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194 results for “Reticulation”
Fig. 5 in A phylogenetic investigation of the taxonomically problematic Eucalyptus odorata complex (E. section Adnataria series Subbuxeales): evidence for extensive interspecific gene flow and reticulate evolution
Fig. 5. Maximum-likelihood phylogeny generated using RAXML, excluding samples with strong evidence for hybridisation and introgression in the combined ddRADseq and DArTseq dataset. Support values on branches are those from the ML and MP analysis, with branches with greater than 80% bootstrapping support in both analyses thickened. Series are labelled as per Nicolle (2019).
Fig. 1 in A phylogenetic investigation of the taxonomically problematic Eucalyptus odorata complex (E. section Adnataria series Subbuxeales): evidence for extensive interspecific gene flow and reticulate evolution
Fig. 1. Distributions of the 12 species of the E. odorata complex, using taxonomic concepts employed a priori in this study. (a) E. viridis and species most commonly considered its closest relatives. (b) E. odorata, E. polybractea and species commonly considered close relatives of these. Distributions are coloured by species and open circles are used to highlight geographically restricted populations. Closed points indicate the collecting localities and seed provenances for samples used in this study. Black circles indicate major regions where members of the E. odorata complex occur as applied in text, which may differ from the actual geographic extent.
Fig. 4 in A phylogenetic investigation of the taxonomically problematic Eucalyptus odorata complex (E. section Adnataria series Subbuxeales): evidence for extensive interspecific gene flow and reticulate evolution
Fig. 4. Maximum-likelihood phylogeny generated using RAXML including all samples in the combined ddRADseq and DArTseq dataset. Support values on branches are those from the ML and MP analysis, with branches with greater than 80% bootstrapping support in both analyses thickened. Series are labelled as per Nicolle (2019).
Phylogenomics of Fargesia and Yushania reveals a history of reticulate evolution
<p>Reticulate evolution is a common and important driving force in angiosperm evolution. In this study, we analyzed the phylogenetic signals of genomic regions with different inheritance patterns to understand the evolutionary process of organisms using species‐rich Himalaya–Hengduan taxa of bamboos (Fargesia Franchet and Yushania Keng). We constructed phylogenetic trees using different sampling strategies and reconstruction methods based on genome skimming and double digest restriction‐site‐associated DNA sequencing data. We assessed the congruence of topologies generated from different datasets and employed several approaches to reveal the causes of phylogenetic incongruence, including the detection of hybridization and introgression using PhyloNetworks and the D‐ statistic test (ABBA‐BABA test). We found that, in the plastome‐based phylogeny, Fargesia bamboos can be clustered into three groups and Yushania was nested within one of them, which contradicts the nuclear–double digest restriction‐site‐associated DNA sequencing‐based phylogeny. Moreover, the genetic variation of chloroplast DNA is significantly correlated with geographical distribution. The strong signal of incomplete lineage sorting, hybridization, introgression, and cytoplasmic gene flow found among genera and species suggests that reticulate evolution is the main cause for the phylogenetic incongruence between nuclear and chloroplast datasets. Our results add evidence that genomes with different inheritance patterns can reveal distinct evolutionary histories of species and suggest that reticulate evolution is prevalent in rapidly diversifying groups.</p>
Deep-time reticulation and ancient mitochondrial genome capture during the radiation of Jamaican Anolis lizards (Squamata; Iguanidae)
<p>Gene flow and reticulation are increasingly recognized as important processes in the diversification of many taxonomic groups. With the increasing ease of collecting genomic data and the development of multispecies coalescent network approaches, such reticulations can be accounted for when inferring phylogeny and diversification. Caribbean <i>Anolis</i> lizards are a classic example of an adaptive radiation in which species have independently radiated on the islands of the Greater Antilles into the same ecomorph classes. Within the Jamaican radiation at least one species, <i>A. opalinus</i>, has been documented to be polyphyletic in its mitochondrial DNA, which could be the result of an ancient reticulation event or incomplete lineage sorting. Here we generate mtDNA and genotyping-by-sequencing (GBS) data and implement gene-tree, species-tree, and multispecies coalescent network methods to infer the diversification of this group. Our mtDNA gene-tree recovers the same relationships previously inferred for this group, which is strikingly different from the species-tree inferred from our GBS data. Posterior predictive simulations suggest that our genomic data violate commonly adopted assumptions of the multispecies coalescent model, so we use network approaches to infer phylogenetic relationships. The inferred network topology contains a reticulation event but does not explain the mtDNA polyphyly observed in this group, however coalescent simulations suggest that the observed mtDNA topology is likely the result of past introgression. How common a signature of gene flow and reticulation is across the radiation of <i>Anolis</i> is unknown; however, the reticulation events that we demonstrate here may have allowed for adaptive evolution, as has been suggested in other, more recent adaptive radiations.</p>
Fig. 2 in A phylogenetic investigation of the taxonomically problematic Eucalyptus odorata complex (E. section Adnataria series Subbuxeales): evidence for extensive interspecific gene flow and reticulate evolution
Fig. 2. Neighbour-net networks of E. odorata complex taxa and co-occurring members of E. section Adnataria created in Splitstree V.4 using uncorrelated-P distances of SNPs generated by A. ddRADseq and B. DArTseq. Tips are coloured by species, with shapes used to distinguish different major groups: E. series Hetereophloiae (inverse triangles), E. series Melliodorae (hexagons), E. series Buxeales (triangles), the grey-box taxa (diamonds), mallee members of E. series Subbuxeales not in the E. odorata complex (squares), and the E. odorata complex (circles) coloured consistent with Fig. 1.
The phylogeny of Triticeae Dumort. (Poaceae): resolution and reticulation based on a genome-wide selection of nuclear loci.
<p>Chloroplast-genome and nuclear-locus phylogenetic datasets for the wheat tribe Triticeae.</p>
FIGURE 5 in A new reticulated beetle (Coleoptera: Cupedidae) from Mexico with a catalogue of Cupedidae species of the world
FIGURE 5. Female terminalia of Paracupes mexicanus sp. nov.: A) Tergite VIII; B) Sternite VIII; C) Ovipositor. Cox: Coxites; Sty: Styli.
FIGURE 4 in A new reticulated beetle (Coleoptera: Cupedidae) from Mexico with a catalogue of Cupedidae species of the world
FIGURE 4. Posterior fold of procoxae and elytral apex of P. mexicanus sp. nov. and P. brasiliensis. Posterior fold of procoxae: A) P. mexicanus sp. nov.; B) P. brasiliensis. Elytral apex: C) P. mexicanus sp. nov.; D) P. brasiliensis.
FIGURE 2 in A new reticulated beetle (Coleoptera: Cupedidae) from Mexico with a catalogue of Cupedidae species of the world
FIGURE 2. Scales of Paracupes spp. Head scales: A) P. mexicanus sp. nov.; B) P. brasiliensis; C) P. ascius. Pronotal scales: D) P. mexicanus sp. nov.; E) P. brasiliensis; F) P. ascius. Elytral scales: G) P. mexicanus sp. nov.; H) P. brasiliensis; I) P. ascius.
FIGURE 5. Sculptures. A. Punctate. B. Granulate. C. Reticulate rugose. D in Dryinidae of the Afrotropical region (Hymenoptera, Chrysidoidea)
FIGURE 5. Sculptures. A. Punctate. B. Granulate. C. Reticulate rugose. D. Striate. (from Olmi 1984).
Fig. 5 in Cladogenesis and reticulation in Cuscuta sect. Denticulatae (Convolvulaceae)
Fig. 5 Host ranges of Cuscuta sect. Denticulatae species visualized as a bipartite network. Four Cuscuta species nodes on the left are connected with the corresponding nodes of their hosts on the right. Thickness of the lines representing the edges of the network indicates the frequency of the parasite-host association. Frequencies higher than 10% are indicated in the graph while the rest of the host frequencies are available in Suppl. Table S1. Hosts indicated with gray dots on white are shared between C. denticulata and C. nevadensis. Note the 100% host specificity of C. veatchii and C. psorothamnensis
Fig. 6 A in Cladogenesis and reticulation in Cuscuta sect. Denticulatae (Convolvulaceae)
Fig. 6 A summary model of relationships within Cuscuta sect. Denticulatae synthesized from all data presented in this study (molecular, cytological, and morphological), showing the reconstruction of cladogenesis (thick lines) and reticulation (thin lines). Hypothesized relative time frame is indicated. Abbreviations: D, C. denticulata (DD, autopolyploid); N, C. nevadensis; nuc, nuclear ribosomal arrays (biparentally inherited; lost copy shown as a dotted line); PS, C. psorothamnensis; pt., plastid genes (maternally inherited); V, C. veatchii
Fig. 1 in Cladogenesis and reticulation in Cuscuta sect. Denticulatae (Convolvulaceae)
Fig. 1 Distribution of Cuscuta sect. Denticulatae species across their geographic ranges in western North America. Potential extent of distribution for C. denticulata is outlined and that of C. nevadensis is shaded. Approximate positions of sampling sites used in this study are indicated (for details, see Appendix 1). Circles (solid and open) represent sampling sites for populations of C. denticulata, squares (solid and open) represent those of C. nevadensis, triangles those of C. veatchii, while X symbols stand for the newly described species, C. psorothamnensis. Encircled symbols represent material obtained from herbaria; all others are sampled directly in the field, including multiple individuals per population. Solid and open symbols correspond to different haplo- and ribotypes of C. denticulata and C. nevadensis (see text for details)
Fig. 7 in Cladogenesis and reticulation in Cuscuta sect. Denticulatae (Convolvulaceae)
Fig. 7 Morphology of Cuscuta psorothamnensis. a Flower, lateral view (note the axillary floral bud indicating the development of a second flower). b Flowers, top view. c Calyces after the removal of corolla. d, e Dissected calyx imaged with both diffuse (d) and transmitted light (e). f Corollas after the removal of calyces. g Dissected corolla. h, i Infrastaminal scale variation, attached to corolla tube (h) and detached from it (i). j Gynoecium. k Indehiscent capsule. l Embryo still surrounded by endosperm; note the globose structure characteristic to sect. Denticulatae. Scale bars = 1 mm except i which is 0.5 mm
Fig. 4 in Cladogenesis and reticulation in Cuscuta sect. Denticulatae (Convolvulaceae)
Fig. 4 Principal Coordinate Analysis (PCoA) using all morphological characters (Appendix 2). The first coordinate axis (62.621% of the variance) separated C. nevadensis from C. denticulata and C. veatchii togeth- er with C. psorothamnesis. The second coordinate axis (9.297% of the variance) clearly separated C. denticulata from C. veatchii/C.
Fig. 2 in Cladogenesis and reticulation in Cuscuta sect. Denticulatae (Convolvulaceae)
Fig. 2 Schematic overview of the phylogenetic relationships in Cuscuta sect. Denticulatae derived from plastid (trnL-F) and nuclear (nrITS) sequence data. For simplicity, only the moderately to strongly supported backbone nodes are shown as resolved. Unresolved groups are represent- ed with a box symbol. For full details, compare with Suppl. Figs. S1 and S2. Symbols are the same as described in Fig. 1
Fig. 3 in Cladogenesis and reticulation in Cuscuta sect. Denticulatae (Convolvulaceae)
Fig. 3 Karyology of Cuscuta sect. Denticulatae. Mitotic metaphases and interphase nuclei of a diploid C. denticulata (2n = 30), b tetraploid C. denticulata (2n = 60), c C. nevadensis (2n = 30), d C. veatchii (2n = 60), and e C. psorothamnensis (2n = 60). f Diakinesis of C. veatchii showing n = 30 bivalents. Note the scale bar is the same across and corresponds to 5 μm
FIGURE 2. Reissantia sessiliflora A. Stem showing reticulation. B. Flowering twigs. C. Inflorescence showing sessile flowers. D. Fruit. E in A new species of Reissantia (Celastraceae) from coastal Karnataka, India
FIGURE 2. Reissantia sessiliflora A. Stem showing reticulation. B. Flowering twigs. C. Inflorescence showing sessile flowers. D. Fruit. E. Torn capsule showing seeds.
Discordance in a South African Memecylon clade (Melastomataceae): Evidence for reticulate evolution
<p><em>Premise of research. </em>Evergreen forests in eastern South Africa have high biodiversity but are limited in extent and have a highly fragmented distribution. Populations of forest plants are thus geographically isolated, and fine-scale evolutionary studies of these lineages might yield important insights into the history and assembly of the forests themselves. Despite their morphological diversity, a prior study showed that three South African <em>Memecylon</em> taxa in Melastomataceae (<em>M. natalense</em>, <em>M. bachmannii</em>, and <em>M. australissimum</em>) had almost identical nuclear ribosomal spacer sequences. Our study investigates phylogenetic relationships within this clade using multiple samples collected across populations and a next-generation phylogenomic approach.</p> <p><em>Methodology. </em>We used 87 low-copy nuclear (LCN) loci to examine relationships among these taxa using both concatenated and coalescent methods. We further used LCN loci to estimate phylogenetic networks and SNPs derived from LCN genes for STRUCTURE analysis of South African <em>Memecylon</em> populations. Finally, we employed two approaches (flow cytometry and SNPs) to infer the ploidy levels of these three taxa.</p> <p><em>Pivotal results. </em>Our investigations showed discordance among gene trees and the species tree, and low statistical support for relationships indicating that species monophyly cannot be recovered from this phylogenomic analysis. Phylogenetic networks and population structures showed that the South African <em>Memecylon </em>clade may be affected by gene flow and reticulate evolution. Flow cytometry and SNP-based estimations provided evidence for polyploidy within this group.</p> <p><em>Conclusions.</em> We found no evidence of monophyly for species within the South African <em>Memecylon</em> clade, which we infer to be the consequence of reticulation and recent and rapid evolution. More cytological studies and genomic data are needed to elucidate the evolutionary history of this group. Additionally, our study identifies priority populations within the South African Memecylon clade for conservation.</p>
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