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Wiley Online Library : Cladistics
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October 28, 2014
The asidine darkling beetles (Coleoptera: Tenebrionidae: Asidini) are a diverse tribe of flightless tenebrionids found in many arid and sub-arid habitats around the world. The 263 currently described North American species are contained in ten genera, all of which are restricted to the western half of the continent. The Asidini, like all members of the subfamily Pimeliinae, lack defensive glands. Instead, several phenotypic traits occur within the tribe that may help limit predation. These include the contrasting defensive strategies of crypsis, through either background matching or pattern disruption, and Batesian mimicry of the chemically defended genus Eleodes. Dorsal elytral morphology was assessed between 53 North American asidine species and 13 common Eleodes model species using multiple methodologies to assess similarities between species in the two groups that might indicate mimetic relationships. A phylogeny of the North American asidines is used to map the occurrence of differing defensive strategies within the tribe. Crypsis is reconstructed as the ancestral state, with two origins for Batesian mimicry and multiple reversals. The combination of strongly to weakly cryptic species and varying levels of mimetic fidelity to Eleodes model species make the asidines a promising lineage upon which to further explore the evolution of defensive phenotypes.
Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not minimization of operationally defined total cost or minimization of equally weighted transformations
Wheeler (2012) stated that minimization of ad hoc hypotheses as emphasized by Farris (1983) always leads to a preference for trivial optimizations when analysing unaligned sequence data, leaving no basis for tree choice. That is not correct. Farris's framework can be expressed as maximization of homology, a formulation that has been used to overcome the problems with inapplicables (it leads to the notion of subcharacters as a quantity to be co-minimized in parsimony analysis) and that is known not to lead to a preference for trivial optimizations when analysing unaligned sequence data. Maximization of homology, in turn, can be formulated as a minimization of ad hoc hypotheses of homoplasy in the sense of Farris, as shown here. These issues are not just theoretical but have empirical relevance. It is therefore also discussed how maximization of homology can be approximated under various weighting schemes in heuristic tree alignment programs, such as POY, that do not take into account subcharacters. Empirical analyses that use the so-called 3221 cost set (gap opening cost three, transversion and transition costs two, and gap extension cost one), the cost set that is known to be an optimal approximation under equally weighted homology in POY, are briefly reviewed. From a theoretical point of view, maximization of homology provides the general framework to understand such cost sets in terms that are biologically relevant and meaningful. Whether or not embedded in a sensitivity analysis, this is not the case for minimization of a cost that is defined in operational terms only. Neither is it the case for minimization of equally weighted transformations, a known problem that is not addressed by Kluge and Grant's (2006) proposal to invoke the anti-superfluity principle as a rationale for this minimization.
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
Phylogeny and historical biogeography of the cocosoid palms (Arecaceae, Arecoideae, Cocoseae) inferred from sequences of six WRKY gene family loci
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
Phylogeny of the North American vaejovid scorpion subfamily Syntropinae Kraepelin, 1905, based on morphology, mitochondrial and nuclear DNA
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
Going further on an intricate and challenging group of nudibranchs: description of five novel species and a more complete molecular phylogeny of the subfamily Nembrothinae (Polyceridae)
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
A global plastid phylogeny of the brake fern genus Pteris (Pteridaceae) and related genera in the Pteridoideae
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.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution