scholarly journals Genetic footprint of population fragmentation and contemporary collapse in a freshwater cetacean

2016 ◽  
Author(s):  
Minmin Chen ◽  
Michael C. Fontaine ◽  
Yacine Ben Chehida ◽  
Jinsong Zheng ◽  
Frédéric Labbe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Habitat Degradation ◽  
Field Studies ◽  
Mitigation Strategies ◽  
Ice Age ◽  
Background Information ◽  
Conservation Strategies ◽  
Low Genetic Diversity ◽  
Neophocaena Asiaeorientalis Asiaeorientalis

AbstractUnderstanding demographic trends and patterns of gene flow in an endangered species is crucial for devising conservation strategies. Here, we examined the extent of population structure and recent evolution of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). By analysing genetic variation at the mitochondrial and nuclear microsatellite loci for 148 individuals, we identified three populations along the Yangtze River, each one connected to a group of admixed ancestry. Each population displayed extremely low genetic diversity, consistent with extremely small effective size (≤92 individuals). Habitat degradation and distribution gaps correlated with highly asymmetric gene-flow that was inefficient in maintaining connectivity between populations. Genetic inferences of historical demography revealed that the populations in the Yangtze descended from a small number of founders colonizing the river from the sea during the last Ice Age. The colonization was followed by a rapid population split during the last millennium predating the Chinese Modern Economy Development. However, genetic diversity showed a clear footprint of population contraction over the last 50 years leaving only ~2% of the pre-collapsed size, consistent with the population collapses reported from field studies. This genetic perspective provides background information for devising mitigation strategies to prevent this species from extinction.

scholarly journals Genetic Diversity and Population Structure of Medemia argun (Mart.) Wurttenb. ex H.Wendl. Based on Genome-Wide Markers

2021 ◽  
Vol 9 ◽  
Author(s):  
Sakina Elshibli ◽  
Helena Korpelainen
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Conservation Status ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Nucleotide Polymorphisms ◽  
Genetic Structuring ◽  
Ancestral Gene ◽  
Low Genetic Diversity

Medemia argun is a wild, dioecious palm, adapted to the harsh arid environment of the Nubian Desert in Sudan and southern Egypt. There is a concern about its conservation status, since little is known about its distribution, abundance, and genetic variation. M. argun grows on the floodplains of seasonal rivers (wadis). The continuing loss of suitable habitats in the Nubian Desert is threatening the survival of this species. We analyzed the genetic diversity, population genetic structure, and occurrence of M. argun populations to foster the development of conservation strategies for M. argun. Genotyping-by-sequencing (GBS) analyses were performed using a whole-genome profiling service. We found an overall low genetic diversity and moderate genetic structuring based on 40 single-nucleotide polymorphisms (SNPs) and 9,866 SilicoDArT markers. The expected heterozygosity of the total population (HT) equaled 0.036 and 0.127, and genetic differentiation among populations/groups (FST) was 0.052 and 0.092, based on SNP and SilicoDArT markers, respectively. Bayesian clustering analyses defined five genetic clusters that did not display any ancestral gene flow among each other. Based on SilicoDArT markers, the results of the analysis of molecular variance (AMOVA) confirmed the previously observed genetic differentiation among generation groups (23%; p < 0.01). Pairwise FST values indicated a genetic gap between old and young individuals. The observed low genetic diversity and its loss among generation groups, even under the detected high gene flow, show genetically vulnerable M. argun populations in the Nubian Desert in Sudan. To enrich and maintain genetic variability in these populations, conservation plans are required, including collection of seed material from genetically diverse populations and development of ex situ gene banks.

The Response to Past Climate Perturbations Explains Extremely Low Genetic Diversity in the Genome of an Abundant Ice-Age Remnant, the Alpine Marmot

2018 ◽  
Author(s):  
Toni I. Gossmann​ ◽  
Achchuthan Shanmugasundram​ ◽  
Stefan Börno ◽  
Ludovic Duvaux ◽  
Christophe Lemaire​ ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ice Age ◽  
Past Climate ◽  
Low Genetic Diversity ◽  
Alpine Marmot

Weak genetic structuring suggests historically high genetic connectivity among recently fragmented urban populations of the scincid lizard, Ctenotus fallens

2015 ◽  
Vol 63 (4) ◽  
pp. 279 ◽  
Author(s):  
Josef Krawiec ◽  
Siegfried L. Krauss ◽  
Robert A. Davis ◽  
Peter B. S. Spencer
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Large Population ◽  
Geographic Distance ◽  
Genetic Erosion ◽  
Genetic Connectivity ◽  
Genetic Structuring ◽  
Low Genetic Diversity ◽  
Population Sizes

Populations in fragmented urban remnants may be at risk of genetic erosion as a result of reduced gene flow and elevated levels of inbreeding. This may have serious genetic implications for the long-term viability of remnant populations, in addition to the more immediate pressures caused by urbanisation. The population genetic structure of the generalist skink Ctenotus fallens was examined using nine microsatellite markers within and among natural vegetation remnants within a highly fragmented urban matrix in the Perth metropolitan area in Western Australia. These data were compared with samples from a large unfragmented site on the edge of the urban area. Overall, estimates of genetic diversity and inbreeding within all populations were similar and low. Weak genetic differentiation, and a significant association between geographic and genetic distance, suggests historically strong genetic connectivity that decreases with geographic distance. Due to recent fragmentation, and genetic inertia associated with low genetic diversity and large population sizes, it is not possible from these data to infer current genetic connectivity levels. However, the historically high levels of gene flow that our data suggest indicate that a reduction in contemporary connectivity due to fragmentation in C. fallens is likely to result in negative genetic consequences in the longer term.

scholarly journals Genetic Diversity Analysis, Population Structure and Gene-flow Estimates among Citrus Macroptera Mont. Collections from Garo Hills, Meghalaya using SPAR Approach

2021 ◽  
Vol 4 (1) ◽  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Gene Diversity ◽  
Time Frame ◽  
Conservation Strategies ◽  
North East India ◽  
Information Index ◽  
North East ◽  
Garo Hills ◽  
Single Primer

North East India is extremely rich in natural resources and is a biodiversity hotspot. Many plant species, including Citrus are known to have originated from this region. Citus macroptera Mont. is a wild, endangered species which have been found to exist naturally in various parts of this region, including Meghalaya. To access the genetic variability among genotypes and their phylogeny, 30 genotypes of wild C. macroptera Mont. were collected from Garo Hills of Meghalaya. Single primer based DNA markers viz. RAPD, ISSR, DAMD were utilized to ascertain genetic diversity. The percentage polymorphic bands for RAPD, ISSR, DAMD were found to be 97.71%, 94.67% and 100% respectively. ISSR showed the highest values for both RP (7.67) and MI (5.03) highlighting its efficacy in determining genetic variations. A concatenated approach, Single Primer Amplification Reaction (SPAR) was also followed to assess their genetic diversity. Dendogram generated from SPAR data showed that the South-West Garo Hills population is the most recently evolved amongst all others while West Garo Hills collections retain an ancestral position in the evolutionary time-frame. Population genetics parametres such as Gene flow (Nm) and the diversity among populations (GST) were found to be 1.9894 and 0.2009 respectively. Gene flow estimates (Nm>1) suggests appreciable gene flow in the populations. AMOVA data further supported this with high percentage of variations (92%) within populations whereas variations among populations were about 8% only. Shannon’s information index (I) values and Nei’s gene diversity (h) varied between 0.303-0.423and 0.201-0.285 respectively. The use of SPAR method yields a clear and concise picture of the underlying genetic variabilities, and a detailed and comprehensive data analysis will help conceive efficient and sustainable conservation strategies for this important plant.

scholarly journals Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity

2019 ◽  
Vol 29 (10) ◽  
pp. 1712-1720.e7 ◽  
Author(s):  
Toni I. Gossmann ◽  
Achchuthan Shanmugasundram ◽  
Stefan Börno ◽  
Ludovic Duvaux ◽  
Christophe Lemaire ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ice Age ◽  
Low Genetic Diversity ◽  
Alpine Marmot

scholarly journals Genetic variation in the emblematic Puya raimondii (Bromeliaceae) from Huascarán National Park, Peru

2013 ◽  
Vol 13 (1) ◽  
pp. 67-74 ◽  
Author(s):  
Claudia Teresa Hornung-Leoni ◽  
Victoria Sosa ◽  
June Simpson ◽  
Katia Gil
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Variability ◽  
National Park ◽  
Conservation Strategies ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Mountain Systems

Puya raimondii, the giant Peruvian and Bolivian terrestrial bromeliad, is an emblematic endemic Andean species well represented in Huascarán National Park in Peru. This park is the largest reserve of puna (high altitude plateau) vegetation. The objective of this study is to report on genetic variation in populations of P. raimondii from Huascarán and neighboring areas. AFLP profiles with four selective primer combinations were retrieved for 60 individuals from different zones. Genetic variability was estimated and a total of 172 bands were detected, of which 79.1% were polymorphic loci. The results showed genetic differentiation among populations, and gene flow. A cluster analysis showed that individuals of P. raimondii populations located in different mountain systems could be grouped together, suggesting long distance dispersal. Thus, conservation strategies for P. raimondii have to take into account exchange between populations located far apart in distance in order to preserve the genetic diversity of this showy species.

Genetic diversity and structure in the northern populations of European hazelnut (Corylus avellana L.)

Genome ◽  
2019 ◽  
Vol 62 (8) ◽  
pp. 537-548
Author(s):  
Pirjo Tanhuanpää ◽  
Maarit Heinonen ◽  
Lidija Bitz ◽  
Veli-Matti Rokka
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Plant Conservation ◽  
Corylus Avellana ◽  
Ice Age ◽  
Genetic Structuring ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Genetic Diversity And Structure ◽  
Corylus Avellana L

European hazelnut (Corylus avellana L.) is a strictly cross-pollinated diploid tree species, which has its northernmost populations in Fennoscandia, and it was one of the first species to recolonize northern Europe after the last ice age. Hazelnut produces edible nuts in Finland but nowadays they are underutilized as food, and currently no breeding programmes exist. In the present study, 300 hazelnut specimens were collected from 20 different locations (= populations) in Finland, and they were genetically analyzed using nine simple sequence repeat (SSR) markers. Most of the genetic diversity existed within populations (83%). According to different genetic analyses (STRUCTURE, principal coordinates analysis, and clustering), a general lack of structure was observed, suggesting extensive gene flow among hazelnuts between 17 investigated populations. However, genetic structuring was clearly observed in three populations: Hakavuori, Mustiala, and Pähkinämäki, which might have become isolated due to geographical barriers that kept them separate, diminishing gene flow from other populations. Studying the diversity of European hazelnut is of great interest for understanding population genetics of a species distributed in its marginal areas in the north, and the results are also valuable for further uses in plant conservation, selection, and possible future breeding actions in Finland.

scholarly journals Gene Flow, Recombination, and Selection in Cyanobacteria: Population Structure of Geographically Related Planktothrix Freshwater Strains

2012 ◽  
Vol 79 (2) ◽  
pp. 508-515 ◽  
Author(s):  
Hanne Sogge ◽  
Thomas Rohrlack ◽  
Trine B. Rounge ◽  
Jørn Henrik Sønstebø ◽  
Ave Tooming-Klunderud ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Variants ◽  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Split Decomposition ◽  
Content Type ◽  
Low Genetic Diversity ◽  
Peptide Synthetase ◽  
Similar Range

ABSTRACTSeveralPlanktothrixstrains, each producing a distinct oligopeptide profile, have been shown to coexist within Lake Steinsfjorden (Norway). Using nonribosomal peptide synthetase (NRPS) genes as markers, it has been shown that thePlanktothrixcommunity comprises distinct genetic variants displaying differences in bloom dynamics, suggesting aPlanktothrixsubpopulation structure. Here, we investigate thePlanktothrixvariants inhabiting four lakes in southeast of Norway utilizing both NRPS and non-NRPS genes. Phylogenetic analyses showed similar topologies for both NRPS and non-NRPS genes, and the lakes appear to have similar structuring ofPlanktothrixgenetic variants. The structure of distinct variants was also supported by very low genetic diversity within variants compared to the between-variant diversity. Incongruent topologies and split decomposition revealed recombination events betweenPlanktothrixvariants. In several strains the gene variants seem to be a result of recombination. Both NRPS and non-NRPS genes are dominated by purifying selection; however, sites subjected to positive selection were also detected. The presence of similar and well-separatedPlanktothrixvariants with low internal genetic diversity indicates gene flow withinPlanktothrixpopulations. Further, the low genetic diversity found between lakes (similar range as within lakes) indicates gene flow also betweenPlanktothrixpopulations and suggests recent, or recurrent, dispersals. Our data also indicate that recombination has resulted in new genetic variants. Stability within variants and the development of new variants are likely to be influenced by selection patterns and within-variant homologous recombination.

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