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1,751 results for “molecular phylogenetics”
Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales)
Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the "portullugo" (Caryophyllales), a moderately sized lineage of flowering plants (∼2200 species) that includes the cacti and harbors many evolutionary transitions to C4 and CAM photosynthesis. Including multi-gene families allowed us to simultaneously infer a robust phylogeny and construct a dense sampling of sequences for a major enzyme of C4 and CAM photosynthesis, which revealed the accumulation of adaptive amino acid substitutions associated with C4 and CAM origins in particular paralogs. Our final set of matrices for phylogenetic analyses included 75–218 loci across 74 taxa, with ∼50% matrix completeness across datasets. Phylogenetic resolution was greatly improved across the tree, at both shallow and deep levels. Concatenation and coalescent-based approaches both resolve the sister lineage of the cacti with strong support: Anacampserotaceae + Portulacaceae, two lineages of mostly diminutive succulent herbs of warm, arid regions. In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees. Our results add to the growing number of examples illustrating the complexity of phylogenetic signals in genomic-scale data.
Files for phylogenetic analyses and molecular diagnosis between Diplomystidae catfish species
<p>Diplomystidae is an early-diverged family of freshwater catfish endemic to southern South America. We have recently collected five juvenile specimens belonging to this family from the Bueno River Basin, a basin which the only previous record was a single juvenile specimen collected in 1996. This finding confirms the distribution of the family further South in northern Patagonia, but poses new questions about the origin of this population in an area with a strong glacial history. We used phylogenetic analyses to evaluate three different hypotheses that could explain the origin of this population in the basin. First, the population could have originated in Atlantic basins (East of the Andes) and dispersed to the Bueno Basin after the Last Glacial Maximum (LGM) via river reversals, as it has been proposed for other population of <em>Diplomystes </em>as well as for other freshwater species from Patagonia. Second, the population could have originated in the geographically close Valdivia Basin (West of the Andes) and dispersed south to its current location in the Bueno Basin. Third, regardless of its geographic origin (West or East of the Andes), the Bueno Basin population could have a longer history in the basin, surviving in situ through the LGM. In addition, we conducted species delimitation analyses using a recently developed method that uses a protracted model of speciation. Our goal was to test the species status of the Bueno Basin population along with another controversial population in Central Chile (Biobío Basin), which appeared highly divergent in previous studies with mtDNA. The phylogenetic analyses showed that the population from the Bueno Basin is more related to Atlantic than to Pacific lineages, although with a deep divergence that predated the LGM, supporting in situ survival rather than postglacial dispersal. In addition, these analyses also showed that the species <em>D. nahuelbutaensis</em> is polyphyletic, supporting the need for a taxonomic reevaluation. The species delimitation analyses supported two new species which are described using molecular diagnostic characters: <em>Diplomystes arratiae</em> sp. nov. from the Biobío, Carampangue, and Laraquete basins, maintaining <em>D. nahuelbutaensis</em> valid only for the Imperial Basin, and <em>Diplomystes habitae</em> sp. nov. from the Bueno Basin. This study greatly increases the number of species within both the family Diplomystidae and Patagonia, and contributes substantially to the knowledge of the evolution of southern South American freshwater biodiversity during its glacial history. Given the important contribution to the phylogenetic diversity of the family, we recommend a high conservation priority for both new species. Finally, this study highlights an exemplary scenario where species descriptions based only on DNA data are particularly valuable, bringing additional elements to the ongoing debate on DNAbased taxonomy.</p>
Molecular Phylogenetics and Trait Evolution in Stigmatodon (Bromeliaceae, Tillandsioideae), an Endemic Genus to Brazilian Rocky Outcrops
<p><strong><em>Abstract</em></strong>—The genus <em>Stigmatodon</em> occurs in steep granite slopes, typical of the inselbergs from the Brazilian Atlantic Forest. Here, we present the first broad phylogenetic analysis focused on <em>Stigmatodon</em>, sampling a total of 83 terminals, including 16 of the 20 species of the genus and the morphologically similar species of <em>Vriesea</em>. We conducted a phylogenetic analysis using two plastid markers (<em>matK </em>and <em>rps16-trnK</em>) and the nuclear gene <em>PHYC</em> to infer phylogenetic relationships and reconstruct ancestral states for ecological and morphological characters. Our results suggest the monophyly of <em>Stigmatodon</em> as originally circumscribed is only possible with the inclusion of morphologically and ecologically similar <em>Vriesea</em> species. In addition, the morphological and anatomical traits led us to propose a new circumscription for the genus, combining eight species of <em>Vriesea </em>to <em>Stigmatodon</em>. The stomata positioned above the ordinary epidermal cells, the adaxial water-storage parenchyma with axially elongated cells, the stamens positioned in two groups of three on each side of the corolla and the tubo-laciniate stigma are exclusive to <em>Stigmatodon</em> in its new circumscription. This new morphological and phylogenetic results constitute a relevant contribution to the taxonomy and evolution of Bromeliaceae, one of the most diverse and ecologically important families of flowering plants of the Neotropics.</p>
The impact of molecular data on the phylogenetic position of the putative oldest crown crocodilian and the age of the clade
The use of molecular data for living groups is vital for interpreting fossils, especially when morphology-only analyses retrieve problematic phylogenies for living forms. These topological discrepancies impact on the inferred phylogenetic position of many fossil taxa. In Crocodylia, morphology-based phylogenetic inferences differ fundamentally in placing <i>Gavialis</i> basal to all other living forms, whereas molecular data consistently unite it with crocodylids. The Cenomanian <i>Portugalosuchus azenhae </i>was recently described as the oldest crown crocodilian, with affinities to <i>Gavialis</i>, based on morphology-only analyses, thus representing a potentially important new molecular clock calibration. Here we performed analyses incorporating DNA data into these morphological datasets, using scaffold and supermatrix (total evidence) approaches, in order to evaluate the position of basal crocodylians including <i>Portugalosuchus</i>. Our analyses incorporating DNA data robustly recovered <i>Portugalosuchus</i> outside Crocodylia (as well as thoracosaurs, planocraniids and <i>Borealosuchus</i> spp.), questioning the status of <i>Portugalosuchus</i> a crown crocodilian and any future use as a node calibration in molecular clock studies. Finally, we discuss how, with the increasing size of phylogenomic datasets, the molecular scaffold might be an efficient (though imperfect) approximation of more rigorous but demanding supermatrix analyses.
Phylogenetic position of Centroglossa and Dunstervillea (Ornithocephalus clade: Oncidiinae: Orchidaceae) based on molecular and morphological data
<p><span>Even though the monophyly of the <em>Ornithocephalus </em>clade (Oncidiinae) is currently well defined, the systematic positioning of <em>Centroglossa </em>and <em>Dunstervillea </em>remains obscure in the clade due to the absence in previous phylogenetic studies. <em>Centroglossa </em>has a very similar habit and is indistinguishable from <em>Zygostates</em>, whereas <em>Dunstervillea </em>has as its main characteristic the calcarate labellum, also found in <em>Centroglossa</em>. We clarify the systematic and phylogenetic positioning of Centroglossa and Dunstervillea in the <em>Ornithocephalus </em>clade (OC) through analysis of maximum likelihood, <em>Bayesian </em>inference, and maximum parsimony from molecular data (nrITS and <em>matK </em>cpDNA) and morphology. Our results indicate that Dunstervillea is phylogenetically close to <em>Eloyella</em>; both genera have a psigmoid habit, single-sided and flattened leaves, floral perianth with the same coloring, petals with entire margins, and a short rostellum. <em>Centroglossa </em>appears as a subclade within <em>Zygostates</em>. In addition to several homoplastic features, these two genera have the dorsal position of viscidium as a synapomorphy. The calcarate labellum, common to <em>Centroglossa </em>and <em>Dunstervillea</em>, originated more than once in the OC. Based on the phylogenetic results, we propose the nomenclatural changes to include <em>Dunstervillea </em>in <em>Eloyella </em>and Centroglossa in Zygostates. Lectotypes are indicated to <em>Centroglossa macroceras </em>and <em>C</em>. <em>glaziovii</em>.</span></p>
Comparative analysis of chloroplast genomes of Sanguisorba species and insights into phylogenetic implications and molecular dating
<pre class="js_message_plain ng-binding"><em>Sanguisorba</em> is a small genus, which consists of about 15 species widely distributed in North America and Eurasia. Previous studies on <em>Sanguisorba</em> are useful for understanding of phylogeny and chloroplast (cp) genome evolution of <em>Sanguisorba</em>. However, the cp genome resources of <em>Sanguisorba</em> are still limited, and the phylogeny and molecular dating for <em>Sanguisorba</em> and its relatives still need further explored. Here, we reported four cp genomes of <em>Sanguisorba</em> and conducted comparative analysis of the four <em>Sanguisorba</em> cp genomes plus five previously published ones. The nine cp genomes of <em>Sanguisorba</em> have typical tetrad quadripartite structure, with a total length of 154 282 to 155 730 bp, and their gene content, gene structure, and gene order are relatively conservative. The analysis of single copy (SC)/inverted repeat (IR) boundaries shows very slight boundary differences in <em>Sanguisorba</em> cp genomes. Eight variation hotspots were screened as excellent candidate markers of <em>Sanguisorba</em>. Phylogenetic analysis indicated <em>Sanguisorba</em> was monophyletic and was a member of tribe Agrimonieae subtribe Sanguisorbinae. Within <em>Sanguisorba</em>, <em>S. filiformis</em> is a sister group of six other taxa in the present sampling. Estimation of the divergence times indicated that subtribes Agrimoniinae and Sanguisorbinae diverged at the transition between the Oligocene and the Miocene, and divergent times of Agrimonieae genera ranged from the late Miocene to the Middle Pleistocene. This study enriches the available cp genome resources of <em>Sanguisorba</em>, and it is of great significance to further study the phylogeny and evolution of <em>Sanguisorba</em> and its relatives.</pre>
Data from: Out of Africa to Madagascar - then back? Molecular phylogenetics and biogeography of tribe Tarchonantheae (Asteraceae: Tarchonanthoideae)
<p>Premise of research. Molecular data have revolutionized inferences of phylogenetic relationships and historical biogeography of flowering plants. Two small genera, Brachylaena and Tarchonanthus, are the only members of Asteraceae tribe Tarchonantheae (subfamily Tarchonanthoideae). The tribe is morphologically distinct within Asteraceae and is resolved as monophyletic with molecular markers. It is distributed in southern Africa and Madagascar. The purposes of the present study were to determine whether molecular data resolve the two genera as monophyletic and to infer the origin and dispersals that produced the current distribution of the tribe.</p> <p>Methodology. Sequences from the nuclear ribosomal ITS and ETS and plastid rpl16 intron were analyzed using maximum likelihood and Bayesian analyses to resolve phylogenetic relationships within the tribe. An ancestral trait reconstruction assessed the likely ancestral range for Tarchonantheae using BioGeoBEARS, and BEAST was used for dating divergence.</p> <p>Pivotal results. We resolved Tarchonanthus as a monophyletic group nested within Brachylaena, making the latter genus paraphyletic. All Malagasy species occurred within a strongly supported clade, but also resolved within the clade was the widely distributed African species Brachylaena huillensis. This indicates two dispersal events between Africa and Madagascar—either a single dispersal to Madagascar, followed by back dispersal to Africa, or two independent dispersals from Africa. </p> <p>Conclusions. Tarchonanthus is a monophyletic group nested within Brachylaena, rendering the latter genus paraphyletic. An initial dispersal of Brachylaena from Africa to Madagascar with subsequent speciation, followed by back dispersal to Africa, with minimal morphological divergence between the African species and its sister species in Madagascar could explain the current distribution of Brachylaena. Alternatively, there may have been two dispersal events to Madagascar from Africa during the Miocene, but all within the same subclade. Dispersal of flowering plants back to Africa from Madagascar is very rare, if not unprecedented. These dispersal events, and most diversification within the tribe, including the divergence of Tarchonanthus and Brachylaena, took place during the Miocene.</p>
Data from: Molecular phylogenetics of Distephanus supports the recognition of a new tribe, Distephaneae (Asteraceae)
<p>The genus <em>Distephanus</em> Cass. comprises 43 distinctive species of shrubs and small trees that have been placed historically within the ironweed tribe, Vernonieae (Asteraceae). Utilizing the most expansive sampling of <em>Distephanus </em>to date, this study aims to test the monophyly of this genus and facilitate its classification. Molecular phylogenetic analyses were conducted using four molecular markers from the nuclear and plastid genomes. These data also supported divergence dating analyses that were performed to understand the timing of diversification events within <em>Distephanus</em> and other related genera. Results from this study indicate that as currently circumscribed, Vernonieae is not monophyletic and that <em>Distephanus </em>is actually sister to a clade that comprises Vernonieae and another tribe, Moquinieae, which only includes two species restricted to Brazil. Based on these findings, <em>Distephanus </em>is recognized in a new tribe that we describe here, Distephaneae. This new tribe comprises 41 species of <em>Disptehanus</em> that are easily distinguished from Moquinieae and Vernonieae based on the presence of florets with yellow corollas and trinervate leaves.</p>
Data supplementing the article "Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of OTUs' ecological profiles" F. Keck, V. Vasselon, F. Rimet, A. Bouchez, and M. Kahlert submitted to Molecular Ecology Resources journal
<p>These data supplement the article "Enhancing DNA metabarcoding for biomonitoring with phylogenetic estimation of OTUs' ecological profiles" F. Keck, V. Vasselon, F. Rimet, A. Bouchez, and M. Kahlert submitted to Molecular Ecology Resources journal</p> <p>The directory contains the following files:</p> <p><strong>278 (139 x 2 replicates) samples fastq files.rar </strong>- contains the 278 fastq files provided by the sequencing platform with demultiplexed and contig DNA reads corresponding to the 139 samples with 2 sequencing replicates (A and B).</p> <p><strong>Counts_diatoms.xlsx </strong>- contains the morphological inventories with species list (Omnidia code) and valve abundances for the 139 samples.</p> <p><strong>Sites_list.xlsx </strong>- contains information regarding the 139 samples, including: River name, GPS coordinates, code used for molecular analysis and corresponding to sequencing fastq names.</p>
Fig. 1. – 50 in Enlarging the monotypic Monocarpieae (Annonaceae, Malmeoideae): recognition of a second genus from Vietnam informed by morphology and molecular phylogenetics
Fig. 1. – 50% majority-rule consensus phylogram derived from Bayesian inference of combined seven plastid DNA regions. Bayesian posterior probabilities (PP) indicated on the right; maximum likelihood bootstrap (BS) percentages in the middle; parsimony symmetric resampling (SR) percentages on the left [** denotes BS/SR <50%]. DEN. = Dendrokingstonieae; MAL. = Malmeeae; MIL. = Miliuseae; MON. = Monocarpieae; PIP. = Piptostigmateae. Scale bar unit = substitutions per site.
Figure 1 in Molecular characterization and phylogenetic assessment of agricultural-related noctuids (Lepidoptera: Noctuidae) of South America
Figure 1 Collection sites in Argentina and Brazil, with provinces or states boundaries.
FIGURE 3 in Molecular phylogenetics of the wrens and allies (Passeriformes: Certhioidea), with comments on the relationships of Ferminia
FIGURE 3. Map of primers used in amplification of ZEB1.
Figure 3 in Genus Baseodiscus (Nemertea: Heteronemertea): Molecular identification of a new species in a phylogenetic context
Figure 3. External view of Baseodiscus jonasii sp. nov. Drawing made by Ray Gibson.
Fig. 3 in The Use of Molecular Phylogenetic and Morphological Tools to Identify Cryptic and Paraphyletic Species: Examples from the Diminutive Long-fingered Bats (Chiroptera: Miniopteridae: Miniopterus) on Madagascar
Fig. 3. Photograph of living Miniopterus brachytragos captured near Ambanizana, Masoala Peninsula
Figure 3. Proposed 16S in Phylogenetic relationships of thorny catfishes (Siluriformes: Doradidae) inferred from molecular and morphological data
Figure 3. Proposed 16S rRNA secondary structure model for Doradidae: (A) 5¢ end of the molecule.
Figure 3 in Phylogenetic relationships of thorny catfishes (Siluriformes: Doradidae) inferred from molecular and morphological data
Figure 3. (Continued) Proposed 16S rRNA secondary structure model for Doradidae: (B) 3¢ end.
Molecular phylogenetics of sessile Dolium sedentarium, a petalomonad euglenid
<p>The euglenids are a species-rich group of flagellates with varying modes of nutrition that can be found in diverse habitats. Phagotrophic members of this group gave rise to phototrophs and hold the key to understanding the evolution of euglenids as a whole, including the evolution of complex morphological characters like the euglenid pellicle. Yet to understand the evolution of these characters, a comprehensive sampling of molecular data is needed to correlate morphological and molecular data and to estimate a basic phylogenetic backbone of the group. While the availability of SSU rDNA and, more recently, multigene data from phagotrophic euglenids has improved, several 'orphan' taxa remain without any molecular data whatsoever. <em>Dolium</em> <em>sedentarium</em> is one such taxon: It is a rarely-observed phagotrophic euglenid that inhabits tropical benthic environments and is one of the few known sessile euglenids. Based on morphological characters, it has been thought of as part of the earliest branch of euglenids, the Petalomonadida. We report the first molecular sequencing data for <em>Dolium</em> using single-cell transcriptomics. Both SSU rDNA and multigene phylogenies confirm it as a solitary branch within Petalomonadida.</p>
Data from: The molecular phylogenetics of Trachymyrmex ants and their fungal cultivars provide insights into the origin and co-evolutionary history of 'higher-attine' ant agriculture
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Molecular phylogenetics of sessile Dolium sedentarium, a petalomonad euglenid
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Data from: Evidence of functional divergence in MSP7 paralogous proteins: a molecular-evolutionary and phylogenetic analysis
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