Systematic Biology

The use of mean instead of smallest interspecific distances exaggerates the size of the “barcoding gap” and leads to misidentification [Systematic Biology]

by Guanyang Zhang

Published in 'Systematic Biology'

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

by Jeffrey Townsend

Porque um "fóssil vivo" não pode existir: dedução lógica através de uma abordagem sistemática

by Douglas Riff

Romano, PSR; Riff, D & Oliveira, GR. 2007. Porque um fóssil vivo não pode existir: dedução lógica através de abordagem sistemática. In: Carvalho, I.S.;Cassab, R.C.T.; Schwanke, C.; Carvalho, M.A.; Fernandes, A.C.S.; Rodrigues, M.A.C.; Carvalho, M.S.S.; Arai, M. & Oliveira, M.E.Q. (eds.) Paleontologia: Cenários de Vida, Volume 2. Interciência, p. 51-59.

ISBN: 978-85-7193-185-5

Generally, a ‘living fossil’ may be identifi ed as a living species (or group) that is anatomically very similar to a... more Generally, a ‘living fossil’ may be identifi ed 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 eidoforont 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.

A correction corrected: Consensus over the meaning of Crocodylia and why it matters

by Stéphane Jouve

Brochu, C. A., J. R. Wagner, S. Jouve, C. D. Sumrall, and L. D. Densmore. 2009. A correction corrected: consensus over the meaning of Crocodylia and why it matters. Systematic Biology, 58 (5): 537-543.

Crown clades are an important nexus of study for paleontologists and neontologists. Associating commonly used names... more Crown clades are an important nexus of study for paleontologists and neontologists. Associating commonly used names with crown clades—the crown clade convention—draws their meanings closer to the way they are actually used by the majority of scientists. Molecular, physiological, behavioral, and soft tissue data can usually be unambiguously optimized no deeper than the root of a crown clade, and commonly used names are applied implicitly to the crown group
far more often than to larger groups including extinct relatives (Rowe 1988; Bryant 1996; Gauthier and de Queiroz 2001; Laurin 2002; Joyce et al. 2004; de Queiroz 2007).
The crown clade convention is controversial (Lee 1996; Benton 2000; Anderson 2002; Bateman and DiMichele 2003; Sereno 2005). Crown clade membership and diagnosis may differ from those of more inclusive groups historically associated with the same name. Our knowledge of phylogeny is imperfect, and changes in hypotheses may force changes in the membership and diagnosis of a group.
A recent comment by Martin and Benton (2008; here after Martin and Benton) suggests that the crown definition of Crocodylia—the last common ancestor of Gavialis gangeticus (Indian gharial), Alligator mississippiensis (American alligator), and Crocodylus niloticus (Nile crocodile) and all of its descendants—should be abandoned. They argue that crown clades might not be stable and that a consistent, stable “traditional” Crocodylia already exists. The interests of stability and continuity are best served, they argue, by reverting to this meaning. But their comment does not actually address the stability of crown Crocodylia, which has been remarkably stable since first published by Benton and Clark (1988), and literature cited in support of a consistent “traditional” meaning of Crocodylia reveals no consistency. Here, we discuss stability in the crown convention, show that one cannot identify a particular meaning of Crocodylia as “traditional,” demonstrate that the crown definition has become the standard meaning for Crocodylia and is demonstrably not limited to a small number of authors, and reiterate the reasons why crown clades are highly
beneficial.

Recent trends in molecular phylogenetic analysis: where to next?

by Robert Murphy

Blair, C., and R.W. Murphy. 2011. Recent trends in molecular phylogenetic analysis: where to next? Journal of Heredity 102: 130–138.

Price, B., Barker, N.P. & Villet, M.H. (2007). Patterns and processes underlying evolutionary significant units in the Platypleura stridula L. species complex (Hemiptera: Cicadidae) in the Cape Floristic Region, South Africa.

by Nigel Barker

Molecular Ecology 16: 2574-2588.

Pirie, M.D., Humphreys, A.M., Galley, C., Barker, N.P., Verboom, G.A., Orlovich, D., Draffin, S.J., Lloyd, K., Baeza, C.M., Negritto, M., Ruiz, E., Cota Sanchez, J.H., Reimer, E. & Linder, H.P. (2008). A supermatrix approach resolves phylogenetic relationships in Danthonioid grasses.

by Nigel Barker

Molecular Phylogenetics and Evolution 48: 1106-1119.

Kelly, C.M.R., Barker, N.P., Villet; M.H., Broadley, D.G. & Branch, W.R. (2008). The snake family Psammophiidae (Reptilia: Serpentes): Phylogenetics and species delimitation in the African sand snakes (Psammophis Boie, 1825) and allied genera.

by Nigel Barker

Molecular Phylogenetics & Evolution 47: 1045-1060.

Sauquet, H., Weston, P.H.W., Anderson, C.L., Barker, N.P., Cantrill, D., Mast, A. & Savolainen, V. (2009). Contrasted patterns of hyper-diversification in Mediterranean hotspots.

by Nigel Barker

Proceedings of the National Academy of Sciences, USA 106: 221-225.

Sauquet, H., Weston, P.H., Barker, N.P., Anderson, C.L., Cantrill, D.J. & Savolainen, V. (2009). Using fossils and molecular data to reveal the origins of the Cape proteas (subfamily Proteoideae). Molecular Phylogenetics & Evolution 51: 31-43.

by Nigel Barker

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

Teske, P.R., Winker, H., McQuaid, C.D. & Barker, N.P. (2009). A tropical/subtropical biogeographic disjunction in southeastern Africa separates two Evolutionarily Significant Units of an estuarine prawn. Marine Biology 156: 1265-1275.

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

Between a rock and a hard polytomy: Rapid radiation in the rupicolous girdled lizards (Squamata: Cordylidae)

by Edward Stanley

Accepted to Molecular Phylogenetics and Evolution. Co-authored with Aaron M. Bauer, Todd R. Jackman, William R. Branch, and P. Le Fras N. Mouton.

Girdled lizards (Cordylidae) are sub-Saharan Africa’s only endemic squamate family and contain 80 nominal taxa,... more Girdled lizards (Cordylidae) are sub-Saharan Africa’s only endemic squamate family and contain 80 nominal taxa, traditionally divided into four genera: Cordylus, Pseudocordylus, Chamaesaura and Platysaurus. Previous phylogenetic analysis revealed Chamaesaura and Pseudocordylus to be nested within Cordylus, and the former genera were sunk into the later. This taxonomic revision has received limited support due to the study’s poor taxon sampling, weakly supported results and possible temporary nomenclatural instability. Our study analyzes three nuclear and three mitochondrial genes from 111 specimens, representing 51 ingroup taxa. Parsimony, likelihood and Bayesian analyses of concatenated and partitioned datasets consistently recovered a comb-like tree with 10, well-supported, monophyletic lineages. Our taxonomic reassessment divides the family into 10 genera, corresponding to these well-supported lineages. Short internodes and low support between the non-platysaur lineages are consistent with a rapid radiation event at the base of the viviparous cordylids.

Histone H3K27ac separates active from poised enhancers and predicts developmental state

by Albert Wu Cheng

Creyghton M.P.*, Cheng A.W.*, Welstead, G.W., Koositra, T., Carey, B.W., Steine,E.J.,Hanna,J.,Lodato,M.A.,Frampton,G.M.,Sharp,P.A.,Boyer,L.A., Young,R.A., Jaenisch R.
*contributed equally

Developmental programs are controlled by transcription factors and chromatin regulators, which maintain specific gene... more Developmental programs are controlled by transcription factors and chromatin regulators, which maintain specific gene expression programs through epigenetic modification of the genome. These regulatory events at enhancers contribute to the specific gene expression programs that determine cell state and the potential for differentiation into new cell types. Although enhancer elements are known to be associated with certain histone modifications and transcription factors, the relationship of these modifications to gene expression and developmental state has not been clearly defined. Here we interrogate the epigenetic landscape of enhancer elements in embryonic stem cells and several adult tissues in the mouse. We find that histone H3K27ac distinguishes active enhancers from inactive/poised enhancer elements containing H3K4me1 alone. This indicates that the amount of actively used enhancers is lower than previously anticipated. Furthermore, poised enhancer networks provide clues to unrealized developmental programs. Finally, we show that enhancers are reset during nuclear reprogramming.

Resolving the phylogenetic position of enigmatic New Guinea and Seychelles Scutigeromorpha (Chilopoda): a molecular and morphological assessment of Ballonemini

by Aodhán Butler

Aodhán D. Butler, Gregory D. Edgecombe, Alexander D. Ball and Gonzalo Giribet

Invertebrate Systematics 24(6) 539-559 http://dx.doi.org/10.1071/IS10037

Recent phylogenetic analyses of scutigeromorph centipedes omitted New Guinea endemics for lack of modern data, either... more Recent phylogenetic analyses of scutigeromorph centipedes omitted New Guinea endemics for lack of modern data, either from morphology or molecular sequences. Among these is the tribe Ballonemini, originally established for Ballonema Verhoeff, 1904, and Parascutigera Verhoeff, 1904, based on similar tergal prominences. Subsequent systematic revision led to their separation into different subfamilies. Combined analyses of morphology and sequence data including Ballonema gracilipes Verhoeff, 1904, resolve Ballonema either in a grade of Scutigerinae or as sister to all other Scutigerinae + Thereuoneminae. Confocal laser scanning microscopy (CLSM) of the types of B. gracilipes demonstrates the utility of this technique for non-destructive imaging of historical museum material at a resolution comparable to scanning electron microscopy. A possible record of Ballonema in the Seychelles is dismissed; a collection from Silhouette samples a member of Thereuoneminae described as Seychellonema gerlachi gen. nov. sp. nov. Morphological data, analysed with sequence data for other Scutigeromorpha, ally Seychellonema with the Oriental-Australian genus Thereuopoda, but it displays a novel patterning of its tergal spinula and tarsal papillae. The phylogenetic analyses include sequence data for African Pselliodidae, corroborating a sister group relationship to remaining Scutigeromorpha and generating a more stable result than in earlier analyses using only Neotropical species.