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58 results for “AFLP”
AFLP and MS-AFLP data for Spartina alterniflora and Borrichia frutescens collected from three habitats (i.e. low, medium, and high salt) within five sites, respectively, on Sapelo Island, GA in May 2011
Using amplified fragment length polymorphism (AFLP) and methylation sensitive (MS)-AFLP we assessed genetic and epigenetic variation in two salt marsh perennials, Spartina alterniflora and Borrichia frutescens, in Sapelo Island, Georgia. We sampled Apex (A), Cabretta (C), Hunt Camp (H), Lighthouse (L), and Marsh Landing (M) for S. alterniflora, and C, H, L, M, and Shell Hammock for B. frutescens due to site specific differences in species among the sites. We tested the hypothesis that populatation structure at the habitat level would be due to epigenetic loci and not genetic. The presence and absence AFLP bands and MS-AFLP methylation respresents a genome-wide snapsnot of variation within individuals. We used hierarchical AMOVAs, permutational MANOVA, Bayesian clustering (genetic only), Mantel and partial Mantel tests, and generalized linear models to assess the spatial structure of genetic and epigenetic variation among our two study organisms across five sites for each organism. (Note: genetic and habitat distance tables were normalized for database compatibility. These data must be formatted as a square dissimilarity matrix for input to the code files.)
AFLP and geometric morphometrics for Littorina fabalis
<p>Low dispersal marine intertidal species facing strong divergent selective pressures associated with steep environmental gradients have a great potential to inform us about local adaptation and reproductive isolation. Among these, gastropods of the genus Littorina offer a unique system to study parallel phenotypic divergence resulting from adaptation to different habitats related with wave exposure. In this study, we focused on two Littorina fabalis ecotypes from Northern European shores and compared the patterns of habitat-related phenotypic and genetic divergence across three different geographic levels (local, regional and global). Geometric morphometric analyses revealed that individuals from habitats moderately exposed to waves usually present a larger shell size with a wider aperture than those from sheltered habitats. The phenotypic clustering of L. fabalis by habitat across most locations (mainly in terms of shell size) support an important role of ecology in morphological divergence. A genome scan based on amplified fragment length polymorphisms (AFLPs) revealed a heterogeneous pattern of differentiation across the genome between populations from the two different habitats, suggesting ecotype divergence in the presence of gene flow. The contrasting patterns of genetic structure between nonoutlier and outlier loci, and the decreased sharing of outlier loci with geographic distance among locations are compatible with parallel evolution of phenotypic divergence, with an important contribution of gene flow and/or ancestral variation. In the future, model-based inference studies based on sequence data across the entire genome will help unravelling these evolutionary hypotheses, improving our knowledge about adaptation and its influence on diversification within the marine realm.</p>
AFLP dataset and sequence alignments from a study of Rhododendron ferrugineum across the whole species range.
<p>STRUCTURE DATASET</p> <p>The raw data are in the files:</p> <ol> <li>Rfe_KAR_AAT-CAC2_2017-10-18-16-55-16.zip</li> <li>Rfe_KAR_ATC-CAC_2017-10-25-12-39-28.zip</li> <li>Rfe_KAR_ATG-CTG2_2017-10-24-09-40-25.zip</li> </ol> <p>Population data: populations.txt</p> <p>The final structure file: Rfe.str</p> <p>We analysed the obtained results in GeneMapper (Applied Biosystems) with default settings for AFLP analysis. The combinations of selective starters amplified the following numbers of polymorphic markers: AAT-CAC=127 (mean=40,4; SD=8,1), ATC-CAC=119 (mean=35,3; SD=5,4), ATG-CTG=144 (mean=44,4; SD=5,0). The blank samples yielded 0, 6 and 5 markers, respectively, which were removed from the final data matrix. We also removed the markers present in only one individual. Three samples (one from each of the populations L22, K27 and S05) failed to amplify in one of the selective primer reactions and were thus removed from the final matrix. The estimated error rate was 2.87% and the final matrix comprises of 87 individuals and 254 polymorphic loci.</p> <p>SEQUENCE ALIGNMENTS</p> <ol> <li>Rfe_ITS_align.fas</li> <li>Rfe_rpl32-trnL_align.fas </li> <li>Rfe_RPS12-RPL20_align.fas </li> <li>Rfe_trnfM-trnS_align.fas </li> <li>Rfe_trnLF_align.fas </li> </ol>
AFLP and geometric morphometrics for Littorina fabalis
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Data from: Comparative analyses of plastid and AFLP data suggest different colonization history and asymmetric hybridisation between Betula pubescens and B. nana
Birches (Betula spp.) hybridize readily, confounding genetic signatures of refugial isolation and postglacial migration. We aimed to distinguish hybridization from range-shift processes in the two widespread and cold-adapted species B. nana and B. pubescens, previously shown to share a similarly east–west-structured variation in plastid DNA (pDNA). We sampled the two species throughout their ranges and included reference samples of five other Betula species and putative hybrids. We analysed 901 individual plants using mainly nuclear high-resolution markers (amplified fragment length polymorphisms; AFLPs); a subset of 64 plants was also sequenced for two pDNA regions. Whereas the pDNA variation as expected was largely shared between B. nana and B. pubescens, the two species were distinctly differentiated at AFLP loci. In B. nana, both the AFLP and pDNA results corroborated the former pDNA-based hypothesis that it expanded from at least two major refugia in Eurasia, one south of and one east of the North European ice sheets. In contrast, B. pubescens showed a striking lack of geographic structuring of its AFLP variation. We identified a weak but significant increase in nuclear (AFLP) gene flow from B. nana into B. pubescens with increasing latitude, suggesting hybridization has been most frequent at the postglacial expansion front of B. pubescens and that hybrids mainly backcrossed to B. pubescens. Incongruence between pDNA and AFLP variation in B. pubescens can be explained by efficient expansion from a single large refugium combined with leading-edge hybridization and plastid capture from B. nana during colonization of new territory already occupied by this more cold-tolerant species.
Data from: AFLP diversity and spatial structure of Calycophyllum candidissimum (Rubiaceae), a dominant tree species of Nicaragua's critically endangered seasonally dry forest
The Central American seasonally dry tropical (SDT) forest biome is one of the worlds' most endangered ecosystems, yet little is known about the genetic consequences of its recent fragmentation. A prominent constituent of this biome is Calycophyllum candidissimum, an insect-pollinated and wind-dispersed canopy tree of high socio-economic importance, particularly in Nicaragua. Here, we surveyed amplified fragment length polymorphisms across 13 populations of this species in Nicaragua to elucidate the relative roles of contemporary vs historical factors in shaping its genetic variation. Genetic diversity was low in all investigated populations (mean HE=0.125), and negatively correlated with latitude. Overall population differentiation was moderate (ΦST=0.109, P<0.001), and Bayesian analysis of population structure revealed two major latitudinal clusters (I: 'Pacific North'+'Central Highland'; II: 'Pacific South'), along with a genetic cline between I and II. Population-based cluster analyses indicated a strong pattern of 'isolation by distance' as confirmed by Mantel's test. Our results suggest that (1) the low genetic diversity of these populations reflects biogeographic/population history (colonisation from South America, Pleistocene range contractions) rather than recent human impact; whereas (2) the underlying process of their isolation by distance pattern, which is best explained by 'isolation by dispersal limitation', implies contemporary gene flow between neighbouring populations as likely facilitated by the species' efficient seed dispersal capacity. Overall, these results underscore that even tree species from highly decimated forest regions may be genetically resilient to habitat fragmentation due to species-typical dispersal characteristics, the necessity of broad-scale measures for their conservation notwithstanding.
Data from: AFLP genome scans suggest divergent selection on colour patterning in allopatric colour morphs of a cichlid fish
Genome scan-based tests for selection are directly applicable to natural populations to study the genetic and evolutionary mechanisms behind phenotypic differentiation. We conducted AFLP genome scans in three distinct geographic colour morphs of the cichlid fish Tropheus moorii to assess whether the extant, allopatric colour pattern differentiation can be explained by drift and to identify markers mapping to genomic regions possibly involved in colour patterning. The tested morphs occupy adjacent shore sections in southern Lake Tanganyika and are separated from each other by major habitat barriers. The genome scans revealed significant genetic structure between morphs, but a very low proportion of loci fixed for alternative AFLP alleles in different morphs. This high level of polymorphism within morphs suggested that colour pattern differentiation did not result exclusively from neutral processes. Outlier detection methods identified six loci with excess differentiation in the comparison between a bluish and a yellow-blotch morph and five different outlier loci in comparisons of each of these morphs with a red morph. As population expansions and the genetic structure of Tropheus make the outlier approach prone to false-positive signals of selection, we examined the correlation between outlier locus alleles and colour phenotypes in a genetic and phenotypic cline between two morphs. Distributions of allele frequencies at one outlier locus were indeed consistent with linkage to a colour locus. Despite the challenges posed by population structure and demography, our results encourage the cautious application of genome scans to studies of divergent selection in subdivided and recently expanded populations.
Data from: Influence of parameter settings in automated scoring of AFLPs on population genetic analysis
The use of procedures for the automated scoring of AFLP fragments has recently increased. Corresponding software does not only automatically score the presence or absence of AFLP fragments, but also allows an evaluation of how different settings of scoring parameters influence subsequent population genetic analyses. In this study, we used the automated scoring package RAWGENO to evaluate how five scoring parameters influence the number of polymorphic bins and estimates of pairwise genetic differentiation between populations (Fst). Steps were implemented in R to automatically run the scoring process in RAWGENO for a set of different parameter combinations. While we found the scoring parameters minimum bin width and minimum number of samples per bin to have only weak influence on pairwise Fst values, maximum bin width and bin reproducibility had much stronger effects. The minimum average bin fluorescence scoring parameter affected Fst values in an only moderate way. At a range of scoring parameters around the default settings of RAWGENO, the number of polymorphic bins as well as pairwise Fst values stayed rather constant. This study thus shows the particularities of AFLP scoring, be it either manual or automatical, can have profound effects on subsequent population genetic analysis.
FIGURE. Flower characteristics comparison of A. P. charlesworthii var. lannaense, B. P. papilio-laoticus (photo. by W. Tongkham) and C. P. Little Trouble (P. charlesworthii x P. barbigerum) (photo. by R. Hella) in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE. Flower characteristics comparison of A. P. charlesworthii var. lannaense, B. P. papilio-laoticus (photo. by W. Tongkham) and C. P. Little Trouble (P. charlesworthii x P. barbigerum) (photo. by R. Hella)
FIGURE. Some flower variation of Paphiopedilum charlesworthii var. lannaense, whole plant and flower. (photo. by W. Tongkham) in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE. Some flower variation of Paphiopedilum charlesworthii var. lannaense, whole plant and flower. (photo. by W. Tongkham)
FIGURE. Paphiopedilum charlesworthii var. lannaense, whole plant and flower. A. Flowering plant, B. Flower front view, C. Flower side view and D. Flower back view (photo. by W. Tongkham) in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE. Paphiopedilum charlesworthii var. lannaense, whole plant and flower. A. Flowering plant, B. Flower front view, C. Flower side view and D. Flower back view (photo. by W. Tongkham)
FIGURE. Dendrogram of P. charlesworthii var. lannaense and 10 other Paphiopedilum species in section Paphiopedilum by 7 AFLP primer combinations, 1= first main group, 2= second main group, 2.1= subgroup 2.1 and 2.2 = subgroup 2.2. in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE. Dendrogram of P. charlesworthii var. lannaense and 10 other Paphiopedilum species in section Paphiopedilum by 7 AFLP primer combinations, 1= first main group, 2= second main group, 2.1= subgroup 2.1 and 2.2 = subgroup 2.2.
FIGURE. Flower and leaf characteristics comparison of A. P. charlesworthii var. lannaense, B. P. charlesworthii, C. P. vejvarutianum and D. P. barbigerum var. coccineum (photo. by W. Tongkham) in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE. Flower and leaf characteristics comparison of A. P. charlesworthii var. lannaense, B. P. charlesworthii, C. P. vejvarutianum and D. P. barbigerum var. coccineum (photo. by W. Tongkham)
FIGURE. Dendrogram of P. charlesworthii var. lannaense and 49 other Paphiopedilum species by 6 AFLP primer combinations, 1= Brachypetalum, 2= Cochlopetalum, 3= Parvisepalum, 4= Polyantha, 5= Sigmatopetalum, 6= Paphiopedilum, 7= Laosianum, and 8= Megastaminodium. in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE. Dendrogram of P. charlesworthii var. lannaense and 49 other Paphiopedilum species by 6 AFLP primer combinations, 1= Brachypetalum, 2= Cochlopetalum, 3= Parvisepalum, 4= Polyantha, 5= Sigmatopetalum, 6= Paphiopedilum, 7= Laosianum, and 8= Megastaminodium.
FIGURE. Flower and leaf characteristics of A. P. charlesworthii var. lannaense, B. P. charlesworthii, C. P. barbigerum var. coccineum and D. P. barbigerum var. sulivongii (photo. by W. Tongkham) in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE. Flower and leaf characteristics of A. P. charlesworthii var. lannaense, B. P. charlesworthii, C. P. barbigerum var. coccineum and D. P. barbigerum var. sulivongii (photo. by W. Tongkham)
FIGURE. In situ photos of Paphiopedilum charlesworthii var. lannaense. A. limestone mountain at 1,100–1,200 m elevation, B. P. charlesworthii var. lannaense living on vertical cliffs of limestone, C. P. charlesworthii var. lannaense plant, D. flowering plant with flower bud, E., F. flowering plant (flower color was faded because these photos were taken toward the end of flowering period) (photo. By S. Somboonphon) in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE. In situ photos of Paphiopedilum charlesworthii var. lannaense. A. limestone mountain at 1,100–1,200 m elevation, B. P. charlesworthii var. lannaense living on vertical cliffs of limestone, C. P. charlesworthii var. lannaense plant, D. flowering plant with flower bud, E., F. flowering plant (flower color was faded because these photos were taken toward the end of flowering period) (photo. By S. Somboonphon)
FIGURE. Illustration of Paphiopedilum charlesworthii var. lannaense W. Tongkham, S. Pumikong, N. Potapohn & W. Bundithya A. flower, B. dorsal sepal, C. synsepal, D. petal, E. labellum frontal view, F. labellum side view, G. labellum longitudinal section, H. pedicel, I. pedicel longitudinal section and transverse section, J. stigma and pollen, K. staminode, L. column side view, M. leaf, N. peduncle, bract and pedicel, and O. flowering plant. Drawn by W. Tongkham from S. Pumikong 021001 (holotype QBG! [no. 132572]). in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE. Illustration of Paphiopedilum charlesworthii var. lannaense W. Tongkham, S. Pumikong, N. Potapohn & W. Bundithya A. flower, B. dorsal sepal, C. synsepal, D. petal, E. labellum frontal view, F. labellum side view, G. labellum longitudinal section, H. pedicel, I. pedicel longitudinal section and transverse section, J. stigma and pollen, K. staminode, L. column side view, M. leaf, N. peduncle, bract and pedicel, and O. flowering plant. Drawn by W. Tongkham from S. Pumikong 021001 (holotype QBG! [no. 132572]).
FIGURE. Distribution map of P. charlesworthii var. lannaense (star), P. charlesworthii (square), P. barbigerum var. coccineum (circle), P. papilio-laoticus (triangle), P. barbigerum var. sulivongii (semi-circle) and P. vejvarutianum (pentagon) (drawn by W. Tongkham) in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE. Distribution map of P. charlesworthii var. lannaense (star), P. charlesworthii (square), P. barbigerum var. coccineum (circle), P. papilio-laoticus (triangle), P. barbigerum var. sulivongii (semi-circle) and P. vejvarutianum (pentagon) (drawn by W. Tongkham)
FIGURE 3 in Buddleja caryopteridifolia (Scrophulariaceae), a species to be recognized based on morphology, floral scent, and AFLP data
FIGURE 3. PCoA plots of the first two components of B. crispa (Cr) and B. caryopteridifolia (Ca), based on the AFLP data, 5, 4 populations for each species, and cumulative percentage of three principal components (cum%) of 11.57, 17.65 and 21.94 %. The population labels used are given in Table 1.
FIGURE 4 in Buddleja caryopteridifolia (Scrophulariaceae), a species to be recognized based on morphology, floral scent, and AFLP data
FIGURE 4. UPGMA phenogram based on Nei's genetic distances. The populations of B. crispa and B. caryopteridifolia were indicated using blue and red color, respectively. The population labels used are given in Table 1.
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