Genetic divergence between the sympatric queen morphs of the ant Myrmica rubra

Pairs of obligate social parasites and their hosts, where some of the parasites have recently diverged from their host through intraspecific social parasitism, provide intriguing systems for studying the modes and processes of speciation. Such speciation, probably in sympatry, has also been propounded in the ant Myrmica rubra and its intraspecific social parasite. In this species, parasitism is associated with queen size dimorphism, and the small microgyne has become a social parasite of the large macrogyne. Here, we investigated the genetic divergence of the host and the parasite queen morphs in 11 localities in southern Finland, using nuclear and mitochondrial markers of queens and workers. We formulated and tested four speciation‐related hypotheses that differed in the degree of genetic divergence between the morphs. The queen morphs were genetically distinct from each other with little hybridization. In the nuclear data, when localities were nested within queen morphs in the hierarchical amova , 39% of the genetic variation was explained by the queen morph (standardized F'_CT = 0.63, uncorrected F_CT = 0.39), whereas 18% was explained by the locality (F'_SC = 0.39, F_SC = 0.29). This result corroborated the hypothesis of advanced sympatric speciation. In contrast, the mitochondrial DNA could not settle between the hierarchical levels of locality and queen morph, thus substantiating equally the hypotheses of incipient and advanced sympatric speciation. Together, our results support the view that the microgynous parasite has genetically diverged from its macrogynous host to the level of a nascent species.     

Evidence for nonallopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert

The genetic structure of populations of closely related, sympatric species may hold the signature of the geographical mode of the speciation process. In fully allopatric speciation, it is expected that genetic differentiation between species is homogeneously distributed across the genome. In nonallopatric speciation, the genomes may remain undifferentiated to a large extent. In this article, we analyzed the genetic structure of five sympatric species from the plant genus Heliotropium in the Atacama Desert. We used amplified fragment length polymorphisms (AFLPs) to characterize the genetic structure of these species and evaluate their genetic differentiation as well as the number of loci subject to positive selection using divergence outlier analysis (DOA). The five species form distinguishable groups in the genetic space, with zones of overlap, indicating that they are possibly not completely isolated. Among‐species differentiation accounts for 35% of the total genetic differentiation (F_ST = 0.35), and F_ST between species pairs is positively correlated with phylogenetic distance. DOA suggests that few loci are subject to positive selection, which is in line with a scenario of nonallopatric speciation. These results support the idea that sympatric species of Heliotropium sect. Cochranea are under an ongoing speciation process, characterized by a fluctuation of population ranges in response to pulses of arid and humid periods during Quaternary times.     

Genetic differentiation between two varieties of Oreocharis benthamii (Gesneriaceae) in sympatric and allopatric regions

The pattern of genetic differentiation between diverging species receives much attention as one of the key observable features of speciation. It has often been suggested that introgression between closely related species occurs commonly where their distributions overlap, leading to their becoming more morphologically and genetically similar, but there are a few opposite results. However, most of these studies have been carried out with animals and separate species; few have looked at intraspecific cases, especially in plants. Here, we conduct a comparative study on patterns of genetic differentiation among populations of two varieties of Oreocharis benthamii in allopatry and sympatry based on ISSR data for 754 individuals from 26 populations, in order to understand the processes leading to speciation. Contrary to expectations, the facultative xenogamy (mixed mating) species O. benthamii has a relatively low genetic diversity within populations (H = 0.1014, I = 0.1528) and high genetic differentiation among populations (G_ST = 0.5867, Ф_ST = 0.659), as is typically found for selfing species. Genetic variance between the two varieties in sympatric populations (44%, Ф_ST = 0.444) is significantly more than that in allopatric populations (14%, Ф_ST = 0.138). Consistent with the taxonomical delimitation of the two varieties, all sampled individuals of O. benthamii clustered into two genetic groups. Moreover, the genetic structures of populations of both varieties are correlated with their different geographical origins. Our studies show that significant divergence between sympatric populations of the two varieties could be attributed primarily to reinforcement by genetic divergent selection in sympatry where secondary contact had occurred. The major proportion of the genetic variation in outcrossing and mixed mating plants may exist among populations when the populations are distributed in fragmented habitats, due to the paucity of suitable habitat combined with inefficient seed dispersal mechanism and limited pollinator foraging area that may limit the gene flow.     

Drift happens: Molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests

Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus F_ST = 0.32, F_ST’ = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R² = 0.51) and higher local inbreeding (R² = 0.22). Populations varied greatly in levels of local inbreeding (F_IS = 0.2–0.9) and F_IS increased in more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.     

Mitochondrial DNA diversity of the vulnerable Chinese Egret (Egretta eulophotes) from China

The genetic diversity and population structure of the vulnerable Chinese Egret (Egretta eulophotes) were surveyed in the present study from three archipelagoes that cover the most southerly to the very northerly parts of the Chinese distribution range of this species, using a 433-bp fragment of the mitochondrial control region (CR). Among 90 individual samples, 31 different haplotypes were defined by 30 polymorphic sites. Overall haplotype diversity, nucleotide diversity and mean sequence divergence (p-distance) of this egret were 0.920, 0.0088 and 1.11%, respectively. NJ tree and parsimony network for the CR haplotypes of the Chinese Egret showed little genetic structure, and analysis of molecular variance indicated low but significant genetic differentiation (haplotype-based Φ_ST = 0.03267, P < 0.05 and distance-based Φ_ST = 0.04194, P < 0.05) among populations. The significant Fu’s F _S tests (Fu’s F _S  = −16.946, P < 0.01) and mismatch distribution analysis (τ = 4.463, SSD = 0.0081, P = 0.12) suggested that the low genetic differentiation and little geographical structure of the genetic differentiation might be explained by the population expansion. The Mantel test (haplotype-based F _ST, r = 0.639, P = 0.34 and distance-based F _ST, r = 0.947, P = 0.15) suggest that the significant genetic differentiation among populations was likely due to isolation by distance.     

Genetic differences between continuous and disjunct populations: some insights from sal (<Emphasis Type="Italic">Shorea robusta</Emphasis> Roxb.) in Nepal

Sal (Shorea robusta Gaertn., Dipterocarpaceae) is a wind-pollinated tropical tree species found in southern Asia. We investigated the genetic diversity and structure at four microsatellites of 15 populations comprising continuous-peripheral and disjunct-peripheral populations in Nepal. Estimates of genetic diversity (N _A = 8.98, H _O = 0.62, H _E = 0.69) were similar when compared with those of other tropical tree species. A higher level of genetic diversity was observed in continuous-peripheral populations (N _A = 9.61, H _O = 0.67, H _E = 0.72) as compared to disjunct-peripheral (N _A = 8.04, H _O = 0.55, H _E = 0.64). Population differentiation was higher among disjunct-peripheral populations (F _ST = 0.043) than among continuous peripherals (F _ST = 0.012). There was a significant association between gene flow distances and genetic differentiation (r ² = 0.128, P ≤ 0.007). No spatial arrangement of populations according to their geographical locations was found. Based on observed genetic diversity protection of some populations in continuous-peripheral range are suggested for the sustainable conservation of genetic resources of the species while protection of some disjunct-peripheral populations are also recommended for conserving rare alleles.     

Ecological host fitting of Trypanosoma cruzi TcI in Bolivia: mosaic population structure,hybridization and a role for humans in Andean parasite dispersal

An improved understanding of how a parasite species exploits its genetic repertoire to colonize novel hosts and environmental niches is crucial to establish the epidemiological risk associated with emergent pathogenic genotypes. Trypanosoma cruzi, a genetically heterogeneous, multi‐host zoonosis, provides an ideal system to examine the sylvatic diversification of parasitic protozoa. In Bolivia, T. cruzi I, the oldest and most widespread genetic lineage, is pervasive across a range of ecological clines. High‐resolution nuclear (26 loci) and mitochondrial (10 loci) genotyping of 199 contemporaneous sylvatic TcI clones was undertaken to provide insights into the biogeographical basis of T. cruzi evolution. Three distinct sylvatic parasite transmission cycles were identified: one highland population among terrestrial rodent and triatomine species, composed of genetically homogenous strains (A_r = 2.95; PA/L = 0.61; D_AS = 0.151), and two highly diverse, parasite assemblages circulating among predominantly arboreal mammals and vectors in the lowlands (A_r = 3.40 and 3.93; PA/L = 1.12 and 0.60; D_AS = 0.425 and 0.311, respectively). Very limited gene flow between neighbouring terrestrial highland and arboreal lowland areas (distance ~220 km; F_ST = 0.42 and 0.35) but strong connectivity between ecologically similar but geographically disparate terrestrial highland ecotopes (distance >465 km; F_ST = 0.016–0.084) strongly supports ecological host fitting as the predominant mechanism of parasite diversification. Dissimilar heterozygosity estimates (excess in highlands, deficit in lowlands) and mitochondrial introgression among lowland strains may indicate fundamental differences in mating strategies between populations. Finally, accelerated parasite dissemination between densely populated, highland areas, compared to uninhabited lowland foci, likely reflects passive, long‐range anthroponotic dispersal. The impact of humans on the risk of epizootic Chagas disease transmission in Bolivia is discussed.     

Polymorphic microsatellite loci for the trematode Diplostomum pseudospathaceum

We present primers for five polymorphic microsatellite loci in the eye fluke Diplostomum pseudospathaceum (Trematoda), a widely distributed parasite with a complex life cycle used as a model for parasitology and fish immunology. The loci were identified using a GA/CT‐enriched genomic library by subtractive hybridization with magnetic particles. All five loci were highly polymorphic, displaying 17 to 61 alleles and heterozygosities ranging from 0.53 to 0.92. We isolated populations of parasites within the first (snail) and second (fish) intermediate host and found small but significant genetic differentiation (F_ST = 0.012) between the two life stages of the parasite.     

Evidence for adaptive phenotypic differentiation in Baltic Sea sticklebacks

The evidence for adaptive phenotypic differentiation in mobile marine species remains scarce, partly due to the difficulty of obtaining quantitative genetic data to demonstrate the genetic basis of the observed phenotypic differentiation. Using a combination of phenotypic and molecular genetic approaches, we elucidated the relative roles of natural selection and genetic drift in explaining lateral plate number differentiation in threespine sticklebacks (Gasterosteus aculeatus) across the entire Baltic Sea basin (approximately 392 000 km²). We found that phenotypic differentiation (P_ST = 0.213) in plate number exceeded that in neutral markers (F_ST = 0.008), suggesting an adaptive basis for the observed differentiation. Because a close correspondence was found between plate phenotype and genotype at a quantitative trait loci (QTL; STN381) tightly linked to the gene (Ectodysplasin) underlying plate variation, the evidence for adaptive differentiation was confirmed by comparison of F_ST at the QTL (F_STQ = 0.089) with F_ST at neutral marker loci. Hence, the results provide a comprehensive demonstration of adaptive phenotypic differentiation in a high‐gene‐flow marine environment with direct, rather than inferred, verification for the genetic basis of this differentiation. In general, the results illustrate the utility of P_ST–F_ST–F_STQ comparisons in uncovering footprints of natural selection and evolution and add to the growing evidence for adaptive genetic differentiation in high‐gene‐flow marine environments, including that of the relatively young Baltic Sea.     

QST < FST As a signature of canalization

A key aim of evolutionary biology – inferring the action of natural selection on wild species – can be achieved by comparing neutral genetic differentiation between populations (F_ST) with quantitative genetic variation (Q_ST). Each of the three possible outcomes of comparisons of Q_ST and F_ST (Q_ST > F_ST, Q_ST = F_ST, Q_ST < F_ST) is associated with an inference (diversifying selection, genetic drift, uniform selection, respectively). However, published empirical and theoretical studies have focused on the Q_ST > F_ST outcome. We believe that this reflects the absence of a straightforward biological interpretation of the Q_ST < F_ST pattern. We here report recent evidence of this neglected evolutionary pattern, provide guidelines to its interpretation as either a canalization phenomenon or a consequence of uniform selection and discuss the significant importance this issue will have for the area of evolutionary biology.     

GENETIC DIFFERENTIATION AMONG CHEWING LOUSE POPULATIONS (MALLOPHAGA: TRICHODECTIDAE) IN A POCKET GOPHER CONTACT ZONE (RODENTIA: GEOMYIDAE)

Genetic variation among populations of chewing lice (Geomydoecus actuosi) was examined in relation to chromosomal and electrophoretic variation among populations of their hosts (Thomomys bottae) at a contact zone. Louse demes were characterized by low levels of genetic heterozygosity (H? = 0.039) that may result from founder effects during primary infestation of hosts, compounded by seasonal reductions in louse population size. Louse populations sampled from different hosts showed high levels of genetic structuring both within and among host localities. Microgeographic differentiation of louse populations is high (mean F_ST = 0.092) suggesting that properties of this host–parasite system promote differentiation of louse populations living on different individual hosts. Among-population differentiation in lice (F_ST = 0.240) was similar to that measured among host populations (F_ST = 0.236), suggesting a close association between gene flow in pocket gophers and gene flow in their lice.     

Genetic diversity of the black mangrove (Avicennia germinans L.) in Colombia

This study analyzed the genetic diversity and patterns of genetic structure in Colombian populations of Avicennia germinans L. using microsatellite loci. A lower genetic diversity was found on both the Caribbean (Ho = 0.439) and the Pacific coasts (Ho = 0.277) than reported for the same species in other locations of Central American Pacific, suggesting the deterioration of genetic diversity. All the populations showed high inbreeding coefficients (0.131–0.462) indicating heterozygotes deficience. The genetic structure between the Colombian coasts separated by Central American Isthmus was high (F_RT = 0.39) and the analyses of the genetic patterns of A. germinans revealed a clear differentiation of populations and no-recent gene flow evidence between coasts. Genetic structure was found within each coast (F_ST = 0.10 for the Caribbean coast and F_ST = 0.22 for the Pacific coast). The genetic patterns along the two coasts appear to reflect a forcing by local geomorphology and marine currents. Both coasts constitute a different Evolutionary Significant Unit, so we suggest for future transplantations plans that propagules or saplings of the populations of the Caribbean coast should not be mixed with those of the Pacific Colombian coast. Besides, we suggest that reforestation efforts should carefully distinguish propagules sources within each coast.     

Genetic diversity and differentiation of <Emphasis Type="Italic">Fagus orientalis</Emphasis> Lipsky in Hyrcanian forests revealed by nuclear and chloroplast microsatellite markers

Oriental beech (Fagus orientalis Lipsky) is a widespread monoecious and wind-pollinated tree species. It is one of the major components of the Hyrcanian forests of Iran and it is of both ecological and economical importance. Twelve beech stands were surveyed at 9 chloroplast (cp) and 6 nuclear (n) polymorphic microsatellite loci (simple sequence repeats, SSR) to provide information on distribution of genetic diversity within and among populations and on gene conservation and silvicultural management of this species. High levels of genetic differentiation were detected for the chloroplast genome (F _ST = 0.80 and R _ST = 0.95), in sharp contrast to the nuclear genome (F _ST = 0.06, R _ST = 0.05). The analysis of molecular variance (AMOVA) showed that 48% of the total cpSSR variation was attributable to differences among regions and 30% to differences among populations within regions, suggesting multiple origins of beech populations in Hyrcanian forests. Nuclear SSRs confirmed the presence of significant differentiation among populations and among geographic regions, even if, as expected, this was less pronounced than that found with cpSSRs (based on AMOVA, differences among regions and among populations within regions each contribute 5% to total nSSR variance). A highly significant correlation between genetic (nSSRs) and geographic distances (R ² = 0.522) was estimated, thus showing an isolation by distance effect. The application of spatial analysis of molecular variance (SAMOVA) using both marker data allowed identification of genetically homogeneous groups of populations. Possible applications of these results for the certification of provenances and/or seed lots and for designing conservation programs are presented and discussed.     

Differential introgression from a sister species explains high FST outlier loci within a mussel species

Scanning genomes for loci with high levels of population differentiation has become a standard of population genetics. F_ST outlier loci are most often interpreted as signatures of local selection, but outliers might arise for many other reasons too often left unexplored. Here, we tried to identify further the history and genetic basis underlying strong differentiation at F_ST outlier loci in a marine mussel. A genome scan of genetic differentiation has been conducted between Atlantic and Mediterranean populations of Mytilus galloprovincialis. The differentiation was low overall (F_ST = 0.03), but seven loci (2%) were strong F_ST outliers. We then analysed DNA sequence polymorphism at two outlier loci. The genetic structure proved to be the consequence of differential introgression of alleles from the sister‐hybridizing species Mytilus edulis. Surprisingly, the Mediterranean population was the most introgressed at these two loci, although the contact zone between the two species is nowadays localized along the Atlantic coasts of France and the British Isles. A historical contact between M. edulis and Mediterranean M. galloprovincialis should have happened during glacial periods. It proved difficult to disentangle two hypotheses: (i) introgression was adaptive, implying edulis alleles have been favoured in Mediterranean populations, or (ii) the genetic architecture of the barrier to edulis gene flow is different between the two M. galloprovincialis backgrounds. Five of the seven outliers between M. galloprovincialis populations were also outliers between M. edulis and Atlantic M. galloprovincialis, which would support the latter hypothesis. Differential introgression across semi‐permeable barriers to gene flow is a neglected scenario to interpret outlying loci that may prove more widespread than anticipated.     

Twelve polymorphic expressed sequence tags‐derived markers for Plasmopara halstedii,the causal agent of sunflower downy mildew

Twelve expressed sequence tags‐derived markers were isolated from Plasmopara halstedii (Oomycetes), the causal agent of sunflower downy mildew. A total of 25 single nucleotide polymorphisms and five indels were detected by single‐strand conformation polymorphism analysis and developed for high‐throughput genotyping of 32 isolates. There was a high level of genetic diversity (H_E = 0.484). Observed heterozygosity ranged from 0 to 0.143 indicating that P. halstedii is probably a selfing species. These markers were also useful in detecting significant genetic variations among French populations (F_ST = 0.193) and between French and Russian populations (F_ST = 0.23). Cross‐amplification tests on three closely related species indicated that no loci amplified in other Oomycete species.     

Conservation genetics of the endangered endemic Sambucus palmensis Link (Sambucaceae) from the Canary Islands

Five polymorphic microsatellites (simple sequence repeat; SSR) markers were used to estimate the levels of genetic variation within and among natural populations from different islands of the endangered endemic from the Canary Islands Sambucus palmensis Link (Sambucaceae). Genetic data were used to infer potential evolutionary processes that could have led to present genetic differentiation among islands. The levels of genetic variability of S. palmensis were considerably high; proportion of polymorphic loci (P = 100%), mean number of alleles per locus (A = 6.8), average expected heterozygosity (He = 0.499). In spite of its small population size and endemic character, 58 different multilocus genotypes were detected within the 165 individuals analyzed. All samples located in different islands always presented different multilocus genotypes. Principal Coordinates Analysis, genetic differentiation analysis (F _ST and G _ST ′) and Bayesian Cluster Analysis revealed significant genetic differences among populations located in different islands. However, this genetic differentiation was not recorded among Tenerife and La Gomera populations, possibly revealing the uncontrolled transfer of material between both islands. AMOVA analysis attributed 77% of the variance to differences within populations, whereas 8% was distributed between islands. The levels of genetic differentiation observed among populations, and the genetic diversity distribution within populations in S. palmensis, indicate that management should aim to conserve as many of the small populations as possible. Concentrating conservation efforts only on the few large populations would result in the likelihood of loss of genetic variability for the species.     

Low population genetic differentiation in the Orchidaceae: implications for the diversification of the family

A leading hypothesis for the immense diversity of the Orchidaceae is that skewed mating success and small, disjunct populations lead to strong genetic drift and switches between adaptive peaks. This mechanism is only possible under conditions of low gene flow that lead to high genetic differentiation among populations. We tested whether orchids typically exhibit high levels of population genetic differentiation by conducting a meta‐analysis to compare mean levels of population genetic differentiation (F_ST) between orchids and other diverse families and between rare and common orchids. Compared with other families, the Orchidaceae is typically characterized by relatively low genetic differentiation among populations (mean F_ST = 0.146) at allozyme loci. Rare terrestrial orchids showed higher population genetic differentiation than common orchids, although this value was still lower than the mean for most plant families. All lines of evidence suggest that orchids are typically characterized by low levels of population genetic differentiation, even in species with naturally disjunct populations. As such, we found no strong evidence that genetic drift in isolated populations has played a major role in the diversification of the Orchidaceae. Further research into the diversification of the family needs to unravel the relative roles of biotic and environmental selective pressures in the speciation of orchids.     

Genetic differentiation among European samples of the arctic‐alpine leaf beetle,Chrysomela lapponica

Genetic differentiation within and among isolated populations of the arctic‐alpine leaf beetle, Chrysomela lapponica L. (Coleoptera: Chrysomelidae), specialized on either Salix L. (Salicaceae) or Betula L. (Betulaceae) species, was assessed by F‐statistics analysis at seven allozyme loci. Beetles were collected on Salix spp. in lowland Finland (four samples), at mid elevation in the Black Forest in Germany (450 m) and the Massif Central in France (two samples, 930–1 300 m), and at high elevation in the French Alps (2 300 m). Beetles sampled in the Czech Republic (650 m) fed on Betula pubescens Ehrh. Larvae feeding on Salix spp. secreted host‐derived salicylaldehyde as major toxin; those feeding on B. pubescens secreted isobutyrates and 2‐methylbutyrates of mixed plant–insect origin. In all samples, a heterozygote deficit was observed (0.120<F_IS<0.568), in particular in populations collected at mid or high elevation (F_IS>0.4). The estimated mean level of genetic differentiation among all populations was high (F_ST = 0.276). Differentiation was highly variable between pairs of populations (F_ST = 0.093–0.455, all significant) without any correlation with geographic distance. The sample collected in the Czech Republic, from the only population on B. pubescens, was not the most divergent.     

Population genetic structure of the Korean threadsail filefish (Stephanolepis cirrhifer) based on microsatellite marker analysis

The threadsail filefish Stephanolepis cirrhifer is one of the most important commercial fish resources in Korea. However, its natural populations have declined drastically over the last several decades. To investigate the genetic characteristics of the threadsail filefish for conservation and management purposes, its genetic variation was analyzed in Korean fishing grounds using 11 microsatellite loci. All populations showed moderate genetic diversity (mean number of alleles (N_A) = 8.6, expected heterozygosity (He) = 0.73), representing a slightly lower level of genetic variability than other congeneric species. The presence of a weak genetic population substructure was detected (F_ST = 0.023, R_ST = 0.030, P < 0.001), but this substructure did not feature significant isolation based on the distance between populations. This differentiation may be primarily attributable to genetic differences between populations from Geomundo and other localities, based on relative low level of gene flow, a high level of pairwise F_ST and R_ST or the position of this population in a phylogenetic tree. An analysis of molecular variance (AMOVA) also revealed a greater part of the variation within the population and genetic differentiation among the samples analyzed and identified two genetic clusters. The possibility of a recent genetic bottleneck was observed in some populations of S. cirrhifer. Given the prevailing ocean currents and the intensity of threadsail filefish harvesting activities in Korea, the possibility that human harvest and stock enhancement activities may have partially contributed to our detected genetic pattern cannot be excluded. Management strategies that take these findings into account might lower the risk of harmful genetic change in the species.