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Background: The patterns of inbreeding coefficients (FIS) and fine spatial genetic structure (FSGS) were evaluated regarding the mating system and inbreeding depression of food-deceptive orchids, Dactylorhiza majalis, Dactylorhiza incarnata var. incarnata, and Dactylorhiza fuchsii, from NE Poland. Methods: We used 455 individuals, representing nine populations of three taxa and AFLPs, to estimate percent polymorphic loci and Nei's gene diversity, which are calculated using the Bayesian method; FIS; FST; FSGS with the pairwise kinship coefficient (Fij); and AMOVA in populations. Results: We detected a relatively high proportion of polymorphic fragments (40.4–68.4%) and Nei's gene diversity indices (0.140–0.234). The overall FIS was relatively low to moderate (0.071–0.312). The average Fij for the populations of three Dactylorhiza showed significantly positive values, which were observed between plants at distances of 1–10 m (20 m). FST was significant in each Dactylorhiza taxon, ranging from the lowest values in D. fuchsii and D. majalis (0.080–0.086, p < 0.05) to a higher value (0.163, p < 0.05) in D. incarnata var. incarnata. Molecular variance was the highest within populations (76.5–86.6%; p < 0.001). Conclusions: We observed concordant genetic diversity patterns in three food-deceptive, allogamous, pollinator-dependent, and self-compatible Dactylorhiza. FIS is often substantially higher than Fij with respect to the first class of FSGSs, suggesting that selfing (meaning of geitonogamy) is at least responsible for homozygosity. A strong FSGS may have evolutionary consequences in Dactylorhiza, and combined with low inbreeding depression, it may impact the establishment of inbred lines of D. majalis and D. incarnata var. incarnata. [ABSTRACT FROM AUTHOR]

Context: Land-use intensification can alter small mammal community composition and induce loss of genetic variation in remaining populations. Fragmented landscapes favor generalist and synanthropic species, which are potential reservoirs of pathogens and pose risks to agriculture and forestry. Objectives: This study aimed to evaluate the effects of land-use intensity on small mammal diversity in grassland and forest habitats, as well as on genetic variation patterns driven by geographic (isolation by distance) and environmental distance (isolation by resistance) factors. Methods: We analysed differences in small mammal community diversity on grassland and forest plots with varying land-use intensities. Genetic analyses were conducted on Myodes glareolus and Microtus arvalis populations from each habitat, using microsatellites. Maximum Likelihood Population Effects models were employed to elucidate gene flow patterns and significant differences in genetic structure based on land-use intensity. Results: Small mammal communities in grasslands were significantly less diverse than in forests. Land-use intensity had a significant effect on diversity within grassland but not within forest habitats. M. glareolus showed three genetic groups, while M. arvalis displayed no discernible population structure or landscape-related pattern. Land-use intensity did not significantly influence the genetic structure of either species. Gene flow in M. glareolus is best described by the IBR model. Conclusion: Land-use intensity significantly affects small mammal community composition, particularly in grasslands. Neither species' genetics is directly impacted by land-use intensity but rather by landscape connectivity and distance. Risk assessments for rodent-borne zoonotic pathogens and crop damage should be framed within a habitat connectivity context. [ABSTRACT FROM AUTHOR]

Species distributions are often indicative of historical biogeographical events and contemporary spatial biodiversity patterns. The Harlequin Duck Histrionicus histrionicus is a sea duck of conservation concern that has a disjunct distribution, with discrete portions of its range associated with northern Pacific and Atlantic Ocean basins. Movement data indicate migratory connectivity within regions of each ocean basin but not cross‐continent dispersal, suggesting that genetic structuring could exist at multiple spatial scales. Little is known regarding the impacts of past vicariance events on the species phylogeographical structure and historical demography, or rates of gene flow at different spatial scales. We used data from microsatellite loci and mitochondrial DNA (mtDNA) sequences to quantify levels of genetic diversity within, and the extent of spatial genetic differentiation among locations sampled at multiple spatial scales across the species range. Samples were collected at nonbreeding locations, which represent groupings appropriate for characterizing genetically differentiated subgroups at regional and continental scales. Collectively, genetic data and coalescence modelling suggested that individuals colonized regions currently occupied within both ocean basins in the Holocene from a single refuge in the Atlantic. Further, it seems likely there was secondary contact with lineages derived from populations in Asia, based on the shallow species‐wide mtDNA phylogeny and high incidence of recently derived private mtDNA haplotypes. Estimates of inter‐location variance in microsatellite allele and mtDNA haplotype frequency were moderate and significant between western (Pacific – North America) and eastern (Atlantic – North America, Greenland and Iceland) ocean basins and among sampling groups within each ocean basin. Genetic differentiation among sampling groups was particularly evident at the species distributional margins in the Atlantic (Iceland) and the Pacific (Shemya Island) Ocean basins. Coalescent modelling results suggest that contemporary spatial genetic patterns in the species arose through the combined influences of secondary contact, shared ancestry and gene flow after the last glacial maxima. [ABSTRACT FROM AUTHOR]

Key message: SSR-based characterization revealed a high genetic diversity, negligible genetic differentiation, insignificant inbreeding, and subtle genetic structure in Myrica esculenta populations of Western Himalayas, indicating a high adaptive and evolutionary potential. Myrica esculenta is a high-valued wild edible fruit-bearing tree of sub-Himalayan region experiencing noticeable deterioration in its stand structure. This study aimed to unveil the gene diversity and spatial genetic structure of M. esculenta populations in the Western Himalayas under the state of Uttarakhand (India) using nuclear simple sequence repeat (SSR) markers. By investigating 23 populations at 8 SSR loci, high genetic diversity (expected heterozygosity, He = 0.90; allelic richness, Ar = 13.65) was recorded with little genetic differentiation (fixation index, FST = 0. 025). Bayesian analysis revealed a weak genetic structure with no discrete genetic lineages from which ancestry can be inferred. Furthermore, genetic clustering among populations was conspicuous but not in accordance with their spatial distribution. Geographically separated populations are genetically well connected due to long-distance gene flow via pollen as well as seed. Hence, the meta-population in the Western Himalayas demonstrated a subtle spatial genetic structure with negligible genetic divergence, where genetic admixing is not modulated by geographical constraints. Viewing the substantial anthropogenic pressure over wild populations, conservation strategies must be adopted synergistically based on scientific knowledge. As center of diversity is centered toward the Kumaon region capturing higher allelic richness, we recommend the populations of this region to be prioritized for in situ conservation. Further, it will be important to harvest seeds from genetically diverse populations for raising plantations or ex situ field gene banks. As its fruits are mostly harvested from wild, local communities need to be sensitized and encouraged to establish private plantations or orchards. [ABSTRACT FROM AUTHOR]

Roupala montana var. brasiliensis is a timber tree species native to the Cerrado and Atlantic Forest areas of Brazil. The wood was exploited for international markets, but there is no information on the conservation status of its natural populations, nor on other key aspects, such as mating system, gene flow, and inbreeding depression, essential for the species' sustainable management and conservation. We report the first study of any Roupala species to apply a validated set of species-specific microsatellite markers to genotype adults, juveniles, and seedlings, and analyse genetic diversity, inbreeding, effective population size, and mating system. We studied four populations of the species in areas of mixed Ombrophilous forest with different disturbance levels (undisturbed to strongly disturbed) in southern Brazil. The species occurs at low frequency in the study forests, but the populations are genetically diverse without significant differences in genetic diversity levels related to disturbance. The study also indicated resistance to the severe fragmentation associated with low density of individuals, with a stable mating system showing preferential outcrossing, with some inbreeding (tm ≈ 0.83, F > 0.165). Despite being spatially isolated from each other, the populations are not reproductively isolated, receiving immigrant pollen from long distances, although there was no evidence of gene flow into the populations via seeds. Seedlings from self-fertilization show low levels of inbreeding depression, which may reflect earlier pre-germination selection events. There was loss of allelic wealth in the younger cohorts, which may be a warning of the fragility of the genetic diversity detected in populations. We consider the implications of the results for the development of ex and in situ conservation and tree improvement programs. [ABSTRACT FROM AUTHOR]

The tetraploid Ficaria verna is a common spring geophyte in central Europe and is considered invasive in the USA and Canada. It is considered an almost seed‐sterile taxon, relying on vegetative reproduction by underground tubers and aerial bulbils. Recent studies have revealed high levels of population genetic diversity in F. verna, raising the question of how genetic diversity is maintained and which factors may be responsible for the observed patterns. Polymorphic nuclear microsatellite markers were established to define multi‐locus genotypes (MLGs), to analyze fine‐scale spatial genetic structure (SGS) using grid and cross‐sampling schemes, and to quantify genetic diversity within and between nine populations with different disturbance regimes in central Germany. In total, 115 MLGs were identified among a total of 347 samples. The G/N ratio varied between 0.16 and 0.70 among populations, and in each population several unique MLGs occurred. Genotypes were highly intermingled within populations, suggesting a "guerrilla" dispersal strategy. Significant SGS (negative regression slope of kinship coefficients against inter‐individual distances) was found in four out of nine populations in fine‐scale cross‐sampling (up to 4 m) and in only one population in grid sampling (up to 14.6 m). No single MLG was found in more than one population, while many alleles were shared between populations. Within‐population clonal and allelic diversity increased with greater exposure to both anthropogenic and natural disturbances. Regular gap openings, facilitated propagule establishment, and propagule dispersal by water and mowing machines are likely important factors explaining the positive effects of disturbance on local genetic diversity of F. verna. [ABSTRACT FROM AUTHOR]

Forests are considered as one of the most complex terrestrial ecosystems due to their high level of biodiversity, including genetic diversity. Understanding the genetic diversity of keystone species at a population level is vital to forest managers and policymakers for the conservation and sustainable utilization of forest genetic resources. Quercus semecarpifolia, commonly known as brown oak, is a keystone species of climax community thriving in the alpine zone of the Himalayas, which is presently experiencing population decline and range shift under the changing climate. In the present study, a landscape genetic approach was employed for deciphering the population genetic structure of Q. semecarpifolia in the western Himalayas using nuclear simple sequence repeat (SSR) markers. By analysing 718 individuals of 24 populations at 10 SSR loci, a high gene diversity (expected heterozygosity, He = 0.72; Allelic richness, Ar = 8.37) was recorded with a moderate genetic differentiation (FST = 0.16; P < 0.001). Genetic clustering and STRUCTURE analysis have displayed two major gene pools which appear to be primarily differentiated by the landscape and ecological constraints rather than the linear geographical distances. The hierarchical AMOVA analysis further supports the regional genetic divergence with a substantial proportion of genetic variation detected among the regions. Diversity maps generated by spatial interpolation elucidated the distribution pattern of genetic diversity and structure across the range, and aid in the demarcation of the diversity hotspots for conservation implications. To the best of our knowledge, this is the first comprehensive genetic study carried out in any Himalayan oaks, and the information generated herein is novel and of paramount importance in guiding conservation decisions. [ABSTRACT FROM AUTHOR]

The genetic diversity and spatial genetic structure of Onychodactylus zhaoermii from four geographic populations were studied using 13 microsatellite loci. In total of 69 alleles were detected in 230 samples, and the number of differential alleles (Na) among populations ranged from 1. 538 to 4. 462, with low genetic diversity. Except for the Benxi Xinkai Village population (PopⅣ), there was no significant genetic differentiation among the Xiuyan Huashan Village population (PopⅠ), Liaoyang Jizhua Village population (PopⅡ) and Liaoyang Hanjia Village population (PopⅢ), and genetic variation mainly originated from within the populations. There was a linear correlation between genetic distance and geographic distance, but it was not significant. Some genetic differences were observed when populations were divided by water system. Within 500 m distance, there was a high genetic similarity among individuals of O. zhaoermii. Three barriers existed between the four populations. A significant geographic barrier effect was formed between the Xinkai Village population (PopⅣ) and the other three populations (PopⅠ-Ⅲ). It is recommended that each geographic population should be established as a management unit and the habitat protection should be strengthened to reduce the impact of habitat fragmentation on wild resources of O. zhaoermii. [ABSTRACT FROM AUTHOR]

ABSTRACT Ecological restoration mitigates the negative effects of fragmentation and habitat loss. This practice allows the conservation of key species, such as Ocotea porosa, a tree native to the Araucaria Forest and extremely endangered. A key point in restoration projects is the source of seeds, as well as guidelines for collection. When carried out under technical criteria, the collection allows the maintenance of genetic diversity and adaptive potential in restoration plantations. Given the importance of seed source, genetic diversity, and adaptive potential, this study aimed to define areas and criteria for collecting seeds by characterizing the demography, genetics, and reproductive phenology of an O. porosa population. A plot of 16 hectares was installed in the municipality of Passos Maia, Santa Catarina, Brazil, and a demographic survey of trees with diameter at breast height (DBH) > 15 cm was carried out. Indices of diversity and internal genetic structure (IGS) were estimated using allozyme markers. The reproductive phenology of 67 individuals was evaluated during 8 months. The studied population showed a high density of individuals (10.7 ind. ha-1) with normal diametric distribution. The phenological pattern of the species is regular, seasonal, and annual. The evaluated population showed high genetic diversity, high fixation index, and significant IGS up to 80 meters away. Based on these results, the evaluated fragment can be used as a seed collection area. It has high genetic diversity, density, and area size sufficient to contain several demes. In addition, it is highly recommended that the matrices be at least 80 meters apart to avoid the effects of significant IGS.

Introduction: The dramatic fluctuations of climate conditions since the late Tertiary era have resulted in major species range shifts. These movements were conditioned by geographic barriers and species dispersal capacities. In land plants, gene flow occurs through the movement of male gametes (sperm cells, pollen grains), which carry nDNA, and diaspores (spores, seeds), which carry both cpDNA and nDNA, making them an ideal model to compare the imprints of past climate change on the spatial genetic structures of different genomic compartments. Based on a meta-analysis of cpDNA and nDNA sequence data in western Europe, we test the hypotheses that nDNA genetic structures are similar in bryophytes and spermatophytes due to the similar size of spores and pollen grains, whereas genetic structures derived from the analysis of cpDNA are significantly stronger in spermatophytes than in bryophytes due to the substantially larger size of seeds as compared to spores. Methods: Sequence data at 1-4 loci were retrieved for 11 bryophyte and 17 spermatophyte species across their entire European range. Genetic structures between and within southern and northern populations were analyzed through F and N statistics and Mantel tests. Results and discussion: Gst and Nst between southern and northern Europe derived from cpDNA were significantly higher, and the proportion of significant tests was higher in spermatophytes than in bryophytes. This suggests that in the latter, migrations across mountain ranges were sufficient to maintain a homogenous allelic structure across Europe, evidencing the minor role played by mountain ranges in bryophyte migrations. With nDNA, patterns of genetic structure did not significantly differ between bryophytes and spermatophytes, in line with the hypothesis that spores and pollen grains exhibit similar dispersal capacities due to their size similarity. Stronger levels of genetic differentiation between southern and northern Europe, and within southern Europe, in spermatophytes than in bryophytes, caused by higher long-distance dispersal capacities of spores as compared to seeds, may account for the strikingly higher levels of endemism in spermatophytes than in bryophytes in the Mediterranean biodiversity hotspot. [ABSTRACT FROM AUTHOR]

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RNA-sequencing was used to develop 16 microsatellite markers for the pearly everlasting, Anaphalis margaritacea var. yedoensis (Franch. et Sav.) Ohwi (Asteraceae), which inhabits gravel bars throughout the Japanese archipelago. The mean number of alleles for these 16 markers in two populations in the Hokkaido and Shizuoka Prefectures, was 3.5 and 4.0, respectively, while the mean expected heterozygosity was 0.525 and 0.560, respectively, with a significant genetic differentiation between the two populations. All markers could also be amplified in two conspecific taxa, A. margaritacea var. margaritacea and var. angustifolia, whereas 11 of the 16 markers were amplifiable in two congeneric species, A. sinica and A. alpicola. These newly developed microsatellite markers will support understanding of population genetics and mating systems in A. margaritacea var. yedoensis, and several will potentially be of use in similar studies in other Anaphalis species. [ABSTRACT FROM AUTHOR]

IntroductionThe dramatic fluctuations of climate conditions since the late Tertiary era have resulted in major species range shifts. These movements were conditioned by geographic barriers and species dispersal capacities. In land plants, gene flow occurs through the movement of male gametes (sperm cells, pollen grains), which carry nDNA, and diaspores (spores, seeds), which carry both cpDNA and nDNA, making them an ideal model to compare the imprints of past climate change on the spatial genetic structures of different genomic compartments. Based on a meta-analysis of cpDNA and nDNA sequence data in western Europe, we test the hypotheses that nDNA genetic structures are similar in bryophytes and spermatophytes due to the similar size of spores and pollen grains, whereas genetic structures derived from the analysis of cpDNA are significantly stronger in spermatophytes than in bryophytes due to the substantially larger size of seeds as compared to spores.MethodsSequence data at 1-4 loci were retrieved for 11 bryophyte and 17 spermatophyte species across their entire European range. Genetic structures between and within southern and northern populations were analyzed through F and N statistics and Mantel tests.Results and discussionGst and Nst between southern and northern Europe derived from cpDNA were significantly higher, and the proportion of significant tests was higher in spermatophytes than in bryophytes. This suggests that in the latter, migrations across mountain ranges were sufficient to maintain a homogenous allelic structure across Europe, evidencing the minor role played by mountain ranges in bryophyte migrations. With nDNA, patterns of genetic structure did not significantly differ between bryophytes and spermatophytes, in line with the hypothesis that spores and pollen grains exhibit similar dispersal capacities due to their size similarity. Stronger levels of genetic differentiation between southern and northern Europe, and within southern Europe, in spermatophytes than in bryophytes, caused by higher long-distance dispersal capacities of spores as compared to seeds, may account for the strikingly higher levels of endemism in spermatophytes than in bryophytes in the Mediterranean biodiversity hotspot.

DNA barcoding with the mitochondrial COI gene reveals distinct haplotype subgroups within the monophyletic and parthenogenetic nematode species, Mesocriconema xenoplax. Biological attributes of these haplotype groups (HG) have not been explored. An analysis of M. xenoplax from 40 North American sites representing both native plant communities and agroecosystems was conducted to identify possible subgroup associations with ecological, physiological, or geographic factors. A dataset of 132 M. xenoplax specimens was used to generate sequences of a 712 bp region of the cytochrome oxidase subunit I gene. Maximum-likelihood and Bayesian phylogenies recognized seven COI HG (≥99/0.99 posterior probability/bootstrap value). Species delimitation metrics largely supported the genetic integrity of the HG. Discriminant function analysis of HG morphological traits identified stylet length, total body length, and stylet knob width as the strongest distinguishing features among the seven groups, with stylet length as the strongest single distinguishing morphological feature. Multivariate analysis identified land cover, ecoregion, and maximum temperature as predictors of 53.6% of the total variation (P = 0.001). Within land cover, HG categorized under “herbaceous,” “woody wetlands,” and “deciduous forest” were distinct in DAPC and RDA analyses and were significantly different (analysis of molecular variance P = 0.001). These results provide empirical evidence for molecular, morphological, and ecological differentiation associated with HG within the monophyletic clade that represents the species Mesocriconema xenoplax.

Rhynchocypris oxycephala (Jordan & Snyder 1901) is distributed throughout western Japan. However, populations of this species in the easternmost distribution limit (Izu and Hakone) are suspected to be non-native. Additionally, this species was introduced into some river systems in eastern Japan (Kanto and Tohoku). We estimated the native distribution area of R. oxycephala populations, focusing on the easternmost distribution limit, and investigated the origin and introduction routes of this species into non-native areas using mitochondrial DNA D-loop analysis. Sampling was conducted in 50 river systems throughout the R. oxycephala distribution area, and 303 specimens were used for DNA analysis. D-loop sequences of 931–944 base pairs and 54 haplotypes were identified. Phylogenetic analyses showed that these haplotypes clustered into six geographically cohesive clades, and the haplotypes obtained from Izu and Hakone, Kanto, and Tohoku were identical or similar to those obtained from the Lake Biwa System. These findings indicated that the species populations in these areas were introduced from the Lake Biwa System. Plecoglossus altivelis altivelis and/or salmonid fishes have been transplanted to the river systems where R. oxycephala was introduced (except for one river), thus suggesting that R. oxycephala was unintentionally introduced from the Lake Biwa System via P. a. altivelis and/or salmonid fish transplantation. In contrast, the haplotypes obtained from the Lake Biwa System were not found in and to the west of the Okitsu River System, a region which ranges from Kyushu in the west to Tokai, near the Itoigawa-Shizuoka Tectonic Line in the east. Therefore, we concluded that the native easternmost distribution limit of the R. oxycephala populations was in the Okitsu River System near the ItoigawaShizuoka Tectonic Line. The present study provides biogeographical information on R. oxycephala that may be critical for planning suitable conservation measures. [ABSTRACT FROM AUTHOR]

Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, Epidendrum radicans, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (He = 0.092–0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 vs. 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from in situ reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally smaller on the younger sites (≤3 m vs. ≤8 m). [ABSTRACT FROM AUTHOR]

Background: Tetracentron sinense Oliv. is an ancient relict species in the family Trochodendraceae and a national secondary-level conservation plant in China. It is listed in Appendix III of the Convention of International Trade of Endangered Species, making its international trade subject to regional control. Knowledge of the spatial genetic structure (SGS) of the natural population of T. sinense is of great significance for the effective protection and management of its germplasm resource. Methods: Fifteen pairs of microsatellite primers were used to analyze the fine-scale SGS and gene flow of the national population of T. sinense in Leigong Mountain National Nature Reserve (LGM). Results: Compared with that of other endangered plants, the fine-scale genetic diversity of the T. sinense population was at the middle level. The genetic diversity levels in the four patches of T. sinense were different, resulting in significant genetic differentiation (Fst = 0.071–0.098), and the fine-scale genetic variation of the population was mainly from within patches. There was a significant SGS in the T. sinense population within a range of 400 m, and the quantified Sp value of the SGS was 0.0305. The gene flow of T. sinense in LGM was greatly restricted, and the distance of gene diffusion decreased with an increase in the effective density of the T. sinense population. Conclusions: The T. sinense population in LGM is suffering from the risk of inbreeding decline, and its limited gene flow will increase the accumulation of this risk. The spatial range of its genetic structure is within 20 m, and the individuals are closely related in this range. Therefore, the sampling interval for individuals during ex situ conservation should be 20 m apart to ensure that the collected individuals can exhibit more complete genetic variation.

Winter annuals comprise a large fraction of warm-desert plant species, but the drivers of their diversity are little understood. One factor that has generally been overlooked is the lack of obvious means of long-distance seed dispersal in many desert-annual lineages, which could lead to genetic differentiation at small spatial scales and, ultimately, to speciation and narrow endemism. If our gene-flow hypothesis is correct, individual winter-annual species should have populations with genetic spatial structures implying short distances of gene flow. To test this idea, we sampled six populations of Eschscholzia parishii (Papaveraceae) in three pairs of watersheds within a 28-km radius in southern California. We quantified genetic diversity and structure and inferred the distance of gene flow in these populations using single nucleotide polymorphisms derived from genotyping-by-sequencing. Estimated distances of gene flow were quite small (σ = 10.4–14.9 m), with strong genetic structure observed within and between populations. Kinship declined steeply with ln distance (r 2 = 0.85). Petal size and shape differed significantly between the northernmost and southernmost populations. These findings support the hypothesis that the high diversity of warm-desert winter annuals might result, in part, from genetic differentiation within species at small spatial scales driven by poor seed dispersal. [ABSTRACT FROM AUTHOR]

Resprouting species, such as English holly (Ilex aquifolium L.), can be severely affected by long-lasting forest management. In the present study, the clonal and fine-scale spatial genetic structure (FSGS) of English holly are evaluated in a sub-Mediterranean mixed forest of Central Spain, where this species was subjected to different and intense human interventions for centuries, including coppicing in dense structures and in open woody pastures. Using seven microsatellite loci, we assessed the contribution of clonal and sexual reproduction to the diversity of holly in both areas and the fine-scale genetic structure was evaluated. For the dense coppiced area, the results showed high clonal diversity derived mainly from stem resprouting. Stems were separated an average of 3 m and up to 10 m, and dense aggregations of stems sometimes included various genotypes. The results also showed recent seed recruitment leading to small unique and isolated genotypes. Furthermore, FSGS was detected at close distances as being stronger in the coppiced area than in the open woody pasture area, especially for individuals of greater diameter at breast height. The results obtained suggest that current management strategies are not negatively affecting the genetic diversity of this species. [ABSTRACT FROM AUTHOR]

Abstract Background There has always been controversy over whether clonal plants have lower genetic diversity than plants that reproduce sexually. These conflicts could be attributed to the fact that few studies have taken into account the mating system of sexually reproducing plants and their phylogenetic distance. Moreover, most clonal plants in these previous studies regularly produce sexual progeny. Here, we describe a study examining the levels of genetic diversity and differentiation within and between local populations of fully clonal Zingiber zerumbet at a microgeographical scale and compare the results with data for the closely related selfing Z. corallinum and outcrossing Z. nudicarpum. Such studies could disentangle the phylogenetic and sexually reproducing effect on genetic variation of clonal plants, and thus contribute to an improved understanding in the clonally reproducing effects on genetic diversity and population structure. Results The results revealed that the level of local population genetic diversity of clonal Z. zerumbet was comparable to that of outcrossing Z. nudicarpum and significantly higher than that of selfing Z. corallinum. However, the level of microgeographic genetic diversity of clonal Z. zerumbet is comparable to that of selfing Z. corallinum and even slightly higher than that of outcrossing Z. nudicarpum. The genetic differentiation among local populations of clonal Z. zerumbet was significantly lower than that of selfing Z. corallinum, but higher than that of outcrossing Z. nudicarpum. A stronger spatial genetic structure appeared within local populations of Z. zerumbet compared with selfing Z. corallinum and outcrossing Z. nudicarpum. Conclusions Our study shows that fully clonal plants are able not only to maintain a high level of within-population genetic diversity like outcrossing plants, but can also maintain a high level of microgeographic genetic diversity like selfing plant species, probably due to the accumulation of somatic mutations and absence of a capacity for sexual reproduction. We suggest that conservation strategies for the genetic diversity of clonal and selfing plant species should be focused on the protection of all habitat types, especially fragments within ecosystems, while maintenance of large populations is a key to enhance the genetic diversity of outcrossing species.

Oceanic islands have isolated biota, which typically include many endemic species. However, island endemics are vulnerable due to small population sizes, and they are often threatened by habitat destruction or by introduced pests and predators. Adequate conservation planning requires good information on genetic variability and population structure, also when seemingly viable species are considered. Here, I analysed the genetic structure in the terrestrial orchid Dactylorhiza foliosa, which is endemic to Madeira. This species is a characteristic component of evergreen laurel forests occupying the northern slopes of the island. Levels of diversity in both the plastid genome and in the nuclear genome were comparable to levels of diversity found in congeners growing in continental regions. Within populations, plants separated by distances up to 256 m shared plastid haplotypes significantly more often than plants at random, but when nuclear markers were considered, only plants growing closer than eight metres were significantly more closely related. Analysis of plastid marker variation revealed that gene dispersal by seeds is not sufficiently large to counterbalance the accumulation of mutations that build up divergence between the most distant populations. However, differentiation in the nuclear genome was considerably smaller, suggesting that gene dispersal by pollen is much more efficient than gene dispersal by seeds in D. foliosa. The overall pollen to seed dispersal ratio, mp/ms, was 7.30. Considering genetic parameters, conditions for long-term persistence of D. foliosa on Madeira seem to be good. [ABSTRACT FROM AUTHOR]

Some neotropical rodents are of special interest because they are an important source of animal protein for human indigenous populations throughout Latin America. This is the case of the genus Dasyprocta (agouties). However, we still do not know how many species, taxa, or lineages are within Dasyprocta. To address this issue, we analyzed the complete mitogenomes of 93 specimens in addition to three mitochondrial genes of 128 specimens of Dasyprocta belonging to six supposed species (D. fuliginosa, D. punctata, D. leporina, D. kalinowski, D. ruatanica, and D. azarae). The phylogenetic results indicated five different lineages within D. fuliginosa, with two being polyphyletic (one more related to D. leporina and another more related to D. punctata). D. kalinowski, a species endemic to Peru, was un-differentiable from one of these D. fuliginosa lineages. D. azarae was related with some of the lineages of D. fuliginosa. Within D. leporina, two significant lineages were found (in central Atlantic Brazil and on the Caribbean islands of Trinidad and Tobago). Within D. punctata, three lineages were detected, one in Central America (central and northern), including D. ruatanica, a supposed endemic species on Roatan Island, Honduras, another in central and southern Panama, and another in trans-Andean and Pacific Colombia and Ecuador. Some of the lineages of D. fuliginosa from the western Amazon yielded the most ancestral haplotypes (around 7 million years ago, MYA, Late Miocene). In contrast, haplotypes of a lineage of D. punctata and those of a lineage of D. leporina (Trinidad and Tobago) were the most derived (around 0.2–0.3 MYA, Pleistocene). Other population genetic results showed that all groups or lineages presented elevated levels of genetic diversity, with the exception D. leporina in Trinidad and Tobago. Their lower genetic diversity is probably related to founder effect during the colonization of the Caribbean island, due to a bottleneck. Some of these Dasyprocta taxa showed some population expansions during the Pleistocene, but all of the lineages experienced some population decrease during the last 10,000–20,000 years. Note that some lineages showed a small population increase in the last few centuries. The spatial genetic structure was highly developed throughout the Neotropics for Dasyprocta. According to this study, (1) coat color (routinely used in the systematics of this rodent) is not valuable from a phylogenetic and systematics perspective and (2) two supposedly endemic species (D. kalinowski and D. ruatanica) were not full species. These results are of vital importance for the biological conservation of the different taxa and lineages of this rodent. [ABSTRACT FROM AUTHOR]

Gene dispersal processes shape demographic and microevolutionary dynamics of tree species. Gene dispersal patterns can be studied by spatially explicit methods. Spatial genetic structure (SGS), summarized in the Sp statistic, provides indirect estimates of gene dispersal across generations for a known or assumed population effective density. Sp is modulated by exogenous and endogenous factors including the mating system that can be assessed using outcrossing rates (tm). Knowledge on tm and Sp are particularly important for the conservation of species in fragmented biomes such as seasonally dry tropical forests (SDTF). The main aim of this review was to evaluate putative drivers of Sp and tm, and their consequences for gene dispersal in tree species from SDTF. We reviewed 59 genetic studies on SDTF tree species published between 2000 and 2020 and extracted data on propagule dispersal, successional stages, seasonality, mating system, population density, landscape features, type of molecular markers, pairwise kinship in the first distance class (F1), Sp statistic, mean gene dispersal distance (σg), and multilocus outcrossing rates (tm). Sp was significantly associated with the mating system where Sp(outcrossing) > Sp(mixed-mating), and population density where Sp was higher in high-density populations. Outcrossing rate was significantly associated with the type of propagule dispersal, where tm was higher in populations of plants pollinated by wind, and in those with animal-mediated seed dispersal, tm(zoochory) > tm(anemochory) > tm(autochory), and with successional stage where tm(late-successional) > tm(pioneer). These factors are relevant to inform management actions in conservation and restoration projects. Thus, the knowledge on the determinants of gene dispersal processes can help to rescue SDTF through sustainable management. [ABSTRACT FROM AUTHOR]

Abstract Background Comparative phylogeographic studies on rainforest species that are widespread in Central Africa often reveal genetic discontinuities within and between biogeographic regions, indicating (historical) barriers to gene flow, possibly due to repeated and/or long-lasting population fragmentation during glacial periods according to the forest refuge hypothesis. The impact of forest fragmentation seems to be modulated by the ecological amplitude and dispersal capacities of each species, resulting in different demographic histories. Moreover, while multiple studies investigated the western part of Central Africa (Lower Guinea), few have sufficiently sampled the heart of the Congo Basin (Congolia). In this study, we look for genetic discontinuities between populations of the widespread tropical tree Scorodophloeus zenkeri Harms (Fabaceae, Detarioideae) in Central Africa. Additionally, we characterize genetic diversity, selfing rate and fine-scale spatial genetic structure within populations to estimate the gene dispersal capacity of the species. Results Clear intraspecific genetic discontinuities occur throughout the species’ distribution range, with two genetic clusters in Congolia and four in Lower Guinea, and highest differentiation occurring between these bioregions. Genetic diversity is higher in Lower Guinea than Congolia. A spatial genetic structure characteristic of isolation by distance occurs within the genetic clusters. This allowed us to estimate gene dispersal distances (σg) for this outcrossing species with ballistic seed dispersal, which range between 100 and 250 m in areas where S. zenkeri occurs in high densities, and are in the low range of σg values compared to other tropical trees. Gene dispersal distances are larger in low density populations, probably due to extensive pollen dispersal capacity. Conclusions Fragmentation of S. zenkeri populations seems to have occurred not only in Lower Guinea but also in the Congo Basin, though not necessarily according to previously postulated forest refuge areas. The lower genetic diversity in Congolia compared to Lower Guinea parallels the known gradient of species diversity, possibly reflecting a stronger impact of past climate changes on the forest cover in Congolia. Despite its bisexual flowers, S. zenkeri appears to be mostly outcrossing. The limited dispersal observed in this species implies that genetic discontinuities resulting from past forest fragmentation can persist for a long time before being erased by gene flow.

ABSTRACT Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a crucial disease for wheat worldwide and constantly threatens wheat production in southwestern and northwestern China, where the environment is a good fit for Pst oversummering and overwintering. However, the underlying genetic dynamics of spring epidemic Pst populations across large areas of continuous planting in the southwestern and northwestern regions are poorly understood. A total of 2,103 Pst isolates were sampled in the spring of 2019 from the two agroecosystems and grouped into three horizontal spatial scales (countywide, provincial, and regional subpopulations) and two vertical spatial scales that consisted of elevational and geomorphic subpopulations. A total of 776 multilocus genotypes were identified, with the highest genetic diversity found in the northern and Sichuan populations, particularly in the Ningxia and Sichuan Basins, while the lowest genetic diversity was found in the Yunnan and Guizhou populations. Multivariate discriminant analysis of principal components (DAPC) and STRUCTURE (STRUCTURE 2.3.4) analyses revealed variation in the genotypic compositions of the molecular groups on horizontal and vertical dimensions from north to south or vice versa and from low to high or vice versa, respectively. The regional neighbor-joining tree revealed three large spatial structures consisting of the southwestern, the northwestern, and the Xinjiang regions, while the Tibetan population connected the southwestern and northwestern regions. The isolates of the Sichuan Basin were scattered over the four quartiles by principal coordinate analysis, which indicated frequent genotype interchange with others. Greater genetic differentiation was observed between the southwestern and northwestern regions. Linkage equilibrium (P ≥ 0.05) was detected on different spatial scales, suggesting that Pst populations are using sexual reproduction or mixed reproduction (sexual and clonal reproduction) in southwestern and northwestern China. IMPORTANCE Understanding the epidemiology and population genetics of plant pathogens is crucial to formulate efficient predictions of disease outbreaks and achieve sustainable integrated disease management, especially for pathogens with migratory capability. Here, this study covers the genetic homogeneity and heterogeneity of different geographical Pst populations on broad to fine spatial scales from the key epidemic regions of the two agroecosystems in China, where wheat stripe rust occurs annually. We provide knowledge of the population genetics of Pst and reveal that, for instance, there is greater genetic diversity in northwestern China, there are close genetic relationships between Yunnan and Guizhou and between Gansu-Ningxia and Qinghai, and there are effects of altitude on genetic compositions, etc. All of these findings clarify the genetic relationships and expand the insights into the population dynamics and evolutionary mechanisms of Pst in southwestern and northwestern China, providing a theoretical basis for achieving sustainable control of wheat stripe rust in key epidemic regions.

Abstract Landscape genetic analyses allow detection of fine‐scale spatial genetic structure (SGS) and quantification of effects of landscape features on gene flow and connectivity. Typically, analyses require generation of resistance surfaces. These surfaces characteristically take the form of a grid with cells that are coded to represent the degree to which landscape or environmental features promote or inhibit animal movement. How accurately resistance surfaces predict association between the landscape and movement is determined in large part by (a) the landscape features used, (b) the resistance values assigned to features, and (c) how accurately resistance surfaces represent landscape permeability. Our objective was to evaluate the performance of resistance surfaces generated using two publicly available land cover datasets that varied in how accurately they represent the actual landscape. We genotyped 365 individuals from a large black bear population (Ursus americanus) in the Northern Lower Peninsula (NLP) of Michigan, USA at 12 microsatellite loci, and evaluated the relationship between gene flow and landscape features using two different land cover datasets. We investigated the relative importance of land cover classification and accuracy on landscape resistance model performance. We detected local spatial genetic structure in Michigan's NLP black bears and found roads and land cover were significantly correlated with genetic distance. We observed similarities in model performance when different land cover datasets were used despite 21% dissimilarity in classification between the two land cover datasets. However, we did find the performance of land cover models to predict genetic distance was dependent on the way the land cover was defined. Models in which land cover was finely defined (i.e., eight land cover classes) outperformed models where land cover was defined more coarsely (i.e., habitat/non‐habitat or forest/non‐forest). Our results show that landscape genetic researchers should carefully consider how land cover classification changes inference in landscape genetic studies.

Species reintroductions are successful when established populations maintain both demographic stability and genetic diversity. Such a result may be obtained by ensuring both structural habitat connectivity and genetic connectivity among reintroduced and remnant populations. Nevertheless, prezygotic barriers such as assortative mating can prevent the flow of genetic material between populations, even when migration between populations is high. Limited gene flow may be particularly relevant for reintroductions that were sourced either from captive-bred populations or from disparate locations in the wild. American martens (Martes americana) have been reintroduced repeatedly in the Upper Midwestern United States in an effort to establish self-sustaining populations. We quantified levels of genetic diversity within and spatial genetic variance among four marten populations during two time periods separated by 10 years. Spatially informed and naïve discriminant analysis of principal components were used to assign individuals to populations. Results indicate that heterozygosity declined and inbreeding coefficients increased between the two collection periods, while genetic structure among populations also increased. Data are consistent with assortative mating contributing to reapportioning of genetic variation. Population assignment tests show that migration among populations is apparent, but admixture (based on cluster membership probabilities) is low and declined over time. Specifically, martens may be successfully dispersing between populations but a lack of admixture indicates a lack of reproductive contributions to genetic diversity by migrants. Because marten reintroductions in this region are well-documented and well-monitored, lessons can be derived from results to inform future reintroductions. We encourage a careful balance of supplementing genetic diversity via augmentation while avoiding translocation of animals from disparate populations that may result in reproductive isolation of migrants. In combination with the maintenance of a functionally connected landscape, this strategy would maximize the likelihood of a successful reintroduction in terms both of demography and genetics. [ABSTRACT FROM AUTHOR]

Abstract Many natural systems are subject to profound and persistent anthropogenic influence. Human‐induced gene movement through afforestation and the selective transportation of genotypes might enhance the potential for intraspecific hybridization, which could lead to outbreeding depression. However, the evolutionary legacy of afforestation on the spatial genetic structure of forest tree species has barely been investigated. To do this properly, the effects of anthropogenic and natural processes must be examined simultaneously. A multidisciplinary approach, integrating phylogeography, population genetics, species distribution modeling, and niche divergence would permit evaluation of potential anthropogenic impacts, such as mass planting near‐native material. Here, these approaches were applied to Pinus armandii, a Chinese endemic coniferous tree species, that has been mass planted across its native range. Population genetic analyses showed that natural populations of P. armandii comprised three lineages that diverged around the late Miocene, during a period of massive uplifts of the Hengduan Mountains, and intensification of Asian Summer Monsoon. Only limited gene flow was detected between lineages, indicating that each largely maintained is genetic integrity. Moreover, most or all planted populations were found to have been sourced within the same region, minimizing disruption of large‐scale spatial genetic structure within P. armandii. This might be because each of the three lineages had a distinct climatic niche, according to ecological niche modeling and niche divergence tests. The current study provides empirical genetic and ecological evidence for the site‐species matching principle in forestry and will be useful to manage restoration efforts by identifying suitable areas and climates for introducing and planting new forests. Our results also highlight the urgent need to evaluate the genetic impacts of large‐scale afforestation in other native tree species.

The spatial genetic structures of insects are reflected in their habitats. Coastal insects tend to have less genetic differentiation than subterranean insects. However, the general pattern of population structure of coastal species residing in subterranean habitats is unknown. Thalassoduvalius masidai (Coleoptera: Carabidae: Trechinae), endemic to Japan, is a coastal and subterranean beetle. Here, we hypothesized that T. masidai populations disperse among regions by ocean currents, floods and tsunamis, despite their habitat being underground. To test this hypothesis, we performed a phylogeographical analysis of T. masidai using single nucleotide polymorphism data from multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) and the mitochondrial COI gene. The phylogenetic network and tree and STRUCTURE analyses indicated that T. masidai populations were divided into three groups: the western Seto Inland Sea–Izu Peninsula coasts, the eastern Seto Inland Sea–Kii Peninsula coasts and the Japan Sea coasts. The genetic diversity of T. masidai was higher in sites with lower longitude and latitude. These results suggest that T. masidai migrated and dispersed from the south-western area of Japan by ocean currents, despite its underground habitat. The genetic analysis data from the present study would also be helpful for the conservation and taxonomic revision of this species. [ABSTRACT FROM AUTHOR]

The use of genetically closely related populations as reintroduction sources is crucial in restoration programmes for endangered species because genetically distant populations may cause genetic disturbances. Aporia hippia (Lepidoptera; Pieridae) is an endangered subalpine grassland butterfly in Japan and its distribution area is restricted to the Asama, Yatsugatake and Akaishi Mountains in central Honshu Island. In the Yatsugatake Mountains, its population is probably already extinct, and reintroduction from the other sites is now under consideration. Here, we estimated the genetic diversity and spatial genetic structure of A. hippia in Japan to identify candidate source populations for reintroduction in extinct populations via multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) and mitochondrial DNA sequencing methods. The MIG-seq method indicated the presence of very few genetic differences among the populations. The mitochondrial DNA sequencing method identified two haplotypes: haplotype A in the Asama, Yatsugatake and northern Akaishi Mountains, and haplotype B in the central and southern Akaishi Mountains. The two haplotypes exhibited only a one base pair substitution between them. Implications for insect conservation: Based on these results, we suggest the existence of two conservation units: the first group consisting of populations in the Asama, Yatsugatake, and northern Akaishi Mountains, and the second group consisting of those in the central and southern Akaishi Mountains. According to this genetic proximity, however, all populations of A. hippia in Japan can also be defined as one conservation unit group, given the risk of inbreeding depression or difficulty of adaptation in different environments. [ABSTRACT FROM AUTHOR]

Many orchids are characterized by small, patchily distributed populations. Resolving how they persist is important for understanding the ecology of this hyper-diverse family, many members of which are of conservation concern. Ten populations of the common terrestrial orchid Drakaea glyptodon from south-western Australia were genotyped with ten nuclear and five plastid simple sequence repeat (SSR) markers. Levels and partitioning of genetic variation and effective population sizes (N e) were estimated. Spatial genetic structure of nuclear diversity, together with plastid data, were used to infer the effective number of seed parents per population. We found high genetic diversity, N e values that generally exceed predictions based on the number of flowering individuals and moderate levels of gene flow. Two populations were founded by less than five colonists suggesting some populations are colonized by few seeds, with growth largely resulting from in situ recruitment. A value of 3.65 for m p / m s indicates that pollinators play a greater role than seed in introducing genetic diversity to populations via gene flow. Our results highlight that D. glyptodon is highly effective at persisting in patchily distributed populations. However, it is important to examine how insights from this common, widespread species transfer to species that are rare and/or occur in fragmented landscapes. [ABSTRACT FROM AUTHOR]

Dispersal is a fundamental process in the functioning of animal societies as it regulates the degree to which closely related individuals are spatially concentrated. A species' dispersal pattern can be complex as it emerges from individuals' decisions shaped by the cost–benefit tradeoffs associated with either remaining in the natal group or dispersing. Given the potential complexity, combining long‐term demographic information with molecular data can provide important insights into dispersal patterns of a species. Based on a 15‐year study that integrates multiyear demographic data on six groups with longitudinal and cross‐sectional genetic sampling of 20 groups (N = 169 individuals, N = 21 polymorphic microsatellite loci), we describe the various dispersal strategies of male and female black howler monkeys (Alouatta pigra) inhabiting Palenque National Park, Mexico. Genetically confirmed dispersal events (N = 21 of 59 males; N = 6 of 65 females) together with spatial autocorrelation analyses revealed that the dispersal pattern of black howlers is bisexual with strong sex‐biases in both dispersal rate (males disperse more often than females) and dispersal distance (females disperse farther than males). Observational and genetic data confirm that both males and females can successfully immigrate into established groups, as well as form new groups with other dispersing individuals. Additionally, both males and females may disperse singly, as well as in pairs, and both may also disperse secondarily. Overall, our findings suggest multiple dispersal trajectories for black howler males and females, and longer multiyear studies are needed to unravel which demographic, ecological and social factors underlie individuals' decisions about whether to disperse and which dispersal options to take. [ABSTRACT FROM AUTHOR]

Fish population structure in previously glaciated regions is often influenced by natural colonization processes and human-mediated dispersal, including fish stocking. Endemic populations are of conservation interest because they may contain rare and unique genetic variation. While coregonines are native to certain Michigan inland lakes, some were stocked with fish from Great Lakes sources, calling into question the origin of extant populations. While most stocking targeted lake whitefish (Coregonus clupeaformis), cisco (C. artedi) were also stocked from the Great Lakes to inland waterbodies. We used population genetic data (microsatellite genotypes and mitochondrial (mt)DNA sequences), coalescent modeling, and approximate Bayesian computation to investigate the origins of 12 inland Michigan cisco populations. The spatial distribution of mtDNA haplotypes suggests Michigan is an introgression zone for two ancestral cisco lineages associated with separate glacial refugia. Low levels of genetic diversity and high levels of genetic divergence were observed for populations located well inland of the Great Lakes relative to populations occupying waterbodies near the Great Lakes. Estimates of recent Great Lakes gene flow ranged from 27 to 48% for populations near the Great Lakes shoreline but were substantially lower (under 8%) for populations further inland. Inland lakes with elevated recent gene flow estimates may have been recipients of stocked coregonine fry, including cisco. Low levels of genetic diversity paired with a high likelihood of endemism as indicated by strong genetic divergence and low Great Lakes population inputs suggest the analyzed cisco populations occupying southern Michigan kettle lakes are of elevated conservation interest. [ABSTRACT FROM AUTHOR]

The application of high-density polymorphic single-nucleotide polymorphisms (SNP) markers derived from high-throughput sequencing methods has heralded plenty of biological questions about the linkages of processes operating at micro- and macroevolutionary scales. However, the effects of SNP filtering practices on population genetic inference have received much less attention. By performing sensitivity analyses, we empirically investigated how decisions about the percentage of missing data (MD) and the minor allele frequency (MAF) set in bioinformatic processing of genomic data affect direct (i.e., parentage analysis) and indirect (i.e., fine-scale spatial genetic structure – SGS) gene flow estimates. We focus specifically on these manifestations in small plant populations, and particularly, in the rare tropical plant species Dinizia jueirana-facao, where assumptions implicit to analytical procedures for accurate estimates of gene flow may not hold. Avoiding biases in dispersal estimates are essential given this species is facing extinction risks due to habitat loss, and so we also investigate the effects of forest fragmentation on the accuracy of dispersal estimates under different filtering criteria by testing for recent decrease in the scale of gene flow. Our sensitivity analyses demonstrate that gene flow estimates are robust to different setting of MAF (0.05–0.35) and MD (0–20%). Comparing the direct and indirect estimates of dispersal, we find that contemporary estimates of gene dispersal distance (σrt = 41.8 m) was ∼ fourfold smaller than the historical estimates, supporting the hypothesis of a temporal shift in the scale of gene flow in D. jueirana-facao, which is consistent with predictions based on recent, dramatic forest fragmentation process. While we identified settings for filtering genomic data to avoid biases in gene flow estimates, we stress that there is no ‘rule of thumb’ for bioinformatic filtering and that relying on default program settings is not advisable. Instead, we suggest that the approach implemented here be applied independently in each separate empirical study to confirm appropriate settings to obtain unbiased population genetics estimates.

The application of high-density polymorphic single-nucleotide polymorphisms (SNP) markers derived from high-throughput sequencing methods has heralded plenty of biological questions about the linkages of processes operating at micro- and macroevolutionary scales. However, the effects of SNP filtering practices on population genetic inference have received much less attention. By performing sensitivity analyses, we empirically investigated how decisions about the percentage of missing data (MD) and the minor allele frequency (MAF) set in bioinformatic processing of genomic data affect direct (i.e., parentage analysis) and indirect (i.e., fine-scale spatial genetic structure – SGS) gene flow estimates. We focus specifically on these manifestations in small plant populations, and particularly, in the rare tropical plant species Dinizia jueirana-facao , where assumptions implicit to analytical procedures for accurate estimates of gene flow may not hold. Avoiding biases in dispersal estimates are essential given this species is facing extinction risks due to habitat loss, and so we also investigate the effects of forest fragmentation on the accuracy of dispersal estimates under different filtering criteria by testing for recent decrease in the scale of gene flow. Our sensitivity analyses demonstrate that gene flow estimates are robust to different setting of MAF (0.05–0.35) and MD (0–20%). Comparing the direct and indirect estimates of dispersal, we find that contemporary estimates of gene dispersal distance (σ rt = 41.8 m) was ∼ fourfold smaller than the historical estimates, supporting the hypothesis of a temporal shift in the scale of gene flow in D. jueirana-facao , which is consistent with predictions based on recent, dramatic forest fragmentation process. While we identified settings for filtering genomic data to avoid biases in gene flow estimates, we stress that there is no 'rule of thumb' for bioinformatic filtering and that relying on default program settings is not advisable. Instead, we suggest that the approach implemented here be applied independently in each separate empirical study to confirm appropriate settings to obtain unbiased population genetics estimates. [ABSTRACT FROM AUTHOR]

Abstract Background Understanding the origin of genetic variation is the key to predict how species will respond to future climate change. The genus Quercus is a species-rich and ecologically diverse woody genus that dominates a wide range of forests and woodland communities of the Northern Hemisphere. Quercus thus offers a unique opportunity to investigate how adaptation to environmental changes has shaped the spatial genetic structure of closely related lineages. Furthermore, Quercus provides a deep insight into how tree species will respond to future climate change. This study investigated whether closely related Quercus lineages have similar spatial genetic structures and moreover, what roles have their geographic distribution, ecological tolerance, and historical environmental changes played in the similar or distinct genetic structures. Results Despite their close relationships, the three main oak lineages (Quercus sections Cyclobalanopsis, Ilex, and Quercus) have different spatial genetic patterns and occupy different climatic niches. The lowest level and most homogeneous pattern of genetic diversity was found in section Cyclobalanopsis, which is restricted to warm and humid climates. The highest genetic diversity and strongest geographic genetic structure were found in section Ilex, which is due to their long-term isolation and strong local adaptation. The widespread section Quercus is distributed across the most heterogeneous range of environments; however, it exhibited moderate haplotype diversity. This is likely due to regional extinction during Quaternary climatic fluctuation in Europe and North America. Conclusions Genetic variations of sections Ilex and Quercus were significantly predicted by geographic and climate variations, while those of section Cyclobalanopsis were poorly predictable by geographic or climatic diversity. Apart from the different historical environmental changes experienced by different sections, variation of their ecological or climatic tolerances and physiological traits induced varying responses to similar environment changes, resulting in distinct spatial genetic patterns.

Species range expansions and (re)colonization of landscapes variously dominated by humans occur on a global scale. Understanding such range enlargements and subsequent changes in the composition of ecological communities is important for conservation management, and the golden jackal (Canis aureus) can be considered a model species for regional and continental range expansion. Although this mesopredator has been known from the Adriatic Coast of southeastern Europe for over 500 years, the species is a recent arrival further north, including in Slovenia where jackals were first confirmed in the 1950s. Research from eastern Italy found jackals with ancestry from the Dalmatian region on the Adriatic Coast and the Pannonian region further east. We predicted similar ancestry for Slovenian jackals, and examined samples from Croatia, including Dalmatia and interior regions, Serbia, Hungary, and Slovenia with 25 microsatellite markers to determine population genetic structure. We detected two distinct genetic clusters, representing the Dalmatian and Balkan-Pannonian (Pannonian) jackal populations (FST = 0.157, 95% CI: 0.112–0.209). Contrary to expectations, only few individuals in Slovenia exhibited signs of Dalmatian ancestry, and none appeared to be direct immigrants. Some results suggested a third cluster centered in northern Hungary. These divergent profiles might indicate immigration from outside the study area, and samples from regions further east are required for additional resolution. Based on our results, we hypothesize that Dalmatia has not been a substantial source for recent range expansion of the species, which has likely occurred from the east. Further investigation can help resolve the ancestry and current distribution of the Dalmatian and Pannonian populations, and the ecological relationships resulting from progressively overlapping distributions of canid species. Finally, genomic research could illuminate whether genetic variants from eastern areas might have facilitated jackal expansion into regions characterized by a colder climate, the presence of snow, and extensive forest cover; habitats seemingly avoided by the jackals occupying the Adriatic Coast and surrounding areas in southeastern Europe.

Marine protected areas (MPAs) are one of the most efficient conservation tools to buffer marine biodiversity loss induced by human activities. Beside effective enforcement, an accurate understanding of the eco-evolutionary processes underlying the patterns of biodiversity is needed to reap the benefits of management policies. In this context, integrating population genetics with demographic data, the demo-genetic approach, is particularly relevant to shift from a “species-based pattern” toward an “eco-evolutionary-based processes” conservation. Here, targeting a key species in the Mediterranean coralligenous, the red coral, Corallium rubrum, in an emblematic Mediterranean MPA, the “Réserve Naturelle de Scandola” (France), we applied demo-genetic approaches at two contrasted spatial scales, among populations and within one population, to (i) infer the demographic connectivity among populations in the metapopulation network and (ii) shed new light on the genetic connectivity and on the demographic transitions underlying the dynamics of a near-pristine population. Integrating different spatial and temporal scales, we demonstrated (i) an apparent temporal stability in the pattern of genetic diversity and structure in the MPA in spite of a dramatic demographic decline and (ii) contrasted levels of genetic isolation but substantial demographic connectivity among populations. Focusing on the near-pristine population, we complemented the characterization of red coral demographic connectivity suggesting (iii) temporal variability and (iv) the occurrence of collective dispersal. In addition, we demonstrated (v) contrasted patterns of spatial genetic structure (SGS), depending on the considered stage-class (adults vs. juveniles), in the near-pristine population. This last result points out that the overall SGS resulted from a restricted dispersal of locally produced juveniles (SGS among adults and juveniles) combined to mortality during early life stages (decrease of SGS from juveniles to adults). Demonstrating the occurrence of two management units and the importance of two populations (CAVB and ALE) for the network of connectivity, we made recommendations for the management of the Réserve Naturelle de Scandola. Besides, we contributed to the implementation of scientifically driven restoration protocols in red coral by providing estimates for the size, density, and distances among patches of transplanted colonies.

Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral species using genome-wide single nucleotide polymorphisms (SNPs). In this study, we examined the spatial genetic structure of a deep-sea coral species—the Japanese red coral, Corallium japonicum, sampled off the coast of Kochi, which lies to the southwest of the Shikoku Island in Japan; the Kochi region suffers from over-harvesting because of its high commercial value. We also examined the power of detecting significant spatial genetic structure by changing the number of loci and the proportion of missing data using both de novo analysis and mapping analysis. Similar results were obtained for both de novo and mapping analysis, although a higher number of loci were obtained by the mapping method. In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species.

Spatial genetic variation involves spatial genetic structure (SGS) and genetic diversity is important genetic features of plants. We first evaluated spatial genetic structure (SGS) and genetic diversity among four populations of Alsophila gigantea from Hainan Island, China, using inter-simple sequence repeat (ISSR) markers. Significant but weak FSGS was found in A. gigantea . High genetic diversity was identified at the species level and the population level. AMOVA analysis revealed a low level of genetic differentiation among the four populations with high gene flow. Mantel test showed no significant correlation between genetic distance and geographic distance. It was found that association between annual mean temperature and annual precipitation with FSGS. Combined with these spatial genetic variation, abundant precipitation and suitable temperature create a stable environment for A. gigantea in Hainan Island, which allows the fern to expand rapidly during the LGM. These results further emphasized the role of outcrossing, and history and environmental factors in the evolution of A. gigantea . This study also provided new insights on in local adaptation of A. gigantea to environmental fluctuations, and available genetic data to enhance the conservation for relict tree ferns. [ABSTRACT FROM AUTHOR]

Dispersal constitutes one of the main processes that shape population genetic structure and dynamics. Combining a capture-mark-resighting methodology and molecular genetics analyses, we studied the natal dispersal behaviour of House Wrens (Troglodytes aedon bonariae) inhabiting a naturally fragmented habitat in south temperate Argentina. Based on data collected over 12 breeding seasons (2005–2016), we tested if males and females differ in natal dispersal behaviour at different spatial scales. At local scale (within study sites), both resighting of banded individuals and genetic analysis showed that females dispersed greater distances than males. At a broader spatial scale (between study sites) resighting of banded individuals could not verify that females were the dispersing sex since long-distance dispersal was rare. However, genetic analyses revealed paradoxical evidence: while the females of populations separated by more than 5 km showed slight but significant genotypic differences among them, males showed genetic differences at a greater distance (> 16 km). Given that genetic analyses can provide evidence of both historical and present-day dispersal the observed genetic differentiation does not necessarily imply that the sex dispersal pattern is reversed at a regional scale. We propose that females have a higher probability of acquiring a partner/territory at closer distances due existing male-biased population sex ratio caused but higher female mortality. Also, although males are less likely to disperse, when they do, they must travel greater distances to find a suitable territory or mate. Such movements would prevent the occurrence of genetic differences among male populations. [ABSTRACT FROM AUTHOR]

Density‐dependent recruitment is fundamental to understanding species diversity and community dynamics in plants. Although there is compelling evidence that seeds and seedlings die from conspecific negative density dependence (CNDD) as predicted by the Janzen–Connell hypothesis, characterising adult recruitment remains a challenge for long‐living trees. Previous studies have used the decrease in fine‐scale spatial genetic structure (FSGS) across life stages to indicate CNDD; however, this has not been tested rigorously.We addressed these challenges by integrating dispersal kernels and FSGS. To establish links between density dependence and FSGS, we simulated seedlings based on the estimated dispersal kernels from parentage analyses, and further simulated adults under various seedling‐to‐adult recruitment scenarios, using an individual‐based spatially explicit model. We tested this method in an isolated Cyclobalanopsis glauca population on China's Dajinshan Island.We detected significant FSGS in the seedlings and weaker, though also significant, FSGS in the adults. As expected, the observed FSGS of seedlings was well predicted by the simulated seedlings, with observations falling inside the 95% confidence envelopes over all distance classes. However, the simulations showed that CNDD enhanced the FSGS while positive density dependence dampened it during the seedling‐to‐adult transition. The adult FSGS of our population was therefore explained by positive rather than negative density‐dependent adult recruitment.Synthesis. Our study demonstrates that the change of FSGS in conjunction with dispersal‐based model tests can offer a valuable insight into density‐dependent adult recruitment. The results indicate that the transitions from seedlings to adults in C. glauca are dominantly regulated not by Janzen–Connell effects, but by processes of positive density dependence. More broadly, the findings may provide a caution against extrapolations of widespread Janzen–Connell effects in seeds and seedlings to adult recruits, underscoring a critical gap between mechanisms at early stages and long‐term population and community dynamics. [ABSTRACT FROM AUTHOR]

Gene flow may occur both through pollen movement and seed dispersal, although their relative contribution to overall species gene flow is not understood for most tropical trees, which compromises management recommendations. We investigated the implications of seed dispersal limitation, pollen dispersal capacity, and mating system to the spatial genetic structure of populations of the Neotropical legume tree, Centrolobium tomentosum, in Brazil's Atlantic Forest. We estimated seed dispersal distribution by counting individuals around adult trees; pollen dispersal distribution and outcrossing rates from adult and offspring genotypes, using seven microsatellite loci. Spatial genetic structure was inferred through the correlation among kinship coefficients and geographical distances between pairs of individuals, using nuclear and chloroplast microsatellite markers. We observed restricted seed dispersal, with most seeds (78%) falling up to 10 m from the adult tree trunk. The best-fitted pollen dispersal distribution was the exponential power distribution, with a heavy tail and average pollen dispersal distance of 3191 m. The mating system was preferably allogamous, with an average of eight pollen donors. There was significant spatial genetic structure in all populations, with stronger structure obtained from chloroplast DNA, which suggests that the restricted gene flow by seed dispersal may be compensated by high outcrossing rates and long-distance pollen flow promoted by the large bees that pollinate the species. Our results emphasize the importance of pollination services in fragmented tropical landscapes, where most tree species are pollinated by animals and a large number of species experience seed dispersal limitation. [ABSTRACT FROM AUTHOR]

Seed and pollen dispersal are important for defining sustainable forest management practices. By reducing population density, selective logging could affect not only the seed production of timber species but also the selfing rate and the patterns of seed and pollen rains. To assess these risks, we characterized seed and pollen dispersal patterns and the fine-scale spatial genetic structure (FSGS) of Pericopsis elata, a gregarious, wind-dispersed legume tree which is highly logged in Central Africa and threatened by overexploitation. Eleven microsatellite markers were used to genotype 189 adults and 664 seedlings in a 4 km2 plot in the Democratic Republic of Congo (DRC). According to the neighbourhood model, seed dispersal was extremely leptokurtic, with 80% of seeds dispersal distances <75 m, 15% >500 m. Pollen dispersal was locally more extensive (median distance 260 m), but pollen immigration was not detected, and the selfing rate (54%) appeared particularly high compared to other tropical tree species. Limited gene dispersal resulted in remarkably high FSGS (Sp = 0.072). A decay of inbreeding with age also suggests that the species is prone to inbreeding depression. The reproductive success of trees was positively related to their diameter at breast height (dbh), with half of the progeny mothered by trees with dbh > 97 cm and fathered by trees with dbh > 119 cm. Our study highlights that (1) seed sources must be diversified for plantation or population reinforcement to limit consanguinity, and (2) the legal minimum cutting diameter in DRC (60 cm) should be increased to maintain enough post-logging reproductive potential. [ABSTRACT FROM AUTHOR]

Genetic marker studies can assist restoration practice through selection of seed sources that conserve historical levels of gene diversity and population genetic differentiation. We examined genetic variation and structure within and among mainland and island populations of Elymus glaucus, a perennial bunchgrass species native to western North American grasslands that is targeted for grassland restoration. Island populations of E. glaucus represent sensitive sites and potentially distinctive seed sources for reintroduction, and little is known of their genetic composition. Genetic diversity and structure were estimated using amplified fragment length polymorphism markers for 21 populations and 416 individuals distributed across two coastal California mainland locations and three California Channel Islands. Eight primer combinations resulted in 166 markers, of which 165 (99.4 %) were polymorphic. The number of polymorphic bands was significantly greater among mainland populations relative to island sites, and locally common alleles were present for each sampled island and mainland location. Population structure was high (62.9 %), with most variation (55.8 %) distributed among populations, 7.1 % between mainland and island locations, and the remainder (37.1 %) within populations. Isolation by distance was only apparent among islands. Using marker data to recommend appropriate seed sources for restoration, E. glaucus seeds are best derived within islands with collections representing a large number of individuals from matching environments. Given the limited gene flow and prior evidence of adaptive divergence among populations of this species, regional collections are recommended in all cases to maintain diversity and to avoid long-distance introductions of highly differentiated plant material.