression might be adaptive remain unexplored in most systems. We report on an annotated chromosome-level genome assembly for the Gilbert's skink, Plestiodon gilberti, one of 18 clades of reptiles and amphibians selected for reference genome sequencing in the California Conservation Genomics Project. This assembly was produced using Pacific Biosciences HiFi long reads and Omni-C proximity ligation data. Although members of the Scincidae comprise nearly one-quarter of all lizard species (1785 described species), this de novo assembly represents one of only 10 skink species globally and the first North American skink with a reference genome. The assembly has a total length of ~ 1.57 Gb, a scaffold N50 length of ~ 231.32 Mb, read coverage of ~56X, and BUSCO completeness score of 97.2% based on the Tetrapoda ortholog database. Plestiodon gilberti is a member of the Plestiodon skiltonianus species complex, a group with many of the characteristics of ecological speciation but where ancient hybridization and biased introgression present challenges to retracing the initial patterns of lineage divergence. Combined with dense sampling of resequenced genomes in the California Conservation Genomics Project, including other members of the P. skiltonianus complex, this reference genome will enable future analyses of the links between divergent selection and the genes underlying speciation, as well as the potential for introgression to enable adaptation to new or changing environments.

We present haplotype-resolved whole-genome assemblies from one individual European river lamprey (Lampetra fluviatilis) and one individual brook lamprey (Lampetra planeri), usually regarded as sister species. The genome assembly of L. fluviatilis consists of pseudo-haplotype one, spanning 1073 Mb and pseudo-haplotype two, spanning 963 Mb. Likewise for the L. planeri specimen, the genome assembly spans 1049 Mb and 960 Mb for pseudo-haplotypes one and two, respectively. Both the L. fluviatilis pseudo-haplotypes have been scaffolded into 82 pseudo-chromosomes, with the same number for the L. planeri pseudo-haplotypes. All four pseudo-haplotype assemblies were annotated, identifying 21,479 and 16,973 genes in pseudo-haplotypes one and two for L. fluviatilis, and 24,961 and 21,668 genes in pseudo-haplotypes one and two for L. planeri. A comparison of the genomes of L. fluviatilis and L. planeri, alongside a separate chromosome level assembly of L. fluviatilis from the UK, indicates that they form a species complex, potentially representing distinct ecotypes. This is further supported by phylogenetic analyses of the three reference Lampetra genomes in addition to sea lamprey (Petromyzon marinus).