Restriction Site-associated DNA Sequencing Research Articles

Genome-Wide Data Uncover Cryptic Diversity With Multiple Reticulation Events in the Balkan-Anatolian Cardamine (Brassicaceae) Species Complex.

Plant species diversity may be considerably underestimated, especially in evolutionarily complex genera and in diversity hotspots that have enabled long-term species persistence and diversification, such as the Balkan Peninsula. Here, we address the topic of underexplored plant diversity and underlying evolutionary and biogeographic processes by investigating the hygrophytic mountain species complex of Cardamine acris s.l. distributed in the Balkans (three subspecies within C. acris) and northwestern Anatolia (C. anatolica). We performed a series of phylogenetic and phylogeographic analyses based on restriction-site associated DNA sequencing (RADseq) and target enrichment (Hyb-Seq) data in combination with habitat suitability modelling. We found C. anatolica as a clade nested within the Balkan C. acris, probably resulting from a founder event, and uncovered three allopatric cryptic lineages within C. acris subsp. acris, allowing us to recognise a total of six entities in this complex. We observed the deepest genetic split within C. acris subsp. acris in the western Balkans, which was at odds with taxonomy and showed no distribution gap. We inferred vicariance as the most likely process for population divergence in the Balkans, accompanied by gene flow between the recognised entities, which was consistent with the modelled habitat suitability dynamics. Furthermore, we discovered several polyploid populations in C. acris, representing both pure intra- and inter-lineage hybrid polyploids, but detected only minor traces of hybridization with related congeners. Overall, our results illustrate that diverse evolutionary processes may influence the history of mountain plant species in the Balkan Peninsula, including vicariance, reticulation, polyploidization and cryptic diversification.

Differentiation of wild accessions within the Panax bipinnatifidus complex using newly developed polymorphic microsatellite markers

Abstract Panax L., renowned as ginseng genus, is a famous medicinal group of family Araliaceae. Within this genus, the taxa of Panax bipinnatifidus complex are mainly distributed in Himalayas and Hengduan Mountain areas. Due to the complex evolutionary history and short-term rapid radiation, the relationships among species within the complex have not been clearly resolved, and the taxa identification is difficult due to the intermediate morphological traits. This study aimed to use the available restriction-site associated DNA sequence data from 29 individuals of P. bipinnatifidus complex to mine high-polymorphic simple sequence repeat (SSR) markers, with the goal of evaluating their utility in taxa identification. Eleven polymorphic SSR loci were ultimately selected and validated through polymerase chain reactions amplifying across 63 individuals of P. bipinnatifidus complex and 13 individuals of three outgroup species. The subsequent genetic diversity analysis uncovered 76 alleles in total, ranging from 5 to 15 per locus. Observed heterozygosity spanned 0.241–0.512, while expected heterozygosity ranged between 0.345 and 0.644. The genetic kinship analysis revealed a sister relationship between Panax zingiberensis and Panax vietnamensis. The analysis result also supported the classification of samples from Hunan and Hubei provinces into a single genetic unit within the P. bipinnatifidus complex. These newly developed SSR markers will facilitate the identification of wild ginseng plants.

The origin and morphological character evolution of the paleotropical woody bamboos.

The woody bamboos (Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkable morphological diversity across the subfamily exists within a single hexaploid clade, the paleotropical woody bamboos (PWB), making it ideal to investigate the factors underlying morphological evolution in woody bamboos. However, the origin and biogeographical history of PWB remain elusive, as does the effect of environmental factors on the evolution of their morphological characters. We generated a robust and time-calibrated phylogeny of PWB using single nucleotide polymorphisms retrieved from optimized double digest restriction site associated DNA sequencing, and explored the evolutionary trends of habit, inflorescence, and caryopsis type in relation to environmental factors including climate, soil, and topography. We inferred that the PWB started to diversify across the Oligocene-Miocene boundary and formed four major clades, that is, Melocanninae, Racemobambosinae s.l. (comprising Dinochloinae, Greslanlinae, Racemobambosinae s.str. and Temburongiinae), Hickeliinae and Bambusinae s.l. (comprising Bambusinae s.str. plus Holttumochloinae). The ancestor of PWB was reconstructed as having erect habit, indeterminate inflorescence and basic caryopsis. The characters including climbing/scrambling habit, determinate inflorescence, and nucoid/bacoid caryopsis have since undergone multiple changes and reversals during the diversification of PWB. The evolution of all three traits was correlated with, and hence likely influenced by, aspects of climate, topography, and soil, with climate factors most strongly correlated with morphological traits, and soil factors least so. However, topography had more influence than climate or soil on the evolution of erect habit, whereas both factors had greater effect on the evolution of bacoid caryopsis than did soil. Our results provide novel insights into morphological diversity and adaptive evolution in bamboos for future ecological and evolutionary research.

Genome-wide analysis tracks the emergence of intraspecific polyploids in Phragmites australis

Polyploidization plays an important role in plant speciation and adaptation. To address the role of polyploidization in grass diversification, we studied Phragmites australis, an invasive species with intraspecific variation in chromosome numbers ranging from 2n = 36 to 144. We utilized a combined analysis of ploidy estimation, phylogeny, population genetics and model simulations to investigate the evolution of P. australis. Using restriction site-associated DNA sequencing (RAD-seq), we conducted a genome-wide analysis of 88 individuals sourced from diverse populations worldwide, revealing the presence of six distinct intraspecific lineages with extensive genetic admixture. Each lineage was characterized by a specific ploidy level, predominantly tetraploid or octoploid, indicative of multiple independent polyploidization events. The population size of each lineage has declined moderately in history while remaining large, except for the North American native and the US Land types, which experienced constant population size contraction throughout their history. Our investigation did not identify direct association between polyploidization events and grass invasions. Nonetheless, we observed octoploid and hexaploid lineages at contact zones in Romania, Hungary, and South Africa, suggestively due to genomic conflicts arising from allotetraploid parental lineages.

The Range‐Wide Genetic Structure of a High‐Elevation Conifer Species, Subalpine Larch

ABSTRACTAimSubalpine larch is a long‐lived conifer with a restricted distribution at treeline in the mountains of western North America. Climate change is reducing the availability of this habitat and subalpine larch is unlikely to adapt to its changing environment due to its long generation time, relatively low levels of standing genetic variation and the high degree of habitat fragmentation across the species' range. This study seeks to elucidate the genetic structure of subalpine larch to inform future conservation and management efforts.LocationWestern North America.TaxonSubalpine larch (Larix lyallii Parl.).MethodsTissue was collected from high‐elevation populations across the entire species range. Restriction site associated DNA sequencing was used to generate single nucleotide polymorphism (SNP) data. Population genetic analyses identified genetic differentiation.ResultsClustering analyses performed using 751 neutral SNPs identified three genetically differentiated regions: the Cascade Range, the southern Rocky Mountains and the northern Rocky Mountains. AMOVA confirmed significant genetic differentiation among regions. A discriminant analysis of principal components and a dendrogram of Provesti's genetic distance both supported the hypothesis that genetically distinct lineages arose after dispersal from a single Pleistocene refugium. Significant isolation by distance (IBD) supported the key role of dispersal in shaping modern patterns of genetic variation in subalpine larch.Main ConclusionsPost‐Pleistocene dispersal resulted in genetic differentiation among groups of subalpine larch in the Cascade Range, the southern Rocky Mountains and the northern Rocky Mountains. These three regions should be prioritised for future management.

Identification of Insertion and Deletion (InDel) Markers for Chickpea (Cicer arietinum L.) Based on Double-Digest Restriction Site-Associated DNA Sequencing.

Enhancing the marker repository and the development of breeder-friendly markers in chickpeas is important in relation to chickpea genomics-assisted breeding applications. Insertion-deletion (InDel) markers are widely distributed across genomes and easily observed with specifically designed primers, leading to less time, cost, and labor requirements. In light of this, the present study focused on the identification and development of InDel markers through the use of double-digest restriction site-associated DNA sequencing (ddRADSeq) data from 20 chickpea accessions. Bioinformatic analysis identified 20,700 InDel sites, including 15,031 (72.61%) deletions and 5669 (27.39%) insertions, among the chickpea accessions. The InDel markers ranged from 1 to 25 bp in length, while single-nucleotide-length InDel markers were found to represent the majority of the InDel sites and account for 79% of the total InDel markers. However, we focused on InDel markers wherein the length was greater than a single nucleotide to avoid any read or alignment errors. Among all of the InDel markers, 96.1% were less than 10 bp, 3.6% were between 10 and 20 bp, and 0.3% were more than 20 bp in length. We examined the InDel markers that were 10 bp and longer for the development of InDel markers based on a consideration of the genomic distribution and low-cost genotyping with agarose gels. A total of 29 InDel regions were selected, and primers were successfully designed to evaluate their efficiency. Annotation analysis of the InDel markers revealed them to be found with the highest frequency in the intergenic regions (82.76%), followed by the introns (6.90%), coding sequences (6.90%), and exons (3.45%). Genetic diversity analysis demonstrated that the polymorphic information content of the markers varied from 0.09 to 0.37, with an average of 0.20. Taken together, these results showed the efficiency of InDel marker development for chickpea genetic and genomic studies using the ddRADSeq method. The identified markers might prove valuable for chickpea breeders.

Conservation genomic study of Hopea hainanensis (Dipterocarpaceae), an endangered tree with extremely small populations on Hainan Island, China.

Hopea hainanensis Merrill & Chun is considered a keystone and indicator species in the tropical lowland rainforests of Hainan Island. Owing to its high-quality timber, H. hainanensis has been heavily exploited, leading to its classification as a first-class national protected plant in China and a plant species with extremely small populations (PSESPs). This study analyzed genome-wide single nucleotide polymorphisms obtained through restriction site-associated DNA sequencing from 78 adult trees across 10 H. hainanensis populations on Hainan Island. The nucleotide diversity of the sampled populations ranged from 0.00096 to 0.00138, which is lower than that observed in several other PSESPs and endangered tree species. Bayesian unsupervised clustering, principal component analysis, and neighbor-joining tree reconstruction identified three to five genetic clusters in H. hainanensis, most of which were geographically widespread and shared by multiple populations. Demographic history analysis based on pooled samples indicated that the decline in the H. hainanensis population began approximately 20,000 years ago, starting from an ancestral population size of approximately 10,000 individuals. The reduction in population size accelerated approximately 4,000 years ago and has continued to the present, resulting in a severely reduced population on Hainan Island. Intensified genetic drift in small and isolated H. hainanensis populations may contribute to moderate differentiation between some of them, as revealed by pairwise F st. In conclusion, our conservation genomic study confirms a severe population decline and an extremely low level of nucleotide variation in H. hainanensis on Hainan Island. These findings provide critical insights for the sustainable management and genetic restoration of H. hainanensis on Hainan Island.

How do hydroelectric dams affect non-migratory fish?: genomic evidence for Cichla temensis (Perciformes: Cichlidae) in the Uatumã River, Amazonas, Brazil

Abstract The Balbina hydroelectric dam was built in the 1980s on the Uatumã River to supply electricity to Manaus, capital of the state of Amazonas, Brazil. Its construction caused a drastic change to the alluvial landscape, forming a large, lentic, artificial reservoir rather than a previously dynamic river system. The objective of our research was to evaluate the impact of the hydroelectric dam on the microevolutionary processes of fish, taking as a model Cichla temensis, an iconic non-migratory fish from the Amazon, abundant in this ecosystem. We collected double digest restriction site-associated DNA sequencing data and extracted single nucleotide polymorphisms, which we identified at neutral and adaptive loci, for subsequent analyses. The results showed that the connectivity of the population was affected historically by natural physical barriers, before the construction of the hydroelectric dam, recognizing two independent population units. We detected that the hydroelectric dam increased the differentiation between populations and affected the genetic diversity and effective population sizes, in addition to promoting a recent population expansion upstream of the dam, as a consequence of adaptation to the new environment. This study provides the first evidence that hydroelectric dams can promote local adaptation in some fish, such as non-migratory ones.

Climate change vulnerability and conservation strategies for tertiary relict tree species: Insights from landscape genomics ofTaxus cuspidata.

The unprecedented habitat fragmentation or loss has threatened the existence of many species. Therefore, it is essential to understand whether and how these species can pace with the environmental changes. Recent advantages in landscape genomics enabled us to identify molecular signatures of adaptation and predict how populations will respond to changing environments, providing new insights into the conservation of species. Here, we investigated the pattern of neutral and putative adaptive genetic variation and its response to changing environments in a tertiary relict tree species, Taxus cuspidata Sieb. et Zucc, which is distributed in northeast China and adjacent regions. We investigated the pattern of genetic diversity and differentiation using restriction site-associated DNA sequencing (RAD-seq) and seven nuclear microsatellites (nSSRs) datasets. We further explored the endangered mechanism, predicted its vulnerability in the future, and provided guidelines for the conservation and management of this species. RAD-seq identified 16,087 single nucleotide polymorphisms (SNPs) in natural populations. Both the SNPs and nSSRs datasets showed high levels of genetic diversity and low genetic differentiation in T. cuspidata. Outlier detection by F ST outlier analysis and genotype-environment associations (GEAs) revealed 598 outlier SNPs as putative adaptive SNPs. Linear redundancy analysis (RDA) and nonlinear gradient forest (GF) showed that the contribution of climate to genetic variation was greater than that of geography, and precipitation played an important role in putative adaptive genetic variation. Furthermore, the genetic offset and risk of non-adaptedness (RONA) suggested that the species at the northeast edge may be more vulnerable in the future. These results suggest that although the species has maintained high current genetic diversity in the face of recent habitat loss and fragmentation, future climate change is likely to threaten the survival of the species. Temperature (Bio03) and precipitation (Prec05) variables can be potentially used as predictors of response of T. cuspidata under future climate. Together, this study provides a theoretical framework for conservation and management strategies for wildlife species in the context of future climate change.

Adaptive radiation of the Callicarpa genus in the Bonin Islands revealed through double-digest restriction site-associated DNA sequencing analysis.

The Bonin Islands, comprised of the Mukojima, Chichijima, and Hahajima Islands, are known for their isolated and distinctive habitats, hosting a diverse array of endemic flora and fauna. In these islands, adaptive radiation has played a remarkable role in speciation, particularly evident in the Callicarpa genus that is represented by three species: Callicarpa parvifolia and C. glabra exclusive to the Chichijima Islands, and Callicarpa subpubescens, distributed across the entire Bonin Islands. Notably, C. subpubescens exhibits multiple ecotypes, differing in leaf hair density, flowering time, and tree size. In this study, we aimed to investigate species and ecotype diversification patterns, estimate divergence times, and explore cryptic species within Callicarpa in the Bonin Islands using phenotypic and genetic data (double-digest restriction site-associated DNA sequencing). Genetic analysis revealed that C. parvifolia and C. glabra both formed single, distinct genetic groups. Conversely, C. subpubescens consisted of six genetic groups corresponding to different ecotypes and regions, and a hybrid group resulting from the hybridization between two of these genetic groups. Population demography analysis focusing on six Chichijima and Hahajima Islands-based species/ecotypes indicated that all species and ecotypes except one ecotype diverged simultaneously around 73-77 kya. The star-shaped neighbor-net tree also suggests the simultaneous divergence of species and ecotypes. The species and ecotypes that simultaneously diverged adapted to dry environments and understory forests, suggesting that aridification may have contributed to this process of adaptive radiation. Moreover, leaf morphology, flowering time, and genetic analyses suggested the presence of two cryptic species and one hybrid species within C. subpubescens.

Genomic Regions Associated with Growth and Reproduction Traits in Pink-Eyed White Mink.

In mink breeding, balanced selection for growth and reproductive features is essential because these traits are contradictory. The variables of total number born (TNB), number born alive (NBA), and body weight (BW) are highly valuable in terms of their importance in mink production. A comprehensive understanding of the molecular mechanisms that drive these features could offer vital insights into their genetic compositions. In the present study, the single-nucleotide polymorphism (SNP) genotypes of 219 minks were obtained via double digest restriction-site associated DNA sequencing (ddRAD-seq). Following several rounds of screening, about 2,415,121 high-quality SNPs were selected for a genome-wide association study (GWAS). The GWAS was used to determine BW and reproductive traits in pink-eyed white mink. It was suggested that SLC26A36, STXBP5L, and RPS 29 serve as potential genes for the total number of kits born (TNB), while FSCB, PDPN, NKX 2-1, NFKB 1, NFKBIA, and GABBR1 are key genes for the number born alive (NBA). Moreover, RTTN, PRPF31, MACROD1, and KYAT1 are possible BW genes based on association results and available functional data from gene and mammalian phenotype databases. These results offer essential information about the variety of mink and theoretical principles for applying mink breeds.

Reduced representation sequencing reveals weak genetic differentiation between Canadian and European Larus hyperboreus (Glaucous Gull)

Abstract Climate change poses a significant threat to Arctic ecosystems. Evaluation of genetic diversity within and differentiation among populations is needed to effectively conserve Arctic species and ensure genetic variation is appropriately managed. This research examined population genetic structure in Larus hyperboreus (Glaucous Gull), a circumpolar Arctic species that is declining in parts of its range. Population genetic information is needed to help delineate management units, including information on genetic differences among related species, among subspecies (currently distinguished by subtle morphometric and plumage differences), and among colonies in North America. We conducted double-digest restriction site-associated DNA sequencing for 62 L. hyperboreus, 18 L. argentatus smithsonianus (American Herring Gull), 6 L. a. argentatus (European Herring Gull), and 15 L. glaucescens (Glaucous-winged Gull) sampled across the Canadian and European Arctic. Interspecific analyses using 2,145 loci were unable to distinguish members of this species complex. Despite the geographic distance among sampling locations, molecular assignments and principal coordinates analyses based on 621 loci uncovered only weak population genetic differentiation among sampled European and Canadian colonies of L. hyperboreus. As L. hyperboreus occupying the eastern Canadian Arctic appear to be acting as a single panmictic population, conservation plans that protect Arctic habitat may help slow or reverse population declines. Proactive conservation strategies will benefit both L. hyperboreus and associated coastal Arctic ecosystems.

High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits in Camellia oleifera Based on Double Digest Restriction Site-Associated DNA Sequencing.

Camellia oleifera, an important tree species and source of edible oil in China, has received significant attention owing to the oil's high unsaturated fatty acid content, which has benefits for human health. However, the mechanisms underlying C. oleifera yield and oil quality are largely unknown. In this study, 180 F1 progenies were obtained from two parents with obvious differences in fruit- and oil-related traits. We constructed a high-density genetic map using a double digest restriction site-associated DNA sequencing (ddRAD-Seq) strategy in C. oleifera. This map spanned 3327 cM and anchored 2780 markers in 15 linkage groups (LGs), with an average marker interval of 1.20 cM. A total of 221 quantitative trait loci (QTLs) associated with fruit- and oil-related traits were identified across three years' worth of phenotypic data. Nine QTLs were detected simultaneously in at least two different years, located on LG02, LG04, LG05, LG06, and LG11, and explained 8.5-16.6% of the phenotypic variation in the corresponding traits, respectively. Seventeen major QTLs were obtained that explained 13.0-16.6% of the phenotypic variance. Eleven and five flanking SNPs of major QTLs for fruit- and oil-related traits were detected which could be used for marker-assisted selection in C. oleifera breeding programs. Furthermore, 202 potential candidate genes in QTL regions were identified based on the collinearity of the genetic map and the C. oleifera "CON" genome. A potential regulatory network controlling fruit development and oil biosynthesis was constructed to dissect the complex mechanism of oil accumulation. The dissection of these QTLs will facilitate the gene cloning underlying lipid synthesis and increase our understanding in order to enhance C. oleifera oil yield and quality.

Impact of Long-Term Pyriproxyfen Exposure on the Genetic Structure and Diversity of Aedes aegypti and Aedes albopictus in Manaus, Amazonas, Brazil.

Aedes aegypti and Aedes albopictus are responsible for transmitting major human arboviruses such as Dengue, Zika, and Chikungunya, posing a global threat to public health. The lack of etiological treatments and efficient vaccines makes vector control strategies essential for reducing vector population density and interrupting the pathogen transmission cycle. This study evaluated the impact of long-term pyriproxyfen exposure on the genetic structure and diversity of Ae. aegypti and Ae. albopictus mosquito populations. The study was conducted in Manaus, Amazonas, Brazil, where pyriproxyfen dissemination stations have been monitored since 2014 up to the present day. Double digest restriction-site associated DNA sequencing was performed, revealing that despite significant local population reductions by dissemination stations with pyriproxyfen in various locations in Brazil, focal intervention has no significant impact on the population stratification of these vectors in urban scenarios. The genetic structuring level of Ae. aegypti suggests it is more stratified and directly affected by pyriproxyfen intervention, while for Ae. albopictus exhibits a more homogeneous and less structured population. The results suggest that although slight differences are observed among mosquito subpopulations, intervention focused on neighborhoods in a capital city is not efficient in terms of genetic structuring, indicating that larger-scale pyriproxyfen interventions should be considered for more effective urban mosquito control.

Genetic Diversity and Phylogenetic Relationships of Capsicum frutescens in the Asia–Pacific Region: The Pacific Dispersal Route

AbstractCapsicum peppers are among the oldest domesticated crops in the Americas. Columbus introduced them to Europe, from where they spread to the Far East via Africa, South Asia, and Southeast Asia. However, the details of how Capsicum peppers were introduced into the Asia–Pacific region and their subsequent dispersal remain unknown. Therefore, we investigated the genetic diversity and relationships of Capsicum frutescens in the Asia–Pacific region through restriction site-associated DNA sequencing (RAD-seq) and the sequencing of a variable chloroplast genome locus. The RAD-seq analysis showed that three accessions from Japan are most closely related to those from the Americas and Micronesia, and are distant from most of those from islands and continental Southeast Asia. Although C. frutescens has two chloroplast haplotypes (T and TC), only the T type was found in the Americas and Japan, whereas both types were distributed in other regions. Therefore, we postulate that some C. frutescens accessions were introduced into the Asia–Pacific region from the Americas via the Pacific dispersal route, whereas only the T type was introduced into Japan. Evidence for this Pacific dispersal route of C. frutescens could lead to a reconsideration of the dispersal routes of other crops native to the Americas.

Translocations, rising populations, and phylogeographic consequences: genomic implications for conservation of introduced Aoudad (Ammotragus lervia) in the southwestern United States

Abstract Over the last century, Texas has been inundated with exotic ungulates, with as many as 67 species represented by captive and free-ranging populations. One of the most successful species to have established free-ranging populations is the Aoudad (Ammotragus lervia). Herein, we expand on previous genetic studies in Aoudad by including new genomic profiles based on double-digest restriction site-associated DNA sequencing methods with the intent of better understanding the effects of >70 years of human-mediated translocations, population expansion, and gene flow among populations. Using a range of 4,338 to 5,529 single-nucleotide polymorphisms obtained from 73 individuals that potentially represented A. l. blainei, A. l. lervia, and A. l. sahariensis, we measured genetic patterns of diversity and connectivity between source populations from California and New Mexico and resultant aoudad populations in Texas. Principal component analyses identified phylogeographically structured populations across Texas. Further, we identified a signature of isolation by distance among Texas populations. To assess geographic regions that facilitated or blocked gene flow between populations, we used estimation of effective migration surfaces, which indicated 3 barriers to movement between populations as well as connectivity among populations in close proximity. Comparison of mtDNA haplogroups and nuclear genotypes among the 3 examined subspecies were discordant, indicating that the current subspecific taxonomic classification needs refinement. Given the vulnerable status of Aoudad in their native range of northern Africa and the exponential population growth and potential competition with native ungulates in Texas, we propose that efforts to manage non-native Aoudad should strive to maintain and preserve unique genetic units while minimizing competition and other detriments to native species in Texas. Conservation efforts are especially important given the vulnerable status of Aoudad within their native range of northern Africa.

Population genomics of four co-distributed frog species in a barrier island system

Abstract In nature, small populations are often of concern because of limited genetic diversity, which underlies adaptive potential in the face of environmental change. Assessing patterns of genetic variation within co-distributed species sampled across varied landscapes can therefore illuminate their capacity to persist over time. We sequenced new genome-wide sequence data (double-digest restriction site-associated DNA sequencing) for four frog species (Anaxyrus terrestris, Hyla cinerea, Hyla squirella, and Rana sphenocephala) sampled from two barrier islands and the adjacent mainland of northern Florida. We calculated genomic diversity metrics and analysed spatial patterns of genomic variation for each species. We found higher genomic diversity within mainland individuals compared to island individuals for all species, suggesting a consistent effect of small island area on diversity across species. Three species (all but A. terrestris) showed significant signatures of isolation by distance, and some clustering analyses indicated separation of island and mainland individuals within species. We identified subtle differences in the strength of these patterns among species, with the strongest genetic differentiation observed in R. sphenocephala. Finally, we found evidence of recent migration between island and mainland populations for all species, which likely explains the limited genetic structure observed and contributes to the persistence of these small populations.

Contrasting effect of hybridization on genetic differentiation in three rockfish species with similar life history.

Hybridization can provide evolutionary benefits (e.g., population resilience to climate change) through the introduction of adaptive alleles and increase of genetic diversity. Nevertheless, management strategies may be designed based only on the parental species within a hybrid zone, without considering the hybrids. This can lead to ineffective spatial management of species, which can directly harm population diversity and negatively impact food webs. Three species of rockfish (Brown Rockfish (Sebastes caurinus), Copper Rockfish (S. auriculatus), and Quillback Rockfish (S. maliger)) are known to hybridize within Puget Sound, Washington, but genetic data from these species are used to infer population structure in the entire genus, including in species that do not hybridize. The goal of this project was to estimate the hybridization rates within the region and determine the effect of hybridization on geographic patterns of genetic structure. We sequenced 290 Brown, Copper, and Quillback rockfish using restriction-site associated DNA sequencing (RADseq) from four regions within and outside Puget Sound, Washington. We show that (i) hybridization within Puget Sound was asymmetrical, not recent, widespread among individuals, and relatively low level within the genome, (ii) hybridization affected population structure in Copper and Brown rockfish, but not in Quillback Rockfish and (iii) after taking hybridization into account we found limited directional dispersal in Brown and Copper rockfish, and evidence for two isolated populations in Quillback Rockfish. Our results suggest that rockfish population structure is species-specific, dependent on the extent of hybridization, and cannot be inferred from one species to another despite similar life history.

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.

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.