Potential Gene Flow Research Articles

Inheritance and ecological effects of exogenous genes from transgenic Brassica napus to Brassica juncea hybrids

●With the rapid development of new breeding techniques, the ecological impacts of transgenic plants receive wide concern again, particularly for potential gene flow from transgenic crops to their relatives. The transgene insertion position, number of gene copies, and flanking sequence of exogenous genes integrated into the recipient genome affect the genetic stability and fitness of offspring.●We employed hybrids F1 and F2, six backcross generations BC1-BC6 and BC1F1 from transgenic Brassica napus with Bacillus thuringiensis (Bt) cry1Ac gene and its wild relative B. juncea through hand pollination. We detected exogenous gene copies, mRNA transcription, and protein expression by ddPCR, qRT-PCR and ELISA, and the fitness of hybrid and backcross generations.●Exogenous genes followed Mendelian segregation expectations in hybrid and backcrossed generations, with stable gene copies, mRNA transcription and protein concentration of exogenous genes in offspring. Exogenous gene copies had no significant effects on plant fitness, but had positive effects on mRNA transcription and protein concentration that varied with growth stages in hybrid and backcross generations.●Our study demonstrated inheritance and ecological effects of exogenous genes from transgenic plants to wild relatives, which will help ecological risk management of biotechnological plants released in the nature.

Reconstruction of invasion pathways of East Asian crab species of the genus Hemigrapsus (Decapoda, Brachyura, Varunidae) based on a comparative phylogeographic approach

Abstract Three intertidal varunid crab species of the genus Hemigrapsus, viz. H. penicillatus, H. sanguineus, and H. takanoi, are widely distributed along the East Asian coastline. The first two became globally well-known after their introduction into Atlantic waters of North America and Europe. Since the first record in the late 1980s, they established breeding populations and now live in sympatry with native and other invasive crab species. The aim of this study was to determine the correct species identity and geographic origin of these invasive populations and, if possible, estimate the number of independent invasion events. For that purpose, specimens from the three species were obtained from native populations in Taiwan, Japan, Russia, Korea, and China, and genetically compared to invasive populations from Europe and the U.S.A. Sequences of the mitochondrial cytochrome c oxidase subunit I gene were generated and used for haplotype network and AMOVA analyses, thus providing insights into the potential invasion pathways, gene flow, and phylogeography of the two invasive species. Pronounced geographic structure for all three species is revealed in their native ranges, with a marked differentiation among northern and southern populations. We furthermore provide evidence that all invasions into North America and Europe originated from northern Asian populations, which is in line with similar climatic conditions in Europe, northeastern America and northern Asia. Our results also confirm the recent finding that all European populations previously thought to consist of H. penicillatus should be reclassified as H. takanoi.

Constructing sympatry networks to assess potential introgression pathways within the major oak sections in the contiguous US states

Societal Impact StatementIncreasing evidence indicates gene flow commonly occurs between closely related species in diverse plant genera and can involve numerous species. Here, we present a simple method to quantify and characterize the potential for gene flow among “sympatric” species (they share some part of their geographic distribution), using oaks as a case study. The resulting sympatry networks provide insight into potential interspecific gene flow, from the perspective of each species and across the entire suite of interfertile species. In a rapidly changing world, interspecific gene flow will play an increasingly important role in the conservation of endangered species, both positive and negative.Summary We provide a simple method, using geographic distribution data, to quantify and characterize sympatry networks among a suite of interfertile species to assess potential routes for introgressive hybridization (IH). Sympatry is a necessary condition for IH and is easily determined from widely available geographic distribution data. Oaks, famous for hybridization, present an excellent case study. We use county‐level data for 94 oak species in the contiguous US states to determine patterns of sympatry of species within the four sections, assumed to be interfertile. The pairwise sympatry relationships can generate species‐centric local networks or a syngameon‐wide network. Two different measures of sympatry are used: proportional and relative. Most oak species are exposed to IH from many species, with red oaks having slightly higher local levels of sympatry (5.7 vs. 3.8 spp per county) than white oaks but lower total numbers of sympatric species (13.7 vs. 14.8). The nature of potential IH generally differs for threatened species, which are often embedded in the much larger distributions of widespread species. Potential IH within oak sections is widespread and disproportionately affects rare species. Given that IH has potentially positive or negative impacts on species cohesion, persistence, and adaptation, the geographic connections among species and the ‘local sympatry effect’ can serve as a springboard for hypothesis generation and genetic investigation of introgression patterns.

Divergence of Phyllosphere Microbial Community Assemblies and Components of Volatile Organic Compounds between the Invasive Sphagneticola trilobata, the Native Sphagneticola calendulacea and Their Hybrids, and Its Implications for Invasiveness.

Closely-related plant groups with distinct microbiomes, chemistries and ecological characteristics represent tractable models to explore mechanisms shaping species spread, competitive dynamics and community assembly at the interface of native and introduced ranges. We investigated phyllosphere microbial communities, volatile organic compound (VOC) compositions, and potential interactions among introduced S. trilobata, native S. calendulacea and their hybrid in South China. S. trilobata exhibited higher α diversity but significantly different community composition compared to the native and hybrid groups. However, S. calendulacea and the hybrid shared certain microbial taxa, suggesting potential gene flow or co-existence. The potent antimicrobial VOC profile of S. trilobata, including unique compounds like p-cymene (13.33%), likely contributes to its invasion success. The hybrid's intermediate microbial and VOC profiles suggest possible consequences for species distribution, genetic exchange, and community assembly in heterogeneous environments. This hybrid deserves further study as both an opportunity for and threat to diversity maintenance. These differentiating yet connected plant groups provide insight into ecological and evolutionary dynamics shaping microbiome structure, species co-occurrence and competitive outcomes during biological exchange and habitat transformation. An interdisciplinary approach combining chemical and microbial ecology may reveal mechanisms underlying community stability and change, informing management of species spread in a globalized world.

Unveiling a potential threat to forest ecosystems: molecular diagnosis of Alliaria petiolata, a newly introduced alien plant in Korea.

Identifying stages of a species invasion in a new habitat (i.e., colonization, establishment, and landscape spread) and their primary determinants in biological invasion warrants attention, as it provides vital insights for preventing non-native species from becoming pervasive invaders. However, delineating invasion stages and their associated factors can pose significant challenges due to the ambiguous distinctions between these stages. Alliaria petiolata, one of the most noxious weeds in woodland habitats, has recently been introduced to Korea and observed in a few distant locations. Although the plant's spread has been relatively slow thus far, rapid spread is highly likely in the future, given the high invasive potential reported elsewhere. We indirectly diagnose the current status of A. petiolata invasion in Korea through the assessment of genetic diversity and phylogenetic inferences using genome-wide molecular markers and cytological data. We analyzed 86 individual samples collected from two native and six introduced populations, employing 1,172 SNPs. Our analysis estimated within- and among-population genetic diversity and included two clustering analyses. Furthermore, we investigated potential gene flow and reticulation events among the sampled populations. Our data unraveled that Korean garlic mustard exhibits a hexaploid ploidy level with two distinct chromosome numbers, 2n = 36 and 42. The extent of genetic diversity measured in Korean populations was comparable to that of native populations. Using genome-wide SNP data, we identified three distinct clusters with minor gene flow, while failing to detect indications of reticulation among Korean populations. Based on the multifaceted analyses, our study provides valuable insights into the colonization process and stressed the importance of closely monitoring A. petiolata populations in Korea.

Integrating Multiple Database Resources to Elucidate the Gene Flow in Southeast Asian Pig Populations.

The domestic pig (Sus scrofa) and its subfamilies have experienced long-term and extensive gene flow, particularly in Southeast Asia. Here, we analyzed 236 pigs, focusing on Yunnan indigenous, European commercial, East Asian, and Southeast Asian breeds, using the Pig Genomics Reference Panel (PGRP v1) of Pig Genotype-Tissue Expression (PigGTEx) to investigate gene flow and associated complex traits by integrating multiple database resources. In this study, we discovered evidence of admixtures from European pigs into the genome of Yunnan indigenous pigs. Additionally, we hypothesized that a potential conceptual gene flow route that may have contributed to the genetic composition of the Diannan small-ear pig is a gene exchange from the Vietnamese pig. Based on the most stringent gene introgression scan using the fd statistic, we identified three specific loci on chromosome 8, ranging from 51.65 to 52.45 Mb, which exhibited strong signatures of selection and harbored the NAF1, NPY1R, and NPY5R genes. These genes are associated with complex traits, such as fat mass, immunity, and litter weight, in pigs, as supported by multiple bio-functionalization databases. We utilized multiple databases to explore the potential dynamics of genetic exchange in Southeast Asian pig populations and elucidated specific gene functionalities.

Exploring mtDNA Databases to Evaluate the Population Structure and Genetic Diversity of Tursiops truncatus in the Atlantic Ocean: Implications for the Conservation of a Small, Offshore Population

Inshore and offshore bottlenose dolphin, Tursiops truncatus, ecotypes were distinguished through genetics, distribution, diet, morphology, diversity, and social behaviors. Although T. truncatus is a widely studied species, few studies have focused on offshore populations. Offshore biodiversity is frequently neglected due to the difficulty of data collection, and therefore, it is challenging to assess how threatened these populations are. A small, offshore population of dolphins residing around the Saint Peter Saint Paul Archipelago (SPSPA) in the middle of the Atlantic Ocean has been monitored for several years, and a decrease in the number of dolphin sightings has recently been noticed. We analyzed a comprehensive mtDNA control-region sequence dataset for this species to infer the conservation status and better understand the relationships between the SPSPA population and other offshore populations. We assessed the genetic diversity and population structure of the bottlenose dolphin from inshore and offshore populations of the Atlantic Ocean. Offshore populations are more genetically diverse and have less variation between populations than inshore populations. The offshore populations share haplotypes, indicating potential gene flow. However, the SPSPA population presented the lowest levels of genetic diversity between populations. The conservation status of the SPSPA population is concerning, and it is necessary to apply effective management strategies to guarantee its protection.

Strong philopatry in an estuarine-dependent fish.

Understanding fish movement is critical in determining the spatial scales in which to appropriately manage wild populations. Genetic markers provide a natural tagging approach to assess the degree of gene flow and population connectivity across a species distribution. We investigated the genetic structure of black bream Acanthopagrus butcheri across its entire distribution range in Australia, as well as regional scale gene flow across south-eastern Australia by undertaking a comprehensive analysis of the populations in estuaries across the region. We applied genome-wide sampling of single-nucleotide polymorphism (SNP) markers generated from restriction site-associated DNA sequencing. Genetic structure and potential gene flow was assessed using principal component analyses and admixture analyses (STRUCTURE). Using 33,493 SNPs, we detected broad scale genetic structuring, with limited gene flow among regional clusters (i.e. Western Australia, South Australia and western Victoria; and eastern Victoria, Tasmania and New South Wales). This is likely the result of unsuitable habitats, strong ocean currents (e.g. the Leeuwin Current and the East Australian Current), large water bodies (e.g. Bass Strait) and known biogeographical provinces across the continent. Local-scale genetic structuring was also identified across the south-eastern Australian estuaries sampled, reflecting that the coexistence of both migratory and resident individuals within populations (i.e. partial migration), and the movement of fish into coastal waters, still results in strong philopatry across the region. Instances of movement among estuaries at this spatial scale were primarily found between adjacent estuaries and were likely attributed to lone migrants utilising inshore coastal currents for movement beyond nearby habitats. Targeting SNP markers in A. butcheri at this continental scale highlighted how neither spatial proximity of estuaries nor black bream's ability to move into coastal waters reflects increased gene flow. Overall, our findings highlight the importance of location-specific management.

Chromosome-scale genome assembly of Poa trivialis and population genomics reveal widespread gene flow in a cool-season grass seed production system.

Poa trivialis (L.) is a cool-season grass species found in various environments worldwide. In addition to being a desired turfgrass species, it is a common weed of agricultural systems and natural areas. As a weed, it is an important contaminant of commercial cool-season grass seed lots, resulting in widespread gene flow facilitated by human activities and causing significant economic losses to farmers. To better understand and manage infestations, we assembled and annotated a haploid genome of P. trivialis and studied troublesome field populations from Oregon, the largest cool-season grass seed producing region in the United States. The genome assembly resulted in 1.35 Gb of DNA sequence distributed among seven chromosome-scale scaffolds, revealing a high content of transposable elements, conserved synteny with Poa annua, and a close relationship with other C3 grasses. A reduced-representation sequencing analysis of field populations revealed limited genetic diversity and suggested potential gene flow and human-assisted dispersal in the region. The genetic resources and insights into P. trivialis provided by this study will improve weed management strategies and enable the development of molecular detection tests for contaminated seed lots to limit seed-mediated gene flow. These resources should also be beneficial for turfgrass breeders seeking to improve desirable traits of commercial P. trivialis varieties and help to guide breeding efforts in other crops to enhance the resiliency of agricultural ecosystems under climate change. Significance Statement: The chromosome-scale assembly of Poa trivialis and population genomic analyses provide crucial insights into the gene flow of weedy populations in agricultural systems and contribute a valuable genomic resource for the plant science community.

Evaluation of the YOLO models for discrimination of the alfalfa pollinating bee species

Identifying insect pollinators and their roles in mediating pollen flow is critical to understand the potential gene flow risks of insect pollination-dependent crop species, such as alfalfa. This study was conducted to evaluate and compare the feasibility of You Only Look Once (YOLO) version 3 (YOLOv3), YOLOv5, YOLOv7, and YOLO Representation (YOLOR) to discriminate the three most common alfalfa pollinating bee species, including honeybee, bumblebee, and leafcutting bee. The metrics comparison results showed YOLOv3 and YOLOv5 outperformed YOLOv7 and YOLOR regarding model precision, recall, F1 score, and mAP50 values. YOLOv3 and YOLOv5 could successfully discriminate the three different bee species with an accuracy of almost 100% (99.9%, 99.8%, and 100% accuracy for honeybee, bumblebee, and leafcutting bee for the two models, respectively). Comparatively, YOLOv7 could discriminate honeybee with an accuracy of 95% but was more likely to mistakenly discriminate bumblebee and leafcutting bee due to the relatively lower discriminating accuracy (87.3% and 66.2%, respectively). While the values of determined parameters for YOLOR were lower than YOLOv3 and YOLOv5, the higher precision (0.99680) along with recall (0.98721), F1 (0.99198), mAP50 (0.99323), and mAP50-100 (0.89076) values indicate that this model could be able to obtain a favorable performance in discriminating the three bee species. In summary, the proposed method in this study has the potential for identifying the alfalfa pollinating bee species, studying the bees’ flower-visiting behaviors, evaluating the risks of insect-mediated pollen flow, and thus contributing to the management of genetically engineered (GE) alfalfa transgene flow.

The novel developed microsatellite markers revealed potential hybridization among Cymbidium species and the interspecies sub-division of C. goeringii and C. ensifolium

BackgroundOrchids (Cymbidium spp.) exhibit significant variations in floral morphology, pollinator relations, and ecological habitats. Due to their exceptional economic and ornamental value, Cymbidium spp. have been commercially cultivated for centuries. SSR markers are extensively used genetic tools for biology identification and population genetics analysis.ResultIn this study, nine polymorphic EST-SSR loci were isolated from Cymbidium goeringii using RNA-Seq technology. All nine SSR loci showed transferability in seven other congeneric species, including 51 cultivars. The novel SSR markers detected inter-species gene flow among the Cymbidium species and intra-species sub-division of C. goeringii and C. ensifolium, as revealed by neighborhood-joining and Structure clustering analyses.ConclusionIn this study, we developed nine microsatellites using RNA-Seq technology. These SSR markers aided in detecting potential gene flow among Cymbidium species and identified the intra-species sub-division of C. goeringii and C. ensifolium.

Genetic structure and relatedness of brown trout (Salmo trutta) populations in the drainage basin of the Ölfusá river, South-Western Iceland.

Lake Þingvallavatn in Iceland, a part of the river Ölfusá drainage basin, was presumably populated by brown trout soon after it formed at the end of the last Ice Age. The genetic relatedness of the brown trout in Þingvallavatn to other populations in the Ölfusá drainage basin is unknown. After the building of a dam at the outlet of the lake in 1959 brown trout catches declined, though numbers have now increased. The aim of this study was to assess effects of geographic isolation and potential downstream gene flow on the genetic structure and diversity in brown trout sampled in several locations in the western side of the watershed of River Ölfusá. We hypothesized that brown trout in Lake Þingvallavatn constituted several local spawning populations connected by occasional gene flow before the damming of the lake. We also estimated the effective population size (NE) of some of these populations and tested for signs of a recent population bottleneck in Lake Þingvallavatn. We sampled brown trout inhabiting four lakes and 12 rivers within and near the watershed of River Ölfusá by means of electro- and net- fishing. After stringent data filtering, 2,597 polymorphic loci obtained from ddRADseq data from 317 individuals were ascertained as putative neutral markers. Overall, the genetic relatedness of brown trout in the Ölfusá watershed reflected the connectivity and topography of the waterways. Ancestry proportion analyses and a phylogenetic tree revealed seven distinct clusters, some of which corresponded to small populations with reduced genetic diversity. There was no evidence of downstream gene flow from Lake Þingvallavatn, although gene flow was observed from much smaller mountain populations. Most locations showed low NE values (i.e., ~14.6 on average) while the putative anadromous trout from River Sog and the spawning population from River Öxará, that flows into Lake Þingvallavatn, showed notably higher NE values (i.e., 71.2 and 56.5, respectively). No signals of recent population bottlenecks were detected in the brown trout of Lake Þingvallavatn. This is the first time that the genetic structure and diversity of brown trout in the watershed of River Ölfusá have been assessed. Our results point towards the presence of a metapopulation in the watershed of Lake Þingvallavatn, which has been influenced by restoration efforts and is now dominated by a genetic component originated in River Öxará. Many of the locations studied represent different populations. Those that are isolated in headwater streams and lakes are genetically distinct presenting low genetic diversity, yet they can be important in increasing the genetic variation in downstream populations. These populations should be considered for conservation and direct management.

Variation in floral form of CRISPR knock-outs of the poplar homologs of LEAFY and AGAMOUS after FT heat-induced early flowering.

Plant migration and gene flow from genetically modified or exotic trees to nearby lands or by crossing with wild relatives is a major public and regulatory concern. Many genetic strategies exist to mitigate potential gene flow; however, the long delay in onset of flowering is a severe constraint to research progress. We used heat-induced FT overexpression to speed assessment of the expected floral phenotypes after CRISPR knockout of poplar homologs of the key floral genes, LEAFY and AGAMOUS. We selected events with previously characterized CRISPR-Cas9 induced biallelic changes then re-transformed them with the Arabidopsis thaliana FLOWERING LOCUS T (AtFT) gene under control of either a strong constitutive promoter or a heat-inducible promoter. We successfully obtained flowering in both a male and female clones of poplar, observing a wide range of inflorescence and floral forms among flowers, ramets, and insertion events. Overall, flowers obtained from the selected LFY and AG targeted events were consistent with what would be predicted for loss-of-function of these genes. LFY-targeted events showed small catkins with leaf-like organs, AG-targeted events had nested floral organs consistent with reduction in floral determinacy and absence of well-formed carpels or anthers. These findings demonstrate the great developmental plasticity of Populus flowers during genetically accelerated flowering, which may be of horticultural value. They also provide an informative early view of floral phenotypes and apparent sterility from knockouts of both these gene targets.

Genomic data provide a robust phylogeny backbone for Rhodiola L. (Crassulaceae) and reveal extensive reticulate evolution during its rapid radiation

The Tibetan Plateau and adjacent mountain regions (TP; including the Tibetan Plateau, Himalaya, Hengduan Mountains and Mountains of Central Asia) harbor great biodiversity, some lineages on which may have undergone rapid radiations. However, only a few studies have investigated the evolutionary pattern of such diversification in depth using genomic data. In this study, we reconstructed a robust phylogeny backbone of Rhodiola, a lineage that may have undergone rapid radiation in the TP, using Genotyping-by-sequencing data, and conducted a series of gene flow and diversification analyses. The concatenation and coalescent-based methods yield similar tree topologies, and five well-supported clades were revealed. Potential gene flow and introgression events were detected, both between species from different major clades and closely related species, suggesting pervasive hybridization and introgression. An initial rapid and later slowdown of the diversification rate was revealed, indicating niche filling. Molecular dating and correlation analyses showed that the uplift of TP and global cooling in the mid-Miocene might have played an important role in promoting the rapid radiation of Rhodiola. Our work demonstrates that gene flow and introgression might be an important contributor to rapid radiation possibly by quickly reassembling old genetic variation into new combinations.

Development of microsatellite markers and genetic diversity of the velvetbean caterpillar Anticarsia gemmatalis (Lepidoptera: Erebidae)

AbstractThe velvetbean caterpillar Anticarsia gemmatalis (VBC) is widely distributed in the Americas and causes severe damage to soybean foliage. This insect presents high ecological plasticity, a feature that is of great importance to understand its genetic diversity and potential gene flow to assist in resistance management strategies. With this objective, we developed microsatellite markers for VBC and applied them to five populations from Brazil. Nine primers were polymorphic, with high values of polymorphic information content (PIC > 0.5), and 134 alleles were identified in 155 individuals. These primers indicated deviation from the Hardy–Weinberg equilibrium for all populations (observed heterozygosity, Ho = 0.48, expected heterozygosity, He = 0.76), with moderate to high levels of genetic diversity and a moderate fixation index (FST = 0.14) among the populations. Analysis of population structure indicated the formation of two principal clusters. The northern one can be divided into the two populations that formed the cluster, with high genetic differentiation between them. The other cluster is formed by three populations, and we found evidence of low gene flow between them in the south–north direction, indicating that these populations may be migratory in certain conditions. These findings indicate that the designed primers were effective in describing the genetic diversity of VBC, with major implications for integrated pest management. Given the little gene flow and the high genetic diversity of populations, they present great potential to become resistant to control practices, which can lead to increased management costs.

A circumpolar parasite: Evidence of a cryptic undescribed species of sucking louse, Linognathus sp., collected from Arctic foxes, Vulpes lagopus, in Nunavut (Canada) and Svalbard (Norway).

The North has experienced unprecedented rates of warming over the past few decades, impacting the survival and development of insects and the pathogens that they carry. Since 2019, Arctic foxes from Canada (Nunavut) have been observed with fur loss inconsistent with natural shedding of fur. Adult lice were collected from Arctic foxes from Nunavut (n = 1) and Svalbard (n = 2; Norway) and were identified as sucking lice (suborder Anoplura). Using conventional PCR targeting the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), lice from Canada and Svalbard were 100% similar (8 pooled samples from Nunavut and 3 pooled samples from Svalbard), indicating that there is potential gene flow between ectoparasites on Scandinavian and North American Arctic fox populations. The cox1 sequences of Arctic fox lice and dog sucking lice (Linognathus setosus) had significant differences (87% identity), suggesting that foxes may harbour a cryptic species that has not previously been recognised. Conventional PCR targeting the gltA gene for Bartonella bacteria amplified DNA from an unknown gammaproteobacteria from two pooled louse samples collected from Svalbard foxes. The amplified sequences were 100% identical to each other but were only 78% like Proteus mirabilis reported in GenBank (CP053614), suggesting that lice on Arctic foxes may carry unique microorganisms that have yet to be described.

Ancient vicariance is reinforced by adaptive divergence in the southern beech: Contributions from geogenomics

AbstractAimGeogenomics seeks to understand geological processes linked to lineage divergence. However, the mechanisms that conserve ancient signals in spite of gene flow are still unclear. In the southern beech, the deep lineage divergence produced by vicariant events is associated with ancient marine transgressions. We hereby evaluate the hypothesis that this divergence is maintained by diversifying selection.LocationSouthern Argentina and Chile.Taxon Nothofagus dombeyi. MethodsThe lineage divergence by means of analysis of molecular variance (AMOVA), principal coordinate analysis, assignment tests and multiple matrix regression analyses were assessed using chloroplast DNA and neutral and outlier single nucleotide polymorphisms (SNPs). Several environmental variables were used to characterize potential within‐species niche structuring and genotype–environment associations.ResultsTwo deep‐rooted latitudinally structured lineages resulted from cpDNA, the northern cluster being more genetically diverse than the southern one. Of the total of 2943 SNPs, 33 identified as outliers and produced two genetic clusters. Neutral SNPs yielded no structure by AMOVA, whereas higher (>75%) FST values were obtained for cpDNA and outlier SNPs. Precipitation variables were mostly associated with population clusters and suggested two climatic niches, consisting of cold and dry in the south and more variable precipitation, temperature and soil conditions in the north. Associations of genetic distance with environment and geography suggested isolation‐by‐distance and isolation‐by‐ecology or isolation‐by‐environment effects.Main conclusionsAncient lineage divergence in N. dombeyi, originally driven by vicariance, has been maintained by diversifying selection under distinct environmental conditions that also define distinct within‐species niches. Deeply rooted phylogeographical breaks can be conserved in continuously distributed species in the absence of current geographical barriers. Yet, physical gradients exert differential selective pressures, which are maintained in the face of potential gene flow. As a result, selection can lead to geographically localized and differentially adapted groups of populations that can be detected by a combination of traditional phylogeographical and novel genomic methods.

Is there hybridization between diploid and tetraploid Euphrasia in a secondary contact zone?

Strong postzygotic reproductive isolating barriers are usually expected to limit the extent of natural hybridization between species with contrasting ploidy. However, genomic sequencing has revealed previously overlooked examples of natural cross-ploidy hybridization in some flowering plant genera, suggesting that the phenomenon may be more common than once thought. We investigated potential cross-ploidy hybridization in British eyebrights (Euphrasia, Orobanchaceae), a group from which 13 putative cross-ploidy hybrid combinations have been reported based on morphology. We analyzed a contact zone between diploid Euphrasia rostkoviana and tetraploid E. arctica in Wales. We sequenced part of the internal transcribed spacer (ITS) of nuclear ribosomal DNA and used genotyping by sequencing (GBS) to look for evidence of cross-ploidy hybridization and introgression. Common variant sites in the ITS region were fixed between diploids and tetraploids, indicating a strong barrier to hybridization. Clustering analyses of 356 single-nucleotide polymorphisms (SNPs) generated using GBS clearly separated samples by ploidy and revealed strong genetic structure (FST = 0.44). However, the FST distribution across all SNPs was bimodal, indicating potential differential selection on loci between diploids and tetraploids. Demographic inference suggested potential gene flow, limited to around one or fewer migrants per generation. Our results suggest that recent cross-ploidy hybridization is rare or absent in a site of secondary contact in Euphrasia. While a strong ploidy barrier prevents hybridization over ecological timescales, such hybrids may form in stable populations over evolutionary timescales, potentially allowing cross-ploidy introgression to take place.

Genomic differentiation in Pacific cod using Pool-Seq.

Patterns of genetic differentiation across the genome can provide insight into selective forces driving adaptation. We used pooled whole genome sequencing, gene annotation, and environmental covariates to evaluate patterns of genomic differentiation and to investigate mechanisms responsible for divergence among proximate Pacific cod (Gadus macrocephalus) populations from the Bering Sea and Aleutian Islands and more distant Washington Coast cod. Samples were taken from eight spawning locations, three of which were replicated to estimate consistency in allele frequency estimation. A kernel smoothing moving weighted average of relative divergence (F ST) identified 11 genomic islands of differentiation between the Aleutian Islands and Bering Sea samples. In some islands of differentiation, there was also elevated absolute divergence (d XY) and evidence for selection, despite proximity and potential for gene flow. Similar levels of absolute divergence (d XY) but roughly double the relative divergence (F ST) were observed between the distant Bering Sea and Washington Coast samples. Islands of differentiation were much smaller than the four large inversions among Atlantic cod ecotypes. Islands of differentiation between the Bering Sea and Aleutian Island were associated with SNPs from five vision system genes, which can be associated with feeding, predator avoidance, orientation, and socialization. We hypothesize that islands of differentiation between Pacific cod from the Bering Sea and Aleutian Islands provide evidence for adaptive differentiation despite gene flow in this commercially important marine species.

Forecasting climate change response in an alpine specialist songbird reveals the importance of considering novel climate

AbstractAimSpecies persistence in the face of climate change depends on both ecological and evolutionary factors. Here, we integrate ecological and whole‐genome sequencing data to describe how populations of an alpine specialist, the Brown‐capped Rosy‐Finch (Leucosticte australis) may be impacted by climate change.LocationSouthern Rocky Mountains in North America.MethodsWe sampled 116 Brown‐capped Rosy‐Finches from 11 sampling locations across the breeding range. Using 429,442 genetic markers from whole‐genome sequencing, we described population genetic structure and identified a subset of 436 genomic variants associated with environmental data. We modelled future climate change impacts on habitat suitability using ecological niche models (ENMs) and impacts on putative local adaptation using gradient forest models (a genetic‐environment association analysis; GEA). We used the metric of niche margin index (NMI) to determine regions of forecasting uncertainty due to climate shifts to novel conditions.ResultsPopulation genetic structure was characterized by weak genetic differentiation, indicating potential ongoing gene flow among populations. Precipitation as snow had high importance for both habitat suitability and changes in genetic variation across the landscape. Comparing ENM and gradient forest models with future climate predicted suitable habitat contracting at high elevations and population allele frequencies across the breeding range needing to shift to keep pace with climate change. NMI revealed large portions of the breeding range shifting to novel climate conditions.Main conclusionsOur study demonstrates that forecasting climate vulnerability from ecological and evolutionary factors reveals insights into population‐level vulnerability to climate change that are obfuscated when either approach is considered independently. For the Brown‐capped Rosy‐Finch, our results suggest that persistence may depend on rapid adaptation to novel climate conditions in a contracted breeding range. Importantly, we demonstrate the need to characterize novel climate conditions that influence uncertainty in forecasting methods.