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477 results for “Molecular evolution”
Data from: Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae
Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and used comparative genomic approaches to investigate the transcriptome evolution of the two species. We retrieved 53 929 unigenes from D. aurantiocaulis by de novo transcriptome assemblies using the Illumina HiSeq 2000 platform. Comparing the transcriptomes of both species, we identified 4593 orthologs. Estimation of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks significantly greater than 1, whereas 1273 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. A total of 51 primer pairs were successfully designed from 461 EST-SSRs contained in 4593 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%) produced clear fragments with the expected sizes in all Podophylloideae species. Specifically, 19 different sequences of CYP719A were identified from PCR-amplified genomic DNA of all 12 species of Podophylloideae using primers designed from the assembled transcripts. The data further indicated that CYP719A was likely subject to strong selective constraints maintaining only one copy per genome. In Dysosma, there was relaxed purifying selection or more positive selection for high-elevation species. Overall, this study has generated a wealth of molecular resources potentially useful for pharmacogenetic and evolutionary studies in Dysosma and allied taxa.
Data from: A molecular phylogeny and revised higher-level classification for the leaf-mining moth family Gracillariidae and its implications for larval host-use evolution
Gracillariidae are one of the most diverse families of internally feeding insects, and many species are economically important. Study of this family has been hampered by lack of a robust and comprehensive phylogeny. In the present paper, we sequenced up to 22 genes in 96 gracillariid species, representing all previously recognized subfamilies and genus groups, plus 20 outgroups representing other families and superfamilies. Following objective identification and removal of two rogue taxa, two datasets were constructed: dataset 1, which included 12 loci totalling 9927 bp for 94 taxa, and dataset 2, which supplemented dataset 1 with 10 additional loci for 10 taxa, for a total of 22 loci and 16 167 bp. Maximum likelihood analyses strongly supported the monophyly of Gracillariidae and most previously recognized subfamilies and genus groups. On this basis, we propose a new classification consisting of eight subfamilies, four of which are newly recognized or resurrected: Acrocercopinae Kawahara & Ohshima subfam. n.; Gracillariinae Stainton; Lithocolletinae Stainton; Marmarinae Kawahara & Ohshima subfam. n.; Oecophyllembiinae Réal & Balachowsky; Parornichinae Kawahara & Ohshima subfam. n.; Ornixolinae Kuznetzov & Baryshnikova stat. rev.; and Phyllocnistinae Zeller. The subfamily Gracillariinae is restricted to the monophyletic group comprising Gracillaria Haworth and closely related genera. We also formally transfer Acrocercops scriptulata Meyrick to Ornixolinae and use the name Diphtheroptila Vári, creating Diphtheroptila scriptulata comb. n. An exploratory mapping of larval host-use traits on the phylogeny shows strong conservation of modes of leaf mining but much higher lability of associations with host plant orders and families, suggesting that host shifts could play a significant role in gracillariid diversification.
FIGURE 2. A in Molecular analysis of six Rhynchospio Hartman, 1936 species (Annelida: Spionidae) with comments on the evolution of brooding within the group
FIGURE 2. A, majority rule consensus tree of the Bayesian inference analysis of 2421 bp total of 16S (236 bp), 18S (1580 bp), 28S (287 bp) and Histone 3 (318 bp) of Boccardia, Pygospio and Rhynchospio sequences rooted with sequences of Marenzelleria. B, majority rule consensus tree of the Bayesian inference analysis of 2516 bp total of 16S (284 bp), 18S (1618 bp), 28S (293 bp), and Histone 3 (321 bp) of the only-Rhynchospio sequences. Posterior probabilities are shown on the branches. Species names are followed by the names of the collecting locations (in parentheses).
FIGURE 1 in Molecular analysis of six Rhynchospio Hartman, 1936 species (Annelida: Spionidae) with comments on the evolution of brooding within the group
FIGURE 1. Gamete morphology of Rhynchospio cf. foliosa (fixed material). A, B, developed coelomic oocytes. A, external honey-combed surface of oocyte thick envelope. B, optical section of an oocyte, showing 20–30 vesicles (cortical alveoli, ve) associated with inner surface, germinal vesicle (gv) and single nucleolus (nl). C, D, spermatozoa, showing conical acrosome (ac) with a small dark spherical structure in anterior part and a transparent central part, ovoid nucleus (nu), a few spherical mitochondria, and a long flagellum. Scale bars: A–C = 10 µm; D = 5 µm.
Supplementary material 2 from: Parasram N, Santana W, Vallès Y, Windsor AМ, Vallès H (2024) Morphological and molecular support for Amphithrax verrucosus (H. Milne Edwards, 1832) and Amphithrax aculeatus (Herbst, 1790) (Crustacea, Decapoda, Brachyura) as valid species. Zoosystematics and Evolution 100(1): 15-30. https://doi.org/10.3897/zse.100.109192
Specimens used in the molecular analysis of Windsor and Felder (2014), which were erroneously identified as Amphithrax aculeatus (Herbst, 1790)
Supplementary material 4 from: Vanegas-Ríos JA, Serra Alanís WS, Azpelicueta MM, Litz T, Malabarba LR (2024) Population variation of Diapoma pampeana (Characiformes, Characidae, Stevardiinae) from an isolated coastal drainage in Uruguay, with new records: comparing morphological and molecular data. Zoosystematics and Evolution 100(1): 69-85. https://doi.org/10.3897/zse.100.112778
Cluster analysis (Ward's method) of size-corrected morphometric data of analyzed specimens of Diapoma pampeana
Fig. 5. Combined ITSand trnT-F phylogenybasedonmaximum parsimonyand Bayesian inference. Shadedsectionof thetree highlightsspecies with x in Canary grasses (Phalaris, Poaceae): Molecular phylogenetics, polyploidy and floret evolution
Fig. 5. Combined ITSand trnT-F phylogenybasedonmaximum parsimonyand Bayesian inference. Shadedsectionof thetree highlightsspecies with x = 6, and names shown in bold denote polyploid species. * = nodes collapsed in the strictconsensus maximum parsimony tree. • = unknown chromosome number. Floret types follow the structure defined in Fig. 2. A = annual and P = perennial habit.
Fig. 4. trnT-F in Canary grasses (Phalaris, Poaceae): Molecular phylogenetics, polyploidy and floret evolution
Fig. 4. trnT-F phylogram generated from Bayesian inference. Parsimony bootstrap results are above branches and Bayesian posterior probabilities are below. Shaded section of the tree highlights species with x = 6, and names shown in bold denote polyploid species. * = clade collapsed in the strict consensus maximum parsimony tree. • = unknown chromosome number. Floret types follow Fig. 2. A = annual and P = perennial habit.
Fig. 2 in Canary grasses (Phalaris, Poaceae): Molecular phylogenetics, polyploidy and floret evolution
Fig. 2. Adiagrammatic illustrationof sixfloret typesrecognizablein speciesof Phalaris following Anderson (1961) and Baldini (1995). Notethe central fertile floret and the two lateral sterile lemmas that display successive reduction in size.
Figure 3 in The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses
Figure 3. Divergence-date estimates obtained with the two alternative molecular matrices (black lines, complete; grey lines, RAG2 only). In both cases, the fossil-based calibration scheme used the Diogenornis age constraint (see Table 1). Nodes used in fossil calibration are marked with diamonds.
Figure 2 in The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses
Figure 2. Relationships of the tinamous using a combined matrix of molecular and morphological data as inferred by Bayesian inference (BI) (Supporting Information, Fig. S7). The subtree topology in the inset was recovered under maximum parsimony (MP). Well-supported nodes having support values> 90% under MP and> 0.95 under BI are marked by dots on the cladogram. Differences among the BI topology and the topologies obtained with the MP (Supporting Information, Fig. S6) and maximum likelihood (ML) searches (Supporting Information, Fig. S8) are marked in grey and with an X, respectively.
Figure 1 in The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses
Figure 1. Bayesian inference (BI) majority consensus tree based on the concatenated molecular data, showing the phylogenetic relationships of tinamous (see also Supporting Information, Figs S6–S8). The maximum likelihood (ML) tree topology was identical to that of the BI tree. Clade-support values are indicated above branches (posterior probability under BI/bootstrap values under ML/bootstrap values under maximum parsimony, respectively).
Figure 4 in The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses
Figure 4. Taxonomic distribution and optimization of phenotypic characters: eggshell coloration, development of postacetabular pelvis and changes in plumage pattern (characters 9, 101 and 185, described in more detail in the Supporting Information, Appendix S1). For the data matrix, see the Supporting Information (Appendix S2). Further discussion is provided in the main text.
Mapping and assembly of the Midas cichlid male-specific region supports molecular parallelism in the evolution of a master sex-determining role for amhr2
<p>The evolution of sex chromosomes and their differentiation from autosomes is a major event during genome evolution that happened many times in several lineages. The repeated evolution and lability of sex-determination mechanisms in fishes makes this a well-suited system to test for general and predictable patterns in evolution. According to current theory, differentiation is triggered by the suppression of recombination following the evolution of a new master-sex determining gene. However, the molecular mechanisms that establish recombination suppression are known from few examples, owing to the intrinsic difficulties of assembling sex determining regions (SDRs). Forward-genetics data and the development of long-read sequencing have generated a wealth of data questioning central aspects of the current theory. Here, we demonstrate that sex in Midas cichlids is determined by an XY system, identify and assemble the SDR by combining forward-genetics, long-read sequencing and optical mapping. We show how long-reads aid in the detection of artifacts in genotype-phenotype mapping that arise from incomplete genome assemblies. The male-specific region is restricted to a 100 kb segment on chromosome 4 that harbors transposable elements and a Y-specific duplicate of the anti-Mullerian receptor 2 locus, a known sex-determining gene. Our data suggests that <em>amhr2Y</em> originated by an interchromosomal translocation from chromosome 20 to 4 predating the split of Midas and Flier cichlids. In the later, it is pseudogenized and translocated to another chromosome. Duplication of anti-Mullerian genes is a common route to establishing new sex determiners, highlighting the role of molecular parallelism in the evolution of sex determination.</p>
Supplementary material 1 from: Todisco V, Nazari V, Cesaroni D, Sbordoni V (2017) Preliminary molecular phylogeny and biogeography of the monobasic subfamily Calinaginae (Lepidoptera, Nymphalidae). Zoosystematics and Evolution 93(2): 255-264. https://doi.org/10.3897/zse.93.10744
Adults and genitalia images of dissected specimens : Explanation note: Adult and genitalia images of dissected specimens examined in this study.
Supplementary material 3 from: Bragança PHN, Amorim PF, Costa WJEM (2018) Pantanodontidae (Teleostei, Cyprinodontiformes), the sister group to all other cyprinodontoid killifishes as inferred by molecular data. Zoosystematics and Evolution 94(1): 137-145. https://doi.org/10.3897/zse.94.22173
Maximum Likelihood (A) and Bayesian Inference (B) analysis including the 16S gene. : Explanation note: Maximum Likelihood (A) and Bayesian Inference (B) analysis including segments of the nuclear genes ENC1, GLYT, MYH6, SH3PX3, RAG1, the mitochondrial genes 16S and first and second codon position of the COI. In ML, bootstrap values under 50 are not represented, and posterior probability values under 0.5 are not represented in BI.
Supplementary material 5 from: Bragança PHN, Amorim PF, Costa WJEM (2018) Pantanodontidae (Teleostei, Cyprinodontiformes), the sister group to all other cyprinodontoid killifishes as inferred by molecular data. Zoosystematics and Evolution 94(1): 137-145. https://doi.org/10.3897/zse.94.22173
Bayesian Inference tree : Explanation note: Bayesian inference tree comprising segments of the nuclear genes ENC1, GLYT, MYH6, SH3PX3, RAG1 and first and second codon position of the mitochondrial gene COI (5,083 bp). Numbers on each node are posterior probablity values; values under 50 are not present in the tree.
Fig. 4 in A dated molecular perspective of eucalypt taxonomy, evolution and diversification
Fig. 4. Bayesian analysis using the concatenated dataset of internal transcribed spacer (ITS), external transcribed spacer (ETS), matK and psbA–trnH, labelled with the informal higher-level groups mesicalypts (3 genera) and newcalypt (1 genus), the eucalypt genus Angophora, and all eucalypt subgenera as classified by Nicolle (2015b). Numbers at nodes in the larger phylogeny represent the penalised-likelihood estimated age. Numbers after each name in the inset box represent the number of terminals in the clade and numbers at nodes represent the posterior probability in the Bayesian analysis. Ma represents millions of years as returned for each penalised-likelihood dating analysis (a summary of estimated ages is provided in Table 2).
Fig. 3. Maximum likelihood-2 in A dated molecular perspective of eucalypt taxonomy, evolution and diversification
Fig. 3. Maximum likelihood-2 (ML-2) analysis using the concatenated dataset of internal transcribed spacer (ITS), external transcribed spacer (ETS), matK and psbA–trnH, labelled with the informal higher-level groups mesicalypts (3 genera) and newcalypt (1 genus), the eucalypt genus Angophora, and all eucalypt subgenera as classified by Nicolle (2015b). Numbers at nodes in the larger phylogeny represent the penalised-likelihood estimated age. Numbers after each name in the inset box represent the number of terminals in the clade and numbers at nodes represent the bootstrap value in the ML analysis. Ma represents millions of years as returned for each penalised-likelihood dating analysis (a summary of estimated ages is provided in Table 2).
Fig. 2. Maximum likelihood-1 in A dated molecular perspective of eucalypt taxonomy, evolution and diversification
Fig. 2. Maximum likelihood-1 (ML-1) analysis using the concatenated dataset of internal transcribed spacer (ITS), external transcribed spacer (ETS), matK and psbA–trnH, labelled with the informal higher-level groups mesicalypts (3 genera) and newcalypt (1 genus), the eucalypt genus Angophora, and all eucalypt subgenera as classified by Nicolle (2015b). Numbers at nodes in the larger phylogeny represent the penalised-likelihood estimated age. The numbers after each name in the inset box represent the number of terminals in the clade and numbers at nodes represent the bootstrap value in the ML analysis. Ma represents millions of years as returned for each penalised-likelihood dating analysis (a summary of estimated ages is provided in Table 2).
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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