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Wiley Online Library : Cladistics
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November 17, 2013
Morphology reinforces proposed molecular phylogenetic affinities: a revised classification for Gelechioidea (Lepidoptera)
Gelechioidea are one of the most species rich and least studied superfamilies of Lepidoptera. We examine the interrelationships within the superfamily using the densest taxon sampling to date, combined with the most extensive ever morphological and molecular character data. We perform partitioned and combined analyses using maximum likelihood, Bayesian and parsimony approaches. The combined dataset consists of 155 exemplar species of Gelechioidea, representing nearly all subfamilies recognized in recent classifications. Parsimony analyses are performed with a dataset including 28 additional terminal taxa with only morphological data available. We use eight genes with a total of 6127 bp, and morphological data with 253 characters derived from larval, pupal, and adult morphology. The analyses of combined data yield more resolved trees and significantly better-supported groupings than either dataset when analysed alone. The recurrent monophyletic groupings in all our model-based analyses support a revision of the family classification. Deeper relationships vary between analyses and data partitions, leaving them ambiguous. The place of the root remains a challenge for future research. We propose a revised classification and suggest the division of Gelechioidea into 16 families. We redefine Depressariidae Meyrick, 1883 for a monophylum that includes Acriinae, Aeolanthinae, Cryptolechiinae, Depressariinae, Ethmiinae, Hypercalliinae, Hypertrophinae, Peleopodinae, Oditinae, Stenomatinae, Carcina, and a diversity of predominantly New World taxa previously excluded from Lypusidae (Amphisbatidae s. authors) but left without family position. A monophyletic Oecophoridae s. s., including Deuterogoniinae and Pleurotinae, is obtained for the first time with significant support. Elachistidae s. l. is found to be polyphyletic, and Elachistidae is restricted to comprise Agonoxeninae, Elachistinae, and Parametriotinae. Batrachedridae are polyphyletic, with several genera pending further study. Apart from the core Batrachedra, the taxa previously included in this family are grouped in an expanded Pterolonchidae, together with Coelopoetinae and Syringopainae. Lypusidae s. s. and Chimabachidae form a monophylum; Chimabachinae is united with Lypusidae as a subfamily, stat. n. Our results contradict the subfamily classifications of several families, notably Lecithoceridae and Autostichidae, but due to insufficient sampling of taxa we refrain from comprehensive taxonomic conclusions on the subfamily level, and encourage focused studies to resolve these groups.
November 11, 2013
Multiple family-level subdivisions of Boraginales have been proposed in the past. The relationships of several constituent genera have been enigmatic, including Codon (Codonaceae), Hoplestigma (Hoplestigmataceae), Pholisma (Lennoaceae), Vahlia (Vahliaceae), and Wellstedia (Wellstediaceae), all of which are included in the present study. We present a molecular analysis with four chloroplast loci, including 89 ingroup taxa and a broad outgroup sampling in the asterids. The genus Vahlia is excluded from Boraginales and appears to represent an early branching lineage of Lamiales. The study provides a well supported topology for the relationships within Boraginales, including all of the genera with previously unclear relationships. Within Boraginales, two major clades are recognized, with “herbaceaous” Boraginales I resolved as [Codonaceae,[Wellstediaceae,[Boraginaceae]]] and “woody” Boraginales II resolved as [Hydrophyllaceae I,[Hydrophyllaceae II,[Heliotropiaceae,[Cordiaceae,[Ehretiaceae,Lennoaceae]]]]. A close relationship between Ehretiaceae and Lennoaceae is well supported, but the exact placement of Lennoaceae remains unresolved. The Cordiaceae lineage includes the monotypic genus Coldenia and the aberrant western and central African genus Hoplestigma. Woody Boraginales II are retrieved in two highly supported clades. Hydrophyllaceae are retrieved in two separate clades, but with poor support. There appear to be clear morphological progressions in vegetative, floral, and fruit morphology in both major Boraginales lineages. Thus capsular fruits are found in the first branching lineages of both clades, whereas reduced seed numbers in indehiscent fruits predominate in the more derived phylogenetic positions. Based on these results, we advocate the recognition of eight morphologically well defined clades in the order, namely Boraginaceae s.str., Codonaceae, Cordiaceae (incl. Coldenia and Hoplestigmataceae), Ehretiaceae (incl. Lennoaceae), Heliotropiaceae, Hydrophyllaceae I and Hydrophyllaceae II, and Wellstediaceae.
October 31, 2013
October 22, 2013
Three additional phyletic group types, “periphyletic,” “epiphyletic”, and “anaphyletic” (in addition to Hennigian mono-, para-, and polyphyletic) are defined in terms of trees and phylogenetic networks (trees with directed reticulate edges) via a generalization of the algorithmic definitions of Farris. These designations concern groups defined as monophyletic on trees, but with additional gains or losses of members from network edges. These distinctions should be useful in discussion of systems with non-vertical inheritance such as recombination between viruses, horizontal exchange between bacteria, hybridization in plants and animals, as well as human linguistic evolution. Examples are illustrated with Indo-European language groups.
October 20, 2013
To address the phylogenetic relationships of the centipede order Geophilomorpha (more than 1000 species), we have reinterpreted and expanded the knowledge on their morphological disparity, and have doubled the amount of molecular data available. We performed maximum parsimony and maximum likelihood analyses, using 195 phylogenetically informative morphological characters for 80 species, and DNA sequences of 28S, 18S, 16S rRNA and COI for up to 48 species. We found strong support for the monophyly of Geophilomorpha, the basal dichotomy between Adesmata and Placodesmata = Mecistocephalidae, and the basal dichotomy within Adesmata between two clades that are recognized here as superfamilies Himantarioidea and Geophiloidea. With respect to the families currently in use, Himantarioidea comprises three well supported clades corresponding to (i) Oryidae, (ii) Himantariidae, and (iii) Schendylidae s.l. including Ballophilidae; Geophiloidea comprises another three supported clades corresponding to (iv) a new family Zelanophilidae, (v) Gonibregmatidae s.l. including Eriphantidae and Neogeophilidae, and (vi) Geophilidae s.l. including Aphilodontidae, Dignathodontidae, Linotaeniidae, and Macronicophilidae.
October 8, 2013
Diversity of features of the female reproductive system and other morphological characters in leeches (Citellata, Hirudinida) in phylogenetic conception
An epistemological–evolutionary conception of leeches (Hirudinida) based on features of the female reproductive system in combination with other morphological characters is presented in the spirit of the cladistic school of taxonomy. Characters relating to the structure of the ovary and the course of oogenesis in leeches were interpreted in this manner, for the first time. Each study was conducted on type species of higher taxonomic groups of true leeches. Results of analyses using features of the reproductive system only as well as in combination with other morphological characters show Piscicolidae and Glossiphoniidae as sister clades making Rhynchobdellida a monophyletic group. Also, Hirudiniformes and Erpobdelliformes appeared to be sister clades within Arhynchobdellida. The relationship between the outgroup specimens and leeches remained unresolved, because both Acanthobdella peledina and branchiobdellidans appeared to be in an equivocal relationship to hirudinidans. Characters concerning the structure of the female reproductive system and course of oogenesis thus appeared to be useful, although conservative, for reconstruction of leech phylogeny, and they well reflect phylogenetic relationships of Hirudinida at the family level.
September 30, 2013
The higher-level phylogenetic relationships of the Eumeninae (Insecta, Hymenoptera, Vespidae), with emphasis on Eumenes sensu lato
Cladistic analyses were carried out to infer the phylogenetic relationships among taxa that were originally part of the large genus Eumenes. Terminals belonging to other eumenine lineages were also included, as well as terminals from other vespid subfamilies. Analyses under equal weights and implied weights were carried out, and better results were obtained with the latter. The results corroborated the monophyly of Eumeninae, and recovered Zethini sensu lato as the sister-lineage to the remaining eumenines. Eumenes sensu lato as originally recognized is paraphyletic relative to Odynerus sensu lato. A natural classification at the tribal level congruent with the phylogenetic results may be proposed, and the names Zethini, Odynerini, and Eumenini are already available. This is the most comprehensive phylogeny of the Eumeninae to date. A new generic synonymy is Alfieria Giordani Soika, 1934 = Delta de Saussure, 1855.
September 22, 2013
Winter is coming: Miocene and Quaternary climatic shifts shaped the diversification of Western-Mediterranean Harpactocrates (Araneae, Dysderidae) spiders
Past climatic shifts have played a major role in generating and shaping biodiversity. Quaternary glacial cycles are the better known examples of dramatic climatic changes endured by ecosystems in temperate regions. Although still a matter of debate, some authors suggest that glaciations promoted speciation. Here we investigate the effect of past climatic changes on the diversification of the ground-dwelling spider genus Harpactocrates, distributed across the major mountain ranges of the western Mediterranean. Concatenated and species-tree analyses of multiple mitochondrial and nuclear loci, combined with the use of fossil and biogeographic calibration points, reveal a Miocene origin of most nominal species, but also unravel several cryptic lineages tracing back to the Pleistocene. We hypothesize that the Miocene Climatic Transition triggered major extinction events in the genus but also promoted its subsequent diversification. Under this scenario, the Iberian mountains acted as an island-like system, providing shelter to Harpactocrates lineages during the climate shifts and favouring isolation between mountain ranges. Quaternary glacial cycles contributed further to the diversification of the group by isolating lineages in peripheral refugia within mountain ranges. In addition, we recovered some unique biogeographic patterns, such as the colonization of the Alps and the Apennines from the Iberian Peninsula.
Phylogenetic analyses of Gammaridae crustacean reveal different diversification patterns among sister lineages in the Tethyan region
The Gammaridae shows the greatest disparity in species diversity and distribution pattern in the Amphipoda, with some genera ranging from the Palearctic to Nearctic, while others are limited to the Mediterranean region or ancient Tethyan margins. Here we present the first molecular phylogenetic analysis of the Gammaridae to investigate its evolutionary history using four genetic markers and a comprehensive set of taxa representing 198 species. The phylogenetic results revealed that the Gammaridae originated from the Tethyan region in the Cretaceous, and split into three morphologically and geographically distinct lineages by the end of the Paleocene. Diversification analysis combined with paleogeological evidence suggested that the Tethyan changes induced by sea-level fluctuation and tectonic uplift triggered different diversification modes and range expansions for the three lineages. The Gammarus lineage underwent an early rapid radiation across Eurasia and North America, then declined towards modern species. Pontogammarids maintained stable diversification with restricted distributions around the Tethyan basin, whereas sarothrogammarids experienced evolutionary stasis by stranding on the ancient Tethyan margins. Our findings suggest that environmental changes have played an important role in the diversification of Gammaridae lineages, which could be an opportunity to promote adaptive radiations in new habitats, or constraints resulting in evolutionary relicts.
September 15, 2013
Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM
Oblong, a program with very low memory requirements, is presented. It is designed for parsimony analysis of data sets comprising many characters for moderate numbers of taxa (the order of up to a few hundred). The program can avoid using vast amounts of RAM by temporarily saving data to disk buffers, only parts of which are periodically read back in by the program. In this way, the entire data set is never held in RAM by the program—only small parts of it. While using disk files to store the data slows down searches, it does so only by a relatively small factor (4× to 5×), because the program minimizes the number of times the data must be accessed (i.e. read back in) during tree searches. Thus, even if the program is not designed primarily for speed, runtimes are within an order of magnitude of those of the fastest existing parsimony programs.
The Barcode of Life
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution