Phylogeny Of Taxa Research Articles

Climate Change during Cretaceous/Paleogene as a Driving Force for the Evolutionary Radiation of Physical Dormancy in Fabaceae

Physical dormancy (PY) due to a water-impermeable seed/fruit coat is one of the characteristic features of many species of Fabaceae; however, the timing and context of the evolution of this trait are poorly understood. In this investigation, fossil and molecular data are used to constrain the timing of the evolution of PY. The phylogenetic reconstruction programs GB-to-TNT and BEAUTi/BEAST are used to create chloroplast gene-based (rbcL and matK) phylogenies of taxa with well-represented fossil records. PY and non-dormancy are mapped to the terminals of the phylogeny, and ancestral states are reconstructed using parsimony. The initial evolution of PY in Fabaceae is reconstructed to have occurred sometime in the interval between divergence from Polygalaceae (late Campanian) to the diversification of crown-group Fabaceae (late Paleocene) when Fabaceae is known to have undergone multiple whole genome duplication (WGD) events across the Cretaceous/Paleogene (K/Pg) boundary. As in Nelumbo, another taxon with PY, Fabaceae may have developed PY in association with climatic change and WGD across the K/Pg boundary. The evolution of PY in association with WGD at the K/Pg boundary is an intriguing hypothesis that requires further investigation.

MbImpute: an accurate and robust imputation method for microbiome data

A critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data—mbImpute—to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. We demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances.

Impacts of Genistein on the Gut Microbiota of a Mouse Model of Cystic Fibrosis (P06-070-19)

ObjectivesDysbiosis of the gut microbiota (GM) is observed in both murine models and humans with cystic fibrosis (CF). Laxative treatments are typically used to improve gastric motility and alleviate gastrointestinal symptoms associated with CF. Genistein, a phytochemical in soy, exerts therapeutic benefits by activating intestinal CFTR ion channels but whether genistein affects the GM in CF is unknown. This study aimed to establish whether dietary genistein alters the GM community structure in a murine model of the most common CF-associated mutation, DF508. MethodsIn this 3-arm parallel randomized intervention, 21-day old DF508 mice (n = 24) were fed standard chow (CHOW; n = 11), CHOW plus Colyte (laxative; n = 7), or CHOW plus 600 mg of dietary genistein (GEN) per kg of diet (n = 6) for 45 days. Fecal pellets from day 45 were frozen at –80°C and microbial genomic DNA extracted using a DNeasy PowerSoil Kit. The 16S rRNA gene was sequenced via Illumina MiSeq. Sequences were quality checked and denoised using DADA2 and taxonomy determined using the GreenGenes 13.8 database. Treatment differences in the GM were compared using both alpha (within-sample) and beta (between-sample) diversity metrics (Kruskal-Wallis and PERMANOVA tests). ResultsBoth observed operational taxonomic units (OTUs) and Shannon’s diversity index (alpha diversity richness measures) were greater for CHOW (OTUs: p = < 0.003; Shannon’s: p < 0.003) and Colyte (OTUs: p = 0.012; Shannon’s: p = 0.006) compared to GEN animals. Colyte resulted in significantly lower species richness (OTUs: p < 0.005) compared to CHOW. Species evenness (Pielou’s) did not differ suggesting the importance of species richness over evenness for group differences. Jaccard, Bray-Curtis, unweighted and weighted UniFrac metrics (beta diversity measures) revealed significant group differences (GEN vs. CHOW: p’s < 0.004; GEN vs. Colyte: p’s < 0.005; CHOW vs. Colyte: p’s < 0.006) suggesting that differences in GM community structure were driven by presence/absence, abundance, and phylogeny of taxa. ConclusionsColyte and GEN resulted in lower within-sample diversity and significant differences in beta diversity compared to CHOW mice. Species abundance differences between Colyte and GEN groups and how disease prognosis is impacted require further investigation. Funding SourcesMidwestern University intramural funds (LA) and Arizona State University internal funds (CMW).

Does responsiveness to arbuscular mycorrhizal fungi depend on plant invasive status?

Differences in the direction and degree to which invasive alien and native plants are influenced by mycorrhizal associations could indicate a general mechanism of plant invasion, but whether or not such differences exist is unclear. Here, we tested whether mycorrhizal responsiveness varies by plant invasive status while controlling for phylogenetic relatedness among plants with two large grassland datasets. Mycorrhizal responsiveness was measured for 68 taxa from the Northern Plains, and data for 95 taxa from the Central Plains were included. Nineteen percent of taxa from the Northern Plains had greater total biomass with mycorrhizas while 61% of taxa from the Central Plains responded positively. For the Northern Plains taxa, measurable effects often depended on the response variable (i.e., total biomass, shoot biomass, and root mass ratio) suggesting varied resource allocation strategies when roots are colonized by arbuscular mycorrhizal fungi. In both datasets, invasive status was nonrandomly distributed on the phylogeny. Invasive taxa were mainly from two clades, that is, Poaceae and Asteraceae families. In contrast, mycorrhizal responsiveness was randomly distributed over the phylogeny for taxa from the Northern Plains, but nonrandomly distributed for taxa from the Central Plains. After controlling for phylogenetic similarity, we found no evidence that invasive taxa responded differently to mycorrhizas than other taxa. Although it is possible that mycorrhizal responsiveness contributes to invasiveness in particular species, we find no evidence that invasiveness in general is associated with the degree of mycorrhizal responsiveness. However, mycorrhizal responsiveness among species grown under common conditions was highly variable, and more work is needed to determine the causes of this variation.

Three New Species ofAleurodiscuss.l. (Russulales, Basidiomycota) on Bamboos from East Asia

Abstract Three new species, Aleurodiscus dextrinoideophyses, A. thailandicus and A. verrucosporus, on bamboos are described and illustrated based on morphological and molecular evidence. Aleurodiscus dextrinoideophyses and A. thailandicus, collected from northern Thailand, possess abundant acanthophyses and small smooth basidiospores, and belong to the A. cerussatus group. While A. dextrinoideophyses is characterized by the dextrinoid acanthophyses, A. thailandicus has yellow acanthophyses arranged between subhymenium and basal layer. Aleurodiscus verrucosporus, collected from Fujian Province, southeastern China, is distinguished by the absence of acanthophyses and verrucose basidiospores. All the three species have abundant gloeocystidia and simple-septate generative hyphae. The phylogeny of taxa in Stereaceae was inferred from the combined ITS and nrLSU sequence data. In our phylogenetic analyses, A. dextrinoideophyses and A. thailandicus steadily nested within the A. cerussatus group, whereas A. verruc...

Biometry of neotropical invertebrates inhabiting floodplain rivers: unraveling bionomy

ABSTRACT Currently, it is widely recognized that invertebrates play key roles in neotropical floodplains and in many other environments worldwide. However, little information has been published concerning their biometry, in spite that it represents an essential tool for many different studies. Here, we provided length-mass and length-length relationships by fitting the linearized model (log10 Y = log10a + b log10 X) and several mean biomass ratios ± SE for bivalves, gastropods, quironomids, ephemeropterans, oligochaetes and hirudineans. We measured, weighed, oven dried and incinerated to ashes specimens collected from 2005 to 2014 in the Paraná River, Argentina. The lineal equations had fit levels higher than 75% in most of the significant regressions. Hence, when slopes were compared, differences raised from ontogeny and phylogeny of taxa. Additionally, slopes resulted different from constants of other regions, types of environments and climates. In addition, organic matter ratios resulted significantly different among invertebrates according to their feeding types. The equations and ratios that we provided will facilitate future research on life history, productivity and energy transference in the food webs of invertebrates inhabiting floodplain wetlands and can be used as tools for planning management strategies and in restoration projects of aquatic environments.

Evaluation of composition and individual variability of rumen microbiota in yaks by 16S rRNA high-throughput sequencing technology

The Yak (Bos grunniens) is a unique species of ruminant animals that is important to agriculture of the Tibetan plateau, and has a complex intestinal microbial community. The objective of the present study was to characterize the composition and individual variability of microbiota in the rumen of yaks using 16S rRNA gene high-throughput sequencing technique. Rumen samples used in the present study were obtained from grazing adult male yaks (n = 6) in a commercial farm in Ganzi Autonomous Prefecture of Sichuan Province, China. Universal prokaryote primers were used to target the V4–V5 hypervariable region of 16S rRNA gene. A total of 7200 operational taxonomic units (OTUs) were obtained after sequence filtering and chimera removal. Within these OTUs, 0.56% belonged to Archaea (40 OTUs), 7.19% to unassigned species (518 OTUs), and the remaining OTUs (6642) in all samples were of bacterial origin. When examining the community structure of bacteria, we identified 23 phyla within 159 families after taxonomic summarization. Bacteroidetes and Firmicutes were the predominant phyla accounting for 39.68% (SD = 0.05) and 45.90% (SD = 0.06), respectively. Moreover, 3764 OTUs were identified as shared OTUs (i.e. represented in all yaks) and belonged to 35 genera, exhibiting highly variable abundance across individual samples. Phylogenetic placement of these genera across individual samples was examined. In addition, we evaluated the distance among the 6 rumen samples by adding taxon phylogeny using UniFrac, representing 24.1% of average distance. In summary, the current study reveals a shared rumen microbiome and phylogenetic lineage and presents novel information on composition and individual variability of the bacterial community in the rumen of yaks.

Phylogeny and taxonomy of poroid and lamellate genera in the Auriculariales (Basidiomycota)

The phylogeny of taxa with poroid and lamellate hymenophores in Auriculariales as yet has not been well studied. Here we sequenced the nLSU and ITS regions of poroid and lamellate representatives from the genera Elmerina, Protodaedalea and Protomerulius to establish the phylogenetic position of these morphologically similar taxa. Our analyses suggest that (i) Elmerina foliacea is divergent from all other Elmerina species sampled; (ii) Protodaedalea hispida (the type of monotypic genus Protodaedalea) and Protomerulius efibulatus should be transferred to Elmerina as E. hispida and E. efibulata respectively; (iii) after exclusion of P. efibulatus, Protomerulius becomes monophyletic and represents the core of a “Protomerulius family” clade that potentially includes species from Tremellodendropsis, Heterochaetella and Protodontia; and (iv) the presence or absence of gloeocystidia serves as the most reliable morphological feature in delimiting Elmerina s.l. and Protomerulius. Concepts of Elmerina s.l. and Protomerulius are redefined, and diagnostic keys for these two genera are provided.

Composition and Similarity of Bovine Rumen Microbiota across Individual Animals

The bovine rumen houses a complex microbiota which is responsible for cattle's remarkable ability to convert indigestible plant mass into food products. Despite this ecosystem's enormous significance for humans, the composition and similarity of bacterial communities across different animals and the possible presence of some bacterial taxa in all animals' rumens have yet to be determined. We characterized the rumen bacterial populations of 16 individual lactating cows using tag amplicon pyrosequencing. Our data showed 51% similarity in bacterial taxa across samples when abundance and occurrence were analyzed using the Bray-Curtis metric. By adding taxon phylogeny to the analysis using a weighted UniFrac metric, the similarity increased to 82%. We also counted 32 genera that are shared by all samples, exhibiting high variability in abundance across samples. Taken together, our results suggest a core microbiome in the bovine rumen. Furthermore, although the bacterial taxa may vary considerably between cow rumens, they appear to be phylogenetically related. This suggests that the functional requirement imposed by the rumen ecological niche selects taxa that potentially share similar genetic features.

Optimality of phylogenetic nomenclatural procedures

Nomenclatures resulting from the application of various procedures are viewed as communication tools whose optimality can be compared. The traditional, node-based, branch-based, apomorphy-based, and cladotypic procedures are compared based on theoretical cases. The traditional procedure collects several major drawbacks: endings related to ranks are of low information content on taxa hierarchy; with respect to procedures using uninominal species names, in case of a partly unbalanced and/or partly unresolved phylogeny, the application of the procedure results into supernumerary names; a traditional taxon name is prone to be polysemic, depending upon someone’s opinion on the rank and composition of the taxon, and upon conflicting hypotheses on the phylogenetic position of name-bearing types. Alternative systems vary in merit. Names of apomorphy-defined taxa are prone to be polysemic due to possible ambiguity in the formulation of the defining character state. The cladotypic nomenclatural procedure is similar in that respect, but a set of rules allow ambiguity to be limited. The main issue of node- and branch-based procedures is that cases of synonymy cannot be settled if the inner phylogeny of taxa cannot be resolved. Cases of irresolvable synonymy can occur under apomorphy-based and cladotypic procedures, but the problem can be circumvented by the use of taxa whose defining character state is not subject to ambiguous mapping. Node-, branch- and apomorphy-based definitions as governed by the PhyloCode can produce nonsensical statements, but this problem can be fixed by the adjunction of falsifiable assumptions in use under the cladotypic procedure. Cladotypic definitions must involve a fourth assumption formulated as ‘cladotypes belong to different species’ (cladogenesis assumption). The present contribution suggests that the cladotypic procedure outperforms all other proposed procedures, producing an optimal formal lexicon useful for naming and communicating about species and taxa.

The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans

BackgroundComparative genomics of the early diverging metazoan lineages and of their unicellular sister-groups opens new window to reconstructing the genetic changes which preceded or accompanied the evolution of multicellular body plans. A recent analysis found that the genome of the nerve-less sponges encodes the homologues of most vertebrate post-synaptic proteins. In vertebrate excitatory synapses, these proteins assemble to form the post-synaptic density, a complex molecular platform linking membrane receptors, components of their signalling pathways, and the cytoskeleton. Newly available genomes from Monosiga brevicollis (a member of Choanoflagellata, the closest unicellular relatives of animals) and Trichoplax adhaerens (a member of Placozoa: besides sponges, the only nerve-less metazoans) offer an opportunity to refine our understanding of post-synaptic protein evolution.ResultsSearches for orthologous proteins and reconstruction of gene gains/losses based on the taxon phylogeny indicate that post-synaptic proteins originated in two main steps. The backbone scaffold proteins (Shank, Homer, DLG) and some of their partners were acquired in a unicellular ancestor of choanoflagellates and metazoans. A substantial additional set appeared in an exclusive ancestor of the Metazoa. The placozoan genome contains most post-synaptic genes but lacks some of them. Notably, the master-scaffold protein Shank might have been lost secondarily in the placozoan lineage.ConclusionsThe time of origination of most post-synaptic proteins was not concomitant with the acquisition of synapses or neural-like cells. The backbone of the scaffold emerged in a unicellular context and was probably not involved in cell-cell communication. Based on the reconstructed protein composition and potential interactions, its ancestral function could have been to link calcium signalling and cytoskeleton regulation. The complex later became integrated into the evolving synapse through the addition of novel functionalities.

Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae).

BackgroundMany molecular phylogenetic analyses rely on DNA sequence data obtained from single or multiple loci, particularly mitochondrial DNA loci. However, phylogenies for taxa that have undergone recent, rapid radiation events often remain unresolved. Alternative methodologies for discerning evolutionary relationships under these conditions are desirable. The dolphin subfamily Delphininae is a group that has likely resulted from a recent and rapid radiation. Despite several efforts, the evolutionary relationships among the species in the subfamily remain unclear.ResultsHere, we compare a phylogeny estimated using mitochondrial DNA (mtDNA) control region sequences to a multi-locus phylogeny inferred from 418 polymorphic genomic markers obtained from amplified fragment length polymorphism (AFLP) analysis. The two sets of phylogenies are largely incongruent, primarily because the mtDNA tree provides very poor resolving power; very few species' nodes in the tree are supported by bootstrap resampling. The AFLP phylogeny is considerably better resolved and more congruent with relationships inferred from morphological data. Both phylogenies support paraphyly for the genera Stenella and Tursiops. The AFLP data indicate a close relationship between the two spotted dolphin species and recent ancestry between Stenella clymene and S. longirostris. The placement of the Lagenodelphis hosei lineage is ambiguous: phenetic analysis of the AFLP data is consistent with morphological expectations but the phylogenetic analysis is not.ConclusionFor closely related, recently diverged taxa, a multi-locus genome-wide survey is likely the most comprehensive approach currently available for phylogenetic inference.

Microsatellites retain phylogenetic signals across genera in eucalypts (Myrtaceae)

The utility of microsatellites (SSRs) in reconstructing phylogenies is largely confined to studies below the genus level, due to the potential of homoplasy resulting from allele size range constraints and poor SSR transferability among divergent taxa. The eucalypt genus Corymbia has been shown to be monophyletic using morphological characters, however, analyses of intergenic spacer sequences have resulted in contradictory hypotheses- showing the genus as either equivocal or paraphyletic. To assess SSR utility in higher order phylogeny in the family Myrtaceae, phylogenetic relationships of the bloodwood eucalypts Corymbia and related genera were investigated using eight polymorphic SSRs. Repeat size variation using the average square and Nei's distance were congruent and showed Corymbia to be a monophyletic group, supporting morphological characters and a recent combination of the internal and external transcribed spacers dataset. SSRs are selectively neutral and provide data at multiple genomic regions, thus may explain why SSRs retained informative phylogenetic signals despite deep divergences. We show that where the problems of size-range constraints, high mutation rates and size homoplasy are addressed, SSRs might resolve problematic phylogenies of taxa that have diverged for as long as three million generations or 30 million years.

Historical biogeography of Australian Rhamnaceae, tribe Pomaderreae

AbstractAim To discover the pattern of relationships of areas of endemism for Australian genera in the plant family Rhamnaceae tribe Pomaderreae for comparison with other taxa and interpretation of biogeographical history.Location Australian mainland, Tasmania and New Zealand.Methods A molecular phylogeny and geographic distribution of species within four clades of Pomaderreae are used as a basis for recognition of areas of endemism and analysis of area relationships using paralogy‐free subtrees. The taxon phylogeny is the strict consensus tree from a parsimony analysis of 54 taxa, in four clades, and sequence data for the internal transcribed spacer regions of ribosomal DNA (ITS1‐5.8S‐ITS2) and the plastid DNA region trnL‐F.Results The biogeographical analysis identified five subtrees, which, after parsimony analysis, resulted in a minimal tree with 100% consistency and seven resolved nodes. Three sets of area relationships were identified: the areas of Arnhem and Kimberley in tropical north Australia are related based on the phylogeny of taxa within Cryptandra; the moister South‐west of Western Australia, its sister area the coastal Geraldton Sandplains, the semi‐arid Interzone region and arid Western Desert are related, based on taxa within Cryptandra, Spyridium, Trymalium and Pomaderris; and the eastern regions of Queensland, McPherson‐Macleay, south‐eastern New South Wales (NSW), Victoria, southern Australia, Tasmania and New Zealand are related based on Cryptandra, Pomaderris and Spyridium. Tasmania and NSW are related based entirely on Cryptandra, but the position of New Zealand relative to the other south‐eastern Australian regions is unresolved.Main conclusions The method of paralogy‐free subtrees identified a general pattern of geographic area relationships based on Australian Pomaderreae. The widespread distribution of clades, the high level of endemicity and the age of fossils for the family, suggest that the Pomaderreae are an old group among the Australian flora. Their biogeographical history may date to the early Palaeogene with subsequent changes through to the Pleistocene.

Tree balance, time slices, and evolutionary turnover in cretaceous planktonic foraminifera.

Studies of phylogenetic tree shape often concentrate on the balance of phylogenies of extant taxa. Paleontological phylogenies (which include extinct taxa) can contain additional useful information and can directly document changes in tree shape through evolutionary time. Unfortunately, the inclusion of extinct taxa lowers the power of direct examinations of tree balance because it increases the range of tree shapes expected under null models of evolution (with equal rates of speciation and extinction across lineages). A promising approach for the analysis of tree shape in paleontological phylogenies is to break the phylogeny down into time slices, examining the shape of the phylogeny of taxa alive at each time slice and changes in that shape between successive time slices. This method was illustrated with 57 time slices through a stratophenetic phylogeny of the Cretaceous planktonic foraminiferal superfamily Globotruncanacea. At 3 of 56 intervals between time slices, 93-92.5 million years ago (MYA), 89-88.5 MYA, and 85.5-84 MYA, the group showed steep increases in imbalance. Although none of these increases were significant after Bonferroni correction, these points in the history of the Globotruncanacea were nevertheless identified as deserving of further macroevolutionary investigation. The 84 MYA time slice coincides with a peak in species turnover for the superfamily. Time slices through phylogenies may prove useful for identifying periods of time when evolution was proceeding in a nonstochastic manner.

Molecular systematics of E-strain mycorrhizal fungi: Wilcoxina and its relationship to Tricharina (Pezizales)

Nuclear-encoded ribosomal RNA gene sequences (rDNA) spanning 107 base pairs at the 3′ end of the 18S gene, the 5′ internal transcribed spacer region (ITS1), and across divergent domain D1 near the 5′ end of the 28S gene were analyzed to infer a phylogeny for taxa of the E-strain mycorrhizal fungal genus Wilcoxina and to determine their relationship to representatives of the genus Tricharina. The phylogeny suggests that Wilcoxina and Tricharina, although related, should be maintained as separate genera. Wilcoxina taxa formed a distinct group that exhibited interspecific variation of 37.6% in the ITS1 region. Wilcoxina alaskana was the most distant taxon, which is consistent with its growth on an unusual substrate (rotting wood). It remains to be confirmed that this taxon is mycorrhizal. A cryptic Wilcoxina species, known only from root isolates, was found. Sequence analysis of the ITS1 region distinguished two varieties of Wilcoxina mikolae: var. mikolae and var. tetraspora. Among the taxa of Tricharina examined there was 31.2% variation in the ITS1 region. The most divergent taxon in the Tricharina group was Tricharina praecox, although sequence analysis was unable to distinguish the varieties described within this species. The remaining taxa in Tricharina formed a tight group with only 10.2% interspecific divergence in the ITS1 region. There is sequence evidence that at least two taxa are included in Tricharina gilva as presently delineated. As the sole report of mycorrhiza formation in Tricharina is shown to be based upon a misidentification, it therefore appears that only Wilcoxina taxa are mycorrhizal. Keywords: E-strain, Wilcoxina, Tricharina, mycorrhiza, ribosomal DNA, phylogeny.

Diagnosis and differentiation of the order primates

We contrast our approach to a phylogenetic diagnosis of the order Primates, and its various supraspecific taxa, with definitional procedures. The order, which we divide into the semiorders Paromomyiformes and Euprimates, is clearly diagnosable on the basis of well-corroborated information from the fossil record. Lists of derived features which we hypothesize to have been fixed in the first representative species of the Primates, Euprimates, Strepsirhini, Haplorhini, and Anthropoidea, are presented. Our classification of the order includes both holophyletic and paraphyletic groups, depending on the nature of the available evidence. We discuss in detail the problematic evidence of the basicranium in Paleogene primates and present new evidence for the resolution of previously controversial interpretations. We renew and expand our emphasis on postcranial analysis of fossil and living primates to show the importance of understanding their evolutionary morphology and subsequent to this their use for understanding taxon phylogeny. We reject the much advocated “cladograms first, phylogeny next, and scenario third” approach which maintains that biologically founded character analysis, i.e., functional-adaptive analysis and paleontology, is irrelevant to genealogy hypotheses. Unlike the cladistic rules of operations demand, we advocate and use a priori weighting of characters. We discuss the evidence for the various proposed relationships of the earliest euprimates, the Adapidae and Omomyidae, and show that linking the former with living Strepsirhini and the latter with living Haplorhini does not depend on the assumption of the presence of soft-anatomical characters in the fossils. On the contrary, it is the sharing of derived hard anatomical features of the fossil taxa with the living groups which makes their possession of either strepsirhine or haplorhine “soft” attributes probable. We discuss the relative merits of the use of the grade concept (with its widely recognized implication of polyphyly) in attempts to group primates and maintain that there exists no evidence for either an “archaic primate” or a prosimian or an anthropoid grade. All the characters in the literature attributed to these are inherited from the first representatives of either the semiorder Paromomyiformes or the semiorder Euprimates or the semisuborder Anthropoidea. Consequently, we find neither descriptive nor didactic merit in gradal arrangements, the goals of which can be much better served by a phylogenetic (not cladistic) classification.