Genetic variation in sand pine (Pinusclausa)

Pinusclausa (Chapm. ex Engelm.) Vasey ex Sarg. is a member of subsection Contortae that is restricted to Florida and the southern tip of Alabama. The present distribution of P. clausa is divided into two purported varieties: var. clausa in peninsular Florida and var. immuginata primarily in the Florida panhandle. We determined allozyme diversity and population genetic structure for 12 populations of var. clausa and 9 populations of var. immuginata. At the species level, 88% of the 26 loci examined were polymorphic. The genetic diversity maintained at both the species (Hes = 0.100) and population (Hep = 0.092) levels was low relative to most other pine species. Genetic differentiation among populations was also relatively low (GST = 0.054). Genetic distances between populations of the same variety (mean D = 0.006) were lower than genetic distances between populations of different varieties (mean D = 0.012). Although allele frequencies at individual loci differed significantly between the two varieties, each variety maintained nearly 99% of the genetic variation apparent at the species level (intervarietal differentiation, Gv = 0.014). The lower levels of genetic diversity in P. clausa may have resulted in part from genetic bottlenecks during periods of range retraction.

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Genetic analysis of silver-fir populations in the Beskids

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.2003.015 ◽

2011 ◽

Vol 72 (2) ◽

pp. 115-119 ◽

Cited By ~ 3

Author(s):

Leon Mejnartowicz

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Analysis ◽

Abies Alba ◽

Genetic Distances ◽

Silver Fir ◽

Geographical Distance ◽

Polymorphic Loci ◽

Expected Heterozygosity ◽

Rare Alleles

Twenty-eight isozymic loci were studied in the Beskid Mts., in four populations of common silver-fir (Abies alba): one in Beskid Makowski (BM) and three populations in Beskid Sądecki (BS). Their genetic variation and diversity were analyzed, and Nei's genetic distances between the populations were calculated. The results show that the geographical distance between the BM population and the three BS populations is reflected in genetic distances. The BM population is clearly distinct from the others. It has the lowest genetic diversity (I = 0.42), percentage of polymorphic loci (%PoL = 64.29) and number of rare alleles (NoRa = 5). Besides, the BM population has the highest observed heterozygosity (Ho = 0.291), which exceeds the expected heterozygosity (He = 0.254), estimated on the basis of the Hardy-Weinberg Principle. On the contrary, BS populations are in the state of equilibrium, which is manifested, in similar values of He = 0.262 and Ho = 0.264.

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Genetic diversity and differentiation in populations of invasive Eurasian (Myriophyllum spicatum) and hybrid (Myriophyllum spicatum × Myriophyllum sibiricum) watermilfoil

Invasive Plant Science and Management ◽

10.1017/inp.2020.12 ◽

2020 ◽

Vol 13 (2) ◽

pp. 59-67

Author(s):

Ryan A. Thum ◽

Gregory M. Chorak ◽

Raymond M. Newman ◽

Jasmine A. Eltawely ◽

Jo Latimore ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Population Genetic ◽

Myriophyllum Spicatum ◽

Population Variation ◽

Efficacy Evaluation ◽

Submerged Aquatic Plant ◽

Myriophyllum Sibiricum ◽

Control Response ◽

Herbicide Response

AbstractPopulation genetic studies of within- and among-population genetic variability are still lacking for managed submerged aquatic plant species, and such studies could provide important information for managers. For example, the extent of within-population genetic variation may influence the potential for managed populations to locally adapt to environmental conditions and control tactics. Similarly, among-population variation may influence whether specific control tactics work equally effectively in different locations. In the case of invasive Eurasian watermilfoil (Myriophyllum spicatum L.), including interspecific hybrids with native northern watermilfoil (Myriophyllum sibiricum Kom.), managers recognize that there is genetic variation for growth and herbicide response. However, it is unclear how much overall genetic variation there is, and how it is structured within and among populations. Here, we studied patterns of within- and among-lake genetic variation in 41 lakes in Michigan and 62 lakes in Minnesota using microsatellite markers. We found that within-lake genetic diversity was generally low, and among-lake genetic diversity was relatively high. However, some lakes were genetically diverse, and some genotypes were shared across multiple lakes. For genetically diverse lakes, managers should explicitly recognize the potential for genotypes to differ in control response and should account for this in monitoring and efficacy evaluation and using pretreatment herbicide screens to predict efficacy. Similarly, managers should consider differences in genetic composition among lakes as a source of variation in the growth and herbicide response of lakes with similar control tactics. Finally, laboratory or field information on control efficacy from one lake may be applied to other lakes where genotypes are shared among lakes.

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Genetic diversity of three Aegla species (Decapoda, Anomura) revealed by AFLP and mtDNA markers

Crustaceana ◽

10.1163/15685403-00003873 ◽

2019 ◽

Vol 92 (4) ◽

pp. 445-462

Author(s):

Bianca L. Zimmermann ◽

Jober V. De Vargas Machado ◽

Sandro Santos ◽

Marlise L. Bartholomei-Santos

Keyword(s):

Genetic Diversity ◽

Distinct Species ◽

Genetic Distances ◽

Species Level ◽

Taxonomic Resolution ◽

Similar Species ◽

Southern Brazil ◽

Low Levels ◽

Management And Conservation ◽

Mtdna Markers

Abstract Representatives of the genus Aegla present a conserved morphology; thus, the increased use of molecular markers has raised many taxonomic issues. We used AFLP and mtDNA to investigate the genetic differentiation and phylogenetic relationships of morphologically similar species with overlapping distribution areas in southern Brazil: A. georginae, A. ludwigi, and A. platensis. While A. platensis is widely distributed, the critically endangered A. georginae and A. ludwigi have limited distributions. Although both markers showed populations with low levels of genetic variability, they differed markedly in revealing relationships between populations; according to AFLP, the genetic distances between A. platensis populations were as high as those between distinct species, a result not observed when considering mtDNA data. We emphasize that the use of multiple lines of evidence is necessary for defining correct levels of genetic diversity and a good species-level taxonomic resolution. Such features are essential for the management and conservation of Aegla species.

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Genetic variation in the greater bilby (Macrotis lagotis)

Pacific Conservation Biology ◽

10.1071/pc930046 ◽

1994 ◽

Vol 1 (1) ◽

pp. 46 ◽

Cited By ~ 4

Author(s):

Richard Southgate ◽

Mark Adams

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Variability ◽

Population Genetic ◽

Taxonomic Status ◽

Biological Species ◽

Significant Loss ◽

Allozyme Electrophoresis ◽

Allozyme Data ◽

Data Support

The taxonomic status of and genetic diversity amongst extant populations of the greater bilby, Macrotis lagotis, were assessed using allozyme electrophoresis. A total of 47 bilbies sampled from three geographic areas and two captive colonies were screened for 42 loci, six of which were polymorphic. The results are consistent with the view that all extant populations represent a single biological species. All populations were genetically very similar (Nei D's 0.000 to 0.004) and overall levels of within-population genetic variability were low (Ho 0.004 � 0.004 to 0.0026 � 0.017). The allozyme data support the hypothesis that there has been no significant loss of variability in the captive colonies when compared to the species as a whole.

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Impact of Mycoplasma ovipneumoniae on juvenile bighorn sheep (Ovis canadensis) survival in the northern Basin and Range ecosystem

PeerJ ◽

10.7717/peerj.10710 ◽

2021 ◽

Vol 9 ◽

pp. e10710

Author(s):

Robert S. Spaan ◽

Clinton W. Epps ◽

Rachel Crowhurst ◽

Donald Whittaker ◽

Mike Cox ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Survival Probability ◽

Population Genetic ◽

Bighorn Sheep ◽

Basin And Range ◽

Ovis Canadensis ◽

Juvenile Survival ◽

Adult Females ◽

Mycoplasma Ovipneumoniae

Determining the demographic impacts of wildlife disease is complex because extrinsic and intrinsic drivers of survival, reproduction, body condition, and other factors that may interact with disease vary widely. Mycoplasma ovipneumoniae infection has been linked to persistent mortality in juvenile bighorn sheep (Ovis canadensis), although mortality appears to vary widely across subspecies, populations, and outbreaks. Hypotheses for that variation range from interactions with nutrition, population density, genetic variation in the pathogen, genetic variation in the host, and other factors. We investigated factors related to survival of juvenile bighorn sheep in reestablished populations in the northern Basin and Range ecosystem, managed as the formerly-recognized California subspecies (hereafter, “California lineage”). We investigated whether survival probability of 4-month juveniles would vary by (1) presence of M. ovipneumoniae-infected or exposed individuals in populations, (2) population genetic diversity, and (3) an index of forage suitability. We monitored 121 juveniles across a 3-year period in 13 populations in southeastern Oregon and northern Nevada. We observed each juvenile and GPS-collared mother semi-monthly and established 4-month capture histories for the juvenile to estimate survival. All collared adult females were PCR-tested at least once for M. ovipneumoniae infection. The presence of M. ovipneumoniae-infected juveniles was determined by observing juvenile behavior and PCR-testing dead juveniles. We used a known-fate model with different time effects to determine if the probability of survival to 4 months varied temporally or was influenced by disease or other factors. We detected dead juveniles infected with M. ovipneumoniae in only two populations. Derived juvenile survival probability at four months in populations where infected juveniles were not detected was more than 20 times higher. Detection of infected adults or adults with antibody levels suggesting prior exposure was less predictive of juvenile survival. Survival varied temporally but was not strongly influenced by population genetic diversity or nutrition, although genetic diversity within most study area populations was very low. We conclude that the presence of M. ovipneumoniae can cause extremely low juvenile survival probability in translocated bighorn populations of the California lineage, but found little influence that genetic diversity or nutrition affect juvenile survival. Yet, after the PCR+ adult female in one population died, subsequent observations found 11 of 14 ( 79%) collared adult females had surviving juveniles at 4-months, suggesting that targeted removals of infected adults should be evaluated as a management strategy.

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KoT: an automatic implementation of the K/θ method for species delimitation

10.1101/2021.08.17.454531 ◽

2021 ◽

Author(s):

Yann Spöri ◽

Fabio Stoch ◽

Simon Dellicour ◽

C. William Birky ◽

Jean-François Flot

Keyword(s):

Genetic Diversity ◽

Species Delimitation ◽

Population Genetic ◽

Average Distance ◽

Species Level ◽

Species Boundaries ◽

Fasta File ◽

Genetic Theory ◽

Putative Species ◽

The Impact

K/θ is a method to delineate species that rests on the calculation of the ratio between the average distance K separating two putative species-level clades and the genetic diversity θ of these clades. Although this method is explicitly rooted in population genetic theory, it was never benchmarked due to the absence of a program allowing automated analyses. For the same reason, its application by hand was limited to small datasets of a few tens of sequences. We present an automatic implementation of the K/θ method, dubbed KoT (short for "K over Theta"), that takes as input a FASTA file, builds a neighbour-joining tree, and returns putative species boundaries based on a user-specified K/θ threshold. This automatic implementation avoids errors and makes it possible to apply the method to datasets comprising many sequences, as well as to test easily the impact of choosing different K/θ threshold ratios. KoT is implemented in Haxe, with a javascript webserver interface freely available at https://eeg-ebe.github.io/KoT/ .

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Genetic Diversity and Population Genetic Structure in the Rare Chittering Grass Wattle, Acacia anomala Court

Australian Journal of Botany ◽

10.1071/bt9880273 ◽

1988 ◽

Vol 36 (3) ◽

pp. 273 ◽

Cited By ~ 70

Author(s):

DJ Coates

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

Genetic System ◽

Small Population ◽

Vegetative Multiplication ◽

The Mean ◽

Allozyme Loci

There are 10 known populations of Acacia anomala occurring in two small disjunct groups some 30 km apart. The Chittering populations reproduce sexually whereas the Kalamunda populations appear to reproduce almost exclusively by vegetative multiplication. The level and distribution of genetic variation were studied at 15 allozyme loci. Two loci were monomorphic in all populations. In the Chittering populations the mean number of alleles per locus was 2.0 and the expected panmictic heterozygosity (genetic diversity) 0.209. In the Kalamunda populations the mean number of alleles per locus was 1.15 and the expected panmictic heterozygosity 0.079, although the observed heterozygosity of 0.150 was only marginally less than the Chittering populations (0.177). These data support the contention that the Chittering populations are primarily outcrossing whereas the Kalamunda populations are clonal, with each population consisting of individuals with identical and, in three of the four populations, heterozygous, multilocus genotypes. The level of genetic diversity within the Chittering populations is high for plants in general even though most populations are relatively smsll and isolated. It is proposed that either the length of time these populations have been reduced in size and isolated is insufficient for genetic diversity to be reduced or the genetic system of this species is adapted to small population conditions. Strategies for the adequate conservation of the genetic resources of Acacia anomala are discussed.

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Genetic variation among Iranian alfalfa (Medicago sativa L.) populations based on RAPD markers

Bangladesh Journal of Plant Taxonomy ◽

10.3329/bjpt.v18i2.9296 ◽

2011 ◽

Vol 18 (2) ◽

pp. 93-104 ◽

Cited By ~ 3

Author(s):

Fatemeh Mohammadzadeh ◽

Hassan Monirifar ◽

Jalal Saba ◽

Mostafa Valizadeh ◽

Ahmad Razban Haghighi ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Variation ◽

Breeding Population ◽

Genetic Distances ◽

Analysis Of Molecular Variance ◽

Molecular Variance ◽

Geographical Patterns ◽

Plant Taxon ◽

High Level

Genetic diversity among and within 10 populations of Iranian alfalfa, from different areas of Azarbaijan, Iran was analyzed by screening DNA from seeds of individual plants and bulk samples. In individual study, 10 randomly amplified polymorphic DNA (RAPD) primers produced 156 polymorphic bands and a high level of genetic diversity was observed within populations. The averages of total and within population genetic diversity were 0.2349 and 0.1892, respectively. Results of analysis of molecular variance (AMOVA) showed the great genetic variation existed within populations (81.37%). These Results were in agreement with allogamous and polyploid nature of alfalfa. Cluster analysis was performed based on Nei’s genetic distances resulting in grouping into 3 clusters which could separate breeding population from other populations. Results of cluster analysis were in consistent with morphological and geographical patterns of populations. The results of bulk method were different from individual analysis. Our results showed that RAPD analysis is a suitable method to study genetic diversity and relationships among alfalfa populations.Keywords: Alfalfa; RAPD; Genetic diversity; Analysis of Molecular Variance; Cluster analysis.DOI: http://dx.doi.org/10.3329/bjpt.v18i2.9296Bangladesh J. Plant Taxon. 18: (2): 93-104, 2011 (December)

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Assessment of genetic variation in Bapedi sheep using microsatellite markers

South African Journal of Animal Science ◽

10.4314/sajas.v50i2.15 ◽

2020 ◽

Vol 50 (2) ◽

pp. 318-324

Author(s):

A. Maqhashu ◽

N.O. Mapholi ◽

H.A. O’Neill ◽

K.A. Nephawe ◽

F.V. Ramukhithi ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Microsatellite Markers ◽

South African ◽

Agricultural Research ◽

Germplasm Conservation ◽

Genetic Distances ◽

Fixation Index ◽

Indigenous Sheep ◽

Agricultural Research Council

This study was conducted to assess genetic variation in Bapedi sheep using 14 microsatellite markers. Blood samples were collected from 174 unrelated Bapedi sheep on six farms in various districts of Limpopo and from the Agricultural Research Council Animal Production Institute (ARC-API) in Gauteng. Genotypes from other South African indigenous sheep, namely Zulu (N = 14), Damara (N = 11), Dorper (N = 8), and Namaqua (N = 11), were included to represent reference populations. The effective number of alleles averaged 5.6 for across the Bapedi flocks and was 4.9 for the reference breeds. Among the Bapedi flocks, the observed heterozygosity (Ho) ranged from 0.56 ± 0.05 to 0.69 ± 0.03 and expected heterozygosity (He) values were between 0.75 ± 0.04 and 0.88 ± 0.01. Thus, there is considerable genetic diversity within the Bapedi sheep populations. However, the fixation index was high, indicating the possibility of inbreeding becoming a problem for these flocks. A neighbour-joining tree was constructed from the estimates of Nei’s genetic distances among flocks. The presence of Bapedi sheep flocks on all of the main branches of the tree along with one of the reference breeds suggests the present-day Bapedi is not an entirely distinct breed and that there are genetic differences between flocks of these South African indigenous sheep. Sustainable breeding and conservation programmes are needed to control inbreeding and to foreclose possible genetic dilution of Bapedi sheep. Keywords: genetic diversity, germplasm conservation, inbreeding, indigenous sheep

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Genetic structure analysis of domestic duck populations in eastern China

Chinese Journal of Agricultural Biotechnology ◽

10.1017/s1479236208002295 ◽

2008 ◽

Vol 5 (3) ◽

pp. 183-187

Author(s):

Li Hui-Fang ◽

Song Wei-Tao ◽

Zhu Wen-Qi ◽

Xu Wen-Juan ◽

Tang Qing-Ping

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Structure ◽

Eastern China ◽

Genetic Distances ◽

Domestic Duck ◽

Average Heterozygosity ◽

Rich Diversity ◽

Breed Differences ◽

The Rich

AbstractUsing microsatellite markers, the genetic structure of nine domestic duck (Anas platyrhynchos) populations in eastern China was analysed. The results showed that the heterozygosity was high in these populations, ranging from 0.5137 to 0.6055, with an average heterozygosity of 0.5523, reflecting the rich diversity. Considerable breed differentiation was observed and 25.65% of the total genetic variation came from breed differences; this low differentiation result affirmed that each breed has its own genetic diversity. The DA genetic distances suggested that greater differentiation existed between populations. The duck populations were clustered into four groups based on neighbour joining (NJ) clustering, and the clustering results showed relationships with duck breed distributions and economic utilization.

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