scholarly journals GENETIC DIVERSITY OF Agave cupreata TREL. & BERGER. CONSIDERATIONS FOR ITS CONSERVATION

2011 ◽  
Vol 34 (3) ◽  
pp. 159
Author(s):  
Alejandro Martínez-Palacios ◽  
Juan M. Gómez-Sierra ◽  
Cuauhtémoc Sáenz-Romero ◽  
Nidia Pérez-Nasser ◽  
Nahúm Sánchez-Vargas
Keyword(s):  
Genetic Variation ◽  
Isolation By Distance ◽  
Alcoholic Beverage ◽  
Natural Populations ◽  
Mantel Test ◽  
Ex Situ ◽  
Semiarid Region ◽  
Endemic Plant ◽  
Effective Population ◽  
Conservation Units

Agave cupreata Trel. & Berger is an endemic plant naturally distributed in the Balsas Depression, a semiarid region in the states of Guerrero and Michoacán in Southwestern México. Their populations are heavily decimated because mature individuals just before their single life flowering period are harvested to produce mezcal, an alcoholic beverage. The genetic variation among and within 12 natural populations was examined for nine isozyme loci. Results indicate high average proportion of polymorphic loci (93 %) and expected heterozygosity (He = 0.467), with an excess of observed heterozygotes in relation to Hardy-Weinberg expectations (Ho = 0.521, FIS = -0.1179). These results represent the largest heterozygosity reported for Agave species endemic to México. There is also a statistically significant genetic differentiation among populations (FST = 0.042). An UPGMA dendrogram reveals the absence of a geographic pattern, as confi rmed by a Mantel test (r = -0.110, P = 0.769), which did not show significant isolation by distance. Estimated minimum viable effective population size was very large (Ne =16,165), larger than in any other known natural population. To protect the natural genetic variation, it is suggested to design and manage A. cupreata natural populations as forest genetic resource conservation units (FGRCUs) using realistic and modest Ne sizes, perhaps between 500 and 5000 plants, ideally with intermediate plantations that could serve as pollinator corridors. Commercial plantations and ex situ FGRCUs need to be established to gradually develop a sustainable management, perhaps at higher altitudes than current locations, as a management measure for adaptation to the climatic change.

scholarly journals Genetic diversity and structure of the narrow endemic Seseli farrenyi (Apiaceae): implications for translocation

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10521
Author(s):  
Núria Garcia-Jacas ◽  
Jèssica Requena ◽  
Sergi Massó ◽  
Roser Vilatersana ◽  
Cèsar Blanché ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Decline ◽  
Natural Populations ◽  
Ex Situ ◽  
Endemic Plant ◽  
Genetic Lineages ◽  
Narrow Endemic ◽  
Management Measures ◽  
Genetic Diversity And Structure ◽  
Nw Mediterranean

Seseli farrenyi (Apiaceae) is an extremely narrow endemic plant, which is considered as one of the species of most conservation concern in Catalonia (NW Mediterranean Basin). Given the accelerated fragmentation and reduction of population size (of over 90%), the environmental agency of Catalonia is currently preparing a recovery plan that includes reinforcements of the extant populations. The present study is aimed at providing the necessary knowledge to carry out genetically-informed translocations, by using microsatellites as genetic markers. Fourteen microsatellites have been specifically developed for S. farrenyi, of which nine have been used. Besides the extant natural populations, the three ex situ collections that are known to exist of this species have also been studied, as they would be the donor sources for translocation activities. Our main finding is that levels of genetic diversity in the natural populations of S. farrenyi are still high (He = 0.605), most likely as a result of a predominantly outcrossing mating system in combination with the limited time elapsed since the population decline. However, population fragmentation is showing the first genetic signs, as the values of genetic differentiation are relatively high, and two well-differentiated genetic lineages have been found even in such a narrow geographic range. These genetic results provide important information when designing conservation management measures.

scholarly journals High Level of Phenotypic Differentiation of Common Yew (Taxus baccata L.) Populations in the North-Western Part of the Balkan Peninsula

Forests ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 78
Author(s):  
Katarina Tumpa ◽  
Zlatko Liber ◽  
Zlatko Šatović ◽  
Jasnica Medak ◽  
Marilena Idžojtić ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Isolation By Distance ◽  
Balkan Peninsula ◽  
Mantel Test ◽  
Environmental Data ◽  
Ex Situ ◽  
Phenotypic Traits ◽  
Taxus Baccata ◽  
The North ◽  
North Western

Common or English yew (Taxus baccata L., Taxaceae) is a conifer species, native to Europe, northern Africa, Asia Minor and Caucasus. It is a dioecious, wind-pollinated and animal-dispersed tree, known for its high-quality wood and medicinal properties, albeit poisonous. The species is rare and has been legally protected at the European and national levels. In addition, its low population density and disjunct character of distribution have reinforced the need for its protection as regeneration is mostly lacking. The aim of this study was to phenotypically characterise the north-western Balkan yew populations. Phenotypic diversity was examined for seven populations, using morphometric analysis of nine phenotypic traits of needles. Descriptive and multivariate statistical analyses were conducted to evaluate the inter- and intrapopulation variability. In addition, to test correlations between geographic, climatic and phenotypic data, Mantel test was used. We identified a geographic structure across studied populations that exhibited high levels of variability on intra- and interpopulation levels. Two groups of populations have been defined and are consistent with previously described genetic divergent lineages from separate refugia. In addition, a significant correlation between phenotypic and geographic data were revealed, i.e., isolation by distance (IBD). However, the Mantel test revealed no significant correlation between morphometric and environmental data. In conclusion, our data reveal that the historical events and persistent IBD acted in combination to produce the morphological patterns observed in common yew populations in the north-western part of the Balkan Peninsula. Finally, we suggested conservation measures to be implemented on a stand level, with habitat preservation as the main goal. In addition, ex situ conservation should be considered, both in the form of collections and urban planting, as both provide additional gene pool reserves.

scholarly journals Global diversity and genetic landscape of natural populations and hatchery stocks of largemouth bass micropterus salmoides across American and Asian regions

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Dan Wang ◽  
Hong Yao ◽  
Yan-He Li ◽  
Yong-Jiang Xu ◽  
Xu-Fa Ma ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Largemouth Bass ◽  
Micropterus Salmoides ◽  
Natural Populations ◽  
The United States ◽  
Systematic Evaluation ◽  
Wild Populations ◽  
Effective Population ◽  
Population Genetic Analysis ◽  
The North

Abstract Although largemouth bass Micropterus salmoides has shown its extremely economic, ecological, and aquacultural significances throughout the North American and Asian continents, systematic evaluation of genetic variation and structure of wild and cultured populations of the species is yet to be documented. In this study, we investigated the genetic structure of M. salmoides from 20 wild populations and five cultured stocks across the United States and China using eight microsatellite loci, which are standard genetic markers for population genetic analysis. Our major findings are as follows: (1) the result of Fst showed largemouth bass had high genetic differentiation, and the gene flow indicated the genetic exchange among wild populations is difficult; (2) AMOVA showed that 14.05% of the variation was among populations, and 85.95% of the variation was within populations; (3) The majority of largemouth bass populations had a significant heterozygosity excess, which is likely to indicate a previous population bottleneck; (4) Allelic richness was lower among cultured populations than among wild populations; (5) Effective population size in hatcheries could promote high levels of genetic variation among individuals and minimize loss of genetic diversity; China’s largemouth bass originated from northern largemouth bass of USA. The information provides valuable basis for development of appropriate conservation policies for fisheries and aquaculture genetic breeding programs in largemouth bass.

scholarly journals Genetic structure of natural populations of Cryptocarya moschata Nees (Lauraceae) from southeastern Brazilian Atlantic rain forest

2004 ◽  
Vol 4 (1) ◽  
pp. 01-16 ◽  
Author(s):  
Pedro Luís Rodrigues de Moraes ◽  
Maria Teresa Vitral de Carvalho Derbyshire
Keyword(s):  
Genetic Structure ◽  
Rain Forest ◽  
Evolutionary Dynamics ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Natural Populations ◽  
Conservation Strategies ◽  
Atlantic Rain Forest ◽  
Effective Population ◽  
Allozyme Loci

This study was accomplished on a more comprehensive basis to evaluate previous questions that were raised from a preliminary article about the genetic structure of Cryptocarya moschata populations. Thus, through the analysis of 40 polymorphic allozyme loci, allele frequencies were estimated from 335 individuals of 11 natural populations of C. moschata from six hydrographic basins of São Paulo state and Serra da Estrela, Rio de Janeiro, Brazil. Estimates of Wright's F statistics were done through the analysis of variance, presenting average values of <img border=0 width=32 height=32 id="_x0000_i1026" src="../../../../../../img/revistas/bn/v4n1/img/a04car(f).jpg" align=absmiddle > or = 0.352, <img border=0 width=32 height=32 id="_x0000_i1027" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle > or = 0.285 and <img border=0 width=32 height=32 id="_x0000_i1028" src="../../../../../../img/revistas/bn/v4n1/img/a04car(f2).jpg" align=absmiddle > or = 0.097. These results indicated that individuals within populations must be panmitic, and that the diversity among populations is fairly high, being superior to what would be expected for groups of plants having a full-sib family structure. From estimates of <img border=0 width=32 height=32 id="_x0000_i1029" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle>obtained for populations taken two at a time, the model of isolation by distance was tested; data did not fit the model, showing that <img border=0 width=32 height=32 id="_x0000_i1030" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle>did not increase by the respective increasing of the geographic distance. The estimated gene flow of 0.55 migrants per generation corroborated the pronounced populational differentiation, indicating that drift effects should be more important than the selection ones. The effective population sizes found from the sampled populations showed that there was an adequate genetic representativeness of the samples for those with relatively low values of <img border=0 width=32 height=32 id="_x0000_i1031" src="../../../../../../img/revistas/bn/v4n1/img/a04car(f2).jpg" align=absmiddle>. Though, under a metapopulation context, the effective population size was 17.07 individuals, indicating that sampling performed for the species corresponded to 88.44% of the maximum effective size obtained from 11 populations with a <img border=0 width=32 height=32 id="_x0000_i1032" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle>of 0.285, equivalent to only 5.09% individuals for the total sampled. Management and conservation strategies aimed at preserving high intrapopulation genetic variation in C. moschata would imply in the maintenance of populations with great number of individuals. Moreover, for the preservation of the species as a whole, the maintenance of many such populations would be mandatorily recommended, which denotes that the conservation of large areas of Atlantic rain forest should be necessary to hold its evolutionary dynamics.

scholarly journals Environmental and geographic data optimize ex situ collections and the preservation of adaptive evolutionary potential

2020 ◽  
Author(s):  
Lionel N. Di Santo ◽  
Jill A. Hamilton
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Plant Species ◽  
Isolation By Distance ◽  
Allelic Diversity ◽  
Genetic Data ◽  
Ex Situ ◽  
Evolutionary Potential ◽  
Isolation By Environment ◽  
The Impact

AbstractMaintenance of biodiversity, through seed banks and botanical gardens where the wealth of species’ genetic variation may be preserved ex situ, is a major goal of conservation. However, challenges can persist in optimizing ex situ collections where trade-offs exist between expense, effort, and conserving species evolutionary potential, particularly when genetic data is not available. Within this context, we evaluate the genetic consequences of guiding population preservation using geographic (isolation-by-distance, IBD) and environmental (isolation-by-environment, IBE) data for ex situ collections where provenance data is available. We use 19 genetic and genomic datasets from 15 plant species to (i) assess the proportion of population genetic differentiation explained by geographic and environmental factors, and (ii) simulate ex situ collections prioritizing source populations based on pairwise geographic or environmental distances. Specifically, we test the impact prioritizing sampling based on environmental and geographic distances may have on capturing neutral, functional or putatively adaptive genetic diversity and differentiation. We find that collectively IBD and IBE explain a substantial proportion of genetic differences among functional (median 45%) and adaptive (median 71%) loci, but not for neutral loci (median 21.5%). Simulated ex situ collections reveal that inclusion of IBD and IBE increases both allelic diversity and genetic differentiation captured among populations, particularly for loci that may be important for adaptation. Thus, prioritizing population collections using environmental and geographic distance data can impact genetic variation captured ex situ. This provides value for the vast majority of plant species for which we have no genetic data, informing conservation of genetic variation needed to maintain evolutionary potential within collections.

scholarly journals Effective population sizes and adaptive genetic variation in a captive bird population

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5803 ◽  
Author(s):  
Giridhar Athrey ◽  
Nikolas Faust ◽  
Anne-Sophie Charlotte Hieke ◽  
I. Lehr Brisbin
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Demographic History ◽  
Ex Situ ◽  
Adaptive Genetic Variation ◽  
Effective Population ◽  
B Locus ◽  
Captive Populations ◽  
Chain Of Custody ◽  
Population Sizes

Captive populations are considered a key component of ex situ conservation programs. Research on multiple taxa has shown the differential success of maintaining demographic versus genetic stability and viability in captive populations. In typical captive populations, usually founded by few or related individuals, genetic diversity can be lost and inbreeding can accumulate rapidly, calling into question their ultimate utility for release into the wild. Furthermore, domestication selection for survival in captive conditions is another concern. Therefore, it is crucial to understand the dynamics of population sizes, particularly the effective population size, and genetic diversity at non-neutral and adaptive loci in captive populations. In this study, we assessed effective population sizes and genetic variation at both neutral microsatellite markers, as well as SNP variants from the MHC-B locus of a captive Red Junglefowl population. This population represents a rare instance of a population with a well-documented history in captivity, following a realistic scenario of chain-of-custody, unlike many captive lab populations. Our analyses, which included 27 individuals comprising the entirety of one captive population show very low neutral and adaptive genetic variation, as well as low effective sizes, which correspond with the known demographic history. Finally, our study also shows the divergent impacts of small effective size and inbreeding in captive populations on microsatellite versus adaptive genetic variation in the MHC-B locus. Our study provides insights into the difficulties of maintaining adaptive genetic variation in small captive populations.

scholarly journals Effective population sizes and adaptive genetic variation in a captive bird population

2018 ◽  
Author(s):  
Giridhar Athrey ◽  
Nikolas Faust ◽  
Anne-Sophie Charlotte Hieke ◽  
I. Lehr Brisbin
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Demographic History ◽  
Ex Situ ◽  
Adaptive Genetic Variation ◽  
Effective Population ◽  
B Locus ◽  
Captive Populations ◽  
Chain Of Custody ◽  
Population Sizes

AbstractCaptive populations are considered a key component of ex situ conservation programs. Research on multiple taxa have shown the differential success of maintaining demographic versus genetic stability and viability in captive populations. In typical captive populations, usually founded by few or related individuals, genetic diversity can be lost and inbreeding can accumulate rapidly, calling into question their ultimate utility for release into the wild. Furthermore, domestication selection for survival in captive conditions is another concern. Therefore, it is crucial to understand the dynamics of population sizes, particularly the effective population size, and genetic diversity at non-neutral, at adaptive loci in captive populations.In this study, we assessed effective population sizes and genetic variation at both neutral microsatellite markers, as well as SNP variants from the MHC-B locus of a captive Red Junglefowl population. This population is represents a rare instance of a population with a well-documented history in captivity, following a realistic scenario of chain-of-custody, unlike captive lab populations. Our analysis, which included 27 individuals comprising the entirety of one captive population show very low neutral and adaptive genetic variation, as well as low effective sizes, which are surprising in spite of the known demographic history. Finally, our study also shows the divergent impacts of small effective size and inbreeding in captive populations on microsatellite versus adaptive genetic variation in the MHC-B locus. Our study provides insights into the difficulties of maintaining adaptive genetic variation in small captive populations.

Evaluating genetic variation and relationships among Puccinellia nuttalliana populations using amplified fragment length polymorphism markers

2013 ◽  
Vol 93 (6) ◽  
pp. 1097-1104 ◽  
Author(s):  
Yining Liu ◽  
Yong-Bi Fu ◽  
Bruce E. Coulman
Keyword(s):  
Genetic Variation ◽  
Great Plains ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Natural Populations ◽  
Amplified Fragment Length Polymorphism ◽  
Mantel Test ◽  
Grass Species ◽  
Puccinellia Nuttalliana

Liu, Y., Fu, Y.-B. and Coulman, B. E. 2013. Evaluating genetic variation and relationships among Puccinellia nuttalliana populations using amplified fragment length polymorphism markers. Can. J. Plant Sci. 93: 1097–1104. Nuttall's salt-meadow, or alkali grass [Puccinellia nuttalliana (Shultes) Hitchc.], is a native grass species in North America, well known for its salt tolerance. Little information is available about the genetic diversity of natural populations of this species. Amplified fragment length polymorphism (AFLP) markers were used to examine the inter-population relationships and to compare variances within and among 23 populations collected from the Canadian Great Plains. Five AFLP primer pairs were employed to screen 15 genotypes (five sets of three half-sib plants) from each population, and 185 polymorphic AFLP bands were scored for each sample. The frequencies of these scored bands ranged from 0.02 to 0.99 with a mean of 0.60. The analysis of molecular variance revealed more than 96% of the total AFLP variation resided within populations. Populations were not highly differentiated with only 4% of the total AFLP variation residing among populations. A Mantel test revealed a significant but low correlation between genetic and geographic distances (r=0.29, P=0.024). Implications for P. nuttalliana conservation, germplasm sampling, and cultivar development are discussed.

Taking stock: defining populations of American shad (Alosa sapidissima) in Canada using neutral genetic markers

2010 ◽  
Vol 67 (6) ◽  
pp. 1021-1039 ◽  
Author(s):  
Daniel J. Hasselman ◽  
Rod G. Bradford ◽  
Paul Bentzen
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Isolation By Distance ◽  
Analysis Of Covariance ◽  
American Shad ◽  
Migration Route ◽  
Conservation Units ◽  
Geographic Scale ◽  
Alosa Sapidissima ◽  
Conservation Concern

Knowledge of the scale of population structure is a prerequisite for designating conservation units. American shad ( Alosa sapidissima ) are of increasing conservation concern, but the scale of population structure within the Canadian portion of the species range is unknown. Using 13 microsatellite loci, we examined the partitioning of genetic variation within four and among 12 Canadian drainages. We detected significant (p < 0.05) and temporally stable genetic differentiation among all drainages, supporting the hypothesis that rivers support genetically distinct populations. However, Bayesian methods identified seven clusters and provided evidence for shad metapopulation structure. We observed a significant (p < 0.01) pattern of isolation by distance (IBD) among all drainages. A strong linear IBD (r = 0.98) was observed among rivers that were outside the Bay of Fundy (BoF). A hypothesized counterclockwise migration route explained a greater proportion of genetic variation (r = 0.87) among BoF rivers than direct route based distances (r = 0.14). Although IBD patterns did not differ regionally (analysis of covariance; p > 0.05), the degree of differentiation among BoF rivers was greater than that among non-BoF rivers, regardless of the geographic scale of comparison. Our results suggest that fisheries managers need to be concerned with the loss of shad genetic diversity on both river and regional scales.

scholarly journals Contribution of spatial heterogeneity in effective population sizes to the variance in pairwise measures of genetic differentiation

2015 ◽  
Author(s):  
Jérôme G. Prunier ◽  
Vincent Dubut ◽  
Lounès Chikhi ◽  
Simon Blanchet
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Spatial Heterogeneity ◽  
Landscape Genetics ◽  
Isolation By Distance ◽  
List Type ◽  
Unique Contribution ◽  
Landscape Resistance ◽  
Effective Population ◽  
Population Sizes

SummaryPairwise measures of neutral genetic differentiation are supposed to contain information about past and on-going dispersal events and are thus often used as dependent variables in correlative analyses to elucidate how neutral genetic variation is affected by landscape connectivity. However, spatial heterogeneity in the intensity of genetic drift, stemming from variations in population sizes, may inflate variance in measures of genetic differentiation and lead to erroneous or incomplete interpretations in terms of connectivity. Here, we tested the efficiency of two distance-based metrics designed to capture the unique influence of spatial heterogeneity in local drift on genetic differentiation. These metrics are easily computed from estimates of effective population sizes or from environmental proxies for local carrying capacities, and allow us to introduce the hypothesis of Spatial-Heterogeneity-in-Effective-Population-Sizes (SHNe). SHNe can be tested in a way similar to isolation-by-distance or isolation-by-resistance within the classical landscape genetics hypothesis-testing framework.We used simulations under various models of population structure to investigate the reliability of these metrics to quantify the unique contribution of SHNe in explaining patterns of genetic differentiation. We then applied these metrics to an empirical genetic dataset obtained for a freshwater fish (Gobio occitaniae).Simulations showed that SHNe explained up to 60% of variance in genetic differentiation (measured as Fst) in the absence of gene flow, and up to 20% when migration rates were as high as 0.10. Furthermore, one of the two metrics was particularly robust to uncertainty in the estimation of effective population sizes (or proxies for carrying capacity). In the empirical dataset, the effect of SHNe on spatial patterns of Fst was five times higher than that of isolation-by-distance, uniquely contributing to 41% of variance in pairwise Fst. Taking the influence of SHNe into account also allowed decreasing the signal-to-noise ratio, and improving the upper estimate of effective dispersal distance.We conclude that the use of SHNe metrics in landscape genetics will substantially improve the understanding of evolutionary drivers of genetic variation, providing substantial information as to the actual drivers of patterns of genetic differentiation in addition to traditional measures of Euclidean distance or landscape resistance.

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