Wiley Online Library : Cladistics


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October 19, 2014

We are puzzled by a recent comment that suggested that historical hypotheses can be tested but are unfalsifiable. We argue that phylogenetic hypotheses are falsifiable without the aid of a time machine and that they are like any other hypothesis: they are tentative knowledge propositions capable of falsification with character evidence.

October 17, 2014

Arecaceae tribe Cocoseae is the most economically important tribe of palms, including both coconut and African oil palm. It is mostly represented in the Neotropics, with one and two genera endemic to South Africa and Madagascar, respectively. Using primers for six single copy WRKY gene family loci, we amplified DNA from 96 samples representing all genera of the palm tribe Cocoseae as well as outgroup tribes Reinhardtieae and Roystoneae. We compared parsimony (MP), maximum likelihood (ML), and Bayesian (B) analysis of the supermatrix with three species-tree estimation approaches. Subtribe Elaeidinae is sister to the Bactridinae in all analyses. Within subtribe Attaleinae, Lytocaryum, previously nested in Syagrus, is now positioned by MP and ML as sister to the former, with high support; B maintains Lytocaryum embedded within Syagrus. Both MP and ML resolve Cocos as sister to Syagrus; B positions Cocos as sister to Attalea. Bactridineae is composed of two sister clades, Bactris and Desmoncus in one, for which there is morphological support, and a second comprising Acrocomia, Astrocaryum, and Aiphanes. Two B and one ML gene tree-species estimation approaches are incongruent with the supermatrix in a few critical intergeneric clades, but resolve the same infrageneric relationships. The biogeographic history of the Cocoseae is dominated by dispersal events. The tribe originated in the late Cretaceous in South America. Evaluated together, the supermatrix and species tree analyses presented in this paper provide the most accurate picture of the evolutionary history of the tribe to date, with more congruence than incongruence among the various methodologies.

September 30, 2014

The first rigorous analysis of the phylogeny of the North American vaejovid scorpion subfamily Syntropinae is presented. The analysis is based on 250 morphological characters and 4221 aligned DNA nucleotides from three mitochondrial and two nuclear gene markers, for 145 terminal taxa, representing 47 species in 11 ingroup genera, and 15 species in eight outgroup genera. The monophyly and composition of Syntropinae and its component genera, as proposed by Soleglad and Fet, are tested. The following taxa are demonstrated to be para- or polyphyletic: Smeringurinae; Syntropinae; Vaejovinae; Stahnkeini; Syntropini; Syntropina; Thorelliina; Hoffmannius; Kochius; and Thorellius. The spinose (hooked or toothed) margin of the distal barb of the sclerotized hemi-mating plug is demonstrated to be a unique, unambiguous synapomorphy for Syntropinae, uniting taxa previously assigned to different subfamilies. Results of the analysis demonstrate a novel phylogenetic relationship for the subfamily, comprising six major clades and 11 genera, justify the establishment of six new genera, and they offer new insights about the systematics and historical biogeography of the subfamily, and the information content of morphological character systems.

September 5, 2014

Nembrothinae is a colourful subfamily of nudibranch polycerids, which despite its large size and striking appearance, needs to be more thoroughly studied. The available scientific information about this subfamily is very recent, and pictures of living undescribed species become available every day. Nevertheless, the lack of associated material for morphological, anatomical, and molecular analysis results in scarce additional studies. In this paper, five novel species are described: Roboastra ernsti sp. nov., Roboastra nikolae sp. nov., Tambja brasiliensis sp. nov., Tambja crioula sp. nov., and Tambja kava sp. nov. In addition, Tambja divae (Marcus, ), a species previously known only from the original description, is redescribed and additional data and comments on Tambja cf. amakusana Baba, 1987 and Tambja marbellensis Schick and Cervera, 1998 are provided. Molecular data (H3, COI and 16S genes) for all these novel species and some additional ones were obtained and included in a previous molecular database. Maximum-likelihood, maximum-parsimony and Bayesian analyses were carried out. The phylogeny presented here has revealed Nembrothinae to be an intricate and challenging group of nudibranchs to study. Intermediate missing species seem to be critical to understanding the evolutionary relationships within this group.

September 3, 2014

August 12, 2014

The need for taxonomists to take full advantage of biodiversity informatics has been clear for at least 10 years. Significant progress has been made in providing access to taxonomic resources online, including images of specimens (especially types), original species descriptions, and georeferenced collection data. However, in spite of persuasive calls for e-monography, there are few, if any, completed project, even though monographic research is the only mechanism for reducing synonymous names, which are estimated to comprise 50% of all published names. Caricaceae is an economically important family of flowering plants from Africa and the Neotropics, best known for the fruit crop papaya. There is a large amount of information on the family, especially on chemistry, crop improvement, genomics, and the sex chromosomes of papaya, but up-to-date information on the 230 names and which species they might belong to was not available. A dynamically updated e-monograph of the Caricaceae now brings together all information on this family, including keys, species descriptions, and specimen data relating the 230 names to 34 species and one hybrid. This may be the first taxonomic monograph of a plant family completely published online. The curated information will be continuously updated to improve the monograph's comprehensiveness and utility.

August 6, 2014

July 30, 2014

The brake fern genus Pteris belongs to the Pteridaceae subfamily Pteridoideae. It contains 200–250 species distributed on all continents except Antarctica, with its highest species diversity in tropical and subtropical regions. The monophyly of Pteris has long been in question because of its great morphological diversity and because of the controversial relationships of the Australian endemic monospecific genus Platyzoma. The circumscription of the Pteridoideae has likewise been uncertain. Previous studies typically had sparse sampling of Pteris species and related genera and used limited DNA sequence data. In the present study, DNA sequences of six plastid loci of 146 accessions representing 119 species of Pteris (including the type of the genus) and 18 related genera were used to infer a phylogeny using maximum-likelihood, Bayesian-inference and maximum-parsimony methods. Our major results include: (i) the previous uncertain relationships of Platyzoma were due to long-branch attraction; (ii) Afropteris, Neurocallis, Ochropteris and Platyzoma are all embedded within a well-supported Pteris sensu lato; (iii) the traditionally circumscribed Jamesonia is paraphyletic in relation to a monophyletic Eriosorus; (iv) Pteridoideae contains 15 genera: Actiniopteris, Anogramma, Austrogramme, Cerosora, Cosentinia, Eriosorus, Jamesonia, Nephopteris (no molecular data), Onychium, Pityrogramma, Pteris, Pterozonium, Syngramma, Taenitis and Tryonia; and (v) 15 well-supported clades within Pteris are identified, which differ from one another on molecular, morphological and geographical grounds, and represent 15 major evolutionary lineages.

July 22, 2014

Numerous hypotheses on the evolution of Neotropical biodiversity have stimulated research to provide a better understanding of diversity dynamics and distribution patterns of the region. However, few studies integrate molecular and morphological data with complete sampling of a Neotropical group, and so there has been little synthesis of the multiple processes governing biodiversity through space and time. Here, a total-evidence phylogenetic approach is used to reconstruct the evolutionary history of the butterfly subgenus Heraclides. We used DNA sequences for two mitochondrial genes and one nuclear gene and coded 133 morphological characters of larvae and adults. A robust and well-resolved phylogeny was obtained using several analytical approaches, while molecular dating and biogeographical analyses indicated an early Miocene origin (22 Mya) in the Caribbean Islands. We inferred six independent dispersal events from the Caribbean to the mainland, and three from the mainland to the Caribbean, and we suggest that cooling climates with decreasing sea levels may have contributed to these events. The time-calibrated tree is best explained by a museum model of diversity in which both speciation and extinction rates remained constant through time. By assessing both continental and fine-scale biodiversity patterns, this study provides new findings, for instance that islands may act as source of diversity rather than as a sink, to explain spatio-temporal macroevolutionary processes within the Neotropical region.