Subtle Genetic Structure Research Articles

SSR-based genetic analysis depicted high gene diversity with subtle population genetic structure in Myrica esculenta, a high-valued edible fruit tree of the Western Himalayas

SSR-based genetic analysis depicted high gene diversity with subtle population genetic structure in Myrica esculenta, a high-valued edible fruit tree of the Western Himalayas

RADseq-based population genomic analysis and environmental adaptation of rare and endangered recretohalophyte Reaumuria trigyna.

Genetic diversity reflects the survival potential, history, and population dynamics of an organism. It underlies the adaptive potential of populations and their response to environmental change. Reaumuria trigyna is an endemic species in the Eastern Alxa and West Ordos desert regions in China. The species has been considered a good candidate to explore the unique survival strategies of plants that inhabit this area. In this study, we performed population genomic analyses based on restriction-site associated DNA sequencing to understand the genetic diversity, population genetic structure, and differentiation of the species. Analyses of 92,719 high-quality single-nucleotide polymorphisms (SNPs) indicated that overall genetic diversity of R. trigyna was low (HO=0.249 and HE=0.208). No significant genetic differentiation was observed among the investigated populations. However, a subtle population genetic structure was detected. We suggest that this might be explained by adaptive diversification reinforced by the geographical isolation of populations. Overall, 3513 outlier SNPs were located in 243 gene-coding sequences in the R. trigyna transcriptome. Potential sites under diversifying selection occurred in genes (e.g., AP2/EREBP, E3 ubiquitin-protein ligase, FLS, and 4CL) related to phytohormone regulation and synthesis of secondary metabolites which have roles in adaptation of species. Our genetic analyses provide scientific criteria for evaluating the evolutionary capacity of R. trigyna and the discovery of unique adaptions. Our findings extend knowledge of refugia, environmental adaption, and evolution of germplasm resources that survive in the Ordos area.

Lack of panmixia of Bothnian Bay vendace - Implications for fisheries management

Overexploitation of fisheries is recognized as a major environmental and socioeconomic problem that threats biodiversity and ecosystem functioning. Inappropriate management policies of fish stocks have been applied as a consequence of inadequate characterization of subtle genetic structure in many fish species. In this study, we aim to assess the extent of genetic differentiation and structure of vendace (Coregonus albula) collected from eight locations in the Bothnian Bay, the northernmost part of the Baltic Sea. Specifically, we test if this species forms a single panmictic population or is divided into several genetically distinct units. We used restriction site-associated DNA sequencing (RAD-seq) to identify 21,792 SNPs based on 266 individuals. We identified a clear pattern of genetic differentiation between River Kalix and the other sampling locations, and a weak structuring between samples from Swedish and Finnish coast. Outlier analysis detected 41 SNPs putatively under divergent selection, mainly reflecting the divergence between River Kalix and the other samples. The outlier SNPs were located within or near 25 genes, including voltage-dependent calcium channel subunit alpha-2 (CACNA2D2), cadherin 26 (CDH26) and carbonic anhydrase 4-like (CA4) that have earlier been associated with salt-tolerance and salinity stress. Our study provides the first genome-wide perspective on genetic structuring of Baltic Sea vendace and rejects the hypothesis of panmixia in the Bothnian Bay. As such, our work demonstrates the power of RAD-sequencing to detect low but significant genetic structuring relevant for fisheries management.

Intra‐Alpine Islands: Population genomic inference reveals high degree of isolation between freshwater spring habitats

AbstractAimAlpine spring ecosystems have long been considered as highly isolated, island‐like habitats. This presumption, however, is insufficiently supported empirically and conclusions about spring isolation have been based on indirect evidence. Therefore, we investigated the population genomic structure of Partnunia steinmanni Walter, 1906, a strictly spring‐dwelling water mite (Hydrachnidia) species, to shed light on the degree of interconnection among freshwater spring habitats.LocationProtected areas across the Alps, Central Europe.MethodsPartnunia steinmanni populations were sampled by hand‐net from 12 springs. Population genomic structure was inferred with 2263 polymorphic restriction site‐associated DNA (RADseq) loci of 256 individuals. We assessed genomic admixture, the phylogenetic relationship, isolation by distance, contemporary migration, effective population sizes, and genetic diversity among individuals from different springs.ResultsWe observed strong genetic differentiation between individuals from different springs. Water mites from each spring qualified as well‐delimited distinct populations with only little intra‐spring migration, even when these were located in close geographic proximity. Furthermore, we found subtle shared genetic structure among springs within the same area, and a southwestern genotype associated with the Rhône catchment that extended into eastern populations. Effective population size estimates and standing genetic variation within springs were generally low.Main conclusionsOur findings indicate strong insularity of freshwater springs and headwater areas, likely caused by intra‐alpine Pleistocene isolation and limited dispersal abilities of strictly spring‐bound species like P. steinmanni. Our results support the concept of spring habitat isolation and highlight the importance of alpine protected areas to conserve springs as substantial components of freshwater biodiversity.

Landscape Features Fail to Explain Spatial Genetic Structure in White‐Tailed Deer Across Ohio, USA

ABSTRACTLandscape features influence wildlife movements across spatial scales and have the potential to influence the spread of disease. Chronic wasting disease (CWD) is a fatal prion disease affecting members of the family Cervidae, particularly white‐tailed deer (Odocoileus virginianus), and the first positive CWD case in a wild deer in Ohio, USA, was recorded in 2020. Landscape genetics approaches are increasingly used to better understand potential pathways for CWD spread in white‐tailed deer, but little is known about genetic structure of white‐tailed deer in Ohio. The objectives of our study were to evaluate spatial genetic structure in white‐tailed deer across Ohio and compare the support for isolation by distance (IBD) and isolation by landscape resistance (IBR) models in explaining this structure. We collected genetic data from 619 individual deer from 24 counties across Ohio during 2007–2009. We used microsatellite genotypes from 619 individuals genotyped at 11 loci and haplotypes from a 547‐base pair fragment of the mitochondrial DNA control region. We used spatial and non‐spatial genetic clustering tests to evaluate genetic structure in both types of genetic data and empirically optimized landscape resistance surfaces to compare IBD and IBR using microsatellite data. Non‐spatial genetic clustering tests failed to detect spatial genetic structure, whereas spatial genetic clustering tests indicated subtle spatial genetic structure. The IBD model consistently outperformed IBR models that included land cover, traffic volume, and streams. Our results indicated widespread genetic connectivity of white‐tailed deer across Ohio and negligible effects of landscape features. These patterns likely reflect some combination of minimal resistive effects of landscape features on white‐tail deer movement in Ohio and the effects of regional recolonization or translocation. We encourage continued CWD surveillance in Ohio, particularly in the proximity of confirmed cases. © 2021 The Wildlife Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

Rhipicephalus sanguineus Complex in the Americas: Systematic, Genetic Diversity, and Geographic Insights.

The Rhipicephalus sanguineus group encompasses at least 12 validated species of Palearctic and Afrotropical hard ticks, which are relevant in veterinary medicine and public health. The taxonomy of R. sanguineus s.s., has been particularly intensely debated, due to its wide geographic distribution, morphological variants, parasite-host associations, and its capacity and vectorial competence for the transmission of several pathogens. By sequencing mitochondrial markers, it was possible to identify the existence of multiple lineages, among which the Tropical and the Temperate lineages stand out, particularly in America. However, the northern limit between these lineages is not clear due to the lack of extensive sampling across Mexico. For this reason, the aim of the present study was to determine the genetic diversity and structure of the R. sanguineus group in Mexico and to compare it with the populations reported in the Americas, in order to propose the northern limit of the R. sanguineus Tropical lineage and the potential regions of sympatry with R. sanguineus s.s. The findings of this study now confirm the presence of R. sanguineus s.s. in Mexico, showing a subtle genetic structure and high genetic diversity throughout its distribution in the Americas. In contrast, the Tropical lineage seems to be genetically less diverse in its overall distribution in the Americas. The genetic diversity of these two independent lineages could have important epidemiological implications in the transmission of tick pathogens.

Genome-Wide SNPs Provide Insights on the Cryptic Genetic Structure and Signatures of Climate Adaption in Amorphophallus albus Germplasms.

Domesticated species represent unique systems in which the evolutionary genomic consequences of intensive selective breeding and adaptation can be thoroughly investigated. Amorphophallus albus occurs naturally and is in cultivation throughout the downstream region of the Jinshajiang River in Southwest China. This species is characterised by high konjac glucomannan content, and has been cultivated in China for nearly 2,000 years. To study genetic differentiation and local adaption of A. albus, we sampled 13 distinct local cultivated populations of this species. Restriction site-associated DNA sequencing was conducted with 87 samples, resulting in 24,225 SNPs. The population structure analyses suggest two main genetic groups: one in the relatively upstream region, and one downstream. We found evidence of additional sub-structure within the upstream group, demonstrating the statistical power of genomic SNPs in discovering subtle genetic structure. The environmental and geographic factors were all identified as significant in shaping the genetic differentiation of this species. Notably, the proportion of environmental factors was larger than geographic factors in influencing the population genetic patterns of A. albus. We also discovered loci that were associated with local adaptation. These findings will help us understand the genetic differentiation of this newly domesticated species, thereby informing future breeding programs of A. albus.

Moving past barriers — Sea-drifted seeds shape regional distribution of genetic diversity of a coastal legume in the Indo-West Pacific

Canavalia rosea, a perennial vine of the legume (Fabaceae) family, is commonly found in the tropical and subtropical coasts of the world. The long-distance dispersal ability of its sea-drifted seeds has aided the species to attain a pantropical distribution. While there has been some progress on its global phylogeography, the influence of evolutionary mechanisms on the genetic composition of C. rosea at a regional scale is still unknown. In this study, we used 13 nuclear microsatellite markers and 376 samples of C. rosea from 29 sampling sites to estimate the genetic diversity and assessed the influence of gene flow and demographic features on the population structure of the species in the Indo-West Pacific (IWP) region. We found high genetic diversity and moderate genetic differentiation of C. rosea in this region. Both spatial and non-spatial clustering algorithms revealed a subtle genetic structure created by the oceanic circulation pattern of the South China Sea (SCS), thereby differentiating the sampling sites of northern SCS from the rest and even creating a genetic break within the north of SCS. However, the Bayesian analysis of migration rate and direction revealed that propagules of C. rosea could move around the cryptic barriers of ocean currents and the land barrier of the Malay Peninsula, thereby weakening the genetic differentiation between these population clusters. Although a significant relationship between geographic distance and genetic differentiation was found, our findings suggested that a continuous distribution model of gene flow could have influenced the population structure of C. rosea in this region.

Interglacials are driving speciation and intraspecific differentiation in the cold‐adapted butterfly species group Boloria pales / napaea (Nymphalidae)

AbstractAimCold‐adapted species had their largest distribution areas during glacial periods, whereas the subsequent interglacials led to retreats of these taxa into mountain ranges and more northern regions, but existing data are not sufficient for generalizing these range dynamics. To improve our knowledge of the different phylogeographical patterns existing for cold‐adapted species, we examined two closely related butterfly species of the genus Boloria with alpine disjunct and arctic–alpine distribution respectively.LocationEurope: High mountain areas and Scandinavia.TaxaBoloria pales and B. napaea.MethodsWe sequenced two mitochondrial (COI, ND1/trRNA/16S region) and two nuclear genes (wingless and EF‐1α) for 182 B. pales specimens from 37 localities and 60 B. napaea specimens from 12 localities representing the whole distribution area of both species in Europe. We used existing and known calibration points to date the age of the relevant splits.ResultsWhile nuclear DNA showed no genetic structures, the mitochondrial loci revealed 91 haplotypes belonging to three well‐differenced genetic lineages: (a) all samples of B. napaea from the Alps and Scandinavia, (b) the samples of B. pales from the Alps, Carpathians, High Tatra, Pirin Mountains, Dinaric Alps in Montenegro and the Apennines and (c) all samples of B. pales from the Pyrenees. The time estimates for the splits between these three groups range from 1.3 to 0.84 million years ago (mya). The further within‐groups differentiations are not older than 0.32 mya, but reveal a subtle pattern among and within mountain ranges.Main conclusionsAllopatry during the mid‐Pleistocene has led to differentiation into three major genetic groups, each of which possibly representing a separate species today. Especially within the today widespread mountain group (i.e. the pales sensu stricto group), repeated expansion out of their Alpine centre and a number of different peri‐Alpine glacial distribution areas have produced the subtle genetic structure observed over the late Pleistocene. The two other groups also show substructures, but to a lesser degree, hence, calling for a less disrupted distribution pattern during the late Pleistocene. However, the arctic populations of B. napaea are not derived from the same source as the Alpine ones.

Agriculture creates subtle genetic structure among migratory and nonmigratory populations of burrowing owls throughout North America.

Population structure across a species distribution primarily reflects historical, ecological, and evolutionary processes. However, large‐scale contemporaneous changes in land use have the potential to create changes in habitat quality and thereby cause changes in gene flow, population structure, and distributions. As such, land‐use changes in one portion of a species range may explain declines in other portions of their range. For example, many burrowing owl populations have declined or become extirpated near the northern edge of the species' breeding distribution during the second half of the 20th century. In the same period, large extensions of thornscrub were converted to irrigated agriculture in northwestern Mexico. These irrigated areas may now support the highest densities of burrowing owls in North America. We tested the hypothesis that burrowing owls that colonized this recently created owl habitat in northwestern Mexico originated from declining migratory populations from the northern portion of the species' range (migration‐driven breeding dispersal whereby long‐distance migrants from Canada and the United States became year‐round residents in the newly created irrigated agriculture areas in Mexico). We used 10 novel microsatellite markers to genotype 1,560 owls from 36 study locations in Canada, Mexico, and the United States. We found that burrowing owl populations are practically panmictic throughout the entire North American breeding range. However, an analysis of molecular variance provided some evidence that burrowing owl populations in northwestern Mexico and Canada together are more genetically differentiated from the rest of the populations in the breeding range, lending some support to our migration‐driven breeding dispersal hypothesis. We found evidence of subtle genetic differentiation associated with irrigated agricultural areas in southern Sonora and Sinaloa in northwestern Mexico. Our results suggest that land use can produce location‐specific population dynamics leading to subtle genetic structure even in the absence of dispersal barriers.

New genomic resources for three exploited Mediterranean fishes

Extensive fishing has led to fish stock declines throughout the last decades. While clear stock identification is required for designing management schemes, stock delineation is problematic due to generally low levels of genetic structure in marine species. The development of genomic resources can help to solve this issue. Here, we present the first mitochondrial and nuclear draft genome assemblies of three economically important Mediterranean fishes, the white seabream, the striped red mullet, and the comber. The assemblies are between 613 and 785 Mbp long and contain between 27,222 and 32,375 predicted genes. They were used as references to map Restriction-site Associated DNA markers, which were developed with a single-digest approach. This approach provided between 15,710 and 21,101 Single Nucleotide Polymorphism markers per species. These genomic resources will allow uncovering subtle genetic structure, identifying stocks, assigning catches to populations and assessing connectivity. Furthermore, the annotated genomes will help to characterize adaptive divergence.

Comparing Pool-seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster (Homarus americanus) as a case study.

Unraveling genetic population structure is challenging in species potentially characterized by large population size and high dispersal rates, often resulting in weak genetic differentiation. Genotyping a large number of samples can improve the detection of subtle genetic structure, but this may substantially increase sequencing cost and downstream bioinformatics computational time. To overcome this challenge, alternative, cost‐effective sequencing approaches, namely Pool‐seq and Rapture, have been developed. We empirically measured the power of resolution and congruence of these two methods in documenting weak population structure in nonmodel species with high gene flow comparatively to a conventional genotyping‐by‐sequencing (GBS) approach. For this, we used the American lobster (Homarus americanus) as a case study. First, we found that GBS, Rapture, and Pool‐seq approaches gave similar allele frequency estimates (i.e., correlation coefficient over 0.90) and all three revealed the same weak pattern of population structure. Yet, Pool‐seq data showed F ST estimates three to five times higher than GBS and Rapture, while the latter two methods returned similar F ST estimates, indicating that individual‐based approaches provided more congruent results than Pool‐seq. We conclude that despite higher costs, GBS and Rapture are more convenient approaches to use in the case of species exhibiting very weak differentiation. While both GBS and Rapture approaches provided similar results with regard to estimates of population genetic parameters, GBS remains more cost‐effective in project involving a relatively small numbers of genotyped individuals (e.g., <1,000). Overall, this study illustrates the complexity of estimating genetic differentiation and other summary statistics in complex biological systems characterized by large population size and migration rates.

Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis

Although edge-tolerant species are known to benefit from habitat fragmentation, less is known about the population genetic impacts fragmentation may exert on edge-tolerant species. We examined the landscape genomic structure of an edge-tolerant forest-dependent bird species, the Striped Tit-Babbler Mixornis gularis, in the heavily urbanized island of Singapore to determine if two centuries of fragmentation have led to signs of isolation and loss of population-genetic diversity in different parts of the island. We obtained a high-quality complete reference genome with 78x coverage. Using almost 4000 SNPs from double-digest RAD-Sequencing across 46 individuals, we found that the population has likely experienced a recent contraction in effective population size and presently exhibits low population genetic diversity. Using empirical and simulation-based landscape genomic analyses, we also found that the subtle population genetic structure observed in the Striped Tit-Babbler population in Singapore is likely driven by isolation by distance resulting from limited dispersal. Our results demonstrate that population genetic impoverishment and subdivision can accumulate at relatively rapid rates in edge-tolerant bird species such as the Striped Tit-Babbler as a result of fragmentation, and that subtle spatial genetic structure can be detected over fine spatial and temporal scales using relatively few multilocus genomic SNPs.

Diversity analysis and genetic relationships among local Algerian fig cultivars (Ficus carica l.) using SSR markers

The common fig (Ficus carica L.) is an emblematic fruit tree in Mediterranean basin with complicated misidentification. A good management and conservation of local cultivars involve a prior genetic assessment of the variability presented in germplasm collections. This study characterizes for the first time the genetic variability of Algerian fig cultivars. In total, 34 fig cultivars from a local germplasm collection and a private orchard were analyzed using 24 SSR markers in order to evaluate the genetic diversity and the relationship among local Algerian cultivars. The polymorphic markers amplified a total of 79 fragments with a mean number of 3.59 alleles per locus. The observed heterozygosity ranged from 0.039 to 0.84, with a mean of 0.46. The expected heterozygosity varied from 0.074 to 0.74, with a mean of 0.42. The total value of probability of identity was 3.24×10−8. Unweighted Pair Group Method with Arithmetic Averages (UPGMA) cluster analysis showed cases of synonymies and homonymies in the cultivars analyzed and some groups were related to fruit production type. The combination of only three SSR allowed to unequivocally distinguish 13 cultivars. Bayesian analysis showed a subtle genetic structure and depicted an admixture origin for most accessions.

Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African buffalo representative of the four subspecies. We identified 2534 SNPs with high confidence within the panel by aligning the short sequences to the cattle genome (Bos taurus). The average sequencing depth of the complete aligned set of reads was estimated at 5x, and at 13x when only considering the final set of putative SNPs that passed the filtering criterion. Our set of SNPs was validated by PCR amplification and Sanger sequencing of 15 SNPs. Of these 15 SNPs, 14 amplified successfully and 13 were shown to be polymorphic (success rate: 87%). The fidelity of the identified set of SNPs and potential future applications are finally discussed.

RAD SNP markers as a tool for conservation of dolphinfish Coryphaena hippurus in the Mediterranean Sea: Identification of subtle genetic structure and assessment of populations sex-ratios

Dolphinfish is an important fish species for both commercial and sport fishing, but so far limited information is available on genetic variability and pattern of differentiation of dolphinfish populations in the Mediterranean basin. Recently developed techniques allow genome-wide identification of genetic markers for better understanding of population structure in species with limited genome information. Using restriction-site associated DNA analysis we successfully genotyped 140 individuals of dolphinfish from eight locations in the Mediterranean Sea at 3324 SNP loci. We identified 311 sex-related loci that were used to assess sex-ratio in dolphinfish populations. In addition, we identified a weak signature of genetic differentiation of the population closer to Gibraltar Strait in comparison to other Mediterranean populations, which might be related to introgression of individuals from Atlantic. No further genetic differentiation could be detected in the other populations sampled, as expected considering the known highly mobility of the species. The results obtained improve our knowledge of the species and can help managing dolphinfish stock in the future.

Novel implications on the genetic structure of representative populations of Saccharina japonica (Phaeophyceae) in the Northwest Pacific as revealed by highly polymorphic microsatellite markers

Although the original Saccharina japonica populations in China are assumed to have been accidentally introduced from Japan in 1920s, few investigations have been performed to prove it. Genetic structure analysis is expected to shed light on this question. In the present study, 11 highly polymorphic microsatellite markers were employed to analyze the genetic structure of representative populations of S. japonica in the Northwest Pacific, including the four varieties from Japan. Populations from China had a much lower level of genetic diversity than the ones from Japan in terms of the number of alleles, private alleles and locally common alleles, and the values of heterozygosity, suggestive of the founder effect in the introduced populations. Both the Bayesian model-based and genetic distance-based analyses revealed three major clusters: (1) S. japonica var. japonica, var. religiosa, and var. ochotensis from Hokkaido, as well as the populations from Korea and Russia; (2) populations from China; and (3) var. diabolica. Saccharina japonica var. diabolica harbored the highest number of private alleles, with three of them having a frequency of 1.00 at three loci, which have the potential to be used as specific markers to distinguish this variety from others. Significant genetic differentiation was found between almost all the populations except for a few cultivated populations from China. Populations from China were most closely related to S. japonica var. japonica, which was in turn most close to var. religiosa and the Korean population. The microsatellite markers used in this study were shown to be polymorphic enough to decipher the subtle genetic structure of S. japonica, including the different varieties.

Using dense locality sampling resolves the subtle genetic population structure of the dispersive fish species Plecoglossus altivelis.

In dispersive species with continuous distributions, genetic differentiation between local populations is often absent or subtle and thus difficult to detect. To incorporate such subtle differentiation into management plans, it may be essential to analyse many samples from many localities using adequate numbers of high-resolution genetic markers. Here, we evaluated the usefulness of dense locality sampling in resolving genetic population structure in the ayu (Plecoglossus altivelis), a dispersive fish important in Japanese inland fisheries. Genetic variability in, and differentiation between, ayu populations around the Japan-Ryukyu Archipelago were investigated in 4746 individuals collected from 120 localities by genotyping 12 microsatellite markers. These individuals represented the two subspecies of ayu, namely the Ryukyuan subspecies (Plecoglossus altivelis ryukyuensis) and both amphidromous and landlocked forms of the nominotypical subspecies (P.a.altivelis) along the archipelago. We successfully detected an absence of genetic differentiation within the landlocked form and subtle but significant differentiation and clear geographic patterns of genetic variation among populations of the amphidromous form, which had been considered genetically homogeneous. This suggests that dense locality sampling effectively resolves subtle differences in genetic population structure, reducing stochastic deviation in the detection of genetic differentiation and geographic patterns in local populations of this dispersive species. Resampling analyses based on empirical data sets clearly demonstrate the effectiveness of increasing the number of locality samples for stable and reliable estimations of genetic fixation indices. The genetic population structure observed within the amphidromous form provides useful information for identifying management or conservation units in ayu.

Genomic variation among populations of threatened coral: Acropora cervicornis.

BackgroundAcropora cervicornis, a threatened, keystone reef-building coral has undergone severe declines (>90 %) throughout the Caribbean. These declines could reduce genetic variation and thus hamper the species’ ability to adapt. Active restoration strategies are a common conservation approach to mitigate species' declines and require genetic data on surviving populations to efficiently respond to declines while maintaining the genetic diversity needed to adapt to changing conditions. To evaluate active restoration strategies for the staghorn coral, the genetic diversity of A. cervicornis within and among populations was assessed in 77 individuals collected from 68 locations along the Florida Reef Tract (FRT) and in the Dominican Republic.ResultsGenotyping by Sequencing (GBS) identified 4,764 single nucleotide polymorphisms (SNPs). Pairwise nucleotide differences (π) within a population are large (~37 %) and similar to π across all individuals. This high level of genetic diversity along the FRT is similar to the diversity within a small, isolated reef. Much of the genetic diversity (>90 %) exists within a population, yet GBS analysis shows significant variation along the FRT, including 300 SNPs with significant FST values and significant divergence relative to distance. There are also significant differences in SNP allele frequencies over small spatial scales, exemplified by the large FST values among corals collected within Miami-Dade county.ConclusionsLarge standing diversity was found within each population even after recent declines in abundance, including significant, potentially adaptive divergence over short distances. The data here inform conservation and management actions by uncovering population structure and high levels of diversity maintained within coral collections among sites previously shown to have little genetic divergence. More broadly, this approach demonstrates the power of GBS to resolve differences among individuals and identify subtle genetic structure, informing conservation goals with evolutionary implications.

No divergent evolution, despite restricted connectivity, between Atlantic and Indian Ocean goby populations

Southern Africa is a marine biodiversity hotspot that not only comprises faunal elements from the Atlantic and Indian Oceans, but also large numbers of endemic species. Using mitochondrial and nuclear DNA sequence data, we explored whether genetic structure in the endemic coastal goby Psammogobius knysnaensis, a species whose range straddles both biomes, is linked to the boundary between the two oceans. Subtle genetic structure was identified between Atlantic and Indian Ocean populations, with genetic diversity being lower in the Atlantic, and particularly on the west coast. Our results point to partial isolation between the populations associated with each biome that is most likely driven by the region’s oceanography, but unlike in other species, there is no evidence for distinct regional evolutionary lineages that are likely adapted to the environmental conditions prevalent in each region. The exclusive presence of P. knysnaensis in sheltered habitats (estuaries and lagoons) may protect this species from the severe impacts of cold water upwelling on the west coast.