Dispersal capacities of pollen, seeds and spores: insights from comparative analyses of spatial genetic structures in bryophytes and spermatophytes.

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.

Development and characterization of expressed sequence tag-simple sequence repeat markers for Anaphalis margaritacea var. yedoensis (Asteraceae).

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.

Pollinator type strongly impacts gene flow within and among plant populations for six Neotropical species.

Animal pollinators directly affect plant gene flow by transferring pollen grains between individuals. Pollinators with restricted mobility are predicted to limit gene flow within and among populations, whereas pollinators that fly longer distances are likely to promote genetic cohesion. These predictions, however, remain poorly tested. We examined population genetic structure and fine-scale spatial genetic structure (FSGS) in six perennial understory angiosperms in Andean cloud forests of northwestern Ecuador. Species belong to three families (Gesneriaceae, Melastomataceae, and Rubiaceae), and within each family we paired one insect-pollinated with one hummingbird-pollinated species, predicting that insect-pollinated species have greater population differentiation (as quantified with the FST statistic) and stronger FSGS (as quantified with the SP statistic) than hummingbird-pollinated species. We confirmed putative pollinators through a literature review and fieldwork, and inferred population genetic parameters with a genome-wide genotyping approach. In two of the three species pairs, insect-pollinated species had much greater (>2-fold) population-level genetic differentiation and correspondingly steeper declines in fine-scale genetic relatedness. In the Gesneriaceae pair, however, FST and SP values were similar between species and to those of the other hummingbird-pollinated plants. In this pair, the insect pollinators are euglossine bees (as opposed to small bees and flies in the other pairs), which are thought to forage over large areas, and therefore may provide similar levels of gene flow as hummingbirds. Overall, our results shed light on how different animal pollination modes influence the spatial scale of plant gene flow, suggesting that small insects strongly decrease genetic cohesion.

Unexpected genetic integrity boosts hope for the conservation of the red-legged partridge (Alectoris rufa, Galliformes) in Italy.

The red-legged partridge (Alectoris rufa) is a medium-sized galliform endemic to southwestern Europe. In the easternmost part of the species' range, the population inhabiting Elba Island (Tuscan Archipelago National Park, Italy) is of undisputed conservation value. While we found nuclear and maternal DNA introgression with the exotic chukar partridge (A. chukar) in previous studies based on microsatellite DNA (n = 25) and two mitochondrial markers (n = 103), respectively, we disclosed a limited or null admixture in a few Elban partridges (n = 4) in a recent genomic investigation relying on 168,675 Single Nucleotide Polymorphisms (SNPs). We herein carried out an extended microsatellite DNA survey including additional 65 samples (total, 90) and six loci (total, 11) to determine both spatial structure and genetic integrity of local A. rufa. A sharp divergence between the subpopulations inhabiting the two sides of the island was disclosed, and the microsatellites indicated that all Elban partridges were not admixed with the chukar, thus fully reflecting the picture inferred using SNPs. We hypothesized that the spreading of chukar genes was constrained by negative selection, with the persistence of only the maternal lineage being indicative of thermal adaptation. The two subpopulations should be treated as distinct Management Units, and an envisaged plan to secure a stock onto nearby Pianosa Island could not only warrant endurance of the Elban population but also establish a source of valuable founders for the ex-situ management of the species in Italy. Our study exemplifies how a suitable samples/loci combination is the key to solve wildlife issues dealing with introgression.

Comparative reproductive ecology of two sister Asarum species (Aristolochiaceae) in relation to the evolution of elongated floral appendage.

Genus Asarum (Aristolochiaceae) shows diverse floral morphology and is hypothesized to have diversified as a result of pollinator-mediated selection. Yet most aspects of their reproductive ecology, including pollinators, remain unclear. This study focuses on A. costatum and A. minamitanianum in Japan, a sister species pair having remarkable differences in calyx lobe length (10-20 mm and 70-180 mm, respectively). The objectives of this study are to elucidate multiple aspects of reproductive ecology of these two species and obtain evolutionary insights into floral organ elongation. We adopted combined approaches, including field observations, molecular analyses and cultivation experiments, such as pollinator observation for 3 years, fine-scale spatial genetic analysis of 769 individuals, paternity analysis based on 566 seeds over 4 years, and control pollination experiments. Both Asarum species had strong spatial genetic structures, indicating limited seed dispersal. Pollinator observation revealed that flies and ground-dwelling insects visited flowers of both species, but that the pollinator fauna differed between the species. The visitation rate of flies was extremely low but was more than twice as high in the species with an elongated floral appendage. Paternity analysis revealed A. minamitanianum was predominantly outcrossing, while A. costatum showed a wide range of selfing rates among fruits. These two Asarum species are likely adapted to fly pollination in the shady forest understorey, where available pollinator fauna is limited. In addition, although its function remains unclear, the elongated calyx lobe of A. minamitanianum could have evolved for effective pollen dispersal by attracting fly visitors.

Ecological and Morphological Differentiation Among COI Haplotype Groups in the Plant Parasitic Nematode Species Mesocriconema Xenoplax.

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.

Genetic Relationships of Puccinia striiformis f. sp. tritici in Southwestern and Northwestern China.

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.

Dispersal patterns in black howler monkeys (Alouatta pigra): Integrating multiyear demographic and molecular data.

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.

La dispersión es un proceso fundamental en el funcionamiento de las sociedades animales, ya que regula el grado en que los individuos parentados se concentran espacialmente. El patrón de dispersión de una especie puede ser complejo ya que surge de las decisiones de los individuos conformadas por las compensaciones de costo-beneficio asociadas con permanecer en el grupo natal o dispersarse. Dada esta posible complejidad, la combinación de información demográfica a largo plazo con datos moleculares puede proporcionar información importante sobre los patrones de dispersión de una especie en particular. Basado en un estudio de 15 años que integra datos demográficos de seis grupos sociales con muestreo genético longitudinal y transversal de 20 grupos (N = 169 individuos, N = 21 loci de microsatélites polimórficos), describimos las diversas estrategias de dispersión de machos y hembras del mono aullador negro (Alouatta pigra) que habitan el Parque Nacional Palenque, México. Los eventos de dispersión confirmados genéticamente (N = 21 de 59 machos; N = 6 de 65 hembras), junto con los análisis de autocorrelación espacial revelaron que el patrón de dispersión de los monos aulladores negros es bisexual con fuertes sesgos sexuales en ambas tasas de dispersión (los machos se dispersan más a menudo que las hembras) y distancia de dispersión (las hembras se dispersan más lejos que los machos). Los datos de observación y genéticos confirman que tanto machos como hembras pueden inmigrar con éxito a grupos ya establecidos, así como formar nuevos grupos con otros individuos que se están dispersando. Además, tanto los machos como las hembras pueden dispersarse individualmente, así como en parejas, y ambos también pueden dispersarse secundariamente. En general, nuestros hallazgos sugieren múltiples trayectorias de dispersión para aulladores negros de los dos sexos, y se necesitan más estudios para desentrañar qué factores demográficos, ecológicos y sociales subyacen en las decisiones de los individuos sobre si dispersarse y qué opciones de dispersión tomar.

There Is No 'Rule of Thumb': Genomic Filter Settings for a Small Plant Population to Obtain Unbiased Gene Flow 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 r t = 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.

Environmental Heterogeneity Leads to Spatial Differences in Genetic Diversity and Demographic Structure of Acer caudatifolium.

Under climate fluctuation, species dispersal may be disturbed by terrain and local climate, resulting in uneven spatial-genetic structure. In addition, organisms at different latitudes may be differentially susceptible to climate change. Here, we tracked the seed dispersal of Acer caudatifolium using chloroplast DNA to explore the relationships of terrain and local climate heterogeneity with range shifts and demography in Taiwan. Our results showed that the extant populations have shifted upward and northward to the mountains since the Last Glacial Maximum. The distributional upshift of A. caudatifolium is in contrast to the downward expansion of its closest relative in Taiwan, A. morrisonense. The northern populations of A. caudatifolium have acquired multiple-source chlorotypes and harbor high genetic diversity. However, effective gene flow between the north and south is interrupted by topography, geographic distance, north-south differences in October rainfall, and other climate heterogeneities, blocking southward genetic rescue. In addition, winter monsoon-driven rainfall may cause regional differences in the phenological schedule, resulting in adaptive effects on the timing of range shift and the genetic draft of chlorotype distribution. Terrain, distance, and local climate also differentiate the northernmost populations from the others, supporting the previous taxonomic treatment of Acer kawakamii var. taitonmontanum as an independent variety.

Fine-scale spatial genetic structure across the species range reflects recent colonization of high elevation habitats in silver fir (Abies alba Mill.).

Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations' resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine-scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies alba Mill.) population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1,368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east-west isolation-by-distance pattern consistent with the post-glacial colonization history of the species. Genetic differentiation among sites (FCT = 0.148) was an order of magnitude greater than between elevations within sites (FSC = 0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modelling revealed that elevation and, to a lesser extent, post-glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non-spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees.

Population genetic structure and connectivity of a riparian selfing herb Caulokaempferia coenobialis at a fine-scale geographic level in subtropical monsoon forest.

BACKGROUND: Rivers and streams facilitate movement of individuals and their genes across the landscape and are generally recognized as dispersal corridors for riparian plants. Nevertheless, some authors have reported directly contrasting results, which may be attributed to a complex mixture of factors, such as the mating system and dispersal mechanisms of propagules (seed and pollen), that make it difficult to predict the genetic diversity and population structure of riparian species. Here, we investigated a riparian self-fertilizing herb Caulokaempferia coenobialis, which does not use anemochory or zoochory for seed dispersal; such studies could contribute to an improved understanding of the effect of rivers or streams on population genetic diversity and structure in riparian plants. Using polymorphic ISSR and cpDNA loci, we studied the effect at a microgeographic scale of different stream systems (a linear stream, a dendritic stream, and complex transverse hydrological system) in subtropical monsoon forest on the genetic structure and connectivity of C. coenobialis populations across Dinghu Mountain (DH) and Nankun Mountain (NK). RESULTS: The results indicate that the most recent haplotypes (DH: H7, H8; NK: h6, h7, h11, h12) are not shared among local populations of C. coenobialis within each stream system. Furthermore, downstream local populations do not accumulate genetic diversity, whether in the linear streamside local populations across DH (H: 0.091 vs 0.136) or the dendritic streamside local populations across NK (H: 0.079 vs 0.112, 0.110). Our results show that the connectivity of local C. coenobialis populations across DH and NK can be attributed to historical gene flows, resulting in a lack of spatial genetic structure, despite self-fertilization. Selfing C. coenobialis can maintain high genetic diversity (H = 0.251; I = 0.382) through genetic differentiation (GST = 0.5915; FST = 0.663), which is intensified by local adaptation and neutral mutation and/or genetic drift in local populations at a microgeographic scale. CONCLUSION: We suggest that streams are not acting as corridors for dispersal of C. coenobialis, and conservation strategies for maintaining genetic diversity of selfing species should be focused on the protection of all habitat types, especially isolated fragments in ecosystem processes.

Genetic variation and population structure of clonal Zingiber zerumbet at a fine geographic scale: a comparison with two closely related selfing and outcrossing Zingiber species.

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.

Evidence of past forest fragmentation in the Congo Basin from the phylogeography of a shade-tolerant tree with limited seed dispersal: Scorodophloeus zenkeri (Fabaceae, Detarioideae).

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.

Spatial genetic structure and landscape connectivity in black bears: Investigating the significance of using different land cover datasets and classifications in landscape genetics analyses.

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.

Asymmetric contributions of seed and pollen to gene dispersal in the marsh orchid Dactylorhiza umbrosa in Asia Minor.

Orchids differ from other plants in their extremely small and partly air-filled seeds that can be transported long distances by wind. Seed dispersal in orchids is expected to contribute strongly to overall gene flow, and orchids generally express low levels of genetic differentiation between populations and low pollen to seed flow ratios. However, studies in orchids distributed in northern Europe have often found a poor geographic structuring of genetic variation. Here, we studied geographic differentiation in the marsh orchid Dactylorhiza umbrosa, which is widely distributed in upland regions from Asia Minor to Central Asia. These areas were less affected by Pleistocene ice ages than northern Europe and the orchid should have been able to survive the last ice age in local refugia. In the plastid genome, which is dispersed by seeds, populations at close distance were clearly divergent, but the differentiation still increased with geographic distance, and a significant phylogeographic structure had developed. In the nuclear genome, which is dispersed by both seeds and pollen, populations showed an even stronger correlation between genetic and geographic distance, but average levels of differentiation were lower than in the plastid genome, and no phylogeographic structure was evident. Combining plastid and nuclear data, we found that the ratio of pollen to seed dispersal (mp/ms) decreases with physical distance. Comparison with orchids that grow in parts of Europe that were glaciated during the last ice suggests that a balanced structure of genetic diversity develops only slowly in many terrestrial orchids, despite efficient seed dispersal.

Optimising the conservation of genetic diversity of the last remaining population of a critically endangered shrub.

An understanding of genetic diversity and the population genetic processes that impact future population viability is vital for the management and recovery of declining populations of threatened species. Styphelia longissima (Ericaceae) is a critically endangered shrub, restricted to a single fragmented population near Eneabba, 250 km north of Perth, Western Australia. For this population, we sought to characterize population genetic variation and its spatial structure, and aspects of the mating portfolio, from which strategies that optimize the conservation of this diversity are identified. A comprehensive survey was carried out and 220 adults, and 106 seedlings from 14 maternal plants, were genotyped using 13 microsatellite markers. Levels of genetic variation and its spatial structure were assessed, and mating system parameters were estimated. Paternity was assigned to the offspring of a subsection of plants, which allowed for the calculation of realized pollen dispersal. Allelic richness and levels of expected heterozygosity were higher than predicted for a small isolated population. Spatial autocorrelation analysis identified fine-scale genetic structure at a scale of 20 m, but no genetic structure was found at larger scales. Mean outcrossing rate (t m = 0.66) reflects self-compatibility and a mixed-mating system. Multiple paternity was low, where 61 % of maternal siblings shared the same sire. Realized pollen dispersal was highly restricted, with 95 % of outcrossing events occurring at 7 m or less, and a mean pollen dispersal distance of 3.8 m. Nearest-neighbour matings were common (55 % of all outcross events), and 97 % of mating events were between the three nearest-neighbours. This study has provided critical baseline data on genetic diversity, mating system and pollen dispersal for future monitoring of S. longissima. Broadly applicable conservation strategies such as implementing a genetic monitoring plan, diluting spatial genetic structure in the natural population, genetically optimizing ex situ collections and incorporating genetic knowledge into translocations will help to manage the future erosion of the high genetic variation detected.

Evolutionary legacy of a forest plantation tree species (Pinus armandii): Implications for widespread afforestation.

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.

Fine-Scale Patterns of Genetic Structure in the Host Plant Chamaecrista fasciculata (Fabaceae) and Its Nodulating Rhizobia Symbionts.

In natural plant populations, a fine-scale spatial genetic structure (SGS) can result from limited gene flow, selection pressures or spatial autocorrelation. However, limited gene flow is considered the predominant determinant in the establishment of SGS. With limited dispersal ability of bacterial cells in soil and host influence on their variety and abundance, spatial autocorrelation of bacterial communities associated with plants is expected. For this study, we collected genetic data from legume host plants, Chamaecrista fasciculata, their Bradyrhizobium symbionts and rhizosphere free-living bacteria at a small spatial scale to evaluate the extent to which symbiotic partners will have similar SGS and to understand how plant hosts choose among nodulating symbionts. We found SGS across all sampled plants for both the host plants and nodulating rhizobia, suggesting that both organisms are influenced by similar mechanisms structuring genetic diversity or shared habitat preferences by both plants and microbes. We also found that plant genetic identity and geographic distance might serve as predictors of nodulating rhizobia genetic identity. Bradyrhizobium elkanii was the only type of rhizobia found in nodules, which suggests some level of selection by the host plant.

Three arenaviruses in three subspecific natal multimammate mouse taxa in Tanzania: same host specificity, but different spatial genetic structure?

Mastomys natalensis is widespread in sub-Saharan Africa and hosts several arenavirus species, including the pathogenic zoonotic Lassa virus in West Africa. Mitochondrial lineages sub-divide the range of M. natalensis and have been associated with cryptic structure within the species. To test specificity of arenaviruses to hosts carrying these lineages, we screened 1772 M. natalensis in a large area of Tanzania where three mitochondrial lineages meet. We detected fifty-two individuals that were positive for one of three arenaviruses: Gairo, Morogoro, and Luna virus. This is the first record of Luna virus in Tanzania. We confirmed the specificity of each arenavirus to a distinct host mitochondrial lineage except for three cases in one locality at the centre of a host hybrid zone. No arenaviruses were detected in a large part of the study area. Morogoro and Gairo virus showed differences in prevalence (Morogoro virus lower than Gairo virus) and in genetic structure (Morogoro virus more structured than Gairo virus). However, both viruses have genetic neighbourhood size estimates of the same order of magnitude as Lassa virus. While differences in arenavirus and/or host evolutionary and ecological dynamics may exist, Tanzanian arenaviruses could be suited to model Lassa virus dynamics in M. natalensis.