A similar phylogeographical structure among sympatric North American birches (Betula) is better explained by introgression than by shared biogeographical history

AimA comparative analysis of the chloroplast (cp) DNA structure of eastern North American birches (Betula) was undertaken to infer the impacts of Quaternary climate change on the phylogeographical structure of these species.LocationEastern North America.MethodsGenetic variation in chloroplast microsatellites (cpSSRs) and the psbA–trnH intergenic spacer in Betula papyrifera, Betula alleghaniensis and Betula lenta was analysed in samples from 65, 80 and 12 populations, respectively. Co‐occurring Betula uber, Betula populifolia and Betula cordifolia were also sampled to examine haplotype relationships and account for potential introgression. Haplotype networks, Bayesian analysis and comparisons of RST and GST values were used to evaluate the phylogeographical structure. Genetic diversity within and among species was compared using rarefaction analysis.ResultsThe two most widespread species, B. papyrifera and B. alleghaniensis, showed high levels of haplotype diversity, while the Appalachian endemic B. lenta possessed a single haplotype. Bayesian analysis revealed three main phylogeographical groups for B. papyrifera and four groups for B. alleghaniensis, and these two species showed extensive regional haplotype sharing and a high introgression ratio.Main conclusionsWe postulate that at least three separate refugia contributed to the recolonization of B. papyrifera and B. alleghaniensis within eastern North America, while B. lenta appears to have recolonized from a single refugium. A high haplotype diversity of B. papyrifera and B. alleghaniensis in the Great Lakes region may reflect biogeographical contact between eastern and western lineages, with the potential influence of periglacial refugia. Similar phylogeographical patterns in the distantly related B. papyrifera and B. alleghaniensis represent a geographical turnover of the same locally shared haplotypes, pointing to introgression rather than shared biogeographical history as the mechanism. Although similar phylogeographical patterns are often interpreted as evidence for common biogeographical histories, our study demonstrates that such patterns can also arise through introgression.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110577/1/jbi12394.pd

Phylogeny of Populus (Salicaceae) based on nucleotide sequences of chloroplast TRNT-TRNF region and nuclear rDNA

The species of the genus Populus, collectively known as poplars, are widely distributed over the northern hemisphere and well known for their ecological, economical, and evolutionary importance. The extensive interspecific hybridization and high morphological diversity in this group pose difficulties in identifying taxonomic units for comparative evolutionary studies and systematics. To understand the evolutionary relationships among poplars and to provide a framework for biosystematic classification, we reconstructed a phylogeny of the genus Populus based on nucleotide sequences of three noncoding regions of the chloroplast DNA (intron of trnL and intergenic regions of trnT-trnL and trnL-trnF) and ITS1 and ITS2 of the nuclear rDNA. The resulting phylogenetic trees showed polyphyletic relationships among species in the sections Tacamahaca and Aigeiros. Based on chloroplast DNA sequence data, P. nigra had a close affinity to species of section Populus, whereas nuclear DNA sequence data suggested a close relationship between P. nigra and species of the section Aigeiros, suggesting a possible hybrid origin for P. nigra. Similarly, the chloroplast DNA sequences of P. tristis and P. szechuanica were similar to that of the species of section Aigeiros, while the nuclear sequences revealed a close affinity to species of the section Tacamahaca, suggesting a hybrid origin for these two Asiatic balsam poplars. The incongruence between phylogenetic trees based on nuclear- and chloroplast-DNA sequence data suggests a reticulate evolution in the genus Populus

Microsatellite analysis reveals genetically distinct populations of red pine (Pinus resinosa, Pinaceae)

Red pine (Pinus resinosa Ait.) is an ecologically and economically important forest tree species of northeastern North America and is considered one of the most genetically depauperate conifer species in the region. We have isolated and characterized 13 nuclear microsatellite loci by screening a partial genomic library with di-, tri-, and tetranucleotide repeat oligonucleotide probes. In an analysis of over 500 individuals representing 17 red pine populations from Manitoba through Newfoundland, five polymorphic microsatellite loci with an average of nine alleles per locus were identified. The mean expected and observed heterozygosity values were 0.508 and 0.185, respectively. Significant departures from Hardy-Weinberg equilibrium with excess homozygosity indicating high levels of inbreeding were evident in all populations studied. The population differentiation was high with 28–35% of genetic variation partitioned among populations. The genetic distance analysis showed that three northeastern (two Newfoundland and one New Brunswick) populations are genetically distinct from the remaining populations. The coalescence-based analysis suggests that "northeastern" and "main" populations likely became isolated during the most recent Pleistocene glacial period, and severe population bottlenecks may have led to the evolution of a highly selfing mating system in red pine

Patterns of nucleotide diversity and phenotypes of two domestication related genes (OsC1 and Wx) in indigenous rice varieties in Northeast India

Background During the domestication of crops, individual plants with traits desirable for human needs have been selected from their wild progenitors. Consequently, genetic and nucleotide diversity of genes associated with these selected traits in crop plants are expected to be lower than their wild progenitors. In the present study, we surveyed the pattern of nucleotide diversity of two selected trait specific genes, Wx and OsC1, which regulate amylose content and apiculus coloration respectively in cultivated rice varieties. The analyzed samples were collected from a wide geographic area in Northeast (NE) India, and included contrasting phenotypes considered to be associated with selected genes, namely glutinous and nonglutinous grains and colored and colorless apiculus. Results No statistically significant selection signatures were detected in both Wx and OsC1gene sequences. However, low level of selection that varied across the length of each gene was evident. The glutinous type varieties showed higher levels of nucleotide diversity at the Wx locus (πtot = 0.0053) than nonglutinous type varieties (πtot = 0.0043). The OsC1 gene revealed low levels of selection among the colorless apiculus varieties with lower nucleotide diversity (πtot = 0.0010) than in the colored apiculus varieties (πtot = 0.0023). Conclusions The results revealed that functional mutations at Wx and OsC1genes considered to be associated with specific phenotypes do not necessarily correspond to the phenotypes in indigenous rice varieties in NE India. This suggests that other than previously reported genomic regions may also be involved in determination of these phenotypes. PMID:2493534

Conservation of microsatellites among tropical trees (Leguminosae)

Although microsatellites or simple sequence repeats (SSRs) have become a popular tool in genetic mapping and gene flow studies, their utility is limited due to paucity of information about DNA sequences in plants. We tested the utility of microsatellite markers characterized for the tropical tree Pithecellobium elegans as a genetic tool for related species. The results indicate that SSR loci are conserved among closely related species, and SSR primers developed for P. elegans could be successfully used as a genetic tool in several species of the tribe Ingeae. This study indicates that there is high potential for the transfer of SSR markers among closely related taxa, circumventing laborious cloning and screening procedures involved in characterizing SSR loci for many species

Functional Androdioecy in Critically Endangered Gymnocladus assamicus (Leguminosae) in the Eastern Himalayan Region of Northeast India

Gymnocladus assamicus is a critically endangered tree species endemic to Northeast India, and shows sexual dimorphism with male and hermaphrodite flowers on separate trees. We studied phenology, reproductive biology and mating system of the species. The flowers are small, tubular, odorless and last for about 96 hours. Pollen grains in both morphs were viable and capable of fertilization leading to fruit and seed set. Scanning electron micrographs revealed morphologically similar pollen in both male and hermaphrodite flowers. The fruit set in open pollinated flowers was 43.61 percent, while controlled autogamous and geitonogamous pollinations yielded 76.81 and 65.58 percent fruit set respectively. Xenogamous pollinations between male and hermaphrodite flowers resulted in 56.85 percent fruit set and pollinations between hermaphrodite flowers yielded 67.90 percent fruit set. This indicates a functionally androdioecious mating system and pollination limited fruit set in G. assamicus. Phylogenetic analyses of Gymnocladus and the sister genus Gleditsia are needed to assess if the androdioecious mating system in G. assamicus evolved from dioecy as a result of selection for hermaphrodites for reproductive assurance during colonization of pollination limited high altitude ecosystems

Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India

The Eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which may serve as a valuable genetic resource for future crop improvement to meet the ever-increasing demand for food production. However, these varieties are rapidly being lost due to changes in land-use and agricultural practices, which favor agronomically improved varieties. A detailed understanding of the genetic structure and diversity of indigenous rice varieties is crucial for efficient utilization of rice genetic resources and for developing suitable conservation strategies. To explore the genetic structure and diversity of rice varieties in NE India, we genotyped 300 individuals of 24 indigenous rice varieties representing sali, boro, jum and glutinous types, 5 agronomically improved varieties, and one wild rice species (O. rufipogon) using seven SSR markers. A total of 85 alleles and a very high level of gene diversity (0.776) were detected among the indigenous rice varieties of the region. Considerable level of genetic variation was found within indigenous varieties whereas improved varieties were monoporphic across all loci. The comparison of genetic diversity among different types of rice revealed that sali type possessed the highest gene diversity (0.747) followed by jum (0.627), glutinous (0.602) and boro (0.596) types of indigenous rice varieties, while the lowest diversity was detected in agronomically improved varieties (0.459). The AMOVA results showed that 66% of the variation was distributed among varieties indicating a very high level of genetic differentiation in rice varieties in the region. Two major genetically defined clusters corresponding to indica and japonica groups were detected in rice varieties of the region. Overall, traditionally cultivated indigenous rice varieties in NE India showed high levels of genetic diversity comparable to levels of genetic diversity reported from wild rice populations in various parts of the world. The efforts for conservation of rice germplasm in NE India should consider saving rice varieties representing different types with specific emphasis given to sali and jum types. The protection against the loss of vast genetic diversity found in indigenous rice varieties in NE India is crucial for maintaining future food security in the changing world

Genetic structure and diversity of natural and domesticated populations of Citrus medica L. in the Eastern Himalayan region of Northeast India

Citron (Citrus medica L.) is a medicinally important species of citrus native to India and occurs in natural forests and home gardens in the foothills of the eastern Himalayan region of northeast India. The wild populations of citron in the region have undergone rapid decline due to natural and anthropogenic disturbances and most of the remaining individuals of citron are found in fragmented natural forests and home gardens in the region. In order to assess the genetic structure and diversity of citron in wild and domesticated populations, we analyzed 219 individuals of C. medica collected from four wild and eight domesticated populations using microsatellite markers. The genetic analysis based on five polymorphic microsatellite loci revealed an average of 13.40 allele per locus. The mean observed and expected heterozygosity values ranged between 0.220–0.540 and 0.438–0.733 respectively among the wild and domesticated populations. Domesticated populations showed close genetic relationships as compared to wild populations and pairwise Nei’s genetic distance ranged from 0.062 to 2.091 among wild and domesticated populations. Analysis of molecular variance (AMOVA) showed higher genetic diversity among- than within populations. The analysis of population structure revealed five groups. Mixed ancestry of few individuals of different populations revealed exchange of genetic materials among farmers in the region. Citron populations in the region show high genetic variation. The knowledge gained through this study is invaluable for devising genetically sound strategies for conservation of citron genetic resources in the region

Ecological niche modeling for conservation planning of an endemic snail in the verge of becoming a pest in cardamom plantations in the Western Ghats biodiversity hotspot

Conservation managers and policy makers are often confronted with a challenging dilemma of devising suitable strategies to maintain agricultural productivity while conserving endemic species that at the early stages of becoming pests of agricultural crops. Identification of environmental factors conducive to species range expansion for forecasting species distribution patterns will play a central role in devising management strategies to minimize the conflict between the agricultural productivity and biodiversity conservation. Here, we present results of a study that predicts the distribution of Indrella ampulla, a snail endemic to the Western Ghats biodiversity hotspot, which is becoming a pest in cardamom (Ellettaria cardamomum) plantations. We determined the distribution patterns and niche overlap between I. ampulla and Ellettaria cardamomum using maximum entropy (MaxEnt) niche modeling techniques under current and future (2020–2080) climatic scenarios. The results showed that climatic (precipitation of coldest quarter and isothermality) and soil (cation exchange capacity of soil [CEC]) parameters are major factors that determine the distribution of I. ampulla in Western Ghats. The model predicted cardamom cultivation areas in southern Western Ghats are highly sensitive to invasion of I. ampulla under both present and future climatic conditions. While the land area in the central Western Ghats is predicted to become unsuitable for I. ampulla and Ellettaria cardamomum in future, we found 71% of the Western Ghats land area is suitable for Ellettaria cardamomum cultivation and 45% suitable for I. ampulla, with an overlap of 35% between two species. The resulting distribution maps are invaluable for policy makers and conservation managers to design and implement management strategies minimizing the conflicts to sustain agricultural productivity while maintaining biodiversity in the region

Sphaeridiotrema globulus and Sphaeridiotrema pseudoglobulus (Digenea): Species Differentiation Based On mtDNA (Barcode) and Partial LSU–rDNA Sequences

Flukes belonging to Sphaeridiotrema are important parasites of waterfowl, and 2 morphologically similar species Sphaeridiotrema globulus and Sphaeridiotrema pseudoglobulus, have been implicated in waterfowl mortality in North America. Cytochrome oxidase I (barcode region) and partial LSU-rDNA sequences from specimens of S. globulus and S. pseudoglobulus, obtained from naturally and experimentally infected hosts from New Jersey and Quebec, respectively, confirmed that these species were distinct. Barcode sequences of the 2 species differed at 92 of 590 nucleotide positions (15.6%%) and the translated sequences differed by 13 amino acid residues. Partial LSU-rDNA sequences differed at 29 of 1,208 nucleotide positions (2.4%%). Additional barcode sequences from specimens collected from waterfowl in Wisconsin and Minnesota and morphometric data obtained from specimens acquired along the north shore of Lake Superior revealed the presence of S. pseudoglobulus in these areas. Although morphometric data suggested the presence of S. globulus in the Lake Superior sample, it was not found among the specimens sequenced from Wisconsin or Minnesota