Molecular Systematics

Molecular evidence for the presence of cryptic evolutionary lineages in the freshwater copepod genus Hemidiaptomus GO Sars, 1903 (Calanoida, Diaptomidae)

by Federico Marrone

Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence dates

by Jeffrey Townsend

Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary.

by Sergios-Orestis Kolokotronis

BMC Evolutionary Biology

Systematics of genus Gnomoniopsis (Gnomoniaceae, Diaporthales)

by Donald Walker

Abstract:

Species of Gnomoniopsis are leaf- and stem-inhabiting
pyrenomycetes that infect plants... more Abstract:

Species of Gnomoniopsis are leaf- and stem-inhabiting
pyrenomycetes that infect plants in Fagaceae,
Onagraceae and Rosaceae. Morphology and
analyses of DNA sequences from three ribosomal
DNA and protein coding regions, namely b-tubulin,
translation elongation factor 1a (tef-1a) and the ITS
region including ITS1, 5.8S rDNA and ITS2, were
used to define species in Gnomoniopsis. Secondary
structural alignment of the ITS region across four
genera in Gnomoniaceae was used to increase the
potential number of homologous positions in the ITS
alignment. Ascospore isolates were grown from newly
collected specimens. Type specimens were compared
with these specimens to determine their identity. In
this paper a recent concept of Gnomoniopsis is
confirmed with phylogenetic resolution of additional
species. Four new combinations and one new species
are proposed. Nine species are described and
illustrated, and a key is provided to the 13 species
currently recognized in Gnomoniopsis.

A Functional Phylogenomic View of the Seed Plants

by Sergios-Orestis Kolokotronis

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

Diversification of the American bulb-bearing Oxalis (Oxalidaceae): Dispersal to North America and modification of the tristylous breeding system.

by Eve Emshwiller

Gardner, Andy G., Magdalena Vaio, Marcelo Guerra, Eve Emshwiller Accepted by American Journal of Botany

Premise of the study: The American bulb-bearing Oxalis (Oxalidaceae) have diverse heterostylous breeding systems and... more Premise of the study: The American bulb-bearing Oxalis (Oxalidaceae) have diverse heterostylous breeding systems and are distributed in mountainous areas from Patagonia to the northeastern United States. To study the evolutionary processes leading to this diversity we construct the first molecular phylogeny for the American bulb-bearing Oxalis, using it to infer biogeographic history and breeding system evolution.
Methods: We use DNA sequence data (nrITS, trnL-trnL-trnF, trnT-trnL, and psbJ-petA) to infer phylogenetic history via parsimony, likelihood, and Bayesian analyses. We use Bayes Multistate to infer ancestral geographic distributions at well-supported nodes of the phylogeny. The Shimodaira-Hasegawa (SH) test distinguishes among hypotheses of single or multiple transitions from South America to North America, and tristyly to distyly.
Key Results: The American bulb-bearing Oxalis include sampled members of sections Ionoxalis and Pseudobulbosae, and are derived from a larger clade including members of sections Palmatifoliae, Articulatae and the African species. The American bulb-bearing Oxalis comprise two clades: one distributed in SE South America, the other in the Andes and North America. An SH test supports multiple dispersals to North America. Most sampled distylous species form a single clade, but there are at least two other, independent distylous lineages, supported by the SH tests.
Conclusions: Phylogenetic results suggest the American bulb-bearing Oxalis originated in southern South America, dispersed repeatedly to North America, and had multiple transitions from tristyly to distyly. This study adds to our understanding of biogeographic history and breeding system evolution and provides a foundation for more precise inferences about the study group.

A NEW CRYPTIC SPECIES OF SALAMANDER, GENUS OEDIPINA (CAUDATA: PLETHODONTIDAE), FROM PREMONTANE ELEVATIONS IN NORTHERN NICARAGUA, WITH COMMENTS ON THE SYSTEMATIC STATUS OF THE NICARAGUAN PARATYPES OF O. PSEUDOUNIFORMIS BRAME, 1968

by Josiah Townsend

We describe a new species of Oedipina (subgenus Oedipina) from premontane elevations of three isolated mountains in... more We describe a new species of Oedipina (subgenus Oedipina) from premontane elevations of three isolated mountains in northern Nicaragua. The new cryptic species differs in molecular characters from its closest relatives: Oedipina cyclocauda (an Atlantic lowland species with a distributional range from central Panama to extreme southeastern Nicaragua) and Oedipina pseudouniformis. We regard all Nicaraguan specimens previously referred to as O. pseudouniformis to be conspecific with the new species herein described and restrict O. pseudouniformis as a Costa Rican endemic species. We also record the fourth known locality (and southernmost) of the Nicaraguan endemic O. nica and discuss additional species of Oedipina that are likely to be found in Nicaragua as field research continues in the country.

Scanlon, J.D. and Lee, M.S.Y.. 2004. The phylogeny of Australasian venomous snakes (Elapidae, Hydrophiidae) based on phenotypic and molecular evidence. Zoologica Scripta 33: 335-366.

by Michael S. Y. Lee

Oliver, P.M., Adams, M., Lee, M.S.Y, Hutchinson, M.N., Doughty, P., 2009. The taxonomic impediment in vertebrates: DNA sequence, allozyme and chromosomal data double estimates of species diversity in a lineage of Australian lizards (Diplodactylus, Gekkota). Proceedings of the Royal Society of London, B. 276: 2001-2007

by Michael S. Y. Lee

For related coverage, see here!

http://www.abc.net.au/news/2009-03-04/genes-check-leads-to-gecko-discovery/1608474
http://www.australasianscience.com.au/article/issue-june-2011/cryptic-clues-species-diversity.html
http://www.adelaidenow.com.au/news/in-depth/lizard-species/story-fn34ojgi-1225799393040

Lee, M.S.Y., 2009. Hidden support from unpromising datasets strongly unites snakes and anguimorph lizards. Journal of Evolutionary Biology 22: 1308-1316.

by Michael S. Y. Lee

Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis.

by Sergios-Orestis Kolokotronis

PLoS Biology

The Diploblast-Bilateria Sister hypothesis: parallel evolution of a nervous system may have been a simple step.

by Sergios-Orestis Kolokotronis

Communicative and Integrative Biology

Dense Taxonomic EST Sampling and Its Applications for Molecular Systematics of the Coleoptera (Beetles)

by Stuart Longhorn

Expressed sequence tag (EST) sequences can provide a wealth of data for phylogenetic and genomic studies, but the... more Expressed sequence tag (EST) sequences can provide a wealth of data for phylogenetic and genomic studies, but the utility of these resources is restricted by poor taxonomic sampling. Here, we use small EST libraries (<1,000 clones) to generate phylogenetic markers across a broad sample of insects, focusing on the species-rich Coleoptera (beetles). We sequenced over 23,000 ESTs from 34 taxa, which produced 8,728 unique sequences after clustering nonredundant sequences. Between taxa, the sequences could be grouped into 731 gene clusters, with the largest corresponding to mitochondrial DNA transcripts and gene families chymotrypsin, actin, troponin, and tubulin. While levels of paralogy were high in most gene clusters, several midsized clusters including many ribosomal protein (RP) genes appeared to be free of expressed paralogs. To evaluate the utility of EST data for molecular systematics, we curated available transcripts for 66 RP genes from representatives of the major groups of Coleoptera. Using supertree and supermatrix approaches for phylogenetic analysis, the results were consistent with the emerging phylogenetic conclusions about basal relationships in Coleoptera. Numerous small EST libraries from a taxonomically densely sampled lineage can provide a core set of genes that together act as a scaffold in phylogenetic reconstruction, comparative genomics, and studies of gene evolution.

Cryptic diversity in Chortis Highland moss salamanders (Caudata: Plethodontidae: Nototriton) revealed using mtDNA barcodes and phylogenetics, with a new species from eastern Honduras

by Josiah Townsend

The systematic study of Central American moss salamanders has been a challenge to researchers due to their cryptic... more The systematic study of Central American moss salamanders has been a challenge to researchers due to their cryptic nature and subsequent difficulty in sampling. In an effort to elucidate relationships among moss salamanders from the Chort´ıs Highlands, we quantified intra- and interspecific variation using data from the mitochondrial genes 16S (the amphibian barcoding gene), cytochrome b (cyt b; widely used in phylogenetic studies of neotropical salamanders), and cytochrome oxidase subunit I (COI, the universal metazoan barcoding gene). All three loci exhibit a bimodal ‘barcoding gap’ between ranges of intra- and interspecific variation, demonstrating unambiguous species boundaries with respect to the mitochondrial loci. A barcoding approach and Bayesian and maximum likelihood analyses of the mtDNA dataset revealed that the nominal species N. barbouri represents a species complex, with two of three populations assigned to this taxon being paraphyletic with respect to a sample from the type locality. These data also revealed an undescribed species from eastern Honduras, and confirmed the identity of allopatric populations of N. lignicola and N. limnospectator. Sequence data from cyt b presented an analytical challenge due to a high level of substitution saturation at the third codon position for some samples. Phylogenetic analyses of the entire dataset including and omitting the third position of cyt b resulted in conflicting results with respect to the position of the new species and N. tomamorum. Based on the molecular data, supplemented with data from external morphology and osteology, we formally describe a new species from Sierra de Agalta.

A global study of forensically significant calliphorids: implications for identification

by Martin Villet

Strong morphological support for the molecular evolutionary tree of placental mammals

by Aaron Camens

The emerging molecular evolutionary tree for placental mammals differs greatly from morphological trees, leading to... more The emerging molecular evolutionary tree for placental mammals differs greatly from morphological trees, leading to repeated suggestions that morphology is uninformative at this level. This view is here refuted empirically, using an extensive morphological and molecular dataset totalling 17 431 characters. When analysed alone, morphology indeed is highly misleading, contradicting nearly every clade in the preferred tree (obtained from the molecular or the combined data). Widespread homoplasy overrides historical signal. However, when added to the molecular data, morphology surprisingly increases support for most clades in the preferred tree. The homoplasy in the morphology is incongruent with all aspects of the molecular signal, while the historical signal in the morphology is congruent with (and amplifies) the historical signal in the molecular data. Thus, morphology remains relevant in the genomic age, providing vital independent corroboration of the molecular tree of mammals.

Resolution of the Hylobates Phylogeny: Congruence of Mitochondrial D-Loop Sequences With Molecular, Behavioral, and Morphological Data Sets

by Danielle Whittaker

Evolutionary Genetics of Kloss's Gibbons (Hylobates Klossii): Systematics, Phylogeography, and Conservation

by Danielle Whittaker

Molecular Phylogenetic affinities of the Simakobu Monkey (Simias Concolor)

by Danielle Whittaker