Interpopulation Relationships Research Articles

Влияние экологических факторов на генетический полиморфизм в природных популяциях Fragaria vesca

Genetic polymorphism of natural cenopopulations of wild strawberry (Fragaria vesca) from the Republic of Mari El was measured by randomly amplified polymorphic DNA (RAPD). The method of molecular genome marking based on RAPD-PCR makes it possible to determine the genetic status of populations and establish interpopulation relationships. The cenopopulations that we selected for the analysis were confined to different stages of the forest phytocenosis succession: the climatic phytocenosis and the area of the forest felling. These F. vesca cenopopulations differed in the ratio of sexual and vegetative reproduction during the maintenance of the cenopopulation size. In a felling area in conditions of greater illumination the intensity of sexual and vegetative reproduction increases. However, specimens of seed origin were not found in the felling area, since in conditions of high competition with ruderal and meadow plants, slowly developing strawberry seedlings died. The germination of seeds and plants of seed origin was noted under conditions of climatic phytocenosis. For the cenopopulation confined to the climax forest, Shannon’s diversity index and Nei’s genetic distance were 0.5179 and 0.3613 respectively. In a felling area vegetative reproduction processes predominate, so Shannon’s diversity index and Nei’s genetic distance were lower, 0.4573 and 0.3132 respectively. In a felling area revealed the loss of certain genetic clusters present in the climax forest. This indicates the loss of a strawberry genetic diversity in the transition to vegetative reproduction due to anthropogenic impact. Our data confirm the idea that climax communities with their more stable conditions can act as regenerative niches of the species.

Morphometric variability of Praomys misonnei (Rodentia: Muridae) in west central African forests reveals complex relationships between populations

This study addresses the morphological biometrics of Praomys misonnei and the signatures of its population history through a survey of external morphological characters measured on 133 individuals from eight West Central African (Gabon and Cameroon) localities. Four standard external characters were measured: head + body length, tail length, hindfoot length, and ear length. Using univariate and multivariate statistics, we inferred inter-population relationships from these morphometric characteristics and tested hypotheses of historical patterns of local adaptation (phylogenetic relationships) or of association with ecological gradients. We also tested the influence of sex on morphometric parameters. Our results support the existence of two morphometrically distinct groups of P. misonnei. The first one includes individuals from northern, central, and southern Gabon, while the second one includes individuals from southern Cameroon and one locality in southern Gabon (Mbaya). This result could be explained by the fact that the first group inhabits an area mainly covered by dense rainforest (about 90% of Gabon), while the second group is found in degraded forest or mosaics of forest-savanna habitats (Cameroon and southeastern Gabon). Another reason could be seasonal reversal, which has been postulated right at border between Gabon and Cameroon. The pattern of morphometric variation was correlated with local environmental factors. No sexual dimorphism was recorded.

Influence of genetic substructuring of statistical forensic parameters on genetic short tandem repeat markers in the populations of Southeastern Europe

AimTo investigate the influence of specific intrapopulation genetic structures on interpopulation relationships. Special focus was the influence of island population isolation on the substructuring of the Croatian population, and the influence of regional population groups on the substructuring of Southeast European populations.MethodsAutosomal short tandem repeat (STR) loci were analyzed by using four forensic parameters: matching probability (PM), power of discrimination (PD), power of exclusion (PE), and polymorphic information content (PIC) on a sample of 2877 unrelated participants of both sexes. A sample set comprising 590 participants was analyzed for the first time, and 2287 participants were included from previous studies. The analysis was performed with PowerStats v. 1.2.ResultsThe analysis of forensic parameters for all nine loci in the Croatian subpopulations showed the largest deviations in the populations of the islands of Korčula and Hvar. The smallest deviations were found in the mainland population. As for Southeast European populations, the largest deviations were found in the population of North Macedonia, followed by Romania, Albanians from Kosovo, and Montenegro, while the smallest deviations were found in the population of Hungary.ConclusionThe comparison of forensic parameters between different subpopulations of Croatia and Southeast Europe indicates that the isolation of individual Croatian subpopulations and rare alleles in their gene pool affect the values of forensic parameters. Specific features of (sub)populations should be taken into account for appropriate sampling of the total population when creating a DNA database of STR markers.

Microsatellite based genetic diversity of Mediterranean fruit fly(Ceratitis capitata, Diptera: Tephritidae) populations from Southwest Turkey

Various pests cause economic losses in some agricultural products, especially in citrus fruits, which are grown in many countries and have a very important role in consumption and export. The Mediterranean fruit fly, Ceratitis capitata Wied. (Diptera: Tephritidae), which spreads throughout the Mediterranean basin, Europe, the Middle East, Central, and South America, and Australia, is considered the most destructive pest in the world. Turkey is an important part of the Eastern Mediterranean basin and, maybe plays a role in the colonization of this pest. This polyphagous species causes huge economic losses by negatively affecting yield and quality in many countries. In this study, population genetic structure and inter-population relationships of the Mediterranean fruit fly were studied by using eight microsatellite markers sampled from the Mediterranean and Aegean regions of Turkey. The results represent a high level of genetic diversity in the Mediterranean fruit fly populations in Turkey and there is no geographical clustering observed when the populations are evaluated in the geographical sense. As a result of the study for 7 provinces, the average number of alleles (n$_{a}$) was 6.95, the average number of effective alleles (n$_{e}$) was 3.58, the observed (H$_{o}$) and expected (H$_{e}$) heterozygosity values were 0.61 and 0.67, respectively. The gene flow (Nem) level among populations was found as Nem = 1.13. Higher genetic diversity values point out that Turkey may have an important role in the colonization of this organism.

Mitochondrial Sequence Variation, Haplotype Diversity, and Relationships Among Dromedary Camel-Types.

Dromedary camels are outstanding livestock that developed efficient abilities to tolerate desert conditions. Many dromedary camel-types (i.e., named populations) exist but lack defined specific breed standards, registries, and breeders’ governing organizations. The breed status of dromedary camel-types can partly be assessed by exploring mitochondrial DNA (mtDNA) variation. Accordingly, this study aimed to examine the breed status and the inter-population relationships of dromedary camel-types by analyzing sequence variation in the mtDNA control region and in three coding genes [cytochrome b, threonine, and proline tRNA, and part of the displacement loop (D-loop)] (867 bp region). Tail hair samples (n = 119) that represent six camel-types from Kuwait were collected, extracted, sequenced, and compared to other publicly available sequences (n = 853). Within the sequenced mitochondrial region, 48 polymorphic sites were identified that contributed to 82 unique haplotypes across 37 camel-types. Haplotype names and identities were updated to avoid previous discrepancies. When all sequences were combined (n = 972), a nucleotide diversity of 0.0026 and a haplotype diversity of 0.725 was observed across the dromedary-types. Two major haplogroups (A and B) were identified and the B1 haplotype was predominant and found in almost all dromedary-types whereas the A haplotypes were more abundant in African regions. Non-metric multidimensional scaling revealed an increased similarity among Arabian Peninsula “Mezayen” camel-types, despite their defining coat colors. The relationships among dromedary camel-types can partly be explained by mtDNA. Future work aimed at a deeper understanding of camel-type breed status should focus on a high number of nuclear markers.

Expanding the Geographic Characterisation of Epstein-Barr Virus Variation through Gene-Based Approaches.

The Epstein–Barr Virus (EBV) infects the vast majority of human individuals worldwide (~90%) and is associated with several diseases, including different types of cancer and multiple sclerosis, which show wide variation in incidence among global geographical regions. Genetic variants in EBV genomic sequences have been used to determine the geographical structure of EBV isolates, but our understanding of EBV diversity remains highly incomplete. We generated sequences for 13 pivotal EBV genes derived from 103 healthy individuals, expanding current EBV diversity datasets with respect to both geographic coverage and number of isolates per region. These newly generated sequences were integrated with the more than 250 published EBV genomes, generating the most geographically comprehensive data set of EBV strains to date. We report remarkable variation in single-gene phylogenies that, when analysed together, show robust signals of population structure. Our results not only confirm known major global patterns of geographic variation, such as the clear separation of Asian isolates from the rest, and the intermixed relationships among African, European and Australian isolates, but yield novel phylogenetic relationships with previously unreported populations. We provide a better understanding of EBV’s population structure in South America, Africa and, by the inclusion of Turkey and Georgia, we also gain insight into EBV diversity in Western Asia, a crossroads connecting Europe, Africa and Asia. In summary, our results provide a detailed world-wide characterisation of EBV genetic clusters, their enrichment in specific geographic regions, novel inter-population relationships, and a catalogue of geographically informative EBV genetic variants.

Genetic diversity and relationship among indigenous Turkish Karayaka sheep subpopulations.

The Karayaka is the most populous sheep breed in the Black Sea region of Turkey. In the present study, we investigated the intra- and inter-population genetic relationships among indigenous Karayaka sheep subpopulations. Nine microsatellites were genotyped for 64 individuals from Samsun, Ordu, Giresun and Tokat provinces. The average number of alleles (), allelic richness (), observed heterozygosity (), expected heterozygosity (), polymorphism information content (PIC) and inbreeding coefficient () for all subpopulations were estimated as , , , , and , respectively. The observed and expected heterozygosity ranged from 0.171 (Giresun) to 0.376 (Ordu) and 0.757 (Samsun) to 0.845 (Ordu), respectively. It was determined that a 10.5 % of total genetic variation ( %) in Karayaka sheep corresponded to genetic differences among subpopulations (), whereas 63.0 % was explained by genetic difference among individuals (). This study gives the first evidence about genetic relationships of Karayaka subpopulations. The results show that Karayaka sheep subpopulations are genetically different from each other. These findings revealed that the Karayaka breed has discrete subpopulations and should be taken into consideration when preparing conservation programs and future breeding strategies.

The biogeography of Elaphe sauromates (Pallas, 1814), with a description of a new rat snake species.

BackgroundThe rat snake genus Elaphe once comprised several dozens of species distributed in temperate through tropical zones of the New and Old World. Based on molecular-genetic analyses in early 2000s, the genus was split into several separate genera, leaving only 15 Palearctic and Oriental species as its members. One of the three species also occurring in Europe is Elaphe sauromates, a robust snake from the Balkans, Anatolia, Caucasus, Ponto-Caspian steppes, and Levant that has been suspected to be composed of two or more genetically diverse populations. Here, we studied the genetic structure and morphological variation of E. sauromates, aiming to better understand its inter-population relationships and biogeography, and subsequently revise its taxonomy.MethodsWe reconstructed the phylogeography and analyzed the genetic structure of E. sauromates populations originating from most of its geographic range using both mitochondrial (COI, ND4) and nuclear (C-MOS, MC1R, PRLR, RAG1) DNA gene fragments. We employed Maximum likelihood and Bayesian inference methods for the phylogenetic tree reconstructions, supplemented with species delimitation methods, analysis of haplotype networks, and calculation of uncorrected p-distances. Morphological variation in 15 metric and 18 meristic characters was studied using parametric univariate tests as well as multivariate general linearized models. In total, we analyzed sequences originating from 63 specimens and morphological data from 95 specimens of E. sauromates sensu lato.ResultsThe molecular phylogeny identified two clearly divergent sister lineages within E. sauromates, with both forming a lineage sister to E. quatuorlineata. The genetic distance between them (5.80–8.24% in mtDNA) is similar to the distances among several other species of the genus Elaphe. Both lineages are also moderately morphologically differentiated and, while none of the characters are exclusively diagnostic, their combination can be used for confident lineage identification. Here, following the criteria of genetic and evolutionary species concepts, we describe the lineage from eastern Anatolia and parts of the Lesser and Great Caucasus as a new species E. urartica sp. nov.DiscussionElaphe urartica sp. nov. represents a cryptic species whose ancestors presumably diverged from their common ancestor with E. sauromates around the Miocene-Pliocene boundary. The intraspecific genetic structure indicates that the recent diversity of both species has been predominantly shaped by Pleistocene climatic oscillations, with glacial refugia mainly located in the Balkans, Crimea, and/or Anatolia in E. sauromates and Anatolia and/or the Caucasus in E. urartica sp. nov.

Evaluating sample size to estimate genetic management metrics in the genomics era.

Inbreeding and relationship metrics among and within populations are useful measures for genetic management of wild populations, but accuracy and precision of estimates can be influenced by the number of individual genotypes analysed. Biologists are confronted with varied advice regarding the sample size necessary for reliable estimates when using genomic tools. We developed a simulation framework to identify the optimal sample size for three widely used metrics to enable quantification of expected variance and relative bias of estimates and a comparison of results among populations. We applied this approach to analyse empirical genomic data for 30 individuals from each of four different free-ranging Rocky Mountain bighorn sheep (Ovis canadensis canadensis) populations in Montana and Wyoming, USA, through cross-species application of an Ovine array and analysis of approximately 14,000 single nucleotide polymorphisms (SNPs) after filtering. We examined intra- and interpopulation relationships using kinship and identity by state metrics, as well as FST between populations. By evaluating our simulation results, we concluded that a sample size of 25 was adequate for assessing these metrics using the Ovine array to genotype Rocky Mountain bighorn sheep herds. However, we conclude that a universal sample size rule may not be able to sufficiently address the complexities that impact genomic kinship and inbreeding estimates. Thus, we recommend that a pilot study and sample size simulation using R code we developed that includes empirical genotypes from a subset of populations of interest would be an effectiveapproach to ensure rigour in estimating genomic kinship and population differentiation.

Massively parallel sequencing of 124 SNPs included in the precision ID identity panel in three East Asian minority ethnicities

Massively parallel sequencing (MPS) technologies can sequence many targeted regions of multiple samples simultaneously and are gaining great interest in the forensic community. The Precision ID Identity Panel contains 90 autosomal SNPs and 34 upper Y-Clade SNPs, which was designed with small amplicons and optimized for forensic degraded or challenging samples. Here, 184 unrelated individuals from three East Asian minority ethnicities (Tibetan, Uygur and Hui) were analyzed using the Precision ID Identity Panel and the Ion PGM System. The sequencing performance and corresponding forensic statistical parameters of this MPS-SNP panel were investigated. The inter-population relationships and substructures among three investigated populations and 30 worldwide populations were further investigated using PCA, MDS, cladogram and STRUCTURE. No significant deviation from Hardy-Weinberg equilibrium (HWE) and Linkage Disequilibrium (LD) tests was observed across all 90 autosomal SNPs. The combined matching probability (CMP) for Tibetan, Uygur and Hui were 2.5880 × 10−33, 1.7480 × 10−35 and 4.6326 × 10−34 respectively, and the combined power of exclusion (CPE) were 0.999999386152271, 0.999999607712827 and 0.999999696360182 respectively. For 34 Y-SNPs, only 16 haplogroups were obtained, but the haplogroup distributions differ among the three populations. Tibetans from the Sino-Tibetan population and Hui with multiple ethnicities with an admixture population have genetic affinity with East Asian populations, while Uygurs of a Eurasian admixture population have similar genetic components to the South Asian populations and are distributed between East Asian and European populations. The aforementioned results suggest that the Precision ID Identity Panel is informative and polymorphic in three investigated populations and could be used as an effective tool for human forensics.

Endemic course of epidemic diarrhea of pigs in the stabilized focus of infection

Porcine epidemic diarrhea virus (PEDV) has been circulating in Ukraine since 2014 and induces an especially dangerous viral infection with a lethal diarrheal syndrome in newborn piglets, with the initial appearance at the focus of infection. The number of infected cases and lethality among diseased piglets of 1–5 days of age can reach 100%, which together with the forced anti-epizootic measures brings significant economic losses. PED can spread to all pigs, but the emergent quality of infectious pathology appears in newborn piglets. No effective and biologically safe means of specific antiviral prophylaxis, which substantially halts the epizootic process is registered, and etiopathogenetic therapy is not developed, therefore PED is an emergent infection which is difficult tocontrol. Over time there appear stationary foci of infection, where evolutionary changes in relationships in the host-parasite system take place fairly rapidly, since pigs are prolific and fast maturing animals able to replace each generation up to three times each year. This leads to a significant variability in interpopulation relationships and the induction of biodiversity in the molecular mechanisms of adaptation and processing of the viral genome. Clinically, genetic modifications of local variants of PEDV – populations are manifested in the form of changes in epizootic peculiarities in the course of infectious pathology in different age groups of animals. Modifications of PEDV may be accompanied by a slight weakening of the intensity of the infectious process, a decrease in mortality and a decrease in the severity of the pathogenesis of diarrheal syndrome. At the same time, the age range of severe abdominal lesions expands from newborn piglets to fattening animals of older age groups of 28, 32, 70 days. Using a set of measures to combat the PED, including “reverse feeding” recycled infected biomaterial from convalescent pigs, eradication of the pathogen from the environment of the host macroorganisms through a total disinfection regime and strict compliance with veterinary and sanitary rules of animal husbandry provide temporary positive results, but in theory this approach is incorrect, since contamination of animals leads to the dispersal of the virus and the formation of endemic foci of infection. The persistence of the virus in convalescent organisms is not fixed, the external inanimate environment can only be a mechanical factor in transmission of the pathogen preserving the viability of PEDV over time. Stabilization of the epizootic foci of infection is possible due to three factors: a) dissemination of the virus in “reverse feeding”; b) preservation of the virus in the external environment as a result of poor-quality disinfection; c) occurrence of a non-immune element among the convalescent young gilts, who as a result of juvenile insufficiency of the immune system have a low titer accumulation of colostral antibodies to the virus received in the biomaterial through reverse feeding. Due to the lack of “lactogenic immunity”, neonatal pigs as biological indicators for the presence of PEDV in the environment begin reproducing the virus in the enterocytes and develop a typical diarrheal syndrome PED.

CYP2D6 in Amerindians from Southern Mexico: low variability and higher frequency of functional alleles

Several functional and nonfunctional CYP2D6 variants have been associated with interindividual and interethnic variability in pharmacological responses. The aim of this article was to study the diversity and the interpopulation relationships of CYP2D6 variants of south Native Mexicans to define predicted phenotypes. A fully systematic review of CYP2D6 variants reported in Amerindian populations before 2015 was performed (NCBI, Google Scholar, and 1000 Genomes Project databases). Allele data were analyzed by methods such as heat map, dissimilarity matrix, dendogram, and principal component analysis using complete-linkage clustering method. Five original studies on CYP2D6 covering 13 Native Mexican populations were identified; three of these described CYP2D6 allele frequencies were in south Native Mexican populations. Overall, CYP2D6 allele variability is scarce in southern Native Mexican populations: besides the functional alleles *1 and *2 and the null variant *4, the other variants have frequencies <0.05. This implies that most of the southern Native Mexican populations may be considered CYP2D6 extended metabolizers. The statistical analyses tend to cluster the native communities by their geographical origin, but in a disperse pattern suggesting distinct subpopulation structures. CYP2D6 functional variants are prevalent in Native Mexicans, and they may be predicted as extended drug metabolizers. In addition, allele frequencies are related to the geographic distribution of the Amerindian groups and display important population stratification.

A new population and habitat for Neotricula aperta in the Mekong river of northeastern Thailand: a DNA sequence-based phylogenetic assessment confirms identifications and interpopulation relationships.

Neotricula aperta (Gastropoda: Pomatiopsidae), the snail intermediate host of Schistosoma mekongi, is found in Cambodia, Laos, and Thailand. We update information on the distribution of this species in the Mekong River and its tributary, the Mun River, in Thailand. DNA sequences of a portion of the mitochondrial cytochrome c oxidase subunit 1 were obtained from N. aperta collected from different locations and used to confirm species and strain identities. Specimens of the β-strain were found in the Mun River, whereas specimens of the γ-strain were found in the Mekong River. The γ-strain (with molecular confirmation of identity) is newly reported from Nong Khai Province, where it occurred in a habitat novel for this species: under paving slabs instead of under natural bed rocks, where agal aufwuchs is extensively located on the islet in the middle of the Mekong River. The new location is approximate 400 km upstream from the nearest previously known site for this species.

Observer error, dental wear, and the inference of new world sundadonty.

Dental morphology provides important information on human evolution and interpopulation relationships. Dental wear is one of the major limitations of morphological data analysis. Wear figures heavily in existing debates about patterns of New World dental variation with some scholars finding evidence for a more generalized dentition in early New World populations (Powell: Doctoral Dissertation, Texas A&M University, TX (1995)) and others questioning these findings based on the probable effects of dental wear on trait scores (Turner, The First Americans: the Pleistocene Colonization of the New World. San Francisco: California Academy of Sciences (2002) 123-158; Turner: Am J Phys Anthropol 130 (2006) 455-461; Turner and Scott, Handbook of paleoanthropology, Vol. III: Phylogeny of Hominids. New York: Springer (2007) 1901-1941). Here we evaluate these competing claims using data from the Early Archaic Windover sample. Results confirm the dental distinctiveness of Windover with respect to other Old World Asian (i.e., sinodont/sundadont) populations. However, comparison of our results to those of Powell (1995) also highlights significant interobserver error. Statistical analysis of matched wear and morphology scores suggests trait downgrading for some traits. Patterns of missing data present a more challenging (and potentially serious) problem. Use of Little's MCAR test for missing data mechanisms indicates a complex process of data collection in which incidental and opportunistic recording of both highly worn and unerupted teeth introduce a "missing not at random" mechanism into our dataset that biases dental trait frequencies. We conclude that patterns of missingness and formal research designs for "planned missingness" are needed to help mitigate this bias.

Isolation and characterization of polymorphic microsatellites in the genome of Yak (Bos grunniens)

The researches on yak genetics and breeding were extremely restricted due to lacking of reliable DNA molecular markers. The microsatellites with repeat motif (AC)n/(GT)n in yak genome were enriched by Dynal magnetic beads and the gene libraries containing (AC)n/(GT)n were constructed. Among the 92 identified and sequenced positive clones, 40 contained perfect repeats (43.48%), 41 contained imperfect repeats (44.57%) and 11 contained compound repeats (11.96%). As compared with the percentage of perfect repeats, no significant increases of imperfect repeats were observed in yak genome, which indicated that the level of adaptive evolution of the ability to repair damaged genomic DNA for yaks were high enough to endure the natural pressure of nucleotide substitution resulted from ultraviolet irradiation in high-altitude areas. Totally 19 polymorphic microsatellite loci were screened and genotyped on the basis of electropherograms on an ABI 310 Genetic Analyzer. All the loci exhibited moderate to high-level polymorphisms in a test population of Bos grunniens and the polymorphic information content ranged from 0.299 to 0.861 (mean 0.678). The newly isolated (AC)n/(GT)n repeats from yak genome will display their potential values in examining intra-population genetic structure and inter-population relationships, and also in investigating molecular markers for production and adaptive traits of individual/population.

Intra- and interpopulation relationships and taxonomic status of Pinus nigra Arnold in Croatia according to morphology and anatomy of needles

Intra- and interpopulational relationships and taxonomic status of six natural black pine populations (&lt;em&gt;Pinus nigra&lt;/em&gt; Arnold) from Croatia were analyzed. Special attention in this research was paid to the establishment of taxonomic status and distribution of stenoendemic Dalmatian black pine (&lt;em&gt;Pinus nigra&lt;/em&gt; Arnold subsp. &lt;em&gt;dalmatica&lt;/em&gt; (Vis.) Franco). Three morphological and twenty-one anatomical traits of needles were used as well as analysis by the methods of multivariate statistics. Most of the researched individuals showed strong population affiliation, whereas a clinal transition of morphological and anatomical traits of needles was determined among the populations. The opinion of the existence of three subspecies of black pine on the territory of Republic of Croatia (&lt;em&gt;Pinus nigra&lt;/em&gt; Arnold subsp. &lt;em&gt;nigra&lt;/em&gt;, &lt;em&gt;Pinus nigra&lt;/em&gt; Arnold subsp. &lt;em&gt;dalmatica&lt;/em&gt; (Vis.) Franco and &lt;em&gt;Pinus nigra&lt;/em&gt; Arnold subsp. &lt;em&gt;illyrica&lt;/em&gt; (Vid.) Fukarek) was confirmed. For each of the three subspecies new ranges were represented. Four Croatian populations were included in the stenoendemic subspecies of the Dalmatian black pine (Brač, Hvar, Grobnik and Pelješac), and a new distribution, broken in two, was suggested. Since the Dalmatian black pine has been reduced to several populations only, and there are some signs of continuous diminishing of its range, this research points out the need of making an action plan to preserve all natural populations of this subspecies.

Evaluating genetic variation and relationships amongPuccinellia nuttallianapopulations using amplified fragment length polymorphism markers

Liu, Y., Fu, Y.-B. and Coulman, B. E. 2013. Evaluating genetic variation and relationships among Puccinellia nuttalliana populations using amplified fragment length polymorphism markers. Can. J. Plant Sci. 93: 1097–1104. Nuttall's salt-meadow, or alkali grass [Puccinellia nuttalliana (Shultes) Hitchc.], is a native grass species in North America, well known for its salt tolerance. Little information is available about the genetic diversity of natural populations of this species. Amplified fragment length polymorphism (AFLP) markers were used to examine the inter-population relationships and to compare variances within and among 23 populations collected from the Canadian Great Plains. Five AFLP primer pairs were employed to screen 15 genotypes (five sets of three half-sib plants) from each population, and 185 polymorphic AFLP bands were scored for each sample. The frequencies of these scored bands ranged from 0.02 to 0.99 with a mean of 0.60. The analysis of molecular variance revealed more than 96% of the total AFLP variation resided within populations. Populations were not highly differentiated with only 4% of the total AFLP variation residing among populations. A Mantel test revealed a significant but low correlation between genetic and geographic distances (r=0.29, P=0.024). Implications for P. nuttalliana conservation, germplasm sampling, and cultivar development are discussed.

Evaluating genetic variation and relationships among Puccinellia nuttalliana populations using amplified fragment length polymorphism markers

Liu, Y., Fu, Y.-B. and Coulman, B. E. 2013. Evaluating genetic variation and relationships amongPuccinellia nuttallianapopulations using amplified fragment length polymorphism markers. Can. J. Plant Sci. 93: 1097-1104. Nuttall's salt-meadow, or alkali grass [Puccinellia nuttalliana (Shultes) Hitchc.], is a native grass species in North America, well known for its salt tolerance. Little information is available about the genetic diversity of natural populations of this species. Amplified fragment length polymorphism (AFLP) markers were used to examine the inter-population relationships and to compare variances within and among 23 populations collected from the Canadian Great Plains. Five AFLP primer pairs were employed to screen 15 genotypes (five sets of three half-sib plants) from each population, and 185 polymorphic AFLP bands were scored for each sample. The frequencies of these scored bands ranged from 0.02 to 0.99 with a mean of 0.60. The analysis of molecular variance revealed more than 96% of the t...

Genetic variability among male populations of a minor mangrove Excoecaria agallocha L. as evident by chromosome morphology and DNA markers

Genetic diversity analysis was done in five male populations of Excoecaria agallocha L. (Family Euphorbiaceae) obtained from east coast of India. Karyotype analysis could not differentiate five male populations studied here which reports high numbers of small sized somatic chromosomes (2n = 130). A total of 303 amplicons were generated from RAPD and ISSR primers of which 43.6% were polymorphic. Cluster analysis obtained from RAPD and ISSR profile exhibited prominent patterns of inter-population relationships. A high degree of genetic divergence was evident among the populations II, IV and V; however, a low genetic variation was detected between populations I and III. A prominent RAPD marker of ∼1,000 bp of population III using OPN-04 primer and two such population specific DNA markers ∼1,100 and ∼2,000 bp with OPD-12 primer could differentiate populations I and III. ISSR 2 primer (CT)8A produced unique bands of ∼650, ∼900 and ∼1,250 bp in populations III, V and I, respectively. ISSR 5 primer (GGAGA)5 separate population III with the help of marker DNA bands of ∼600 and ∼1,200 bp. Population I from Gopalpur and population III from Chilka showed lower genetic divergence as compared to rest of the examined populations (P < 0.05). AMOVA test revealed 23.6% and 53.5% genetic variability among populations and within populations, respectively. Genetic differentiation among the populations from Chandipur (population II), Paradeep (population IV) and Bhitarkanika (population V) were significant. This study suggests that ocean currents, land barriers and limited dispersal ability of seeds play important role in the occurrence of genetic diversity in sexually reproduced and dioeciously represented species E. agallocha.

Morphological and allozymic variation within and between populations of Bythinella Moquin-Tandon, 1855 (Gastropoda: Prosobranchia). II. Phenetic analysis

Phylogenetic relationships among 20 Central European populations of the genus Bythinella have been reconstructed on the basis of morphological characters and allozymic variation presented in our previous papers. Fitch-Margoliash additive trees based on Euclidean distances were constructed for morphological data, and genetic distances (Prevosti, unbiased Nei, Cavalli-Sforza and Edwards arc distances) were computed. Of all the genetic trees which were fairly similar, those based on Cavalli-Sforza and Edwards arc distances seem to reflect the phylogeny best. 21 discrete morphological character states were used to reconstruct phylogenies by means of the parsimony method. Allele frequencies were used directly to compute a tree of interpopulation relationships by means of the frequency-parsimony method. The inferred morphological and allozymic phylogenies differ in their topology and the amount of evolution (measured as the number of changes averaged over all reconstructions) along the corresponding branches; the correlation between them is statistically insignificant. The species rank of most of the postulated morphospecies seems doubtful and requires a further study.