Gene Flow Research Articles

Partitioning genetic structure of a subterranean rodent at multiple spatial scales: accounting for isolation by barriers, distance, and environment

ContextUnderstanding genetic structure at multiple spatial scales and identifying drivers of genetic isolation are important for developing comprehensive conservation plans including for grassland conservation efforts. However, few studies account for multiple genetic isolation processes nor partition genetic variance among these processes.ObjectivesWe assess key processes that can create spatial genetic patterns including isolation by barrier (IBB), isolation by distance (IBD), and isolation by environment (IBE) for a widespread pocket gopher species (Geomys bursarius) and a spatially restricted subspecies (Geomys bursarius illinoensis). We further partition genetic variation to each isolating effect and identify genetic variation that was shared between processes.MethodsWe used seven microsatellites to determine spatial genetic clustering and identify environmental factors impacting genetic similarities. Then, we used redundancy analysis to partition variance explained by IBB, IBD, and IBE.ResultsMajor rivers including the Mississippi River acted as barriers and explained the most genetic variation across the species. In contrast, IBD explained the most genetic variation for G. b. illinoensis. Gophers had genetic associations to soil sand percent and soil color, but IBE uniquely explained a small amount of genetic structure for G. bursarius, with additional variation shared with other isolating processes.ConclusionsGopher genetic structure resulted from barriers, distance, and environmental factors at the species range as well as for a subspecies’ region, but the relative amount of genetic variance assigned to unique isolating processes differed between scales. Delineation of conservation units should consider major rivers as natural boundaries, and finer-scale management should identify and protect areas close to source populations with similar soil friability. Our study exemplifies how analyzing gene flow at rangewide and regional scales can aid managers in developing localized strategies that fit within broader conservation units.

Hybrid speciation driven by multilocus introgression of ecological traits

Hybridization allows adaptations to be shared among lineages and may trigger the evolution of new species1,2. However, convincing examples of homoploid hybrid speciation remain rare because it is challenging to demonstrate that hybridization was crucial in generating reproductive isolation3. Here we combine population genomic analysis with quantitative trait locus mapping of species-specific traits to examine a case of hybrid speciation in Heliconius butterflies. We show that Heliconius elevatus is a hybrid species that is sympatric with both parents and has persisted as an independently evolving lineage for at least 180,000 years. This is despite pervasive and ongoing gene flow with one parent, Heliconius pardalinus, which homogenizes 99% of their genomes. The remaining 1% introgressed from the other parent, Heliconius melpomene, and is scattered widely across the H. elevatus genome in islands of divergence from H. pardalinus. These islands contain multiple traits that are under disruptive selection, including colour pattern, wing shape, host plant preference, sex pheromones and mate choice. Collectively, these traits place H. elevatus on its own adaptive peak and permit coexistence with both parents. Our results show that speciation was driven by introgression of ecological traits, and that speciation with gene flow is possible with a multilocus genetic architecture.

Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages

Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.

Genetic barriers more than environmental associations explain Serratia marcescens population structure

Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigate the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses reveal a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets reveals only a partial habitat separation of the clusters. Globally, two clusters only show a separate gene composition coherent with ecological adaptations. These results suggest that genetic isolation has preceded ecological adaptations in the shaping of the species diversity, an evolutionary scenario coherent with the Evolutionary Extended Synthesis.

The Net of Life, a short story: Intricate patterns of gene flows across hundreds of extant genomes, all the way to LUCA

Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role. The 'Net of Life' not only impacts our understanding of genome evolution but also has profound implications for classification systems, the rapid appearance of new traits, and the spread of diseases. Here, we explore the core tenets of the 'Net of Life' and its implications for genome-scale phylogenetic divergence, providing a comprehensive framework for further investigations in evolutionary biology.

Same landscape, different connectivity: contrasting patterns of gene flow in two sympatric ungulates in a mountain area

Comparative landscape genetics studies provide insights on the impact of landscape elements on gene flow patterns of different species inhabiting the same geographic area. We investigated the population genetic structure of two sympatric ungulates, roe deer Capreolus capreolus and Northern chamois Rupicapra rupicapra, in a mountain area of the central Italian Alps (Trentino, northern Italy). A total of 122 chamois and 72 roe deer samples were genotyped by two species-specific panels of 11 polymorphic microsatellite loci and analyzed by aspatial and spatially explicit analyses. While the roe deer population resulted unstructured, a clear population structure was detected in chamois, with two main groups, one inhabiting the eastern and the other spread in the western part of the study area. Landscape genetics analysis confirmed these scenarios and revealed a different effect of landscape on gene flow. An IBD (Isolation-By-Distance) model best explained genetic variation in roe deer, while IBR (Isolation-By-Resistance) was found as the process underlying genetic variation patterns in chamois, suggesting arable lands, coniferous forests, watercourses, and main roads as potential barriers. Species distribution and landscape use might explain these results: roe deer mostly occupy valley floors relatively connected to each other, and their spatial behavior may promote gene flow across areas. On the other hand, chamois prefer higher elevations and their movements may be hindered by valleys, rivers, and road networks. This study highlights the different impacts of natural and anthropic landscape elements on gene flow in two sympatric species, resulting from their different ecological requirements.

Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex.

Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which triggered the adaptive radiation of the clade. Within clownfishes, the "skunk complex" is particularly interesting. Besides ecological speciation, interspecific gene flow and hybrid speciation are thought to have shaped the evolution of the group. We investigated the mechanisms characterizing the diversification of this complex. By taking advantage of their disjunct geographical distribution, we obtained whole-genome data of sympatric and allopatric populations of the three main species of the complex (Amphiprion akallopisos, A. perideraion and A. sandaracinos). We examined population structure, genomic divergence and introgression signals and performed demographic modelling to identify the most realistic diversification scenario. We excluded scenarios of strict isolation or hybrid origin of A. sandaracinos. We discovered moderate gene flow from A. perideraion to the ancestor of A. akallopisos + A. sandaracinos and weak gene flow between the species in the Indo-Australian Archipelago throughout the diversification of the group. We identified introgressed regions in A. sandaracinos and detected in A. perideraion two large regions of high divergence from the two other species. While we found that gene flow has occurred throughout the species' diversification, we also observed that recent admixture was less pervasive than initially thought, suggesting a role of host repartition or behavioural barriers in maintaining the genetic identity of the species in sympatry.

Local adaptation to an altitudinal gradient: The interplay between mean phenotypic trait variation and phenotypic plasticity in Mimulus laciniatus

Organisms can adapt to environmental heterogeneity through two mechanisms: (1) expression of population genetic variation or (2) phenotypic plasticity. In this study we investigated whether patterns of variation in both trait means and phenotypic plasticity along elevational and latitudinal clines in a North American endemic plant, Mimulus laciniatus, were consistent with local adaptation. We grew inbred lines of M. laciniatus from across the species’ range in two common gardens varying in day length to measure mean and plastic trait expression in several traits previously shown to be involved in adaptation to M. laciniatus’s rocky outcrop microhabitat: flowering time, size-related traits, and leaf shape. We tested for phenotypic plasticity and GxE, examined correlations between the mean phenotype and plasticity, and tested for a relationship between trait variation and population elevation and latitude. We did not find a strong correlation between mean and plastic trait expression at the individual genotype level suggesting that they operate under independent genetic controls. We identified multiple traits that show patterns consistent with local adaptation to elevation: critical photoperiod, flowering time, flower size, mean leaf lobing, and leaf lobing plasticity. These trends occur along multiple geographically independent altitudinal clines indicating that selection is a more likely cause of this pattern than gene flow among nearby populations with similar trait values. We also found that population variation in mean leaf lobing is associated with latitude. Our results indicate that both having more highly lobed leaves and greater leaf shape plasticity may be adaptive at high elevation within M. laciniatus. Our data strongly suggest that traits known to be under divergent selection between M. laciniatus and close relative Mimulus guttatus are also under locally varying selection within M. laciniatus.

Uncovering glacial footprints and identifying phylogeographic units in the freshwater crab Potamon elbursi Pretzmann, 1962 (Decapoda: Potamidae) based on mitochondrial data

The current patterns of biodiversity have significantly been affected by glacial-interglacial cycles during the Pleistocene period. True freshwater crabs are considered as poor dispersers and terrestrial barriers restrict gene flow between their local populations. Recent studies, however, suggest that certain environmental conditions, such as periods of heavy rainfall and humidity, can facilitate their between-drainage dispersal and will result in the evolution of homogenous genetic patterns among different drainage systems. Here we tested this hypothesis by comparing populations of the endemic freshwater crab Potamon elbursi Pretzmann, 1962 distributed in two drainage systems, the Caspian Sea and Namak Lake, in northern Iran. Our results based on the genetic analysis of 70 new and 61 previously published sequences of the mitochondrial cytochrome oxidase subunit I gene revealed a substantial haplotype diversity in some populations and high levels of local population structuring in others. Initially, we found mixed evidence of genetic differentiation and connectivity among drainages and populations. Genetic differentiation between the two drainages only became apparent after the Sepirdood population (which belongs to the Caspian Sea drainage) was excluded. Subsequently, the two drainages showed significant genetic distinctions, with a limited gene flow between them. Our demographic analyses supported recent population bottlenecks, followed by a rapid demographic and/or spatial expansion dating back to the Pleistocene climatic fluctuations. Species distribution modelling suggests that precipitation during warm weather conditions profoundly affects the distribution of P. elbursi. This study indicates that freshwater crabs can override short land barriers under favorable weather conditions and will have conservation implications in the face of contemporary climatic fluctuations.

Anthropogenetic study of the Arabic - speaking population of Chaouia Ouardigha (Morocco) based on autosomal STRs

BackgroundThe Chaouia - Ouradigha is a historical and ethno-geographic region of Morocco. Despite its historical relevance, this region has not received sufficient attention in terms of population genetic exploration. The present study aims to provide new data on the genetic background of the Chaouia-Ouardigha population, the Arabic-speaking North African population in the western center of Morocco, and to examine the relationship between this population and other reference populations based on our dataset as well as previously published population data. Genetic exploration will enable the reconstruction of past gene flows that have influenced the genetic makeup of this particular population. We utilized the Investigator® IDplex Plus PCR amplification kit (Qiagen, Germany) to establish the allelic frequencies and forensic statistical parameters of 15 autosomal Short Tandem Repeats (STRs) included in the kit in 153 random healthy unrelated individuals from the Chaouia-Ourdigha region.ResultsThe Chaouia-Ouardigha population, which speaks Arabic, exhibits a high degree of genetic diversity with heterozygosity values ranging from 0.670 to 0.879. The loci with the highest allele frequencies, namely D7S820 and TPOX, have the lowest heterozygosity values (0.670 and 0.672, respectively), resulting in lower exclusion power (PE) and typical relatedness index (TPI) values (PE = 0.427 and TPI = 1.66 for TPOX; PE = 0.442 and TPI = 1.72 for D7S820). Phylogenetic analysis showed that the Arabic-speaking population of Chaouia-Ouardigha was found to be distinct from Sub-Saharan, East Asian, and Latin American populations.ConclusionsOur study provides insights into the genetic connections of the Chaouia Ouardigha population, highlighting how historical events, socio-cultural influences, and geographical proximity have contributed to shaping their genetic structure. It demonstrates the substantial impact of historical events and geographical closeness in fostering affinities between the Chaouia Ouardigha community and neighboring populations in North Africa, Southern Europe, and the Middle East. Additionally, the study has generated valuable data confirming the effectiveness of these 15 genetic markers for forensic applications across the broader population.

Comparative population genomics reveals convergent and divergent selection in the Apricot-Peach-Plum-Mei Complex

Abstract The economically significant genus Prunus includes fruit and nut crops that have been domesticated for shared and specific agronomic traits, however, the genomic signals of convergent and divergent selection have not been elucidated. In this study, we aim to detect genomic signatures of convergent and divergent selection by conducting comparative population genomic analyses of the Apricot-Peach-Plum-Mei (APPM) complex, utilizing a haplotype-resolved telomere-to-telomere (T2T) genome assembly and population resequencing data. The haplotype-resolved T2T reference genome for the plum cultivar was assembled through HiFi and Hi-C reads, resulting in two haplotypes with 251.25 Mb and 251.29 Mb in size, respectively. Comparative genomics reveals a chromosomal translocation of approximately 1.17 Mb in the apricot genomes compared to peach, plum, and mei. Notably, the translocation involves the D locus, significantly impacting acidity (TA), pH, and sugar content. Population genetic analysis detected substantial gene flow between plum and apricot, with introgression regions enriched in post-embryonic development and pollen germination processes. Comparative population genetic analyses revealed convergent selection for stresses, flower development, and fruit ripening, along with divergent selection shaping crop-specific genes, such as somatic embryogenesis in plum, pollen germination in mei, and hormone regulation in peach. Notably, selective sweeps on chromosome 7 coincide with a chromosomal co-linearity from the comparative genomics, impacting key fruit-softening genes such as PG, regulated by ERF and RMA1H1. Overall, this study provides insights into the genetic diversity, evolutionary history, and domestication of the APPM complex, offering valuable implications for genetic studies and breeding programs of Prunus crops.

Altai Mountains – cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)

AbstractMountains form a diverse mosaic of microhabitats over small distances created by changes in climate, soil, and water availability. A key to adaptation of plants to such microhabitats is genetic variation; however, natural accumulation of genetic variation through mutation is slow and often not sufficient alone. Adaptive introgression via hybridization is an alternative to generate genetic variation. Here, we investigate hybridization and discuss its adaptive role in Veronica subg. Pseudolysimachium at their Altai Mountains distribution. To support our hypotheses of frequent hybridization, we genotyped thousands of SNPs for 233 individuals from 10 species and 7 putative hybrids previously described based on morphology. We employed Bayesian and likelihood statistical models and supported our results by morphometric analysis and genomic in situ hybridization (GISH). The results suggest that almost all the individuals of the putative hybrids are of F1 type. The GISH investigation in one case strongly supports homoploid hybridization (origin of V. ×schmakovii from V. longifolia and V. porphyriana. Divergence times of Altai Veronica species are estimated to be within 1–2 million years ago with high probability of gene flow over that time. Our results also demonstrate that the direction of gene flow is mainly from the locally endemic V. porphyriana. We hypothesize that the large Siberian plains and topographically diverse foreland of the Altai Mountains provide an ideal setting for hybridization with the potential for adaptive introgression of alleles conferring tolerance to cooler climates, to the lowland species migrating into the Altai Mountains.

Global assessment of effective population sizes: Consistent taxonomic differences in meeting the 50/500 rule.

Effective population size (Ne) is a particularly useful metric for conservation as it affects genetic drift, inbreeding and adaptive potential within populations. Current guidelines recommend a minimum Ne of 50 and 500 to avoid short-term inbreeding and to preserve long-term adaptive potential respectively. However, the extent to which wild populations reach these thresholds globally has not been investigated, nor has the relationship between Ne and human activities. Through a quantitative review, we generated a dataset with 4610 georeferenced Ne estimates from 3829 populations, extracted from 723 articles. These data show that certain taxonomic groups are less likely to meet 50/500 thresholds and are disproportionately impacted by human activities; plant, mammal and amphibian populations had a <54% probability of reaching = 50 and a <9% probability of reaching = 500. Populations listed as being of conservation concern according to the IUCN Red List had a smaller median than unlisted populations, and this was consistent across all taxonomic groups. was reduced in areas with a greater Global Human Footprint, especially for amphibians, birds and mammals, however relationships varied between taxa. We also highlight several considerations for future works, including the role that gene flow and subpopulation structure plays in the estimation of in wild populations, and the need for finer-scale taxonomic analyses. Our findings provide guidance for more specific thresholds based on Ne and help prioritise assessment of populations from taxa most at risk of failing to meet conservation thresholds.

Circular genetic structure of the Abies nephrolepis species complex shaped by the circular landform of Northeast Asia

AbstractAimPinaceae have been noted for their tendency towards reticulation as a result of interspecific hybridization. Here, we demonstrated the phylogeographic dynamics of the native Northeast Asian sub‐alpine conifer, Abies nephrolepis species complex (ANSC), evolving in circular overlaps along the Northeast Asian landform, which functions as a corridor with the sea, thus acting as a geographic barrier.LocationNortheast Asia: the Korean Peninsula, Japanese Archipelago, Russian Far East and northeastern China.TaxonAbies nephrolepis species complex (Family Pinaceae, Genus Abies, Section Balsamea, Abies nephrolepis, A. koreana, A. veitchii and A. sachalinensis).MethodsA total of 728 individuals from 38 ANSC populations were analysed using multiplexed inter‐simple sequence repeat genotyping by sequencing to capture variations in biparental nuclear genomes. Eight mitochondrial regions and eight chloroplast regions of each individual were sequenced using the MiSeq platform and Sanger sequencing. Species distribution models were generated.ResultsBayesian clustering with 507 nuclear single nucleotide polymorphisms and the discrepancy between cytoplasmic and nuclear genome lineages implied contemporary and ancient connections between neighbouring species in the form of circular overlap. This genetic connectivity was supported by principal component analysis. Strong correlations between genetic distance and geographic distance were observed, suggesting that gene flow occurs through a continuous chain around the sea. We also found that gene flow direction and intensity changed over time, with support from palaeodistribution modelling.ConclusionPast hybridization events were captured in cytoplasmic genomes, generating heterogeneity across maternal ancestries. This intensive phylogeographic study demonstrates speciation with incomplete reproductive isolation (continuous gene flow) among neighbouring species with an alteration of the direction and intensity of gene flow due to climate change. The divergence of ANSC due to repeated isolation and reconnection caused by heterogenous physiological environments and climate fluctuation provides a model to solve evolutionary scenarios for reticulate evolution in Pinaceae and other plants.

Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations

The blue wildebeest (Connochaetes taurinus) is a keystone species in savanna ecosystems from southern to eastern Africa, and is well known for its spectacular migrations and locally extreme abundance. In contrast, the black wildebeest (C. gnou) is endemic to southern Africa, barely escaped extinction in the 1900s and is feared to be in danger of genetic swamping from the blue wildebeest. Despite the ecological importance of the wildebeest, there is a lack of understanding of how its unique migratory ecology has affected its gene flow, genetic structure and phylogeography. Here, we analyze whole genomes from 121 blue and 22 black wildebeest across the genus’ range. We find discrete genetic structure consistent with the morphologically defined subspecies. Unexpectedly, our analyses reveal no signs of recent interspecific admixture, but rather a late Pleistocene introgression of black wildebeest into the southern blue wildebeest populations. Finally, we find that migratory blue wildebeest populations exhibit a combination of long-range panmixia, higher genetic diversity and lower inbreeding levels compared to neighboring populations whose migration has recently been disrupted. These findings provide crucial insights into the evolutionary history of the wildebeest, and tangible genetic evidence for the negative effects of anthropogenic activities on highly migratory ungulates.

Genetic differentiation of the Capparis spinosa group in the Mediterranean area

The Capparis spinosa group is represented in the Mediterranean by a complex of taxa widespread in North Africa, the Middle East, and southern Europe. The taxonomy of this group used to be based on morphological characters with little work on the genetics of the group, and there is still much to be learned about its evolutionary history and diversification. We sampled 431 individuals of two subspecies and five varieties of C. spinosa and analysed them using highly informative EST-SSR markers to evaluate the population genetic diversity, structure and differentiation of the species in the Mediterranean. In addition, comparisons with the genetic profiles of C. spinosa subsp. cartilaginea, the putative ancestral taxon were made to investigate the phylogeographic history and possible gene flow across taxa. Integrated Bayesian approaches showed: i) a high divergence among C. spinosa subsp. spinosa var. canescens, C. spinosa subsp. spinosa var. aegyptia and the three varieties belonging to C. spinosa subsp. rupestris (var. rupestris, var. ovata and var. myrtifolia), with a clear separation between var. aegyptia and var. canescens which allows to consider var. aegyptia as a subspecies of C. spinosa; ii) a significant correlation between genetic divergence and geographic distance between the five varieties studied; iii) that the different varieties in the Mediterranean may have been derived from C. spinosa subsp. cartilaginea. Further genomic investigations are required to confirm our results. However, the findings presented allows us to suggest the genus Capparis can be considered a model for the study of the gene flow and differentiation in species occurring in a wide range of habitats.

Highly structured populations of copepods at risk to deep-sea mining: Integration of genomic data with demogenetic and biophysical modelling.

Copepoda is the most abundant taxon in deep-sea hydrothermal vents, where hard substrate is available. Despite the increasing interest in seafloor massive sulphides exploitation, there have been no population genomic studies conducted on vent meiofauna, which are known to contribute over 50% to metazoan biodiversity at vents. To bridge this knowledge gap, restriction-site-associated DNA sequencing, specifically 2b-RADseq, was used to retrieve thousands of genome-wide single-nucleotide polymorphisms (SNPs) from abundant populations of the vent-obligate copepod Stygiopontius lauensis from the Lau Basin. SNPs were used to investigate population structure, demographic histories and genotype-environment associations at a basin scale. Genetic analyses also helped to evaluate the suitability of tailored larval dispersal models and the parameterization of life-history traits that better fit the population patterns observed in the genomic dataset for the target organism. Highly structured populations were observed on both spatial and temporal scales, with divergence of populations between the north, mid, and south of the basin estimated to have occurred after the creation of the major transform fault dividing the Australian and the Niuafo'ou tectonic plate (350 kya), with relatively recent secondary contact events (<20 kya). Larval dispersal models were able to predict the high levels of structure and the highly asymmetric northward low-level gene flow observed in the genomic data. These results differ from most studies conducted on megafauna in the region, elucidating the need to incorporate smaller size when considering site prospecting for deep-sea exploitation of seafloor massive sulphides, and the creation of area-based management tools to protect areas at risk of local extinction, should mining occur.

Does selection favour the maintenance of porous species boundaries?

The endpoint of speciation has been viewed as complete isolation and the absence of gene flow between species. If the influx of genes from another species is maladaptive because species have different adaptations and genetic backgrounds, selection should favour the closing of species boundaries and zero gene flow, a process known as reinforcement. Recently, numerous cases of gene flow between species have been identified, many of which involved adaptive introgression of beneficial alleles. These cases could reflect transient states on the way to closed species boundaries or the result of declining strength or efficacy of selection for reinforcement as the level of gene flow approaches zero. An alternative hypothesis, however, is that selection favours porous species boundaries that allow beneficial alleles to cross, especially in changing environments. This perspective evaluates the conditions that would be needed for selection to favour porous species boundaries and the evidence for them. A contrast is made between hybridization in sexual eukaryotes and gene transfer via homologous recombination in bacteria. Current evidence is inconclusive on whether non-zero gene flow is favoured by selection. Studies are needed that quantify selection gradients on rates of gene flow and test for evolution towards intermediate values, especially experiments that manipulate conditions and track evolution for multiple generations. Estimation of gene flow networks for more clades and regional assemblages using emerging genome data will also allow the evolutionary determinants of interspecific gene flow to be better understood.

Keeping the door ajar: when is a little gene flow a good thing?

Keeping the door ajar: when is a little gene flow a good thing?

Development and characterization of microsatellite markers for population genetics of the cocoa pod borer Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae).

The cocoa pod borer (CPB) Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae) is one of the major constraints for cocoa production in South East Asia. In addition to cultural and chemical control methods, autocidal control tactics such as the Sterile Insect Technique (SIT) could be an efficient addition to the currently control strategy, however SIT implementation will depend on the population genetics of the targeted pest. The aim of the present work was to search for suitable microsatellite loci in the genome of CPB that is partially sequenced. Twelve microsatellites were initially selected and used to analyze moths collected from Indonesia, Malaysia, and the Philippines. A quality control verification process was carried out and seven microsatellites found to be suitable and efficient to distinguish differences between CPB populations from different locations. The selected microsatellites were also tested against a closely related species, i.e. the lychee fruit borer Conopomorpha sinensis (LFB) from Vietnam and eight loci were found to be suitable. The availability of these novel microsatellite loci will provide useful tools for the analysis of the population genetics and gene flow of these pests, to select suitable CPB strains to implement the SIT.