Facilitate Gene Flow Research Articles

Experimentally testing mate preference in an avian system with unidirectional bill color introgression.

Mating behavior can play a key role in speciation by inhibiting or facilitating gene flow between closely related taxa. Hybrid zones facilitate a direct examination of mating behavior and the traits involved in establishing species barriers. The long-tailed finch (Poephila acuticauda) has two hybridizing subspecies that differ in bill color (red and yellow), and the yellow bill phenotype appears to have introgressed ~350 km eastward following secondary contact. To examine the role of mate choice on bill color introgression, we performed behavioral assays using natural and manipulated bill colors. We found an assortative female mating preference for males of their own subspecies when bill color was not manipulated. However, we did not find this assortative preference in trials based on artificially manipulated bill color. This could suggest that assortative preference is not fixed entirely on bill color and instead may be based on a different trait (e.g., song) or a combination of traits, or alternatively may be due to lower statistical power alongside the bill manipulations being unconvincing to the female choosers. Intriguingly, we find a bias in the inheritance of bill color in captive bred F1 hybrid females. Previous modeling suggests that assortative mate preference and this kind of partial dominance in the underlying genes may together contribute to introgression, making the genetic architecture of bill color in this system a priority for future research.

A test of genetic divergence of a bird existing in the Sichuan Basin and its surrounding mountain ranges

Island ecosystems, serving as natural laboratories, facilitate geographical isolation, ecological specialization, and species divergence. The Sichuan Basin, surrounded by mountain ranges, represents a typical continental island due to its marked environmental spatial heterogeneity. This heterogeneity may contribute to geographical isolation and habitat heterogeneity, resulting in genetic divergence within populations. Therefore, we used the White-browed Laughingthrush (Garrulax sannio) as a model specimen to investigate the genetic divergence in the Sichuan Basin and its surrounding mountain ranges, given its presence in various habitats within and beyond this basin. Employing a RAD-seq dataset of 140 G. sannio individuals from 17 distinct ecological zones in the Sichuan Basin and its surrounding mountain ranges, we conducted PCA, population structure analysis, phylogenetic tree construction, and gene flow analysis to comprehensively analyze G. sannio groups. Additionally, in conjunction with geographical and ecological data, we performed isolation by distance, isolation by environment, PCA, and latent factor mixed model analysis to identify factors influencing the genetic divergence among these G. sannio groups. In summary, the 17 G. sannio groups were categorized into high-elevation, medium-elevation, and low-elevation groups. Genetic divergence in G. sannio may be attributed to both geographical distance and key ecological factors, particularly elevation and key climatic variables. Notably, the high-elevation group exhibited a greater number of SNPs and selected genes associated with the key ecological factors compared to the low-elevation group. The ADCY9 gene and several associated key pathways were identified as crucial elements driving ecological adaptation (elevation and key climatic variables) in the high-elevation group. Furthermore, climate changes during the glacial cycles may have facilitated gene flow among these groups residing in the Sichuan Basin and its surrounding mountain ranges. Our findings provide evidence of genetic divergence in G. sannio influenced by the geographical distance and key ecological factors between the Sichuan Basin and its surrounding mountain ranges. These results lay the groundwork for future research on the molecular systematics of continental islands.

A wide hybrid zone mediated by precipitation contributed to confused geographical structure of Scutiger boulengeri.

Confused geographical structure of a population and mitonuclear discordance are shaped by a combination of rapid changes in population demographics and shifts in ecology. In this study, we generated a time-calibrated phylogeny of Scutiger boulengeri, an endemic Xizang alpine toad occurring in mountain streams on the Qinghai-Xizang (Tibet) Plateau (QTP). Based on three mitochondrial DNA (mtDNA) genes, eight clades were assigned to three deeply divergent lineages. Analysis of nuclear DNA (nuDNA) genes revealed three distinct clusters without geographic structure, indicating significantly high rates of gene flow. Coalescent theory framework analysis (approximate Bayesian computation model DIYABC and Migrate-N) suggested that divergence of the main intraspecific clusters was the result of hybridization after secondary contact in the Holocene around 0.59 million years ago (Ma). The ratio of mtDNA F ST (fixation index) to nuDNA F ST was 2.3, thus failing to show male-biased dispersal. Geographic cline analysis showed that a wide hybrid zone was initially established in southwestern China, without significant reproductive isolation but with strong introgression in S. boulengeri, suggesting high hybrid fitness. Furthermore, mtDNA genes exhibited isolation by distance (IBD) while nuDNA genes exhibited significant isolation by environment (IBE). Results suggested that mitonuclear discordance may have initially been caused by geographic isolation, followed by precipitation-mediated hybridization, producing a wide hybrid zone and geographic structure confusion of nuDNA genes in S. boulengeri. This study indicated that complicated historical processes may have led to specific genetic patterns, with a specific climate factor facilitating gene flow in the system.

Time-calibrated phylogeny and ecological niche models indicate Pliocene aridification drove intraspecific diversification of brushtail possums in Australia.

Major aridification events in Australia during the Pliocene may have had significant impact on the distribution and structure of widespread species. To explore the potential impact of Pliocene and Pleistocene climate oscillations, we estimated the timing of population fragmentation and past connectivity of the currently isolated but morphologically similar subspecies of the widespread brushtail possum (Trichosurus vulpecula). We use ecological niche modeling (ENM) with the current fragmented distribution of brushtail possums to estimate the environmental envelope of this marsupial. We projected the ENM on models of past climatic conditions in Australia to infer the potential distribution of brushtail possums over 6 million years. D-loop haplotypes were used to describe population structure. From shotgun sequencing, we assembled whole mitochondrial DNA genomes and estimated the timing of intraspecific divergence. Our projections of ENMs suggest current possum populations were unlikely to have been in contact during the Pleistocene. Although lowered sea level during glacial periods enabled connection with habitat in Tasmania, climate fluctuation during this time would not have facilitated gene flow over much of Australia. The most recent common ancestor of sampled intraspecific diversity dates to the early Pliocene when continental aridification caused significant changes to Australian ecology and Trichosurus vulpecula distribution was likely fragmented. Phylogenetic analysis revealed that the subspecies T.v.hypoleucus (koomal; southwest), T.v.arnhemensis (langkurr; north), and T.v.vulpecula (bilda; southeast) correspond to distinct mitochondrial lineages. Despite little phenotypic differentiation, Trichosurus vulpecula populations probably experienced little gene flow with one another since the Pliocene, supporting the recognition of several subspecies and explaining their adaptations to the regional plant assemblages on which they feed.

Commentary: using prey naïveté to inform ecological management.

Commentary: using prey naïveté to inform ecological management.

Biogeography in the deep: Hierarchical population genomic structure of two beaked whale species

The deep sea is the largest ecosystem on Earth, yet little is known about the processes driving patterns of genetic diversity in its inhabitants. Here, we investigated the macro- and microevolutionary processes shaping genomic population structure and diversity in two poorly understood, globally distributed, deep-sea predators: Cuvier’s beaked whale (Ziphius cavirostris) and Blainville’s beaked whale (Mesoplodon densirostris). We used double-digest restriction associated DNA (ddRAD) and whole mitochondrial genome (mitogenome) sequencing to characterise genetic patterns using phylogenetic trees, cluster analysis, isolation-by-distance, genetic diversity and differentiation statistics. Single nucleotide polymorphisms (SNPs; Blainville’s n = 43 samples, SNPs=13988; Cuvier’s n = 123, SNPs= 30479) and mitogenomes (Blainville’s n = 27; Cuvier’s n = 35) revealed substantial hierarchical structure at a global scale. Both species display significant genetic structure between the Atlantic, Indo-Pacific and in Cuvier’s, the Mediterranean Sea. Within major ocean basins, clear differentiation is found between genetic clusters on the east and west sides of the North Atlantic, and some distinct patterns of structure in the Indo-Pacific and Southern Hemisphere. We infer that macroevolutionary processes shaping patterns of genetic diversity include biogeographical barriers, highlighting the importance of such barriers even to highly mobile, deep-diving taxa. The barriers likely differ between the species due to their thermal tolerances and evolutionary histories. On a microevolutionary scale, it seems likely that the balance between resident populations displaying site fidelity, and transient individuals facilitating gene flow, shapes patterns of connectivity and genetic drift in beaked whales. Based on these results, we propose management units to facilitate improved conservation measures for these elusive species.

Breeding system and geospatial variation shape the population genetics of Triodanis perfoliata.

Both intrinsic and extrinsic forces work together to shape connectivity and genetic variation in populations across the landscape. Here we explored how geography, breeding system traits, and environmental factors influence the population genetic patterns of Triodanis perfoliata, a widespread mix‐mating annual plant in the contiguous US. By integrating population genomic data with spatial analyses and modeling the relationship between a breeding system and genetic diversity, we illustrate the complex ways in which these forces shape genetic variation. Specifically, we used 4705 single nucleotide polymorphisms to assess genetic diversity, structure, and evolutionary history among 18 populations. Populations with more obligately selfing flowers harbored less genetic diversity (π: R 2 = .63, p = .01, n = 9 populations), and we found significant population structuring (F ST = 0.48). Both geographic isolation and environmental factors played significant roles in predicting the observed genetic diversity: we found that corridors of suitable environments appear to facilitate gene flow between populations, and that environmental resistance is correlated with increased genetic distance between populations. Last, we integrated our genetic results with species distribution modeling to assess likely patterns of connectivity among our study populations. Our landscape and evolutionary genetic results suggest that T. perfoliata experienced a complex demographic and evolutionary history, particularly in the center of its distribution. As such, there is no singular mechanism driving this species' evolution. Together, our analyses support the hypothesis that the breeding system, geography, and environmental variables shape the patterns of diversity and connectivity of T. perfoliata in the US.

Rapid large-scale genomic introgression in Arabidopsis suecica via an autoallohexaploid bridge.

Gene flow between species in the genus Arabidopsis occurs in significant amounts, but how exactly gene flow is achieved is not well understood. Polyploidization may be one avenue to explain gene flow between species. One problem, however, with polyploidization as a satisfying explanation is the occurrence of lethal genomic instabilities in neopolyploids as a result of genomic exchange, erratic meiotic behavior, and genomic shock. We have created an autoallohexaploid by pollinating naturally co-occurring diploid Arabidopsis thaliana with allotetraploid Arabidopsis suecica (an allotetraploid composed of A. thaliana and Arabidopsis arenosa). Its triploid offspring underwent spontaneous genome duplication and was used to generate a multigenerational pedigree. Using genome resequencing, we show that 2 major mechanisms promote stable genomic exchange in this population. Legitimate meiotic recombination and chromosome segregation between the autopolyploid chromosomes of the 2 A. thaliana genomes occur without any obvious bias for the parental origin and combine the A. thaliana haplotypes from the A. thaliana parent with the A. thaliana haplotypes from A. suecica similar to purely autopolyploid plants. In addition, we repeatedly observed that occasional exchanges between regions of the homoeologous chromosomes are tolerated. The combination of these mechanisms may result in gene flow leading to stable introgression in natural populations. Unlike the previously reported resynthesized neoallotetraploid A. suecica, this population of autoallohexaploids contains mostly vigorous, and genetically, cytotypically, and phenotypically variable individuals. We propose that naturally formed autoallohexaploid populations might serve as an intermediate bridge between diploid and polyploid species, which can facilitate gene flow rapidly and efficiently.

Green infrastructure can promote plant functional connectivity in a grassland species around fragmented semi‐natural grasslands in NW‐Europe

Species may benefit from green infrastructure, i.e. the network of natural and anthropogenic habitat remnants in human‐dominated landscapes, if it helps isolated populations in remaining habitat patches to be functionally connected. The importance of green infrastructure is therefore increasingly emphasized in conservation policy to counter biodiversity loss. However, there is limited evidence, particularly in plants, that green infrastructure promotes functional connectivity, i.e. supports the colonization of habitat patches across a landscape. We applied landscape genetics to test whether the green infrastructure supports structural and functional connectivity in the grassland perennial Galium verum, in 35 landscapes in Belgium, Germany and Sweden. We used multivariate genetic clustering techniques, nestedness analyses and conditional inference trees to examine landscape‐scale patterns in genetic diversity and structure of plant populations in the green infrastructure surrounding semi‐natural grasslands. Inferred functional connectivity explained genetic variation better than structural connectivity, yielding positive effects on genetic variation. The road verge network, a major structural component of the green infrastructure and its functional connectivity, most effectively explained genetic diversity and composition in G. verum. Galium verum ramets occupying the surrounding landscape proved to be genetic subsets of focal grassland populations, shaping a nested landscape population genetic structure with focal grasslands, particularly ancient ones, harbouring unique genetic diversity. This nested pattern weakened as road network density increased, suggesting road verge networks enable high landscape occupancy by increased habitat availability and facilitates gene flow into the surrounding landscape. Our study proposes that green infrastructure can promote functional connectivity, providing that a plant species can survive outside of core habitat patches. As this often excludes habitat specialist species, conservation practice and policy should primarily focus on ancient, managed semi‐natural grasslands. These grasslands both harbour unique genetic diversity and act as primary gene and propagule sources for the surrounding landscape, highlighting their conservation value.

Genetic diversity, gene flow, and differentiation among wild, semiwild, and landrace chile pepper (Capsicum annuum) populations in Oaxaca, Mexico.

Capsicum annuum (Solanaceae) was originally domesticated in Mexico, where wild (C. annuum var. glabriusculum) and cultivated (C. annuum var. annuum) chile pepper populations (>60 landraces) are common, and wild-resembling individuals (hereafter semiwild) grow spontaneously in anthropogenic environments. Here we analyze the role of elevation and domestication gradients in shaping the genetic diversity in C. annuum from the state of Oaxaca, Mexico. We collected samples of 341 individuals from 28 populations, corresponding to wild, semiwild (C. annuum var. glabriusculum) and cultivated C. annuum, and closely related species Capsicum frutescens and C. chinense. From the genetic variation of 10 simple sequence repeat (SSR) loci, we assessed the population genetic structure, inbreeding, and gene flow through variance distribution analyses, genetic clustering, and connectivity estimations. Genetic diversity (HE ) did not differ across domestication levels. However, inbreeding coefficients were higher in semiwild and cultivated chiles than in wild populations. We found evidence for gene flow between wild populations and cultivated landraces along the coast. Genetic structure analysis revealed strong differentiation between most highland and lowland landraces. Gene flow between wild and domesticated populations may be mediated by backyards and smallholder farms, while mating systems may facilitate gene flow between landraces and semiwild populations. Domestication and elevation may overlap in their influence on genetic differentiation. Lowland Gui'ña dani clustered with highland landraces perhaps due to the social history of the Zapotec peoples. In situ conservation may play an important role in preserving semiwild populations and private alleles found in landraces.

Spatial Variation of Acanthophlebia cruentata (Ephemeroptera), a Mayfly Endemic to Te Ika-a-Māui-North Island of Aotearoa, New Zealand.

Simple SummaryPatterns of variation within a widespread species can provide evidence of population history. Adjacent stable populations with gene flow show clinal genetic divergence forming a pattern of isolation by distance. Populations that have grown due to an increase in potential habitat such as forest cover since the last glacial maximum will have low genetic variation showing patterns of range expansion. The mayfly Acanthophlebia cruentata of Aotearoa, New Zealand, is widespread in streams of North Island but absent from the cooler South Island. Mayfly nymphs are restricted to streams but adults fly, facilitating gene flow among catchments. We detected higher genetic diversity at lower latitudes of this mayfly’s range compared to most of its distribution, concordant with predictions of limited forest cover in New Zealand during Pleistocene glacial periods. A signature of recent range expansion was observed in the higher latitudes. Despite initial observation suggesting mayfly size correlated with latitude, we found sex, elevation and sampling date were significant predictors of size, and some size variation is also explained by three regional groups based on haplotype distribution.The mayfly Acanthophlebia cruentata of Aotearoa, New Zealand, is widespread in Te Ika-a-Māui North Island streams, but has never been collected from South Island despite land connection during the last glacial maximum. Population structure of this mayfly might reflect re-colonisation after volcanic eruptions in North Island c1800 years ago, climate cycling or conceal older, cryptic diversity. We collected population samples from 33 locations to estimate levels of population genetic diversity and to document phenotypic variation. Relatively low intraspecific haplotype divergence was recorded among mitochondrial cytb sequences from 492 individuals, but these resolved three geographic-haplotype regions (north, west, east). We detected a signature of isolation by distance at low latitudes (north) but evidence of recent population growth in the west and east. We did not detect an effect of volcanic eruptions but infer range expansion into higher latitudes from a common ancestor during the last glacial period. As judged from wing length, both sexes of adult mayflies were larger at higher elevation and we found that haplotype region was also a significant predictor of Acanthophlebia cruentata size. This suggests that our mitochondrial marker is concordant with nuclear genetic differences that might be explained by founder effect during range expansion.

Quantifying the effects of recent glacial history and future climate change on a unique population of mountain goats

Human disturbance and climate change can impact populations by disrupting movement corridors and reducing important habitat. Characterizing how animals respond to such environmental changes is valuable for conservation as many species can experience reduced genetic diversity when deleterious habitat change occurs, leading to an increased likelihood of extirpation. Mountain goats (Oreamnos americanus) exemplify this conservation challenge; their geographically isolated habitat can inhibit gene flow, making them susceptible to population declines in the face of anthropogenic-induced change. To facilitate biologically informed population management of mountain goats in Glacier Bay National Park, Alaska, we characterized the fine-scale genetic population structure and examined how future climate change could impact population density. Our results indicated that three genetically distinct subpopulations exist in Glacier Bay and that the genealogical history is reflective of the historic landscape patterns. Climate modeling predicted that demographic productivity was likely to be reduced for all subpopulations; additionally, we found that climate change likely degrades the suitability of movement corridors that facilitate gene flow between subpopulations, ultimately increasing the cost of travel. Understanding such fine-scale patterns are key to managing subpopulations, particularly with impending changes to the landscape.

Males Are Capable of Long-Distance Dispersal in a Social Bee

Pollinator conservation is aided by knowledge of dispersal behavior, which shapes gene flow and population structure. In many bees, dispersal is thought to be male-biased, and males’ movements may be critical to maintaining gene flow in disturbed and fragmented habitats. Yet male bee movements are challenging to track directly and male dispersal ability remains poorly understood in most species. Here, we combine field manipulations and models to assess male dispersal ability in a stingless bee (Tetragonula carbonaria). We placed colonies with virgin queens at varying distances apart (1–48 km), genotyped the males that gathered at mating aggregations outside each colony, and used pairwise sibship assignment to determine the distribution of likely brothers across aggregations. We then compared simulations of male dispersal to our observed distributions and found best-fit models when males dispersed an average of 2–3 km (>2-fold female flight ranges), and maximum of 20 km (30-fold female flight ranges). Our data supports the view that male bee dispersal can facilitate gene flow over long-distances, and thus play a key role in bee populations’ resilience to habitat loss and fragmentation. In addition, we show that the number of families contributing to male aggregations can be used to estimate local stingless bee colony densities, allowing population monitoring of these important tropical pollinators.

Functional connectivity in sympatric spiny rats reflects different dimensions of Amazonian forest‐association

AbstractAimUnderstanding how the landscape influences gene flow is important in explaining biodiversity, especially when co‐distributed taxa across heterogeneous landscapes exhibit species‐specific habitat associations. Here, we test predictions about the effects of forest‐type on population connectivity in two sympatric species of spiny rats that differ in their forest associations. Specifically, we evaluate the hypothesis that seasonal floodplain forests (várzea) provide linear connectivity, facilitating gene flow among individuals, while non‐flooded forests (terra‐firme) may diminish the functional connectivity.LocationWestern Amazon, South America.TaxonProechimys simonsi (non‐flooded forests, terra‐firme) and Proechimys steerei (seasonal floodplain forests, várzea).MethodsWe analyse about 13,000 single nucleotide polymorphisms along with characterizations of landscape heterogeneity for two forest types to test for differences in the functional connectivity. Influence of the landscape and environmental variables are quantified using maximum‐likelihood population effect models to identify the relative importance of variables in explaining the gene flow.ResultsThere are significant differences in functional connectivity between species. However, the genomic data does not support the conventional hypotheses of higher connectivity for inhabitants of várzea than those of terra‐firme. Stronger genetic structure in P. steerei than P. simonsi based on isolation by distance models suggests reduced gene flow in species associated with várzea forests. Isolation by resistance reinforces that wetland habitats inhibit and promote the functional connectivity in P. simonsi and P. steerei, respectively, although large distances along the rivers can prevent gene flow in P. steerei.Main conclusionInterpreting differences between connectivity in taxa apparent from genetic analyses through the lens of a single dimension of Amazonian heterogeneity—that is, forest type—may be an oversimplification. Our statistical modelling and fit of the data to different models points to specific environmental and habitat differences between the ecological divergent spiny rat species that may contribute to differences in the genetic structure of these sympatric taxa.

Species-landscape interactions drive divergent population trajectories in four forest-dependent Afromontane forest songbird species within a biodiversity hotspot in South Africa.

Species confined to naturally fragmented habitats may exhibit intrinsic population complexity which may challenge interpretations of species response to anthropogenic landscape transformation. In South Africa, where native forests are naturally fragmented, forest‐dependent birds have undergone range declines since 1992, most notably among insectivores. These insectivores appear sensitive to the quality of natural matrix habitats, and it is unknown whether transformation of the landscape matrix has disrupted gene flow in these species. We undertook a landscape genetics study of four forest‐dependent insectivorous songbirds across southeast South Africa. Microsatellite data were used to conduct a priori optimization of landscape resistance surfaces (land cover, rivers and dams, and elevation) using cost‐distances along least‐cost pathway (LCP), and resistance distances (IBR). We detected pronounced declines in effective population sizes over the past two centuries for the endemic forest specialist Cossypha dichroa and Batis capensis, alongside recent gene flow disruption in B. capensis, C. dichroa and Pogonocichla stellata. Landscape resistance modelling showed both native forest and dense thicket configuration facilitates gene flow in P. stellata, B. capensis and C. dichroa. Facultative dispersal of P. stellata through dense thicket likely aided resilience against historic landscape transformation, whereas combined forest‐thicket degradation adversely affected the forest generalist B. capensis. By contrast, Phylloscopus ruficapilla appears least reliant upon landscape features to maintain gene flow and was least impacted by anthropogenic landscape transformation. Collectively, gene flow in all four species is improved at lower elevations, along river valleys, and riparian corridors— where native forest and dense thicket better persist. Consistent outperformance of LCP over IBR land‐cover models for P. stellata, B. capensis and C. dichroa demonstrates the benefits of wildlife corridors for South African forest‐dependent bird conservation, to ameliorate the extinction debts from past and present anthropogenic forest exploitation.

Stable climate corridors promote gene flow in the Cape sand snake species complex (Psammophiidae)

AbstractClimate shifts during the Quaternary Period have driven changes in regional range dynamics for many species, influencing population structure of species and in some cases promoting speciation. Within southern Africa, the psammophine snakes Psammophis trinasalis and P. namibensis were historically considered subspecies of P. leightoni but were elevated to species rank based on ecological differences. Preliminary phylogenetic analyses suggested intraspecific, not interspecific genetic variation between these taxa, but this finding was based on very limited data and could not be confirmed. To assess the level of genetic differentiation within the P. leightoni species complex, we explored the evolutionary history of these snakes by combining phylogenetic analyses, species distribution modelling and an examination of morphology. We generated a comprehensive, multi‐gene phylogeny for Psammophis that included wider geographic sampling of the three species in the complex. Using this phylogeny, Bayesian and distance‐based species delimitation analyses showed intraspecific, not interspecific divergences between taxa in the complex, suggesting that they collectively represent a single taxon. Furthermore, non‐metric multidimensional scaling analysis of scalation characters showed no differences between the species. Moreover, palaeo‐modelling at three time periods since the last interglacial period suggest that there have been varying levels of connectivity between these taxa, which has likely facilitated gene flow between them. Given the evidence, we propose that the P. leightoni complex represents a single species and therefore formally synonymise the three species.

Phylogeography of the smooth greensnake, Opheodrys vernalis (Squamata: Colubridae): divergent lineages and variable demographics in a widely distributed yet enigmatic species

Abstract Phylogeographic studies can uncover robust details about the population structure, demographics, and diversity of species. The smooth greensnake, Opheodrys vernalis, is a small, cryptic snake occupying mesic grassland and sparsely wooded habitats. Although O. vernalis has a wide geographical range, many metapopulations are patchy and some are declining. We used mitochondrial DNA and double digest restriction-site associated DNA sequencing to construct the first phylogeographic assessment of O. vernalis. Genomic analysis of 119 individuals (mitochondrial DNA) and a subset of another 45 smooth greensnakes (nuclear DNA; N = 3031 single nucleotide polymorphisms) strongly supports two longitudinally separated lineages, with admixture in the Great Lakes region. Post-Pleistocene secondary contact best explains admixture from populations advancing northwards. Overall, populations expressed low heterozygosity, variable inbreeding rates, and moderate to high differentiation. Disjunct populations in the Rocky Mountains and central Great Plains regions might be contracting relicts, whereas northerly populations in more continuous mesic habitats (e.g., Prairie Pothole region, southern Canada) had signals of population expansion. Broadly, conservation management efforts should be focused on local populations, because habitat connectivity may facilitate gene flow and genetic diversity.

Location and Species Matters: Variable Influence of the Environment on the Gene Flow of Imperiled, Native and Invasive Cottontails.

The environment plays an important role in the movement of individuals and their associated genes among populations, which facilitates gene flow. Gene flow can help maintain the genetic diversity both within and between populations and counter the negative impact of genetic drift, which can decrease the fitness of individuals. Sympatric species can have different habitat preferences, and thus can exhibit different patterns of genetic variability and population structure. The specialist-generalist variation hypothesis (SGVH) predicts that specialists will have lower genetic diversity, lower effective population sizes (Ne), and less gene flow among populations. In this study, we used spatially explicit, individual-based comparative approaches to test SGVH predictions in two sympatric cottontail species and identify environmental variables that influence their gene flow. New England cottontail (Sylvilagus transitionalis) is the only native cottontail in the Northeast US, an early successional habitat specialist, and a species of conservation concern. Eastern cottontail (S. floridanus) is an invasive species in the Northeast US and a habitat generalist. We characterized each species’ genomic variation by developing double-digest Restriction-site Associated DNA sequence single nucleotide polymorphism markers, quantified their habitat with Geographic Information System environmental variables, and conducted our analyses at multiple scales. Surprisingly, both species had similar levels of genetic diversity and eastern cottontail’s Ne was only higher than New England cottontail in one of three subregions. At a regional level, the population clusters of New England cottontail were more distinct than eastern cottontail, but the subregional levels showed more geographic areas of restricted gene flow for eastern cottontail than New England cottontail. In general, the environmental variables had the predicted effect on each species’ gene flow. However, the most important environmental variable varied by subregion and species, which shows that location and species matter. Our results provide partial support for the SGVH and the identification of environmental variables that facilitate or impede gene flow can be used to help inform management decisions to conserve New England cottontail.

Metapopulation connectivity retains genetic diversity following a historical bottleneck in a federally endangered seabird

AbstractDespite intensive management since the 1970s, recovery of the endangered northwestern Atlantic population of the Roseate Tern (Sterna dougallii dougallii) has not offset low productivity from a female-biased sex ratio, low adult survival, and habitat constriction. Now, >90% of individuals breed at three sites within 200 km from Long Island, NY, to Buzzards Bay, MA (warm-water subregion). To characterize the impact of historical bottlenecks, metapopulation structure, and demographic fluctuations on genetic variation, Roseate Terns from the warm-water (1870s, 1970s, 1997, 2016) and cold-water (Nova Scotia, Canada; 2018) subregions were genotyped at 8–16 microsatellites and 2–3 mitochondrial regions. Diversity declined in the warm-water subregion from the 1870s (expected heterozygosity [HE] = 0.44, allelic richness [AR] = 2.86) and 1970s (HE = 0.53, AR = 3.25) to 1997 (HE = 0.38, AR = 2.58). Genetic signatures of bottlenecks persisted in 1997 (P = <0.001–0.003) and 2016 (P = <0.001–0.005), but an increase in variation occurred by 2016 (HE = 0.50, AR = 2.85). Weak structure was detected between contemporary warm- and cold-water subregions (θ = 0.06) and within the warm-water subregion (θ = 0.04). Both demographic (3,439–3,821) and genetic (3,040) estimates suggested effective population size (Ne) stability over the last 100 years, despite large fluctuations in census size (4,000–8,662). Results suggest that 50 years of management (restoring habitat, preventing gull encroachment, controlling predators) at colony sites supported a small, stable Ne and maintained a hierarchical metapopulation that allowed gene flow to redistribute genetic variation throughout the northwest Atlantic. The metapopulation remains highly vulnerable to stochastic events but harbors resiliency and redundancy through gene flow and a stable Ne. For long-term persistence from a genetic perspective, managers must maintain the major source colonies, increase the availability of high-quality peripheral breeding sites, and protect concentrated nonbreeding sites that facilitate gene flow.

Plant Breeding Integrated with Genomic-Enabled Prediction

Plant breeding programs have used conventional breeding methods, such as hybridization, induced mutations, and other methods to manipulate the plant genome within the species' natural genetic boundaries to improve crop varieties. However, repeatedly using conventional breeding methods might lead to the erosion of the gene reservoir, thereby rendering crops vulnerable to environmental stresses and hampering future progress in crop production, food and nutritional security, and socio-economic benefits. Integrating innovative technologies in breeding programs to accelerate gene flow is critical for sustaining global plant production. Genomic prediction is a promising tool to assist the rapid selection of premiere genotypes and accelerate breeding gains for climate-resilient plant varieties. This review surveys the annals and principles of genomic-enabled prediction. Based on the problem that is investigated through the prediction, as well as several other factors, such as trait heritability, the relationship between the individuals to be predicted and those used to train the models for prediction, the number of markers, sample size, and the interaction between genotype and environment, different levels of accuracy have been reported. Genomic prediction might play a decisive role and facilitate gene flow from gene bank accessions to elite lines in future breeding programs.