Systematic Biology

Many research groups are estimating trees containing anywhere from a few thousands to hundreds of thousands of species, toward the eventual goal of the estimation of a Tree of Life, containing perhaps as many as several million leaves. These phylogenetic estimations present enormous computational challenges, and current computational methods are likely to fail to run even on data sets in the low end of this range. One approach to estimate a large species tree is to use phylogenetic estimation methods (such as maximum likelihood) on a supermatrix produced by concatenating multiple sequence alignments for a collection of markers; however, the most accurate of these phylogenetic estimation methods are extremely computationally intensive for data sets with more than a few thousand sequences. Supertree methods, which assemble phylogenetic trees from a collection of trees on subsets of the taxa, are important tools for phylogeny estimation where phylogenetic analyses based upon maximum likelihood (ML) are infeasible. In this paper, we introduce SuperFine, a metamethod that utilizes a novel two-step procedure in order to improve the accuracy and scalability of supertree methods. Our study, using both simulated and empirical data, shows that SuperFine-boosted supertree methods produce more accurate trees than standard supertree methods, and run quickly on very large data sets with thousands of sequences. Furthermore, SuperFine-boosted matrix representation with parsimony (MRP, the most well-known supertree method) approaches the accuracy of ML methods on supermatrix data sets under realistic conditions.

BACKGROUND:
In spite of its indusrial usefulness and varied daily uses, lead (Pb) pollution is a widespread ecological problem that faces the humans in the 21th century. Pb was found to produces a wide range of toxic effects including neurotoxicity especially to the developing and young offspring. Recently, the utilization of herbal plants has received a significant attention where there has been rising awareness in their therapeutic use; among these is the garlic.
AIM OF THE WORK:
In light of the above, the current study is designed experimentally in female pregnant rats in order to investigate the beneficial role of garlic extract in the protection from the maternal and fetal cerebellar damage that produced by administration of different doses of Pb during pregnancy.
MATERIALS AND METHODS:
Positively pregnant female rats were divided into five groups; one control group, two Pb-treated groups (exposed to 160 and 320 mg/kg b.wt. of Pb, respectively) and two groups treated with both Pb and garlic (exposed to Pb as previous groups together with 250 mg/ kg b.wt. /day of garlic extract). Treatments started from day 1 till day 20 of pregnancy, where the mother rats of different experimental groups were sacrified to obtain the fetuses. Pb level in the maternal nd fetal blood and cerebellum was estimated by spectrophotometry. Specimens of the cerebellum of different mother and fetal groups were processed to histological and immunohistochemical staining for microscopic examination.
RESULTS:
The results showed that administration of Pb to pregnant rats resulted in a dose-dependent toxicity for both mothers and fetuses in the form of decrease of maternal weight gain, placental and fetal weights, brain weight and diminished fetal growth parameters, which were prominent in rat's group treated with larger dose of Pb. In Pb-treated rats, Pb level in blood and cerebellum was high when compared to the control. The histopathological examination of the cerebellum of treated dams and fetuses showed marked alterations mainly in the form of Purkinje cell degeneration and lack of deveopmet of fetal cerebellum. Co-treatment of garlic extract along with Pb resulted in a significant decrease in Pb levels as compared with those treated with Pb alone with improvement of the histopathological changes.
CONCLUSIONS:
This study was useful in evaluating the hazardous effects of uncontrolled use of Pb in general and in assessing the developmental and neurotoxicity of fetuses due to exposure during pregnancy in particular. Co-administration of garlic has beneficial effects in amelioration of Pb-induced neurotoxicity and reversing the histopathological changes of the cerebellum of mother rats and fetuses.
KEYWORDS:
garlic; glial fibrillary acidic protein; lead; purkinje cells

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication . A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/. [Bootstrap analysis; branch testing; LRT and aLRT; maximum likelihood; NNI; phylogenetic software; SPR; tree search algorithms.]

The highlands of northeastern Honduras remain under-characterized in terms of biological diversity, as exemplified by the regularity of new amphibian and reptile taxa discoveries. Following the recent description of a new species of Nototriton from the Sierra de Agalta in northeastern Honduras, we report the discovery of a second new species of Nototriton from the nearby Parque Nacional Montaña de Botaderos. This new taxon, Nototriton mime sp. nov., is distinguished from other Nototriton by its distinctive pale brown dorsal coloration in adult males, relatively large nares, a relatively broad head, mitochondrial sequence divergence, and phylogenetic relationships, and is geographically isolated from other populations of Nototriton.

International Journal on Bioinformatics & Biosciences (IJBB) is a Quarterly peer-reviewed and refereed open access journal that publishes articles which contribute new results in all areas of the Bioinformatics & Biosciences. Bioinformatics is the application of information science and technology to the field of biology to increase the understanding of all biological process. The aim of this journal is to publish all the latest and outstanding research articles in all areas of bioinformatics and Biometrics. Researchers and scientists from the fields of biology, computer science, mathematics, statistics, and physics are invited to share their developments and new techniques in the fields of Biometrics and Bioinformatics.

International Journal on Bioinformatics & Biosciences (IJBB) is a Quarterly peer-reviewed and refereed open access journal that publishes articles which contribute new results in all areas of the Bioinformatics & Biosciences. Bioinformatics is the application of information science and technology to the field of biology to increase the understanding of all biological process. The aim of this journal is to publish all the latest and outstanding research articles in all areas of bioinformatics and Biometrics. Researchers and scientists from the fields of biology, computer science, mathematics, statistics, and physics are invited to share their developments and new techniques in the fields of Biometrics and Bioinformatics.

Co-authored chapters:

Johnson, Jerry D., Larry David Wilson, and Josiah H. Townsend. Summary of recent changes in higher taxonomic categories of Mesoamerican amphibians and reptiles. Pp. 18–27.

Townsend, Josiah H., and Larry David Wilson. Conservation of the Honduran herpetofauna: Issues and imperatives. Pp. 460–487.

Townsend, Josiah H., and Larry David Wilson. Biogeography and conservation of the Honduran subhumid forest herpetofauna. Pp. 686–705.

Wilson, Larry David, and Josiah H. Townsend. The Herpetofauna of Mesoamerica: Biodiversity significance, conservation status, and future challenges. Pp. 760–812.

Late Mesozoic palaeobiogeography has been characterized by a distinction between the northern territories of Laurasia and the southern landmasses of Gondwana. The repeated discovery of Gondwanan lineages in Laurasia has led to the proposal of alternative scenarios to explain these anomalous occurrences. A new biogeographical model for late Mesozoic terrestrial ecosystems is here proposed in which Europe and "Gondwanan" territories possessed a common Eurogondwanan fauna during the earliest Cretaceous. Subsequently, following the Hauterivian, the European territories severed from Africa and then connected to Asiamerica resulting in a faunal interchange. This model explains the presence of Gondwanan taxa in Laurasia and the absence of Laurasian forms in the southern territories during the Cretaceous. In order to test this new palaeobiogeographical model, tree reconciliation analyses (TRAs) were performed based on biogeographical signals provided by a supertree of late Mesozoic archosaurs. The TRAs found significant evidence for the presence of an earliest Cretaceous Eurogondwanan fauna followed by a relatively short-term Gondwana-Laurasia dichotomy. The analysis recovered evidence for a biogeographical reconnection of the European territories with Africa and South America-Antarctica during the Campanian to Maastrichtian time-slice. This biogeographical scenario appears to continue through the early Tertiary and sheds light on the trans-Atlantic disjunct distributions of several extant plant and animal groups.

DNA barcoding as a method for species identification is rapidly increasing in popularity. However, there are still relatively few rigorous methodological tests of DNA barcoding. Current distance-based methods are frequently criticized for treating the nearest neighbor as the closest relative via a raw similarity score, lacking an objective set of criteria to delineate taxa, or for being incongruent with classical character-based taxonomy. Here, we propose an artificial intelligence-based approach-inferring species membership via DNA barcoding with back-propagation neural networks (named BP-based species identification)-as a new advance to the spectrum of available methods. We demonstrate the value of this approach with simulated data sets representing different levels of sequence variation under coalescent simulations with various evolutionary models, as well as with two empirical data sets of COI sequences from East Asian ground beetles (Carabidae) and Costa Rican skipper butterflies. With a 630-to 690-bp fragment of the COI gene, we identified 97.50% of 80 unknown sequences of ground beetles, 95.63%, 96.10%, and 100% of 275, 205, and 9 unknown sequences of the neotropical skipper butterfly to their correct species, respectively. Our simulation studies indicate that the success rates of species identification depend on the divergence of sequences, the length of sequences, and the number of reference sequences. Particularly in cases involving incomplete lineage sorting, this new BP-based method appears to be superior to commonly used methods for DNA-based species identification. [Back-propagation; DNA barcoding; incomplete lineage sorting; neural networks; species identification.]

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Previous phylogenetic analyses of tetrapod 18S ribosomal RNA (rRNA) sequences support the grouping of birds with mammals, whereas other molecular data, and morphological and paleontological data favor the grouping of birds with crocodiles. The 18S rRNA gene has consequently been considered odd, serving as "definitive evidence of different genes providing significantly different estimates of phylogeny in higher organisms" (p. 156; Huelsenbeck et al., 1996, Trends Ecol. Evol. 11:152-158). Our research indicates that the previous discrepancy of phylogenetic results between the 18S rRNA gene and other genes is caused mainly by (1) the misalignment of the sequences, (2) the inappropriate use of the frequency parameters, and (3) poor sequence quality. When the sequences are aligned with the aide of the secondary structure of the 18S rRNA molecule and when the frequency parameters are estimated either from all sites or from the variable domains where substitutions have occurred, the 18S rRNA sequences no longer support the grouping of the avian species with the mammalian species. [alignment; 18S rRNA; RNA secondary structure; Indel; molecular phylogenetics; tetrapod phylogeny.]

The origins and monophyly of the bulbous habit in the eudicot genus Oxalis  are uncertain, but key character state transitions in the evolution of true bulbs are currently thought to be reflected in extant pseudobulbous and other geophytic taxa. We test the relationships between the two major groups of bulbous Oxalis taxa, namely the southern African lineage which is centered in the speciose Cape Floristic Region (CFR), and the New World section Ionoxalis, by including the rhizomatous geophyte Oxalis acetosella, the caudiciform stem succulent Oxalis articulata, and the rhizomiform pseudobulbous Oxalis triangularis, in combined phylogenetic analyses of nrITS and trnL-F sequence data. We optimize several key bulbous characters in ancestral state reconstructions on produced phylogenies. Results of our analyses indicate that the evolution of bulbous characters in the genus is more complex than previously thought. Although the two major bulb types are homologous, the rhizomiform pseudobulbous habit arises from within true bulbs, and in most reconstructions the caudiciform stem succulent O. articulata is inferred to have secondarily lost several distinctive bulbous characters. O. acetosella  is not as closely related to the bulbous lineage as previously thought. More sampling from other key taxa are needed before the order in which key bulbous characters were acquired can be verified. We discuss these results in terms of the taxonomic and ecological implications for the CFR Oxalis taxa.

Generally, a ‘living fossil’ may be identified as a living species (or group) that is anatomically very similar to a fossil species which occurs very early in the history of a lineage. This concept is failed since must authors recognize “living fossils” based on an arbitrary character that stay unchanged in the lineages. A concept of species followed by several systematists recognizes it as an evolutionary entity that changes in space and time, named eidoforont by Willi Hennig. Although not every change in an eidophoront may be accessed, it is implicit that it occurs in the lineages as well as in the origin of new lineages (respectively, anagenesis and cladogenesis processes). Hence, if the identification of stability in some lineages is merely a sample problem, a “living fossil” is impossible to be rigorously identified. Therefore, we suggest that the term must be abandoned.

Fruiting body evolution is one of the central topics in fungal evolutionary biology. A number of hypotheses have been developed to explain the contemporary diversity of fruiting body forms, but their evaluation has been hampered by the lack of well-sampled data sets and suitable statistical methods. Phylogenetic evidence of the physiological changes that accompany switches in fruiting body type is lacking, and very little is known about the age of major events of fruiting body evolution. Based on a new multigene phylogeny, by using Bayesian methods, we demonstrate the existence of correlation between a number of morphological features and switches from nondeliquescent to deliquescent (autodigesting) fruiting bodies in the mushroom family Psathyrellaceae. Our results show that switches in the anatomy of two types of spacer cells (cystidia and pseudoparaphyses) and basidia (bimorphic or monomorphic) as well as the structure of the mushroom cap follow the evolution of deliquescent fruiting bodies, which suggests strong functional linkage between these traits. We performed Bayes factor-based tests, referred hereafter to as evolutionary pathway test (EPT), to decide which of the correlated characters were gained first during evolution. The EPTs strongly suggest that deliquescence was gained first, followed after short waiting times by the other morphological features. Bayesian relaxed molecular clock analyses suggest that the various events of switching between fruiting body types occurred independently at various ages during the history of the family. The utility of two mushroom fossils (Archaemarasmius and Protomycena), the only ones with unambiguous taxonomic positions, for the calibration of agaric trees were also examined. Based on our results, we suggest that the evolutionary benefit of deliquescence may be prevention against desiccation via accelerated ontogeny of the fruiting body. Hypotheses regarding the functional significance of the correlated evolution are presented and discussed. Further, we argue that the changes in fruiting body types in mushrooms in general can be attributed to independent events (e.g., dispersal and adaptation) and not to particular geologic ages.

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

Superimposition methods for comparing configurations of landmarks in two or more specimens are reviewed. These methods show differences in shape among specimens as residuals after rotation, translation, and scaling them so that they align as well as possible. A new method is presented that generalizes Siegel and Benson's (1982) resistant-fit theta-rho analysis so that more than two objects can be compared at the same time. Both least-squares and resistant-fit approaches are generalized to allow for affine transformations (uniform shape change). The methods are compared, using artificial data and data on 18 landmarks on the wings of 127 species of North American mosquitoes. Graphical techniques .are also presented to help summarize the patterns of differences in shape among the objects being compared.

A new species of Tantilla is described from Refugio de Vida Silvestre Texiguat in northern Honduras. The new species is allocated to the Tantilla taeniata group, which currently contains 20 of the 63 species in the genus, but it differs from all congeners on the basis of its dorsal body pattern and scutellation. The new species has a pale mid-dorsal stripe composed of narrow spots, confined to the mid-dorsal row, and a lateral coloration of pale spots on each of rows 1, 2, and 4 with dark brown pigment on the lateral edges of the ventrals. The new species appears to have no
close affinities within the T. taeniata group. Refugio de Vida Silvestre Texiguat is one of the most important cloud and premontane rain forest reserves in eastern nuclear Central America with respect to evolution, species endemism, and conservation. Nonetheless, areas of this reserve are seriously imperiled, especially on the leeward side due to continuing illegal logging and forest clearing for subsistence agriculture.

This paper reviews some of the important properties of geometric morphometric shape variables and discusses the advantages and limitations of the use of such data in studies of phylogeny. A method for fitting morphometric data to a phylogeny (i.e., estimating ancestral states of the shape variables) is presented using the squared-change parsimony criterion for estimation. These results are then used to illustrate shape change along a phylogeny as a deformation of the shape of any other node on the tree (e.g., the estimated root of the tree). In addition, a method to estimate the digitized image of an ancestor is given that uses averages of unwarped images. An example dataset with 18 wing landmarks for 11 species of mosquitoes is used to illustrate the methods.

The Cover A circular tree of life inferred from ribosomal RNA genes, superimposed on the genome of a triploid parthenogenetic species of gecko (Heteronotia binoei complex). The chromosomes were stained by fluorescent in situ hybridization for the ribosomal DNA arrays in a study of concerted evolution of repeated genes (see Hillis et al., 1991, Science 251:308-310). The photographs represent a sampling of multicellular species from the tips of the tree of life. Photographs by David Hillis. Graphic design by Janet Young.

Knowledge of phylogenetic relationships among species is fundamental to understanding basic patterns in evolution and underpins nearly all research programs in biology and paleontology. However, most methods of phylogenetic inference typically used by paleontologists do not accommodate the idiosyncrasies of fossil data and therefore do not take full advantage of the information provided by the fossil record. The advent of Bayesian “tip-dating” approaches to phylogeny estimation is especially promising for paleo-systematists because time-stamped comparative data can be combined with probabilistic models tailored to accommodate the study of fossil taxa. Under a Bayesian framework, the recently developed fossilized birth‒death process (FBD) provides a more realistic tree prior model for paleontological data that accounts for macroevolutionary dynamics, preservation, and sampling when inferring phylogenetic trees containing fossils. In addition, FBD tree prior also allows for the possibility of sampling ancestral morphotaxa. Although paleontologists are increasingly embracing probabilistic phylogenetic methods, these recent developments have not previously been applied to the deep-time invertebrate fossil record. Here, I examine phylogenetic relationships among Ordovician through Devonian crinoids using a Bayesian tip-dating approach. Results support several clades recognized in previous analyses sampling only Ordovician taxa, but also reveal instances where phylogenetic affinities are more complex and extensive revisions are necessary, particularly among the Cladida. The name Porocrinoidea is proposed for a well-supported clade of Ordovician ‘cyathocrine’ cladids and hybocrinids. The Eucladida is proposed as a clade name for the sister group of the Flexibilia herein comprised of cladids variously considered ‘cyathocrines’, ‘dendrocrines’, and/or ‘poteriocrines’ by other authors.

The Oxalis tuberosa alliance is a group of morphologically similar Oxalis species allied to the Andean tuber crop oca, O. tuberosa. Originally described by cytologists as a dozen species sharing a base chromosome number rare in Oxalis (x = 8), the alliance as defined here includes additional species for which cytological information is not yet available but which are supported as members on molecular and/or morphological grounds. The alliance includes members found in the Andean region from Venezuela to northern Argentina, with one species at high elevations in Central America. They occur from the high Andean steppes (páramo and puna) to the cloud forests of middle elevations and include both restricted endemics and variable widespread species complexes. Geographical and altitudinal distributions of members of the alliance and selected Oxalis species outside the alliance were compared with a combined phylogenetic analysis of DNA sequence data of ITS and ncpGS (chloroplast-expressed glutamine synthetase). Groups within the alliance (i.e., major clades on the molecular trees) occur across widespread, overlapping regions in the Andes, with only partial ecological separation. The hypothesis that the O. tuberosa alliance may have developed in the Andes of southern Peru and northwestern Bolivia and radiated southward and, especially, northward along the Andean axis is suggested by patterns of distributions of members of the alliance and outgroups. In spite of uncertain species delimitations, it is clear that the alliance includes many endemic species and ecotypes that have very restricted distributions. As relatives of the Andean tuber crop Oxalis tuberosa, the genetic diversity represented by this geographical variability should be a high priority for conservation.

Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of North American freshwater fishes. With a near-complete taxon sampling of close to 250 species, we aim to investigate strategies for efficient multilocus data sampling and the estimation of divergence times using relaxed-clock methods when a clade lacks a fossil record. Our phylogenetic data set comprises a single mitochondrial DNA (mtDNA) gene and two nuclear genes sampled from 245 of the 248 darter species. This dense sampling allows us to determine if a modest amount of nuclear DNA sequence data can resolve relationships among closely related animal species. Darters lack a fossil record to provide age calibration priors in relaxed-clock analyses. Therefore, we use a near-complete species-sampled phylogeny of the perciform clade Centrarchidae, which has a rich fossil record, to assess two distinct strategies of external calibration in relaxed-clock divergence time estimates of darters: using ages inferred from the fossil record and molecular evolutionary rate estimates. Comparison of Bayesian phylogenies inferred from mtDNA and nuclear genes reveals that heterospecific mtDNA is present in approximately 12.5% of all darter species. We identify three patterns of mtDNA introgression in darters: proximal mtDNA transfer, which involves the transfer of mtDNA among extant and sympatric darter species, indeterminate introgression, which involves the transfer of mtDNA from a lineage that cannot be confidently identified because the introgressed haplotypes are not clearly referable to mtDNA haplotypes in any recognized species, and deep introgression, which is characterized by species diversification within a recipient clade subsequent to the transfer of heterospecific mtDNA. The results of our analyses indicate that DNA sequences sampled from single-copy nuclear genes can provide appreciable phylogenetic resolution for closely related animal species. A well-resolved near-complete species-sampled phylogeny of darters was estimated with Bayesian methods using a concatenated mtDNA and nuclear gene data set with all identified heterospecific mtDNA haplotypes treated as missing data. The relaxed-clock analyses resulted in very similar posterior age estimates across the three sampled genes and methods of calibration and therefore offer a viable strategy for estimating divergence times for clades that lack a fossil record. In addition, an informative rank-free clade-based classification of darters that preserves the rich history of nomenclature in the group and provides formal taxonomic communication of darter clades was constructed using the mtDNA and nuclear gene phylogeny. On the whole, the appeal of mtDNA for phylogeny inference among closely related animal species is diminished by the observations of extensive mtDNA introgression and by finding appreciable phylogenetic signal in a modest sampling of nuclear genes in our phylogenetic analyses of darters.

Species designations are critically important scientific hypotheses that serve as the foundational units in a wide range of biological subdisciplines. A growing realization that some classes of data fail to delimit species under certain conditions has led to increasingly more integrative taxonomies, whereby species discovery and hypothesis testing are based on multiple kinds of data (e.g., morphological, molecular, behavioral, ecological, etc.). However, although most taxonomic descriptions have been based on morphology, some key morphological features, such as color, are rarely quantified and incorporated into integrative taxonomic studies. In this article, we applied a new method of ultraviolet digital photography to measure plumage variation in a color-variable avian species complex, the varied tit (Sittiparus varius). Plumage measurements corroborated species limits defined by morphometric, mitochondrial DNA, and nuclear DNA disjunctions and provided the only evidence for distin...