POPTREE2: Software for Constructing Population Trees from Allele Frequency Data and Computing Other Population Statistics with Windows Interface

Takezaki, Naoko; Nei, Masatoshi; Tamura, Koichiro

doi:10.1093/molbev/msp312

Cited by 615 publications

(390 citation statements)

References 13 publications

Supporting

Mentioning

386

Contrasting

Unclassified

Order By: Relevance

“…Consensus DNA contigs from combined forward primer and reverse primer sequencing results were created manually in MEGA (Tamura et al, 2013) (Nei et al, 1983) were prepared in POPTREE2 (Takezaki et al, 2010) with 1000 bootstrap replicates.…”

Section: Discussionmentioning

confidence: 99%

Evolution of nickel hyperaccumulation and serpentine adaptation in the Alyssum serpyllifolium species complex

et al. 2016

View full text Add to dashboard Cite

Metal hyperaccumulation is an uncommon but highly distinctive adaptation found in certain plants that can grow on metalliferous soils. Here we review what is known about evolution of metal hyperaccumulation in plants and describe a population-genetic analysis of the Alyssum serpyllifolium (Brassicaceae) species complex that includes populations of nickelhyperaccumulating as well as non-accumulating plants growing on serpentine (S) and non-serpentine (NS) soils, respectively. To test whether the S and NS populations belong to the same or separate closely related species, we analysed genetic variation within and between four S and four NS populations from across the Iberian peninsula. Based on microsatellites, genetic variation was similar in S and NS populations (average H o = 0.48). The populations were significantly differentiated from each other (overall F ST = 0.23), and the degree of differentiation between S and NS populations was similar to that within these two groups. However, high S versus NS differentiation was observed in DNA polymorphism of two genes putatively involved in adaptation to serpentine environments, IREG1 and NRAMP4, whereas no such differentiation was found in a gene (ASIL1) not expected to play a specific role in ecological adaptation in A. serpyllifolium. These results indicate that S and NS populations belong to the same species and that nickel hyperaccumulation in A. serpyllifolium appears to represent a case of adaptation to growth on serpentine soils. Further functional and evolutionary genetic work in this system has the potential to significantly advance our understanding of the evolution of metal hyperaccumulation in plants.

show abstract

Section: Discussionmentioning

confidence: 99%

Evolution of nickel hyperaccumulation and serpentine adaptation in the Alyssum serpyllifolium species complex

et al. 2016

View full text Add to dashboard Cite

show abstract

“…I analyzed relationships among populations by constructing a neighbor-joining tree with 1000 bootstrap replicates using the DA measure of genetic distance (Nei et al 1983) in the program POPTREE2 (Takezaki et al 2010). …”

Section: Microsatellite Marker Amplification (I III Iv)mentioning

confidence: 99%

Influences of geographic differentiation in the forewing warning signal of the wood tiger moth in Alaska

Hegna

Mappes

2014

Evol Ecol

View full text Add to dashboard Cite

Geographic Variation in the WarningSignals of the Wood Tiger Moth (Parasemia plantaginis; Arctiidae)Esitetään Jyväskylän yliopiston matemaattis-luonnontieteellisen tiedekunnan suostumuksella julkisesti tarkastettavaksi yliopiston Ylistönrinteellä, salissa YAA303 marraskuun 8. päivänä 2013 kello 12.Academic dissertation to be publicly discussed, Warning signals are not expected to be diverse because they are under stabilizing selection. This dissertation aims to study historic and contemporary selection mechanisms underlying the geographic warning signal diversity in the wood tiger moth (Parasemia plantaginis). In the first study, I explored the variation in hindwing warning color frequencies across the distribution of P. plantaginis and the phylogeography of the species. Males have polymorphic hindwing color (yellow or white) across much of their distribution but turn reddish in the Caucasus and mostly white in Japan, which coincide with mitogenetic divergence. Females vary continuously in hindwing warning color between yellow and red, becoming yellow east of the Ural mountain range, but does not correspond to mitogenetic divergence. Post-glacial isolation may be one contributing factor to the genetic divergence and the hindwing warning signal differences in the Caucasus region. In the second study, I found that thermoregulation benefits of melanin can trade-off with a larger more effective warning signal, which contributes to variation in melanization within Europe. In the third study, I found that forewing patterns function as warning signals and that generalization by predators might play an important role in warning signal diversity along with frequency dependent selection. In the fourth chapter, I found three populations in Japan differing in warning signal traits with some gene flow suggesting both selection and isolation may be underlying causes. Overall, my results suggest that historical and abiotic factors contribute to the observed warning signal diversity in P. plantaginis, rather than predation alone. This adds to our understanding of how historical factors along with environmental heterogeneity in biotic and abiotic factors can promote warning signal diversity. My results highlight the need to take an integrated approach to studying geographic diversity in warning signals.

show abstract

“…Bootstrap tests (Felsenstein 1985) were performed using 1000 replicates with the POPTREE2 software (Takezaki et al 2010). Phylogenetic relationships were depicted as an unrooted tree and visualized with MEGA 5 (Tamura et al 2011).…”

Section: Characterization Of Local Fruitsmentioning

confidence: 99%

Genetic characterization of chestnut (Castanea sativa Mill.) orchards and traditional nut varieties in El Bierzo, a glacial refuge and major cultivation site in northwestern Spain

Quintana

Contreras

Merino

et al. 2014

Tree Genetics & Genomes

View full text Add to dashboard Cite

This paper presents a detailed genetic study of Castanea sativa in El Bierzo, a major nut production region with interesting features. It is located within a glacial refuge at one extreme of the distribution area (northwest Spain); it has a centenary tradition of chestnut management; and more importantly, it shows an unusual degree of genetic isolation. Seven nuclear microsatellite markers were selected to analyze the genetic variability and structure of 169 local trees grafted for nut production. We analyzed in the same manner 62 local nuts. The selected loci were highly discriminant for the genotypes studied, giving a combined probability of identity of 6.1 x 10~6. An unprecedented density of trees was sampled for this project over the entire region, and nuts were collected representing 18 cultivars marketed by local producers. Several instances of misclassification by local growers were detected. Fixation index estimates and analysis of molecular variance (AMOVA) data are supportive of an unexpectedly high level of genetic differentiation in El Bierzo, larger than that estimated in a previous study with broader geographical scope but based on limited local sampling (Pereira-Lorenzo et al., Tree Genet Genomes 6: 701-715, 2010a). Likewise, we have determined that clonality due to grafting had been previously overestimated. In line with these observations, no significant spatial structure was found using both a modelbased Bayesian procedure and Mantel's tests. Taken together, our results evidence the need for more fine-scale genetic studies if conservation strategies are to be efficiently improved.

show abstract

POPTREE2: Software for Constructing Population Trees from Allele Frequency Data and Computing Other Population Statistics with Windows Interface

Cited by 615 publications

References 13 publications

Evolution of nickel hyperaccumulation and serpentine adaptation in the Alyssum serpyllifolium species complex

Evolution of nickel hyperaccumulation and serpentine adaptation in the Alyssum serpyllifolium species complex

Influences of geographic differentiation in the forewing warning signal of the wood tiger moth in Alaska

Genetic characterization of chestnut (Castanea sativa Mill.) orchards and traditional nut varieties in El Bierzo, a glacial refuge and major cultivation site in northwestern Spain

Contact Info

Product

Resources

About