Phylogenetic studies

Biogeography and variation of the Malaysian fruit bat, Cynopterus brachyotis, in Sunda Shelf 2003

by M.T. Abdullah, PhD

Five more studies by BU, UKM & UNIMAS had tested and confirmed similar findings in this 2003 PhD study.

There are more then one species in the Malayan fruit bat, Cynopterus brachyotis, species complex based on the... more There are more then one species in the Malayan fruit bat, Cynopterus brachyotis, species complex based on the mophological and MtDNA cytochorome b analyses. The small form is found in the closed canopy forest while the larger form utilised the open habitat. There is a new species within the C. brachyotis populations yet to be described.

Profiling Phylogenetic Informativeness

by Jeffrey Townsend

The resolution of four controversial topics in phylogenetic experimental design hinges upon the informativeness of... more The resolution of four controversial topics in phylogenetic experimental design hinges upon the informativeness of characters about the historical relationships among taxa. These controversies regard the power of different classes of phylogenetic character, the relative utility of increased taxonomic versus character sampling, the differentiation between lack of phylogenetic signal and a historical rapid radiation, and the design of taxonomically broad phylogenetic studies optimized by taxonomically sparse genome-scale data. Quantification of the informativeness of characters for resolution of phylogenetic hypotheses during specified historical epochs is key to the resolution of these controversies. Here, such a measure of phylogenetic informativeness is formulated. The optimal rate of evolution of a character to resolve a dated four-taxon polytomy is derived. By scaling the asymptotic informativeness of a character evolving at a nonoptimal rate by the derived asymptotic optimum, and by normalizing so that net phylogenetic informativeness is equivalent for all rates when integrated across all of history, an informativeness profile across history is derived. Calculation of the informativeness per base pair allows estimation of the cost-effectiveness of character sampling. Calculation of the informativeness per million years allows comparison across historical radiations of the utility of a gene for the inference of rapid adaptive radiation. The theory is applied to profile the phylogenetic informativeness of the genes BRCA1, RAG1, GHR, and c-myc from a muroid rodent sequence data set. Bounded integrations of the phylogenetic profile of these genes over four epochs comprising the diversifications of the muroid rodents, the mammals, the lobe-limbed vertebrates, and the early metazoans demonstrate the differential power of these genes to resolve the branching order among ancestral lineages. This measure of phylogenetic informativeness yields a new kind of information for evaluation of phylogenetic experiments. It conveys the utility of the addition of characters a phylogenetic study and it provides a basis for deciding whether appropriate phylogenetic power has been applied to a polytomy that is proposed to be a rapid radiation. Moreover, it provides a quantitative measure of the capacity of a gene to resolve soft polytomies.

Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic Inference

by Jeffrey Townsend

Optimal rates of evolution and the informativeness of characters for phylogenetic inference have received increasing... more Optimal rates of evolution and the informativeness of characters for phylogenetic inference have received increasing attention as the effort to distinguish phylogenetic signal and noise from large data sets intensifies. Ascertaining optimal rates for character evolution and predicting sequences featuring high phylogenetic utility are challenging tasks for which little theory has been developed. We argue for the usage of predictive theoretical tools that identify phylogenetic signal for quartets of taxa. We demonstrate analytically that, under an infinite states model, phylogenetically optimal rates of character evolution increase with greater taxon sampling. Finally, we argue for the development of increasingly sophisticated tools for the prediction of phylogenetic informativeness that incorporate higher taxon sampling and that directly account for phylogenetic noise.

In a recent paper, Klopfstein et al. (2010) evaluate and critique profiles of phylogenetic informativeness (Townsend 2007), a method designed to inform the choice of markers for phylogenetic inference, and to interpret of the power of data sets to resolve short deep internodes in the history of life. To motivate their critique, Klopfstein et al. (2010) provide two analyses. First, they profile the phylogenetic informativeness of CO1 and 28S rRNA and reconstruct phylogeny for diplazontine parasitoid wasps. Second, they perform simulations to test the optimal rate of character change against a prediction based on four-taxon theory in Townsend (2007), addressing data sets of increasing numbers of taxa. With regard to their empirical data set, Klopfstein et al. (2010) find fault with the relation between the quartet-based (Townsend 2007) phylogenetic informativeness profile and the results of phylogenetic inference. Furthermore, they argue that their simulations indicate a dramatic trend in the optimal rate of change of a character for phylogenetic inference, such that the greater the taxon sampling, the slower the optimal rate of change of the characters.

Here, we dispute these claims. …

PhyDesign: an online application for profiling phylogenetic informativeness

by Jeffrey Townsend

Background

The rapid increase in number of sequenced genomes for species across of the tree of life is... more Background

The rapid increase in number of sequenced genomes for species across of the tree of life is revealing a diverse suite of orthologous genes that could potentially be employed to inform molecular phylogenetic studies that encompass broader taxonomic sampling. Optimal usage of this diversity of loci requires user-friendly tools to facilitate widespread cost-effective locus prioritization for phylogenetic sampling. The Townsend (2007) phylogenetic informativeness provides a unique empirical metric for guiding marker selection. However, no software or automated methodology to evaluate sequence alignments and estimate the phylogenetic informativeness metric has been available.


Results

Here, we present PhyDesign, a platform-independent online application that implements the Townsend (2007) phylogenetic informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions. An easy-to-use interface facilitates uploading of alignments and ultrametric trees to calculate and depict profiles of informativeness over specified time ranges, and provides rankings of locus prioritization for epochs of interest.


Conclusions

By providing these profiles, PhyDesign facilitates locus prioritization increasing the efficiency of sequencing for phylogenetic purposes compared to traditional studies with more laborious and low capacity screening methods, as well as increasing the accuracy of phylogenetic studies. Together with a manual and sample files, the application is freely accessible at http://phydesign.townsend.yale.edu webcite.

Use of paleontological and molecular data in supertrees for comparative studies: the example of lissamphibian femoral microanatomy

by Michel Laurin

Baeza, J.A. 2010. Molecular systematics of peppermint and cleaner shrimps: phylogeny and taxonomy of the genera Lysmata and Exhippolysmata (Crustacea: Caridea: Hippolytidae). Zoological Journal of the Linnean Society 160: 254–265

by Antonio Baeza

Investigating the presence of Wolbachia pipientis in various mosquito species

by Ravi Dinakar

To view the FREE full pdf full text of this article please go to www.jes2s.com/pdfs/kang_article.pdf

Also visit the homepage, www.jes2s.com, to view the October 2011 issue.

Authors: Yuan Kang and Brian Dempsey*
Department of Science
Acton Boxborough Regional High School, 36 Charter Road, Acton, MA 01720
*Correspondence: bdempsey@mail.ab.mec.edu

The Journal of Experimental Secondary Science, July 2011
Publisher: Ravi Dinakar

Wolbachia pipientis are endosymbionts that
infect many insects, arachnids, and nematodes.
By comparing the... more Wolbachia pipientis are endosymbionts that
infect many insects, arachnids, and nematodes.
By comparing the Wolbachia DNA sequences
contained in different infected insect species,
one can investigate the evolutionary history of
arthropods and the modes of transmission of this
reproductive parasite. We collected and extracted
DNA from several mosquito species to test for
the presence of Wolbachia. Multiple positive
sequences were generated by PCR and DNA
sequencing of 16S DNA from Culex restuans
samples. When these sequences were analyzed
using the NCBI BLAST database, we confirmed
the occurrence of transmission of Wolbachia
DNA in insects and arachnids. However, due
to contamination of multiple samples, we were
unable to conclusively compare the Wolbachia
sequences between different mosquito species.

Mitochondrial DNA analysis reveals Plio-Pleistocene diversification within

by Riashna Sithaldeen

Phylogenetic position of Diania challenged

by Ross Mounce

Mounce, R. C. P. & Wills, M. A. Phylogenetic position of diania challenged. Nature 476, E1 (2011). URL http://dx.doi.org/10.1038/nature10266.

Liu et al. describe a new and remarkable fossil, Diania cactiformis. This animal apparently combined the soft trunk of... more Liu et al. describe a new and remarkable fossil, Diania cactiformis. This animal apparently combined the soft trunk of lobopodians (a group including the extant velvet worms in addition to many Palaeozoic genera) with the jointed limbs that typify arthropods.
They go on to promote Diania as the immediate sister group to the arthropods, and conjecture that sclerotized and jointed limbs may therefore have evolved before articulated trunk tergites in the immediate arthropod stem. The data published by Liu et al. do not un-ambiguously support these conclusions; rather, we believe that Diania probably belongs within an unresolved clade or paraphyletic grade of lobopodians.

Historical male-mediated introgression in horseshoe bats revealed by multilocus DNA sequence data

by Stephen Rossiter

Genetic divergence and echolocation call frequency in cryptic species of Hipposideros larvatus sl (Chiroptera: Hipposideridae) from the Indo‐Malayan region

by Stephen Rossiter

Phylogenetic and population genetic divergence correspond with habitat for the pathogen Colletotrichum cereale and allied taxa across diverse grass communities

by Jo Anne Crouch

Over the past decade, the emergence of anthracnose disease has newly challenged the health of turfgrasses on North... more Over the past decade, the emergence of anthracnose disease has newly challenged the health of turfgrasses on North American golf courses, resulting in considerable economic loss. The fungus responsible for the outbreaks, Colletotrichum cereale, has also been identified from numerous natural grasses and cereal crops, although disease symptoms are generally absent. Here we utilize phylogenetic and population genetic analyses to determine the role of ecosystem in the advancement of turfgrass anthracnose and assess whether natural grass and/or cereal inhabitants are implicated in the epidemics. Using a four-gene nucleotide data set to diagnose the limits of phylogenetic species and population boundaries, we find that the graminicolous Colletotrichum diverged from a common ancestor into distinct lineages correspondent with host physiology (C3 or C4 photosynthetic pathways). In the C4 lineage, which includes the important cereal pathogens Colletotrichum graminicola, C. sublineolum, C. falcatum, C. eleusines, C. caudatum and several novel species, host specialization predominates, with host-associated lineages corresponding to isolated sibling species. Although the C3 lineage--C. cereale--is comprised of one wide host-range species, it is divided into 10 highly specialized populations corresponding to ecosystem and/or host plant, along with a single generalist population spread across multiple habitat types. Extreme differentiation between the specialized C. cereale populations suggests that asymptomatic nonturfgrass hosts are unlikely reservoirs of infectious disease propagules, but gene flow between the generalist population and the specialized genotypes provides an indirect mechanism for genetic exchange between otherwise isolated populations and ecosystems.

Systematic analysis of the falcate-spored graminicolous Colletotrichum and a description of six new species from warm-season grasses

by Jo Anne Crouch

Species limits in the fungal genus Colletotrichum are traditionally distinguished by appressorial and/or conidial... more Species limits in the fungal genus Colletotrichum are traditionally distinguished by appressorial and/or conidial morphology or through host plant association, but both criteria are criticized for their inability to resolve distinct taxa. In previous research eight novel falcate-spored Colletotrichum species were identified from graminicolous hosts using multilocus molecular phylogenetic analysis. In the present work formal descriptions and illustrations are provided for six of the new taxa: C. hanaui sp. nov., C. nicholsonii sp. nov., C. paspali sp. nov., C. jacksonii sp. nov., C. miscanthi sp. nov. and C. axonopodi sp. nov.; and an emended description with epitypification is provided for C. eleusines. Comparison of hyphopodial appressoria and host association against phylogenetic species boundaries and evolutionary relationships in the graminicolous Colletotrichum group demonstrate that, while these characters can be useful in combination for the purpose of species diagnosis, erroneous identification is possible and species boundaries might be underestimated if these characters are used independently, as exemplified by the polyphyletic taxa C. falcatum. Appressoria have been subject to convergent evolution and were not predictive of phylogenetic relationships. Despite these limitations, the results of this work establish that in combination appressorial and host range characters could be used to generate informative dichotomous identification keys for Colletotrichum species groups when an underlying framework of evolutionary relationships, taxonomic criteria and nomenclature have been satisfactorily derived from molecular systematic treatments.

Clark, V.R., Barker, N.P. & Mucina, L. (2009). The Sneeuberg: A new centre of floristic endemism on the Great Escarpment, South Africa. South African Journal of Botany 75: 196-238.

by Nigel Barker

Kelly, C.M.R., Barker, N.P., Villet, M.H. & Broadley, D.G. (2009). Phylogeny, biogeography and classification of the snake Superfamily Elapoidea: A rapid radiation in the late Eocene. Cladistics 25: 38-63.

by Nigel Barker

Howis, S., Barker, N.P. & Mucina, L. (2009). Globally grown, but poorly known: Species limits and biogeography of Gazania Gaertn. (Asteraceae) inferred from chloroplast and nuclear DNA sequence data. Taxon58: 871-882.

by Nigel Barker

Schrire, B.D., Lavin, M., Barker, N.P. & Forest, F. (2009). Phylogeny of the tribe Indigofereae (Leguminosae – Papilionoideae): Geographically structured more in succulent-rich and temperate settings than in grass-rich environments. American Journal of Botany 96: 816-852.

by Nigel Barker

Teske, P.R., McLay, C.L Sandoval-Castillo, J., Papadopoulos, I., Newman, B.K., Griffiths, C.L., McQuaid, C.D., Barker, N.P., Borgonie, G. & Beheregaray, L.B. (2009). Tri-locus sequence data reject a “Gondwanan origin hypothesis” for the African/South Pacific crab genus Hymenosoma. Molecular Phylogenetics & Evolution 53: 23-33.

by Nigel Barker

Ramdhani, S., Barker, N.P. & Cowling, R.M. (2010). Phylogeography of Schotia (Fabaceae): recent evolutionary processes in an ancient thicket biome lineage. International Journal of Plant Sciences 171: 626-640.

by Nigel Barker

Hohenbergia mesoamericana (Bromeliaceae), first record of the genus for Mesoamerica

by William Cetzal Ix

Ramírez, I., G. Carnevali & W. Cetzal Ix. 2010. Revista Mexiana de Biodiversidad 81: 21-26.

Hohenbergia mesoamericana I. Ramírez, Carnevali et Cetzal is proposed as new, described, and illustrated. Because the... more Hohenbergia mesoamericana I. Ramírez, Carnevali et Cetzal is proposed as new, described, and illustrated. Because the genus was previously known only from the Antilles, Colombia, Venezuela, and Brazil, this new species represents the first record of Hohenbergia for Mexico and Mesoamerica. The new species is morphologically similar to the Jamaican H. spinulosa Mez in having the bracts subtending the spikes far exceeding them (especially the lowermost) and green petals, but differs in several characters, including a more elongate peduncle and rachis resulting in a less dense inflorescence, shorter fl oral bracts, and pedicellate spikes. The conservation status of the new species is evaluated as critically endangered (CR) according to IUCN criteria.

Key words: Bromelioideae, biogeographical disjunction, conservation, IUCN criteria, Mexico, Yucatán Peninsula.

Resumen. Hohenbergia mesoamericana I. Ramírez, Carnevali et Cetzal se propone como especie nueva, se describe y se ilustra. El género era conocido solamente de las Antillas, Brasil, Venezuela y Colombia; por ello, este nuevo taxón representa el primer registro de Hohenbergia para Mesoamérica y México. Hohenbergia mesoamericana es morfológicamente similar a H. spinulosa Mez de Jamaica, por presentar las brácteas de las espigas muy largas (especialmente las basales) y los pétalos verdes. Sin embargo, difi ere de ella en varios caracteres, incluyendo el pedúnculo y raquis de la infl orescencia más largos, brácteas fl orales más cortas y espigas pediceladas. El estado de conservación de la especie nueva es evaluado como críticamente amenazado (CR) según los criterios del IUCN.

Palabras clave: Bromelioideae, conservación, criterios IUCN, disyunción geográfi ca, México, península de Yucatán.