Comparative population genetics of swimming crab host (Portunus pelagicus) and common symbiotic barnacle (Octolasmis angulata) in Vietnam

Background By comparing spatial geographical structures of host populations with that of their symbionts light can be shed on their biological interactions, and the degree of congruence between host and symbiont phylogeographies should reflect their life histories and especially dispersal mechanisms. Methods Here, we analyzed the genetic diversity and structure of a host, the blue swimming crab, Portunus pelagicus, and its symbiotic pedunculate barnacle Octolasmis angulata from six location sites representing three geographic regions (north, central and south) along the Vietnam coastline. High levels of congruence in their phylogeographic patterns were expected as they both undergo planktonic larval stages. Results Based on the COI mtDNA markers, O. angulata populations showed higher genetic diversity in comparison with their host P. pelagicus (number of haplotype/individuals, haplotype and nucleotide diversity are 119/192, 0.991 ± 0.002 and 0.02; and 89/160, 0.913 ± 0.02 and 0.015, respectively). Pairwise Fst and AMOVA analyses showed a more pronounced population structure in the symbiotic barnacle than in its crab host. The DAPC analyses identified three genetic clusters. However, both haplotype networks and scatter plots supported connectivity of the host and the symbiotic barnacle throughout their distribution range, except for low subdivision of southern population. Isolation by distance were detected only for the symbiont O. angulata (R2 = 0.332, P = 0.05), while dbMEM supported spatial structure of both partners, but only at MEM-1 (Obs. 0.2686, P < 0.01 and Obs. 0.2096, P < 0.01, respectively).

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Population genetic structure and variability in Lindera glauca (Lauraceae) indicates low levels of genetic diversity and skewed sex ratios in natural populations in mainland China

PeerJ ◽

10.7717/peerj.8304 ◽

2020 ◽

Vol 8 ◽

pp. e8304 ◽

Cited By ~ 2

Author(s):

Biao Xiong ◽

Limei Zhang ◽

Shubin Dong ◽

Zhixiang Zhang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Isolation By Distance ◽

Sex Ratios ◽

Mainland China ◽

Small Sample ◽

Chloroplast Microsatellites ◽

Wild Populations ◽

Haplotype Networks ◽

Low Levels

Lindera glauca (Lauraceae) is a tree of economic and ecological significance that reproduces sexually and asexually via apomictic seeds. It is widely distributed in the low-altitude montane forests of East Asia. Despite the potential implications of a mixed reproductive system in terms of genetic diversity, few studies have focused on this aspect. In this study, the genetic structure of wild populations of L. glauca was investigated via genetic analyses. Overall, 13 nuclear microsatellites (nSSRs) and five chloroplast microsatellites (cpSSRs) were used to genotype 300 individual plants, taken from 20 wild populations (a small sample size in some wild populations is due to the limitation of its specific reproduction, leading to certain limitations in the results of this study) and two cultivated populations ranging across nearly the entire natural distribution of mainland China. The populations exhibited low levels of genetic diversity (nSSR: AR = 1.75, Ho = 0.32, He = 0.36; cpSSR: Nb = 2.01, Hrs = 0.40), and no significant effect of isolation by distance between populations existed, regardless of marker type (nSSR: R2 = 0.0401, P = 0.068; cpSSR: R2 = 0.033, P = 0.091). Haplotype networks showed complex relationships among populations, and the H12 haplotype was predominant in most populations. Analyses of molecular variance obtained with nuclear markers (Fsc = 0.293, FST = 0.362) and chloroplast markers (Fsc = 0.299, FST = 0.312) were similar. The migration ratio of pollen flow versus seed flow in this study was negative (r = −1.149). Results suggest that weak barriers of dispersal between populations and/or the similarity of founders shared between neighbors and distant populations are indicative of the gene flow between populations more likely involving seeds. Wild L. glauca in mainland China was inferred to have highly skewed sex ratios with predominant females. In addition, some populations experienced a recent bottleneck effect, especially in Gujianshan, Chongqing, and southwest China (population GJS). It is suggested that few wild male individuals should be conserved in order to maintain overall genetic diversity in the wild populations of this species. These findings provide important information for the sustainable utilization and preservation of the overall genetic diversity of L. glauca.

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Diverging Genetic Structure of Coexisting Populations of the Black Storm-Petrel and the Least Storm-Petrel in the Gulf of California

Tropical Conservation Science ◽

10.1177/1940082920949177 ◽

2020 ◽

Vol 13 ◽

pp. 194008292094917

Author(s):

Misael D. Mancilla-Morales ◽

Santiago Romero-Fernández ◽

Araceli Contreras-Rodríguez ◽

José J. Flores-Martínez ◽

Víctor Sánchez-Cordero ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Population Genetic Structure ◽

Mate Selection ◽

Gulf Of California ◽

Population Genetic ◽

Life Histories ◽

Gene Diversity ◽

Isolation By Distance ◽

Storm Petrel

Estimations on the influence of evolutionary and ecological forces as drivers of population gene diversity and genetic structure have been performed on a growing number of colonial seabirds, but many remain poorly studied. In particular, the population genetic structure of storm-petrels (Hydrobatidae) has been evaluated in only a few of the 24 recognized species. We assessed the genetic diversity and population structure of the Black Storm-Petrel ( Hydrobates melania) and the Least Storm-Petrel ( Hydrobates microsoma) in the Gulf of California. The two species were selected because they are pelagic seabirds with comparable ecological traits and breeding grounds. Recent threats such as introduced species of predators and human disturbance have resulted in a decline of many insular vertebrate populations in this region and affected many different aspects of their life histories (ranging from reproductive success to mate selection), with a concomitant loss of genetic diversity. To elucidate to what extent the population genetic structure occurs in H. melania and H. microsoma, we used 719 base pairs from the mitochondrial cytochrome oxidase c subunit I gene. The evaluation of their molecular diversity, genetic structure, and gene flow were performed through diversity indices, analyses of molecular and spatial variance, and isolation by distance (IBD) across sampling sites, respectively. The population genetic structure (via AMOVA and SAMOVA) and isolation by distance (pairwise p-distances and FST/1– FST (using ΦST) were inferred for H. microsoma. However, for H. melania evidence was inconclusive. We discuss explanations leading to divergent population genetic structure signatures in these species, and the consequences for their conservation.

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Genetic diversity and structure of Jatropha curcas L. in its centre of origin

Plant Genetic Resources ◽

10.1017/s1479262114000550 ◽

2014 ◽

Vol 13 (1) ◽

pp. 9-17 ◽

Cited By ~ 17

Author(s):

M. Salvador-Figueroa ◽

J. Magaña-Ramos ◽

J. A. Vázquez-Ovando ◽

M. L. Adriano-Anaya ◽

I. Ovando-Medina

Keyword(s):

Genetic Diversity ◽

Jatropha Curcas ◽

Isolation By Distance ◽

Random Mating ◽

Mantel Test ◽

Reproductive Pattern ◽

Chain Reactions ◽

Polymerase Chain Reactions ◽

Centre Of Origin ◽

Genetic Diversity And Structure

To investigate the genetic diversity and structure of Jatropha curcas L. oilseed plant, in this study, native populations from Chiapas, Mexico, were evaluated, using microsatellite DNA markers. A total of 93 representative samples were selected from seven sites in two regions in the state of Chiapas grouped by geographical proximity, where leaf samples were collected to isolate the genomic DNA. Individual polymerase chain reactions were carried out with ten pairs of specific oligonucleotides for the microsatellites of J. curcas, separating the products of amplification by acrylamide electrophoresis. Twenty-seven fragments were detected (77% polymorphic) with which heterozygous individuals were distinguished. The most informative microsatellite was Jcps20 (nine alleles, polymorphic index content 0.354). The average polymorphism per population was 58%. The Hardy–Weinberg tests revealed a reproductive pattern of non-random mating. The diversity descriptors and the analysis of molecular variance revealed that the populations were structured and moderately differentiated (FST 0.087) and that this differentiation was not due to isolation by distance, as the Mantel test was not significant (P= 0.137), but rather due to allopatry. Bayesian analysis revealed that the accessions belonged to only four genetic groups and confirmed the differentiation between the regions. Because some loci were in Hardy–Weinberg disequilibrium, it is proposed that differentiation is due to the clonal reproduction of J. curcas practised by farmers in Chiapas, along with the anthropogenic dispersion at regional levels. The results of this study reveal that J. curcas in Chiapas has genetic diversity that is greater than that reported in other parts of the world, which represents a potential germplasm pool for the selection of genotypes.

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Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus?

PeerJ ◽

10.7717/peerj.3842 ◽

2017 ◽

Vol 5 ◽

pp. e3842 ◽

Cited By ~ 2

Author(s):

Daniela Lazo-Cancino ◽

Selim S. Musleh ◽

Cristian E. Hernandez ◽

Eduardo Palma ◽

Enrique Rodriguez-Serrano

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Isolation By Distance ◽

Landscape Fragmentation ◽

Native Forest ◽

Least Cost Path ◽

Natural Habitats ◽

Forest Patches ◽

Genetic Diversity And Structure ◽

Oligoryzomys Longicaudatus

Background Fragmentation of native forests is a highly visible result of human land-use throughout the world. In this study, we evaluated the effects of landscape fragmentation and matrix features on the genetic diversity and structure of Oligoryzomys longicaudatus, the natural reservoir of Hantavirus in southern South America. We focused our work in the Valdivian Rainforest where human activities have produced strong change of natural habitats, with an important number of human cases of Hantavirus. Methods We sampled specimens of O. longicaudatus from five native forest patches surrounded by silvoagropecuary matrix from Panguipulli, Los Rios Region, Chile. Using the hypervariable domain I (mtDNA), we characterized the genetic diversity and evaluated the effect of fragmentation and landscape matrix on the genetic structure of O. longicaudatus. For the latter, we used three approaches: (i) Isolation by Distance (IBD) as null model, (ii) Least-cost Path (LCP) where genetic distances between patch pairs increase with cost-weighted distances, and (iii) Isolation by Resistance (IBR) where the resistance distance is the average number of steps that is needed to commute between the patches during a random walk. Results We found low values of nucleotide diversity (π) for the five patches surveyed, ranging from 0.012 to 0.015, revealing that the 73 sampled specimens of this study belong to two populations but with low values of genetic distance (γST) ranging from 0.022 to 0.099. Likewise, we found that there are no significant associations between genetic distance and geographic distance for IBD and IBR. However, we found for the LCP approach, a significant positive relationship (r = 0.737, p = 0.05), with shortest least-cost paths traced through native forest and arborescent shrublands. Discussion In this work we found that, at this reduced geographical scale, Oligoryzomys longicaudatus shows genetic signs of fragmentation. In addition, we found that connectivity between full growth native forest remnants is mediated by the presence of dense shrublands and native forest corridors. In this sense, our results are important because they show how native forest patches and associated routes act as source of vector species in silvoagropecuary landscape, increasing the infection risk on human population. This study is the first approach to understand the epidemiological spatial context of silvoagropecuary risk of Hantavirus emergence. Further studies are needed to elucidate the effects of landscape fragmentation in order to generate new predictive models based on vector intrinsic attributes and landscape features.

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Abundance and spatial distribution of blue swimming crab (Portunus pelagicus) larvae during east monsoon in the East Lampung waters, Indonesia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d190420 ◽

2018 ◽

Vol 19 (4) ◽

pp. 1326-1333 ◽

Cited By ~ 2

Author(s):

DURANTA D. KEMBAREN ◽

ZAIRION ZAIRION ◽

MOHAMMAD M. KAMAL ◽

YUSLI WARDIATNO

Keyword(s):

Spatial Distribution ◽

Early Stage ◽

Mass Density ◽

Sampling Site ◽

Water Environment ◽

Larval Abundance ◽

Swimming Crab ◽

Portunus Pelagicus ◽

Important Species ◽

Larval Stages

Kembaren DD, Zairion, Kamal MM, Wardiatno Y. 2018. Abundance and spatial distribution of blue swimming crab (Portunuspelagicus) larvae during east monsoon in the East Lampung waters, Indonesia. Biodiversitas 19: 1326-1333. The blue swimmingcrab/BSC, Portunus pelagicus, is an economically important species in fishery industry and continuously being exploited, particularly inthe East Lampung waters. BSC research in Indonesia during the last decade was only restricted to the adult phase, while research ontheir larval dynamics in nature has not been done yet. This study aimed to assess the abundance and the distribution of BSC larvae, andto describe their correlation to its environmental conditions. This study was conducted in June 2017 (during east monsoon) in the EastLampung waters. Sampling was done in surface water during the daylight hours on nine sites with three replicates on each site. Planktonabundance and oceanographic profile were also recorded from the same sampling site. The result from this study showed that the waterquality from the environment was suitable for the development of BSC larvae. The abundance of the early-stage larvae (Z1-Z3) wasrelatively higher than the late-stage larvae (Z4 and M). The larval stages of BSC were dispersed and completed their development in themid-shore and offshore waters. There was a tendency that the early-stage was more abundant in the northern part, while the late-stagewas more abundant in the southern part of the study area. The highest larval abundance was found in the mid-shore, particularly in sitenumber five, which was influenced by the water mass density and current direction during the east monsoon. Moreover, oxygenconcentration and salinity of the water environment influenced the early-stage larvae abundance more than the late-stages abundance.

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Geographically structured genetic diversity in the cave beetle Darlingtonea kentuckensis Valentine, 1952 (Coleoptera, Carabidae, Trechini, Trechina)

Subterranean Biology ◽

10.3897/subtbiol.34.46348 ◽

2020 ◽

Vol 34 ◽

pp. 1-23 ◽

Cited By ~ 1

Author(s):

Olivia F. Boyd ◽

T. Keith Philips ◽

Jarrett R. Johnson ◽

Jedidiah J. Nixon

Keyword(s):

Genetic Diversity ◽

Isolation By Distance ◽

A Priori ◽

Coi Gene ◽

Population Isolation ◽

Eastern Kentucky ◽

Eastern Usa ◽

Genetic Clusters ◽

Cave Beetle ◽

Mantel Correlations

Cave beetles of the eastern USA are one of many poorly studied groups of insects and nearly all previous work delimiting species is based solely on morphology. This study assesses genetic diversity in the monotypic cave carabid beetle genus DarlingtoneaValentine 1952, to test the relationship between putative geographical barriers to subterranean dispersal and the boundaries of genetically distinct groups. Approximately 400bp of the mitochondrial cytochrome oxidase I (COI) gene was sequenced from up to four individuals from each of 27 populations, sampled from caves along the escarpments of the Mississippian and Cumberland plateaus in eastern Kentucky, USA. The 81 individuals sequenced yielded 28 unique haplotypes. Hierarchical analyses of molecular variance (AMOVA) within and among geographically defined groups tested two a priori hypotheses of structure based on major and minor river drainages, as well as genetic distance clusters defined a posteriori from an unrooted analysis. High genetic differentiation (FST) between populations was found across analyses. The influence of isolation by distance could potentially account for much but not all of the variation found among geographically defined groups at both levels. High variability among the three northernmost genetic clusters (FCT), low variability among populations within clusters (FSC), and low within-cluster Mantel correlations indicate the importance of unidentified likely intra-karst barriers to gene flow separating closely grouped cave populations. Overall phylogeographic patterns are consistent with previous evidence of population isolation among cave systems in the region, revealing geographically structured cryptic diversity in Darlingtonea over its distribution. The landscape features considered a priori in this study were not predictive of the genetic breaks among the three northern clusters, which are genetically distinct despite their close geographic proximity.

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Genetic diversity and differentiation in the swimming crab, Portunus trituberculatus (Miers, 1876) (Decapoda, Brachyura) along the coast of China based on fluorescent AFLP markers: implications for conservation and genetic improvement

Crustaceana ◽

10.1163/15685403-00003398 ◽

2015 ◽

Vol 88 (1) ◽

pp. 1-17

Author(s):

Xiaoying Li ◽

Zhiguo Dong ◽

Hongbo Su ◽

Qingqi Zhang ◽

Huan Gao ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Genetic Improvement ◽

The Other ◽

Aflp Markers ◽

Ex Situ ◽

Portunus Trituberculatus ◽

Swimming Crab ◽

Species Introduction ◽

Genetic Diversity And Structure

Using fluorescent AFLP-markers, the genetic diversity and structure of six geographical populations of the swimming crab,Portunus trituberculatus(Miers, 1876), from the coast of China were analysed to assess their genetic resource state. Eight primer combinations generated 925 loci among 85 individuals, and revealed a high polymorphism within these populations that varied from 57.41% (Zhoushan population) to 76.86% (Dalian population). According to the combination of percentage of polymorphic loci (PPL) and Shannon’s information index (I), the populations from Zhangzhou, Dongying and Dalian showed more genetic variation than the Lianyungang, Zhanjiang and Zhoushan populations. The gene flow () and across all populations overall were 1.935 and 0.205, respectively, showing moderate genetic differentiation. Differentiation was highest in the Zhoushan and Zhanjiang populations, and the geographical distribution and UPGMA cluster tree were not fully accordant. Neutrality test results revealed that the Zhangzhou population faced a smaller selective pressure than the other five populations (). In general, a high genetic diversity among theP. trituberculatuspopulations was observed along the coast of China, especially in the Zhangzhou, Dongying, Dalian and Lianyungang populations, while a pronounced level () of genetic differentiation has occurred between the Zhoushan population and the other populations. Therefore, these findings have the following implications for conservation and genetic improvement: (1) high diversity levels and good genetic resources, especially in the Zhangzhou population, which could lay the foundations for breeding research and genetic improvement; (2) the importance of preventing species escape and gene pool contamination in ex-situ conservation and species introduction programs in the Zhoushan population.

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Genetic differentiation between estuarine and open coast ecotypes of a dominant ecosystem engineer

Marine and Freshwater Research ◽

10.1071/mf17392 ◽

2019 ◽

Vol 70 (7) ◽

pp. 977 ◽

Cited By ~ 6

Author(s):

M. A. Coleman ◽

J. S. Clark ◽

M. A. Doblin ◽

M. J. Bishop ◽

B. P. Kelaher

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Ecosystem Engineer ◽

Isolation By Distance ◽

Spatial Scales ◽

Random Mating ◽

Rocky Shores ◽

Open Coast ◽

Key Species ◽

Genetic Diversity And Structure

Temperate intertidal shores globally are often dominated by habitat-forming seaweeds, but our knowledge of these systems is heavily biased towards northern hemisphere species. Rocky intertidal shores throughout Australia and New Zealand are dominated by a single monotypic species, Hormosira banksii. This species plays a key role in facilitating biodiversity on both rocky shores and estuarine habitats, yet we know little about the processes that structure populations. Herein we characterise the genetic diversity and structure of Hormosira and demonstrate strong restrictions to gene flow over small spatial scales, as well as between estuarine and open coast populations. Estuarine ecotypes were often genetically unique from nearby open coast populations, possibly due to extant reduced gene flow between habitats, founder effects and coastal geomorphology. Deviations from random mating in many locations suggest complex demographic processes are at play within shores, including clonality in estuarine populations. Strong isolation by distance in Hormosira suggests that spatial management of intertidal habitats will necessitate a network of broad-scale protection. Understanding patterns of genetic diversity and gene flow in this important ecosystem engineer will enhance the ability to manage, conserve and restore this key species into the future.

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Development of the Larval Stages of the Blue Swimming Crab Portunus pelagicus L. (Portunidae : Decapoda : Crustacea)

Marine and Freshwater Research ◽

10.1071/mf9790485 ◽

1979 ◽

Vol 30 (4) ◽

pp. 485 ◽

Cited By ~ 12

Author(s):

L Shinkarenko

Keyword(s):

Scylla Serrata ◽

Gastric Mill ◽

Swimming Crab ◽

Portunus Pelagicus ◽

Larval Stages ◽

Mechanical Breakdown

The four zoeal stages and megalopa of P. pelagicus were reared in culture and are described. Each appendage or structure is described showing the changes that occur during the zoeal phase. P. pelagicus larvae have similar types and location of setae as the larvae of P. spinicarpus. The positions of the chromatophores in the zoeal stages are described. The megalopa has the same types of setae as the zoea with the addition of two types of modified serrate setae. The zoea has no gastric mill and the capture and mechanical breakdown of the prey is the function of the mouthparts: the labrum, mandibles, maxillules and maxillae; and the serrated setae in the curve of the telson. The mouthparts of the megalopa are composed of the same appendages as in the zoea with the incorporation of the first, second and third maxillipeds. There are discrepancies between the descriptions in the present study and that of Prasad and Tampi (1953) whose second and third zoea and megalopa were obtained from the plankton. P. pelagicus larvae are compared with those of Scylla serrata to see if they could be distinguished, morphologically.

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Genetic diversity and structure of the treeManilkara zapotain a naturally fragmented tropical forest

Journal of Tropical Ecology ◽

10.1017/s0266467417000268 ◽

2017 ◽

Vol 33 (4) ◽

pp. 285-294 ◽

Cited By ~ 1

Author(s):

Daniela A. Martínez-Natarén ◽

Víctor Parra-Tabla ◽

Miguel A. Munguía-Rosas

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Tropical Forest ◽

Isolation By Distance ◽

Allelic Diversity ◽

Long Distance ◽

Population Genetic Differentiation ◽

Continuous Forest ◽

Genetic Diversity And Structure ◽

Degree Of Isolation

Abstract:Forest fragmentation, habitat loss and isolation may have a strong effect on biodiversity in tropical forests. This can include modification of the genetic diversity and structure of plant populations. In this study, we assessed the genetic diversity and structure of the treeManilkara zapotain 15 naturally formed fragments of semi-evergreen tropical forest, as well as in an adjacent continuous forest for comparison. Forest fragments were scattered within a matrix of wetlands and were highly variable in terms of size and degree of isolation. The naturally fragmented populations ofM.zapotahad slightly less allelic diversity (Ar: 3.4) than those of the continuous forest (Ar: 3.6), when corrected for sample size. However, populations in the fragments and continuous forest had very similar heterozygosity levels (HE: 0.59 in both cases). Low levels of genetic differentiation were observed among populations (FST: 0.026) and genetic structure was not consistent with isolation by distance, indicating high levels of gene flow. Genetic diversity was not explained by fragment size or degree of isolation. The relatively high genetic diversity and low inter-population genetic differentiation observed inM. zapotamay be the result of long-distance pollen and seed dispersal, as well as the high proximity among patches.

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