Hierarchical Genetic Structure Research Articles

Genetic Diversity and Genetic Structure of Three Sympatric Oak Species in Serbian Landscape of Outstanding Features "Kosmaj" Assessed by Nuclear Microsatellites

Quercus petraea (Matt.) Liebl., Q. pubescens Willd., and Q. frainetto Ten. grow naturally in sympatry in the Landscape of Outstanding Features "Kosmaj" (Mt. Kosmaj) in Serbia, in the Western Balkans. The levels of genetic diversity and genetic structure in populations of these species (160 trees in total) was assessed by means of 14 nuclear microsatellites. The number of alleles detected in overall sample was 314, with the locus QrZAG90 being the most informative one in all three species (31, 35 and 36 alleles in Q. frainetto, Q. pubescens and Q. petraea, respectively). The levels of genetic diversity of all three species were relatively high (HE = 0.824, 0.834, and 0.794 in Q. petraea, Q. pubescens and Q. frainetto, respectively). Low but statistically significant inbreeding was detected in all three species (F = 0.100, 0.131 and 0.065 in Q. petraea, Q. pubescens and Q. frainetto, respectively), which, however, most likely reflects population substructure, which was observed in the STRUCTURE analysis. The optimal number of genetic groups revealed by Bayesian clustering analysis did not coincide with the number of analyzed species as it amounted to four (one gene pool was observed in each of the two species, Q. petraea and Q. pubescens, while two gene pools were observed in Q. pubescens). Furthermore, a higher level of hierarchical genetic structure, with six gene pools was found, with Q. frainetto being the only oak species in which population substructure was not observed. Genetic differentiation of three sympatric oak species was relatively low but statistically significant, with the highest FST value found among Q. petraea and Q. frainetto (FST = 0.047, P = 0.001), and the lowest between Q. petraea and Q. pubescens (FST = 0.032, P = 0.001). Our results reveal rather high levels of genetic diversity in all three studied oak species, which retained their genetic integrity despite sympatric distribution, indicating low levels of interspecific hybridization, and pronounced genetic structure of Q. pubescens and Q. petraea.

The eco‐evolutionary role of fire in shaping terrestrial ecosystems

Abstract Fire is an inherently evolutionary process, even though much more emphasis has been given to ecological responses of plants and their associated communities to fire. Here, we synthesize contributions to a Special Feature entitled ‘Fire as a dynamic ecological and evolutionary force’ and place them in a broader context of fire research. Topics covered in this Special Feature include a perspective on the impacts of novel fire regimes on differential forest mortality, discussions on new approaches to investigate vegetation‐fire feedbacks and resulting plant syndromes, synthesis of fire impacts on plant–fungal interactions, and a meta‐analysis of arthropod community responses to fire. We conclude by suggesting pathways forward to better understand the ecological and evolutionary consequences of fire. These include developing ecological and evolutionary databases for fire ecology, integrating hierarchical genetic structure or phylogenetic structure, and developing new experimental frameworks that limit context‐dependent outcomes. Read the free Plain Language Summary for this article on the Journal blog.

Functional connectivity of an imperilled Arctic ungulate – where melting sea ice and human trails increase isolation

Sea ice loss, disturbance, and habitat modification by humans can alter functional landscape connectivity, with negative impacts on wildlife. Connectivity facilitates movement and gene flow, and contributes to genetic diversity, metapopulation dynamics, and species range-shifts under climate change. For Arctic ungulates, which disperse over large areas including sea ice, environmental change threatens further isolation. Protecting habitat and its linkages is critical and depends on identifying such areas at commensurate, broad scales. Using caribou, the world's most vagile species, we modelled and mapped the drivers of connectivity across ca. 2 million km2 of the Canadian Arctic Archipelago — where the pace of climate change is among the fastest and caribou are threatened with extinction. First, we quantified hierarchical genetic structure and identified two discrete groups. Next, using circuit theory and simultaneous multi-surface optimization, we tested whether land- and sea-scape heterogeneity or geographic distance better accounted for movement and gene flow within each group. We show that anthropogenic interference is far-reaching. High Arctic Peary caribou displayed isolation-by-resistance, where glacier cover, low sea-ice concentrations during fall, and human trails impeded connectivity. In contrast, more southerly barren-ground caribou displayed largely unrestricted gene flow. These divergent outcomes underscore that organism-landscape relationships can vary across space and highlight the importance of intra-specific structure and responses. By leveraging genetic data, our study demonstrates how critical movement pathways can be identified, even for remote and imperilled species. Such knowledge supports broad-scale conservation planning, in particular, by accounting for complex organism-landscape relationships, across vast, heterogeneous ecosystems.

A Comparison of Entropic Diversity and Variance in the Study of Population Structure.

AMOVA is a widely used approach that focuses on variance within and among strata to study the hierarchical genetic structure of populations. The recently developed Shannon Informational Diversity Translation Analysis (SIDTA) instead tackles exploration of hierarchical genetic structure using entropic allelic diversity. A mix of artificial and natural population data sets (including allopolyploids) is used to compare the performance of SIDTA (a 'q = 1' diversity measure) vs. AMOVA (a 'q = 2' measure) under different conditions. An additive allelic differentiation index based on entropic allelic diversity measuring the mean difference among populations (ΩAP) was developed to facilitate the comparison of SIDTA with AMOVA. These analyses show that the genetic population structure seen by AMOVA is notably different in many ways from that provided by SIDTA, and the extent of this difference is greatly affected by the stability of the markers employed. Negative among group values are lacking with SIDTA but occur with AMOVA, especially with allopolyploids. To provide more focus on measuring allelic differentiation among populations, additional measures were also tested including Bray-Curtis Genetic Differentiation (BCGD) and several expected heterozygosity-based indices (e.g., GST, G″ST, Jost's D, and DEST). Corrections, such as almost unbiased estimators, that were designed to work with heterozygosity-based fixation indices (e.g., FST, GST) are problematic when applied to differentiation indices (eg., DEST, G″ST, G'STH).

Hierarchical genetic structure in a direct-developing whelk (Buccinum undatum) throughout the western North Atlantic

Direct-developing marine species lack a pelagic larval phase and are therefore predicted to have limited dispersal capacity and exhibit strong genetic structure over small spatial scales. Nevertheless, empirical work suggests that developmental mode, alone, cannot always explain realized connectivity patterns. We characterized spatial genetic structure within the western North Atlantic lineage of the waved whelk ( Buccinum undatum) , a direct-developing gastropod that is the target of an emerging fishery. We genotyped individuals throughout Atlantic Canada using 1052 single nucleotide polymorphisms, documenting strong hierarchical genetic structuring throughout this region. Overall, pairwise genetic structure estimates were high, with two major genetic clusters separating southwestern and northeastern sites. But more complex patterns emerged at smaller spatial scales. Notably, pairs of sites on deeper offshore habitat exhibited panmixia, despite being separated by up to 100 km, whereas inshore and intertidal populations spaced at comparable distances were strongly genetically divergent. Collectively, our multi-scale analyses revealed that direct developers can exhibit genetic patterns that do not conform to simple geographic expectations. Future exploration of potential depth-variable connectivity is warranted, especially among harvested populations.

Unraveling the hierarchical genetic structure of tea green leafhopper, Matsumurasca onukii, in East Asia based on SSRs and SNPs.

Matsumurasca onukii (Matsuda, R. (1952). Oyo‐Kontyu Tokyo, 8(1): 19–21), one of the dominant pests in major tea production areas in Asia, currently is known to occur in Japan, Vietnam, and China, and severely threatens tea production, quality, and international trade. To elucidate the population genetic structure of this species, 1633 single nucleotide polymorphisms (SNPs) and 18 microsatellite markers (SSRs) were used to genotype samples from 27 sites representing 18 geographical populations distributed throughout the known range of the species in East Asia. Analyses of both SNPs and SSRs showed that M. onukii populations in Yunnan exhibit high‐genetic differentiation and structure compared with the other populations. The Kagoshima (JJ) and Shizuoka (JS) populations from Japan were separated from populations from China by SNPs, but clustered with populations from Jinhua (JH), Yingde (YD), Guilin (GL), Fuzhou (FZ), Hainan (HQ), Leshan (CT), Chongqing (CY), and Zunyi (ZY) tea plantations in China and the Vietnamese Vinh Phuc (VN) population based on the SSR data. In contrast, CT, CY, ZY, and Shaanxi (SX) populations clustered together based on SNPs, but were separated by SSRs. Both marker datasets identified significant geographic differentiation among the 18 populations. Various environmental and anthropogenic factors, including geographical barriers to migration, human transport of hosts (Camellia sinesis [L.] O. Kuntze) and adaptation of M. onukii to various local climatic zones possibly account for the rapid spread of this pest in Asia. The results demonstrate that SNPs from high‐throughput genotyping data can be used to reveal subtle genetic substructure at broad scales in r‐strategist insects.

Accounting for population structure in genomic predictions of Eucalyptus globulus.

Genetic groups have been widely adopted in tree breeding to account for provenance effects within pedigree-derived relationship matrices. However, provenances or genetic groups have not yet been incorporated into single-step genomic BLUP ("HBLUP") analyses of tree populations. To quantify the impact of accounting for population structure in Eucalyptus globulus, we used HBLUP to compare breeding value predictions from models excluding base population effects and models including either fixed genetic groups or the marker-derived proxies, also known as metafounders. Full-sib families from 2 separate breeding populations were evaluated across 13 sites in the "Green Triangle" region of Australia. Gamma matrices (Γ) describing similarities among metafounders reflected the geographic distribution of populations and the origins of 2 land races were identified. Diagonal elements of Γ provided population diversity or allelic covariation estimates between 0.24 and 0.56. Genetic group solutions were strongly correlated with metafounder solutions across models and metafounder effects influenced the genetic solutions of base population parents. The accuracy, stability, dispersion, and bias of model solutions were compared using the linear regression method. Addition of genomic information increased accuracy from 0.41 to 0.47 and stability from 0.68 to 0.71, while increasing bias slightly. Dispersion was within 0.10 of the ideal value (1.0) for all models. Although inclusion of metafounders did not strongly affect accuracy or stability and had mixed effects on bias, we nevertheless recommend the incorporation of metafounders in prediction models to represent the hierarchical genetic population structure of recently domesticated populations.

Hierarchical genetic structure and implications for conservation of the world\u2019s largest salmonid, Hucho taimen

Population genetic analyses can evaluate how evolutionary processes shape diversity and inform conservation and management of imperiled species. Taimen (Hucho taimen), the world’s largest freshwater salmonid, is threatened, endangered, or extirpated across much of its range due to anthropogenic activity including overfishing and habitat degradation. We generated genetic data using high throughput sequencing of reduced representation libraries for taimen from multiple drainages in Mongolia and Russia. Nucleotide diversity estimates were within the range documented in other salmonids, suggesting moderate diversity despite widespread population declines. Similar to other recent studies, our analyses revealed pronounced differentiation among the Arctic (Selenge) and Pacific (Amur and Tugur) drainages, suggesting historical isolation among these systems. However, we found evidence for finer-scale structure within the Pacific drainages, including unexpected differentiation between tributaries and the mainstem of the Tugur River. Differentiation across the Amur and Tugur basins together with coalescent-based demographic modeling suggests the ancestors of Tugur tributary taimen likely diverged in the eastern Amur basin, prior to eventual colonization of the Tugur basin. Our results suggest the potential for differentiation of taimen at different geographic scales, and suggest more thorough geographic and genomic sampling may be needed to inform conservation and management of this iconic salmonid.

Context-dependent dispersal determines relatedness and genetic structure in a patchy amphibian population.

Dispersal is a central process in ecology and evolution with far reaching consequences for the dynamics and genetics of spatially structured populations (SSPs). Individuals can adjust their decisions to disperse according to local fitness prospects, resulting in context-dependent dispersal. By determining dispersal rate, distance and direction, these individual-level decisions further modulate the demography, relatedness and genetic structure of SSPs. Here, we examined how context-dependent dispersal influences the dynamics and genetics of a great crested newt (Triturus cristatus) SSP. We collected capture-recapture data of 5564 individuals and genetic data of 950 individuals across an SSP in northern Germany. We added genetic data from six sites outside this SSP to assess genetic structure and gene flow at a regional level. Dispersal rates within the SSP were high but dispersal distances were short. Dispersal was context-dependent: individuals preferentially immigrated into high-quality ponds where breeding probabilities were higher. The studied SSP behaved like a patchy population, where subpopulations at each pond were demographically interdependent. High context-dependent dispersal led to weak but significant spatial genetic structure and relatedness within the SSP. At the regional level, a strong hierarchical genetic structure with very few first-generation migrants as well as low effective dispersal rates suggest the presence of independent demographic units. Overall, our study highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in SSPs. Limited capacity for long-distance dispersal seems to increase genetic structure within a population and leads to demographic isolation in anthropogenic landscapes.

Landscape Genetics of American Beaver in Coastal Oregon

ABSTRACTAmerican beaver (Castor canadensis) have been translocated for population restoration, reduction of human‐wildlife conflict, and enhancement of ecosystem function. Yet few studies have assessed dispersal of beaver, making it difficult to determine at what scale translocations are appropriate. Genetic studies can provide inferences about gene flow, and thus dispersal. We used a landscape genetic approach to evaluate whether landscape features influenced gene flow among beaver in the Coast Range of western Oregon, USA, using samples collected April–September 2014. We collected genetic samples from live‐captured (n = 232), road‐killed (n = 2) and trapper‐provided (n = 58) tissue samples and genotyped them at 10 microsatellite loci. We mapped records of beaver translocations into or within the study area during the twentieth century to consider the effect of those movements on genetic structure. We used population assignment tests to delimit genetic clusters, evaluated correspondence of those clusters with watershed boundaries and translocation history, and then estimated differentiation between clusters and between watersheds using model‐based and model‐free approaches. We evaluated how individual genetic differences varied with geographic distance, and investigated related pairs within clusters. We developed landscape resistance models incorporating slope, distance to water, and watershed boundaries at 2 scales, and estimated effective distances between sample locations with least cost path and circuit theoretic analyses. We evaluated the correlation of individual genetic distances with effective distances using a pseudo‐bootstrapping approach. Landscape genetic models did not explain spatial variation in genetic structure better than geographic distance, but hierarchical genetic structure corresponded with watershed boundaries and suggested influences from historical translocations. Pairwise individual genetic distances were positively correlated with geographic distances to 61 km; highly‐related pairs mostly were detected <1 km apart (median = 1.0 km, = 14.6 ± 2.3 [SE] km, n = 77). We concluded that slope and distance to water did not strongly limit dispersal and gene flow by beaver in this system, but concordance of genetic structure with watershed boundaries suggests that dispersal is more common within than between watersheds. Genetic differentiation of beaver within this topographically complex system was much greater than reported in a study at similar spatial scales in relatively flat topography. We recommend that translocation efforts of American beaver in topographically complex landscapes occur within watersheds when possible but conclude that dispersal can occur across watersheds. © 2021 The Wildlife Society. This article is a U.S. Government work and is in the public domain in the USA.

Genomic data support management of anadromous Arctic Char fisheries in Nunavik by highlighting neutral and putatively adaptive genetic variation.

Distinguishing neutral and adaptive genetic variation is one of the main challenges in investigating processes shaping population structure in the wild, and landscape genomics can help identify signatures of adaptation to contrasting environments. Arctic Char (Salvelinus alpinus) is an anadromous salmonid and the most harvested fish species by Inuit people, including in Nunavik (Québec, Canada), one of the most recently deglaciated regions in the world. Unlike many other anadromous salmonids, Arctic Char occupy coastal habitats near their natal rivers during their short marine phase restricted to the summer ice‐free period. Our main objective was to document putatively neutral and adaptive genomic variation in anadromous Arctic Char populations from Nunavik and bordering regions to inform local fisheries management. We used genotyping by sequencing (GBS) to genotype 18,112 filtered single nucleotide polymorphisms (SNP) in 650 individuals from 23 sampling locations along >2000 km of coastline. Our results reveal a hierarchical genetic structure, whereby neighboring hydrographic systems harbor distinct populations grouped by major oceanographic basins: Hudson Bay, Hudson Strait, Ungava Bay, and Labrador Sea. We found genetic diversity and differentiation to be consistent both with the expected postglacial recolonization history and with patterns of isolation‐by‐distance reflecting contemporary gene flow. Results from three gene–environment association methods supported the hypothesis of local adaptation to both freshwater and marine environments (strongest associations with sea surface and air temperatures during summer and salinity). Our results support a fisheries management strategy at a regional scale, and other implications for hatchery projects and adaptation to climate change are discussed.

Genetic differentiation over a small spatial scale in the smooth newt (Lissotriton vulgaris)

Understanding the distribution of genetic variation is central for both population biology and conservation genetics. Genetic population structure can be primarily affected by the species’ dispersal ability, which is assumed to be limited in many amphibians. In this study, we estimated allelic differentiation metrics and FST indices to investigate genetic variation among natural breeding ponds of smooth newts (Lissotriton vulgaris) over a small spatial scale. Based on six microsatellite loci, we found a small, but significant allelic differentiation among clusters of natural breeding ponds (i.e. ‘local regions’), which result was in line with the calculation of corresponding hierarchical FST values. Analysis of molecular variance also indicated significant between-region variation in the study area. Pairwise estimations showed that only the furthermost regions differed from each other in both differentiation measures, but this difference was not attributable to geographic distances between ponds. Our results provide evidence that hierarchical genetic structure can be characteristic to breeding ponds of smooth newts on a small spatial scale in their natural breeding habitat, but dispersal distance may be less limited than previously thought in these philopatric caudates.

Hybrid performance as related to genomic diversity and population structure in public sorghum inbred lines

AbstractThe low‐cost next‐generation sequencing technologies provide tremendous opportunities for dissecting complex traits in crop species. The objective of this study was to assess the relationship between genomic diversity, population structure, and hybrid performance in public sorghum [Sorghum bicolor (L.) Moench] inbred lines. A total of 279 public sorghum inbred lines (228 R‐lines and 51 B‐lines) developed across more than two decades were studied. The inbreds were genotyped using genotyping‐by‐sequencing (GBS) platform, which generated 282,536 single nucleotide polymorphisms (SNPs). After filtering at a ≤5% threshold for minor allele frequency (MAF) and <20% missing data, a total of 66,265 SNPs were returned and used for analysis. Mean polymorphic information content (PIC) was 0.35, and gene diversity across the inbreds was 0.46. The neighbor‐joining tree, principal component, and STRUCTURE analyses clustered the inbreds into three subgroups. One‐hundred and two test‐cross hybrids, 50 between closely related parents and 52 between distantly related parents, were developed and evaluated along with two commercial checks in two environments using three replications. Data were obtained on plant height, maturity, yield, and yield components. Mean performance of hybrids derived from closely related and distantly related parents was compared to determine the value of genomics‐based genetic distance to predict hybrid performance. The results revealed the presence of robust genetic variability and hierarchical genetic structure among inbred parents, but marker‐based genetic distance was not a good predictor of yield performance.

Common barriers, but temporal dissonance: Genomic tests suggest ecological and paleo-landscape sieves structure a coastal riverine fish community.

Assessments of spatial and temporal congruency across taxa from genetic data provide insights into the extent to which similar processes structure communities. However, for coastal regions that are affected continuously by cyclical sea-level changes over the Pleistocene, congruent interspecific response will not only depend upon codistributions, but also on similar dispersal histories among taxa. Here, we use SNPs to test for concordant genetic structure among four codistributed taxa of freshwater fishes (Teleostei: Characidae) along the Brazilian Atlantic coastal drainages. Based on population relationships and hierarchical genetic structure analyses, we identify all taxa share the same geographic structure suggesting the fish utilized common passages in the past to move between river basins. In contrast to this strong spatial concordance, model-based estimates of divergence times indicate that despite common routes for dispersal, these passages were traversed by each of the taxa at different times resulting in varying degrees of genetic differentiation across barriers with most divergences dating to the Upper Pleistocene, even when accounting for divergence with gene flow. Interestingly, when this temporal dissonance is viewed through the lens of the species-specific ecologies, it suggests that an ecological sieve influenced whether species dispersed readily, with an ecological generalist showing the highest propensity for historical dispersal among the isolated rivers of the Brazilian coast (i.e., the most recent divergence times and frequent gene flow estimated for barriers). We discuss how our findings, and in particular what the temporal dissonance, despite common geographic passages, suggest about past dispersal structuring coastal communities as a function of ecological and paleo-landscape sieves.

Hierarchical genetic and spatial structure among varieties and populations of Hymenaea stigonocarpa (Fabaceae) in Brazilian savannah

Approaches in population genetics decompose species genetic variation at hierarchical level, understanding the action of microevolutionary processes at spatial scales. We evaluated the taxonomically complex species Hymenaea stigonocarpa, a tree species distributed in central Brazil, presenting three botanical varieties weakly distinguished by morphological traits. We aimed to investigate the spatial genetic structure of populations of H. stigonocarpa along Cerrado biome, assessing genetic differentiation and the existence of hybridization zones in this species. We genotyped 901 plants from 28 local populations using nine nuclear microsatellite loci. Analyses of genetic diversity, Bayesian inference estimated genetic differentiation and migration rate among populations and varieties. Mantel tests and sPCA evaluated spatial pattern of genetic variation. We observed that H. stigonocarpa var. brevipetiolata presented larger genetic differentiation compared to H. stigonocarpa var. stigonocarpa and H. stigonocarpa var. pubescens (FCT = 0.175). Bayesian approaches supported a genetic different cluster and hybridization process in sympatric populations for H. stigonocarpa var. brevipetiolata. Migration rate was high and not significantly higher among varieties, confirming the existence of hybridization. Spatial correlations were relatively low, but with exponential decrease of genetic similarity along of the geographic space. Spatial genetic structure was higher for H. stigonocarpa var. brevipetiolata and local structures were found with sPCA, indicating that neighboring populations are genetically different mainly in populations of eastern Cerrado. The genetic clusters are not congruent with the vegetative characters used to recognize the three botanical varieties, which should be viewed with skepticism. Our genetic analyses strongly support the need for a taxonomic review.

Genetic Diversity, Population Structure, and Linkage Disequilibrium of Pearl Millet.

Mapping of GBS reads of 398 accessions to the draft genome sequence identified 82,112 SNPs Model-based clustering analysis revealed a hierarchical genetic structure of six subgroups Greater LD decay in the west-African subpopulation is likely due to long history of recombination Genetic differentiation analysis among subpopulations revealed variation in selection signatures Pearl millet [Cenchrus americanus (L.) Morrone syn. Pennisetum glaucum (L.) R. Br.] is one of the most extensively cultivated cereals in the world, after wheat (Triticum aestivum L.), maize (Zea mays L.), rice (Oryza sativa L.), barley (Hordeum vulgare L.), and sorghum [Sorghum bicolor (L.) Moench]. It is the main component of traditional farming systems and a staple food in the arid and semiarid regions of Africa and southern Asia. However, its genetic improvement is lagging behind other major cereals and the yield is still low. Genotyping-by-sequencing (GBS)-based single-nucleotide polymorphism (SNP) markers were screened on a total of 398 accessions from different geographic regions to assess genetic diversity, population structure, and linkage disequilibrium (LD). By mapping the GBS reads to the reference genome sequence, 82,112 genome-wide SNPs were discovered. The telomeric regions of the chromosomes have the higher SNP density than in pericentromeric regions. Model-based clustering analysis of the population revealed a hierarchical genetic structure of six subgroups that mostly overlap with the geographic origins or sources of the genotypes but with differing levels of admixtures. A neighbor-joining phylogeny analysis revealed that germplasm from western Africa rooted the dendrogram with much diversity within each subgroup. Greater LD decay was observed in the west-African subpopulation than in the other subpopulations, indicating a long history of recombination among landraces. Also, genome scan of genetic differentiatation detected different selection histories among subpopulations. These results have potential application in the development of genomic-assisted breeding in pearl millet and heterotic grouping of the lines for improved hybrid performance.

Fine-scale hierarchical genetic structure and kinship analysis of the ascidian Pyura chilensis in the southeastern Pacific.

Studying population structure and genetic diversity at fine spatial scales is key for a better understanding of demographic processes that influence population connectivity. This is particularly important in marine benthic organisms that rely on larval dispersal to maintain connectivity among populations. Here, we report the results of a genetic survey of the ascidian Pyura chilensis from three localities along the southeastern Pacific. This study follows up on a previous report that described a genetic break in this region among localities only 20 km apart. By implementing a hierarchical sampling design at four spatial levels and using ten polymorphic microsatellite markers, we test whether differences in fine‐scale population structure explain the previously reported genetic break. We compared genetic spatial autocorrelations, as well as kinship and relatedness distributions within and among localities adjacent to the genetic break. We found no evidence of significant autocorrelation at the scale up to 50 m despite the low dispersal potential of P. chilensis that has been reported in the literature. We also found that the proportion of related individuals in close proximity (<1 km) was higher than the proportion of related individuals further apart. These results were consistent in the three localities. Our results suggest that the spatial distribution of related individuals can be nonrandom at small spatial scales and suggests that dispersal might be occasionally limited in this species or that larval cohorts can disperse in the plankton as clustered groups. Overall, this study sheds light on new aspects of the life of this ascidian as well as confirms the presence of a genetic break at 39°S latitude. Also, our data indicate there is not enough evidence to confirm that this genetic break can be explained by differences in fine‐scale genetic patterns among localities.

Comparative genetic isolation patterns for multiple headwater fishes in three geographic regions.

Headwater-resident fishes may be prone to a high rate of isolation and a pronounced hierarchical genetic structure due to a combination of niche preference and dendritic effects of river networks. Genetic isolation patterns were compared using microsatellites in six headwater fishes, Fundulus olivaceus, Semotilus atromaculatus, Erimyzon claviformis, Etheostoma artesiae, Etheostoma whipplei and Etheostoma parvipinne, in three geographic regions that included drainages of small, medium and large sizes in the southern United States. All species showed hierarchical nesting of genetic populations and there were clear and mostly consistent differences between species and regions that were identified through summary statistics derived from two independent analyses. For species comparisons, a high isolation grouping (increased number of isolated genetic clusters or sites within regions) and a low-isolation grouping (decreased number of clusters or sites) were identified. Species group placement was related to niche breadth along the river continuum and presumed abundance and variability of preferred microhabitats, with increased headwater specialization among species being associated with placement in the high-isolation grouping. There was a weakly significant positive effect of drainage size on the number of isolated clusters or sites across all species. Regional patterns were shared in two species, with the region containing the smallest drainages having lower rates of isolation in both datasets. This study shows the effects of regional and species characteristics on genetic isolation for headwater species, which are especially prone to isolation due to spatial, dendritic effects of river networks.

Hierarchical genetic structure of native masu salmon populations in Hokkaido, Japan

Identification of the spatial extent of genetic structuring that may be influenced by evolutionary, ecological and historical factors is critical for effective conservation or management strategies. Masu salmon Oncorhynchus masou is commonly distributed in Far East, however, many local populations have been under threats of decline due to habitat destruction, overexploitation, and genetic introgression. To reveal the spatial genetic structure of native masu salmon populations in Hokkaido, masu salmon samples were collected from 16 rivers in which there was no official record of artificial releases of any masu salmon stock and were analyzed using 15 microsatellite loci. A Bayesian assignment test revealed that masu salmon populations were divided into two genetically distinct groups: the northeastern and southwestern groups. For within-group genetic structure, all populations, except for geographically proximate populations, were significantly different from each other. AMOVA revealed that genetic variation at among-group level based on groups identified assignment test was greater than that of groups based on geographic locations. There was no significant IBD for the 16 populations. However, the Mantel test revealed significant IBD for the northeastern group, but did not for the southwestern group. This study suggested that native masu salmon populations in Hokkaido exhibit a hierarchical genetic structure that is largely a result of their precise homing behavior. The results of this study also highlight the importance of defining populations by using genetic data rather than by using predefined populations based on geographic locations for the correct determination of genetic structure.

Spatial genetic structure in brittlebush (Encelia farinosa, Asteraceae) in the southwestern deserts of North America: a comparison of nuclear and chloroplast DNA sequences

A previous study of spatial genetic structure in brittlebush in the southwestern deserts based on chloroplast DNA variation revealed strongly differentiated populations and statistically significant associations between geography and genetic diversity, presumably associated with Pleistocene climatic oscillations. To expand this work and understand the spatial genetic structure of brittlebush populations more completely, we sought to compare the genetic diversity and structure of chloroplast DNA with that of nuclear ribosomal DNA (internal transcribed spacer) and a low-copy nuclear region developed for the Asteraceae (D22). Here we obtained 192 ITS and 206 D22 sequences from individuals sampled throughout the range and analyzed them with network, population genetic, demographic, hierarchical, spatial, and Bayesian analyses. Although there are differences in the signal present in each genetic region, several large-scale spatial patterns are congruent, including a split between the Sonoran and Mojave Deserts and differentiation of a taxonomic variety from the Cape Region of Baja California. In general, the distribution of genetic variation observed in D22 confirms and even refines patterns previously observed in the chloroplast region. In contrast, there is little to no geographic structure in the genetic variation of ITS, possibly due to the effects of multiple gene copies, reticulation, homoplasy, and concerted evolution. Hierarchical genetic structure differs sharply between nuclear regions and the chloroplast region, and this is likely due to differences not only in the evolution and inheritance of these regions, but also in the dispersal of pollen and seeds among brittlebush populations.