Scenario Of Gene Flow Research Articles

Individual small in-stream barriers contribute little to strong local population genetic structure five strictly aquatic macroinvertebrate taxa.

Water flow in river networks is frequently regulated by man‐made in‐stream barriers. These obstacles can hinder dispersal of aquatic organisms and isolate populations leading to the loss of genetic diversity. Although millions of small in‐stream barriers exist worldwide, their impact on dispersal of macroinvertebrates remains unclear. Therefore, we, therefore, assessed the effects of such barriers on the population structure and effective dispersal of five macroinvertebrate species with strictly aquatic life cycles: the amphipod crustacean Gammarus fossarum (clade 11), three snail species of the Ancylus fluviatilis species complex and the flatworm Dugesia gonocephala. We studied populations at nine weirs and eight culverts (3 pipes, 5 tunnels), built 33–109 years ago, mainly in the heavily fragmented catchment of the river Ruhr (Sauerland, Germany). To assess fragmentation and barrier effects, we generated genome‐wide SNP data using ddRAD sequencing and evaluated clustering, differentiation between populations up‐ and downstream of each barrier and effective migration rates among sites and across barriers. Additionally, we applied population genomic simulations to assess expected differentiation patterns under different gene flow scenarios. Our data show that populations of all species are highly isolated at regional and local scales within few kilometers. While the regional population structure likely results from historical processes, the strong local differentiation suggests that contemporary dispersal barriers exist. However, we identified significant barrier effects only for pipes (for A. fluviatilis II and III) and few larger weirs (>1.3 m; for D. gonocephala). Therefore, our data suggest that most small in‐stream barriers can probably be overcome by all studied taxa frequently enough to prevent fragmentation. However, it remains to be tested if the strong local differentiation is a result of a cumulative effect of small barriers, or if larger in‐stream barriers, land use, chemical pollution, urbanization, or a combination of these factors impede gene flow.

Broadly Distributed but Genetically Fragmented: Demographic Consequences of Pleistocene Climatic Oscillations in a Common Iberian Grasshopper

Abstract Although the genetic consequences of contemporary landscape composition and range shifts driven Pleistocene climatic oscillations have been studied fairly well in alpine organisms, we know much less about how these factors have shaped the demography of taxa with broader climatic niches and distributions. Here, we use high-throughput sequencing data to study the processes underlying spatial patterns of genomic variation in Omocestus panteli (Bolívar, 1887) (Orthoptera: Acrididae), a common Iberian grasshopper distributed across numerous habitat types and a wide elevational range (from sea level to >2,000 m). Although the species is broadly distributed, our analyses support that its contemporary populations show significant genetic fragmentation that dates back to the last glacial period. Accordingly, spatially explicit testing of alternative gene flow scenarios and demographic inference analyses revealed that genetic differentiation between populations and their long-term effective population sizes are best explained by the spatial configuration of environmentally suitable habitats during the last glacial maximum (ca. 21 ka). At that time, the species experienced net demographic expansions but interspersed unsuitable areas might have disrupted gene flow and created opportunity for geographical diversification. Collectively, our analyses indicate that the genetic makeup of contemporary populations is not well explained by current environmental factors or geographical barriers to dispersal but mostly reflects genetic fragmentation during the last glacial period followed by postglacial admixture among previously isolated gene pools. Taken together, these results support that the Pleistocene ‘species pump’ model might be also useful in explaining demographic dynamics and geographical diversification in taxa characterized by broad climatic niches.

When are populations not connected like a circuit? Identifying biases in gene flow from coalescent times.

Connectivity and movement patterns of populations are influenced by past and present environmental and biotic factors, which are reflected in genetic relatedness among populations. Methods that estimate the "commute time" between populations based on electrical resistance (i.e., isolation-by-resistance [IBR]) have been widely applied to either infer movement patterns directly from environmental factors or detect possible barriers to gene flow given empirical genetic relatedness. Yet, the commute time is only equivalent to the coalescence time between populations under symmetric migration with isotropic landscapes. Asymmetric gene flow is relatively common when populations are expanding, retreating, or with source-sink dynamics. In a From the Cover paper in this issue of Molecular Ecology Resources, Lundgren and Ralph (Molecular Ecology Resources, 19, 2019) describe a Bayesian method to infer bidirectional gene flow rates and population sizes without the assumption of symmetry. The method shows great accuracy in connectivity estimations under symmetric, as well as asymmetric gene flow scenarios where resistance methods fail. However, computational complexity limits the method to a few populations, preventing its application to finescale environmental maps. Also, as a discrete-deme static model, the inferred differences in gene flow rates are sensitive to population discretization and cannot be directly used to differentiate among processes (e.g., past expansion vs. current barrier). Here, we discuss scenarios where the new method can best be utilized and provide potential directions to identify the underlying processes causing deviations in gene flow patterns.

Coalescent Theory of Migration Network Motifs

Natural populations display a variety of spatial arrangements, each potentially with a distinctive impact on genetic diversity and genetic differentiation among subpopulations. Although the spatial arrangement of populations can lead to intricate migration networks, theoretical developments have focused mainly on a small subset of such networks, emphasizing the island-migration and stepping-stone models. In this study, we investigate all small network motifs: the set of all possible migration networks among populations subdivided into at most four subpopulations. For each motif, we use coalescent theory to derive expectations for three quantities that describe genetic variation: nucleotide diversity, FST, and half-time to equilibrium diversity. We describe the impact of network properties on these quantities, finding that motifs with a high mean node degree have the largest nucleotide diversity and the longest time to equilibrium, whereas motifs with low density have the largest FST. In addition, we show that the motifs whose pattern of variation is most strongly influenced by loss of a connection or a subpopulation are those that can be split easily into disconnected components. We illustrate our results using two example data sets—sky island birds of genus Sholicola and Indian tigers—identifying disturbance scenarios that produce the greatest reduction in genetic diversity; for tigers, we also compare the benefits of two assisted gene flow scenarios. Our results have consequences for understanding the effect of geography on genetic diversity, and they can assist in designing strategies to alter population migration networks toward maximizing genetic variation in the context of conservation of endangered species.

The Origin and Population History of the Endangered Golden Snub-Nosed Monkey (Rhinopithecus roxellana).

The origin and population history of the endangered golden snub-nosed monkey (Rhinopithecus roxellana) remain largely unavailable and/or controversial. We here integrate analyses of multiple genomic markers, including mitochondrial (mt) genomes, Y-chromosomes, and autosomes of 54 golden monkey individuals from all three geographic populations (SG, QL, and SNJ). Our results reveal contrasting population structures. Mt analyses suggest a division of golden monkeys into five lineages: one in SNJ, two in SG, and two in QL. One of the SG lineages (a mixed SG/QL lineage) is basal to all other lineages. In contrast, autosomal analyses place SNJ as the most basal lineage and identify one QL and three SG lineages. Notably, Y-chromosome analyses bear features similar to mt analyses in placing the SG/QL-mixed lineage as the first diverging lineage and dividing SG into two lineages, while resembling autosomal analyses in identifying one QL lineage. We further find bidirectional gene flow among all three populations at autosomal loci, while asymmetric gene flow is suggested at mt genomes and Y-chromosomes. We propose that different population structures and gene flow scenarios are the result of sex-linked differences in the dispersal pattern of R. roxellana. Moreover, our demographic simulation analyses support an origin hypothesis suggesting that the ancestral R. roxellana population was once widespread and then divided into SNJ and non-SNJ (SG and QL) populations. This differs from previous mt-based "mono-origin (SG is the source population)" and "multiorigin (SG is a fusion of QL and SNJ)" hypotheses. We provide a detailed and refined scenario for the origin and population history of this endangered primate species, which has a broader significance for Chinese biogeography. In addition, this study highlights the importance to investigate multiple genomic markers with different modes of inheritance to trace the complete evolutionary history of a species, especially for those exhibiting differential or mixed patterns of sex dispersal.

Fuzzy species limits in Mediterranean gorgonians (Cnidaria, Octocorallia): inferences on speciation processes

The study of the interplay between speciation and hybridization is of primary importance in evolutionary biology. Octocorals are ecologically important species whose shallow phylogenetic relationships often remain to be studied. In the Mediterranean Sea, three congeneric octocorals can be observed in sympatry: Eunicella verrucosa, Eunicella cavolini and Eunicella singularis. They display morphological differences and E. singularis hosts photosynthetic Symbiodinium, contrary to the two other species. Two nuclear sequence markers were used to study speciation and gene flow between these species, through network analysis and Approximate Bayesian Computation (ABC). Shared sequences indicated the possibility of hybridization or incomplete lineage sorting. According to ABC, a scenario of gene flow through secondary contact was the best model to explain these results. At the intraspecific level, neither geographical nor ecological isolation corresponded to distinct genetic lineages in E. cavolini. These results are discussed in the light of the potential role of ecology and genetic incompatibilities in the persistence of species limits.

Extreme mitochondrial variation in the Atlantic gall crab Opecarcinus hypostegus (Decapoda: Cryptochiridae) reveals adaptive genetic divergence over Agaricia coral hosts

The effectiveness of migration in marine species exhibiting a pelagic larval stage is determined by various factors, such as ocean currents, pelagic larval stage duration and active habitat selection. Direct measurement of larval movements is difficult and, consequently, factors determining the gene flow patterns remain poorly understood for many species. Patterns of gene flow play a key role in maintaining genetic homogeneity in a species by dampening the effects of local adaptation. Coral-dwelling gall crabs (Cryptochiridae) are obligate symbionts of stony corals (Scleractinia). Preliminary data showed high genetic diversity on the COI gene for 19 Opecarcinus hypostegus specimens collected off Curaçao. In this study, an additional 176 specimens were sequenced and used to characterize the population structure along the leeward side of Curaçao. Extremely high COI genetic variation was observed, with 146 polymorphic sites and 187 unique haplotypes. To determine the cause of this high genetic diversity, various gene flow scenarios (geographical distance along the coast, genetic partitioning over depth, and genetic differentiation by coral host) were examined. Adaptive genetic divergence across Agariciidae host species is suggested to be the main cause for the observed high intra-specific variance, hypothesised as early signs of speciation in O. hypostegus.

Application of PE-RADSeq to the study of genomic diversity and divergence of two Brazilian marmoset species (Callithrix jacchus and C. penicillata).

Callithrix jacchus and C. penicillata are among the smallest anthropoid primates, are highly specialized tree gougers, and largely occupy Brazil's most extreme, semi-arid biomes. However, the underlying genomic factors that underpin the evolution of these species and their unique traits are under-investigated. Additionally, exotic populations of these two species are widely established throughout Brazil and hybridize with threatened native congers. Thus, both genomic and conservation factors call for a better understanding of C. jacchus and C. penicillata evolution. Here, we applied PE-RADseq to characterize genomic variation in these two species, using six C. jacchus and seven C. penicillata individuals. We identified an average of 7,463 and 5,180 SNPs/individual in C. penicillata and C. jacchus, respectively, and also found 1,395 variable sites that were represented in both species. C. penicillata showed overall higher levels of genetic diversity than C. jacchus at the variable sites present in both species. Additionally, among these variable sites, 106 showed relative interspecific divergence levels that were significantly higher than the genome-wide average. We further compared relative and absolute divergence for C. penicillata and C. jacchus between RAD loci associated with the 106 significantly diverged variable sites and all other RAD loci present in both species. The former RAD loci set showed significantly elevated relative and absolute divergence measures in comparison to the latter set. This convergence suggests that C. jacchus and C. penicillata may have diverged under a scenario of gene flow under secondary contact. Here, we demonstrate that RADseq is an efficient method to simultaneously discover and genotype a large number of markers and validate the utility of RADseq for examining Callithrix evolution.

Jackknife resampling for precision measurement of direct gene flow estimates

Gene flow from outside pollen sources reduces the expected genetic gain of seed orchards, and has been quantified by genotyping seed samples from crop years to determine the proportion of seed sired by outside sources. Random bulk seed sampling and microsatellite genotyping allows for fast, unbiased identification of orchard contamination rates. Bulk seed sampling has been employed in multiple studies of seed orchard gene flow, but a method of determining precision of gene flow estimates from this sampling method has yet to be described. In this study, we used jackknife resampling to generate random samples of migrant and within-population genotypes obtained from an empirical sample of Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) genotypes of five microsatellite loci. We generated samples of 50, 100, 150, 200, and 250 genotyped individuals from a sample of 400 seeds, with genotypes corresponding to low (6%), moderate (14%), or high (56%) pollen contamination levels. The mean gene flow estimate and confidence interval were calculated for each sample size and gene flow scenario to determine the precision of gene flow estimates obtained from each sample size in each contaminant gene flow scenario. Genotyping 150 individuals was sufficient to produce gene flow estimates with calculated confidence interval values below ± 1%, indicating that 150 genotyped individuals were sufficient for precise gene flow estimation in this population. This resampling method will enable precise and unbiased estimation of gene flow into seed orchards for future monitoring of gene flow, to allow better management of seed orchard genetic resources.

Refugial isolation and divergence in the Narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data

Glacial-interglacial cycles of the Pleistocene are hypothesized as one of the foremost contributors to biological diversification. This is especially true for cold-adapted montane species, where range shifts have had a pronounced effect on population-level divergence. Gartersnakes of the Thamnophis rufipunctatus species complex are restricted to cold headwater streams in the highlands of the Sierra Madre Occidental and southwestern USA. We used coalescent and multilocus phylogenetic approaches to test whether genetic diversification of this montane-restricted species complex is consistent with two prevailing models of range fluctuation for species affected by Pleistocene climate changes. Our concatenated nuDNA and multilocus species analyses recovered evidence for the persistence of multiple lineages that are restricted geographically, despite a mtDNA signature consistent with either more recent connectivity (and introgression) or recent expansion (and incomplete lineage sorting). Divergence times estimated using a relaxed molecular clock and fossil calibrations fall within the Late Pleistocene, and zero gene flow scenarios among current geographically isolated lineages could not be rejected. These results suggest that increased climate shifts in the Late Pleistocene have driven diversification and current range retraction patterns and that the differences between markers reflect the stochasticity of gene lineages (i.e. ancestral polymorphism) rather than gene flow and introgression. These results have important implications for the conservation of T.rufipunctatus (sensu novo), which is restricted to two drainage systems in the southwestern US and has undergone a recent and dramatic decline.

Making inferences about speciation using sophisticated statistical genetics methods: look before you leap

Understanding speciation is a fundamental aim of evolutionary biology and a very challenging one. Speciation can be viewed as the dynamics of genetic differentiation between populations resulting in substantial reproductive isolation (Gavrilets 2003). It was generally accepted that very small levels of migration prevent genetic differentiation among populations and, therefore, speciation. However, recent theoretical work showed that sympatric speciation is possible (Gavrilets 2003). Nevertheless, providing empirical evidence that gene flow occurred during speciation is challenging because several gene flow scenarios can explain observed patterns of genetic differentiation. Positive migration rate estimates alone do not prove ongoing gene flow during divergence. We also need to know whether migration took place before, during or after speciation. There is no statistical method specifically aimed at estimating gene flow timing, but several studies used the isolation with migration model (Hey & Nielsen 2004, 2007; Hey 2010b) to estimate this parameter and make inferences about speciation scenarios. It is tempting to use statistical methods to estimate important evolutionary parameters even if they do not appear explicitly in the inference model. Nevertheless, before doing so, we need to determine whether they can provide reliable results. In this issue of Molecular Ecology, Strasburg and Rieseberg (2011) present a simulation study that examines the degree to which gene flow timing estimates obtained from IMa2 (Hey 2010b) can be used to make inferences about speciation mode. Their results are sobering; gene flow timing estimates obtained in this way are not reliable and cannot be used to unequivocally establish if gene flow was ongoing during speciation.

Genetic diversity of the endangered Brazilian endemic herb Cunila menthoides Benth. (Lamiaceae) and its implications for conservation

Cunila menthoides is classified as a xylopodiferous subshrub found in fragmented environments threatened by local agriculture and pasture activities. The species presents strong and pleasant smell, and is commonly used in south Brazilian folk medicine. Based on the species’ medicinal and aromatic potential, the aim of this work was to examine the genetic variation within and among C. menthoides populations, focusing on the conservation of this species. In this context, six C. menthoides populations collected in Rio Grande do Sul, Brazil, were analyzed by ISSR. The populations were sorted as four clusters according to geographic distribution. The six C. menthoides populations analyzed presented low genetic variability, indicating that each population derives from a limited number of plants in a low gene flow scenario. In situ and ex situ conservation approaches may be useful in this species. Conservation strategies for the species should be based on in situ and ex situ approaches.

Erratum

Molecular EcologyVolume 18, Issue 11 p. 2543-2543 Free Access Erratum First published: 22 May 2009 https://doi.org/10.1111/j.1365-294X.2009.04230.xAboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat In Saenz-Agudelo et al. (2009), the wrong version of Fig. 3 was published. Please see the correct version below. Fig. 3 Parentage analysis results using FAMOZ software. (A) Number of juveniles assigned in Bootless Bay when the test was carried out using genotypes from Bootless Bay excluding Taurama (B-T), Bootless Bay all sites (B) and Bootless Bay and Schumann Island (B + S). Columns show assignments divided in to five categories: (i) juveniles assigned when test was carried out excluding Taurama B-T (white fill); (ii) juveniles reassigned within the four previous sites when Taurama was included (B) (light grey fill); (iii) new juveniles assigned to/from Taurama (dark grey fill); (iv) new assignments within the four sites data set that were not reassigned when Taurama was included in the test (dashed fill); (v) juveniles from Schumann Island assigned to Bootless Bay (black fill). (B) Juveniles assigned when the test was carried out using genotypes from Schumann Island alone (S), and Schumann Island and Bootless Bay (S + B). (i) Juveniles assigned when test was carried out only with S (white fill); (ii) juveniles reassigned within S when Bootless Bay was included (light grey fill); (iii) new assignments within Schumann that were not assigned in test S (dashed fill); (iv) juveniles from Bootless Bay assigned to Schumann Island (black fill). We apologise for this error. Reference Saenz-Agudelo P, Jones GP, Thorrold SR, Planes S (2009) Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios. Molecular Ecology, 18, 1765– 1776. Wiley Online LibraryCASPubMedWeb of Science®Google Scholar Volume18, Issue11June 2009Pages 2543-2543 ReferencesRelatedInformation

Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios

The application of spatially explicit models of population dynamics to fisheries management and the design marine reserve network systems has been limited due to a lack of empirical estimates of larval dispersal. Here we compared assignment tests and parentage analysis for examining larval retention and connectivity under two different gene flow scenarios using panda clownfish (Amphiprion polymnus) in Papua New Guinea. A metapopulation of panda clownfish in Bootless Bay with little or no genetic differentiation among five spatially discrete locations separated by 2-6 km provided the high gene flow scenario. The low gene flow scenario compared the Bootless Bay metapopulation with a genetically distinct population (F(ST )= 0.1) located at Schumann Island, New Britain, 1500 km to the northeast. We used assignment tests and parentage analysis based on microsatellite DNA data to identify natal origins of 177 juveniles in Bootless Bay and 73 juveniles at Schumann Island. At low rates of gene flow, assignment tests correctly classified juveniles to their source population. On the other hand, parentage analysis led to an overestimate of self-recruitment within the two populations due to the significant deviation from panmixia when both populations were pooled. At high gene flow (within Bootless Bay), assignment tests underestimated self-recruitment and connectivity among subpopulations, and grossly overestimated self-recruitment within the overall metapopulation. However, the assignment tests did identify immigrants from distant (genetically distinct) populations. Parentage analysis clearly provided the most accurate estimates of connectivity in situations of high gene flow.

Gene flow scenarios with transgenic maize in Mexico

Maize diversity is widespread in Mexico and it has been stewarded by campesinos in small communities until the present. With the arrival of transgenic maize, the objective of this study is to analyze possible scenarios that could result if genetically modified maize were not regulated and openly available in Mexico. By applying a simple logistic model based on the conditions of maize production in Mexico, the dispersion of transgenic maize in different situations within fields of farmers is described. In traditional open systems of freely exchanged seed within communities it is concluded that the most likely outcome of GM maize release is the incorporation of transgenes in the genome of Mexican germplasm and possibly in that of teosinte.

Cryptic speciation in a high gene flow scenario in the oviparous marine sponge Chondrosia reniformis

Sponge systematics has been traditionally based on the study of the skeleton (spicules and spongin fibres). However, sponges of the genus Chondrosia are devoid of those skeletal features, making it difficult to distinguish between different species in the genus. Chondrosia reniformis Nardo, 1847, the type species of the genus, was described from the Mediterranean Sea. The lack of distinguishing morphological features may have been responsible for the widespread assignment of specimens of the genus to this species; as a result C. reniformis is considered to be a cosmopolitan species. In this work, populations of C. reniformis from the western Mediterranean (France) and the West Atlantic (Bermuda and Brazil) were analysed using allozyme electrophoresis for 13 enzyme loci. Levels of mean heterozygosity were high (Bermuda and Brazil H=0.27 and W Mediterranean H=0.12), as is often observed in sponge species. Gene identities observed between West Atlantic and Mediterranean populations were low (I=0.40–0.52, typical values for congeneric species), including the presence of four diagnostic loci. This level of divergence clearly shows that they are not conspecific. Hence, a worldwide or cosmopolitan distribution of C. reniformis would seem improbable. However, the West Atlantic samples (Bermuda and Brazil) were genetically similar (gene identity, I=0.88–0.95) over a distance of 8,000 km. This is the first report of genetic homogeneity in a sponge species over such a large geographical distance.