Genomic assessment reveals signal of adaptive selection in populations of the Spotted rose snapper Lutjanus guttatus from the Tropical Eastern Pacific.

Background: The lack of barriers in the marine environment has promoted the idea of panmixia in marine organisms. However, oceanographic conditions and habitat characteristics have recently been linked to genetic structure in marine species. The Tropical Eastern Pacific (TEP) is characterized by dynamic current systems and heterogeneous oceanographic conditions. The Gulf of Panama (part of the equatorial segment for the TEP) is influenced by a complex current system and heterogeneous environment, which has been shown to limit the gene flow for shoreline species. Next Generation Sequencing (NGS) has contributed to detect genetic differences in previously reported panmictic species by the assessment of loci associated with selection and to understand how selection acts affects marine populations. Lutjanus guttatus is a species distributed in the TEP for which previous studies using mitochondrial data recovered a panmictic pattern along its distributional range. In this study, we used SNP data of L. guttatus individuals sampled along its range to evaluate population genetic structure and investigate whether oceanographic factors influence the species' genetic architecture. Finally, we assessed the role of adaptive selection by evaluating the contribution of outlier and neutral loci to genetic divergence. Methods: The RADcap method was used to obtain 24 million paired reads for 123 individuals of L. guttatus covering nearly all its distributional area. Genetic variation was assessed using both spatial and non-spatial methods by comparing three different data sets: (i) a Combined Loci (CL dataset = 2003 SNPs); a search for putative loci under selection allowed the evaluation of (ii) Neutral Loci (NL dataset = 1858 SNPs) and (iii) Outlier Loci (OL dataset = 145 SNPs). We used the estimating effective migration surface (EEMS) approach to detect possible barriers to gene flow. Results: Genetic differences were found in the OL dataset, showing two clusters (Northern and Southern), whereas NL showed no differences. This result may be related to the Selection-Migration balance model. The limit between the Northern and Southern groups was in the Gulf of Panama, which has been previously identified as a barrier to gene flow for other species, mainly due to its heterogeneous oceanographic conditions. The results suggest that selection plays an important role in generating genetic differences in Lutjanus guttatus. A migration corridor was detected that coincides with the Costa Rica Coastal Current that flows from Central America to the Gulf of California, allowing the homogenization of the northern population. In the Southern cluster, a migration corridor was observed with the OL from Panama to Colombia, which could be associated with the currents found in the Gulf of Panama. Genetic variation found in the OL of Lutjanus guttatus highlights the usefulness of NGS data in evaluating the role of selection in population differentiation.

Assessment of potential impacts associated with gene flow from transgenic hybrids to Mexican maize landraces.

Genetically modified (GM) maize has been grown and safely consumed on a global scale since its commercialization in 1996. However, questions have been raised about the potential impact that GM maize could have on native maize landraces in Mexico, which is the center of origin and diversity of maize. This research was conducted to evaluate potential changes to maize landraces in an unlikely event of transgene introgression. For this study, two GM traits that confer insect protection and herbicide tolerance in maize (MON 89034 and MON 88017), designated as VT3Pro, were introgressed into two Mexican landraces, Tuxpeño and Tabloncillo. Field trials were conducted across four environments to assess phenotypic characteristics, plant response to stressors, and kernel composition of landraces with and without VT3Pro traits. Furthermore, materials from four backcrossing generations were analyzed for segregation of these GM traits. Generally, no significant differences were observed between landraces with and without VT3Pro traits for the evaluated characteristics and the segregation analysis showed that GM traits, when introgressed into landraces, followed Mendelian principles. These results support the conclusion that, if inadvertently introgressed into landraces, VT3Pro traits are not expected to alter phenotypic or kernel characteristics, plant response to stressors (except for targeted insect protection and herbicide tolerance traits) and would segregate like any endogenous gene. These results should be taken into consideration when discussing benefits and risks associated with commercial production of GM maize hybrids in the centers of origin and diversity of maize.

Assessment of the potential for gene flow from transgenic maize (Zea mays L.) to eastern gamagrass (Tripsacum dactyloides L.).

Eastern gamagrass (Tripsacum dactyloides L.) belongs to the same tribe of the Poaceae family as maize (Zea mays L.) and grows naturally in the same region where maize is commercially produced in the USA. Although no evidence exists of gene flow from maize to eastern gamagrass in nature, experimental crosses between the two species were produced using specific techniques. As part of environmental risk assessment, the possibility of transgene flow from maize to eastern gamagrass populations in nature was evaluated with the objectives: (1) to assess the seeds of eastern gamagrass populations naturally growing near commercial maize fields for the presence of a transgenic glyphosate-tolerance gene (cp4 epsps) that would indicate cross-pollination between the two species, and (2) to evaluate the possibility of interspecific hybridization between transgenic maize used as male parent and eastern gamagrass used as female parent. A total of 46,643 seeds from 54 eastern gamagrass populations collected in proximity of maize fields in Illinois, USA were planted in a field in 2014 and 2015. Emerged seedlings were treated with glyphosate herbicide and assessed for survival. An additional 48,000 seeds from the same 54 eastern gamagrass populations were tested for the presence of the cp4 epsps transgene markers using TaqMan® PCR method. The results from these trials showed that no seedlings survived the herbicide treatment and no seed indicated presence of the herbicide tolerant cp4 epsps transgene, even though these eastern gamagrass populations were exposed to glyphosate-tolerant maize pollen for years. Furthermore, no interspecific hybrid seeds were produced from 135 hand-pollination attempts involving 1529 eastern gamagrass spikelets exposed to maize pollen. Together, these results indicate that there is no evidence of gene flow from maize to eastern gamagrass in natural habitats. The outcome of this study should be taken in consideration when assessing for environmental risks regarding the consequence of gene flow from transgenic maize to its wild relatives.

The relationship between least-cost and resistance distance.

Least-cost modelling and circuit theory are common analogs used in ecology and evolution to model gene flow or animal movement across landscapes. Least-cost modelling estimates the least-cost distance, whereas circuit theory estimates resistance distance. The bias added in choosing one method over the other has not been well documented. We designed an experiment to test whether both methods were linearly related. We also tested the sensitivity of these metrics to variation in Euclidean distance, spatial autocorrelation, the number of pixels representing the landscape, and data aggregation. We found that least-cost and resistance distance were not linearly related unless a transformation was applied. Resistance distance was less sensitive to the number of pixels representing a landscape and was also less sensitive than least-cost distance to the Euclidean distance between nodes. Spatial autocorrelation did not affect either method or the relationship between methods. Resistance distance was more sensitive to aggregation in any form compared to least-cost distance. Therefore, the metric used to infer movement or gene flow and the manipulations applied to the data used to calculate these metrics may govern findings.

Efficient computation in the IM model.

In this paper we analyze the isolation-with-migration model in a continuous-time Markov chain framework, and derive analytical expressions for the probability densities of gene tree topologies with an arbitrary number of lineages. We combine these densities with both nucleotide-substitution and infinite sites mutation models and derive probabilities for use in maximum likelihood estimation. We demonstrate how to apply lumpability of continuous-time Markov chains to achieve a significant reduction in the size of the state-space under consideration. We use matrix exponentiation and spectral decomposition to derive explicit expressions for the case of two diploid individuals in two populations, when the data is given as alignment columns. We implement these expressions in order to carry out a maximum likelihood analysis and provide a simulation study to examine the performance of our method in terms of our ability to recover true parameters. Finally, we show how the performance depends on the parameters in the model.

Dissimilarity of contemporary and historical gene flow in a wild carrot (Daucus carota) metapopulation under contrasting levels of human disturbance: implications for risk assessment and management of transgene introgression.

BACKGROUND AND AIMS: Transgene introgression from crops into wild relatives may increase the resistance of wild plants to herbicides, insects, etc. The chance of transgene introgression depends not only on the rate of hybridization and the establishment of hybrids in local wild populations, but also on the metapopulation dynamics of the wild relative. The aim of the study was to estimate gene flow in a metapopulation for assessing and managing the risks of transgene introgression. METHODS: Wild carrots (Daucus carota) were sampled from 12 patches in a metapopulation. Eleven microsatellites were used to genotype wild carrots. Genetic structure was estimated based on the FST statistic. Contemporary (over the last several generations) and historical (over many generations) gene flow was estimated with assignment and coalescent methods, respectively. KEY RESULTS: The genetic structure in the wild carrot metapopulation was moderate (FST = 0·082) and most of the genetic variation resided within patches. A pattern of isolation by distance was detected, suggesting that most of the gene flow occurred between neighbouring patches (≤1 km). The mean contemporary gene flow was 5 times higher than the historical estimate, and the correlation between them was very low. Moreover, the contemporary gene flow in roadsides was twice that in a nature reserve, and the correlation between contemporary and historical estimates was much higher in the nature reserve. Mowing of roadsides may contribute to the increase in contemporary gene flow. Simulations demonstrated that the higher contemporary gene flow could accelerate the process of transgene introgression in the metapopulation. CONCLUSIONS: Human disturbance such as mowing may alter gene flow patterns in wild populations, affecting the metapopulation dynamics of wild plants and the processes of transgene introgression in the metapopulation. The risk assessment and management of transgene introgression and the control of weeds need to take metapopulation dynamics into consideration.

Assessment of genetic diversity in the sorghum reference set using EST-SSR markers.

Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. In the present study, a reference set representing a wide range of sorghum genetic diversity was screened with 40 EST-SSR markers to validate both the use of these markers for genetic structure analyses and the population structure of this set. Grouping of accessions is identical in distance-based and model-based clustering methods. Genotypes were grouped primarily based on race within the geographic origins. Accessions derived from the African continent contributed 88.6 % of alleles confirming the African origin of sorghum. In total, 360 alleles were detected in the reference set with an average of 9 alleles per marker. The average PIC value was 0.5230 with a range of 0.1379-0.9483. Sub-race, guinea margaritiferum (Gma) from West Africa formed a separate cluster in close proximity to wild accessions suggesting that the Gma group represents an independent domestication event. Guineas from India and Western Africa formed two distinct clusters. Accessions belongs to the kafir race formed the most homogeneous group as observed in earlier studies. This analysis suggests that the EST-SSR markers used in the present study have greater discriminating power than the genomic SSRs. Genetic variance within the subpopulations was very high (71.7 %) suggesting that the germplasm lines included in the set are more diverse. Thus, this reference set representing the global germplasm is an ideal material for the breeding community, serving as a community resource for trait-specific allele mining as well as genome-wide association mapping.

Marked population structure and recent migration in the critically endangered Sumatran orangutan (Pongo abelii).

A multitude of factors influence how natural populations are genetically structured, including dispersal barriers, inhomogeneous habitats, and social organization. Such population subdivision is of special concern in endangered species, as it may lead to reduced adaptive potential and inbreeding in local subpopulations, thus increasing the risk of future extinctions. With only 6600 animals left in the wild, Sumatran orangutans (Pongo abelii) are among the most endangered, but also most enigmatic, great ape species. In order to infer the fine-scale population structure and connectivity of Sumatran orangutans, we analyzed the most comprehensive set of samples to date, including mitochondrial hyper-variable region I haplotypes for 123 individuals and genotypes of 27 autosomal microsatellite markers for 109 individuals. For both mitochondrial and autosomal markers, we found a pronounced population structure, caused by major rivers, mountain ridges, and the Toba caldera. We found that genetic diversity and corresponding long-term effective population size estimates vary strongly among sampling regions for mitochondrial DNA, but show remarkable similarity for autosomal markers, hinting at male-driven long-distance gene flow. In support of this, we identified several individuals that were most likely sired by males originating from other genetic clusters. Our results highlight the effect of natural barriers in shaping the genetic structure of great ape populations, but also point toward important dispersal corridors on northern Sumatra that allow for genetic exchange.

The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes.

The idea that molecular data should contain information on the recent evolutionary history of populations is rather old. However, much of the work carried out today owes to the work of the statisticians and theoreticians who demonstrated that it was possible to detect departures from equilibrium conditions (e.g., panmictic population/mutation-drift equilibrium) and interpret them in terms of deviations from neutrality or stationarity. During the last 20 years the detection of population size changes has usually been carried out under the assumption that samples were obtained from populations that can be approximated by a Wright-Fisher model (i.e., assuming panmixia, demographic stationarity, etc.). However, natural populations are usually part of spatial networks and are interconnected through gene flow. Here we simulated genetic data at mutation and migration-drift equilibrium under an n-island and a stepping-stone model. The simulated populations were thus stationary and not subject to any population size change. We varied the level of gene flow between populations and the scaled mutation rate. We also used several sampling schemes. We then analyzed the simulated samples using the Bayesian method implemented in MSVAR, the Markov Chain Monte Carlo simulation program, to detect and quantify putative population size changes using microsatellite data. Our results show that all three factors (genetic differentiation/gene flow, genetic diversity, and the sampling scheme) play a role in generating false bottleneck signals. We also suggest an ad hoc method to counter this effect. The confounding effect of population structure and of the sampling scheme has practical implications for many conservation studies. Indeed, if population structure is creating "spurious" bottleneck signals, the interpretation of bottleneck signals from genetic data might be less straightforward than it would seem, and several studies may have overestimated or incorrectly detected bottlenecks in endangered species.

Effects of colonization asymmetries on metapopulation persistence.

Ocean currents, prevailing winds, and the hierarchical structures of river networks are known to create asymmetries in re-colonization between habitat patches. The impacts of such asymmetries on metapopulation persistence are seldom considered, especially rarely in theoretical studies. Considering three classical models (the island, the stepping stone and the distance-dependent model), we explore how metapopulation persistence is affected by (i) asymmetry in dispersal strength, in which the colonization rate between two patches differs in direction, and (ii) asymmetry in connectivity, in which the overall colonization pattern displays asymmetry (circulating or dendritic networks). Viability can be drastically reduced when directional bias in dispersal strength is higher than 25%. Re-colonization patterns that allow for strong local connectivity provide the highest persistence compared to systems that allow circulation. Finally, asymmetry has relatively weak effects when metapopulations maintain strong general connectivity.

How can tsetse population genetics contribute to African trypanosomiasis control?

In sub-Saharan Africa, tsetse transmitted Trypanosomiases have an enormous impact on human health and economic development. Both the World Health Organisation and African countries through the Pan African Tsetse and Trypanosomiasis Eradication Campaign (PATTEC) have recently asserted their determination to rid the sub-continent of these diseases, and it is increasingly recognised that vector control should play an important role. This review mainly focuses on population genetics of tsetse of the palpalis group, the main vectors of sleeping sickness, and reports recent results on tsetse population structure and on measures of gene flow between populations. Implications of these studies for large-scale tsetse control programmes being undertaken in West Africa are important, particularly regarding control strategies (suppression or eradication).

Modelling pollen-mediated gene flow in rice: risk assessment and management of transgene escape.

Fast development and commercialization of genetically modified plants have aroused concerns of transgene escape and its environmental consequences. A model that can effectively predict pollen-mediated gene flow (PMGF) is essential for assessing and managing risks from transgene escape. A pollen-trap method was used to measure the wind-borne pollen dispersal in cultivated rice and common wild rice, and effects of relative humidity, temperature and wind speed on pollen dispersal were estimated. A PMGF model was constructed based on the pollen dispersal pattern in rice, taking outcrossing rates of recipients and cross-compatibility between rice and its wild relatives into consideration. Published rice gene flow data were used to validate the model. Pollen density decreased in a simple exponential pattern with distances to the rice field. High relative humidity reduced pollen dispersal distances. Model simulation showed an increased PMGF frequency with the increase of pollen source size (the area of a rice field), but this effect levelled off with a large pollen-source size. Cross-compatibility is essential when modelling PMGF from rice to its wild relatives. The model fits the data well, including PMGF from rice to its wild relatives. Therefore, it can be used to predict PMGF in rice under diverse conditions (e.g. different outcrossing rates and cross-compatibilities), facilitating the determination of isolation distances to minimize transgene escape. The PMGF model may be extended to other wind-pollinated plant species such as wheat and barley.

Genetic evidence for female-biased dispersal and gene flow in a polygynous primate.

Many models of sex-biased dispersal predict that the direction of sex-bias depends upon a species' mating system. In agreement with this, almost all polygynous mammals show male-biased dispersal whereas largely monogamous birds show female-biased dispersal (FBD). The hamadryas baboon (Papio hamadryas hamadryas) is polygynous and so dispersal is predicted to be male biased, as is found in all other baboon subspecies, but there are conflicting field data showing both female and male dispersal. Using 19 autosomal genetic markers genotyped in baboons from four Saudi Arabian populations, we found strong evidence for FBD in post-dispersal adults but not, as expected, in pre-dispersal infants and young juveniles, when we compared male and female: population structure (F(st)), inbreeding (F(is)), relatedness (r), and the mean assignment index (mAIc). Furthermore, we found evidence for female-biased gene flow as population genetic structure (F(st)), was about four times higher for the paternally inherited Y, than for either autosomal markers or for maternally inherited mtDNA. These results contradict the direction of sex-bias predicted by the mating system and show that FBD has evolved recently from an ancestral state of male-biased dispersal. We suggest that the cost-benefit balance of dispersal to males and females is tightly linked to the unique hierarchical social structure of hamadryas baboons and that dispersal and social organization have coevolved.