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14,185 results for “phylogenies”
Data from: Delimitation of the new tribe Parartocarpeae (Moraceae) is supported by a 333- gene phylogeny and resolves tribal level Moraceae taxonomy
Here we describe the new tribe, Parartocarpeae, within the Moraceae (mulberry family). The tribe comprises two small Malesian genera, Parartocarpus and Hullettia, and brings the total number of Moraceae tribes to seven. Evidence for this new designation comes from a phylogeny based on 333 nuclear genes sequenced using target enrichment via hybridization (hybseq). Morphological characters that set Parartocarpeae apart from other Moraceae tribes include the combination of the following characters: lateral nonamplexicaul stipules, spirally arranged leaves without annulate stipule scars, the presence of a single layer of involucral inflorescence bracts, and the lack of perianth tissue, wherein flowers are embedded in cavities of the receptacle. With the designation of Parartocarpeae, the tribe-level circumscription of Moraceae is now well-supported by phylogenetic methods. Because the phylogenetic markers employed here work well throughout Moraceae, they can facilitate much needed work at the genus level in the family.
Data from: Phylogeny and evolution of the neotropical radiation of Lachemilla (Rosaceae): uncovering a history of reticulate evolution and implications for infrageneric classification
Reticulate evolution often leads to incongruence between nuclear and plastid phylogenies and comparisons between them have been used as a first approximation to disentangle patterns of hybridization. Because other processes like incomplete lineage sorting and phylogenetic error also produce similar incongruence patterns, additional sources of evidence must be incorporated. Here we focus on reconstructing the phylogeny of genus Lachemilla using nuclear ribosomal ITS and plastid trnL-F DNA sequences, and explore widespread patterns of cytonuclear discordance in this group. Lachemilla is a highly morphologically variable group of perennial herbs and shrubs, and a nearly ubiquitous member of the diverse Neotropical high-altitude grasslands. Our analyses identified four major clades within Lachemilla that are in part congruent with previous morphological classifications of the group. Furthermore, using multiple sources of evidence, including a procrustean approach to cophylogeny estimation, coalescent-based simulations, phylogenetic networks, chromosome counts, and genome size estimations, we also revealed a large-scale pattern of incongruence between the plastid and nuclear phylogenies in Lachemilla, which is mainly the result of widespread hybridization and polyploidy. We also estimated that the origin of Lachemilla in South America (~14.5 mya) predates the "rapid-uplift" diversification model that has been suggested for other high species-richness Andean plant clades, but following the formation of the high-elevation Andean grasslands during the last 5 mya, a rapid accumulation of particular nested lineages occurred has contributed to the ubiquitous presence of Lachemilla in these biomes.
Data from: Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions
<p>Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread use of analytical sampling corrections for sparsely sampled phylogenies of higher taxonomic groups. In particular, corrections based on "sampling fractions" can lead to low statistical power to infer rate variation when it is present, depending on the likelihood function used for inference. In the extreme, the sampling fraction correction can lead to spurious patterns of diversification that are driven solely by unbalanced sampling across the tree in concert with low overall power to infer shifts. Stochastic polytomy resolution provides an alternative to sampling fraction approaches that avoids some of these biases. We show that stochastic polytomy resolvers can greatly improve the power of common analyses to estimate shifts in diversification rates. We introduce a new stochastic polytomy resolution method (TACT: Taxonomic Addition for Complete Trees) that uses birth-death-sampling estimators across an ultrametric phylogeny to estimate branching times for unsampled taxa, with taxonomic information to compatibly place new taxa onto a backbone phylogeny. We close with practical recommendations for diversification inference under several common scenarios of incomplete sampling.</p>
Data from: Phylogeny and morphologic evolution of the Ordovician Camerata (Class Crinoidea, Phylum Echinodermata)
The subclass Camerata (Crinoidea, Echinodermata) is a major group of Paleozoic crinoids that represents an early divergence in the evolutionary history and morphologic diversification of class Crinoidea, yet phylogenetic relationships among early camerates remain unresolved. This study conducted a series of quantitative phylogenetic analyses using parsimony methods to infer relationships of all well-preserved Ordovician camerate genera (52 taxa), establish the branching sequence of early camerates, and test the monophyly of traditionally recognized higher taxa, including orders Monobathrida and Diplobathrida. The first phylogenetic analysis identified a suitable outroup for rooting the Ordovician camerate tree and assessed affinities of the atypical dicyclic family Reteocrinidae. The second analysis inferred the phylogeny of all well-preserved Ordovician camerate genera. Inferred phylogenies confirm: (1) the Tremadocian genera Cnemecrinus and Eknomocrinus are sister to the Camerata; (2) as historically defined, orders Monobathrida and Diplobathrida do not represent monophyletic groups; (3) with minimal revision, Monobathrida and Diplobathrida can be re-diagnosed to represent monophyletic clades; (4) family Reteocrinidae is more closely related to camerates than to other crinoid groups currently recognized at the subclass level; and (5) several genera in subclass Camerata represent stem taxa that cannot be classified as either true monobathrids or true diplobathrids. The clade containing Monobathrida and Diplobathrida, as recognized herein, is termed Eucamerata to distinguish its constituent taxa from more basally positioned taxa, termed stem eucamerates. The results of this study provide a phylogenetic framework for revising camerate classification, elucidating patterns of morphologic evolution, and informing outgroup selection for future phylogenetic analyses of post-Ordovician camerates.
Data from: Descriptions of four new species of Minyomerus Horn, 1876 sec. Jansen & Franz, 2018 (Coleoptera: Curculionidae), with notes on their distribution and phylogeny
This contribution adopts the taxonomic concept approach, including the use of taxonomic concept labels (name sec. [according to] source) and region connection calculus-5 (RCC–5) articulations and alignments. Prior to this study, the broad-nosed weevil genus Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Curculionidae [non-focal]: Entiminae [non-focal]: Tanymecini [non-focal]) contained 17 species distributed throughout the desert and plains regions of North America. In this review of Minyomerus sec. Jansen & Franz, 2018, we describe the following four species as new to science: Minyomerus ampullaceus sec. Jansen & Franz, 2018 (henceforth: [JF2018]), new species, Minyomerus franko [JF2018], new species, Minyomerus sculptilis [JF2018], new species, and Minyomerus tylotos [JF2018], new species. The four new species are added to, and integrated with, the preceding revision, and an updated key and phylogeny of Minyomerus [JF2018] are presented. A cladistic analysis using 52 morphological characters of 26 terminal taxa (5/21 outgroup/ingroup) yielded a single most-parsimonious cladogram (Length = 99 steps, consistency index = 60, retention index = 80). The analysis reaffirms the monophyly of Minyomerus [JF2018] with eight unreversed synapomorphies. The species-group placements, possible biogeographic origins, and natural history of the new species are discussed in detail.
Data from: Archipelago-wide survey of Philippine forest dragons (Agamidae: Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot
We utilize robust geographical genetic sampling, a multilocus dataset, and coalescent-based species delimitation statistics to provide the first phylogenetic inferences of relationships of Philippine Gonocephalus, combined with estimates of putative species diversity in this virtually unknown island radiation. Our results reveal startling levels of undocumented diversity, genetically partitioned at a number of geographic levels across the archipelago. In this paper we present the first survey of genetic lineage diversity, coupled with an archipelago-wide elucidation of geographic structure in a unique archipelago-endemic radiation. Philippine Gonocephalus have previously escaped the attention of biogeographers, due to taxonomic confusion associated with low numbers of preserved specimens in museum collections. With new vouchered material and genetic sampling from a comprehensive, archipelago-wide vertebrate biodiversity inventory, our findings join many recent studies highlighting the unprecedented faunal diversity in one of the world's most unique biodiversity conservation hotspots.
A genome-skimmed phylogeny of a widespread bryozoan family, Adeonidae
<p>Understanding the phylogenetic relationships among species is one of the main goals of systematic biology. Simultaneously, credible phylogenetic hypotheses are often the first requirement for unveiling the evolutionary history of traits and for modelling macroevolutionary processes. However, many non-model taxa have not yet been sequenced to an extent such that statistically well-supported molecular phylogenies can be constructed for these purposes. Here, we use a genome-skimming approach to extract sequence information for 15 mitochondrial and 2 ribosomal operon genes from the cheilostome bryozoan family, the Adeonidae, Busk, 1884, whose current systematics is based purely on morphological traits. The members of the Adeonidae are, like all cheilostome bryozoans, benthic, colonial, marine organisms. Adeonids are also geographically widely-distributed, often locally common, and are sometimes important habitat-builders. Results We successfully genome-skimmed 35 adeonid colonies representing 6 genera (Adeona, Adeonellopsis, Bracebridgia, Adeonella, Laminopora and Cucullipora). We also contributed 16 new, circularised mitochondrial genomes to the eight previously published for cheilostome bryozoans. Using the aforementioned mitochondrial and ribosomal genes, we inferred the relationships among these 35 samples. Contrary to some previous suggestions, the Adeonidae is a robustly supported monophyletic clade. However, the genera Adeonella and Laminopora are in need of revision: Adeonella is polyphyletic and Laminopora paraphyletically forms a clade with some Adeonella species. Additionally, we assign a sequence clustering identity using cox1 barcoding region of 99% at the species and 83% at the genus level. Conclusions We provide sequence data, obtained via genome-skimming, that greatly increases the resolution of the phylogenetic relationships within the adeonids. We present a highly-supported topology based on 17 genes and substantially increase availability of circularised cheilostome mitochondrial genomes, and highlight how we can extend our pipeline to other bryozoans.</p>
Data from: Reticulate evolution in nuclear Middle America causes discordance in the phylogeny of palm‐pitvipers (Viperidae: Bothriechis)
Aim: A number of processes can lead to weak or conflicting phylogenetic signals, especially in geographically dynamic regions where unstable landscapes and climates promote complex evolutionary histories. The Middle American pitviper genus Bothriechis has a complex biogeographic distribution and previous phylogenetic analyses have recovered conflicting topologies based on the data type used. Here, we tested whether historic conflicts in the phylogeny were the result of reticulate evolution and whether the inferred biogeographic history of the group would enable contact among reticulate lineages. Location: Middle America Taxon: Palm-Pitvipers (genus Bothriechis) Methods: We generated a phylogenomic dataset using an anchored phylogenomics approach and inferred a genomics-based species tree and mitochondrial tree to assess incongruence among datasets. We then generated a dated phylogeny and conducted ancestral area reconstruction to examine the biogeographic history surrounding the diversification of these species. We additionally tested whether the discordance among trees is better explained by lineage sorting or reticulate evolution by testing models of reticulate evolution inferred through multiple methods. Results: We found strong support for discordance in the phylogeny of <i>Bothriechis</i> and corresponding evidence for reticulate evolution among lineages with incongruent placement. Ancestral area reconstruction placed these taxa in adjacent regions during the time period when reticulation was projected to take place and suggested a biogeographic history heavily influenced by vicariant processes. Main conclusions: Reticulation among geographically proximate lineages has driven apparent genomic discordance in Bothriechis and is responsible for historical incongruence in the phylogeny. Inference of the order of events suggests that reticulation in Nuclear Middle American occurred during a time of geologic upheaval, promoting lineage divergence and secondary contact. Reticulate evolution and similar processes can have substantial impacts on the evolutionary trajectory of taxa and are important to explicitly test for in biogeographically complex regions. Main conclusions: Reticulation among geographically proximate lineages has driven apparent genomic discordance in Bothriechis and is responsible for historical incongruence in the phylogeny. Inference of the order of events suggests that reticulation in Nuclear Middle American occurred during a time of geologic upheaval, promoting lineage divergence and secondary contact. Reticulate evolution and similar processes can have substantial impacts on the evolutionary trajectory of taxa and are important to explicitly test for in biogeographically complex regions.
Data from: Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae)
Phylogenetic relationships among recently diverged species are often difficult to resolve due to insufficient phylogenetic signal in available markers and/or conflict among gene trees. Here we explore the use of reduced-representation genome sequencing, specifically in the form of restriction-site associated DNA (RAD), for phylogenetic inference and the detection of ancestral hybridization in non-model organisms. As a case study, we investigate Pedicularis section Cyathophora, a systematically recalcitrant clade of flowering plants in the broomrape family (Orobanchaceae). Two methods of phylogenetic inference, maximum likelihood and Bayesian concordance, were applied to data sets that included as many as 40,000 RAD loci. Both methods yielded similar topologies that included two major clades: a "rex-thamnophila" clade, composed of two species and several subspecies with relatively low floral diversity, and geographically widespread distributions at lower elevations, and a "superba" clade, composed of three species characterized by relatively high floral diversity and isolated geographic distributions at higher elevations. Levels of molecular divergence between subspecies in the rex-thamnophila clade are similar to those between species in the superba clade. Using Patterson's D-statistic test, including a novel extension of the method that enables finer-grained resolution of introgression among multiple candidate taxa by removing the effect of their shared ancestry, we detect significant introgression among nearly all taxa in the rex-thamnophila clade, but not between clades or among taxa within the superba clade. These results suggest an important role for geographic isolation in the emergence of species barriers, by facilitating local adaptation and differentiation in the absence of homogenizing gene flow.
Data from: Phylogeny and biogeography of the core babblers (Aves: Timaliidae)
The avian family Timaliidae is a species rich and morphologically diverse component of African and Asian tropical forests. The morphological diversity within the family has attracted interest from ecologists and evolutionary biologists, but systematists have long suspected that this diversity might also mislead taxonomy, and recent molecular phylogenetic work has supported this hypothesis. We produced and analyzed a dataset of six genes and almost 300 individuals to assess the evolutionary history of the family. Although phylogenetic analysis required extensive adjustment of program settings, we ultimately produced a well-resolved phylogeny for the family. The resulting phylogeny provided strong support for major subclades within the family but extensive paraphyly of genera. Only three genera represented by more than three species were monophyletic. Biogeographic reconstruction indicated a mainland Asian origin for the family and most major clades. Colonization of Africa, Sundaland, and the Philippines occurred relatively late in the family's history and was mostly unidirectional. Several putative babbler genera, such as Robsonius, Malia, Leonardina, and Micromacronus are only distantly related to the Timaliidae.
Phylogeny and biogeography of the hollies (Ilex L., Aquifoliaceae)
<p>The holly genus, <em>Ilex</em> L., in the monogeneric Aquifoliaceae, is the largest woody dioecious genus (>664 spp.), with a near‐cosmopolitan distribution in mesic environments. We constructed a phylogeny based on two nuclear genes, representing 177 species spread across the geographical range, and dated using macrofossil records. The five main clades had a common ancestor in the early Eocene, much earlier than previously suggested. <em>Ilex</em> originated in subtropical Asia and extant clades colonized South America by 30 Ma, North America by 23 Ma, Australia by 8 Ma, Europe by 6 Ma, and Africa by 4 Ma. South and North America were colonized multiple times. <em>Ilex</em> also reached Hawaii (10 Ma) and other oceanic islands. Macrofossil and pollen records show the genus has tracked mesic climates through time and space, and had a wider distribution before late Miocene global cooling. Our phylogeny provides a framework for studies in comparative ecology and evolution.</p>
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.
Data from: A worldwide molecular phylogeny provides new insight on cryptic diversity within the moonworts (Botrychium s. s., Ophioglossaceae)
The moonwort genus, Botrychium s. s., includes diploid and polyploid taxa that occur primarily in the northern hemisphere. Their evolutionary history, morphologically cryptic taxa and deep divergence of the family in the phylogeny of ferns has long fascinated pteridologists. Previous molecular studies did not include a complete taxonomic sampling of the taxa in the genus, nor multiple specimens from throughout the known geographical range of each taxon. Therefore, to investigate evolutionary relationships of the major clades of Botrychium s. s., we increased both taxonomic representativeness (multiple accessions per taxa), as well as phylogenetic resolution by including additional new chloroplast markers. To confirm identification and provide evidence from both maternal and paternal parentage of allopolyploids, we also included specimens that have been characterized by allozyme profiles determined by electrophoretic analysis of 20 nuclear enzyme loci for each taxon. We analyzed four chloroplast regions (matK intron, trnHGUG —psbA, andtrnLUAA —trnFGAA intergenic spacers, and rpL16 intron region) of 365 specimens fromAsia, Europe, North America, Oceania, and South America, sampling the geographical range of 34 of 35 accepted Botrychium s. s. taxa and thirteen putatively new taxa. We conducted a phylogenetic analysis of maternal lineages based on 2,385 aligned nucleotides using maximum likelihood and Bayesian inference to explore genetic diversity and phylogenetic relationships among taxa. We found strong support for themonophyly of three major clades: Lanceolatum, Lunaria, and Simplex-Campestre, and resolved 15 subclades. Our results suggest multiple origins for at least four polyploid taxa (B. boreale, B. michiganense, B. yaaxudakeit, and B. watertonense). The Simplex-Campestre clade had the largest number of species, despite having a similar total number of haplotypes as the Lunaria clade (62 and 59, respectively), which has the broadest worldwide distribution. In total, our new molecular phylogeny comprises 47 taxa, of which thirteen are discussed for possible taxonomic recognition.
Data alignment and phylogenetic trees from Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales
<p>Alignment and tree files from Ruck et al. 2016:</p> <p>Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales</p>
FIGURE 5. Cyt b in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 5. Cyt b tree for Monitilorinae and Lucininae, expanded from Figure 4.
FIGURE 3. Combined gene tree for Lucininae, expanded from Figure 1 in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 3. Combined gene tree for Lucininae, expanded from Figure 1.
FIGURE 2. Combined gene tree for Codakiinae, expanded from Figure 1 in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 2. Combined gene tree for Codakiinae, expanded from Figure 1.
Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)
Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)
Figure 10. - Maximum-likelihood phylogeny of Epicephala species based on sequences of the COI, ArgK and EF1α genes. Numbers above nodes are maximum-likelihood bootstrap support values based on 1,000 replications. The Japanese Epicephala species are marked in blue. Symbols right to species names donate ovipositor morphology: inverted U-shape, rounded apically; inverted V-shape, acute apically.
Figure 10. - Maximum-likelihood phylogeny of Epicephala species based on sequences of the COI, ArgK and EF1α genes. Numbers above nodes are maximum-likelihood bootstrap support values based on 1,000 replications. The Japanese Epicephala species are marked in blue. Symbols right to species names donate ovipositor morphology: inverted U-shape, rounded apically; inverted V-shape, acute apically.
The phylogeny of fossil whip spiders
<p>Additional files for the publication The phylogeny of fossil whip spiders, published in BMC Evolutionary Biology. </p> <p>Additional file 1. File format: .vaxml (see [38]). Title: Tomographic reconstruction of <em> Graeophonus anglicus</em> Pocock, 1911. Description: A 3D mesh model of Graeophonus anglicus in the VAXML interchange format. </p> <p>Additional file 2. File format: .pdf. Title: Character statements. Description: Morphological characters statements for the characters used in the current analysis. </p> <p>Additional file 3. File format: .tnt (see [45]). Title: Cladistic matrix. Description: Cladistic matrix used in the current analysis, in a TNT ready format. </p> <p>Additional file 4. A video showing the tomographic reconstruction of<em> Graeophonus anglicus </em>Pocock, 1911 presented herein; inferred/reconstructed anatomy partially transparent.</p>
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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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