Patterns Of Gene Flow Research Articles

Staying close: short local dispersal distances on a managed forest of two Patagonian Nothofagus species

Abstract Understanding the impact of management on the dispersal potential of forest tree species is pivotal in the context of global change, given the implications of gene flow on species evolution. We aimed to determine the effect of logging on gene flow distances in two Nothofagus species from temperate Patagonian forests having high ecological relevance and wood quality. Therefore, a total of 778 individuals (mature trees and saplings) of Nothofagus alpina and N. obliqua, from a single plot managed 20 years ago (2.85 hectares), were mapped and genotyped at polymorphic nuclear microsatellite loci. Historical estimates of gene dispersal distance (based on fine-scale spatial genetic structure) and contemporary estimates of seed and pollen dispersal (based on spatially explicit mating models) were obtained. The results indicated restricted gene flow (gene distance ≤ 45 m, both pollen and seed), no selfing and significant seed and pollen immigration from trees located outside the studied plot but in the close surrounding area. The size of trees (diameter at breast height and height) was significantly associated with female and/or male fertility. The significant fine-scale spatial genetic structure was consistent with the restricted seed and pollen dispersal. Moreover, both estimates of gene dispersal (historical and contemporary) gave congruent results. This suggests that the recent history of logging within the study area has not significantly influenced on patterns of gene flow, which can be explained by the silviculture applied to the stand. The residual tree density maintained species composition, and the homogeneous spatial distribution of trees allowed the maintenance of gene dispersal. The short dispersal distance estimated for these two species has several implications both for understanding the evolution of the species and for defining management, conservation and restoration actions. Future replication of this study in other Nothofagus Patagonian forests would be helpful to validate our conclusions.

First steps towards the identification of evolutionarily significant units in Mexican native trout: An assessment of microsatellite variation

In the remote high-elevation streams and rivers in the northwest of Mexico, there is an endemic and highly diverse group of native trout related to the rainbow trout lineage (Oncorhynchus mykiss). Currently, only two species have been formally described from this trout complex, the Mexican golden trout, O. chrysogaster, and the San Pedro Martir rainbow trout, O. m. nelsoni, but only the former occurs in the Sierra Madre Occidental (SMO). South and north of the O. chrysogaster range, there are other undescribed trout that have been recently discovered. Given the various human impacts on aquatic systems occupied by these Mexican native trout, the lack of taxonomic descriptions and the imminent risk of losing populations without their even being documented, we sought to infer a hierarchical population structure of the Mexican native trout, determine the geographic patterns of genetic diversity and gene flow among them, and identify evolutionarily significant units for a prompt conservation strategy. The allelic diversity across eleven microsatellite loci was used to assess genetic divergences of wild trout collected throughout its range in Mexico. Our results reject the old hypothesis that many of the trout in Mexico are introduced or translocated hatchery-reared rainbow trout and strongly support the new hypothesis of distinct genetic populations and lineages in the northwest of Mexico. According to the different statistical analysis of the genetic data, we distinguish between species and subspecies (O. chrysogaster, O. mykiss, and O. m. nelsoni) of the other regional lineages of undescribed trout (northern and southern) inhabiting the SMO. We also found a strong genetic substructure within these large clusters. We propose the presence of seven Evolutionarily Significant Units in the drainage basins of the SMO (two occur in the northern region, four in the southern, and one for the area of distribution of O. chrysogaster) and one in north-western Baja California. Based in microsatellite data a minimum gene flow among populations is evidenced, resulting the presence the highly divergent populations.

Genetic diversity, population structure, and immigration, in a partially hunted puma population of south-central Argentina

AbstractCarnivores are decreasing globally due in part to anthropogenic ecological disturbances. In Argentina, human activities have fragmented wildlife habitat, thereby intensifying puma–livestock conflict and leading to population control of the predator species by hunting. We investigated genetic variability and population structure of pumas (Puma concolor) from three south-central Argentine provinces with two different management policies for the species: full protection versus legal hunting. All genetic estimates were based on 83 individuals genotyped at 25 species-specific microsatellite loci. The overall genetic diversity was high (observed heterozygosity = 0.63), but lower than in other South American populations. Spatial analyses revealed the presence of two bottlenecked genetic clusters with very similar diversity and low gene flow (3% per generation) between them. However, analyses based on a priori separated groups showed that gene flow follows increasing values of hunting pressure, converging to the area with the greatest number of individuals harvested. Our results suggest that hunting pressure likely is contributing to the gene flow pattern, limiting pumas’ movements and creating a metapopulation dynamic among geographic subpopulations. Integrated demographic and genetic approaches are needed to better understand pumas’ movements across the landscape and adopt successful management plans to achieve long-term population viability.

Genetic consequences of being a dwarf: do evolutionary changes in life-history traits influence gene flow patterns in populations of the world's smallest goldenrod?

Contrasting life-history traits can evolve through generations of dwarf plant ecotypes, yet such phenotypic changes often involve decreased plant size and reproductive allocation, which can configure seed dispersal patterns and, subsequently, population demography. Therefore, evolutionary transitions to dwarfism can represent good study systems to test the roles of life-history traits in population demography by comparing genetic structure between related but phenotypically divergent ecotypes. In this study, we examined an ecotypic taxon pair of the world's smallest goldenrod (stem height 2.6 cm) in alpine habitats and its closely related lowland taxon (30-40 cm) found on Yakushima Island, Japan. Genetic variation in chloroplast DNA sequences, nuclear microsatellites and genome-wide single-nucleotide polymorphisms were used to investigate 197 samples from 16 populations, to infer the population genetic demography and compare local genetic structure of the ecotypes. We found a pronounced level of genetic differentiation among alpine dwarf populations, which were much less geographically isolated than their lowland counterparts. In particular, several neighbouring dwarf populations (located ~500 m apart) harboured completely different sets of chloroplast haplotypes and nuclear genetic clusters. Demographic modelling revealed that the dwarf populations have not exchanged genes at significant levels after population divergence. These lines of evidence suggest that substantial effects of genetic drift have operated on these dwarf populations. The low-growing stature and reduced fecundity (only 3.1 heads per plant) of the dwarf plants may have reduced gene flow and rare long-distance seed dispersal among habitat patches, although the effects of life-history traits require further evaluation using ecological approaches.

Isolation and characterization of microsatellite loci in Astroniumgraveolens (Anacardiaceae) and cross amplification in related species.

Microsatellite markers are a useful genetic tool to answer ecological and conservation genetics questions. Microsatellite primers were developed and characterized to evaluate forest fragmentation effects on genetic structure, diversity and gene flow patterns in the dioecious tropical tree Astroniumgraveolens (Anacardiaceae). Using genomic library enrichment, sixteen microsatellite loci were developed for A.graveolens. Polymorphism was evaluated in 80 individuals from four localities in Mexico. The overall number of alleles detected was 63, average alleles per locus 3.9 with a range from one to 11 per locus. Cross amplification trails on related species in the Anacardiaceae family: Spondiaspurpurea and Amphipterygiumadstringens, achieved successful amplification for all primers. Microsatellite markers described here are the first to be characterized for A.graveolens. These genetic markers will be a useful tool to assess the genetic consequences of habitat fragmentation and selective logging on A.graveolens populations. Cross amplification success on S.purpureaandA.adstringens suggest that they may be used for population genetic studies in other species within the family.

Geography and spawning season drive genetic divergence among populations of the hard coral Acropora tenuis from Indonesia and Western Australia

It has long been hypothesized that Western Australian coral reefs are genetically connected to those in Indonesia via long-distance dispersal, and that this connection may influence the timing of annual mass coral spawning on Western Australian coral reefs. This genetic connection has not been tested, and it requires re-evaluation because spawning patterns of Western Australian corals are not as synchronous or seasonal as originally thought. Here, we used population genetics to examine patterns of gene flow among populations of the scleractinian coral Acropora tenuis in Indonesia and Western Australia. Analysis of microsatellite data showed that Indonesian and Australian populations are highly genetically differentiated. Importantly, this genetic divergence is associated with differences in the seasonal spawning time of A. tenuis between the two regions, with Indonesian populations dominated by ‘spring’ spawners and Western Australian populations dominated by ‘autumn’ spawners, indicating that spawning season has an important influence on genetic structure. Furthermore, negligible gene flow between Indonesia and Western Australia indicates that the recolonization of inshore Western Australian populations since the Last Glacial Maximum was independent of input from Indonesian populations.

The Potential for Discrepancies in Population History Signatures from Different Segments of the Human Skeleton

The use of metric data from skeletal remains to assess models of evolutionary processes is a well‐established substitute for genomic data. However, it has been suggested in previous research that certain osteological elements retain population history signatures better than others because they are likely less subject to natural selection. This study examines the potential for differences in gene flow models using human crania (traits shown to evolve through neutral processes) versus postcrania (traits provisionally shown to have evolved in response to selection). In this study, we sampled from four large pueblos in the American Southwest representing a short temporal period and small geographic area (Arizona, c. 1200–1400, N=267). Based on a robust archaeological record detailing changes in material culture, researchers hypothesize immigration into this region from non‐local populations.The study uses gene flow models based on variance comparison methods developed by Relethford and Blangero. Metric data were analyzed using the R statistical environment and RMET 5.0, a program based on the Relethford‐Blangero statistics. Under a quantitative genetic model, gene flow results in higher‐than‐expected variance in a population, which RMET examines. Likewise, gene flow decreases the biodistance between populations sharing genes, and so these were compared through Mahalanobis D2 distances.Cranial and postcranial dimensions generally result in different patterns of gene flow. Comparing residual phenotypic variances from the Relethford‐Blangero model, only one of the four sites presents the same pattern of gene flow between cranial and postcranial results. Biodistance analyses show that the Pueblo population that is the greatest distance remains consistent in both crania and postcrania, but which of the other three is closest changes between the two body regions. This incongruence has implications for local disparities in the variance and in the mean differences between aspects of morphology.Either the upper or lower limb elements may be driving the discrepancies, as limb bones are shown to respond dissimilarly to selection on a global scale. We conducted analyses comparing results of the upper and lower limbs. The results indicate upper limb residual variances are higher, but only the lower limb matches the patterns observed in the overall postcranial analysis. Biological distance relationships are very similar between the limbs, though the lower limb data is closer in magnitude to the overall postcranial distance. It is possible that the lower limb is driving the variance results for the postcrania, a result that provisionally reflects the evolution of femoral traits in recent humans in response to neutral processes. This has implications for how we evaluate population history using phenotypic data, particularly considering which phenotypic data to employ.Support or Funding InformationThis research was partially funded by the University of Tennessee Department of Anthropology through a Kneberg‐Lewis Scholarship.

Biome stability predicts population structure of a southern African aridland bird species.

Environments are heterogeneous in space and time, and the permeability of landscape and climatic barriers to gene flow may change over time. When barriers are present, they may start populations down the path toward speciation, but if they become permeable before the process of speciation is complete, populations may once more merge. In Southern Africa, aridland biomes play a central role in structuring the organization of biodiversity. These biomes were subject to substantial restructuring during Plio‐Pleistocene climatic fluctuations, and the imprint of this changing environment should leave genetic signatures on the species living there. Here, we investigate the role of adjacent aridland biome boundaries in structuring the genetic diversity within a widespread generalist bird, the Cape Robin‐chat (Cossypha caffra). We find evidence supporting a central role for aridland biomes in structuring populations across Southern Africa. Our findings support a scenario wherein populations were isolated in different biome refugia, due to separation by the exceptionally arid Nama Karoo biome. This biome barrier may have arisen through a combination of habitat instability and environmental unsuitability, and was highly unstable throughout the Plio‐Pleistocene. However, we also recovered a pattern of extensive contemporary gene flow and admixture across the Nama Karoo, potentially driven by the establishment of homesteads over the past 200 years. Thus, the barrier has become permeable, and populations are currently merging. This represents an instance where initial formation of a barrier to gene flow enabled population differentiation, with subsequent gene flow and the merging of populations after the barrier became permeable.

Landscape drivers of connectivity for a forest rodent in a coffee agroecosystem

The majority of remaining tropical forests exist as fragments embedded in a matrix of agricultural production. Understanding the effects of these agricultural landscapes on species dispersal is crucial in the development of successful conservation planning. The objective of this study was to examine the influence of five landscape features within a coffee agroecosystem (i.e., slope, elevation, streams, riparian effect, and tree cover) on Heteromys desmarestianus goldmani gene flow. We expected that landscape variables linked to more intense agricultural management (e.g., low tree cover, riparian effect) would reduce gene flow in H. d. goldmani. This study was conducted in a 4 km × 2 km area within the coffee growing region of Soconusco in Chiapas, Mexico. We used 12 microsatellite markers to calculate individual-based estimates of gene flow as a measure of dispersal. We used resistance surface modelling, using ResistanceGA (Peterman in Methods Ecol Evol 9:1638–1647, 2018) to identify if any of the landscape features analyzed explained the patterns of gene flow. Our results showed patterns of population structure and weak isolation-by-distance, as found previously for H. d. goldmani by Otero Jimenez et al. (Conserv Genet 19:495–499, 2018). Slope and tree cover were the two landscape features that could best explain gene flow patterns. More specifically, intermediate slopes and tree cover represent the lowest resistance to gene flow for H. d. goldmani and, thus, have a role in promoting gene flow in this species. This study highlights the potential of integrating molecular and landscape data to explore population connectivity of elusive species, such as terrestrial small mammals. Our study adds to the growing body of literature in landscape genetics by demonstrating that a rodent species shows population structure at a small scale resulting from landscape factors linked to agricultural management.

Genetic structure, gene flow pattern, and association analysis of superior germplasm resources in domesticated upland cotton (Gossypium hirsutum L.)

Gene flow patterns and the genetic structure of domesticated crops like cotton are not well understood. Furthermore, marker-assisted breeding of cotton has lagged far behind that of other major crops because the loci associated with cotton traits such as fiber yield and quality have scarcely been identified. In this study, we used 19 microsatellites to first determine the population genetic structure and patterns of gene flow of superior germplasm resources in upland cotton. We then used association analysis to identify which markers were associated with 15 agronomic traits (including ten yield and five fiber quality traits). The results showed that the upland cotton accessions have low levels of genetic diversity (polymorphism information content = 0.427), although extensive gene flow occurred among different ecological and geographic regions. Bayesian clustering analysis indicated that the cotton resources used in this study did not belong to obvious geographic populations, which may be the consequence of a single source of domestication followed by frequent genetic introgression mediated by human transference. A total of 82 maker–trait associations were examined in association analysis and the related ratios for phenotypic variations ranged from 3.04% to 47.14%. Interestingly, nine SSR markers were detected in more than one environmental condition. In addition, 14 SSR markers were co-associated with two or more different traits. It was noteworthy that NAU4860 and NAU5077 markers detected at least in two environments were simultaneously associated with three fiber quality traits (uniformity index, specific breaking strength and micronaire value). In conclusion, these findings provide new insights into the population structure and genetic exchange pattern of cultivated cotton accessions. The quantitative trait loci of domesticated cotton identified will also be very useful for improvement of yield and fiber quality of cotton in molecular breeding programs.

Janzen-Connell effects shape gene flow patterns and realized fitness in the tropical dioecious tree Spondias purpurea (ANACARDIACEAE)

Pollination and seed dispersal patterns determine gene flow within plant populations. In tropical forests, a high proportion of trees are dioecious, insect pollinated and dispersed by vertebrates. Dispersal vectors and density dependent factors may modulate realized gene flow and influence the magnitude of Fine Scale Genetic Structure (FSGS), affecting individual fitness. Spondias purpurea is a vertebrate-dispersed, insect-pollinated dioecious tropical tree. We assessed the influence of sex ratio, effective and realized gene flow on genetic diversity, FSGS and individual fitness within a 30 ha plot in the tropical dry forest reserve of Chamela-Cuixmala, Mexico. All individuals within the plot were tagged, geo-referenced and sampled for genetic analysis. We measured dbh and monitored sex expression during two reproductive seasons for all individuals. We collected seeds directly from maternal trees for effective pollen dispersal analysis, and analyzed established seedlings to assess realized pollen and seed dispersal. Nine microsatellite loci were used to describe genetic diversity parameters, FSGS and gene flow patterns among different size classes. A total of 354 individuals were located and classified into three size classes based on their dbh (<10, 10–20, and >20 cm). Population sex ratios were male biased and diametric size distributions differed among sexes, these differences may be the result of precocious male reproduction at early stages. Autocorrelation analyses indicate low FSGS (Fj <0.07) across all size classes. Long realized pollen and seed dispersal and differences among effective and realized gene flow were detected. In our study site low FSGS is associated with high gene flow levels. Effective and realized gene flow indicate a population recruitment curve indicating Janzen-Connell effects and suggesting fitness advantages for long-distance pollen and seed dispersal events.

Recent kuru-induced female gene flow disrupted the coevolution of genes and languages in the Papua New Guinea highlands.

The island of New Guinea was settled by modern human over 50,000 years ago, and is currently characterized by a complex landscape and contains one-seventh of the world's languages. The Eastern Highlands of New Guinea were also the home to the devastating prion disease called kuru that primarily affected Fore-speaking populations, with some 68% of cases involving adult females. We characterized the mitochondrial DNA (mtDNA) diversity of highlanders from Papua New Guinea (PNG) to: (a) gain insight into the coevolution of genes and languages in situ over mountainous landscapes; and (b) evaluate the recent influence of kuru mortality on the pattern of female gene flow. We sequenced the mtDNA hypervariable segment 1 of 870 individuals from the Eastern and Southern Highlands of PNG using serums collected in the 1950s to 1960s. These highlanders were selected from villages representing 15 linguistic groups within the Trans-New Guinea phylum. Genetic, linguistic, and geographic distances were calculated separately and correlations among those distance matrices were assessed using the Mantel test. Geographic, genetic, and linguistic patterns were independently correlated with each other (p < .05). Increased mtDNA diversity in kuru-affected populations and low Fst estimates between kuru-affected linguistic groups were observed. In general, the genetic structure among the Highland populations was shaped by both geography and language, and language is a good predictor of mtDNA affinity in the PNG Highlands. High kuru female mortality increased female gene flow locally, disrupting coevolutionary pattern among genes, languages, and geography.

Anthropogenic disturbance drives dispersal syndromes, demography, and gene flow in amphibian populations

AbstractThere is growing evidence that anthropogenic landscapes can strongly influence the evolution of dispersal, particularly through fragmentation, and may drive organisms into an evolutionary trap by suppressing dispersal. However, the influence on dispersal evolution of anthropogenic variation in habitat patch turnover has so far been largely overlooked. In this study, we examined how human‐driven variation in patch persistence affects dispersal rates and distances, determines dispersal‐related phenotypic specialization, and drives neutral genetic structure in spatially structured populations. We addressed this issue in an amphibian, Bombina variegata, using an integrative approach combining capture–recapture modeling, demographic simulation, common garden experiments, and population genetics. B. variegata reproduces in small ponds that occur either in habitat patches that are persistent (i.e., several decades or more), located in riverine environments with negligible human activity, or in patches that are highly temporary (i.e., a few years), created by logging operations in intensively harvested woodland. Our capture–recapture models revealed that natal and breeding dispersal rates and distances were drastically higher in spatially structured populations (SSPs) in logging environments than in riverine SSPs. Population simulations additionally showed that dispersal costs and benefits drive the fate of logging SSPs, which cannot persist without dispersal. The common garden experiments revealed that toadlets reared in laboratory conditions have morphological and behavioral specialization that depends on their habitat of origin. Toadlets from logging SSPs were found to have higher boldness and exploration propensity than those from riverine SSPs, indicating transgenerationally transmitted dispersal syndromes. We also found contrasting patterns of neutral genetic diversity and gene flow in riverine and logging SSPs, with genetic diversity and effective population size considerably higher in logging than in riverine SSPs. In parallel, intrapatch inbreeding and relatedness levels were lower in logging SSPs. Controlling for the effect of genetic drift and landscape connectivity, gene flow was found to be higher in logging than in riverine SSPs. Taken together, these results indicate that anthropogenic variation in habitat patch turnover may have an effect at least as important as landscape fragmentation on dispersal evolution and the long‐term viability and genetic structure of wild populations.

Gene Flow Patterns among Aedes aegypti (Diptera: Culicidae) Populations in Sri Lanka

In Sri Lanka, dengue is the most serious arboviral disease. Recent increases in dengue cases suggest a higher infection rate and spread of the disease to new areas. The present study explores gene flow patterns of Ae. aegypti, the main vector of dengue disease, among 10 collection sites including major ports and inland cities using variations at 11 microsatellite loci. Discriminant analysis of principal components (DAPC) and k-means clustering estimated eight genetic clusters. Analysis of Molecular Variance (AMOVA) estimated equal variances among cities and among collections in Colombo, Sri Lanka. Significant evidence, although weak, was detected for isolation by distance. Analysis of gene flow rates and directions using MIGRATE-n indicated that populations throughout the island served as a source of immigrants for Colombo with abundant gene flow among major commercial cities in Sri Lanka, which appear to receive migrant mosquitoes from throughout Sri Lanka. The observed patterns probably arise through human movement of Ae. aegypti during commerce from throughout Sri Lanka into Colombo increasing the risk of spread. The patterns uncovered in this study are significant for global health as Sri Lanka is situated along a key international shipping route.

Carnivore population structure across an urbanization gradient: a regional genetic analysis of bobcats in southern California

In human-dominated landscapes, habitat fragmentation and barriers to movement can interrupt gene flow. While often considered at a local extent, regional analyses are also needed to reveal broader landscape-mediated population processes. To explore the relationship between patterns of gene flow and fragmentation resulting from urbanization across southern California, we used the bobcat as an indicator species. We assembled data for a landscape level genetic analysis across southern California from both archived and new samples, including two northern Californian populations for comparison, to identify local and regional areas affected by isolation. Our regional analyses focused on a dataset of 19 microsatellite loci for 118 individuals and a dataset of 422 individuals genotyped at 11 loci. We examined population genetic structure and examined how pairwise genetic distance of all population clusters aligned with geographic distance. We employed a landscape genetic analysis based on resistance to determine which features of the landscape likely play a role in determining the patterns of genetic structure we observed. Study populations generally exhibited a pattern of isolation by distance and localized areas of genetic isolation. The landscape genetic analysis suggested that, in southern California, these patterns are driven by overall landscape permeability. Although local studies are key to examining the effects of urbanization and habitat fragmentation on populations, we demonstrate the importance of combining local and regional analyses for wide-ranging species to understand and maintain connectivity at local scales, while also improving and establishing sustainable linkages to habitats at the regional scale.

Bachelor groups in primate multilevel society facilitate gene flow across fragmented habitats.

In the face of ongoing habitat fragmentation, many primate species have experienced reduced gene flow resulting in a reduction of genetic diversity, population bottlenecks, and inbreeding depression, including golden snub-nosed monkeys Rhinopithecus roxellana. Golden snub-nosed monkeys live in a multilevel society composed of several 1 male harem units that aggregate to form a cohesive breeding band, which is followed by one or more bachelor groups composed of juvenile, subadult, and adult male members. In this research, we examine the continuous landscape resistance surface, the genetic diversity and patterns of gene flow among 4 isolated breeding bands and 1 all-male band in the Qinling Mountains, China. Landscape surface modeling suggested that human activities and ecological factors severely limit the movement of individuals among breeding bands. Although these conditions are expected to result in reduced gene flow, reduced genetic diversity, and an increased opportunity for a genetic bottleneck, based on population genetic analyses of 13 microsatellite loci from 188 individuals inhabiting 4 isolated breeding bands and 1 all-male band, we found high levels of genetic diversity but low levels of genetic divergence, as well as high rates of gene flow between males residing in the all-male band and each of the 4 breeding bands. Our results indicate that the movement of bachelor males across the landscape, along with their association with several different breeding bands, appears to provide a mechanism for promoting gene flows and maintaining genetic diversity that may counteract the otherwise isolating effects of habitat fragmentation.

Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters.

A background study is important for the conservation and stock management of a species. Terapon jarbua is a coastal Indo-Pacific species, sourced for human consumption. This study examined 134 samples from the central west and east coasts of Peninsular (West) Malaysia and East Malaysia. A 1446-bp concatenated dataset of mtDNA COI and Cyt b sequences was used in this study and 83 haplotypes were identified, of which 79 are unique haplotypes and four are shared haplotypes. Populations of T. jarbua in Malaysia are genetically heterogenous as shown by the high level of haplotype diversity ranging from 0.9167–0.9952, low nucleotide diversity ranging from 0.0288–0.3434, and high FST values (within population genetic variation). Population genetic structuring is not distinct as shown by the shared haplotypes between geographic populations and mixtures of haplotypes from different populations within the same genetic cluster. The gene flow patterns and population structuring observed among these regions are likely attributed to geographical distance, past historical events, allopatric speciation, dispersal ability and water currents. For instance, the mixture of haplotypes revealed an extraordinary migration ability of T. jarbua (>1200 km) via ancient river connectivity. The negative overall value of the neutrality test and a non-significant mismatch distribution are consistent with demographic expansion(s) in the past. The median-joining network concurred with the maximum likelihood haplotype tree with three major clades resolved. The scarcity of information on this species is an obstacle for future management and conservation purposes. Hence, this study aims to contribute information on the population structure, genetic diversity, and historical demography of T. jarbua in Malaysia.

Exploring the role of genetic diversity and relatedness in tree seedling growth and mortality: A multispecies study in a Bornean rainforest

Abstract Where conspecific seedlings occur at high densities, density‐dependent processes tend to depress their performance and survival relative to co‐occurring heterospecifics. We extend this observation to within‐species genetic diversity and relatedness. We posit that seedling growth and survival increase where there is higher genetic diversity, and lower relatedness, among seedling populations, under the expectation that increased genetic dissimilarity among conspecific seedlings affords greater resistance to pathogens. We used estimates of individual seedling genetic diversity (multilocus heterozygosity (sMLH)) and genetic relatedness among conspecific seedlings (pairwise kinship coefficients (LRI)), under high and low conspecific seedling density, coupled with censuses of seedling growth and mortality over 30 months to explore the role of genetic diversity and relatedness on growth and mortality of 1,485 seedlings of four dipterocarp species in an undisturbed Bornean tropical rainforest. We hypothesized that more genetically diverse and less related co‐occurring seedlings would display higher survival and growth rates. In three of our four species, lower genetic diversity increased the probability of mortality over 30 months. We observed no effect of genetic diversity on relative growth rates. Contrary to our expectations, only one species showed a negative effect of increased relatedness on mortality. In two of the four species studied, seedlings that were more genetically related to neighbouring conspecific seedlings in the sample plot were less likely to die, but grew more slowly. Synthesis. Our results confirm that genetic diversity and relatedness among seedlings shape survival probabilities differentially across species. In contrast, we found no differences in mortality and growth rates between plots with low and high seedling density. Our results suggest that a greater abundance of pollen donors could contribute to cohort seedling survival in some species, though not all, and the specific mechanisms by which genetic relatedness determines seedling demography remain uncertain. These results have conservation and management implications in view of changing patterns of gene flow in fragmented, exploited and degraded tropical rainforests, which might differentially influence natural regeneration among species.

Using genetics to inform restoration and predict resilience in declining populations of a keystone marine sponge

Genetic tools can have a key role in informing conservation management of declining populations. Genetic diversity is an important determinant of population fitness and resilience, and can require careful management to ensure sufficient variation is present. In addition, population genetics data reveal patterns of connectivity and gene flow between locations, enabling mangers to predict recovery and resilience, identify areas of local adaptation, and generate restoration plans. Here, we demonstrate a conservation genetics approach to inform restoration and management of the loggerhead sponge (Spheciospongia vesparium) in the Florida Keys, USA. This species is a dominant, habitat-forming component of marine ecosystems in the Caribbean region, but in Florida has suffered numerous mass mortality events. We developed microsatellite markers and used them to genotype sponges from 14 locations in Florida and a site each in The Bahamas, Belize and Barbuda. We found that genetic diversity levels were similar across all sites, but inbreeding and bottleneck signatures were present in Florida. Populations are highly structured at the regional scale, whilst within Florida connectivity is present in a weak isolation by distance pattern, coupled with chaotic genetic patchiness. Evidence of a weak barrier to gene flow was found in Florida among sites situated on opposite sides of the islands in the Middle Keys. Loggerhead sponge populations in Florida are vulnerable in the face of mass mortalities due to low connectivity with other areas in the region, as well as distance-limited and unpredictable local connectivity patterns. However, our discovery of Florida’s high genetic diversity increases hope for resilience to future perturbations. These results provide valuable insight for sponge restoration practice in Florida.

Complex patterns of differentiation and gene flow underly the divergence of aposematic phenotypes in Oophaga poison frogs.

Hybridization and introgression can have complex consequences for both species evolution and conservation. Here, we investigated the origin and characteristics of a putative hybrid zone between two South American poison dart frog species, Oophaga anchicayensis and the critically endangered Oophaga lehmanni, which are heavily sought after on the illegal pet market. Using a combination of phenotypic (49 traits) and genomic (ddRADseq) data, we found that the putative hybrids are morphologically distinct from their parental species and confirmed genomic signatures of admixture in these populations. Several lines of evidence (hybrid indices, interspecific hybrid heterozygosity, genomic clines, comparisons with simulated hybrids and demographic modelling) support the conclusion that these populations are not comprised of early-generation hybrids and thus, they probably did not arise as a result of illegal translocations associated with wildlife trafficking. Instead, they probably represent an independent lineage which has persisted through isolation and has only relatively recently re-established gene flow with both parental species. Furthermore, we detected signals of differential introgression from parental species into these hybrid populations which suggest relaxed stabilizing selection on these aposematic colour morphs, potentially via context-dependent female choice. These populations thus provide a fascinating window into the role of hybridization, isolation and female choice in the diversification of South American poison dart frogs. In addition, our results underline the importance of landscape conservation measures to protect, not only known localities of nominal species, but also the phenotypic and genomic variation harbored by admixed lineages which represent crucial repositories for the impressive diversity in this system.