Population Genetic Structure of the Grasshopper Eyprepocnemis plorans in the South and East of the Iberian Peninsula

The grasshopper Eyprepocnemis plorans subsp. plorans harbors a very widespread polymorphism for supernumerary (B) chromosomes which appear to have arisen recently. These chromosomes behave as genomic parasites because they are harmful for the individuals carrying them and show meiotic drive in the initial stages of population invasion. The rapid increase in B chromosome frequency at intrapopulation level is thus granted by meiotic drive, but its spread among populations most likely depends on interpopulation gene flow. We analyze here the population genetic structure in 10 natural populations from two regions (in the south and east) of the Iberian Peninsula. The southern populations were coastal whereas the eastern ones were inland populations located at 260–655 m altitude. The analysis of 97 ISSR markers revealed significant genetic differentiation among populations (average G_ST =  0.129), and the Structure software and AMOVA indicated a significant genetic differentiation between southern and eastern populations. There was also significant isolation by distance (IBD) between populations. Remarkably, these results were roughly similar to those found when only the markers showing low or no dropout were included, suggesting that allelic dropout had negligible effects on population genetic analysis. We conclude that high gene flow helped this parasitic B chromosome to spread through most of the geographical range of the subspecies E. plorans plorans.     

Population Genetic Structure of a Widespread Bat-Pollinated Columnar Cactus

Bats are the main pollinators and seed dispersers of Stenocereus thurberi, a xenogamous columnar cactus of northwestern Mexico and a good model to illustrate spatial dynamics of gene flow in long-lived species. Previous studies in this cactus showed differences among populations in the type and abundance of pollinators, and in the timing of flowering and fruiting. In this study we analyzed genetic variability and population differentiation among populations. We used three primers of ISSR to analyze within and among populations genetic variation from eight widely separated populations of S. thurberi in Sonora, Mexico. Sixty-six out of 99 of the ISSR bands (P = 66.7%) were polymorphic. Total heterozygosity for all populations sampled revealed high genetic diversity (H_sp = 0.207, H_BT = 0.224). The AMOVA showed that most of the genetic variation was within populations (80.5%). At the species level, estimates of population differentiation, θ = 0.175 and θ^B = 0.194, indicated moderate gene flow among populations. The absence of a significant correlation between genetic and geographic distances indicated little isolation by geographic distance. The large genetic variation and diversity found in S. thurberi is consistent with its open reproductive system and the high mobility of bats, a major pollinator. However, small changes in number or kind of pollinators and seed dispersal agents, in the directionality of migratory routes, and/or in the timing of flowering and fruiting among populations, can critically affect gene flow dynamics.     

Isolation by landscape in populations of a prized edible mushroom Tricholoma matsutake

Tricholoma matsutake, a wild edible ectomycorrhizal mushroom, is revered for its distinguished flavor and iconic significance. Here, we test for landscape effects on T. matsutake gene flow and population structure in the Eastern Himalayas. Using single-nucleotide polymorphic (SNP) DNA markers, isolation by distance patterns were tested on eight populations within and between watersheds. We find that high, treeless ridgelines are effective barriers to gene flow, even at distances less than 65 km, whereas populations located within watersheds are structured at greater distances. Mantel tests demonstrated a significant positive correlation between F _st and a “landscape distance” measured as the shortest distance between population pairs below treeline r = 0.574, P = 0.002, whereas strict euclidian distances do not correlate. AMOVA analysis revealed significant partitioning with 91% of the genetic variance found within populations and 7% found between watersheds, indicative of sexually recombining populations with limited gene flow between watersheds. We show that landscape is an important determinant of air-dispersed ectomycorrhizal species population structure in heterogeneous landscapes.     

Limited gene flow among brown bear populations in far Northern Europe? Genetic analysis of the east–west border population in the Pasvik Valley

Noninvasively collected genetic data can be used to analyse large‐scale connectivity patterns among populations of large predators without disturbing them, which may contribute to unravel the species’ roles in natural ecosystems and their requirements for long‐term survival. The demographic history of brown bears (Ursus arctos) in Northern Europe indicates several extinction and recolonization events, but little is known about present gene flow between populations of the east and west. We used 12 validated microsatellite markers to analyse 1580 hair and faecal samples collected during six consecutive years (2005–2010) in the Pasvik Valley at 70°N on the border of Norway, Finland and Russia. Our results showed an overall high correlation between the annual estimates of population size (N_c), density (D), effective size (N_e) and N_e/N_c ratio. Furthermore, we observed a genetic heterogeneity of ～0.8 and high N_e/N_c ratios of ～0.6, which suggests gene flow from the east. Thus, we expanded the population genetic study to include Karelia (Russia, Finland), Västerbotten (Sweden) and Troms (Norway) (477 individuals in total) and detected four distinct genetic clusters with low migration rates among the regions. More specifically, we found that differentiation was relatively low from the Pasvik Valley towards the south and east, whereas, in contrast, moderately high pairwise F_ST values (0.91–0.12) were detected between the east and the west. Our results indicate ongoing limits to gene flow towards the west, and the existence of barriers to migration between eastern and western brown bear populations in Northern Europe.     

Rapid suppression of drive for a parasitic B chromosome

The persistence of parasitic B chromosomes in natural populations depends on both B ability to drive and host response to counteracting it. In the grasshopper Eyprepocnemis plorans, the B24 chromosome is the most widespread B chromosome variant in the Torrox area (Málaga, Spain). Its evolutionary success, replacing its ancestral neutralized B variant, B2, was based on meiotic drive in females, as we showed in a sample caught in 1992. In females collected six years later, mean B24 transmission ratio (k(B)) was 0.523, implying a very rapid decrease from the 0.696 observed in 1992. This shows that B24 neutralization is running very fast and suggests that it might most likely be based on a single gene of major effect.     

Population genetic structure of wild boars in the West Balkan region

We investigated the population genetic structure of wild boars from Vojvodina (Serbia), Slavonija (Croatia) and Bosnia using four microsatellite markers. All loci presented a high degree of polymorphism and a total of 76 alleles (mean 19 alleles per locus) were detected. Average observed heterozygosity (H _o) value was 0.60. Deviation from Hardy-Weinberg equilibrium was found due to significant heterozygote deficiency detected for three of the four analyzed loci and for all populations. F _IS value over all loci and all populations was 0.29, and the effective number of migrants based on private alleles was 1.64. Sufficient levels of gene flow were found between all populations and the spatial structure showed slightly closer nuclear gene pool affinity of Vojvodina and Slavonija populations in relation of Bosnia population.     

Comparative phylogeography of brown (Sula leucogaster) and red-footed boobies (S. sula): The influence of physical barriers and habitat preference on gene flow in pelagic seabirds

To test the hypothesis that both physical and ecological barriers to gene flow drive population differentiation in tropical seabirds, we surveyed mitochondrial control region variation in 242 brown boobies (Sula leucogaster), which prefer inshore habitat, and 271 red-footed boobies (S. sula), which prefer pelagic habitat. To determine the relative influence of isolation and gene flow on population structure, we used both traditional methods and a recently developed statistical method based on coalescent theory and Bayesian inference (Isolation with Migration). We found that global population genetic structure was high in both species, and that female-mediated gene flow among ocean basins apparently has been restricted by major physical barriers including the Isthmus of Panama, and the periodic emergence of the Sunda and Sahul Shelves in Southeast Asia. In contrast, the evolutionary history of populations within ocean basins differed markedly between the two species. In brown boobies, we found high levels of population genetic differentiation and limited gene flow among colonies, even at spatial scales as small as 500 km. Although red-footed booby colonies were also genetically differentiated within ocean basins, coalescent analyses indicated that populations have either diverged in the face of ongoing gene flow, or diverged without gene flow but recently made secondary contact. Regardless, gene flow among red-footed booby populations was higher than among brown booby populations. We suggest that these contrasting patterns of gene flow within ocean basins may be explained by the different habitat preferences of brown and red-footed boobies.     

A SNP haplotype associated with a gene resistant to Xanthomonas axonopodis pv. malvacearum in upland cotton (Gossypium hirsutum L.)

An F_4:5 population of 285 families with each tracing back to a different F₂ plant, derived from a cotton bacterial blight resistant line ‘DeltaOpal’ and a susceptible line ‘DP388’, was artificially inoculated with bacterial blight race 18 (Xanthomonas axonopodis pv. malvacearum) to assay their resistance or susceptibility to the disease. The segregation in the F_4:5 population indicates that the resistance was conditioned by a single dominant gene designated B _12. Simple sequence repeat (SSR) markers identified as putatively linked to the resistance gene by bulked segregant analysis were confirmed on the entire F_4:5 population. Three SSR markers, CIR246, BNL3545 and BNL3644 on chromosome 14, were found closely linked to B ₁₂ . The association between CIR246 and B ₁₂ was validated among 354 plants of 16 diverse varieties. Based on Monsanto SSR/single nucleotide polymorphism (SNP) consensus map, SNP markers closely linked to CIR246 were used to screen ‘DeltaOpal’ and ‘DP388’ for polymorphism. The polymorphic SNP markers were run on the F_4:5 population and the four SNP markers spanning 3.4 cM were found to flank the resistance gene on chromosome 14. The linkage between B ₁₂ and the 4-SNP marker haplotype was validated using 18 elite cotton lines. This 4-SNP marker haplotype can be used for marker assisted selection for bacterial blight resistance breeding programs or for screening germplasm collections for this locus rapidly.     

Assessment of genetic diversity and population structure of Bergenia stracheyi (Saxifragaceae) in the Western Himalaya (India)

Genetic diversity and population structure in Bergenia stracheyi, a threatened medicinal herb in the Western Himalaya of India was analysed using directed amplification of minisatellite DNA (DAMD) and inter simple sequence repeats (ISSR) markers. A total of 41 accessions of B. stracheyi representing three populations (Khillenmarg –KLM, Jalori Pass-JLP and Rohtang-RTG) were considered in the present study. The cumulative data analysis for 26 (10 DAMD + 16 ISSR) markers revealed 87.1% polymorphism. The maximum inter-population genetic distance was found between KLM and JLP, whereas the minimum genetic distance was found between RTG and JLP populations. The analysis of molecular variance (AMOVA) revealed maximum percentage of variation among individuals within populations (75%) than among the populations (25%). Clustering pattern of the three sample populations in STRUCTURE and PCoA analyses showed high genetic variation at population level. The present study revealed that distribution patterns, high altitudinal ranges, high habitat specificity, relatively high gene flow, small and isolated population size have shaped the current population structure of B. stracheyi in the Western Himalayan region. DAMD and ISSR markers have provided significant insights into characterization of B. stracheyi populations, and facilitate selection of appropriate accessions for further utilization in conservation and bioprospecting programmes.     

Quantitative analysis of NOR expression in a B chromosome of the grasshopper <Emphasis Type="Italic">Eyprepocnemi</Emphasis>s <Emphasis Type="Italic">ploran</Emphasis>s

The B₂₄ chromosome in the Torrox population of the grasshopper Eyprepocnemis plorans is recurrently attached to a nucleolus in diplotene cells, indicating the activity of its distally located ribosomal DNA (rDNA). The frequency of males expressing the B chromosome nucleolus organizer region (B-NOR) almost doubled in 4 years. The likelihood of expressing the B-NOR increased with the B number and, in males expressing it, about 20% of their cells showed a nucleolus attached to the B. When active, the B-NOR contributed more than 25% of total cell nucleolar area (NA). Within males expressing the B-NOR, total cell NA did not differ between cells showing the active or inactive B-NOR, suggesting that total cell NA is tightly regulated in this species. However, this parameter tended to increase in this population from 1999 to 2004, in parallel to the neutralization process which is taking place in this population. Finally, an analysis of A chromosome NOR interdependence for activity revealed a positive correlation among autosomes but a negative correlation between autosomes and the X chromosome, the manifestation of which depends on B-NOR activity. These results are discussed in the context of the nucleolus as a sensor of the stress caused by parasitic B chromosomes.     

Genetic diversity and differentiation of the extremely dwarf Ficus tikoua in Southwestern China

Fig wasps are short-lived, weak fliers, and their long-distance dispersal depends on the ability to enter fast-flowing air above the canopy. Therefore, growth form of fig species may affect fig wasps’ dispersal. We employed six microsatellite markers to examine gene flow in Chinese populations of the dioecious Ficus tikoua, a prostrate shrub with figs partially buried in the soil. Moderate genetic diversity was found within populations of F. tikoua. Differentiation among six F. tikoua populations (F_ST = 0.196, p < 0.001) was higher than those of other dioecious figs, and significant differentiation was found between each pair of populations, indicating potential restricted gene flow. This was further demonstrated by significant isolation-by-distance pattern (p = 0.039), because low gene flow among population was needed to balance the minor effect of genetic drift, given F. tikoua was locally common. Restricted gene flow suggests that growth form may determine differences in gene flow between fig species.     

Genetic differentiation in the mud crab Scylla serrata (Decapoda: Portunidae) within the Indian Ocean

Scylla serrata (Decapoda: Portunidae) is a swimming crab that is widespread in the Indo-Pacific region and commonly found in estuarine and mangrove waters. An extended planktonic larval phase suggests high dispersal potential and the possibility of extensive gene flow between conspecific populations at least on a geographic mesoscale (tens to hundreds of kilometres).Intraspecific variation of the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) gene was investigated in 77 individuals from four representative mangrove swamps of the African tropics (Kenya and Zanzibar) by means of DNA sequencing. We examined 535 base pairs (bp) and identified 24 different haplotypes. Each population sample is characterised by a single most frequent haplotype, shared among all four populations, and a small number of rare ones, typically present in only one or two individuals and representative of a specific population.Analysis of molecular variance (AMOVA), F_ST statistics and χ² contingency analysis of spatial distribution of mtDNA haplotype frequencies revealed in toto a significant genetic differentiation among populations. These results could indicate that gene flow might be reduced, even between geographically close sites, despite the high potential for dispersal; anyway, at the recorded level of divergence and owing to the abundance of rare haplotypes and singletons in our data set, repeated sampling over time is necessary to establish whether the recorded pattern of genetic differentiation is stable and biologically significant.Finally, integration of our data with those reported by Gopurenko et al. [Mar. Biol. 134 (1999) 227] on S. serrata from South Africa, Red Sea and Mauritius Islands allowed to infer S. serrata population structure within a larger area of the Indian Ocean region.     

Genetic consequences of fragmentation in “arbor vitae,” eastern white cedar (Thuja occidentalis L.), toward the northern limit of its distribution range

We tested the hypothesis that marginal fragmented populations of eastern white cedar (EWC) are genetically isolated due to reduced pollen and gene flow. In accordance with the central-marginal model, we predicted a decrease in population genetic diversity and an increase in differentiation along the latitudinal gradient from the boreal mixed-wood to northern coniferous forest. A total of 24 eastern white cedar populations were sampled along the north-south latitudinal gradient for microsatellite genotyping analysis. Positive F_is values and heterozygote deficiency were observed in populations from the marginal (F_is = 0.244; P_HW = 0.0042) and discontinuous zones (F_is = 0.166; P_HW = 0.0042). However, populations from the continuous zone were in HW equilibrium (F_is = −0.007; P_HW = 0.3625). There were no significant latitudinal effects on gene diversity (H_s), allelic richness (AR), or population differentiation (F_st). Bayesian and NJT (neighbor-joining tree) analyses demonstrated the presence of a population structure that was partly consistent with the geographic origins of the populations. The impact of population fragmentation on the genetic structure of EWC is to create a positive inbreeding coefficient, which was two to three times higher on average than that of a population from the continuous zone. This result indicated a higher occurrence of selfing within fragmented EWC populations coupled with a higher degree of gene exchange among near-neighbor relatives, thereby leading to significant inbreeding. Increased population isolation was apparently not correlated with a detectable effect on genetic diversity. Overall, the fragmented populations of EWC appear well-buffered against effects of inbreeding on genetic erosion.     

Divergence and gene flow between the East Sea and the Southeast Atlantic populations of North Pacific light fish Maurolicus japonicus Ishikawa

In the present study, we examined the divergence time and the magnitude of gene flow between two distantly separated populations of North Pacific light fish Maurolicus japonicus, one in the southern part of the East Sea (off Korea) and the other in the Southeast Atlantic Ocean (off Namibia). The mitochondrial 16SrDNA sequences (524 base pairs) obtained from the two populations were analyzed using the isolation with migration (IM) coalescent method as well as the conventional F _ST statistic and a phylogeographic method. A significant nonzero F _ST value (0.176, P<0.05) indicated genetic differentiation between the two populations. The low level of nucleotide diversity compared to the moderately high level of haplotype diversity implied that the populations have experienced a bottleneck followed by rapid growth in both populations. IM analysis suggested that these two populations most likely split approximately 500?C800 K years ago during the Pleistocene climatic oscillations and that gene flow has occurred unidirectionally from the Southeast Atlantic population to the East Sea population. Nested clade phylogeographic analysis supports restricted gene flow between the two populations.     

Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection

The study of recent natural selection in human populations has important applications to human history and medicine. Positive natural selection drives the increase in beneficial alleles and plays a role in explaining diversity across human populations. By discovering traits subject to positive selection, we can better understand the population level response to environmental pressures including infectious disease. Our study examines unusual population differentiation between three large data sets to detect natural selection. The populations examined, African Americans, Nigerians, and Gambians, are genetically close to one another (F_ST < 0.01 for all pairs), allowing us to detect selection even with moderate changes in allele frequency. We also develop a tree-based method to pinpoint the population in which selection occurred, incorporating information across populations. Our genome-wide significant results corroborate loci previously reported to be under selection in Africans including HBB and CD36. At the HLA locus on chromosome 6, results suggest the existence of multiple, independent targets of population-specific selective pressure. In addition, we report a genome-wide significant (p = 1.36 × 10⁻¹¹) signal of selection in the prostate stem cell antigen (PSCA) gene. The most significantly differentiated marker in our analysis, rs2920283, is highly differentiated in both Africa and East Asia and has prior genome-wide significant associations to bladder and gastric cancers.     

Population genetic structure of three major river Populations of rohu,Labeo rohita (Cyprinidae: Cypriniformes) using microsatellite DNA markers

Determining the genetic structure is essential for developing conservation and stock improvement plans. Four dinucleotide microsatellite loci were analysed to reveal population genetic structure of the Indian major carp,Labeo rohita collected from three major rivers namely the Halda, the Jamuna, and the Padma in Bangladesh. The four loci were polymorphic (P ₉₅) in all the populations. The populations varied in the number and frequencies of alleles as well as heterozygosities in the loci analyzed. Population differentiation (F _ST) value between the Halda and the Jamuna population was significant (P<0.05). Relatively high level of gene flow and low level ofF _ST values were found between the Padma and the Jamuna population. The unweighted pair group method with averages (UPGMA) dendrogram based on genetic distance resulted in two clusters: the Halda population was alone in one cluster whereas the Jamuna and the Padma made another cluster. The results revealed a relatively low level of genetic variability in the river populations ofL. rohita in Bangladesh.     

High Connectivity among Blue Crab (Callinectes sapidus) Populations in the Western South Atlantic

Population connectivity in the blue crab Callinectes sapidus was evaluated along 740 km of the Western South Atlantic coast. Blue crabs are the most exploited portunid in Brazil. Despite their economic importance, few studies report their ecology or population structure. Here we sampled four estuarine areas in southern Brazil during winter 2013 and summer 2014 in order to evaluate diversity, gene flow and structure of these populations. Nine microsatellite markers were evaluated for 213 adult crabs, with identification of seven polymorphic loci and 183 alleles. Pairwise F_ST values indicated low population structure ranging from -0.00023 to 0.01755. A Mantel test revealed that the geographic distance does not influence genetic (r = -0.48), and structure/migration rates confirmed this, showing that even the populations located at the opposite extremities of our covered region presented low F_ST and exchanged migrants. These findings show that there is a significant amount of gene flow between blue crab populations in South Brazil, likely influenced by local current dynamics that allow the transport of a high number of larvae between estuaries. Considering the elevated gene flow, the populations can be considered a single genetic stock. However, further information on population size and dynamics, as well as fishery demands and impacts at different regions, are necessary for harvest management purposes.     

Genetic differentiation in spite of high gene flow in the dominant rainforest tree of southeastern Australia,Nothofagus cunninghamii

Nothofagus cunninghamii is a long-lived, wind-pollinated tree species that dominates the cool temperate rainforests of southeastern Australia. The species'' distribution is more or less continuous in western Tasmania but is fragmented elsewhere. However, it is unknown whether this fragmentation has affected the species'' genetic architecture. Thus, we examined N. cunninghamii using 12 nuclear microsatellites and 633 individuals from 18 populations spanning the species'' natural range. Typical of wind-pollinated trees, there was low range-wide genetic structure (F_ST=0.04) consistent with significant gene flow across most of the species'' range. However, gene flow was not high enough to overcome the effects of drift across some disjunctions. Victorian populations (separated from Tasmania by the 240 km wide Bass Strait) formed a genetic group distinct from Tasmanian populations, had lower diversity (mean allelic richness (Ar)=5.4 in Victoria versus 6.9 in Tasmania) and were significantly more differentiated from one another than those in Tasmania (F_ST=0.045 in Victoria versus 0.012 in Tasmania). Evidence for bottlenecking was found in small populations that were at least 20 km from other populations. Interestingly, we found little divergence in microsatellite markers between the extremes of genetically based morphological and physiological altitudinal clines suggesting adaptive differentiation is strongly driven by selection because it is likely to be occurring in the presence of gene flow. Even though the cool temperate rainforests of Australia are highly relictual, the species is relatively robust to population fragmentation due to high levels of genetic diversity and gene flow, especially in Tasmania.