Spatial Scale Patterns of Genetic Diversity and Gene Flow in Populations of Sweet Detar (Detarium microcarpum Guill. & Perr.; Fabaceae)

Abstract The main objective of this study is to investigate the patterns of genetic diversity and phylogenetic relationships within populations of Detarium microcarpum (Fabaceae) relative to different spatial conditions. Seventy-eight (78) accessions of D. microcarpum belonging to six populations (Phytogeographic districts) were sampled. In order to have very good quality DNA for molecular analysis, an optimization of the DNA isolation protocol was made. The molecular analysis of the accessions was carried out using 7 chloroplast microsatellite markers. The polymorphism rate (P) is 85.71% and the Polymorphism Information Content (PIC) was in the range of 0.43 (Ntcp_9) to 0.73 (Ccmp_2) with an average of 0.59. Allelic richness (A) ranged from 1.41 to 2.85 with an average of 2.04. The observed heterozygosity (Ho) ranged from 0.23 to 0.60 with an average of 0.39. The expected heterozygosity (He) ranged from 0.43 to 0.60 with a mean of 0.50. Wright's fixation index (FIS) ranged from − 0.17 to 0.47. The effective allele (Ae) is between 1.77 and 2.53 with an average of 2.02. Wright differentiation index (FST) was 0.024. Phylogenetic analysis revealed that the NST value was significantly higher than the GST value (NST = 0.452; GST = 0.190; P < 0.05). A relatively low hd haplotype diversity is obtained (Hd = 0.320). AMOVA analysis showed that 17.35% of the variation existed within populations but 45.80% among populations within the species. Neighbor-Joining phylogenetic tree of D. microcarpum revealed three non-distinct clusters haplotypes showing the existence of gene flow between populations of the species. Our findings of genetic structure and gene flow of D. microcarpum populations based on different spatial conditions is caused by evolutionary forces such as scattering and pollination.

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Climate change and conservation in a warm North American desert: effect in shrubby plants

PeerJ ◽

10.7717/peerj.6572 ◽

2019 ◽

Vol 7 ◽

pp. e6572 ◽

Cited By ~ 2

Author(s):

Victoria Sosa ◽

Israel Loera ◽

Diego F. Angulo ◽

Marilyn Vásquez-Cruz ◽

Etelvina Gándara

Keyword(s):

Climate Change ◽

Genetic Diversity ◽

Gene Flow ◽

North American ◽

Chihuahuan Desert ◽

Haplotype Diversity ◽

Sierra Madre Oriental ◽

Ecological Resistance ◽

Sierra Madre ◽

Shrubby Species

Background Deserts are biologically rich habitats with a vast array of animals and plants adapted to xeric conditions, and most deserts are among the planet’s last remaining areas of total wilderness. Among North American deserts, the Chihuahuan Desert has the highest levels of diversity and endemism. To understand the effect of future climate change on plants distributed in this arid land and propose effective conservation planning, we focused on five endemic shrubby species that characterize the Chihuahuan Desert and used an integrative approach. Methods Ecological niche-based modeling, spatial genetics and ecological resistance analyses were carried out to identify the effect of global warming on the studied five shrubby species. Key areas that need to be preserved were identified taking into account the existing protected areas within the Chihuahuan Desert. Results The extent of future distribution will vary among these species, and on average expansion will occur in the western part of the Chihuahuan Desert. For most species low environmental resistance to gene flow was predicted, while higher future resistance was predicted for one species that would lead to increased population isolation. The highest haplotype diversity was identified in three hotspots. Based on future suitability of habitat and in the haplotype diversity we suggest preserving two hotspots of genetic diversity in the Sierra Madre Oriental, located in areas without protection. The third hotspot was detected in the well preserved Tehuacán-Cuicatlán Man and Biosphere Reserve. Conclusion Global climate change will have an effect in arid adapted plants, favoring expansion in the western of the Chihuahuan Desert however negatively affecting others with high ecological resistance disrupting gene flow. Two hotspots of genetic diversity in the Sierra Madre Oriental should be protected.

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Genetic differentiation among Parastichopus regalis populations from Western Mediterranean Sea: potential effects of its fishery and current connectivity.

Mediterranean Marine Science ◽

10.12681/mms.1020 ◽

2015 ◽

Vol 16 (3) ◽

pp. 489 ◽

Cited By ~ 7

Author(s):

C. MAGGI ◽

M. GONZÁLEZ-WANGÜEMERT

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Haplotype Diversity ◽

Western Mediterranean ◽

Mediterranean Coast ◽

Morphological Data ◽

Coi Gene ◽

Fixation Index ◽

Morphological Description ◽

Western Mediterranean Sea

Parastichopus regalis (Cuvier, 1817) is the most expensive seafood product on the catalonian market (NE Spain), with prices around 130 €/Kg (fresh weight). Despite its ecological and economic importance, biological and genetic information on this sea cucumber species is scarce. We provided the first insight on the genetic structure of P. regalis using sequences of cytochrome oxidase I (COI) and 16S genes, as well as a morphological description of its populations. Individuals were collected in six locations along the Spanish Mediterranean coast, including an area under fishery pressure (Catalonia). We found high haplotype diversity and low nucleotide diversity for both genes, with higher levels of genetic diversity observed on COI gene. Population pairwise fixation index (FST), AMOVA and correspondence analysis (CA) based on COI, revealed significant genetic differentiation among some locations. However, further analysis using nuclear markers (e.g. microsatellites) would be necessary to corroborate these results. Moreover, the genetic and morphological data may indicate fishery effects on the Catalonian population with decrease of the size and weight average and lower genetic diversity compared to locations without fishery pressure. For an appropriate management of this species, we suggest: 1) an accurate assessment of the stocks status along the Spanish coasts; 2) the study of the reproductive cycle of this target species and the establishment of a closed fishery season according to it; 3) the founding of protected areas (i.e. not take zones) to conserve healthy populations and favour the recruitment on the nearby areas.

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Post-Disturbance Genetic Changes: The Impact of the 2010 Mega-Earthquake and Tsunami on Chilean Sandy Beach Fauna

Scientific Reports ◽

10.1038/s41598-019-50525-1 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Antonio Brante ◽

Garen Guzmán-Rendón ◽

Erwin M. Barría ◽

Marie-Laure Guillemin ◽

Iván Vera-Escalona ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Haplotype Diversity ◽

Population Expansion ◽

Adult Survival ◽

Genetic Changes ◽

Species Response ◽

Emerita Analoga ◽

Mtdna Sequence ◽

The Impact

Abstract Earthquake/tsunamis can have profound impacts on species and their genetic patterns. It is expected that the magnitude of this impact might depend on the species and the time since the disturbance occurs, nevertheless these assumptions remain mostly unexplored. Here we studied the genetic responses of the crustacean species Emerita analoga, Excirolana hirsuticauda, and Orchestoidea tuberculata to the 27F mega-earthquake/tsunami that occurred in Chile in February 2010. mtDNA sequence analyses revealed a lower haplotype diversity for E. analoga and E. hirsuticauda in impacted areas one month after the 27F, and the opposite for O. tuberculata. Three years after the 27F we observed a recovery in the genetic diversity of E. analoga and E. hirsuticauda and decrease in the genetic diversity in O. tuberculata in 2/3 of sampled areas. Emerita analoga displayed decrease of genetic differentiation and increase in gene flow explained by long-range population expansion. The other two species revealed slight increase in the number of genetic groups, little change in gene flow and no signal of population expansion associated to adult survival, rapid colonization, and capacity to burrow in the sand. Our results reveal that species response to a same disturbance event could be extremely diverse and depending on life-history traits and the magnitude of the effect.

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Genetic diversity analysis of Dermacentor nuttalli within Inner Mongolia, China

Parasites & Vectors ◽

10.1186/s13071-021-04625-5 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Zheng Gui ◽

Lin Wu ◽

Hao Cai ◽

Lan Mu ◽

Jing-Feng Yu ◽

...

Keyword(s):

Genetic Diversity ◽

16S Rrna ◽

Genetic Differentiation ◽

Inner Mongolia ◽

Haplotype Diversity ◽

Fixation Index ◽

Rrna Gene ◽

Human Beings ◽

Autonomous Region ◽

Inner Mongolia Autonomous Region

Abstract Background Ticks (Arthropoda, Ixodida), after mosquitoes, are the second most prevalent vector of infectious diseases. They are responsible for spreading a multitude of pathogens and threatening the health and welfare of animals and human beings. However, given the history of tick-borne pathogen infections in the Inner Mongolia Autonomous Region of China, surprisingly, neither the genetic diversity nor the spatial distribution of haplotypes within ticks has been studied. Methods We characterized the haplotype distribution of Dermacentor nuttalli in four main pastoral areas of the Inner Mongolia Autonomous Region, by sampling 109 individuals (recovered from sheep) in April–August 2019. The 16S rRNA gene, cytochrome c oxidase subunit I (COI), and the internal transcribed spacer 2 region (ITS2) were amplified and sequenced from extracted DNA. Results Twenty-six haplotypes were identified using 16S rRNA sequences, 57 haplotypes were identified with COI sequences, and 75 haplotypes were identified with ITS2 sequences. Among the three genes, total haplotype diversity was greater than 0.7, while total nucleotide diversity was greater than 0.06. Neutrality tests revealed a significantly negative Tajima’s D result, while Fu's Fs was not significantly positive. Fixation index values (FST) indicated that the degree of genetic differentiation among some sampled populations was small, while for others it was moderate. Analysis of molecular variance (AMOVA) revealed that the variation within populations was greater than that among populations. The mismatch analysis of D. nuttalli exhibited double peaks. Conclusion The genetic diversity of D. nuttalli populations in our region can likely adapt to different geographical environments, thereby leading to genetic diversity, and creating genetic differentiation among different populations. However, genetic differentiation is cryptic and does not form a pedigree geographical structure.

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Geographic variation and genetic structure in the Bahama Oriole (Icterus northropi), a critically endangered synanthropic species

PeerJ ◽

10.7717/peerj.1421 ◽

2015 ◽

Vol 3 ◽

pp. e1421

Author(s):

Melissa R. Price ◽

Carl Person ◽

William K. Hayes

Keyword(s):

Gene Flow ◽

Haplotype Diversity ◽

Bird Species ◽

Critically Endangered ◽

Fixation Index ◽

Population Differences ◽

Genetic Structuring ◽

Island Endemic ◽

Population Structuring ◽

Andros Island

Bird species may exhibit unexpected population structuring over small distances, with gene flow restricted by geographic features such as water or mountains. The Bahama Oriole (Icterus northropi) is a critically endangered, synanthropic island endemic with a declining population of fewer than 300 individuals. It now remains only on Andros Island (The Bahamas), which is riddled with waterways that past studies assumed did not hinder gene flow. We examined 1,858 base pairs of mitochondrial DNA sequenced from four gene regions in 14 birds (roughly 5% of the remaining population) found on the largest land masses of Andros Island (North Andros and Mangrove Cay/South Andros). We sought to discern genetic structuring between the remaining subpopulations and its relationship to current conservation concerns. Four unique haplotypes were identified, with only one shared between the two subpopulations. Nucleotide and haplotype diversity were higher for the North Andros subpopulation than for the Mangrove Cay/South Andros subpopulation. Analysis of molecular variance (AMOVA) yielded a Wright’s fixation index (Fst) of 0.60 (PFst= 0.016), with 40.2% of the molecular variation explained by within-population differences and 59.8% by among-population differences. Based on the mitochondrial regions examined in this study, we suggest the extant subpopulations of Bahama Oriole exhibit significant population structuring over short distances, consistent with some other non-migratory tropical songbird species.

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Microsatellites for detecting inconsistencies in Capsicum cultivars registration in Brazilian database: more than meets the eye

Horticultura Brasileira ◽

10.1590/s0102-053620190306 ◽

2019 ◽

Vol 37 (3) ◽

pp. 285-293

Author(s):

Carlos Diego de O Azevedo ◽

Rosana Rodrigues ◽

Cláudia P Sudré

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Molecular Analysis ◽

Microsatellite Loci ◽

Principal Coordinate Analysis ◽

Fixation Index ◽

National Register ◽

Genetic Purity ◽

Low Genetic Diversity ◽

Capsicum Spp

ABSTRACT In Brazil, cultivars are registered by National Register of Cultivars (RNC), which besides enabling commercialization of cultivar propagative material, also guarantees the producers genetic purity and identity of propagules. However, it is possible that the information about registration and commercialization of some cultivars is inaccurate. This study aims to analyze the use of microsatellite markers to detect inconsistencies in data of Capsicum spp. cultivars obtained from the official database (CultivarWeb). Seven cultivars were evaluated, three of them were through genetic identity analysis (Amarela Comprida, De Cayenne and Cayenne Long Slin) and the others were used as standard for the species C. annuum, C. frutescens and C. chinense. Thirty-three microsatellite loci were polymorphic and presented 76 alleles (an average of 2.3 alleles/locus). Fixation Index (F) showed high homozygosis and estimators of genetic diversity (Ho and I) presented low genetic diversity among cultivars. The molecular analysis, represented in a dendrogram and in Principal Coordinate Analysis Chart (PCOA), showed that the investigated cultivars belong to C. annuum, contrary to what is registered in CultivarWeb, which indicates that such cultivars belong to the species C. frutescens. Thus, the authors recommend that the data in the CultivarWeb should be checked and enhanced.

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Gene exchange across a postglacial contact zone in Fraxinus excelsior L.

Silvae Genetica ◽

10.1515/sg-2012-0003 ◽

2012 ◽

Vol 61 (1-6) ◽

pp. 18-27 ◽

Cited By ~ 1

Author(s):

D. Gömöry ◽

L. Paule ◽

D. Krajmerová ◽

I. Romšáková ◽

J. Piecka

Keyword(s):

Gene Flow ◽

Bayesian Analysis ◽

Contact Zone ◽

Haplotype Diversity ◽

Glacial Refugia ◽

Fraxinus Excelsior ◽

Chloroplast Microsatellite ◽

The Czech Republic ◽

Chloroplast Haplotype ◽

Haplotype Frequencies

Abstract Hybridization between divergent lineages of common ash Fraxinus excelsior L. was studied in Slovakia and adjacent regions of Hungary, the Czech Republic and Poland in the contact zone between two postglacial colonization routes originating from different glacial refugia. Thirty-eight common ash populations were studied using a combination of 6 maternally inherited chloroplast microsatellite markers and 7 biparentally inherited nuclear microsatellites (nSSR). Two predominant chloroplast lineages were identified, between which the boundary was very sharp. Populations containing a mixture of different haplotypes were found only in the immediate proximity of the boundary. Bayesian analysis of population structure based on nSSR loci revealed the existence of two clusters, which largely coincided with chloroplast lineages. Both haplotype frequencies and proportions of clusters identified by the Bayesian analysis exhibited a clinal transition over the hybrid zone, with cline widths of 36 km for chloroplast haplotype frequencies (reflecting gene flow by seeds) and 275 km for Bayesian clusters based on nSSR (reflecting gene flow by pollen and seeds). Chloroplast haplotype diversity increased along the boundary between lineages not only because of admixture, but also due to the presence of rare haplotypes. In contrast, diversity at nuclear loci did not exhibit any geographical trend.

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Genetic diversity of the cyprinid fish Capoeta trutta (Heckel, 1843) populations from Euphrates and Tigris rivers in Turkey based on mtDNA COI sequences

Indian Journal of Fisheries ◽

10.21077/ijf.2017.64.1.62396-03 ◽

2017 ◽

Vol 64 (1) ◽

pp. 18 ◽

Cited By ~ 1

Author(s):

Arif Parmaksız ◽

Esra Eksi

Keyword(s):

Genetic Diversity ◽

Haplotype Diversity ◽

Data Set ◽

Mtdna Coi ◽

Gene Sequence Analysis ◽

Different Populations ◽

The Mean ◽

Neutrality Tests ◽

Coi Sequences ◽

Amova Analysis

In this study, genetic diversity of Capoeta trutta (Heckel, 1843) populations from Euphrates and Tigris rivers in Turkey was evaluated based on gene sequence analysis of mitochondrial DNA cytochrome c oxidase subunit I (mtDNA COI) locus. Six polymorphic sites and seven haplotypes were detected in 47 samples collected from four populations viz., Adiyaman, Birecik, Bismil and Batman. The mean haplotype diversity (h) and nucleotide diversity (π) were calculated as h = 0,6420 and π = 0,00138 respectively. Pairwise FST statistics of different populations were found to be negative, low and were insignificant, indicating gene flow. AMOVA analysis showed Fst = 0.09865 and p = 0.00489, indicating that the populations were isolated. The results of Neutrality tests showed an increase in Adiyaman, Birecik and Bismil populations and a decline in Batman population, all values being statistically insignificant (p>0.05). Three haplotypes determined for mtDNA COI locus in the present study form important data set for genetic diversity of this species.

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Genetic Diversity Analysis of Dermacentor Nuttalli within Inner Mongolia, China

10.21203/rs.3.rs-117759/v1 ◽

2020 ◽

Author(s):

Zheng Gui ◽

Lin Wu ◽

Hao Cai ◽

Fu-Shaoyin ◽

Jing Feng Yu ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Inner Mongolia ◽

Haplotype Diversity ◽

Fixation Index ◽

Rrna Gene ◽

Human Beings ◽

Autonomous Region ◽

Negative Results ◽

Inner Mongolia Autonomous Region

Abstract BackgroundTicks (Arthropoda, Ixodida), after mosquitoes, are the next most prevalent vector of infectious diseases; and are responsible for spreading a multitude of pathogens and threatening the health and welfare of animals and human beings. Yet, given the history of tick-borne pathogen infections in the Inner Mongolia Autonomous region of China, neither the genetic diversity nor the spatial distribution of haplotypes within ticks has been studied. MethodsWe characterized the haplotype distribution of Dermacentor nuttalli in four main pastoral areas of the Inner Mongolia Autonomous region, by sampling 109 individuals (recovered from sheep) in April-August 2019. The 16S rRNA gene, Cytochrome c Oxidase Subunit Ⅰ, and the Internal Transcribed Spacer 2 region were amplified and sequenced from extracted DNA.Results 82 haplotypes were identified, the most prevalent of which was H32. 12 sequences (11 of all sequences) represented the most abundant haplotypes, with a highly scattered distribution. Total haplotype diversity was 0.98318, while total nucleotide diversity was 0.11369. Neutrality tests revealed negative results in the four locations analyzed, which is indicative of an excess of recently derived haplotypes. Fixation index values (FST) indicate that the degree of genetic differentiation amongst some sampled populations were small, while others were moderate. Conclusion The genetic diversity of D.nuttalli populations in our region can likely adapt to different geographical environments, thereby leading to genetic diversity, and creating genetic differentiation amongst different populations. However, genetic differentiation is cryptic and does not form the pedigree geographical structure.

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Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation

Diversity ◽

10.3390/d11040062 ◽

2019 ◽

Vol 11 (4) ◽

pp. 62 ◽

Cited By ~ 12

Author(s):

Yasmin G. S. Carvalho ◽

Luciana C. Vitorino ◽

Ueric J. B. de Souza ◽

Layara A. Bessa

Keyword(s):

Genetic Diversity ◽

Life History ◽

Plant Species ◽

Life History Traits ◽

Demographic History ◽

Haplotype Diversity ◽

Molecular Techniques ◽

Fixation Index ◽

Relative Contribution ◽

Recent Trends

Genetic diversity and its distribution, both within and between populations, may be determined by micro-evolutionary processes, such as the demographic history of populations, natural selection, and gene flow. In plants, indices of genetic diversity (e.g., k, h and π) and structure (e.g., FST) are typically inferred from sequences of chloroplast markers. Given the recent advances and popularization of molecular techniques for research in population genetics, phylogenetics, phylogeography, and ecology, we adopted a scientometric approach to compile evidence on the recent trends in the use of cpDNA sequences as markers for the analysis of genetic diversity in botanical studies, over the years. We also used phylogenetic modeling to assess the relative contribution of relatedness or ecological and reproductive characters to the genetic diversity of plants. We postulated that genetic diversity could be defined not only by microevolutionary factors and life history traits, but also by relatedness, so that species more closely related phylogenetically would have similar genetic diversities. We found a clear tendency for an increase in the number of studies over time, confirming the hypothesis that the advances in the area of molecular genetics have supported the accumulation of data on the genetic diversity of plants. However, we found that the vast majority of these data have been produced by Chinese authors, and refer specifically to populations of Chinese plants. Most of the data on genetic diversity have been obtained for species in the International Union for Conservation of Nature (IUCN) category NE (Not Evaluated), which indicates a relative lack of attention on threatened species. In general, we observed very high FST values in the groups analyzed and, as we focused primarily on species that have not been evaluated by the IUCN, the number of plant species that are threatened with extinction may be much greater than that indicated by the listing of this organization. We also found that the number of haplotypes (k) was influenced by the type of geographic distribution of the plant, while haplotype diversity (h) was affected by the type of flower, and the fixation index (FST), by the type of habitat. The plant species most closely-related phylogenetically have similar levels of genetic diversity. Overall, then, it will important to consider phylogenetic dependence in future studies that evaluate the effects of life-history traits on plant genetic diversity.

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