High Levels Of Gene Flow Research Articles

Genetic diversity and population connectivity of the sea urchin Tripneustes gratilla along the South African coast

The collector sea urchin Tripneustes gratilla has been identified as a species with potential for aquaculture production in South Africa. The species’ roe is considered a culinary delicacy in Asia and Europe. However, T. gratilla remains genetically uncharacterised in South Africa. Therefore, the purpose of this study was to provide baseline genetic information consisting of estimates of genetic diversity and population stratification, which may aid in future sustainable use of this urchin resource. A total of 22 species-specific microsatellite markers were used for the genetic characterisation of T. gratilla samples from along the South African coast, at Haga Haga, Coffee Bay, Hibberdene, Ballito Bay and Sodwana Bay. A moderate level of genetic diversity was observed, with an average number of alleles of 7.89 and an average effective number of alleles of 6.57, as well as an average observed heterozygosity of 0.55. Population differentiation tests suggest that the geographically representative samples form part of a single, large interbreeding population, with a global Fst estimate of 0.02 (p > 0.05). This finding is likely explained by high levels of gene flow between these locations caused by extensive larval dispersal during the planktonic larval stage. The panmixia observed within these natural populations of T. gratilla indicate that they could be managed as a single genetic stock.

Spatial and temporal assessments of genetic structure in an endangered Garry oak ecosystem on Vancouver Island

Garry oak (Quercus garryana Douglas ex Hook.) is a deciduous tree whose ecosystem is listed “at risk” throughout its range in British Columbia (BC), Canada, under the Canadian Species at Risk Act. Garry oak ecosystems host the most diverse flora for coastal BC, yet they account for less than 0.3% of the province’s land coverage. Due to the loss and degradation of Garry oak habitat, many associated plant and animal species that rely on these sensitive ecosystems are endangered. Microsatellite markers were used to investigate temporal changes in fine-scale population genetic structure of 121 Garry oak trees from the Nanaimo region (Vancouver Island, BC) using diameter at breast height as a proxy for age. Overall, allelic diversity was moderate, ranging from 3.0 to 7.5 alleles per locus with a mean of 4.4 (±0.4 SE) across all loci. Global fixation indices (FST) of 0.06 and 0.09 suggest significant departures from Hardy–Weinberg equilibrium among all populations and age-classified subpopulations, respectively. We found no evidence for change in genetic diversity across generations. Our results indicate low levels of differentiation within populations and high levels of gene flow among populations, suggesting an adaptive potential for Garry oaks in response to future climate change events.

Color patterns of the hermit crab Calcinus tibicen (Herbst, 1791) fail to indicate high genetic variation within COI gene

Abstract Apart from traditional characters, other data have been used for taxonomy, like color patterns. Based on the different colors (green and orange) observed for some Calcinus tibicen (Herbst, 1761) specimens, we evaluated the genetic distance for cytochrome oxidase subunit I mitochondrial gene of individuals collected in Pernambuco (northern Brazil) and in Sao Paulo (southeast Brazil). We found low genetic variation (0.2-1.1%), and no evidence of isolation on our molecular tree based on genetic distance. We suggest high levels of gene flow between specimens with different color patterns, which are polymorphisms and might be related to the kind of nutrition as well different ecological and evolutionary predation characteristics.

Life histories predict genetic diversity and population structure within three species of octopus targeted by small-scale fisheries in Northwest Mexico.

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species targeted by artisanal fisheries in the region with distinct life histories, the lack of basic biological information about the distribution, metapopulation size and structure of each species could impede effective fisheries management to avoid overexploitation. We tested if different life histories of three species of octopus could help predict observed patterns of genetic diversity, population dynamics, structure and connectivity and how this information could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the west coast of the Baja California peninsula. We tested five hypotheses derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We discovered that Octopus bimaculoides with low fecundity and direct development (without a planktonic phase) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, than the other two species. These features indicated limited dispersal and high local recruitment. In contrast, O. bimaculatus and O. hubbsorum with higher fecundity and planktonic phase as paralarvae had higher effective population size and genetic diversity, and overall lower kinship and population structure than O. bimaculoides. These observations supported higher levels of gene flow over a larger geographical scale. O. bimaculatus with the longest planktonic paralarval duration and therefore larger dispersal potential had differences in the calculated parameters possibly associated with increased connectivity. We propose O. bimaculoides is more susceptible to over exploitation of small, isolated populations and could have longer recovery times than the other two species. This species may benefit from distinct fishery management within each local population. O. bimaculatus and O. hubbsorum may benefit from fishery management that takes into account metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal driven by ocean currents and population connectivity among individuals of each locality. The distribution of each species and variations in their reproductive phenology is also important to consider when establishing marine reserves or seasonal fishing closures.

Population structure and genetic diversity of Rhipicephalus microplus in Zimbabwe

Recently there was an expansion in the geographic range of Rhipicephalus microplus in Zimbabwe. In order to understand gene flow patterns and population structure in this highly invasive and adaptable cattle tick, a population genetics study was carried out. Eighty-seven R. microplus tick samples drawn from 5 distinct populations were genotyped using eight polymorphic microsatellite loci. Genetic diversity (He) was high (0.755–0.802) in all the populations, suggesting high levels of gene flow with 97% of genetic variation found within populations and 3% amongst populations. No isolation by distance was observed with low but significant genetic differentiation amongst the populations (0–0.076). Most of the sampled individuals had admixed genetic backgrounds, except for those from Matabeleland North whose genetic makeup appeared different from the rest. Rhipicephalus microplus was recently recorded in this area and the environmental conditions do not support survival of the tick there. These results confirm recent range expansion of the tick and the lowest genetic diversity recorded in the Matabeleland North population is suggestive of a founder effect, which may lead to genetic drift. Generally, the very low levels of genetic differentiation amongst the populations could be a result of the frequent movement of livestock from one area to another, which will have implications for disease control. This study offers further opportunities to study evolutionary adaptation of R. microplus in Zimbabwe and southern Africa.

Genetic diversity and differentiation of the riparian relict tree <i>Pterocarya fraxinifolia</i> (Juglandaceae) along altitudinal gradients in the Hyrcanian forest (Iran)

Riparian trees, especially relict trees, are attractive and important for research to understand both past and recent biogeographical and evolutionary processes. Our work is the first study to elucidate the genetic diversity and spatial genetic structure of the canopy-dominating riparian (Juglandaceae) along two altitudinal gradients in different river systems of the Hyrcanian forest, which is one of the most important refugium of relict trees in Western Eurasia. Altitudinal gradients were chosen along two river systems at 100, 400 and 900 m a.s.l. Leaf samples were collected from 116 trees, and the genetic diversity was evaluated with eight SSR markers. Overall, 39 alleles were identified for all of the populations studied. The observed heterozygosity (Ho) varied from 0.79 to 0.87 (with a mean of 0.83). The results of the AMOVA analysis indicated that the variation within populations was 88%, whereas the variation among populations was 12% for all of the gradients. A structure analysis indicated that 93% of the trees were grouped in the same gradient. The genetic distance based on Fst confirmed the structure result and indicated a high rate of gene flow among the investigated populations. Based on high gene flow (low differentiation of the population along the same river) and the clearly distinct genetic structure of the investigated gradients, it can be concluded that rivers are the main seed dispersal vector among populations. The genetic diversity of did not show any trend from upstream to downstream. The high level of gene flow and uniform genetic diversity along each river suggest the “classical” metapopulation structure of the species. Pterocarya fraxinifoliaP. fraxinifoliaP. fraxinifolia

Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (Lateolabrax maculatus).

The marine species usually show high dispersal capabilities accompanied by high levels of gene flow. On the other hand, many physical barriers distribute along the continental marginal seas and may prevent dispersals and increase population divergence. These complexities along the continental margin generate serious challenges to population genetic studies of marine species. Chinese sea bass Lateolabrax maculatus distributes broad latitudinal gradient spanning from the tropical to the mid-temperate zones in the continental margin seas of the Northwest Pacific Ocean. Using the double digest restriction-site-associated DNA tag sequencing (ddRAD) approach, we genotyped 10,297 SNPs for 219 Chinese seabass individuals of 12 populations along the Chinese coast in the Northwest Pacific region. Genetic divergence among these populations was evaluated, and population structure was established. The results suggested that geographically distant populations in the Bohai Gulf and the Beibu Gulf retain significant genetic divergence, which are connected by a series of intermediate populations in between. The results also suggested that Leizhou Peninsula, Hainan Island, and Shandong Peninsula are major physical barriers and substantially block gene flow and genetic admixture of L. maculatus. We also investigated the potential genetic basis of local adaptation correlating with population differentiation of L. maculatus. The sea surface temperature is a significantly differentiated environmental factor for the distribution of L. maculatus. The correlation of water temperature and genetic variations in extensively distributed populations was investigated with Bayesian-based approaches. The candidate genes underlying the local selection in geographically divergent populations were identified and annotated, providing clues to understand the potential mechanisms of adaptive evolution. Overall, our genome scale population genetic analysis provided insight into population divergence and local adaptation of Chinese sea bass in the continental marginal seas along Chinese coast.

The absence of reproductive isolation between non-sister and deeply diverged mitochondrial lineages of the black-throated tit (Aegithalos concinnus) revealed by a multilocus genetic analysis in a contact zone

BackgroundA deep divergence of mitochondrial DNA is common in species delimitated by morphological traits. Several hypotheses can explain such variations, such as cryptic species, introgression, allopatric divergence and ancestral lineage. The black-throated tit harbors several deeply divergent mitochondrial lineages. Two lineages with 5% divergence, but having a high level of gene flow, have been detected in its subspecies, A. C. concinnus and A. c. talifuenses. In this study, we conducted a genetic analysis at a contact zone of these two lineages to identify whether these lineages either reflect a high level of intraspecific variation in mitochondrial loci or represent incipient speciation. Mitochondrial ND2 and 11 microsatellite loci were used to conduct phylogenetic and population structure analyses.ResultsND2 haplotypes actually diverged into two groups within subspecies A. c. talifuenses; however, they formed a non-sister relationship when including all available GenBank ND2 sequences. Analyses of microsatellite data indicated no existing population structure and showed a pattern of isolation by distance. Individuals sampled at the contact zone were almost identified as F2 hybrids.ConclusionsIsolation for 2.4 Ma, as suggested by a previous study, appeared to be insufficient to develop robust reproductive barriers. Reproductive barriers were weak, or even absent between the divergent lineages, highlighting that incipient speciation was unlikely to be the case. Considering the results from previous studies, the divergent lineages may be better explained by secondary contact after allopatric isolation because of Pleistocene climate changes, but other hypotheses cannot be definitively ruled out because of the lack of representative samples from the other distribution region and its relatives. Considering that divergence in morphology was hardly observed and the particular split in genetics, the two subspecies might be better merged. The current findings also highlight the likely contribution of male-biased dispersal to male-biased gene flow among mitochondrial lineages; more efforts are needed to illustrate the evolutionary history of the black-throated tit.

Assessment of genetic diversity of an endangered tooth-carp, Aphanius farsicus (Teleostei: Cyprinodontiformes: Cyprinodontidae) using microsatellite markers.

Genetic structure of an endemic tooth-carp fish, Aphanius farsicus from four different water bodies in the Maharlu Lake basin was investigated by applying five microsatellite markers. All of the five examined microsatellite loci showed polymor-phism pattern. A total of four alleles were detected at five microsatellite loci, with an average of 2.8 to 3.5 alleles per locus. Average values of observed and expected heterozygosity were 0.95±0.09 and 0.64±0.02 respectively. None of the tests of linkage disequilibrium were significant between each pair of loci and no deviation from Hardy-Weinberg equilibrium were detected to test for heterozygote deficiency within populations. The Nei's genetic distance values ranged between 0.03 – 0.13. Analysis of pairwise genetic differentiation between each pair of the populations revealed that fixation index (FST) values ranged from 0.013 to 0.039 and RST ranged from 0.005 to 0.065. High genetic diversity observed within the populations (99%) and low diversity (1%) among them indicating probably high level of gene flow among the studied populations of Fars tooth-carp at the present time or in the past. Regarding low genetic differentiation among the studied populations and results of population assignment test, two hypotheses are suggested and supporting evidence for each hypothesis are provided.

Population genetic structure of the endemic rosewoods Dalbergia cochinchinensis and D.oliveri at a regional scale reflects the Indochinese landscape and life-history traits.

Indochina is a biodiversity hot spot and harbors a high number of endemic species, most of which are poorly studied. This study explores the genetic structure and reproductive system of the threatened endemic timber species Dalbergia cochinchinensis and Dalbergia oliveri using microsatellite data from populations across Indochina and relates it to landscape characteristics and life‐history traits. We found that the major water bodies in the region, Mekong and Tonle Sap, represented barriers to gene flow and that higher levels of genetic diversity were found in populations in the center of the distribution area, particularly in Cambodia. We suggest that this pattern is ancient, reflecting the demographic history of the species and possible location of refugia during earlier time periods with limited forest cover, which was supported by signs of old genetic bottlenecks. The D. oliveri populations had generally high levels of genetic diversity (mean H e = 0.73), but also strong genetic differentiation among populations (global GST = 0.13), while D. cochinchinensis had a moderate level of genetic diversity (mean H e = 0.55), and an even stronger level of differentiation (global GST = 0.25). These differences in genetic structure can be accounted for by a higher level of gene flow in D. oliveri due to a higher dispersal capacity, but also by the broader distribution area for D. oliveri, and the pioneer characteristics of D. cochinchinensis. This study represents the first detailed analysis of landscape genetics for tree species in Indochina, and the found patterns might be common for other species with similar ecology.

Population genetic structure and expansion patterns of the cotton pest Adelphocoris fasciaticollis

Understanding the population genetic structure and demographic dynamics of important agricultural pest insects is very important in studying insecticide resistance and control strategies. The plant bug Adelphocoris fasciaticollis (Reuter) (Hemiptera: Miridae) is one of the main insect pests on cotton in Northern China. We studied large-scale genetic structure and genetic diversity patterns and explored the demographic history. We also employed a phylogeographical approach on A. fasciaticollis samples using sequence data from mitochondrial DNA (mtDNA) and nuclear DNA (ncDNA). MtDNA showed a significant correlation between genetic and geographical distances, but ncDNA did not support this correlation. Both datasets revealed that A. fasciaticollis populations had experienced recent expansion and lacked a geographical structure. One reason for lack of a genetic structure is a high level of gene flow among the populations. We suggest that the strong flight capability of A. fasciaticollis has been aided by the East Asian monsoon and cold fronts to accelerate the rate of range expansion. In addition, decreased insecticide usage and disturbances from human activities may all have contributed to population expansion. The low effective population number was based on two datasets. It is suggested that the host crop use, local climate conditions, and the recent population expansion might be the main influencing factors.

Population genetic structure of the sword prawn Parapenaeopsis hardwickii (Miers, 1878) (Decapoda: Penaeidae) in the Yellow Sea and East China Sea

The genetic structure of the populations of the sword prawn Parapenaeopsis hardwickii (Miers, 1878) in the Yellow Sea and East China Sea, an economically and ecologically important species in the Indo-West Pacific region, is described. Based on partial mtDNA COI gene, 27 COI haplotypes are recognized from 130 samples collected from seven locations. Nucleotide and haplotype diversities of the Yellow Sea and East China Sea populations were 0.00187 +/- 0.00021 and 0.818 +/- 0.049, and 0.00215 +/- 0.00023 and 0.822 +/- 0.042, respectively. AMOVA and pairwise FST reveal no significant genetic differentiation of the populations. Neither the Bayesian inference tree nor haplotype network reveals clades with geographic pattern, indicating high levels of gene flow between prawn populations of each sea. Mismatch distribution and neutrality tests suggest an historical population expansion of P. hardwickii, with Pleistocene glacial cycles likely having impacted this species' historical demography. This study provides background information for sustainable improvement and fisheries management of P. hardwickii in the Yellow Sea and East China Sea.

Tests of fit of historically-informed models of African American Admixture.

African American populations in the U.S. formed primarily by mating between Africans and Europeans over the last 500 years. To date, studies of admixture have focused on either a one-time admixture event or continuous input into the African American population from Europeans only. Our goal is to gain a better understanding of the admixture process by examining models that take into account (a) assortative mating by ancestry in the African American population, (b) continuous input from both Europeans and Africans, and (c) historically informed variation in the rate of African migration over time. We used a model-based clustering method to generate distributions of African ancestry in three samples comprised of 147 African Americans from two published sources. We used a log-likelihood method to examine the fit of four models to these distributions and used a log-likelihood ratio test to compare the relative fit of each model. The mean ancestry estimates for our datasets of 77% African/23% European to 83% African/17% European ancestry are consistent with previous studies. We find admixture models that incorporate continuous gene flow from Europeans fit significantly better than one-time event models, and that a model involving continuous gene flow from Africans and Europeans fits better than one with continuous gene flow from Europeans only for two samples. Importantly, models that involve continuous input from Africans necessitate a higher level of gene flow from Europeans than previously reported. We demonstrate that models that take into account information about the rate of African migration over the past 500 years fit observed patterns of African ancestry better than alternative models. Our approach will enrich our understanding of the admixture process in extant and past populations.

Genetic structure of Apis mellifera carnica in Slovakia based on microsatellite DNA polymorphism

AbstractCarniolan honeybee (

Effects of Habitat Fragmentation on Genetic Diversity in Cycas Balansae (Cycadaceae)

Habitat fragmentation is a serious threat to species survival. In Vietnam, Cycas balansae has been considered as threatened species because of the reduction and fragmentation of its habitats and over-exploitation. We assessed genetic variability and the pattern of population structure among six populations sampled in four provinces: Hoa Binh, Ha Nam, Ninh Binh and Quang Ninh. Polyacrylamide gel electrophoresis was performed on leaf tissues from 152 individuals representing 6 populations of C. balansae. Six of twelve enzyme systems were used to estimate genetic diversity at population and species levels. Eleven loci were examined. The allozyme data showed high levels of genetic diversity within all populations, ranging from 0.538 in Ba Sao to 0.628 in Tan Dan (average 0.576). The maintenance of high levels of expected heterozygosity (average 0.571) and low in observed heterozygosity (average 0.347) might be related to great heterozygote deficiency and increased frequencies of rare alleles. Genetic differentiation among populations was low (Dst = 0.036 and Gst = 0.064), indicating high level of gene flow (Nm = 3.22). Isolation by geographical distance was observed, however, no significant relationship between genetic distances and geographical distances was recorded. Our studies suggest small population sizes of cycads brought about by fragmentation of its habitats, over-exploitation, and increasing number of inbred individuals within populations.

Diversidad Genética del Caballo Criollo (Equus caballus) mediante Genes Asociados al Pelaje en Valencia, Colombia

El objetivo de este trabajo fue estudiar la variabilidad genética de caballos criollos (Equus caballus) mediante genes asociados al pelaje. Se realizaron muestreos entre enero y mayo de 2016 en cinco poblaciones de la ciudad de Valencia. Se realizó la caracterización fenotípica de los animales adultos presentes en las fincas, atendiendo a los marcadores autosómicos de codificación morfológica Extension, Agouti, Cream, Gris, White, Tobiano, Overo y Roan. Los resultados mostraron ausencia de los marcadores White y Overo, mientras que los marcadores Extension y Agouti fueron los de mayores frecuencias, posiblemente favorecidas por selección artificial, debido a temperamento y astucia respectivamente. Las poblaciones se encontraron en equilibrio de Hardy-Weinberg, exhibieron exceso de homocigotos y altos valores de flujo genético.

Local selection in the presence of high levels of gene flow: Evidence of heterogeneous insecticide selection pressure across Ugandan Culex quinquefasciatus populations.

BackgroundCulex quinquefasciatus collected in Uganda, where no vector control interventions directly targeting this species have been conducted, was used as a model to determine if it is possible to detect heterogeneities in selection pressure driven by insecticide application targeting other insect species.Methodology/Principal findingsPopulation genetic structure was assessed through microsatellite analysis, and the impact of insecticide pressure by genotyping two target-site mutations, Vgsc-1014F of the voltage-gated sodium channel target of pyrethroid and DDT insecticides, and Ace1-119S of the acetylcholinesterase gene, target of carbamate and organophosphate insecticides. No significant differences in genetic diversity were observed among populations by microsatellite markers with HE ranging from 0.597 to 0.612 and low, but significant, genetic differentiation among populations (FST = 0.019, P = 0.001). By contrast, the insecticide-resistance markers display heterogeneous allelic distributions with significant differences detected between Central Ugandan (urban) populations relative to Eastern and Southwestern (rural) populations. In the central region, a frequency of 62% for Vgsc-1014F, and 32% for the Ace1-119S resistant allele were observed. Conversely, in both Eastern and Southwestern regions the Vgsc-1014F alleles were close to fixation, whilst Ace1-119S allele frequency was 12% (although frequencies may be underestimated due to copy number variation at both loci).Conclusions/SignificanceTaken together, the microsatellite and both insecticide resistance target-site markers provide evidence that in the face of intense gene flow among populations, disjunction in resistance frequencies arise due to intense local selection pressures despite an absence of insecticidal control interventions targeting Culex.

Microsatellite analysis of genetic diversity and genetic structure of the Chinese freshwater mussel Solenaia carinata (Bivalvia: Unionidae)

Abstract The freshwater mussels (Unionidae) in the Yangtze River basin of China are among the most diverse assemblages on Earth. Freshwater mussels provide valuable ecosystem services (e.g. natural water filtration) and economic value (shell, pearls, and food), but are experiencing global declines as a result of pollution, habitat alteration, and overharvest. Despite the diversity and value of freshwater mussels in the Yangtze River basin, relatively little is known about the biology of the many species endemic to the region. Solenaia carinata is an endemic and potentially imperilled freshwater mussel (Bivalvia: Unionidae) in China that is distributed in a single major tributary of the middle Yangtze; the Poyang Lake basin in Jiangxi Province. This study represents the first analyses of the genetic diversity and population genetic structure of S. carinata. Solenaia carinata specimens (n=64) were collected from three sites in large tributary rivers of Poyang Lake. Using 19 polymorphic microsatellite markers, the results showed that S. carinata had a moderate level of genetic diversity (PIC ranged from 0.464 to 0.484), limited evidence of a recent genetic bottleneck, little genetic differentiation (FST ranged from 0.021 to 0.045), high levels of gene flow (Nm ranged from 3.675 to 33.227) and limited genetic structure among the three sampling locations. Given that S. carinata inhabits a highly interconnected system of large rivers and lakes, the results of low differentiation and high gene flow among geographically proximate sampling locations (sites separated by between 8 and 20 km of water) are not surprising. The results indicate that specimens can be used and moved from anywhere across the distribution of S. carinata for the purposes of captive propogation and translocation.

Seascape genetics of a flatfish reveals local selection under high levels of gene flow

Local adaptation is often found to be in a delicate balance with gene flow in marine species with high dispersal potential. Genotyping with mapped transcriptome-derived markers and advanced seascape statistical analyses are proven tools to uncover the genomic basis of biologically relevant traits under environmental selection. Using a panel of 426 gene-linked single nucleotide polymorphisms (SNPs), we scanned 17 samples (n¼539) of sole (Solea solea L.) from the Northeast Atlantic Ocean and applied a node-based seascape analysis. Neutral loci confirmed a clear distinction between the North Sea–Baltic Sea transition zone and the other Eastern Atlantic samples. At a more subtle level, the latter unit split in an English Channel and North Sea group, and a Bay of Biscay and Atlantic Iberian coast group. A fourth group, the Irish and Celtic Sea, was identified with 19 outlier loci. A pattern of isolation by distance (IBD) characterized the latitudinal distribution. Seascape analyses identified winter seawater temperature, food availability and coastal currents to explain a significant component of geographically distributed genetic variation, suggesting that these factors act as drivers of local adaptation. The evidence for local adaptation is in line with the current understanding on the impact of two key ecological factors, the life-history trait winter mortality and the behaviour of inshore/offshore spawning. We conclude that the subtle differentiation between two metapopulations (North Sea and Bay of Biscay) mirrors local adaptation. At least three genomic regions with strong population differentiation point to locally divergent selection. Further functional characterization of these genomic regions should help with formulating adaptive management policies.

The complex evolutionary history and phylogeography of Caridina typus (Crustacea: Decapoda): long-distance dispersal and cryptic allopatric species

The evolutionary history of the old, diverse freshwater shrimp genus Caridina is still poorly understood, despite its vast distribution – from Africa to Polynesia. Here, we used nuclear and mitochondrial DNA to infer the phylogeographic and evolutionary history of C. typus, which is one of only four species distributed across the entire range of the genus. Despite this species’ potential for high levels of gene flow, questions have been raised regarding its phylogeographic structure and taxonomic status. We identified three distinct lineages that likely diverged in the Miocene. Molecular dating and ancestral range reconstructions are congruent with C. typus’ early dispersal to Africa, possibly mediated by the Miocene Indian Ocean Equatorial Jet, followed by back dispersal to Australasia after the Jet’s closure. Furthermore, several different species delimitation methods indicate each lineage represents a distinct (cryptic) species, contradicting current morphospecies delimitation of a single C. typus taxon. The evolutionary history of C. typus lineages is complex, in which ancient oceanic current systems and (currently unrecognised) speciation events preceded secondary sympatry of these cryptic species.