Restriction Site-associated DNA Sequencing Research Articles

Striking genetic homogeneity in the widespread South American bracken.

Bracken (Pteridium, Dennstaedtiaceae) is a cosmopolitan genus of aggressive disturbance colonizers that are toxic to agricultural livestock. The taxonomy of Pteridium has been treated in multiple schemes, ranging from one to six species worldwide, with numerous subspecies and varieties. Recent work has focused on the worldwide distribution and systematics of the bracken fern, but South America has been poorly represented. We present the first continent-wide sampling and analysis of Pteridium esculentum, a Southern Hemisphere diploid species. Within South America, P. esculentum has several morphotypes, distinguished into subspecies by variation in indument and lamina architecture. We used double digest restriction site-associated DNA sequencing (ddRADSeq) to assess the phylogenetic relationships of P. esculentum subspecies. We found a striking genetic homogeneity in the species, being able to support only two morphotypes from molecular data: P. e. arachnoideum and P. e. campestre. We had high confidence for shallow and deep phylogenetic relationships, but less support for relationships among crown groups. We describe an east-west geographic pattern that would explain the relationships between populations; and, in contrast to previous studies, we detected differences with P. esculentum from Australia. These results will lay the foundations for studying variations in this species' behavior as a weed, as well as its impact on the production of agricultural livestock in South America.

Neutral markers reveal complex population structure across the range of a widespread songbird.

Understanding how both contemporary and historical physical barriers influence gene flow is key to reconstructing evolutionary histories and can allow us to predict species' resilience to changing environmental conditions. During the last glacial maximum (LGM), many high latitude North American bird species were forced into glacial refugia, including mountain bluebirds (Silia currucoides). Within their current breeding range, mountain bluebirds still experience a wide variety of environmental conditions and barriers that may disrupt gene flow and isolate populations. Using single nucleotide polymorphisms (SNPs) obtained through restriction site-associated DNA sequencing, we detected at least four genetically distinct mountain bluebird populations. Based on this structure, we determined that isolation-by-distance, the northern Rocky Mountains, and discontinuous habitat are responsible for the low connectivity and the overall history of each population going back to the last glacial maximum. Finally, we identified five candidate genes under balancing selection and three loci under diversifying selection. This study provides the first look at connectivity and gene flow across the range of these high-altitude and high latitude songbirds.

Neutral markers reveal complex population structure across the range of a widespread songbird.

Understanding how both contemporary and historical physical barriers influence gene flow is key to reconstructing evolutionary histories and can allow us to predict species' resilience to changing environmental conditions. During the last glacial maximum (LGM), many high latitude North American bird species were forced into glacial refugia, including mountain bluebirds (Silia currucoides). Within their current breeding range, mountain bluebirds still experience a wide variety of environmental conditions and barriers that may disrupt gene flow and isolate populations. Using single nucleotide polymorphisms (SNPs) obtained through restriction site-associated DNA sequencing, we detected at least four genetically distinct mountain bluebird populations. Based on this structure, we determined that isolation-by-distance, the northern Rocky Mountains, and discontinuous habitat are responsible for the low connectivity and the overall history of each population going back to the last glacial maximum. Finally, we identified five candidate genes under balancing selection and three loci under diversifying selection. This study provides the first look at connectivity and gene flow across the range of these high-altitude and high latitude songbirds.

Conservation genomics assessment of Tharp's bluestar (Amsonia tharpii) with comparisons to widespread (A. longilora) and narrowly endemic (A. fugatei) congeners.

Land-use change and habitat fragmentation are threats to biodiversity. The decrease in available habitat, increase in isolation, and mating within populations can lead to elevated inbreeding, lower genetic diversity, and poor fitness. Here we investigate the genetics of two rare and threatened plant species, Amsonia tharpii and A. fugatei, and we compare them to a widespread congener A. longiflora. We also report the first phylogenetic study of the genus Amsonia (Apocynaceae), including 10 of the 17 taxa and multiple sampling locations, to understand species relationships. We used a double digest restriction-site associated DNA sequencing (ddRADseq) approach to investigate the genetic diversity and gene flow of each species and to create a maximum likelihood phylogeny. The ddRADseq data was mapped to a reference genome to separate out the chloroplast and nuclear markers for population genetic analysis. Our results show that genetic diversity and inbreeding were low across all three species. The chloroplast and nuclear dataset in A. tharpii were highly structured, whereas they showed no structure for A. fugatei, while A. longiflora lacked structure for nuclear data but not chloroplast. Phylogenetic results revealed that A. tharpii is distinct and sister to A. fugatei, and together they are distantly related to A. longiflora. Our results demonstrated that evolutionary history and contemporary ecological processes largely influences genetic diversity within Amsonia. Interestingly, we show that in A. tharpii there was significant structure despite being pollinated by large, bodied hawkmoths that are known to be able to carry pollen long distances, suggesting that other factors are contributing to the structure observed among A. tharpii populations. Conservation efforts should focus on protecting all of the A. tharpii populations, as they contain unique genetic diversity, and a protection plan for A. fugatei needs to be established due to its limited distribution.

Which contributes more to the relict flora distribution pattern in East Asia, geographical processes or climate change? New evidence from the phylogeography of Rehderodendron kwangtungense

BackgroundRelict species are important for enhancing the understanding of modern biogeographic distribution patterns. Although both geological and climatic changes since the Cenozoic have affected the relict flora in East Asia, the contributions of geographical processes remain unclear. In this study, we employed restriction-site associated DNA sequencing (RAD-seq) and shallow genome sequencing data, in conjunction with ecological niche modeling (ENM), to investigate the spatial genetic patterns and population differentiation history of the relict species Rehderodendron kwangtungense Chun.ResultsA total of 138 individuals from 16 populations were collected, largely covering the natural distribution of R. kwangtungense. The genetic diversity within the R. kwangtungense populations was extremely low (HO = 0.048 ± 0.019; HE = 0.033 ± 0.011). Mantel tests revealed isolation-by-distance pattern (R2 = 0.38, P < 0.001), and AMOVA analysis showed that the genetic variation of R. kwangtungense occurs mainly between populations (86.88%, K = 7). Between 23 and 21 Ma, R. kwangtungense underwent a period of rapid differentiation that coincided with the rise of the Himalayas and the establishment of the East Asian monsoon. According to ENM and population demographic history, the suitable area and effective population size of R. kwangtungense decreased sharply during the glacial period and expanded after the last glacial maximum (LGM).ConclusionOur study shows that the distribution pattern of southern China mountain relict flora may have developed during the panplain stage between the middle Oligocene and the early Miocene. Then, the flora later fragmented under the force of orogenesis, including intermittent uplift during the Cenozoic Himalayan orogeny and the formation of abundant rainfall associated with the East Asian monsoon. The findings emphasized the predominant role of geographical processes in shaping relict plant distribution patterns.

Whole-genome selection signature differences between Chaohu and Ji'an red ducks.

Assessing the genetic structure of local varieties and understanding their genetic data are crucial for effective management and preservation. However, the genetic differences among local breeds require further explanation. To enhance our understanding of their population structure and genetic diversity, we conducted a genome-wide comparative study of Chaohu and Ji'an Red ducks using genome sequence and restriction site-associated DNA sequencing technology. Our analysis revealed a distinct genetic distinction between the two breeds, leading to divided groups. The phylogenetic tree for Chaohu duck displayed two branches, potentially indicating minimal impact from artificial selection. Additionally, our ROH (runs of homozygosity) analysis revealed that Chaohu ducks had a lower average inbreeding coefficient than Ji'an Red ducks. We identified several genomic regions with high genetic similarity in these indigenous duck breeds. By conducting a selective sweep analysis, we identified 574 candidate genes associated with muscle growth (BMP2, ITGA8, MYLK, and PTCH1), fat deposits (ELOVL1 and HACD2), and pigmentation (ASIP and LOC101797494). These results offer valuable insights for the further enhancement and conservation of Chinese indigenous duck breeds.

Low-coverage sequencing and Wahlund effect severely bias estimates of inbreeding, heterozygosity and effective population size in North American wolves.

vonHoldt etal. ((2024), Molecular Ecology, 33, e17231) (vH24) used low-coverage (average ~ 7X read depth) restriction site-associated DNA sequence data to estimate individual inbreeding and heterozygosity, and recent effective population size (Ne), in Great Lakes (GL) and Northern Rocky Mountain (RM) wolves. They concluded that RM heterozygosity rapidly declined between 1991 and 2020, and that Ne declined substantially in GL and RM over the last 50 generations. Here, we evaluate the effects of low sequence coverage and sampling strategy on vH24's findings and provide general recommendations for using sequence data to evaluate inbreeding, heterozygosity and Ne. Low-coverage sequencing resulted in downwardly biased estimates of individual inbreeding and heterozygosity, and an erroneous large temporal decline in RM heterozygosity due to declining read depth through time. Additionally, vH24's sampling strategy-which combined individuals from several genetically differentiated populations and across at least eight wolf generations-is expected to have resulted in severe downward bias in estimates of recent Ne for RM. We recommend using high-coverage sequence data ( 15-20X) to estimate inbreeding and heterozygosity. Carefully filtering individuals, loci and genotypes, and using genotype imputation or likelihoods can help to minimise bias when low-coverage sequence data must be used. For estimation of contemporary Ne, the marginal benefits of using more than 103-104 loci are small, so aggressive filtering of loci with low average read depth potentially can retain most individuals without sacrificing much precision. Individuals are relatively more valuable than loci because analyses of contemporary Ne should focus on roughly single-generation samples from local breeding populations.

Development of 51 K liquid-phased probe array for Loblolly and Slash pines and its application to GWAS of Slash pine breeding population

Loblolly pine (Pinus taeda) and Slash pine (Pinus elliottii) are important economically and ecologically tree species worldwide. To implement genomic based breeding strategy, genotyping large number of samples is needed. However, huge and complex pines genome make it difficult to obtain abundant and cost-effectively markers. In this study, we designed a SNP array containing 51 K liquid-phased probes based on the published SNPs and probes of the two species, novel Slash pine-specific long-read transcript, and SNPs obtained from a double digest Restriction-Site Associated DNA sequencing (ddRADseq). We performed targeted capture sequencing using the developed SNP array on three pine species of Loblolly, Slash, and Caribbean pine (Pinus caribaea). The probe capture had an efficiency of 68.26% on average. Principal Component Analysis (PCA), phylogenetic analysis, and genetic structure analysis of 28,670 SNPs genotyped for the three pine species demonstrated the transferability of the SNP array for the three pines. Furthermore, we genotyped 221 range-wide Slash pine genotypes, analyzed their genetic diversity and performed a genome-wide association study (GWAS). We identified 95 SNPs significantly associated with growth and wood quality traits of Slash pine. We have identified potential roles of the MYB2 and MYB46 transcription factors in regulating cell cycle and differentiation in Slash pine, while also suggesting that AP2/ERF and Glycosyl hydrolase may play significant roles in wood formation processes. This new SNP array can be widely applied in future molecular breeding research of conifers.

Genomic evaluation of mud sunfish in the atlantic slope drainage

Mud Sunfish (Acantharchus pomotis, Baird), a cryptic species native to the Atlantic and Gulf slope drainages of North America, have experienced a documented reduction in their geographic range. Atlantic Slope populations of Mud Sunfish were evaluated to determine the population structure, assess genetic diversity, and to identify presence of evolutionary significant units (ESU) in order to develop fundamental understandings of its occurrence. Tissue samples were collected from across the Atlantic Slope for genomic comparison. Restriction site Associated DNA Sequencing (RAD-Seq) was performed on 95 individuals from 14 populations. Mantel test provided evidence of a correlation between genetic and geographical distances, suggesting a pattern of isolation-by-distance. Differences among populations of Mud Sunfish largely occur along a north-south latitudinal gradient. Bayesian clustering of putatively outlier SNP loci, suggests that regional adaptive pressure is occurring. Despite a large geographic distance and significant differences between the majority of the populations of Mud Sunfish, Bayesian clustering analysis suggests that two unresolved clades are persisting within the Atlantic Slope Drainage: a northern clade of Mud Sunfish ranging from New Jersey to North Carolina and a southern clade ranging from South Carolina to Florida. A population of Mud Sunfish in Florida appears distinct from all others in the Atlantic Coastal plain and likely represents a distinct management unit.

Genome-wide association study reveals candidate genes critical for skin pigmentation in common carp (Cyprinus carpio) strains including koi

The differentiation and variation of body color in fish is an important component of biological evolution and phylogenetic research, and is influenced by several factors such as heredity, nutrition, physiological hormones and rearing conditions, with heredity being the most critical factor. An improved comprehension of the genetic regulation in different carp populations will facilitate future applications of precision breeding and pigment cell development-related genes editing. In this study, we used restriction site-associated DNA sequencing (2d-RAD) to determine the distribution characteristics of single nucleotide polymorphisms (SNPs) in eight common carp strains including six koi strains, i.e., Kohaku (Hb), Taisho (Dz), Showa (Zh), Golden (Hj), Matsukawabake (Sch) and Five-color (Ws), and two genetically improved breeding strains, i.e., FFRC No. 2 strain (Fr) and red FFRC strain (Hfr), and then SNP markers to resolve genetic information on the population structure and skin color formation of these strains. We found that most individuals of eight strains were clearly divided into eight clades. Genetic diversity within Fr, Sch and Ws is relatively high, while it is low within Dz, Hb and Hfr. A comparison between the populations revealed that Hfr and Ws have the highest degree of genetic differences, while Hb and Dz have the lowest. The GWAS analysis for two strategies identified several SNPs that are significantly related to skin color variation and affect melanin synthesis (ephrinb2, slc22a23, herc2, ephb2), carotenoid metabolism (oca2, bcmo1, bco2) and circadian rhythm(cipc). To summarize, our study provides some information on the genetic structure and diversity of Japanese koi and Chinese FFRC carp. Furthermore, based on the data obtained on relevant genes related to skin color differentiation and pigmentation, it can provide a theoretical basis for the subsequent integration of dominant traits and precision breeding in carps.

Genetic diversity and population structure of four Anatolian sheep revealed by genome-wide ddRADseq data

This is the first wide-scale study to reveal next-generation sequencing-based and comprehensive study to reveal genetic diversity, population structure, and phylogenetic relationships of some of Türkiye's indigenous fat-tailed sheep breeds. A total of 80 animals belonging to Akkaraman (AKR), Güney Karaman (GKR), Morkaraman (MKR), and Karakaş (KRK) sheep breeds were genotyped with genome-wide of 296.097 single nucleotide polymorphisms (SNPs) data recovered from double digest restriction site-associated DNA sequencing (ddRADseq) libraries processed by Illumina HiSeq X Ten instrument. Minor allele frequency (MAF) ranged from 0.311 (MKR) to 0.316 (AKR and GKR). Observed heterozygosity (HO) values were higher than expected values (HE) across all populations with a mean of 0.307. Negative inbreeding coefficient (FIS) values were observed in four sheep populations varying between −0.034 (AKR) to −0.060 (MKR). Cross-entropy criterion-based ADMIXTURE analysis demonstrated that four Anatolian sheep breeds were represented by two ancestral populations in which GKR and AKR were distinct, while KRK and MKR were mixed populations. Genetic distance-based tree, discriminant analysis of principal components (DAPC), and ADMIXTURE analyses confirmed that GKR, which is believed to be derived from the AKR breed, has become genetically different from other sheep populations. Moreover, no migration from and into the GKR breed was detected, while a migration edge was drawn from the KRK and MKR clade into the AKR breed by the TreeMix algorithm. This study confirmed that high-density SNP data obtained from advanced next-generation sequencing (NGS) platforms are efficient in genetically distinguishing animal breeds, even varieties. It is recommended that further NGS-based studies could be carried out to better characterize different indigenous livestock populations raised in Türkiye.

Genetic divergence and adaptation of an isolated European lobster population in the Netherlands

Abstract Identifying isolated populations is a key step towards enacting effective conservation management. European lobsters (Homarus gammarus) from Oosterschelde in the Netherlands are subject to fishery pressure and have previously been reported as genetically differentiated. They are also putatively of transplanted origin and have subsequently endured recent bottlenecking and environmental change. We assessed Oosterschelde lobsters to evaluate their demographic independence and appraise potential founder effects and evolutionary responses to isolation. Using restriction-site associated DNA sequencing, we genotyped 6185 single nucleotide polymorphisms across 188 individuals from 27 sites across the Atlantic range of H. gammarus to investigate population genetic diversity, structure, and potential adaptation. Our results show that Oosterschelde lobsters are genetically divergent from other stocks. We evidence extensive differentiation via both neutral and outlier loci, indicative of strong biophysical and demographic isolation, and detect signatures of reduced genetic diversity that may reflect weak founder effects or subsequent population contractions. Among outlier loci, we identify candidates for range-wide local adaptation via variants in genes of important biological functionality and link a private allele of Oosterschelde to a locus potentially conveying adaptive tolerance to environmental hypoxia. Given our findings, we advise proactive monitoring of Oosterschelde lobsters to explore whether existing management measures effectively conserve this discrete, self-recruiting population.

A Diverging Species within the Stewartia gemmata (Theaceae) Complex Revealed by RAD-Seq Data.

Informed species delimitation is crucial in diverse biological fields; however, it can be problematic for species complexes. Showing a peripatric distribution pattern, Stewartia gemmata and S. acutisepala (the S. gemmata complex) provide us with an opportunity to study species boundaries among taxa undergoing nascent speciation. Here, we generated genomic data from representative individuals across the natural distribution ranges of the S. gemmata complex using restriction site-associated DNA sequencing (RAD-seq). Based on the DNA sequence of assembled loci containing 41,436 single-nucleotide polymorphisms (SNPs) and invariant sites, the phylogenetic analysis suggested strong monophyly of both the S. gemmata complex and S. acutisepala, and the latter was nested within the former. Among S. gemmata individuals, the one sampled from Mt. Tianmu (Zhejiang) showed the closest evolutionary affinity with S. acutisepala (which is endemic to southern Zhejiang). Estimated from 2996 high-quality SNPs, the genetic divergence between S. gemmata and S. acutisepala was relatively low (an Fst of 0.073 on a per-site basis). Nevertheless, we observed a proportion of genomic regions showing relatively high genetic differentiation on a windowed basis. Up to 1037 genomic bins showed an Fst value greater than 0.25, accounting for 8.31% of the total. After SNPs subject to linkage disequilibrium were pruned, the principal component analysis (PCA) showed that S. acutisepala diverged from S. gemmata along the first and the second PCs to some extent. By applying phylogenomic analysis, the present study determines that S. acutisepala is a variety of S. gemmata and is diverging from S. gemmata, providing empirical insights into the nascent speciation within a species complex.

Intergeneric hybrid origin of the invasive tetraploid Cirsium vulgare.

The invasive tetraploid Cirsium vulgare hybridizes with both Cirsium and Lophiolepis. Its conflicted position in molecular phylogenies, and its peculiar combination of morphological, anatomical, and genomic features that are alternatively shared with representatives of Cirsium or Lophiolepis, strongly suggest its intergeneric hybrid origin. Genetic relationships of C. vulgare (8 samples) with genus Lophiolepis (11 species) and other representatives of genus Cirsium (12 species) were evaluated using restriction site-associated DNA sequencing (RADseq) and examined using analytical and imaging approaches, such as NeighborNet, Heatmap, and STRUCTURE, to identify nuclear genomes admixture. Estimation of the intensity of spontaneous hybridization within and between Cirsium and Lophiolepis was based on herbarium revisions and published data for all reported hybrids pertinent to taxa currently included in Cirsium or Lophiolepis. The genome of any examined Cirsium species is more similar to C. vulgare than to any Lophiolepis species, and vice versa. The nuclear genome of the tetraploid C. vulgare is composed of two equivalent parts, each attributable either to Lophiolepis or to Cirsium; the organellar RADseq data clustered C. vulgare with the genus Cirsium. Spontaneous hybridization between Cirsium and Lophiolepis is significantly less intensive than within these genera. Our analyses provide compelling evidence that the invasive species C. vulgare has an allotetraploid intergeneric origin, with the maternal parent from Cirsium and the paternal from Lophiolepis. For the purpose of delimiting monophyletic genera, we propose keeping Lophiolepis separate from Cirsium and segregating C. vulgare into the hybridogenous genus Ascalea.

Different reference genomes determine different results: Comparing SNP calling in RAD-seq of Engelhardia roxburghiana using different reference genomes

Advances in next-generation sequencing (NGS) have significantly reduced the cost and improved the efficiency of obtaining single nucleotide polymorphism (SNP) markers, particularly through restriction site-associated DNA sequencing (RAD-seq). Meanwhile, the progression in whole genome sequencing has led to the utilization of an increasing number of reference genomes in SNP calling processes. This study utilized RAD-seq data from 242 individuals of Engelhardia roxburghiana, a tropical tree of the walnut family (Juglandaceae), with SNP calling conducted using the STACKS pipeline. We aimed to compare both reference-based approaches, namely, employing a closely related species as the reference genome versus the species itself as the reference genome, to evaluate their respective merits and limitations. Our findings indicate a substantial discrepancy in the number of obtained SNPs between using a closely related species as opposed to the species itself as reference genomes, the former yielded approximately an order of magnitude fewer SNPs compared to the latter. While the missing rate of individuals and sites of the final SNPs obtained in the two scenarios showed no significant difference. The results showed that using the reference genome of the species itself tends to be prioritized in RAD-seq studies. However, if this is unavailable, considering closely related genomes is feasible due to their wide applicability and low missing rate as alternatives. This study contributes to enrich the understanding of the impact of SNP acquisition when utilizing different reference genomes.

Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data.

Islands provide a great system to explore the processes that maintain genetic diversity and promote local adaptation. We explored the genomic diversity of the Balearic lizard Podarcis lilfordi, an endemic species characterized by numerous small insular populations with large phenotypic diversity. Using the newly available genome for this species, we characterized more than 300,000 SNPs, merging genotyping-by-sequencing (GBS) data with previously published restriction site-associated DNA sequencing (RAD-Seq) data, providing a dataset of 16 island populations (191 individuals) across the range of species distribution (Menorca, Mallorca, and Cabrera). Results indicate that each islet hosts a well-differentiated population (F ST = 0.247 ± 0.09), with no recent immigration/translocation events. Contrary to expectations, most populations harbor a considerable genetic diversity (mean nucleotide diversity, P i = 0.144 ± 0.021), characterized by overall low inbreeding values (F IS < 0.1). While the genetic diversity significantly decreased with decreasing islet surface, maintenance of substantial genetic diversity even in tiny islets suggests variable selection or other mechanisms that buffer genetic drift. Maximum-likelihood tree based on concatenated SNP data confirmed the existence of the two major independent lineages of Menorca and Mallorca/Cabrera. Multiple lines of evidence, including admixture and root testing, robustly placed the origin of the species in the Mallorca Island, rather than in Menorca. Outlier analysis mainly retrieved a strong signature of genome differentiation between the two major archipelagos, especially in the sexual chromosome Z. A set of proteins were target of multiple outliers and primarily associated with binding and catalytic activity, providing interesting candidates for future selection studies. This study provides the framework to explore crucial aspects of the genetic basis of phenotypic divergence and insular adaptation.

Genomic signatures of hybridization between Ixodes ricinus and Ixodes persulcatus in natural populations.

Identifying hybridization between common pathogen vectors is essential due to the major public health implications through risks associated with hybrid's enhanced pathogen transmission potential. The hard-ticks Ixodes ricinus and Ixodes persulcatus are the two most common vectors of tick-borne pathogens that affect human and animal health in Europe. Ixodes ricinus is a known native species in Finland with a well-known distribution, whereas I. persulcatus has expanded in range and abundance over the past 60 years, and currently it appears the most common tick species in certain areas in Finland. Here we used double-digest restriction site-associated DNA (ddRAD) sequencing on 186 ticks (morphologically identified as 92 I. ricinus, and 94 I. persulcatus) collected across Finland to investigate whether RAD generated single nucleotide polymorphisms (SNPs) can discriminate tick species and identify potential hybridization events. Two different clustering methods were used to assign specific species based on how they clustered and identified hybrids among them. We were able to discriminate between the two tick species and identified 11 putative hybrids with admixed genomic proportions ranging from approximately 24 to 76 percent. Four of these hybrids were morphologically identified as I. ricinus while the remaining seven were identified as I. persulcatus. Our results thus indicate that RAD SNPs are robust in identifying both species of the ticks as well as putative hybrids. These results further suggest ongoing hybridization between I. ricinus and I. persulcatus in their natural populations in Finland. The unique ability of RAD markers to discriminate between tick species and hybrids adds a useful aspect to tick evolutionary studies. Our findings align with previous studies and suggest a shared evolutionary history between the species, with instances of individuals possessing a considerable proportion of the other species' genome. This study is a significant step in understanding the formation of hybridization zones due to range expansion potentially associated with climate change.

Niche conservatism and spread explain introgression between native and invasive fish.

Hybridisation can be an important driver of evolutionary change, but hybridisation with invasive species can have adverse effects on native biodiversity. While hybridisation has been documented across taxa, there is limited understanding of ecological factors promoting patterns of hybridisation and the spatial distribution of hybrid individuals. We combined the results of ecological niche modelling (ENM) and restriction site-associated DNA sequencing to test theories of niche conservatism and biotic resistance on the success of invasion, admixture, and extent of introgression between native and non-native fishes. We related Maxent predictions of habitat suitability based on the native ranges of invasive Eastern Banded Killifish (Fundulus diaphanus diaphanus Lesueur 1817) and native Western Banded Killifish (Fundulus diaphanus menona Jordan and Copeland 1877) to admixture indices of individual Banded Killifish. We found that Eastern Banded Killifish predominated at sites predicted as suitable from their ENM, consistent with niche conservatism. Admixed individuals were more common as Eastern Banded Killifish habitat suitability declined. We also found that Eastern Banded Killifish were most common at sites closest to the presumed source of this invasion, whereas the proportion of admixed individuals increased with distance from the source of invasion. Lastly, we found little evidence that habitat suitability for Western Banded Killifish provides biotic resistance from either displacement by, or admixture with, invasive Eastern Banded Killifish. Our study demonstrates that ENMs can inform conservation-relevant outcomes between native and invasive taxa while emphasising the importance of protecting isolated Western Banded Killifish populations from invasive conspecifics.

Comprehensive genome assembly reveals genetic diversity and carcass consumption insights in critically endangered Asian king vultures

The Asian king vulture (AKV), a vital forest scavenger, is facing globally critical endangerment. This study aimed to construct a reference genome to unveil the mechanisms underlying its scavenger abilities and to assess the genetic relatedness of the captive population in Thailand. A reference genome of a female AKV was assembled from sequencing reads obtained from both PacBio long-read and MGI short-read sequencing platforms. Comparative genomics with New World vultures (NWVs) and other birds in the Family Accipitridae revealed unique gene families in AKV associated with retroviral genome integration and feather keratin, contrasting with NWVs’ genes related to olfactory reception. Expanded gene families in AKV were linked to inflammatory response, iron regulation and spermatogenesis. Positively selected genes included those associated with anti-apoptosis, immune response and muscle cell development, shedding light on adaptations for carcass consumption and high-altitude soaring. Using restriction site-associated DNA sequencing (RADseq)-based genome-wide single nucleotide polymorphisms (SNPs), genetic relatedness and inbreeding status of five captive AKVs were determined, revealing high genomic inbreeding in two females. In conclusion, the AKV reference genome was established, providing insights into its unique characteristics. Additionally, the potential of RADseq-based genome-wide SNPs for selecting AKV breeders was demonstrated.

Development and utilization of genome-wide InDel markers in Sorghum [Sorghum bicolor (L.) Moench

Sorghum (Sorghum bicolor L. Moench) has become an increasingly valuable crop for food, feed, and especially bioenergy feedstock production, which makes the crop extremely attractive for studying genomics and genetic diversity. Molecular markers and genomics play essential roles in sorghum breeding. The rapid development of next-generation sequencing technology has facilitated the identification of genome-wide insertion-deletion (InDel) polymorphisms, enabling the efficient construction of InDel markers that are suitable for user-friendly PCR. This study was conducted with the objective of discovering and developing InDel markers using double digest restriction site-associated DNA sequencing (ddRAD-Seq) data. A total of 19,226 InDels distributed across 10 chromosomes in the sorghum genome was identified. Of those, deletions constituted 65.7% while the remain was insertions. A comprehensive analysis of all the chromosomes revealed a total of 80 InDel sites with a minimum length of 10 bp. For a good conversion of the InDel regions to beneficial molecular markers, specific primers were designed for the amplification of 47 InDel regions that were selected for further investigation. A diverse panel of sorghum consisting of 16 accessions served a source for the developed InDel markers validation. Of the 47 InDel markers, 14 were tested across 16 sorghum accessions and were demonstrated their helpfulness for marker-assisted selection in sorghum. The polymorphic information content (PIC) values of the 16 markers varied between 0.11 and 0.38, with an average of 0.28. The findings of this study indicated that the identification of InDels and the development of molecular markers for sorghum were accomplished using the ddRAD-Seq data.