scholarly journals Investigation of population structure in Gulf of MexicoSeepiophila jonesi(Polychaeta, Siboglinidae) using cross-amplified microsatellite loci

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2366 ◽  
Author(s):  
Chunya Huang ◽  
Stephen W. Schaeffer ◽  
Charles R. Fisher ◽  
Dominique A. Cowart
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Microsatellite Loci ◽  
Deep Sea ◽  
Larval Dispersal ◽  
Cold Seeps ◽  
Dispersal Patterns ◽  
Separate Species ◽  
Significant Gene ◽  
Species Specific

BackgroundVestimentiferan tubeworms are some of the most recognizable fauna found at deep-sea cold seeps, isolated environments where hydrocarbon rich fluids fuel biological communities. Several studies have investigated tubeworm population structure; however, much is still unknown about larval dispersal patterns at Gulf of Mexico (GoM) seeps. As such, researchers have applied microsatellite markers as a measure for documenting the transport of vestimentiferan individuals. In the present study, we investigate the utility of microsatellites to be cross-amplified within the escarpiid clade of seep vestimentiferans, by determining if loci originally developed forEscarpiaspp. could be amplified in the GoM seep tubeworm,Seepiophila jonesi. Additionally, we determine if cross-amplified loci can reliably uncover the same signatures of high gene flow seen in a previous investigation ofS. jonesi.MethodsSeventy-sevenS. jonesiindividuals were collected from eight seep sites across the upper Louisiana slope (<1,000 m) in the GoM. Forty-eight microsatellite loci that were originally developed forEscarpia laminata(18 loci) andEscarpia southwardae(30 loci) were tested to determine if they were homologous and polymorphic inS. jonesi. Loci found to be both polymorphic and of high quality were used to test for significant population structuring inS. jonesi.ResultsMicrosatellite pre-screening identified 13 (27%) of theEscarpialoci were homologous and polymorphic inS. jonesi, revealing that microsatellites can be amplified within the escarpiid clade of vestimentiferans. Our findings uncovered low levels of heterozygosity and a lack of genetic differentiation amongstS. jonesifrom various sites and regions, in line with previous investigations that employed species-specific polymorphic loci onS. jonesiindividuals retrieved from both the same and different seep sites. The lack of genetic structure identified from these populations supports the presence of significant gene flow via larval dispersal in mixed oceanic currents.DiscussionThe ability to develop “universal” microsatellites reduces the costs associated with these analyses and allows researchers to track and investigate a wider array of taxa, which is particularly useful for organisms living at inaccessible locations such as the deep sea. Our study highlights that non-species specific microsatellites can be amplified across large evolutionary distances and still yield similar findings as species-specific loci. Further, these results show thatS. jonesicollected from various localities in the GoM represents a single panmictic population, suggesting that dispersal of lecithotrophic larvae by deep sea currents is sufficient to homogenize populations. These data are consistent with the high levels of gene flow seen inEscarpiaspp., which advocates that differences in microhabitats of seep localities lead to variation in biogeography of separate species.

scholarly journals Population Structure, Larval Dispersal, and Gene Flow in the Queen Conch,Strombus gigas, of the Caribbean

1989 ◽  
Vol 177 (3) ◽  
pp. 356-362 ◽  
Author(s):  
JEFFRY B. MITTON ◽  
CARL J. BERG ◽  
KATHERINE S. ORR
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Larval Dispersal ◽  
Strombus Gigas ◽  
Queen Conch ◽  
The Caribbean

Contrasting population structures of three Pristis sawfishes with different patterns of habitat use

2017 ◽  
Vol 68 (3) ◽  
pp. 452 ◽  
Author(s):  
N. M. Phillips ◽  
J. A. Chaplin ◽  
S. C. Peverell ◽  
D. L. Morgan
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Habitat Use ◽  
Microsatellite Loci ◽  
Spatial Scales ◽  
Marine Waters ◽  
Male And Female ◽  
Entire Life ◽  
Population Structures ◽  
Using Data

This research demonstrates how population structure differs in elasmobranchs with different patterns of habitat use. Population structure was assessed using data at microsatellite loci in three species of Pristis sawfishes in northern Australian waters. Statistically significant population structure was found in each of P. clavata (FST = 0.021, F′ST = 0.151, P < 0.001) and P. zijsron (FST = 0.026, F′ST = 0.130, P < 0.001), which spend their entire life in marine waters. In contrast, there was no evidence of significant population structure in P. pristis, which uses freshwater rivers as juveniles and marine waters as adults (FST = 0.004, F′ST = 0.029, P = 0.210). When combined with the results of mtDNA analyses from a previous study, the results suggested that dispersal in P. pristis is male-biased, whereas both male and female gene flow are restricted at large spatial scales in each of P. clavata and P. zijsron in Australian waters. The present study has provided the first evidence of sex-biased dispersal in a sawfish.

scholarly journals Range-Wide and Regional Patterns of Population Structure and Genetic Diversity in the Gopher Tortoise

2017 ◽  
Vol 8 (2) ◽  
pp. 497-512 ◽  
Author(s):  
D. Gaillard ◽  
J.R. Ennen ◽  
B.R. Kreiser ◽  
C.P. Qualls ◽  
S.C. Sweat ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Microsatellite Loci ◽  
Spatial Scales ◽  
Demographic History ◽  
Genetic Admixture ◽  
Gopher Tortoise ◽  
Regional Patterns ◽  
Genetic Groups

Abstract The gopher tortoise (Gopherus polyphemus) has experienced dramatic population declines throughout its distribution in the southeastern United States and is federally listed as threatened in the area west of the Tombigbee and Mobile rivers. While there is molecular support for recognizing the listed portion of the range as genetically distinct, other research has suggested that additional population structure exists at both range-wide and regional scales. In this study, we sought to comprehensively define genetic population structure at both spatial scales by doubling the data available in terms of the number of sampling sites, individuals, and microsatellite loci compared to previously published work. We also compared patterns of genetic diversity, gene flow, and demographic history across the range. We collected 933 individuals from 47 sampling sites across the range and genotyped them for 20 microsatellite loci. Our range-wide analyses supported the recognition of five genetic groups (or regions) delineated by the Tombigbee and Mobile rivers, Apalachicola and Chattahoochee rivers, and the transitional areas between several physiographic province sections of the Coastal Plains (i.e., Eastern Gulf, Sea Island, and Floridian). We found genetic admixture at sampling sites along the boundaries of these genetically defined groups. We detected some degree of additional genetic structure within each of the five regions. Notably, within the range listed as threatened under the Endangered Species Act, we found some support for two additional genetic groups loosely delineated by the Pascagoula and Chickasawhay rivers, and we detected four more genetic groups within the Florida region that seemed to reflect the influence of the local physiography. Additionally, our range-wide analysis found the periphery of the range had lower levels of genetic diversity relative to the core. We suggest that the five main genetic groups delineated in our study warrant recognition as management units in terms of conservation planning. Intraregional population structure also points to the potential importance of other barriers to gene flow at finer spatial scales, although additional work is needed to better delineate these genetic groups.

scholarly journals Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Cristhian Danilo Joya ◽  
Ricardo Marcel Landínez-García ◽  
Edna Judith Márquez
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Anthropogenic Activities ◽  
Lower Section ◽  
Habitat Disturbances ◽  
Genetic Groups ◽  
Lack Of Information ◽  
Species Specific

ABSTRACT Pimelodus yuma (formerly Pimelodus blochii) is a freshwater fish, endemic to the Colombian Magdalena-Cauca and Caribbean basins that experiences habitat disturbances resulting from anthropogenic activities. Due to the lack of information about the population genetics of this species, this study developed 14 species-specific microsatellite loci to assess the genetic diversity and population structure of samples from the lower section of the Cauca River. The studied species showed genetic diversity levels higher than the average values reported for Neotropical Siluriformes and significant inbreeding levels as was described for some congeners. Furthermore, P. yuma comprises two coexisting genetic groups that exhibit gene flow along the lower section of the Cauca River. This information constitutes a baseline for future monitoring of the genetic diversity and population structure in an anthropic influenced sector of the Magdalena-Cauca basin.

scholarly journals Population genetics of Anopheles arabiensis, the primary malaria vector in the Republic of Sudan

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Mashair Sir El Khatim Mustafa ◽  
Zairi Jaal ◽  
Sumia Abu Kashawa ◽  
Siti Azizah Mohd Nor
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Gene Flow ◽  
Malaria Vector ◽  
Microsatellite Loci ◽  
Anopheles Arabiensis ◽  
Isolation By Distance ◽  
Gene Pools ◽  
High Gene Flow ◽  
High Gene

Abstract Background Anopheles arabiensis is a member of Anopheles gambiae complex and the main malaria vector in Sudan. There is insufficient population genetics data available on An. arabiensis for an understanding of vector population structure and genetics, which are important for the malaria vector control programmes in this country. The objective of this investigation is to study the population structure, gene flow and isolation by distance among An. arabiensis populations for developing control strategies. Methods Mosquitoes were collected from six sites located in three different states in Sudan, Khartoum, Kassala and Sennar, using pyrethrum spray catch of indoor resting mosquitoes. Anopheline mosquitoes were identified morphologically and based on species specific nucleotide sequences in the ribosomal DNA intergenic spacers (IGS). Seven published An. gambiae microsatellite loci primers were used to amplify the DNA of An. arabiensis samples. Results PCR confirmed that An. arabiensis was the main malaria vector found in the six localities. Of the seven microsatellite loci utilized, six were found to be highly polymorphic across populations, with high allelic richness and heterozygosity with the remaining one being monomorphic. Deviation from Hardy–Weinberg expectations were found in 21 out of 42 tests in the six populations due to heterozygote deficiency. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes four and the other includes two populations. The clusters were not grouped according to the three states but were instead an admixture. The genetic distances between pairs of populations ranged from 0.06 to 0.24. Significant FST was observed between all pairwise analyses of An. arabiensis populations. The Kassala state population indicated high genetic differentiation (FST ranged from 0.17 to 0.24) from other populations, including one which is also located in the same state. High gene flow (Nm = 1.6–8.2) was detected among populations within respective clusters but limited between clusters particularly with respect to Kassala state. There was evidence of a bottleneck event in one of the populations (Al Haj Yousif site). No isolation by distance pattern was detected among populations. Conclusions This study revealed low levels of population differentiation with high gene flow among the An. arabiensis populations investigated in Sudan, with the exception of Kassala state.

scholarly journals Widespread Dispersal of the Crown-of-Thorns Sea Star,Acanthaster planci, across the Hawaiian Archipelago and Johnston Atoll

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Molly A. Timmers ◽  
Kimberly R. Andrews ◽  
Chris E. Bird ◽  
Marta J. deMaintenton ◽  
Russell E. Brainard ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Larval Dispersal ◽  
Hawaiian Islands ◽  
Marine Species ◽  
Sea Star ◽  
Acanthaster Planci ◽  
The West ◽  
Geographic Population ◽  
Hawaiian Archipelago

The population structure of marine species is variable along the Hawaiian Archipelago; thus, it is important to understand dispersal and recruitment patterns for economically and ecologically important taxa to inform Ecosystem-based Management. Connectivity of the coral-eating crown-of-thorns sea star,Acanthaster planci, was examined from Johnston Atoll and 12 locations across the Hawaiian Archipelago. Sequences of mitochondrial DNA from 383 individuals were analyzed to infer patterns of gene flow among the Northwestern Hawaiian Islands (NWHIs), the main Hawaiian Islands, and Johnston Atoll. Population samples were genetically similar across the Hawaiian Archipelago with the exception of the west side of the Big Island of Hawaii, which was significantly differentiated from the majority of Hawaiian samples (pairwise , ). Although differentiated, Hawai`i West shares haplotypes with every other site across the Hawaiian Archipelago. Johnston Atoll was genetically distinct from every location (pairwise , ) except French Frigate Shoals (, ), supporting connectivity between the central NWHIs and Johnston Atoll. Taken together with the lack of geographic population structure and haplotypes shared among all populations, these results indicate widespread larval dispersal with few restrictions to gene flow along the archipelago.

Population Genetic of Anopheles Arabiensis Patton(Diptera: Culicidae) the Malaria Vector in the Republic of Sudan.

2020 ◽  
Author(s):  
Mashair Mustafa ◽  
Zairi Jaal ◽  
Sumia Abu Kashawa ◽  
Siti Azizah Mohd Nor
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Malaria Vector ◽  
Microsatellite Loci ◽  
Population Genetic ◽  
Anopheles Arabiensis ◽  
Isolation By Distance ◽  
Gene Pools ◽  
High Gene Flow ◽  
High Gene

Abstract Background Anopheles arabiensis is a member of An. gambiae complex and a main malaria vector in Sudan. There is no sufficient An. arabiensis population genetic data available an understanding of vector population structure and genetics are important to the malaria vector control programs. The objective of this investigation is to study the population structure, gene flow and isolation by distance among An. arabiensis for developing control strategies Methods Mosquitoes were collected from six sites in Sudan using pyrethrum spray catch of indoor resting mosquitoes. Anopheline mosquitos were identified morphologically and based on species specific nucleotide sequences in the ribosomal DNA intergenic spacers (IGS). Seven microsatellite loci published An. gambiae primers were used to amplify the DNA of An. arabiensis samples. Results PCR confirmed that An. arabiensis was the main malaria vector found in the six localities. Of the seven microsatellite loci utilized, six were found to be highly polymorphic across populations, with high allelic richness and heterozygosity with the remaining one being monomorphic. Deviation from Hardy-Weinberg expectations were found in 21 out of 42 tests in the six populations due to heterozygotes deficiency. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes four and the other includes two populations. The genetic distances between pairs of populations ranged from 0.06 to 0.24. Significant F ST was observed between all An. arabiensis populations . Kr population indicated high genetic differentiation (F ST ranged from 0.17 to 0.24). High gene flow (Nm= 1.6–8.2) was detected between clusters. There was evidence of a bottleneck event in the Hj population. No isolation by distance pattern was detected among populations. Conclusions This study revealed low levels of population differentiation with high gene flow among six An. arabiensis populations in Sudan.

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