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Wiley Online Library : Cladistics
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May 12, 2015
A protocol for the delimitation of areas of endemism and the historical regionalization of the Brazilian Atlantic Rain Forest using harvestmen distribution data
The concept of areas of endemism (AoEs) has rarely been discussed in the literature, even though the use of methods to ascertain them has recently increased. We introduce a grid-based protocol for delimiting AoEs using alternative criteria for the recognition of AoEs that are empirically tested with harvestmen species distributions in the Atlantic Rain Forest. Our data, comprising 778 records of 123 species, were analysed using parsimony analysis of endemicity and endemicity analysis on four different grids (two cell sizes and two cell placements). Additionally, we employed six qualitative combined criteria for the delimitation of AoEs and applied them to the results of the numerical analyses in a new protocol to objectively delimit AoEs. Twelve AoEs (the most detailed delimitation of the Atlantic Rain Forest so far) were delimited, partially corroborating the main divisions previously established in the literature. The results obtained with the grid-based methods were contradictory and were plagued by artefacts, probably due to the existence of different endemism patterns in one cell or to a biogeographical barrier set obliquely to latitudinal and longitudinal axes, for example. Consequently, the congruence patterns found by them should not be considered alone; qualitative characteristics of species and clade distributions and abiotic factors should be evaluated together. Mountain slopes are the main regions of endemism, and large river valleys are the main divisions. Refuges, marine transgressions and tectonic activity seem to have played an important role in the evolution of the Atlantic Rain Forest.
May 5, 2015
April 16, 2015
A phylogenetic analysis of the early branching lineages of the monocotyledons is performed using data from two plastid genes (rbcL and matK), five mitochondrial genes (atp1, ccmB, cob, mttB and nad5) and morphology. The complete matrix includes 93 terminals representing Acorus, the 14 families currently recognized within Alismatales, and numerous lineages of monocotyledons and other angiosperms. Total evidence analysis results in an almost completely resolved strict consensus tree, but all data partitions, genomic as well as morphological, are incongruent. The effects of RNA editing and potentially processed paralogous sequences are explored and discussed. Despite a decrease in incongruence length differences after exclusion of edited sites, the major data partitions remain significantly incongruent. The 14 families of Alismatales are all found to be monophyletic, but Acorus is found to be included in Alismatales rather than being the sister group to all other monocotyledons. The placement is strongly supported by the mitochondrial data, atp1 in particular, but it cannot be explained as an artifact caused by patterns of editing or by sampling of processed paralogues.
April 1, 2015
Molossidae is a large (roughly 100 species) pantropically distributed clade of swift aerially insectivorous bats for which the phylogeny remains relatively unknown and little studied compared with other speciose groups of bats. We investigated phylogenetic relationships among 62 species, representing all extant molossid genera and most of the subgenera, using 102 morphological characters from the skull, dentition, postcrania, external morphology, tongue, and penis, based on direct observation and literature reports. Both parsimony and Bayesian analyses were used in phylogenetic reconstruction. Our analysis supports two main clades of molossids, both of which mingle Old World and New World taxa. One clade is comprised of Mormopterus,Platymops, Sauromys, Neoplatymops, Molossops, Cynomops, Cheiromeles, Molossus, and Promops. The other clade includes Tadarida, Otomops, Nyctinomops, Eumops, Chaerephon, and Mops. The position of Myopterus with respect to these two groups is unclear. As in other recent analyses, we find that several genera do not appear to be monophyletic (e.g. Tadarida, Chaerephon, and Molossops sensu lato). We recommend that the subgenera of Molossops sensu lato and Austronomus be recognized at the generic level. We conclude that much more data are needed to investigate lower level problems (generic monophyly and relationships within genera) and to resolve the higher-level branching pattern of the family.
March 20, 2015
Phylogenetic relationships of toads of the Rhinella granulosa group (Anura: Bufonidae): a molecular perspective with comments on hybridization and introgression
The Rhinella granulosa group consists of 13 species of toads distributed throughout open areas of South America and Panama. In this paper we perform a phylogenetic analysis considering all but one species of the group, employing five nuclear and four mitochondrial genes, for up to 7910 bp per specimen. Separate phylogenetic analyses under direct optimization (DO) of nuclear and mitochondrial sequences recovered the R. granulosa group as monophyletic and revealed topological incongruence that can be explained mainly by multiple events of hybridization and introgression, both mitochondrial and nuclear. The DO combined analysis, after the exclusion of putatively introgressed or heterozygous genomes, resulted in a phylogenetic hypothesis for the R. granulosa group in which most of the species are recovered as monophyletic, but with interspecific relationships poorly supported. The optimization of morphological (adult and larval), chromosomal, and behavioural characters resulted in 12 putative phenotypic synapomorphies for this species group and some other synapomorphies for internal clades. Our results indicate the need for additional population genetic studies on R. dorbignyi and R. fernandezae to corroborate the taxonomic status of both taxa. Finally, we discuss biological and genetic characteristics of Bufonidae, as possible explanations for the common occurrence of hybridization and introgression observed in some lineages of this family.
March 19, 2015
The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae)
Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) generated using the anchored phylogenomics sequencing method (66 loci, derived from conserved genome regions, for 48 taxa) and Sanger sequencing (seven loci for up to 142 taxa) to tackle this problem. We assess the effects of character sampling, taxon sampling, analytical methods and assumptions in phylogenetic inference of microhylid frogs. The phylogeny of microhylids shows high susceptibility to different analytical methods and datasets used for the analyses. Clades inferred from maximum-likelihood are generally more stable across datasets than those inferred from parsimony. Parsimony trees inferred within a tree-alignment framework are generally better resolved and better supported than those inferred within a similarity-alignment framework, even under the same cost matrix (equally weighted) and same treatment of gaps (as a fifth nucleotide state). We discuss potential causes for these differences in resolution and clade stability among discovery operations. We also highlight the problem that commonly used algorithms for model-based analyses do not explicitly model insertion and deletion events (i.e. gaps are treated as missing data). Our results corroborate the monophyly of Microhylidae and most currently recognized subfamilies but fail to provide support for relationships among subfamilies. Several taxonomic updates are provided, including naming of two new subfamilies, both monotypic.
March 10, 2015
Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification
Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty-six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB-rbcL and trnL-F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum-parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three-colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well-supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.
Effects of sequence diversity and recombination on the accuracy of phylogenetic trees estimated by kSNP
kSNP v2 is a powerful tool for single nucleotide polymorphism (SNP) identification from complete microbial genomes and for estimating phylogenetic trees from the identified SNPs. kSNP can analyse finished genomes, genome assemblies, raw reads or any combination of those and does not require either genome alignment or reference genomes. This study uses sequence evolution simulations to evaluate the topological accuracy of kSNP trees and to assess the effects of diversity and recombination on that accuracy. The accuracies of kSNP trees are strongly affected by increasing diversity, with parsimony accuracy > maximum-likelihood accuracy > neighbour-joining accuracy. Accuracy is also strongly influenced by recombination; as recombination increases accuracy decreases. Reliable trees are arbitrarily defined as those that have ≥ 90% topological accuracy. It is determined that the best predictor of topological accuracy is the ratio of r/m, a measure of the effect of recombination, to FCK (the fraction of core kmers), a measure of diversity. Tools are available to allow investigators to determine both r/m and FCK, and the relationship between topological accuracy and the ratio of r/m to FCK is determined. The practical implication of this study is that kSNP is an effective tool for estimating phylogenetic trees from microbial genome sequences provided that both recombination and sequence diversity are within acceptable ranges.
March 9, 2015
300 million years of diversification: elucidating the patterns of orthopteran evolution based on comprehensive taxon and gene sampling
Orthoptera is the most diverse order among the polyneopteran groups and includes familiar insects, such as grasshoppers, crickets, katydids, and their kin. Due to a long history of conflicting classification schemes based on different interpretations of morphological characters, the phylogenetic relationships within Orthoptera are poorly understood and its higher classification has remained unstable. In this study, we establish a robust phylogeny of Orthoptera including 36 of 40 families representing all 15 currently recognized superfamilies and based on complete mitochondrial genomes and four nuclear loci, in order to test previous phylogenetic hypotheses and to provide a framework for a natural classification and a reference for studying the pattern of divergence and diversification. We find strong support for monophyletic suborders (Ensifera and Caelifera) as well as major superfamilies. Our results corroborate most of the higher-level relationships previously proposed for Caelifera, but suggest some novel relationships for Ensifera. Using fossil calibrations, we provide divergence time estimates for major orthopteran lineages and show that the current diversity has been shaped by dynamic shifts of diversification rates at different geological times across different lineages. We also show that mitochondrial tRNA gene orders have been relatively stable throughout the evolutionary history of Orthoptera, but a major tRNA gene rearrangement occurred in the common ancestor of Tetrigoidea and Acridomorpha, thereby representing a robust molecular synapomorphy, which has persisted for 250 Myr.
March 8, 2015
$1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen-rich samples
Several of the biggest challenges in taxonomy and systematics are related to a toxic mixture of small size, abundance, and rarity. There are too many species in groups with too few taxonomists and many of these species are very rare and hard to find because they are hidden in mass samples. To make matters worse, these species often have life-history stages that are morphologically so different that it is difficult to identify them as semaphoronts of the same species. We demonstrate that these biodiversity challenges can be addressed with cost-effective molecular markers. Here, we describe a next-generation-sequencing protocol that can yield barcodes at a chemical cost of
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution