Phylogeography of the tailed frog (Ascaphus truei) in British Columbia

2000 ◽  
Vol 78 (10) ◽  
pp. 1749-1758 ◽  
Author(s):  
Kermit Ritland ◽  
Linda A Dupuis ◽  
Fred L Bunnell ◽  
Wesley LY Hung ◽  
John E Carlson
Keyword(s):  
British Columbia ◽  
Genetic Distance ◽  
Range Expansion ◽  
Gene Diversity ◽  
Distinct Group ◽  
Strong Relationship ◽  
Physical Distance ◽  
Genetic Distances ◽  
Coastal Regions ◽  
Ascaphus Truei

The tailed frog (Ascaphus truei) is highly philopatric, with naturally disjunct populations. To infer the historical pattern of range expansion and contraction in A. truei of British Columbia (B.C.), we conducted a randomly ampli fied polymorphic DNA (RAPD) survey, using 16 primers, of 469 individuals sampled from 22 populations in four regions. Genetic distances, based on 169 putative RAPD loci, clustered populations into three clear groups: mid/north-coastal B.C., south-coastal B.C., and interior B.C. The interior populations were the most distinct group, but their genetic distance from other groups equals that expected from isolation by physical distance alone, as opposed to taxonomic differentiation. FST values within coastal regions were moderately low (0.02-0.05) but were high in the interior (0.12) and across all populations (0.18). Within the mid/north-coastal and south-coastal regions, genetic distance showed no relationship with physical distance, while among regions and within the interior region there was a strong relationship. Gene diversity varied significantly among regions, with both the interior and south-coastal populations showing about 25% less diversity than the mid/north-coastal populations. These data indicate a complex history of geographic restrictions to multiple refugia, followed by various types of range expansion. The implications of these results for conservation efforts in this species are discussed.

Detection of genetic diversity in rough fescue (Festuca campestris Rydb) populations of southern Alberta and British Columbia, Canada, using RAPD markers

2008 ◽  
Vol 88 (2) ◽  
pp. 307-312
Author(s):  
Zhao Mengli ◽  
Han Bing ◽  
Walter D Willms
Keyword(s):  
Genetic Diversity ◽  
British Columbia ◽  
Genetic Distance ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Distance ◽  
Genetic Distances ◽  
Gene Frequencies ◽  
Southern Alberta ◽  
Potential Adaptation ◽  
Rough Fescue

Mountain rough fescue (Festuca campestris Rydb.) is a tufted native grass in southern Alberta and British Columbia, Canada, and has attracted interest for use in reclamation. However, its seed is often available from only a few localized sources and may not be adapted for areas removed from the collection site. We conducted a study to determine the genetic variability among rough fescue populations to assess its potential adaptation. Thirty plants were collected from each of six populations and analyzed using Random Amplified Polymorphic DNA (RAPD). One population (Kamloops, BC) was separated by several mountain ranges from the five easterly Alberta populations.The Kamloops population was also separated from the Alberta populations by genetic distance in two clusters. Of the total genetic variation present in the data, 21% was found among populations while the remaining (79%) was found within populations. Nei’s genetic distances among populations were related to their geographical distances. Genetic differences among populations appeared to be caused primarily by differences in gene frequencies rather than rare genes. Also, genetic diversity appeared to increase from west to east suggesting that the more easterly populations had greater adaptation potential. We speculate that the more easterly populations are less likely to share genes since the prevailing winds are from the west. Germplasm from the more easterly populations may be used with suitable precautions within Alberta and possibly around Kamloops. Key words: Genetic distance, geographic distance, reclamation, potential adaptation

Population genetic structure of tailed frogs (Ascaphus truei) in clearcut and old-growth stream habitats in south coastal British Columbia

2005 ◽  
Vol 83 (11) ◽  
pp. 1460-1468 ◽  
Author(s):  
T R Wahbe ◽  
C Ritland ◽  
F L Bunnell ◽  
K Ritland
Keyword(s):  
British Columbia ◽  
Genetic Structure ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Physical Distance ◽  
Future Research ◽  
Ecological Data ◽  
Old Growth ◽  
Ascaphus Truei ◽  
Coastal British Columbia

Ascaphus truei Stejneger, 1899 relies on cool, fast-flowing, forested mountain streams, which receive little protection from logging activities. During recovery of post-logging habitats, local extirpation of Ascaphus is a concern because their recolonization may be slow. In British Columbia, Oregon, and California, coastal Ascaphus populations are designated as "at risk". To infer fragmentation impacts from patterns of genetic structure, we used RAPD molecular markers and compared population genetic structures of Ascaphus larvae in an old growth with an adjacent clearcut stream located in coastal British Columbia. In the clearcut, larvae were less genetically diverse than in the old growth and exhibited no relationship between physical distance and genetic relatedness, whereas in the old growth, genetic similarity decreased with physical distance. Patterns of gene flow between the clearcut and old-growth streams were significantly different. The clearcut population went through a bottleneck/founding event, but also exhibited greater dispersal. The frogs were perhaps searching for new habitat (which would lower isolation by distance) and suffering mortality (which would decrease diversity). Most problems in conservation will require genetic and ecological data, and future research should aim to incorporate methodologies from both fields.

Isozyme variation and the conservation genetics of Garry oak

2005 ◽  
Vol 83 (11) ◽  
pp. 1478-1487 ◽  
Author(s):  
K. Ritland ◽  
L.D. Meagher ◽  
D.G.W. Edwards ◽  
Y.A. El-Kassaby
Keyword(s):  
British Columbia ◽  
Gene Diversity ◽  
Keystone Species ◽  
Vancouver Island ◽  
Genetic Distances ◽  
Quercus Garryana ◽  
White Oak ◽  
Isolated Populations ◽  
Island Populations ◽  
Inbreeding Coefficients

Garry oak ( Quercus garryana Dougl. ex Hook) has a long north–south distribution along the inland Pacific coast. In British Columbia, it is a keystone species in a unique and endangered “Garry oak meadow” ecosystem. Here, we apply isozyme markers to address issues in the conservation and phylogeography of Garry oak. Among 42 populations and 23 gene loci, gene diversity (expected heterozygosity) averaged 0.17, and number of alleles per locus averaged 1.84. These values are about one-half of those found in other white oak species. Using progeny arrays, we found outcrossing rates in two Vancouver Island populations to average 0.96, with no detectable biparental inbreeding; also inbreeding coefficients of the 42 populations averaged near zero (0.025); thus inbreeding is not a significant concern. Cluster analysis of genetic distances identified two major groups of populations: southern Washington – Oregon and Vancouver Island – Gulf Islands; populations within the island region were particularly homogenous. An isolated mainland British Columbia population near Sumas, British Columbia, perhaps of anthropogenic origin, showed the least genetic variability and greatest genetic distance. Generally, geographically isolated populations were more genetically depauperate, which may place handicaps on their survival, but also more genetically distinct, providing a greater evolutionary legacy to the species.

scholarly journals Genetic diversity analysis of tropical sugar beet (Beta vulgaris L.) varieties in Bangladesh using RAPD markers

Genetika ◽  
2016 ◽  
Vol 48 (1) ◽  
pp. 151-164
Author(s):  
Saidin Saclain ◽  
Abdul Latif ◽  
Babul Bala ◽  
Mithun Mallik ◽  
Shahidul Islam
Keyword(s):  
Genetic Variation ◽  
Sugar Beet ◽  
Genetic Distance ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Similarity Index ◽  
Genetic Distances ◽  
Group Method ◽  
Pair Group ◽  
Major Cluster

Knowledge on intra-specific genetic variation of an organism is important for its genetic improvement and conservation. In order to estimate genetic variation and relatedness in eleven tropical Sugar beet varieties we used randomly amplified polymorphic DNA (RAPD) markers. The RAPD analysis was performed using six decamer random primers, which amplified a total of 63 DNA fragments of which 43 (68.25%) were found polymorphic. The average polymorphic bands per primer was 7.17 and the overall gene diversity was 0.24. Among the 43 polymorphic loci studied, 2 were specific for 2K 310, 1 for Shubraha, 1 for Natura and 1 for HI-0473 varieties. Pair wise genetic distance and similarity indices were ranged from 0.12-0.51 and 66.73-92.91, respectively. Cauvery and 2K 310 were found to be the most distantly related with a higher genetic distance value (GD = 0.51) and lower similarity index (SI = 66.73), while Aranka and Serenada were the most closely related with their lower GD (0.12) and higher SI(92.91) values. In an unweighted pair group method of arithmetic mean dendrogram constructed on the basis of genetic distances, the eleven varieties grouped into two main clusters: 2K 310 alone was in one cluster whereas 10 other varieties grouped into a major cluster. This indicates that 2K 310 was distantly related with each of the other varieties. Distantly related varieties based on estimated genetic variation could be selected for future breeding program that could result in improvement of this crop.

scholarly journals Efficiency of different PCR-based marker systems for assessment of Iris pumila genetic diversity

Biologia ◽  
2013 ◽  
Vol 68 (4) ◽  
Author(s):  
Olena Bublyk ◽  
Igor Andreev ◽  
Ruslan Kalendar ◽  
Kateryna Spiridonova ◽  
Viktor Kunakh
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Issr Markers ◽  
Genetic Distances ◽  
Resolving Power ◽  
Abiotic Stress Response ◽  
Genetic Population ◽  
Iris Pumila ◽  
Polymorphic Bands

AbstractWe investigated informativeness and effectiveness of different marker types (ISSR, IRAP, REMAP, RGAP and LP-PCR that employ primers based on the conservative sequences of abiotic stress response genes) to study genetic diversity of Iris pumila L. By the number of amplicons per primer, number of polymorphic amplicons per primer and resolving power index (Rp), ISSR-markers were the most efficient followed by LP-PCR-markers. In order of decreasing value of indicators of genetic diversity “the percentage of polymorphic bands”, and “the average Jaccardś genetic distance between plants”, marker systems may be arranged as follows: ISSR > RAPD > LP-PC > RGAP ≈ IRAP. For ISSR-markers, the percentage of polymorphic bands was 1.3–1.7 times higher than for the others, and the average genetic distance was 1.2–1.3 times higher. Different marker systems were ranked by the value of Neiś gene diversity and the Shannonś index as follows: ISSR > RAPD ≈ LP-PCR > RGAP ≈ IRAP, with the highest and the lowest values differing 1.4 times. Genetic population structure was investigated with program Structure 2.3. The data of all marker systems suggest that all genomes under study belonged to one population. The PCoA and cluster analyses based on genetic distances showed distinctions in clustering generated from different markers data and summarized data, as well as the lack of strong clusters. Mantel test revealed significant positive correlation between the matrices of genetic distances generated by the data of almost all marker systems. The strongest correlation was found between RGAP- and IRAP-markers (r = 0.452, p = 0.01) and between RGAP and ISSR (r = 0.430, p = 0.01). ISSR, RAPD and LP-PCR proved to be more effective for the study of I. pumila genetic diversity, nevertheless, joint use of different marker systems will provide a more comprehensive assessment of variation in different genomic regions.

scholarly journals Estimation of Genetic Diversity among Canola Accessions using Simple Sequence Repeat Markers

2021 ◽  
Vol 8 (4) ◽  
pp. 86-94
Author(s):  
Jaleel Ahmad ◽  
Muhammad Baber ◽  
Wajid Nazeer ◽  
Sana Hamdullah ◽  
Aleena Ahmad Somroo
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Molecular Genetic ◽  
Genetic Distances ◽  
Genetic Studies ◽  
Molecular Genetic Basis ◽  
Ssr Primers ◽  
Minimum Genetic Distance ◽  
Simple Sequence

Genetic studies through molecular markers proved important to find out the genetic diversity of canola. In this study, 50 lines of canola were used to find the polymorphism using 15 SSR primers and investigated the genetic diversity, PIC values, frequency-based genetic distance, and allelic frequencies. Mean gene diversity, frequency-based genetic distance, and PIC values were 0.8777, 0.233 and 0.8666, respectively for the canola lines. A good range of genetic diversity was found among studied canola lines with value 85.91% polymorphism. Maximum and minimum genetic distances among 50 lines were 1 and 0.26, respectively. Accessions ACC-26068, ACC-24241, ACC-24244, ACC-24233, ACC-24423 and ACC-24224 have maximum genetic distance. Accessions ACC-24879 and ACC-24169 had minimum genetic distance i.e., 0.26. Dendrogram based on genetic distances showed four main clusters that were further dividing into several sub-clusters. The primers utilized in the present study, were valuable to identify different accessions of canola to find the variability present. This variability will be helpful to initiate the breeding program with their molecular genetic basis.

Molecular Characterization and Genetic Diversity Study in F3 Population of Rice

2013 ◽  
Vol 20 (1-2) ◽  
pp. 1-8
Author(s):  
MM Rahman ◽  
L Rahman ◽  
SN Begum ◽  
F Nur
Keyword(s):  
Genetic Distance ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Polymorphic Loci ◽  
Rice Genotypes ◽  
High Level ◽  
Genetic Diversity Study ◽  
Diversity Study

Random Amplified Polymorphic DNA (RAPD) assay was initiated for molecular genetic analysis among 13 F3 rice lines and their parents. Four out of 15 decamer random primers were used to amplify genomic DNA and the primers yielded a total of 41 RAPD markers of which 37 were considered as polymorphic with a mean of 9.25 bands per primer. The percentage of polymorphic loci was 90.24. The highest percentage of polymorphic loci (14.63) and gene diversity (0.0714) was observed in 05-6 F3 line and the lowest polymorphic loci (0.00) and gene diversity (0.00) was found in 05-12 and 05-15 F3 lines. So, relatively high level of genetic variation was found in 05-6 F3 line and it was genetically more diverse compared to others. The average co-efficient of gene differentiation (GST) and gene flow (Nm) values across all the loci were 0.8689 and 0.0755, respectively. The UPGMA dendrogram based on the Nei’s genetic distance differentiated the rice genotypes into two main clusters: PNR-519, 05-19, 05-14, 05-12 and 05-17 grouped in cluster 1. On the other hand, Baradhan, 05-9, 05-13, 05-11, 05-5, 05-6, 05-1, 05-4, 05-15 and 05-25 were grouped in cluster 2. The highest genetic distance (0.586) was found between 05-4 and 05-17 F3 lines and they remain in different cluster.DOI: http://dx.doi.org/10.3329/pa.v20i1-2.16839 Progress. Agric. 20(1 & 2): 1 – 8, 2009

scholarly journals Genetic distance as an alternative to physical distance for definition of gene units in association studies

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 408 ◽  
Author(s):  
Cristina Rodriguez-Fontenla ◽  
Manuel Calaza ◽  
Antonio Gonzalez
Keyword(s):  
Genetic Distance ◽  
Association Studies ◽  
Physical Distance ◽  
Definition Of

scholarly journals Genetic Variation Among Colletotrichum graminicola Isolates from Four Hosts Using Isozyme Analysis

Plant Disease ◽  
2004 ◽  
Vol 88 (4) ◽  
pp. 402-406 ◽  
Author(s):  
B. J. Horvath ◽  
J. M. Vargas
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Geographic Origin ◽  
Creeping Bentgrass ◽  
Genetic Distances ◽  
Colletotrichum Graminicola ◽  
Annual Bluegrass ◽  
Close Relationship ◽  
Host Origin ◽  
Serious Disease

Anthracnose basal rot (ABR) is a serious disease of turfgrasses that is caused by the pathogen Colletotrichum graminicola. The relationships of isolates causing ABR on turfgrasses to those causing disease on important crop hosts (maize, sorghum) remain unresolved. Genetic variation among isolates from annual bluegrass, creeping bentgrass, maize, and sorghum was evaluated based on host origin and geographic origin. Isozymes were used to estimate the genetic variation of the isolates. Five enzyme systems comprising 16 alleles from 5 loci were used. Allele frequencies, genetic distance, and linkage disequilibrium values were calculated for isolates based on both host and geographic origin. Isolates from creeping bentgrass and annual bluegrass were the most closely related based on Nei's genetic distance, while isolates from maize and sorghum were the most distantly related, consistent with their known species-level relationship. Isolates from annual bluegrass and creeping bentgrass had different genetic distances to isolates from both maize and sorghum. Annual bluegrass isolates from different geographic regions had the smallest genetic distance values observed in this study, indicating a very close relationship regardless of geographic origin. Based on these data, it appears that host origin, not geographic origin, plays a more important role in the genetic diversity of these fungi.

Ampelographic characterization of white grapevine cul-tivars (Vitis vinifera L.) grown in Palestine

2015 ◽  
Vol 3 (1) ◽  
pp. 1-11
Author(s):  
Rezq Basheer-Salimia
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Vitis Vinifera L ◽  
Similarity Matrix ◽  
Breeding Programs ◽  
Local Varieties ◽  
Synonymies And Homonymies

Abstract: In Palestine, grape culture consists of ecotypes and cultivars (also called local varieties), for which a large number of homonymous and synonymous designations exist as well as misnaming of cultivars. The present study is the first report using detailed ampelographic characterizations (39 informative traits) to assess genetic diversity and detect similarities among sixteen accessions collected from putative diverse grape genotypes In general, 30 descriptors presented highly and satisfactory divergent genotypes, whereas the remaining traits showed no or very little ampelographic variation. Based on the similarity matrix and the resulting dendrogram of these ampelographic data, distinguishable genotypes as well as some cases of synonymies and homonymies clearly exist. A synonymy case seemed to be in four genotypes including Jandali-Mfarad, Jan-dali-Mrazraz, Jandali, and Hamadani-Mattar, which indeed showed genetic distances of less than 0.5, sug-gesting their relatedness, and the possibility that they are the same genotype, but with different names. In addition, homonym cases also occur in the following pairs of “Marawi’s, Hamadani’s, and Zaini’s genotypes, in which each pair seems to be two distinctive genotypes. Finally, among the 16 examined genotypes, the Zaini-Baladi genotype tended to show the highest genetic distance values from the others and thus could be potentially incorporated into any further local or regional breeding programs as well as germplasm conservation.

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