Observed Gene Flow Research Articles

Genetic structuring of Fishers in British Columbia, Canada: implications for population conservation and management

Abstract In the westernmost Canadian province of British Columbia, fishers (Pekania pennanti) occur in low-elevation forested ecosystems in the central and northern portions of the province, with several substantial mountain ranges and rivers bisecting this distribution. The effect of these geographic features on gene flow and population structuring is unknown and may contribute to fishers differentiating into 2 or more populations within the province. To better understand population structuring within the range of fishers in British Columbia, we collected tissue samples from 491 fishers from throughout the province and evaluated variation of neutral genetic markers using a 385-base pair section of the mitochondrial DNA control region and 13 microsatellite loci. Fishers appeared to be genetically structured as hierarchical stepping-stone populations where an upper hierarchical level of genetic partitioning resulted in 2 populations at the provincial scale, with 3 subpopulations occurring in the central interior region. We observed gene flow of 2 to 5 migrants per generation between the 2 upper populations, which was substantially less than the 90 migrants per generation estimated as needed to maintain genetic homogeneity. This resulted in differentiated upper populations (haplotype FST = 0.272, microsatellite FST = 0.049) characterized by relatively low Ne (Columbian population = 252, 95% CI = 185 to 332; Boreal population [British Columbia only] = 136, 95% CI = 92 to 234). The consequence of low gene flow and resultant population structuring is that the Columbian population likely receives relatively little genetic and demographic support from other populations and, combined with precipitous recent declines in its numbers, puts this population at heightened conservation risk. As a result, swift and effective actions are needed to conserve this vulnerable population of fishers.

Extensive gene flow in secondary sympatry after allopatric speciation.

In the conventional view, species are separate gene pools delineated by reproductive isolation (RI). In an alternative view, species may also be delineated by a small set of 'speciation genes' without full RI, a view that has gained broad acceptance. A recent survey, however, suggested that the extensive literature on 'speciation with gene flow' is mostly (if not all) about exchanges in the early stages of speciation. There is no definitive evidence that the observed gene flow actually happened after speciation is completed. Here, we wish to know whether 'good species' (defined by the 'secondary sympatry' test) do continue to exchange genes and, importantly, under what conditions such exchanges can be observed. De novo whole-genome assembly and re-sequencing of individuals across the range of two closely related mangrove species (Rhizophora mucronata and R. stylosa) reveal the genomes to be well delineated in allopatry. They became sympatric in northeastern Australia but remain distinct species. Nevertheless, their genomes harbor ∼4000-10 000 introgression blocks averaging only about 3-4 Kb. These fine-grained introgressions indicate continual gene flow long after speciation as non-introgressable 'genomic islets,' ∼1.4 Kb in size, often harbor diverging genes of flower or gamete development. The fine-grained introgression in secondary sympatry may help settle the debate about sympatric vs. micro-allopatric speciation. In conclusion, true 'good species' may often continue to exchange genes but the opportunity for detection is highly constrained.

Genetic Diversity and Population Structure of Fusarium commune Causing Strawberry Root Rot in Southcentral China

Strawberry plants and fruits are vulnerable to infections by a broad range of pathogens and pests. However, knowledge about the epidemiology of pathogens causing strawberry diseases is limited. In this study, we analyzed Fusarium commune, a major fungal pathogen causing strawberry root rot, from diseased strawberry root tissues in southcentral China. A total of 354 isolates were obtained from 11 locations that spanned about 700 km from both south to north and east to west. Multilocus genotypes of all isolates were obtained using seven polymorphic simple sequence repeat markers developed in this study. Our analyses revealed significant genetic diversity within each of the 11 local populations of F. commune. STRUCTURE analysis revealed that the optimal number of genetic populations for the 354 strains was two, with most local geographic populations containing isolates in both genetic clusters. Interestingly, many isolates showed allelic ancestry to both genetic clusters, consistent with recent hybridization between the two genetic clusters. In addition, though alleles and genotypes were frequently shared among local populations, statistically significant genetic differentiations were found among the local populations. However, the observed F. commune population genetic distances were not correlated with geographic distances. Together, our analyses suggest that populations of F. commune causing strawberry root rot are likely endemic to southcentral China, with each local population containing shared and unique genetic elements. Though the observed gene flow among geographic regions was relatively low, human activities will likely accelerate pathogen dispersals, resulting in the generation of new genotypes through mating and recombination.

Diversity, Dispersal and Mode of Reproduction of Amanita exitialis in Southern China.

Amanita exitialis is a poisonous mushroom and has caused many deaths in southern China. In this study, we collected 118 fruiting bodies of A. exitialis from seven different sites in Guangdong Province in southern China and investigated their genetic relationships using 14 polymorphic molecular markers. These 14 markers grouped the 118 fruiting bodies into 20 multilocus genotypes. Among these 20 genotypes, eight were each found only once while the remaining 12 were each represented by two to 54 fruiting bodies. Interestingly, among the 12 shared genotypes, four were shared between/among local populations that were separated by as far as over 80 km, a result consistent with secondary homothallic reproduction and long-distance spore dispersal. Despite the observed gene flow, significant genetic differentiations were found among the local populations, primarily due to the over-representation of certain genotypes within individual local populations. STRUCTURE analyses revealed that the 118 fruiting bodies belonged to three genetic clusters, consistent with divergence within this species in this geographic region. Interestingly, we found an excess of heterozygous individuals at both the local and the total sample level, suggesting potential inbreeding depression and heterozygous advantage in these populations of A. exitialis. We discuss the implications of our results for understanding the life cycle, dispersal, and evolution of this poisonous mushroom.

Genetic diversity of the Ankober Serin (Crithagra ankoberensis) at Simien Mountains National Park and Guassa Community Conservation Area, Ethiopia

The genetic diversity of the Ethiopian endemic Ankober Serin Crithagra ankoberensis was studied in two populations at Simien Mountains National Park and Guassa Community Conservation Area using five microsatellite markers. Blood samples were taken from 16 and 14 birds, respectively. Three molecular markers resulted in relatively low, though noticeable differences between the two populations. The analysis also showed the presence of shared alleles, indicating current gene flow between the two populations. Two markers from Simien Mountains National Park and two markers from Guassa Community Conservation Area revealed obvious deviations from the Hardy–Weinberg equilibrium. We interpret these deviations in both populations as limited population size and restricted gene flow. The genetic differentiation between the two populations thus could be explained by their geographical separation (more than 360 km), reinforced by barriers, such as steep mountains, deep valleys and extensive plains (isolation by distance). On the other hand, a stepping-stone mechanism between geographically intermediate populations across small distances might explain the observed gene flow. Further studies are needed to better reconstruct the biogeographic history and conservation needs of the Ankober Serin populations in Ethiopia.

Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing.

Phylogenomic analyses of bacteria from the phylum Thermotogota have shown extensive lateral gene transfer with distantly related organisms, particularly with Firmicutes. One likely mechanism of such DNA transfer is viruses. However, to date, only three temperate viruses have been characterized in this phylum, all infecting bacteria from the Marinitoga genus. Here we report 17 proviruses integrated into genomes of bacteria belonging to eight Thermotogota genera and induce viral particle production from one of the proviruses. All except an incomplete provirus from Mesotoga fall into two groups based on sequence similarity, gene synteny and taxonomic classification. Proviruses of Group 1 are found in the genera Geotoga, Kosmotoga, Marinitoga, Thermosipho and Mesoaciditoga and are similar to the previously characterized Marinitoga viruses, while proviruses from Group 2 are distantly related to the Group 1 proviruses, have different genome organization and are found in Petrotoga and Defluviitoga. Genes carried by both groups are closely related to Firmicutes and Firmicutes (pro)viruses in phylogenetic analyses. Moreover, one of the groups show evidence of recent gene exchange and may be capable of infecting cells from both phyla. We hypothesize that viruses are responsible for a large portion of the observed gene flow between Firmicutes and Thermotogota.

Different population size change and migration histories created genetic diversity of three oaks in Tokai region, central Japan.

To understand genetic diversity in focal species, it is important to consider the possibility of speciation with gene flow, especially in species with porous genomes such as oaks. We studied genetic diversity and structure in three oaks, Quercus mongolica var. mongolicoides (QM), Q. mongolica var. crispula (QC) and Q. serrata (QS), growing in the Tokai region, central Japan. QM is semi-endemic to the region while the others are common taxa. We also conducted demographic modeling to infer their population size change and migration histories using an approximate Bayesian computation (ABC) approach. The three taxa showed distinct genetic structures but there was genetic admixture among the taxa, especially between QM and QC. ABC analysis of population size change revealed that the population size of QM was stable during and after the last glacial period, while QC and QS showed population expansion after the last glacial maximum. ABC analysis of population divergence and migration revealed that continuous gene flow between QM and QC after their divergence was supported, while between QM and QS, and between QC and QS, secondary contact after sufficient isolation was supported. These historical migration patterns among the three taxa indicate that QM and QC are currently in the early stage or gray zone of speciation, whereas speciation of the other two taxon pairs is considered to have almost been established. Observed gene flow patterns and strength between QM and QC, and between QM and QS, were explained by both flowering patterns and historical distributions, but those between QC and QS were not.

Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species.

Species invasion and range expansion are currently under scrutiny due to increasing anthropogenic impact on the natural environment. This is also true for harmful algal blooms, which have been reported to have increased in frequency. However, this research is challenging due to the ephemeral nature, small size and mostly low concentrations of microalgae in the environment. One such species is the nuisance microalga Gonyostomum semen (Raphidophyceae), which has increased in occurrence in northern Europe in recent decades. The question of whether the species has expanded its habitat range or if it was already present in the lakes but was too rare to be detected remains unanswered. The aim of the present study was to determine the genetic structure and dispersal pathways of G. semen using RAD (restriction-site-associated DNA) tag sequencing. For G. semen, which has a huge genome (32Gbp), we faced particular challenges, but were nevertheless able to recover over 1000 single nucleotide polymorphisms at high coverage. Our data revealed a distinct population genetic structure, demonstrating a divide of western and eastern populations that probably represent different lineages. Despite significant genetic differentiation among lakes, we found only limited isolation-by-distance. While we had expected a pattern of recent expansion northwards, the data demonstrated gene flow from the northeast/east towards the southwest/west. This genetic signature suggests that the observed gene flow may be due to dispersal by autumn migratory birds, which act as dispersal vectors of resistant resting propagules that form at the end of the G. semen blooms.

Population Genetic Structure and Connectivity of the European Lobster Homarus gammarus in the Adriatic and Mediterranean Seas.

Highly selective fishing has the potential to permanently change the characteristics within a population and could drive the decline of genetic diversity. European lobster is an intensively fished crustacean species in the Adriatic Sea which reaches high market value. Since knowledge of population structure and dynamics is important for effective fisheries management, in this study, we used 14 neutral microsatellites loci and partial mitochondrial COI region sequencing to explore population connectivity and genetic structure by comparing samples from the Adriatic Sea and the adjacent basins of the Mediterranean Sea. The obtained results suggest that neutral genetic diversity has not been significantly affected by decrease in population size due to overfishing, habitat degradation and other anthropogenic activities. Global genetic differentiation across all populations was low (FST = 0.0062). Populations from the Adriatic Sea were panmictic, while genetic differentiation was found among populations from different Mediterranean basins. Observed gene flow for European lobster suggest that populations in the north eastern Adriatic act as a source for surrounding areas, emphasizing the need to protect these populations by establishing interconnected MPAs that will be beneficial for both fisheries and conservation management.

Genome-wide investigation of a Korean synthetic breed, Woori-Heukdon using the Illumina PorcineSNP60K BeadChip.

Woori-Heukdon (KWH) is a Korean synthetic pig breed generated using Chookjin-Duroc (KCD), Chookjin-Chamdon (KCC), and their crossbreds. Currently, there is a severe lack of studies investigating the Korean breed populations including wild boars (KWB) throughout the genome. This study was performed to investigate the genetic characteristics of Korean pig populations at the genome-wide level. Using the SNP dataset derived from genotyped and downloaded datasets using the Illumina PorcineSNP60K BeadChip, we compared the genomes of 532 individuals derived from 23 pig breeds to assess the genetic diversity, inbreeding coefficient, genetic differentiation, and population structure. KWB showed the lowest average expected heterozygosity (HE = 0.1904), while KWH showed the highest genetic diversity (HE = 0.02859) among Korean populations. We verified that the genetic composition of KWH, showing USD of 74.8% and KCC of 25.2% in ADMIXTURE analysis. In population structure analyses, KCC was consistently shown to be separated from other pig populations. In addition, we observed gene flow from Western pigs to a part of Chinese populations. This study showed that Korean native pigs, KCC have genetic differences in comparison with Chinese and Western pigs; despite some historical records and recent genetic studies, we could not find any clear evidence that KCC was significantly influenced by Chinese or Western breeds in this study. We also verified the theoretical genomic composition of KWH at the molecular level in structure analyses. To our knowledge, this is the first genomic study to investigate the genomic characteristics of KWH and KCC.

CERRADO RUPESTRE DO ESPINHAÇO: diversidade genética de espécie endêmica

O objetivo do trabalho foi de caracterizar a diversidade e a estrutura genética de 82 indivíduos de P. adamantinum, espécie de campos rupestres e de altitude do Cerrado brasileiro, na região central de Minas Gerais, divididos em 02 populações de 41 indivíduos. Foram utilizados 08 primers ISSR que amplificaram 135 locos, com 108 (80%) locos polimórficos entre as populações e média de 16,9 locos por primer. O valor médio de PIC foi de 0,375. Os valores médios do índice de Shannon (I) e da diversidade genética de Nei (He) foram de 0,491 e 0,341, respectivamente. O índice da proporção da diversidade genética (GST = 0,047) demonstrou que a variabilidade entre e dentro das populações contribuiu com 4,7% e 95,3% da heterozigosidade total (HT), respectivamente. O fluxo gênico observado foi alto (Nm = 10,213), o que contrapõe os efeitos da deriva genética. Foi observada a ocorrência de baixa estruturação genética espacial (EGE) (Sp= 0,058) e coancestria positiva nas duas populações (Fij = 0,016; P < 0,123 em POP01 e Fij = 0,018; P < 0,057 em POP02), ambas avaliadas até a segunda classe de distância. Mesmo com a presença de fatores favoráveis à endogamia, P. adamantinum apresentou altos índices de diversidade genética. O elevado fluxo gênico registrado pode terr amenizado os efeitos do acasalamento de indivíduos aparentados. Palavras-chave: ISSR. Fluxo Gênico. Cerrado. Espécie Endêmica. Estrutura Espacial. THE CAMPOS RUPESTRES OF ESPINHAÇO: mountain range: genetic diversity of endemic species ABSTRACT The objective of the study was to characterize the diversity and genetic structure of 82 individuals of P. adamantinum, divided into 02 populations of 41 individuals. We used 08 ISSR primers that amplified 135 loci, with 108 (80%) polymorphic loci between the populations and a mean of 16.9 loci per primer. The mean value of PIC was 0.375. The mean values ​​of the Shannon index (I) and the genetic diversity of Nei (He) were 0.491 and 0.341, respectively. The genetic diversity ratio index (GST = 0.047) showed that the variability between and within the populations contributed with 4.7% and 95.3% of the total heterozygosity (HT), respectively. The observed gene flow was high (Nm = 10,213), which contrasts the effects of genetic drift. The occurrence of low spatial genetic structuration (EGE) (Sp = 0.058) and positive coancestry in both populations (Fij = 0.0161; P < 0.123 in POP01 and Fij = 0.018; P < 0, 057 in POP02), both evaluated up to the second distance class. Even with the presence of factors favorable to inbreeding, P. adamantinum presented high levels of genetic diversity. The high recorded gene flow was responsible for mitigating the effects of mating of related individuals Keywords: ISSR. Gene Flow. Cerrado. Endemic Specie. Spatial Structure. CERRADO RUPESTRE DEL ESPINHAÇO: diversidad genética de especie endémica RESUMEN El objetivo del estudio fue caracterizar la diversidad y la estructura genética de 82 individuos de P. adamantinum, una especie típica del Cerrado brasileño, en la región central de Minas Gerais, dividida en 02 poblaciones de 41 individuos. Se utilizaron 08 cebadores ISSR que amplificaron 135 loci, con 108 (80%) loci polimórficos entre poblaciones y un promedio de 16.9 loci por cebador. El valor medio de PIC fue 0.375. Los valores medios del índice de Shannon (I) y la diversidad genética de Nei (He) fueron 0.491 y 0.341, respectivamente. El índice de la proporción de diversidad genética (GST = 0.047) demostró que la variabilidad entre y dentro de las poblaciones contribuyó con 4.7% y 95.3% de la heterocigosidad total (HT), respectivamente. El flujo de genes observado fue alto (Nm = 10.213), lo que se opone a los efectos de la deriva genética. Se observó la ocurrencia de baja estructura genética espacial (EGE) (Sp = 0.058) y coancestria positivo en ambas poblaciones (Fij = 0.016; P <0.123 en POP01 y Fij = 0.018; P <0.057 en POP02), ambos evaluados hasta el segundo clase de distancia. Incluso con la presencia de factores favorables a la endogamia, P. adamantinum mostró altas tasas de diversidad genética. El alto flujo de genes registrado fue responsable de mitigar los efectos del apareamiento de individuos relacionados. Palabras clave: ISSR. Flujo de genes. Cerrado. Especies endêmicas. Estructura espacial.

Gene flow and Bayesian phylogeography of serogroup C meningococci circulating in Italy.

Hyperinvasive strains of Neisseria meningitidis serogroup C have caused outbreaks of severe disease in Italy. Here, we report the analysis of the migration patterns of C:P1.5-1,10-8:F3-6:ST-11(cc11) meningococcal strains from different Italian regions collected between 2012 and 2017. N. meningitidis genomes were sequenced through the whole genome sequencing (WGS) method and were analyzed using the BIGSdb Genome Comparator tool. The phylogeography was performed using BEAST. The gene flows in Italy were tested by using MacClade. The C:P1.5-1,10-8:F3-6:ST-11(cc11) hyperinvasive meningococcal strain, for the data available at the time of the analysis, from UK reached at first Emilia Romagna region, and then, in 2012, was detected in the outbreak occurred in the port of Livorno. The "Tuscany-outbreak strain" was likely introduced in Italy between 2013 and 2014. Most of the observed gene flow events occurred from the Center to Northern part of Italy. The phylogeographic analysis allowed to track the dissemination of C:P1.5-1,10-8:F3-6:ST-11(cc11) strains in the country.

Climate connectivity of the bobcat in the Great Lakes region.

The Great Lakes and the St. Lawrence River are imposing barriers for wildlife, and the additive effect of urban and agricultural development that dominates the lower Great Lakes region likely further reduces functional connectivity for many terrestrial species. As the climate warms, species will need to track climate across these barriers. It is important therefore to investigate land cover and bioclimatic hypotheses that may explain the northward expansion of species through the Great Lakes. We investigated the functional connectivity of a vagile generalist, the bobcat, as a representative generalist forest species common to the region. We genotyped tissue samples collected across the region at 14 microsatellite loci and compared different landscape hypotheses that might explain the observed gene flow or functional connectivity. We found that the Great Lakes and the additive influence of forest stands with either low or high canopy cover and deep lake‐effect snow have disrupted gene flow, whereas intermediate forest cover has facilitated gene flow. Functional connectivity in southern Ontario is relatively low and was limited in part by the low amount of forest cover. Pathways across the Great Lakes were through the Niagara region and through the Lower Peninsula of Michigan over the Straits of Mackinac and the St. Marys River. These pathways are important routes for bobcat range expansion north of the Great Lakes and are also likely pathways that many other mobile habitat generalists must navigate to track the changing climate. The extent to which species can navigate these routes will be important for determining the future biodiversity of areas north of the Great Lakes.

Genes and speciation: is it time to abandon the biological species concept?

The biological species concept (BSC) is the cornerstone of neo-Darwinian thinking. In BSC, species do not exchange genes either during or after speciation. However, as gene flow during speciation is increasingly being reported in a substantial literature, it seems time to reassess the revered, but often doubted, BSC. Contrary to the common perception, BSC should expect substantial gene flow at the onset of speciation, not least because geographical isolation develops gradually. Although BSC does not stipulate how speciation begins, it does require a sustained period of isolation for speciation to complete its course. Evidence against BSC must demonstrate that the observed gene flow does not merely occur at the onset of speciation but continues until its completion. Importantly, recent genomic analyses cannot reject this more realistic version of BSC, although future analyses may still prove it wrong. The ultimate acceptance or rejection of BSC is not merely about a historical debate; rather, it is about the fundamental nature of species – are species (and, hence, divergent adaptations) driven by a relatively small number of genes, or by thousands of them? Many levels of biology, ranging from taxonomy to biodiversity, depend on this resolution.

Influence of hydrodynamic connectivity on the genetic structure and gene flow of the common pandora Pagellus erythrinus

Many marine organisms have complex genetic patterns that cannot be easily resolved by data analysis on spatial distribution of variability usually applied in population genetic studies. We propose an analytical framework to evaluate the role of dispersal during early life stages that considers the actual hydrodynamic connectivity in the Mediterranean Sea, as a factor shaping the population structure of demersal fishes. To this purpose, and to test different scenarios of gene flow, genotypes of individuals of Pagellus erythrinus sampled at 12 sites in the central Mediterranean Sea were analyzed at ten microsatellite loci. The results show the lack of genetic structure in western Mediterranean basin and a pattern of gene flow that deviates from an isolation by distance model. The observed gene flow estimates appear to be scale-dependent. At local scale, it is likely the result of multifactorial components, whereas at a larger scale it is mainly driven by the sea currents, directly influencing dispersal of larvae between sites not reachable by adult movements. Our results stress the importance of a quantitative analysis of potential early life stage dispersal in any study focusing on the population structure of fishes with a long larval stage.

Genetic diversity and population structure of African village dogs based on microsatellite and immunity-related molecular markers.

The village and street dogs represent a unique model of canine populations. In the absence of selective breeding and veterinary care, they are subject mostly to natural selection. Their analyses contribute to understanding general mechanisms governing the genetic diversity, evolution and adaptation. In this study, we analyzed the genetic diversity and population structure of African village dogs living in villages in three different geographical areas in Northern Kenya. Data obtained for neutral microsatellite molecular markers were compared with those computed for potentially non-neutral markers of candidate immunity-related genes. The neutral genetic diversity was similar to other comparable village dog populations studied so far. The overall genetic diversity in microsatellites was higher than the diversity of European pure breeds, but it was similar to the range of diversity observed in a group composed of many European breeds, indicating that the African population has maintained a large proportion of the genetic diversity of the canine species as a whole. Microsatellite marker diversity indicated that the entire population is subdivided into three genetically distinct, although closely related subpopulations. This genetical partitioning corresponded to their geographical separation and the observed gene flow well correlated with the communication patterns among the three localities. In contrast to neutral microsatellites, the genetic diversity in immunity-related candidate SNP markers was similar across all three subpopulations and to the European group. It seems that the genetic structure of this particular population of Kenyan village dogs is mostly determined by geographical and anthropogenic factors influencing the gene flow between various subpopulations rather than by biological factors, such as genetic contribution of original migrating populations and/or the pathogen-mediated selection. On the other hand, the study of oldest surviving dogs suggested a biological mechanism, i.e. a possible advantage of the overal heterozygosity marked by the the microsatellite loci analyzed.

Drainage isolation and climate change-driven population expansion shape the genetic structures of Tuber indicum complex in the Hengduan Mountains region.

The orogenesis of the Qinghai-Tibetan Plateau and the Quaternary climate changes have played key roles in driving the evolution of flora and fauna in Southwest China, but their effects on higher fungi are poorly addressed. In this study, we investigated the phylogeographic pattern of the Tuber indicum species complex, an economically important fungal group distributed in the Hengduan Mountains region. Our data confirmed the existence of two distinct lineages, T. indicum and T. himalayense, within this species complex. Three geographic groups (Groups W, N and C) were revealed within T. indicum, with Group W found in the paleo-Lancang River region, while Groups N and C corresponded to the two banks along the contemporary Jinsha River, suggesting that rivers have acted as barriers for gene flow among populations from different drainages. Historical range expansion resulted from climate changes was inferred in Group C, contributing to the observed gene flow among geographic populations within this group. Although no significant geographic structure was identified in T. himalayense, evidence of drainage isolation for this species was also detected. Our findings demonstrate that both topographic changes and Quaternary climate oscillations have played important roles in driving the genetic structures of the T. indicum species complex.

Understanding age‐specific dispersal in fishes through hydrodynamic modelling, genetic simulations and microsatellite DNA analysis

Many marine species have vastly different capacities for dispersal during larval, juvenile and adult life stages, and this has the potential to complicate the identification of population boundaries and the implementation of effective management strategies such as marine protected areas. Genetic studies of population structure and dispersal rarely disentangle these differences and usually provide only lifetime-averaged information that can be considered by managers. We address this limitation by combining age-specific autocorrelation analysis of microsatellite genotypes, hydrodynamic modelling and genetic simulations to reveal changes in the extent of dispersal during the lifetime of a marine fish. We focus on an exploited coral reef species, Lethrinus nebulosus, which has a circum-tropical distribution and is a key component of a multispecies fishery in northwestern Australia. Conventional population genetic analyses revealed extensive gene flow in this species over vast distances (up to 1,500 km). Yet, when realistic adult dispersal behaviours were modelled, they could not account for these observations, implying adult dispersal does not dominate gene flow. Instead, hydrodynamic modelling showed that larval L. nebulosus are likely to be transported hundreds of kilometres, easily accounting for the observed gene flow. Despite the vast scale of larval transport, juvenile L. nebulosus exhibited fine-scale genetic autocorrelation, which declined with age. This implies both larval cohesion and extremely limited juvenile dispersal prior to maturity. The multidisciplinary approach adopted in this study provides a uniquely comprehensive insight into spatial processes in this marine fish.

Gene flow between Zhuang and Han populations in the China–Vietnam borderland

In epidemiological studies, it is easier to glean information from isolated populations with simple genetic backgrounds than from populations with relatively complex genetic backgrounds. Regarded as an isolated population, the Minz (Hei-Yi Zhuang) in Napo County (in the China-Vietnam borderland) has been the subject of numerous recent studies. To assess the genetic isolation of this population, we studied Y chromosome and mitochondrial DNA from Minz and Han in Napo. Both populations exhibited southern Chinese genetic characteristics in both paternal and maternal lineages. Using NETWORK analyses, we found pronounced gene flow between these two populations only in maternal lineages. We also observed gene flow from other populations into the Minz gene pool. We thus concluded that the Minz is not a genetically isolated population and it is increasingly difficult to find isolated populations in mainland East Asia.

A New Bayesian Method to Identify the Environmental Factors That Influence Recent Migration

We present a new multilocus genotype method that makes inferences about recent immigration rates and identifies the environmental factors that are more likely to explain observed gene flow patterns. It also estimates population-specific inbreeding coefficients, allele frequencies, and local population F(ST)'s and performs individual assignments. We generate synthetic data sets to determine the region of the parameter space where our method is and is not able to provide accurate estimates. Our simulation study indicates that reliable results can be obtained when the global level of genetic differentiation (F(ST)) is >1%, the number of loci is only 10, and sample sizes are of the order of 50 individuals per population. We illustrate our method by applying it to Pakistani human data, considering altitude and geographic distance as explanatory factors. Our results suggest that altitude explains better the genetic data than geographic distance. Additionally, they show that southern low-altitude populations have higher migration rates than northern high-altitude ones.