Cladistics

Wiley Online Library : Cladistics

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September 5, 2014

21:09
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

20:12
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

20:08
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

23:10
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.

July 17, 2014

03:41
A recent article published in Cladistics is critical of a number of heuristic methods for phylogenetic inference based on parsimony scores. One of my papers is among those criticized, and I would appreciate the opportunity to make a public response. The specific criticism is that I have re-invented an algorithm for economizing parsimony calculations on trees that differ by a subtree pruning and regrafting (SPR) rearrangement. This criticism is justified, and I apologize for incorrectly claiming originality for my presentation of this algorithm. However, I would like to clarify the intent of my paper, if I can do so without detracting from the sincerity of my apology. My paper is not about that algorithm, nor even primarily about parsimony. Rather, it is about a novel strategy for Markov chain Monte Carlo (MCMC) sampling in a state space consisting of trees. The sampler involves drawing from conditional distributions over sets of trees: a Gibbs-like strategy that had not previously been used to sample tree-space. I would like to see this technique incorporated into MCMC samplers for phylogenetics, as it may have advantages over commonly used Metropolis-like strategies. I have recently used it to sample phylogenies of a biological invasion, and I am finding many applications for it in agent-based Bayesian ecological modelling. It is thus my contention that my 2005 paper retains substantial value.

July 15, 2014

19:59
Protodrilidae is a group of small, superficially simple-looking annelids, lacking chaetae and appendages, except for two prostomial palps. Originally considered to be one of the primitive “archiannelid” families, its affinity within Annelida is still highly debated. Protodrilids are found worldwide in the interstices of intertidal and subtidal marine sediments. Despite their simple appearance they constitute one of the most species-rich interstitial families, with 36 described species in two genera, Protodrilus and the gutless Astomus. Here we present the first phylogenetic study of Protodrilidae employing five gene fragments, 55 morphological characters and 73 terminals (including seven outgroups) analysed under direct optimization and parsimony as well as model-based methods. The large data set includes all 36 described species of Protodrilidae (17 of which are represented only by the morphological partition) as well as 30 undescribed or uncertain species (represented by both morphology and molecules). This comprehensive, inclusive and combined analysis revealed a new perspective on the phylogeny of Protodrilidae: the family is shown to contain six cosmopolitan subclades, each supported by several morphological apomorphies, and with the genus Astomus consistently nested among the other five clades rather than next to these. Consequently, the diagnosis of Protodrilus is emended, Astomus remains unchanged and the four remaining lineages are diagnosed and named Megadrilus n. gen, Meiodrilus gen. nov., Claudrilus n. gen and Lindrilus gen. nov. Character transformations showed that large size and presence of pigmentation, oviducts and eyes are plesiomorphies of the family, retained in Protodrilus, Megadrilus gen. nov. and Lindrilus gen. nov. These features are secondarily lost in the gutless Astomus with epidermal uptake of nutrients, as well as in Meiodrilus gen. nov. and some species of Claudrilus n. gen, with smaller size correlated to life in interstices of finer sediments.

June 30, 2014

20:54
Neriidae are a small family of acalyptratae flies, mostly distributed in the tropics. Very little is known about their biology, and the evolutionary relationships among species have never been evaluated. We perform the first comprehensive phylogenetic analysis of the family, including 48 species from all biogeographic regions inhabited, as well as five species of Micropezidae and one Cypselosomatidae as outgroups. We build a morphological data matrix of 194 characters, including 72 continuous characters. We first explore ways to deal with the issue of scaling continuous characters, including rescaling ranges to unity and using implied weighting. We find that both strategies result in very different phylogenetic hypotheses, and that implied weighting reduces the problem of scaling, but only partially. Furthermore, using implied weighting after rescaling characters improves the congruence between partitions and results in higher values of group support. With respect to the Neriidae, we confirm the monophyly of the family and of most its genera, although we do not obtain any of the currently accepted suprageneric groups. We propose to restrict the Eoneria and Nerius groups exclusively to the Neotropical fauna, and synonymize Glyphidops subgenus Oncopsia Enderlein with Glyphidops subgenus Glyphidops Enderlein, eliminating the subgeneric divisions. This revised phylogeny presents a striking biogeographic consistency, and shows that previous main divisions of the family were based on events of convergence.
20:53
A phylogenetic analysis of a total of 31 species: 27 fossil species from seven families (Glypheidae, Litogastridae, Mecochiridae, Pemphicidae, Erymidae, Clytiopsidae, Chimaerastacidae), and four extant species from three families (Glypheidae, Nephropidae, Stenopodidae) is proposed. Most of the genera considered are coded exclusively based upon their type species and, as much as possible, based upon the type specimens. The cladistic analysis demonstrates that the glypheidean lobsters (infraorder Glypheidea) form a monophyletic group including two superfamilies: Glypheoidea and Pemphicoidea new status. Glypheoidea includes three families: Glypheidae, Mecochiridae and Litogastridae. Litogastridae is the sister group of the clade Glypheidae + Mecochiridae. Pemphicoidea includes a single family: Pemphicidae. A new classification of Glypheidea is proposed and currently known genera are rearranged based upon the phylogenetic analysis.
00:56
The present paper is mainly concerned with homology assessment through phylogenetic analyses. It raises a fundamental question: What are the epistemological differences between modern parsimony and model-based analyses in relation to homology assessment and phylogenetic inference? Although these methods usually achieve concordant topological results, they may generate discordant inferences of character evolution from the same datasets. This indicates that method selection has serious implications for evolutionary scenarios and classificatory arrangements. Notwithstanding that parsimony and model-based approaches use the Hennigian concepts of monophyly and synapomorphy, they employ different epistemological ways of dealing with the monophyly/synapomorphy relationship. Independently of their differences, these analyses should take into account all relevant evidence in support of the phylogenetic inferences. A focus on morphological homologues means that they must be included in data matrices, evaluated as part of the phylogenetic analysis, and cannot be ignored in calculation of the tree(s) length (parsimony), maximum-likelihood (maximum-likelihood), and posterior probabilities (Bayes).

June 25, 2014

20:45
Among the least studied harvestmen are the members of the family Caddidae sensu Shear, , a group of Opiliones with massive eyes and the putative sister group of the remaining Eupnoi. Caddids were originally described as two families, Caddidae and Acropsopilionidae, but these are currently treated as subfamilies of Caddidae. These minute arachnids are rarely collected and present some interesting biogeographical patterns, including a disjunct distribution between East Asia and eastern North America, and some of the few cases of trans-Pacific genera in southern hemisphere Opiliones. We therefore obtained samples from most of the landmasses inhabited by Caddidae and undertook a phylogenetic study using nuclear and mitochondrial genes for as many samples as possible. Our results, based on a broad taxonomic sampling, surprisingly showed polyphyly of Caddidae, with the genus Caddo forming the sister group of the remaining Eupnoi, whereas the southern hemisphere genera, many of which were originally placed in Acropsopilionidae, within Dyspnoi, formed the sister clade of the remaining Dyspnoi. In addition, the more recently described genus Hesperopilio, from Western Australia and Chile, was unrelated to either Caddidae or Acropsopilionidae, despite having the supposedly diagnostic large ocularium, and instead appeared deeply nested within the Eupnoi superfamily Phalangioidea. Our results are robust to analytical treatment and to homology scheme (dynamic vs. static notions of homology), resulting in a new phylogenetic proposal for Eupnoi and Dyspnoi. Ancestral state reconstruction suggests that the ancestral Palpatores was probably a tiny harvestman with an enlarged ocularium and glandular palpal setae in its enlarged and armed palps. We take the following taxonomic actions: Acropsopilionidae is removed from synonymy under Caddidae and its family status and membership in Dyspnoi are restored. Hesperopilio Shear, is removed from Caddoidea/Caddidae and transferred to Phalangioidea, but it is not assigned to any family.

June 24, 2014