Genetic variation characterization of the boreal tree Acer ginnala population in response to environmental change of Northern China

Abstract Background: Acer ginnala is a deciduous shrub/small tree that primarily distributed across the northern regions of China. It comprises a foundation species in many terrestrial ecosystems and has significant ornamental and economic value. Owing to its increased use as an economic resource, overexploitation and environmental destruction have resulted in the vulnerability of this species. Thus, the elucidation of the genetic differentiation and influence of environmental factors on A. ginnala is very critical for its management and future utilization strategies. Results: Our results revealed that high genetic variation occurred in A. ginnala species while low genetic diversity was observed at the population level. Most differentiation has found among populations. A significant correlation existed between genetic and environmental distances. Seven climate variables (bio1, bio2, bio3, bio4, bio13, bio15 and bio18) might explain the substantial levels of genetic variation (> 40%) in populations. The most suitable areas of this species appeared in Shaanxi, Shanxi, Anhui Provinces, and Northeastern China based on ENM results. Compared to the last interglacial (LIG) period, A. ginnala migrated toward Northern and Northeastern China, and extended to the most suitable areas during the last glacial maximum (LGM) period. Shanxi and Anhui Provinces might have served as refugium owing to their relatively high genetic variation. Conclusions: Low genetic diversity at the population level that may be the source of its vulnerability. Climate heterogeneity would play an important role in the pattern of genetic differentiation in A. ginnala populations. The A. ginnala population was isolated by a heterogeneous climate and subsequently began to adapt to local selection processes resulted in high genetic divergence.

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Unusually Low Levels of Genetic Variation among Giardia lamblia Isolates

Eukaryotic Cell ◽

10.1128/ec.00138-07 ◽

2007 ◽

Vol 6 (8) ◽

pp. 1421-1430 ◽

Cited By ~ 52

Author(s):

Smilja Teodorovic ◽

John M. Braverman ◽

Heidi G. Elmendorf

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Giardia Lamblia ◽

Diarrheal Disease ◽

Regulation Of Gene Expression ◽

Genetic Exchange ◽

Disease Etiology ◽

Noncoding Regions ◽

Low Genetic Diversity ◽

Low Levels

ABSTRACT Giardia lamblia, an intestinal pathogen of mammals, including humans, is a significant cause of diarrheal disease around the world. Additionally, the parasite is found on a lineage which separated early from the main branch in eukaryotic evolution. The extent of genetic diversity among G. lamblia isolates is insufficiently understood, but this knowledge is a prerequisite to better understand the role of parasite variation in disease etiology and to examine the evolution of mechanisms of genetic exchange among eukaryotes. Intraisolate genetic variation in G. lamblia has never been estimated, and previous studies on interisolate genetic variation have included a limited sample of loci. Here we report a population genetics study of intra- and interisolate genetic diversity based on six coding and four noncoding regions from nine G. lamblia isolates. Our results indicate exceedingly low levels of genetic variation in two out of three G. lamblia groups that infect humans; this variation is sufficient to allow identification of isolate-specific markers. Low genetic diversity at both coding and noncoding regions, with an overall bias towards synonymous substitutions, was discovered. Surprisingly, we found a dichotomous haplotype structure in the third, more variable G. lamblia group, represented by a haplotype shared with one of the homogenous groups and an additional group-specific haplotype. We propose that the distinct patterns of genetic-variation distribution among lineages are a consequence of the presence of genetic exchange. More broadly, our findings have implications for the regulation of gene expression, as well as the mode of reproduction in the parasite.

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High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous Ciliate Carchesium polypinum in the Grand River Basin (North America)

Applied and Environmental Microbiology ◽

10.1128/aem.00178-09 ◽

2009 ◽

Vol 75 (10) ◽

pp. 3187-3195 ◽

Cited By ~ 28

Author(s):

E. Gentekaki ◽

D. H. Lynn

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

River Basin ◽

Large Subunit ◽

Population Level ◽

Nuclear Markers ◽

Mitochondrial Markers ◽

Intraspecific Genetic Variation ◽

Grand River

ABSTRACT Studies that assess intraspecific genetic variation in ciliates are few and quite recent. Consequently, knowledge of the subject and understanding of the processes that underlie it are limited. We sought to assess the degree of intraspecific genetic variation in Carchesium polypinum (Ciliophora: Peritrichia), a cosmopolitan, freshwater ciliate. We isolated colonies of C. polypinum from locations in the Grand River basin in Southwestern Ontario, Canada. We then used the nuclear markers—ITS1, ITS2, and the hypervariable regions of the large subunit rRNA—and an 819-bp fragment of the mitochondrial cytochrome c oxidase I gene (cox-1) to investigate the intraspecific genetic variation of C. polypinum and the degree of resolution of the above-mentioned markers at the population level. We also sought to determine whether the organism demonstrated any population structure that mapped onto the geography of the region. Our study shows that there is a high degree of genetic diversity at the isolate level, revealed by the mitochondrial markers but not the nuclear markers. Furthermore, our results indicate that C. polypinum is likely not a single morphospecies as previously thought.

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Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

Canadian Journal of Forest Research ◽

10.1139/x26-162 ◽

1996 ◽

Vol 26 (8) ◽

pp. 1454-1462 ◽

Cited By ~ 31

Author(s):

Naoki Tani ◽

Nobuhiro Tomaru ◽

Masayuki Araki ◽

Kihachiro Ohba

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Differentiation ◽

Phylogenetic Trees ◽

Genetic Relationships ◽

Natural Populations ◽

Group Method ◽

Stone Pine ◽

Arithmetic Means ◽

Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

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Genetic variation within and relationships among five subpopulations of Slovak Thoroughbred

Acta Veterinaria Hungarica ◽

10.1556/avet.52.2004.3.2 ◽

2004 ◽

Vol 52 (3) ◽

pp. 259-265

Author(s):

Daniela Šátková-Jakabová ◽

J. Trandžík ◽

Ľudmila Hudecová-Kvasňáková ◽

Erika Hegedüšová-Zetochová ◽

A. Bugarský ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Differentiation ◽

International Society ◽

Microsatellite Loci ◽

Genetic Relationships ◽

Allele Frequencies ◽

Weinberg Equilibrium ◽

Hardy Weinberg Equilibrium

Genetic variation at six microsatellite loci was analysed for five Thoroughbred subpopulations to determine the magnitude of genetic differentiation and the genetic relationships among the subpopulations. Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, with all subpopulations. The genetic diversities and relationships of five Thoroughbred subpopulations were evaluated using six microsatellites recommended by the International Society of Animal Genetics (ISAG). The allele frequencies, the effective numbers of alleles, and the observed and expected heterozygosities were calculated. POPGENE v. 1.31 (Yeh et al., 1997) was used to test for deviations from the Hardy-Weinberg (H-W) equilibrium and to assign FIS estimates (Weir, 1990). The utility of microsatellites for evaluating genetic diversity of horses is discussed.

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Phylogeographical Structure of Liquidambar formosana Hance Revealed by Chloroplast Phylogeography and Species Distribution Models

Forests ◽

10.3390/f10100858 ◽

2019 ◽

Vol 10 (10) ◽

pp. 858 ◽

Cited By ~ 1

Author(s):

Sun ◽

Lin ◽

Huang ◽

Ye ◽

Lai ◽

...

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Species Distribution ◽

Species Distribution Models ◽

Central China ◽

Recent Common Ancestor ◽

Interglacial Period ◽

Last Interglacial ◽

Distribution Models ◽

Last Interglacial Period

To understand the origin and evolutionary history, and the geographical and historical causes for the formation of the current distribution pattern of Lquidambar formosana Hance, we investigated the phylogeography by using chloroplasts DNA (cpDNA) non-coding sequences and species distribution models (SDM). Four cpDNA intergenic spacer regions were amplified and sequenced for 251 individuals from 25 populations covering most of its geographical range in China. A total of 20 haplotypes were recovered. The species had a high level of chloroplast genetic variation (Ht = 0.909 ± 0.0192) and a significant phylogeographical structure (genetic differentiation takes into account distances among haplotypes (Nst) = 0.730 > population differentiation that does not consider distances among haplotypes (Gst) = 0.645; p < 0.05), whereas the genetic variation within populations (Hs = 0.323 ± 0.0553) was low. The variation of haplotype mainly occurred among populations (genetic differentiation coefficient (Fst) = 0.73012). The low genetic diversity within populations may be attributed to the restricted gene flow (Nm = 0.18). The time of the most recent common ancestor for clade V mostly distributed in Southwestern China, Central China, Qinling and Dabieshan mountains was 10.30 Ma (95% Highest posterior density (HPD): 9.74–15.28) dating back to the middle Miocene, which revealed the genetic structure of L. formosana was of ancient origin. These results indicated that dramatic changes since the Miocene may have driven the ancestors of L. formosana to retreat from the high latitudes of the Northern Hemisphere to subtropical China in which the establishment and initial intensification of the Asian monsoon provided conditions for their ecological requirements. This scenario was confirmed by the fossil record. SDM results indicated there were no contraction–expansion dynamics, and there was a stable range since the last interglacial period (LIG, 130 kya). Compared with the population expansion detected by Fu’s Fs value and the mismatch distribution, we speculated the expansion time may happen before the interglacial period. Evidence supporting L. formosana was the ancient origin and table range since the last interglacial period.

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Limited Genetic Diversity and High Differentiation in Angelica Dahurica Resulted by Domestication: Insights to Breeding and Conservation

10.21203/rs.3.rs-1160144/v1 ◽

2021 ◽

Author(s):

Rong Huang ◽

Yinrong Liu ◽

Jianling Chen ◽

Zuyu Lu ◽

Jiajia Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Differentiation ◽

Clustering Analysis ◽

Large Scale ◽

Angelica Dahurica ◽

Significant Genetic Differentiation ◽

Large Scale Analysis ◽

Domestication Process ◽

Resources Conservation

Abstract Background： Angelica dahurica, belonging to the Apiaceae family, whose dry root is a famous traditional Chinese medicine named as “Bai zhi”. There are two cultivars (A. dahurica cv. ‘Hangbaizhi’ and A. dahurica cv. ‘Qibaizhi’), which have been domesticated for thousands of years. Long term artificial selection has led to great changes in root phenotypes of the two cultivars, and also decreased their adaptability to environment. We proposed hypothesis that the cultivars may lose some genetic diversity and highly differentiate from wild A. dahurica during the domestication process. However, few studies have been carried out on how domestication affects the genetic variation of this species. Here, we accessed the levels of genetic variation and differentiation within and between wild A. dahurica and its cultivars using 12 SSR markers. Results: The results revealed that the genetic diversity of the cultivars was much lower than that of wild A. dahurica, and A. dahurica cv. ‘Qibaizhi’ had lower genetic diversity compared to A. dahurica cv. ‘Hangbaizhi’. AMOVA analysis showed significant genetic diﬀerentiation between the wild and cultivated A. dahurica, and between A. dahurica cv. ‘Hangbaizhi’ and A. dahurica cv. ‘Qibaizhi’. The results of Bayesian, UPGMA, NJ and PcoA clustering analysis indicated that all 15 populations were assigned to two genetic clusters corresponding to the wild and cultivated resources. Bayesian clustering analysis further divided the cultivated resources into two sub-clusters corresponding to the two cultivars. Conclusions：Our study suggests that domestication process is likely the major factor resulting in the loss of genetic diversity in cultivated A. dahurica and significant genetic differentiation from the wild resources due to founder effect and/or artificially directional selections. This large-scale analysis of population genetics could provide valuable information for genetic resources conservation and breeding programs of Angelica dahurica.

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Genetic structure and proposed conservation strategy for natural populations of Calycanthus chinensis Cheng et S.Y. Chang (Calycanthaceae)

Canadian Journal of Plant Science ◽

10.4141/cjps07015 ◽

2008 ◽

Vol 88 (1) ◽

pp. 179-186 ◽

Cited By ~ 2

Author(s):

Chu-Chuan Fan ◽

Nicola Pecchioni ◽

Long-Qing Chen

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Differentiation ◽

Genetic Distance ◽

Gene Diversity ◽

Genetic Relationships ◽

Natural Populations ◽

Population Level ◽

Conservation Strategy ◽

Information Index

Calycanthus chinensis Cheng et S.Y. Chang, a tertiary relic species in China, is a shade-loving and deciduous bush withan elegant shape and beautiful flower of high ornamental value. It was widely planted in gardens and miniature scapes in China.The objective of this study was to characterize the genetic variation and structure in the three extant populations of the species, in order to provide useful information for a future conservation strategy. Twenty-two of 120 RAPD primers were selected and a total of 257 stable and clear DNA fragments were scored. Calycanthus chinensis showed a lower level of genetic diversity. At the population level, the percentage of polymorphic loci, Nei's gene diversity and Shannon’s information index were 40.9%, 0.1641 and 0.2386, respectively; while at the species level, the corresponding values were 59.1%, 0.2097 and 0.3123, respectively. The estimates of genetic differentiation based on Shannon’s information index (0.2360), Nei’s gene diversity (0.2175) and AMOVA (24.94%) were very similar, and significantly higher than the average genetic differentiation reported in outcrossed spermatophyte. So it suggested high genetic differentiation emerged among populations of C. chinensis. Genetic relationships among populations were assessed by Nei’s standard genetic distance, which suggested that the Tiantai population was genetically distinct from the other two populations. Moreover, the genetic distance was significantly correlated with geographical distance among populations (r = 0.997, t > t0.05). The gene flow (Nm) was 0.8994, indicating that gene exchange among populations was restricted. A conservation strategy was proposed based on the low gene flow and habitat deterioration, which are contributing to the endangered status of this species. Key words: Genetic diversity, endangered plant, population genetics, RAPD

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Genetic and morphological differentiation among populations of the Rivoli’s Hummingbird (Eugenes fulgens) species complex (Aves: Trochilidae)

The Auk ◽

10.1093/auk/ukaa032 ◽

2020 ◽

Vol 137 (4) ◽

Cited By ~ 1

Author(s):

Luz E Zamudio-Beltrán ◽

Juan Francisco Ornelas ◽

Andreia Malpica ◽

Blanca E Hernández-Baños

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Genetic Differentiation ◽

Species Complex ◽

Ecological Niche Modeling ◽

Demographic History ◽

Morphological Differentiation ◽

Last Interglacial ◽

Haplotype Networks ◽

Isthmus Of Tehuantepec

Abstract Genetic variation and phylogeographic studies have been crucial for understanding mechanisms of speciation. We analyzed genetic variation and phylogeography to reconstruct the demographic history of the Rivoli’s Hummingbird (Eugenes fulgens) species complex and also evaluated their morphological differentiation. This widely distributed species inhabits the highlands of Mexico and northern Central America, with 2 subspecies separated by the Isthmus of Tehuantepec (west: E. f. fulgens, east: E. f. viridiceps). We surveyed genetic variation in 2 mitochondrial DNA markers (mtDNA, with 129 individuals) and nuclear DNA (6 microsatellites, with 85 individuals). We also inferred the demographic history, estimated divergence times, and analyzed morphological variation using 470 vouchered specimens. We modeled the current potential distribution of the species using ecological niche modeling and projected it into the past to model the effects of the Pleistocene climatic cycles. Haplotype networks, pairwise FST comparisons, AMOVA, and morphological analysis revealed differences between geographically isolated populations separated by the Isthmus of Tehuantepec (IT; corresponding to the 2 recognized subspecies: fulgens and viridiceps), and by the Motagua-Polochic-Jocotán (MPJ) system fault. Demographic scenarios revealed a contraction in distribution during the last interglacial, and expansion during the Last Glacial Maximum (LGM) with little change since the LGM. Divergence between groups separated by the Isthmus of Tehuantepec ~59,600 yr ago occurred in the presence of gene flow, suggesting that the Isthmus of Tehuantepec is a semipermeable barrier to gene flow. STRUCTURE analyses of microsatellite data detected 3 genetically differentiated groups. Several results fit a model of recent lineage divergence, including a significant signal of genetic differentiation, demographic expansion, decreased gene flow from past to present, and northward expansion during the LGM and contraction during the interglacial periods. We conclude that the genetic differentiation of E. fulgens in the Madrean Pine-Oak Woodlands resulted from recent geographical isolation of populations separated by natural barriers (IT and MPJ).

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Genetic Variability and Structure of Canadian Populations of the Sapstain Fungus Ceratocystis resinifera

Phytopathology ◽

10.1094/phyto.2004.94.12.1323 ◽

2004 ◽

Vol 94 (12) ◽

pp. 1323-1330 ◽

Cited By ~ 11

Author(s):

Chantal Morin ◽

Colette Breuil ◽

Louis Bernier

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Great Plains ◽

Random Amplified Polymorphic Dna ◽

Eastern Canada ◽

Low Genetic Diversity ◽

Central Canada ◽

Geographical Populations ◽

Coniferous Tree Species ◽

Differentiation Index

Genomic DNA was extracted from 129 isolates of Ceratocystis resinifera, a species belonging to the C. coerulescens complex, and 19 polymorphic random amplified polymorphic DNA markers were used to study the population genetic structure of this fungus. The analysis suggested a moderate value for genetic diversity (HS = 0.209). However, when monomorphic markers and rare alleles, representing 89 markers, also were included in the calculation, the genetic diversity of Canadian populations of C. resinifera appeared to be much lower (HS = 0.045). This could be explained by two hypotheses: (i) recent introduction of this species into North America and (ii) clonal reproduction (by selfing). No specialization by C. resinifera for coniferous tree species was observed based on genetic differentiation index between isolates sampled from Pinus and Picea spp. and on phylogenetic analysis using Dice coefficient of association. In spite of a low genetic diversity, a very high genetic differentiation was observed among the nine geographical populations studied (FST = 20.8%). The genetic differences were especially striking when populations from Eastern Canada were compared with populations from Western Canada (φST = 0.27%; P < 0.001), suggesting that a geographic reproductive barrier occurs in Central Canada. This barrier may be the consequence of a weak migration of insect vectors of C. resinifera due to reduced presence of hosts in the Canadian Great Plains, where extensive agriculture occurs. However, results from pairwise FST matrix and phylogeny of haplotypes suggest that the barrier is not totally impenetrable because some gene flow occurred from the west and from the east in the Big River (Saskatchewan) population located in the middle of the Great Plains.

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Assessing genetic diversity of protected coho salmon (Oncorhynchus kisutch) populations in California

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f06-171 ◽

2007 ◽

Vol 64 (1) ◽

pp. 30-42 ◽

Cited By ~ 11

Author(s):

Katherine A Bucklin ◽

Michael A Banks ◽

Dennis Hedgecock

Keyword(s):

Genetic Diversity ◽

Coho Salmon ◽

Random Mating ◽

Oncorhynchus Kisutch ◽

Legal Protection ◽

Population Level ◽

Population Subdivision ◽

Minimal Impact ◽

Low Genetic Diversity ◽

Microsatellite Dna Markers

California coho salmon (Oncorhynchus kisutch) are under legal protection owing to significant declines in abundance over the last decades. Previously, California coho salmon were characterized as having low genetic diversity and weak population subdivision, attributable potentially to homogenization by out-of-basin hatchery releases. Here, diversity at seven highly polymorphic microsatellite DNA markers is assessed within and among 32 collections of coho salmon from 16 California watersheds. In 71% of local populations, genotypic composition deviates significantly from that expected under the assumption of random mating. We develop and apply methods to adjust for two potential causes of deviation from random mating expectations: (i) Wahlund effects, owing to heterogeneous collections of individuals, and (ii) the "Allendorf–Phelp's effect", owing to closely related juveniles in samples. Such population-level "adjustments" reduce within-region and increase among-region variance; after adjustment, we find strong concordance of genetic and geographic distances. We conclude that stock transfers have had minimal impact on population structure and that California coho salmon populations likely comprise small numbers of endemic breeders, potentially experiencing high levels of genetic drift and inbreeding.

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