Model Of Gene Flow Research Articles

Hybrid Incompatibilities, Local Adaptation, and the Genomic Distribution of Natural Introgression between Species.

Under allopatric speciation, geographic barriers eliminate gene flow between eventual species at all loci in the genome simultaneously. There is increasing evidence, however, that speciation can be complex, with some loci experiencing gene flow during speciation or during bouts of secondary contact. In taxa with heteromorphic sex chromosomes-birds, butterflies, mammals, and Drosophila-the X (or Z) chromosome generally shows reduced levels of gene flow compared to autosomes. To investigate why, we develop population genetic models of secondary contact and gene flow at a neutral locus that is genetically linked to selected loci involved in hybrid incompatibilities and/or local adaptation. Using models that assume weak migration and strong selection, we compare gene flow at X-linked versus autosomal neutral loci as a function of linkage, dominance, sex-specific selection, and sex-specific recombination. For most cases, gene flow at neutral loci on the X is reduced relative to autosomes, as the greater efficacy of hemizygous selection in XY hybrids reduces the opportunity for neutral migrant alleles to escape their genetically linked, locally disfavored alleles via recombination. There are some circumstances, however, involving sex-limited selection and sex-limited recombination that allow neutral loci on the X to introgress more readily than those on autosomes.

The first human settlement of the New World: A closer look at craniofacial variation and evolution of early and late Holocene Native American groups

Abstract During its expansion across the globe, Homo sapiens successfully survived to major adaptive challenges as a species, inviting scientific research to plunge into the particularities of continental settlement dynamics. A recurrent paleoanthropological concern is about the understanding of the great deal of craniofacial diversity that evolved into the Americas, which includes a vector of continuum variation between a generalized morphology observed among humans groups leading the Out-of-Africa dispersion, and a derived set of craniofacial traits classically labeled as “mongoloid” and that would have arise in Asia during the Holocene. Here, we use geometric morphometric techniques and multivariate statistics along with quantitative genetic approaches to look more closely into the human craniofacial evolutionary history during the Late Pleistocene–Early Holocene from Asia and the New World. We detected significant signals of deviation of the neutral evolutionary expectations, suggesting an important action of non-stochastic evolution (e.g. natural selection, phenotypic plasticity) in the Americas. We also found further support to the Recurrent Gene Flow model that refers to an ancestral, founder population experiencing a standstill in Beringia, and exhibiting high within-group craniofacial variation. This original, internally variable stock would have been the ancestral source of variation that fuelled the subsequent local micro evolution of other derived phenotypic patterns, giving origin to the craniofacial diversity observed among Holocene Native American samples.

Design of a decision support tool for managing coexistence between genetically modified and conventional maize at farm and regional levels

Over the last 15years, several studies on coexistence have used simulation results of spatially explicit gene flow models. These models predict the adventitious presence (AP) of GM grains in non-GM fields at the landscape scale. However, result uncertainty is not quantified. Moreover, most of the models require an important amount of input data on climate, land use, and crop management practices which might not always be available. A comprehensive Bayesian statistical approach has been implemented in the case of gene flow. This approach makes it possible to inform the decision-maker on AP, whatever the amount of information available in a given situation, to provide information on the uncertainty of the predictions and to model the variability of AP within a field, which helps set up sampling strategies.The resulting decision-support tool (DST) can compute the expected AP and its probability distribution in non-GM maize fields at different times of the growing season and under different management scenarios. Integrated through a web interface, the DST is designed to be operationally helpful for managing coexistence between GM and non-GM maize crops for a wide range of stakeholders from farmers to policy makers.

The importance of terrestrial dispersal for connectivity among headwater salamander populations

Many organisms are primarily constrained to the channels of the upstream terminus of river networks with limited capacities for both in‐stream and overland dispersal. Dispersal is believed to contribute to gene flow and the demographic stability of headwater populations. While assumed, the importance of overland dispersal to gene flow is largely unexplored in headwater salamanders. Six microsatellite markers were used to assess patterns of genetic population structure for a headwater salamander, Desmognathus fuscus. Tissue samples were collected using a nested hierarchical study design, which specifically addressed the contribution of overland movements to the genetic connectivity of headwater populations. Genetic divergence was significant among all populations (Fst = 0.027–0.405) and at all hierarchical spatial scales. However, lower degrees of genetic population structure were observed among proximal streams that shared no downstream hydrologic connections. Mantel tests indicated a significant relationship between genetic divergence and overland distance, suggesting that D. fuscus populations conform to an isolation‐by‐distance model of gene flow. Estimated dispersal among headwater streams was limited, with an average of less than one effective migrant per generation moving between paired headwater streams. These results indicate that regional patterns of genetic population structure are influenced by overland dispersal and suggest the importance of terrestrial movements in maintaining population connectivity among D. fuscus populations.

Assessment of Genetic Diversity in Wild and Aquaculture Stocks ofMercenaria mercenariain Florida

The northern hard clam Mercenaria mercenaria is one of the most commercially important bivalve species produced via aquaculture in the eastern United States. Breeding practices associated with large-scale hatchery production of hard clamseedmayresultinunintended,potentiallynegativeconsequencesincludinginbreedingandreducedlevelsofgeneticdiversity. Seven microsatellite markers were used to compare levels of genetic diversity in six hatchery stocks and four wild stocks from the state of Florida. Wild stocks of M. mercenaria had slightly higher levels of allelic richness and similar observed heterozygosity (wild ¼Ar ¼3.61,Ho ¼0.448;hatchery ¼Ar ¼3.46,Ho ¼0.452);however,thesedifferenceswerenotstatisticallysignificant(Ar:P ¼ 0.145; Ho: P ¼ 0.931). Differentiation was highest between hatchery stocks (GST ¼ 0.03, SD ¼ 0.007; P < 0.001) but minimal among hatchery-by-wild comparisons. In contrast, wild stocks were not differentiated (GST ¼ -0.002, SD ¼ 0.004; P � 0.58) and Bayesian comparisons of competing gene flow models (panmixia, stepping stone, and full-migration) suggested that wild stocks were effectively panmictic at this scale. Together, these results indicate that some genetic drift has occurred within hatchery populations, possibly as a result of broodstock selection and spawning practices. The genetic divergence between wild and hatchery stocks observed in this study are not as pronounced as seen in other aquaculture bivalve species. Given the large scale of hard clam production in Florida we argue that hatchery practices should incorporate long-term genetic goals (i.e., avoidance of inbreeding) to maintain the integrity of hatchery stocks. A secondary objective of this study was to amplify a congeneric species, Mercenaria campechiensis, using the same suite of microsatellite markers to assess their utility for detecting interspecific hybridization. Amplification success was poor and failed for four of the seven loci. The identification of microsatellite loci for different species of Mercenaria should be identified de novo in the future.

Application of an atmospheric gene flow model for assessing environmental risks from transgenic corn crops

Gene flow data from experiments under limited environmental conditions (e.g. wind speed and direction, atmospheric stability) have only provided limited information for gene flow risk management. It is necessary to apply models to predict the gene flow under a complete set of possible environmental conditions to inform farmers, seed companies, government agencies, and researchers about the risks and potential prevention and precaution methods. In this paper, the previous validated gene flow model developed by the authors was used to predict gene flow from genetically modified (GM) corn crops. The model was used to simulate potential gene flow from GM corn sources of different sizes from one plant area of 0.1 m 2 to an area 3.1×10 6 m 2 under normal weather conditions. In addition, the model was also used to predict the potential gene flow for different source strengths, atmospheric conditions, buffer heights, buffer field sizes, and pollen settling speeds from 10,000 m 2 sources. The model simulations have provided gene flow information for risk management under the above conditions and have shown that the source sizes, source strengths, buffer heights, buffer sizes, atmospheric conditions, and pollen settling speeds had important effects on gene flow. While the atmospheric conditions and pollen settling speeds cannot be controlled, choosing appropriate buffer heights and sizes will effectively prevent gene flow. The lost seed control is crucial to limit gene flow because even a GM corn plant can result in a grand total deposition flux of 646,272 grains/m 2 , an outcrossing ratio of 0.016, and outcrossed seed of 110 kernels/m 2 at 0.8 m from the plant in the non-target field under normal atmospheric

Development and validation of atmospheric gene flow model for assessing environmental risks from transgenic corn crops.

Pollen-mediated gene flow from genetically modified plants to non-target plants is a concern of crop growers, seed companies, the general public, and the scientific communities. Although there have been descriptive and mechanistic models to describe pollen dispersion, there has rarely been a comprehensive mechanistic model to dynamically simulate pollen release, dispersion, and deposition and to finally relate them to the gene flow (outcrossing). This research developed and validated such a comprehensive mechanistic model for corn crop gene flow risk management. Dynamic pollen dispersion and deposition were predicted by a 3-D random walk model according to inputs of weather data and plant and domain characteristics. Actual gene flow (outcrossing ratio) was obtained according to predicted grand total deposition flux at silk height during the whole pollination season. The model was validated by experimental data and was appropriate to predict gene flow with acceptable accuracy under different atmospheric and environmental conditions; on average, the ratios of measured and simulated values ranged from 0.82 to 1.21, while R 2 ranged from 0.56 to 0.68. The model can be easily adapted

Drought survival strategies, dispersal potential and persistence of invertebrate species in an intermittent stream landscape

Summary Intermittent stream systems create a mosaic of aquatic habitat that changes through time, potentially challenging freshwater invertebrate dispersal. Invertebrates inhabiting these mosaics may show stronger dispersal capacity than those in perennial stream systems. To relate different combinations of dispersal and drought survival strategies to species persistence, we compared the distribution and dispersal potential of six invertebrate species across all streams in a montane landscape where drying is becoming increasingly frequent and prolonged. Invertebrates were collected from seventeen streams in the Victoria Range, Grampians National Park, Victoria, Australia. The species analysed were as follows: the caddisflies Lectrides varians Moseley (Leptoceridae) and Agapetus sp. (Glossosomatidae); the mayflies Nousia AV1 and Koorrnonga AV3 (Leptophlebiidae); the water penny beetle Sclerocyphon sp. (Psephenidae); and a freshwater crayfish Geocharax sp. nov. 1 (Parastacidae). These species were widespread in the streams and varied in their dispersal and drought survival strategies. The distribution of each species across the Victoria Range, their drought responses and within‐stream habitat associations were determined. Hypotheses of the dispersal capacity and population structure for each species were developed and compared to four models of gene flow: Death Valley Model (DVM), Stream Hierarchy Model (SHM), Headwater Model (HM) or panmixia (PAN). Molecular genetic methods were then used to infer population structure and dispersal capacity for each species. The large caddisfly Lectrides resisted drought through aestivation and was panmictic (PAN) indicating strong dispersal capacity. Conversely, the small caddisfly Agapetus relied on perennially flowing reaches and gene flow was limited to short distances among stream headwaters, resembling the HM. Both mayflies depended on perennial surface water during drying and showed evidence of gene flow among streams: Koorrnonga mainly dispersed along stream channels within catchments, resembling the SHM, whereas Nousia appeared to disperse across land by adult flight. Sclerocyphon relied on perennial water to survive drying and showed an unusual pattern of genetic structure that indicated limited dispersal but did not resemble any of the models. Geocharax survived drought through aestivation or residence in perennial pools, and high levels of genetic structure indicated limited dispersal among streams, resembling the DVM. Despite good knowledge of species' drought survival strategies, the population structure of four species differed from predictions. Dispersal capacity varied strongly among species; most species were poor dispersers and only one species showed panmixia. Therefore, intermittent stream species may not necessarily be better dispersers than those in perennial streams. Species showing strong drought resistance strategies differed in dispersal capacity. Knowledge of life‐history characteristics, distribution and refuge use does not necessarily enable successful prediction of invertebrate dispersal pathways or population structure. Dispersal among intermittent streams may be restricted to relatively short distances (km) for most invertebrate species. Thus, frequent drought refuges (perennial water) that provide strong connectivity to subpopulations through stream flow (hydrological dispersal), or continuous terrestrial vegetation (flight dispersal), will be critical to maintain genetic diversity, adaptability and population persistence.

The use of habitat and dispersal models in protecting European black poplar (Populus nigra L.) from genetic introgression in Slovenia

European black poplar (Populus nigra L.) has become threatened by the widespread disappearance of riparian forests in Europe. Gene introgression through hybridization with related, non-indigenous poplar taxa may additionally reduce the population size and genetic diversity of native black poplar. We assessed the exposure of native black poplar in Slovenia to genetic introgression using a combination of habitat and gene flow models. The habitat model was built with data mining on forest inventory data employing classification decision trees. Dispersion distances for pollen, seeds and vegetative parts at 0.9% and 0.001% of adventitious presence threshold were assessed using modified gene flow models. To protect native black poplar, protection zones around native black poplar stands were proposed. Since the population of native black poplar may be exposed to various introgression pressures (e.g., the vicinity of exotic, genetically compatible poplar plantations, or feral populations potentially initiated along transport corridors or rivers), we assessed the intensity of introgression pressure by intersecting the occupied and potential habitat with the introgression pressure areas. In 2010, native black poplar occurred on 43,756ha (2.2% of the total Slovenian territory), while the suitable habitat extended up to 108,724ha (5.4%). The protection zones were 0.5–4.6 times larger than the occupied and potential habitat depending on the selected threshold and the type of dispersion vector. In the worst case scenario, 45.1% of protection zones would be exposed to high hybridization pressure. We recommend extending the proposed methodological approach to other regions with endangered black poplar.

Mitochondrial genome diversity at the Bering Strait area highlights prehistoric human migrations from Siberia to northern North America

The patterns of prehistoric migrations across the Bering Land Bridge are far from being completely understood: there still exists a significant gap in our knowledge of the population history of former Beringia. Here, through comprehensive survey of mitochondrial DNA genomes retained in 'relic' populations, the Maritime Chukchi, Siberian Eskimos, and Commander Aleuts, we explore genetic contribution of prehistoric Siberians/Asians to northwestern Native Americans. Overall, 201 complete mitochondrial sequences (52 new and 149 published) were selected in the reconstruction of trees encompassing mtDNA lineages that are restricted to Coastal Chukotka and Alaska, the Canadian Arctic, Greenland, and the Aleutian chain. Phylogeography of the resulting mtDNA genomes (mitogenomes) considerably extends the range and intrinsic diversity of haplogroups (eg, A2a, A2b, D2a, and D4b1a2a1) that emerged and diversified in postglacial central Beringia, defining independent origins of Neo-Eskimos versus Paleo-Eskimos, Aleuts, and Tlingit (Na-Dene). Specifically, Neo-Eskimos, ancestral to modern Inuit, not only appear to be of the High Arctic origin but also to harbor Altai/Sayan-related ancestry. The occurrence of the haplogroup D2a1b haplotypes in Chukotka (Sireniki) introduces the possibility that the traces of Paleo-Eskimos have not been fully erased by spread of the Neo-Eskimos or their descendants. Our findings are consistent with the recurrent gene flow model of multiple streams of expansions to northern North America from northeastern Eurasia in late Pleistocene-early Holocene.

Differential introgression and effective size of marker type influence phylogenetic inference of a recently divergent avian group (Phasianidae: Tympanuchus)

Life history strategies can influence the effective population size (Ne) of loci differently based on their mode of inheritance. Recognizing how this may affect the rate of lineage sorting among marker types is important for studies focused on resolving phylogenetic relationships among recently divergent taxa. In this study, we use gene tree, coalescent-based species tree, and isolation-with-migration analyses to explore the differences between marker types (autosomal, Z-linked, and mitochondrial) in resolving phylogenetic relationships among North American prairie grouse (Tympanuchus). We found that Z-linked loci were more likely to identify monophyletic relationships among prairie grouse species compared to autosomal and mtDNA loci in both species and gene tree analyses, with species tree analyses outperforming gene trees. These results were further supported with isolation-with-migration analyses, where Z-linked loci largely followed a strict isolation model while autosomal loci were more likely to fit a model with gene flow between species following population divergence. While accounting for differences in inheritance pattern (or Ne) for marker type, results suggest that additional factors, such as strong sexual selection and sex-biased introgression (i.e., male-biased postzygotic hybrid behavioral isolation or “unsexy son”), may further explain the decreased diversity levels and increased rate of lineage sorting observed with the Z-linked loci relative to autosomal and mtDNA loci. In fact, to our knowledge no hybrid male prairie grouse have been observed breeding in the wild, yet hybrid females along with backcross females are known to produce viable offspring. Overall, this study highlights that more work is needed to determine how complex models of gene flow (i.e., sex biased introgression) and differences in the effective size among marker types based on differing life history strategies influence divergence date estimation and species delimitation.

Rice transgene flow: its patterns, model and risk management.

Progress has been made in a 12year's systemic study on the rice transgene flow including (i) with experiments conducted at multiple locations and years using up to 21 pollen recipients, we have elucidated the patterns of transgene flow to different types of rice. The frequency to male sterile lines is 10(1) and 10(3) higher than that to O.rufipogon and rice cultivars. Wind speed and direction are the key meteorological factors affecting rice transgene flow. (ii) A regional applicable rice gene flow model is established and used to predict the maximum threshold distances (MTDs) of gene flow during 30years in 993 major rice producing counties of southern China. The MTD0.1% for rice cultivars is basically ≤5m in the whole region, despite climate differs significantly at diverse locations and years. This figure is particularly valuable for the commercialization and regulation of transgenic rice. (iii) The long-term fate of transgene integrated into common wild rice was investigated. Results demonstrated that the F1 hybrids of transgenic rice/O.rufipogon gradually disappeared within 3-5years, and the Bt or bar gene was not detectable in the mixed population, suggesting the O.rufipogon may possess a strong mechanism of exclusiveness for self-protection. (iv) The flowering time isolation and a 2-m-high cloth-screen protection were proved to be effective in reducing transgene flow. We have proposed to use a principle of classification and threshold management for different types of rice.

Distributional dynamics and interspecific gene flow in Picea likiangensis and P. wilsonii triggered by climate change on the Qinghai‐Tibet Plateau

AbstractAimTo address whether climate changes have altered the distributional ranges of cold‐preferring conifer species, and whether this has influenced interspecific divergence.LocationQinghai‐Tibet Plateau (QTP), Asia.MethodsWe obtained DNA sequences at 13 nuclear loci in 229 individuals collected from 32 populations across the range of two cold‐preferring alpine species, Picea likiangensis and Picea wilsonii. Bayesian skyline plots (BSPs) were used to examine historical changes in effective population sizes. Species distributions were reconstructed based on presence‐only data at 134 locations and climate variables from the WorldClim database, and the reconstructed distributions were compared with projected palaeodistributions at the Last Glacial Maximum (LGM, about 20 ka). Four models of interspecific gene flow during the Pleistocene and Holocene were compared using approximate Bayesian computation (ABC).ResultsThe effective population sizes of P. likiangensis and P. wilsonii increased continuously from 5 to 0.2 Ma, but decreased after 0.2 Ma. The distributional ranges during the LGM were wider than at present, confirming the trend of a recent decrease. However, the overlapping area became greater due to their shifted distributions, and these shifts altered the major direction of continuing interspecific gene flow.Main conclusionsThe early increase in the distributions of these two species might have been triggered by enlargements of the available cold habitats brought about by QTP uplift and Pleistocene glaciations. However, the distributional ranges decreased in response to climatic warming since the end of the largest glaciation. These distributional changes further retarded the process of differentiation by altering the pattern of gene flow. Our results shed light on the evolutionary complexity of alpine species in response to climate changes in this climate‐sensitive biodiversity hotspot.

Models of selection, isolation, and gene flow in speciation.

Many marine ecologists aspire to use genetic data to understand how selection and demographic history shape the evolution of diverging populations as they become reproductively isolated species. I propose combining two types of genetic analysis focused on this key early stage of the speciation process to identify the selective agents directly responsible for population divergence. Isolation-with-migration (IM) models can be used to characterize reproductive isolation between populations (low gene flow), while codon models can be used to characterize selection for population differences at the molecular level (especially positive selection for high rates of amino acid substitution). Accessible transcriptome sequencing methods can generate the large quantities of data needed for both types of analysis. I highlight recent examples (including our work on fertilization genes in sea stars) in which this confluence of interest, models, and data has led to taxonomically broad advances in understanding marine speciation at the molecular level. I also highlight new models that incorporate both demography and selection: simulations based on these theoretical advances suggest that polymorphisms shared among individuals (a key source of information in IM models) may lead to false-positive evidence of selection (in codon models), especially during the early stages of population divergence and speciation that are most in need of study. The false-positive problem may be resolved through a combination of model improvements plus experiments that document the phenotypic and fitness effects of specific polymorphisms for which codon models and IM models indicate selection and reproductive isolation (such as genes that mediate sperm-egg compatibility at fertilization).

Asymmetric connectivity of spawning aggregations of a commercially important marine fish using a multidisciplinary approach.

Understanding patterns of larval dispersal is key in determining whether no-take marine reserves are self-sustaining, what will be protected inside reserves and where the benefits of reserves will be observed. We followed a multidisciplinary approach that merged detailed descriptions of fishing zones and spawning time at 17 sites distributed in the Midriff Island region of the Gulf of California with a biophysical oceanographic model that simulated larval transport at Pelagic Larval Duration (PLD) 14, 21 and 28 days for the most common and targeted predatory reef fish, (leopard grouper Mycteroperca rosacea). We tested the hypothesis that source–sink larval metapopulation dynamics describing the direction and frequency of larval dispersal according to an oceanographic model can help to explain empirical genetic data. We described modeled metapopulation dynamics using graph theory and employed empirical sequence data from a subset of 11 sites at two mitochondrial genes to verify the model predictions based on patterns of genetic diversity within sites and genetic structure between sites. We employed a population graph describing a network of genetic relationships among sites and contrasted it against modeled networks. While our results failed to explain genetic diversity within sites, they confirmed that ocean models summarized via graph and adjacency distances over modeled networks can explain seemingly chaotic patterns of genetic structure between sites. Empirical and modeled networks showed significant similarities in the clustering coefficients of each site and adjacency matrices between sites. Most of the connectivity patterns observed towards downstream sites (Sonora coast) were strictly asymmetric, while those between upstream sites (Baja and the Midriffs) were symmetric. The best-supported gene flow model and analyses of modularity of the modeled networks confirmed a pulse of larvae from the Baja Peninsula, across the Midriff Island region and towards the Sonoran coastline that acts like a larval sink, in agreement with the cyclonic gyre (anti-clockwise) present at the peak of spawning (May–June). Our approach provided a mechanistic explanation of the location of fishing zones: most of the largest areas where fishing takes place seem to be sustained simultaneously by high levels of local retention, contribution of larvae from upstream sites and oceanographic patterns that concentrate larval density from all over the region. The general asymmetry in marine connectivity observed highlights that benefits from reserves are biased towards particular directions, that no-take areas need to be located upstream of targeted fishing zones, and that some fishing localities might not directly benefit from avoiding fishing within reserves located adjacent to their communities. We discuss the implications of marine connectivity for the current network of marine protected areas and no-take zones, and identify ways of improving it.

Establishment and optimization of a regionally applicable maize gene-flow model

Because of the rapid development of transgenic maize, the potential effect of transgene flow on seed purity has become a major concern in public and scientific communities. Setting a proper isolation distance in field experiments and seed production is a possible solution to meet seed-quality standards and ensure adventitious contamination of products is below a specific threshold. By using a Gaussian plume model as basis and data recorded by meteorological stations as input, we have established a simple regionally applicable maize gene-flow model for prediction of the maximum threshold distances (MTD) at which gene-flow frequency is equal to or lower than a threshold value of 1 or 0.1% (MTD1%, MTD0.1%). After optimization of the model variables, simulated outcrossing rate was a good fit to data obtained from field experiments (y=1.156x, R (2)=0.8913, n=30, P<P 0.01). In the process of model calibration, it was found that only 15.82% of the total amount of the pollen released by each plant participated in the dispersal process. The variable "a" for genetic pollen competitiveness between donor and recipient was introduced into our model, for the "Zinuo18" and "Su608" used, "a" was 17.47. Finally, the model was successfully used in the spring maize-growing region of Northeast China. The range of MTD1% and MTD0.1% in this region varied from 10m to 49m and from 17m to 125m, respectively.

Breeding programmes for smallholder sheep farming systems: II. Optimization of cooperative village breeding schemes.

A simulation study was conducted to optimize a cooperative village-based sheep breeding scheme for Menz sheep of Ethiopia. Genetic gains and profits were estimated under nine levels of farmers' participation and three scenarios of controlled breeding achieved in the breeding programme, as well as under three cooperative flock sizes, ewe to ram mating ratios and durations of ram use for breeding. Under fully controlled breeding, that is, when there is no gene flow between participating (P) and non-participating (NP) flocks, profits ranged from Birr 36.9 at 90% of participation to Birr 21.3 at 10% of participation. However, genetic progress was not affected adversely. When there was gene flow from the NP to P flocks, profits declined from Birr 28.6 to Birr -3.7 as participation declined from 90 to 10%. Under the two-way gene flow model (i.e. when P and NP flocks are herded mixed in communal grazing areas), NP flocks benefited from the genetic gain achieved in the P flocks, but the benefits declined sharply when participation declined beyond 60%. Our results indicate that a cooperative breeding group can be established with as low as 600 breeding ewes mated at a ratio of 45 ewes to one ram, and the rams being used for breeding for a period of two years. This study showed that farmer cooperation is crucial to effect genetic improvement under smallholder low-input sheep farming systems.

Upstream or downstream? Population structure of the land snail Ventridens ligera (Say, 1821) in the Potomac River drainage basin

Organisms that live in or near watercourses often disperse with the flow of the water and therefore experience asymmetric gene flow. The asymmetric model of gene flow does not hold for organisms capable of dispersing either upstream or by land, such as amphibians and insects. I analysed genetic diversity in populations of the land snail Ventridens ligera over 300 km of the Potomac River drainage system to determine if the river has an effect on gene flow. Samples were analysed by collection site and then by river. A moderate level of genetic differentiation is present between collection sites on the rivers flowing into the Potomac River, suggesting that the upstream sites are genetically isolated. However allelic richness does not increase significantly with downstream flow as would be expected if asymmetric gene flow is present. These contrasting results suggest that V. ligera disperses by two means: (1) overland to local habitats upstream, downstream or away from the river and (2) downstream to more distant habitats by rafting on plants or debris.

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow.

The metaphor of 'genomic islands of speciation' was first used to describe heterogeneous differentiation among loci between the genomes of closely related species. The biological model proposed to explain these differences was that the regions showing high levels of differentiation were resistant to gene flow between species, while the remainder of the genome was being homogenized by gene flow and consequently showed lower levels of differentiation. However, the conditions under which such differentiation can occur at multiple unlinked loci are restrictive; additionally, essentially, all previous analyses have been carried out using relative measures of divergence, which can be misleading when regions with different levels of recombination are compared. Here, we test the model of differential gene flow by asking whether absolute divergence is also higher in the previously identified 'islands'. Using five species pairs for which full sequence data are available, we find that absolute measures of divergence are not higher in genomic islands. Instead, in all cases examined, we find reduced diversity in these regions, a consequence of which is that relative measures of divergence are abnormally high. These data therefore do not support a model of differential gene flow among loci, although islands of relative divergence may represent loci involved in local adaptation. Simulations using the program IMa2 further suggest that inferences of any gene flow may be incorrect in many comparisons. We instead present an alternative explanation for heterogeneous patterns of differentiation, one in which postspeciation selection generates patterns consistent with multiple aspects of the data.

Gene flow within and between catchments in the threatened riparian plant Myricaria germanica.

One of the major distinctions of riparian habitats is their linearity. In linear habitats, gene flow is predicted to follow a one-dimensional stepping stone model, characterized by bidirectional gene flow between neighboring populations. Here, we studied the genetic structure of Myricaria germanica, a threatened riparian shrub which is capable of both wind and water dispersal. Our data led us to reject the ‘one catchment – one gene pool’ hypothesis as we found support for two gene pools, rather than four as expected in a study area including four catchments. This result also implies that in the history of the studied populations, dispersal across catchments has occurred. Two contemporary catchment-crossing migration events were detected, albeit between spatially proximate catchments. Allelic richness and inbreeding coefficients differed substantially between gene pools. There was significant isolation by distance, and our data confirmed the one-dimensional stepping-stone model of gene flow. Contemporary migration was bidirectional within the studied catchments, implying that dispersal vectors other than water are important for M. germanica.