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

2019 ◽  
Vol 70 (7) ◽  
pp. 977 ◽  
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.

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

2014 ◽  
Vol 13 (1) ◽  
pp. 9-17 ◽  
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.

scholarly journals Range reduction of the Oblong Rocksnail, Leptoxis compacta, shapes riverscape genetic patterns

2020 ◽  
Author(s):  
Aaliyah D. Wright ◽  
Nicole L. Garrison ◽  
Ashantye’ S. Williams ◽  
Paul D. Johnson ◽  
Nathan V. Whelan
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Human Impacts ◽  
Isolation By Distance ◽  
Extinction Risk ◽  
River System ◽  
High Genetic Diversity ◽  
Range Contraction ◽  
Genetic Patterns ◽  
Cahaba River

AbstractMany freshwater gastropod species face extinction, including 79% of species in the family Pleuroceridae. The Oblong Rocksnail, Leptoxis compacta, is a narrow range endemic pleurocerid from the Cahaba River basin in central Alabama that has seen rapid range contraction in the last 100 years. Such a decline is expected to negatively affect genetic diversity in the species. However, precise patterns of genetic variation and gene flow across the restricted range of L. compacta are unknown. This lack of information limits our understanding of human impacts on the Cahaba River system and Pleuroceridae. Here, we show that L. compacta has likely seen a species-wide decline in genetic diversity, but remaining populations have relatively high genetic diversity. We also report a contemporary range extension compared to the last published survey. Leptoxis compacta does not display an isolation by distance pattern, contrasting patterns seen in many riverine taxa. Our findings also indicate that historical range contraction has resulted in the absence of common genetic patterns seen in many riverine taxa like isolation by distance as the small distribution of L. compacta allows for relatively unrestricted gene flow across its remaining range despite limited dispersal abilities. Two collection sites had higher genetic diversity than others, and broodstock sites for future captive propagation and reintroduction efforts should utilize sites identified here as having the highest genetic diversity. Broadly, our results support the hypothesis that range contraction will result in the reduction of species-wide genetic diversity, and common riverscape genetic patterns cannot be assumed to be present in species facing extinction risk.

scholarly journals Range reduction of Oblong Rocksnail, Leptoxis compacta, shapes riverscape genetic patterns

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9789
Author(s):  
Aaliyah D. Wright ◽  
Nicole L. Garrison ◽  
Ashantye’ S. Williams ◽  
Paul D. Johnson ◽  
Nathan V. Whelan
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Human Impacts ◽  
Isolation By Distance ◽  
Extinction Risk ◽  
River System ◽  
High Genetic Diversity ◽  
Range Contraction ◽  
Genetic Patterns ◽  
Cahaba River

Many freshwater gastropod species face extinction, including 79% of species in the family Pleuroceridae. The Oblong Rocksnail, Leptoxis compacta, is a narrow range endemic pleurocerid from the Cahaba River basin in central Alabama that has seen rapid range contraction in the last 100 years. Such a decline is expected to negatively affect genetic diversity in the species. However, precise patterns of genetic variation and gene flow across the restricted range of L. compacta are unknown. This lack of information limits our understanding of human impacts on the Cahaba River system and Pleuroceridae. Here, we show that L. compacta has likely seen a species-wide decline in genetic diversity, but remaining populations have relatively high genetic diversity. We also report a contemporary range extension compared to the last published survey. Our findings indicate that historical range contraction has resulted in the absence of common genetic patterns seen in many riverine taxa like isolation by distance as the small distribution of L. compacta allows for relatively unrestricted gene flow across its remaining range despite limited dispersal abilities. Two collection sites had higher genetic diversity than others, and broodstock sites for future captive propagation and reintroduction efforts should utilize sites identified here as having the highest genetic diversity. Broadly, our results support the hypothesis that range contraction will result in the reduction of species-wide genetic diversity, and common riverscape genetic patterns cannot be assumed to be present in species facing extinction risk.

scholarly journals Genetic Structure and Eco-Geographical Differentiation of Lancea tibetica in the Qinghai-Tibetan Plateau

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 97 ◽  
Author(s):  
Xiaofeng Chi ◽  
Faqi Zhang ◽  
Qingbo Gao ◽  
Rui Xing ◽  
Shilong Chen
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Gene Flow ◽  
Tibetan Plateau ◽  
Environmental Changes ◽  
Restricted Gene Flow ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Genetic Diversity And Structure ◽  
Tanggula Mountains

The uplift of the Qinghai-Tibetan Plateau (QTP) had a profound impact on the plant speciation rate and genetic diversity. High genetic diversity ensures that species can survive and adapt in the face of geographical and environmental changes. The Tanggula Mountains, located in the central of the QTP, have unique geographical significance. The aim of this study was to investigate the effect of the Tanggula Mountains as a geographical barrier on plant genetic diversity and structure by using Lancea tibetica. A total of 456 individuals from 31 populations were analyzed using eight pairs of microsatellite makers. The total number of alleles was 55 and the number per locus ranged from 3 to 11 with an average of 6.875. The polymorphism information content (PIC) values ranged from 0.2693 to 0.7761 with an average of 0.4378 indicating that the eight microsatellite makers were efficient for distinguishing genotypes. Furthermore, the observed heterozygosity (Ho), the expected heterozygosity (He), and the Shannon information index (I) were 0.5277, 0.4949, and 0.9394, respectively, which indicated a high level of genetic diversity. We detected high genetic differentiation among all sampling sites and restricted gene flow among populations. Bayesian-based cluster analysis (STRUCTURE), principal coordinates analysis (PCoA), and Neighbor-Joining (NJ) cluster analysis based on microsatellite markers grouped the populations into two clusters: the southern branch and the northern branch. The analysis also detected genetic barriers and restricted gene flow between the two groups separated by the Tanggula Mountains. This study indicates that the geographical isolation of the Tanggula Mountains restricted the genetic connection and the distinct niches on the two sides of the mountains increased the intraspecific divergence of the plants.

Genetic diversity of the lichen-forming alga, Diplosphaera chodatii, in North America and Europe

2013 ◽  
Vol 45 (6) ◽  
pp. 799-813 ◽  
Author(s):  
Kyle M. FONTAINE ◽  
Elfie STOCKER-WÖRGÖTTER ◽  
Tom BOOTH ◽  
Michele D. PIERCEY-NORMORE
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
North America ◽  
Isolation By Distance ◽  
Water Level Fluctuations ◽  
Free Living ◽  
Climatic Zones ◽  
Algal Symbiont ◽  
Low Levels

AbstractDermatocarpon luridum is a subaquatic lichen which is distributed within temperate climatic zones around the world. It colonizes rock substrata along the shoreline of lakes and rivers of watersheds that regularly experience water level fluctuations. The mycobiont produces perithecia with small, simple spores that are thought to be wind dispersed. The photobiont, Diplosphaera chodatii, occurs both free-living and lichenized but little is known about its distribution and dispersal. The goal of this study was to compare the population structure of the photobiont from lakes and rivers in central North America with those of Europe. Specimens were collected in Manitoba, Canada and Austria. Population structure of the algal symbiont was assessed using the internal transcribed spacer (ITS) of ribosomal DNA (rDNA) and actin gene sequences. Results showed that genetic diversity and gene flow was high within local populations, but gene flow was low between continental populations. Low levels of gene flow between the most distant populations support the isolation-by-distance theory. The photobiont on both continents is also reported to be the photobiont for other lichen species contributing to photobiont availability for D. luridum.

scholarly journals Genetic diversity and extent of gene flow in the endangered Japanese population of Hodgson's hawk-eagle, Spizaetus nipalensis

2006 ◽  
Vol 16 (2) ◽  
pp. 113-129 ◽  
Author(s):  
SHIGEKI ASAI ◽  
YOSHIHIRO YAMAMOTO ◽  
SATOSHI YAMAGISHI
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Japanese Population ◽  
Isolation By Distance ◽  
Cladistic Analysis ◽  
Variable Region ◽  
Complete Sequence ◽  
Restricted Gene Flow ◽  
Critical Situation ◽  
Mtdna Sequence

The Japanese subspecies of Hodgson's Hawk-eagle, Spizaetus nipalensis orientalis, is considered threatened and has been designated as Endangered by the Japanese government. We determined the complete mitochondrial DNA (mtDNA) sequence of this species and designed a primer set to amplify a highly variable region of mtDNA, part of the control region (CR), based on this complete sequence. Using the primers, we amplified the CR and then determined the haplotypes of 178 samples collected at different sites in Japan. A nested cladistic analysis indicated that gene flow within some clades was restricted. The inference key implied that isolation by distance had caused the restriction of gene flow. Moreover, the ranges of the clades in which restricted gene flow was detected overlapped with the ranges of other clades. These results suggest that there is no fragmental population of Hodgson's Hawk-eagle in Japan and that this species has dispersed within short distances, at least in some lineages. Genetic diversity was high in comparison with other species. Therefore, at least in terms of genetic diversity, the Japanese population of Hodgson's Hawk-eagle is probably not in a critical situation.

scholarly journals Genetic studies of human diversity in East Asia

2007 ◽  
Vol 362 (1482) ◽  
pp. 987-996 ◽  
Author(s):  
Feng Zhang ◽  
Bing Su ◽  
Ya-ping Zhang ◽  
Li Jin
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
East Asia ◽  
Pacific Islands ◽  
East Asian ◽  
Human Populations ◽  
Genetic Studies ◽  
The North ◽  
Asian Populations ◽  
Genetic Diversity And Structure

East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic history and designing and interpreting genetic studies of human diseases, in recent years researchers in China have made substantial efforts to collect samples and generate data especially for markers on Y chromosomes and mtDNA. The hallmark of these efforts is the discovery and confirmation of consistent distinction between northern and southern East Asian populations at genetic markers across the genome. With the confirmation of an African origin for East Asian populations and the observation of a dominating impact of the gene flow entering East Asia from the south in early human settlement, interpretation of the north–south division in this context poses the challenge to the field. Other areas of interest that have been studied include the gene flow between East Asia and its neighbouring regions (i.e. Central Asia, the Sub-continent, America and the Pacific Islands), the origin of Sino-Tibetan populations and expansion of the Chinese.

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

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3842 ◽  
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.

scholarly journals Genetic structure of Oryza glumaepatula wild rice populations and evidence of introgression from O. sativa in Costa Rica

2015 ◽  
Author(s):  
Eric J Fuchs ◽  
Allan Meneses Martínez ◽  
Amanda Calvo ◽  
Melania Muñoz ◽  
Griselda Arrieta-Espinoza
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Costa Rica ◽  
Genetic Structure ◽  
Wild Species ◽  
Wild Rice ◽  
Wild Rice Species ◽  
Genetic Diversity And Structure ◽  
Diversity Estimates ◽  
Oryza Glumaepatula

Wild crop relatives are an important source of genetic diversity for crop improvement. However, gene flow from cultivated species into wild species may prove detrimental. Introgression may lead to changes in wild species by incorporating alleles from domesticated species, which may increase the likelihood of extinction. The objective of the present study is to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated if there is evidence of introgression between wild rice and commercial varieties of O. sativa since it is cultivated commonly in close proximity to wild rice populations. Individuals from all known O. glumaepatula populations in Costa Rica were collected. With the aid of 455 AFLP markers, we characterized the genetic diversity and structure among seven populations in northern Costa Rica. Given the dominant nature of our markers, Bayesian estimates of genetic structure were used. We also compared genetic diversity estimates between O. glumaepatula individuals and O. sativa commercial rice. Our results show that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. This is likely a result of large population size. Despite the restricted distributions of this wild species, in Costa Rica most populations are composed of several thousand individuals, thus reducing the effects of drift on genetic diversity. Our results also found low but significant structure (\theta=0.03±0.001) among populations that are separated by ~10 Km within a single river. The position of the population along the river did not influence genetic diversity estimates or differences among populations. This river does not have a strong current and meadows or seeds may easily move upstream, thus homogenizing genetic diversity across populations regardless of river position. Ample gene flow through pollen, seeds or detached culms within the same river reduces genetic structure. A Bayesian structure analysis showed that individuals from two populations share a significant proportion of their genomes with O. sativa genome. These results suggest that the low levels of genetic structure found in these populations are likely the result of introgression from cultivated O. sativa populations. These results expose an important biohazard as recurrent hybridization may reduce genetic diversity of this wild rice species. Introgression may transfer commercial traits into the only populations of O. glumaepatula in Costa Rica, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

scholarly journals Population structure and dispersal across small and large spatial scales in a direct developing marine isopod

2020 ◽  
Author(s):  
William S. Pearman ◽  
Sarah J. Wells ◽  
Olin K. Silander ◽  
Nikki E. Freed ◽  
James Dale
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Population Connectivity ◽  
Clear Pattern ◽  
Small Spatial Scale ◽  
Cook Strait ◽  
Genetic Break

AbstractMarine organisms generally exhibit one of two developmental modes: biphasic, with distinct adult and larval morphology, and direct development, in which larvae resemble adults. Developmental mode is thought to significantly influence dispersal, with direct developers expected to have much lower dispersal potential. However, in contrast to our relatively good understanding of dispersal and population connectivity for biphasic species, comparatively little is known about direct developers. In this study, we use a panel of 8,020 SNPs to investigate population structure and gene flow for a direct developing species, the New Zealand endemic marine isopod Isocladus armatus. On a small spatial scale (20 kms), gene flow between locations is extremely high and suggests an island model of migration. However, over larger spatial scales (600km), populations exhibit a clear pattern of isolation-by-distance. Because our sampling range is intersected by two well-known biogeographic barriers (the East Cape and the Cook Strait), our study provides an opportunity to understand how such barriers influence dispersal in direct developers. Our results indicate that I. armatus exhibits significant migration across these barriers, and suggests that ocean currents associated with these locations do not present a barrier to dispersal. Interestingly, we do find evidence of a north-south population genetic break occurring between Māhia and Wellington, two locations where there are no obvious biogeographic barriers between them. We conclude that developmental life history largely predicts dispersal in intertidal marine isopods. However, localised biogeographic processes can disrupt this expectation.

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