Behavioural vs. molecular sources of conflict between nuclear and mitochondrial DNA: the role of male-biased dispersal in a Holarctic sea duck

Genetic studies of waterfowl (Anatidae) have observed the full spectrum of mitochondrial (mt) DNA population divergence, from apparent panmixia to deep, reciprocally monophyletic lineages. Yet, these studies often found weak or no nuclear (nu) DNA structure, which was often attributed to male‐biased gene flow, a common behaviour within this family. An alternative explanation for this ‘conflict’ is that the smaller effective population size and faster sorting rate of mtDNA relative to nuDNA lead to different signals of population structure. We tested these alternatives by sequencing 12 nuDNA introns for a Holarctic pair of waterfowl subspecies, the European goosander (Mergus merganser merganser) and the North American common merganser (M. m. americanus), which exhibit strong population structure in mtDNA. We inferred effective population sizes, gene flow and divergence times from published mtDNA sequences and simulated expected differentiation for nuDNA based on those histories. Between Europe and North America, nuDNA Ф_ST was 3.4‐fold lower than mtDNA Ф_ST, a result consistent with differences in sorting rates. However, despite geographically structured and monophyletic mtDNA lineages within continents, nuDNA Ф_ST values were generally zero and significantly lower than predicted. This between‐ and within‐continent contrast held when comparing mtDNA and nuDNA among published studies of ducks. Thus, male‐mediated gene flow is a better explanation than slower sorting rates for limited nuDNA differentiation within continents, which is also supported by nonmolecular data. This study illustrates the value of quantitatively testing discrepancies between mtDNA and nuDNA to reject the null hypothesis that conflict simply reflects different sorting rates.     

Going with the flow: the role of ocean circulation in global marine ecosystems under a changing climate

Ocean warming, acidification, deoxygenation and reduced productivity are widely considered to be the major stressors to ocean ecosystems induced by emissions of CO₂. However, an overlooked stressor is the change in ocean circulation in response to climate change. Strong changes in the intensity and position of the western boundary currents have already been observed, and the consequences of such changes for ecosystems are beginning to emerge. In this study, we address climatically induced changes in ocean circulation on a global scale but relevant to propagule dispersal for species inhabiting global shelf ecosystems, using a high‐resolution global ocean model run under the IPCC RCP 8.5 scenario. The ¼ degree model resolution allows improved regional realism of the ocean circulation beyond that of available CMIP5‐class models. We use a Lagrangian approach forced by modelled ocean circulation to simulate the circulation pathways that disperse planktonic life stages. Based on trajectory backtracking, we identify present‐day coastal retention, dominant flow and dispersal range for coastal regions at the global scale. Projecting into the future, we identify areas of the strongest projected circulation change and present regional examples with the most significant modifications in their dominant pathways. Climatically induced changes in ocean circulation should be considered as an additional stressor of marine ecosystems in a similar way to ocean warming or acidification.     

Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii)

By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards ( Chlamydosaurus kingii ) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark–recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.     

转基因植物与近缘种之间基因流的研究进展

随着转基因植物的大面积种植,转基因植物的生态风险受到广泛关注,其中主要的风险是转基因植物与近缘物种之间的基因流及其影响。本文综述了目前商业化种植的转基因作物油菜、棉花、玉米和大豆,以及未商业化种植的水稻、小麦的基因流研究进展;分析了不同转基因作物与其近缘种之间发生基因流的频率和最远发生距离;介绍了降低基因流发生的方法。基因流频率受物种亲缘关系、花期重叠时间、风速风向等因素的影响,最远发生距离受气候条件、传粉媒介、地理条件等因素的影响。转基因作物与其近缘种之间的基因流频率与距花粉源的距离呈负相关关系(y=-0.59x-0.46,R²=0.25,P<0.01),亲缘关系近的基因流频率高。为了降低转基因植物与其近缘物种之间的基因流风险,建议采取“分区管理”的策略,并加强基因流发生之后的生态风险评价研究。     

Fire‐induced population reduction and landscape opening increases gene flow via pollen dispersal in Pinus halepensis

Population reduction and disturbances may alter dispersal, mating patterns and gene flow. Rather than taking the common approach of comparing different populations or sites, here we studied gene flow via wind‐mediated effective pollen dispersal on the same plant individuals before and after a fire‐induced population drop, in a natural stand of Pinus halepensis. The fire killed 96% of the pine trees in the stand and cleared the vegetation in the area. Thirteen trees survived in two groups separated by ~80 m, and seven of these trees had serotinous (closed) prefire cones that did not open despite the fire. We analysed pollen from closed pre and postfire cones using microsatellites. The two groups of surviving trees were highly genetically differentiated, and the pollen they produced also showed strong among‐group differentiation and very high kinship both before and after the fire, indicating limited and very local pollen dispersal. The pollen not produced by the survivors also showed significant prefire spatial genetic structure and high kinship, indicating mainly within‐population origin and limited gene flow from outside, but became spatially homogeneous with random kinship after the fire. We suggest that postfire gene flow via wind‐mediated pollen dispersal increased by two putative mechanisms: (i) a drastic reduction in local pollen production due to population thinning, effectively increasing pollen immigration through reduced dilution effect; (ii) an increase in wind speeds in the vegetation‐free postfire landscape. This research shows that dispersal can alleviate negative genetic effects of population size reduction and that disturbances might enhance gene flow, rather than reduce it.     

Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the overlap of ancestral populations. In this study, we performed population genetic analyses, species delimitation, simulations and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito‐nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation–migration analyses, however, revealed near‐zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.     

Widespread gene flow between oceans in a pelagic seabird species complex

Global‐scale gene flow is an important concern in conservation biology as it has the potential to either increase or decrease genetic diversity in species and populations. Although many studies focus on the gene flow between different populations of a single species, the potential for gene flow and introgression between species is understudied, particularly in seabirds. The only well‐studied example of a mixed‐species, hybridizing population of petrels exists on Round Island, in the Indian Ocean. Previous research assumed that Round Island represents a point of secondary contact between Atlantic (Pterodroma arminjoniana) and Pacific species (Pterodroma neglecta and Pterodroma heraldica). This study uses microsatellite genotyping and tracking data to address the possibility of between‐species hybridization occurring outside the Indian Ocean. Dispersal and gene flow spanning three oceans were demonstrated between the species in this complex. Analysis of migration rates estimated using bayesass revealed unidirectional movement of petrels from the Atlantic and Pacific into the Indian Ocean. Conversely, structure analysis revealed gene flow between species of the Atlantic and Pacific oceans, with potential three‐way hybrids occurring outside the Indian Ocean. Additionally, geolocation tracking of Round Island petrels revealed two individuals travelling to the Atlantic and Pacific. These results suggest that interspecific hybrids in Pterodroma petrels are more common than was previously assumed. This study is the first of its kind to investigate gene flow between populations of closely related Procellariiform species on a global scale, demonstrating the need for consideration of widespread migration and hybridization in the conservation of threatened seabirds.     

Seed dispersal and realized gene flow of two forest orchids in a fragmented landscape

• Species with vast production of dust‐like windborne seeds, such as orchids, should not be limited by seed dispersal. This paradigm, however, does not fit recent studies showing that many sites suitable for orchids are unoccupied and most seeds land close to their maternal plant. To explore this issue, we studied seed dispersal and gene flow of two forest orchid species, Epipactis atrorubens and Cephalanthera rubra, growing in a fragmented landscape of forested limestone hills in southwest Bohemia, Czech Republic.
• We used a combination of seed trapping and plant genotyping methods (microsatellite DNA markers) to quantify short‐ and long‐distance dispersal, respectively. In addition, seed production of both species was estimated.
• We found that most seeds landed very close to maternal plants (95% of captured seeds were within 7.2 m) in both species, and dispersal distance was influenced by forest type in E. atrorubens. In addition, C. rubra showed clonal reproduction (20% of plants were of clonal origin) and very low fruiting success (only 1.6% of plants were fruiting) in comparison with E. atrorubens (25.7%). Gene flow was frequent up to 2 km in C. rubra and up to 125 km in E. atrorubens, and we detected a relatively high dispersal rate among regions in both species.
• Although both species occupy similar habitats and have similar seed dispersal abilities, C. rubra is notably rarer in the study area. Considerably low fruiting success in this species likely limits its gene flow to longer distances and designates it more sensitive to habitat loss and fragmentation.

     

Fine-scale spatial genetic structure and gene dispersal in Silene latifolia

Plants are sessile organisms, often characterized by limited dispersal. Seeds and pollen are the critical stages for gene flow. Here we investigate spatial genetic structure, gene dispersal and the relative contribution of pollen vs seed in the movement of genes in a stable metapopulation of the white campion Silene latifolia within its native range. This short-lived perennial plant is dioecious, has gravity-dispersed seeds and moth-mediated pollination. Direct measures of pollen dispersal suggested that large populations receive more pollen than small isolated populations and that most gene flow occurs within tens of meters. However, these studies were performed in the newly colonized range (North America) where the specialist pollinator is absent. In the native range (Europe), gene dispersal could fall on a different spatial scale. We genotyped 258 individuals from large and small (15) subpopulations along a 60 km, elongated metapopulation in Europe using six highly variable microsatellite markers, two X-linked and four autosomal. We found substantial genetic differentiation among subpopulations (global F_ST=0.11) and a general pattern of isolation by distance over the whole sampled area. Spatial autocorrelation revealed high relatedness among neighboring individuals over hundreds of meters. Estimates of gene dispersal revealed gene flow at the scale of tens of meters (5–30 m), similar to the newly colonized range. Contrary to expectations, estimates of dispersal based on X and autosomal markers showed very similar ranges, suggesting similar levels of pollen and seed dispersal. This may be explained by stochastic events of extensive seed dispersal in this area and limited pollen dispersal.     

Demographic and genetic connectivity: the role and consequences of reproduction,dispersal and recruitment in seagrasses

Accurate estimation of connectivity among populations is fundamental for determining the drivers of population resilience, genetic diversity, adaptation and speciation. However the separation and quantification of contemporary versus historical connectivity remains a major challenge. This review focuses on marine angiosperms, seagrasses, that are fundamental to the health and productivity of temperate and tropical coastal marine environments globally. Our objective is to understand better the role of sexual reproduction and recruitment in influencing demographic and genetic connectivity among seagrass populations through an integrated multidisciplinary assessment of our present ecological, genetic, and demographic understanding, with hydrodynamic modelling of transport. We investigate (i) the demographic consequences of sexual reproduction, dispersal and recruitment in seagrasses, (ii) contemporary transport of seagrass pollen, fruits and seed, and vegetative fragments with a focus on hydrodynamic and particle transport models, and (iii) contemporary genetic connectivity among seagrass meadows as inferred through the application of genetic markers. New approaches are reviewed, followed by a summary outlining future directions for research: integrating seascape genetic approaches; incorporating hydrodynamic modelling for dispersal of pollen, seeds and vegetative fragments; integrating studies across broader geographic ranges; and incorporating non‐equilibrium modelling. These approaches will lead to a more integrated understanding of the role of contemporary dispersal and recruitment in the persistence and evolution of seagrasses.     

When genes move farther than offspring: gene flow by male gamete dispersal in the highly philopatric bat species Thyroptera tricolor

For species characterized by philopatry of both sexes, mate selection represents an important behaviour for inbreeding avoidance, yet the implications for gene flow are rarely quantified. Here, we present evidence of male gamete‐mediated gene flow resulting from extra‐group mating in Spix's disc‐winged bat, Thyroptera tricolor, a species which demonstrates all‐offspring philopatry. We used microsatellite and capture–recapture data to characterize social group structure and the distribution of mated pairs at two sites in southwestern Costa Rica over four breeding seasons. Relatedness and genetic spatial autocorrelation analyses indicated strong kinship within groups and over short distances (<50 m), resulting from matrilineal group structure and small roosting home ranges (~0.2 ha). Despite high relatedness among‐group members, observed inbreeding coefficients were low (F_IS = 0.010 and 0.037). Parentage analysis indicated mothers and offspring belonged to the same social group, while fathers belonged to different groups, separated by large distances (~500 m) when compared to roosting home ranges. Simulated random mating indicated mate choice was not based on intermediate levels of relatedness, and mated pairs were less related than adults within social groups on average. Isolation‐by‐distance (IBD) models of genetic neighbourhood area based on father–offspring distances provided direct estimates of mean gamete dispersal distances () > 10 roosting home range equivalents. Indirect estimates based on genetic distance provided even larger estimates of , indicating direct estimates were biased low. These results suggest extra‐group mating reduces the incidence of inbreeding in T. tricolor, and male gamete dispersal facilitates gene flow in lieu of natal dispersal of young.     

Lack of concordance between mtDNA gene flow and population density fluctuations in the bank vole

The genetic structure of bank voles Clethrionomys glareolus was determined from analyses of mitochondrial DNA (mtDNA) sequences, and compared with previous data on geographical synchrony in population density fluctuations. From 31 sample sites evenly spaced out along a 256-km transect in SE Norway a total of 39 distinct mtDNA haplotypes were found. The geographical distribution of the haplotypes was significantly nonrandom, and a cladistic analysis of the evolutionary relationship among haplotypes shows that descendant types were typically limited to a single site, whereas the ancestral types were more widely distributed geographically. This geographical distribution pattern of mtDNA haplotypes strongly indicates that the range and amount of female dispersal is severely restricted and insufficient to account for the previously observed synchrony in population density fluctuations. We conclude that geographical synchrony in this species must be caused by factors that are external to the local population, such as e.g. mobile predators.     

Ecology and genetics of insecticide resistance inHelicoverpa armigera: Interactions between selection and gene flow

Pyrethroid resistance inHelicoverpa armigera provides a model system in which to study evolution in natural populations. Resistance is seen to evolve as a consequence of selection pressure that varies within and between life-stages and gene flow. Although three different mechanisms are involved, present day fluctuations in phenotype frequency can be explained by variation in only one of these, metabolic resistance, that is inherited as a single, incompletely dominant gene,mfo. Selective mortality of phenotypes occurs in both larvae and adults in the presence of the pyrethroid insecticides. Although most individuals of all three genotypes are killed in young larvae, selection in this age-class contributes significantly to evolution of resistance. While there is some evidence of reduced fitness of resistant pupae during winter diapause, most of the decline in resistance frequencies each spring occurs as a result of immigration of susceptible individuals into insecticide-treated populations.     

NM+: software implementing parentage-based models for estimating gene dispersal and mating patterns in plants

NM+ is computer software designed for making inferences on plant gene dispersal and mating patterns by modelling parentage probabilities of offspring based on the spatially explicit neighbourhood model. NM+ requires a sample of mapped and genotyped candidate parents and offspring; however, offspring may optionally be assigned to single maternal parents (forming so-called half-sib progeny arrays). Using maximum likelihood, NM+ estimates a number of parameters, including proportions of offspring due to self-fertilization, pollen immigration from outside of a defined study site, parameters of pollen (and/or seed) dispersal kernels (exponential-power, Weibull, geometric or 2Dt) and selection gradients relating covariates (phenotypic traits) with male (and/or female) reproductive success. NM+ allows for missing data both in parents and in offspring. It accounts for null alleles and their frequencies can optionally be considered as estimable parameters. Data files are formatted in a table-like structure so they can be easily prepared in a spreadsheet software. By default NM+ is for studying plant populations, however, it can be used for any organism as long as data requirements and model assumptions are met. NM+ runs under Windows, but it can be launched under Linux using WINE emulator. NM+ can be downloaded free of charge from http://www.genetyka.ukw.edu.pl/index_pliki/software.htm.     

Sex‐biased dispersal and high levels of gene flow among local populations in the argentine boa constrictor,Boa constrictor occidentalis

Abstract The knowledge of dispersal is essential to understand the ecology of any species, since population dynamics, spatial distribution and genetic structure are closely tied to patterns of movement. In this paper we estimate dispersal patterns in natural populations of the endangered snake Boa constrictor occidentalis (Serpentes, Boidae), using allozymes as genetic markers. Blood samples were obtained from a total of 120 adult individuals of nine localities from two areas, Sobremonte and Pocho, in Argentina. Only four out of a total of 24 loci were polymorphic: 6‐Pgdh‐1, Cat‐1, Ldh and Hp. The values of expected and observed mean heterozygosities, the percentage of polymorphic loci and mean number of alleles per locus for each population confirm the low levels of genetic variability in this snake. F_ST and N_em mean values were 0.0089 and 46.1 for Sobremonte and 0.0379 and 7.46 for Pocho, indicating important levels of gene flow. A comparison of F_ST between genders in both areas suggests a male‐biased dispersal, which could be explained by the characteristics of the mating system: males carry out an active mate search of receptive females, and philopatry could be selected in females due to the benefits of the familiarity with the natal area in the use of local resources.     

Directional seed and pollen dispersal and their separate effects on anisotropy of fine‐scale spatial genetic structure among seedlings in a dioecious,wind‐pollinated,and wind‐dispersed tree species,Cercidiphyllum japonicum

Prevailing directions of seed and pollen dispersal may induce anisotropy of the fine‐scale spatial genetic structure (FSGS), particularly in wind‐dispersed and wind‐pollinated species. To examine the separate effects of directional seed and pollen dispersal on FSGS, we conducted a population genetics study for a dioecious, wind‐pollinated, and wind‐dispersed tree species, Cercidiphyllum japonicum Sieb. et Zucc, based on genotypes at five microsatellite loci of 281 adults of a population distributed over a ca. 80 ha along a stream and 755 current‐year seedlings. A neighborhood model approach with exponential‐power‐von Mises functions indicated shorter seed dispersal (mean = 69.1 m) and much longer pollen dispersal (mean = 870.6 m), effects of dispersal directions on the frequencies of seed and pollen dispersal, and the directions with most frequent seed and pollen dispersal (prevailing directions). Furthermore, the distance of effective seed dispersal within the population was estimated to depend on the dispersal direction and be longest at the direction near the prevailing direction. Therefore, patterns of seed and pollen dispersal may be affected by effective wind directions during the period of respective dispersals. Isotropic FSGS and spatial sibling structure analyses indicated a significant FSGS among the seedlings generated by the limited seed dispersal, but anisotropic analysis for the seedlings indicated that the strength of the FSGS varied with directions between individuals and was weakest at a direction near the directions of the most frequent and longest seed dispersal but far from the prevailing direction of pollen dispersal. These results suggest that frequent and long‐distance seed dispersal around the prevailing direction weakens the FSGS around the prevailing direction. Therefore, spatially limited but directional seed dispersal would determine the existence and direction of FSGS among the seedlings.     

Stable genetic polymorphism in heterogeneous environments: balance between asymmetrical dispersal and selection in the acorn barnacle

Elucidating the processes responsible for maintaining polymorphism at ecologically relevant genes is intimately related to understanding the interplay between selection imposed by habitat heterogeneity and a species' capacity for dispersal in the face of environmental constraints. In this paper, we used a model-based approach to solve equilibria of balanced polymorphism, given values of fitness and larval dispersal among different habitats in the acorn barnacle Semibalanus balanoides from the Gulf of St Lawrence. Our results showed that allele frequencies observed at both MPI* and GPI* loci represented stable equilibria, given empirical estimates of fitness values, and that considerably more larvae dispersed from one region (north) to the other (south) than vice versa. Dispersal conditions were predicted to be similar for the maintenance of polymorphism at both loci. Moreover, the values of asymmetrical dispersal required by the model to reach stable equilibria were compatible with empirical estimates of larval dispersal and oceanic circulation documented in this system. Overall, this study illustrated the usefulness of a modified and computable version of Bulmer's model (1972) in order to test hypotheses of balanced polymorphism resulting from interactions between spatial selection and asymmetrical dispersal.