HCPC: A New Parsimonious Clustering Method based on Hierarchical Characters for Morphological Phylogenetic Reconstruction

Background: Phylogenetic trees are reconstructed frequently to provide a better interpretation of the evolutionary history of species. However, most traditional methods ignore the hierarchical relationships among characters and neglect the inapplicable state that frequently exists in the morphological data, resulting in poor performance of the phylogenetic analysis.Results: In this study, we propose a phylogenetic clustering method based on hierarchical characters. Accordingly, we call our method Hierarchical Characters Parsimonious Clustering(HCPC). To combine prior phylogenetic knowledge and treat the inapplicable state more reasonably, two stages are proposed, i.e., Phylogenetic reconstruction and parsimonious tree search. During phylogenetic reconstruction, HCPC is able to infer the shared ancestral relationships among species. For the search of the parsimonious tree, we use a simulated annealing algorithm to heuristically search the phylogenetic tree based on the parsimony criterion. In addition, HCPC combines asymmetric binary relationships and character hierarchies to solve the problem of the ambiguity of the inapplicable state.Conclusion: The experimental results show that the proposed method provides better performance of phylogenetic analysis than existing methods and a scientific and quantitative basis for biologists to study species evolution.

Rooting morphologically divergent taxa – slow-evolving sequence data might help

When fossils are sparse and the lineages studied are very divergent morphologically, analyses based exclusively on morphology may lead to conflicting and unexpected hypotheses. Through integration of data from conservative genes/gene regions the terminals including these data can anchor or constrain the search, thereby practically circumscribing the search space of the combined analyses. In this study, we revisit the phylogeny of a highly divergent group of mosses, class Polytrichopsida. We supplemented the morphological matrix by adding sequence data of the nuclear gene 18S, chloroplast genes rbcL and rps4, plus the mitochondrial gene nad5. For the phylogenetic analyses we used parsimony as the optimality criterion. Analyses that included all the terminals resulted in one most parsimonious tree with a clade comprised of Alophosia azorica and the fossil Meantoinea alophosioides representing the basal-most lineage. Analyses with different outgroup sampling produced the same topology for most ingroup relationships. An analysis excluding morphological characters and the four terminals for which only morphological characters were scored (the two fossil and two extant terminals) resulted in one optimal tree with identical topology to the one obtained when including all terminals. These results are largely congruent with those obtained in the recent analyses based exclusively on sequence level data of a larger number of terminals. Our results indicate that large size and complexity of the gametophyte have evolved independently in several lineages. Notably, the nodes of the backbone of the most parsimonious tree have very low support values, thus these inferred relationships could change if new additional information conflicts with the current data. Future studies should be aimed at incorporating all terminals into phylogenetic analyses, which is not an unrealistic goal for a group with less than 200 species. Also, additional fossils, some of which await detailed examination and description, need to be included. Whether these will affect the overall pattern of phylogeny presented here remains to be seen. In a group that is obviously very ancient, we cannot assume, a priori, that currently known fossil taxa, which go back in time less than 140 Ma, represent the oldest lineages of the group.

Phylogenetic placement of the monotypic genus Holopodostreptus Carl, 1913 and notes on the systematics of Pseudonannolenidae (Spirostreptida : Cambalidea)

The genus Holopodostreptus Carl, 1913 is a poorly known monotypic genus endemic to Ecuador. It differs from most other Pseudonannolenidae by a set of characteristics of the gnathochilarium and gonopods. Herein, we provide descriptive notes of males of H. braueri Carl, 1913 based on recently collected material. Females of the species are described for the first time, and images of the vulvae are provided. In addition, we attempt for the first time to place Holopodostreptus in a phylogenetic context. With a total of 14 taxa and 41 morphological characters, and under implied weighting (k = 6), a single most-parsimonious tree is recovered (total fit = 35.86). The genus is recovered as sister-group of Physiostreptus Silvestri, 1903. The clade Holopodostreptus + Physiostreptus is supported by one synapomorphy (absence of setae on the prefemoral process of leg-pair 1 in males) and one homoplastic transformation (narrow telopodite). Based on the phylogenetic results, notes on the subfamilies Pseudonannoleninae, Cambalomminae and Physiostreptinae and a key for all pseudonannolenid genera are provided.

Systematics of the genus Aphrophila Edwards with description of fifteen new species (Diptera: Tipulomorpha: Limoniidae)

The genus Aphrophila (Diptera: Limoniidae) is revised. All previously described species are redescribed and illustrated, along with fifteen new species. From the Campbell Island (New Zealand): A. whakapapa sp. n.; from Argentina: A. argentina sp. n., A. huahua sp. n. and A. peuma sp. n.; from Chile: A. aequalitas sp. n., A. alexanderi sp. n., A. dentata sp. n., A. dupla sp. n., A. edwardsi sp. n., A. minuscula sp. n., A. penta sp. n., A. regia sp. n., A. serra sp. n., A. sperancae sp. n. and A. vulcania sp. n. Identification key is provided for all the valid species. A phylogenetic analysis was made which resulted in one single most parsimonious tree with five main groups, classified into five subgenera: A. (Aphrophila) Edwards, A. (Magnodonta) subg. n., A. (Spinalia) subg. n., A. (Sirena) subg. n., A. (Zelandica) subg. n. In order to uncover the biogeographical pattern of the distribution of the species in terms of area relationships, a Paralogy-free subtree analysis was performed, which resulted in the following areagram: ((Campbell Is. + S. America) + New Zealand).

A new species of Polietina (Diptera: Muscidae) from South America, with an updated phylogeny of the genus and a review of species’ identity in GenBank

After a 20 years hiatus, we describe a new species, Polietina ponti sp. nov., from Madre de Dios, Tambopata River, Peru. Additionally, we propose Polietina nigra Couri & Carvalho, 1996 as a junior synonym of Polietina prima (Couri & Medeiros, 1990). A previous phylogenetic hypothesis was updated with the inclusion of the new taxon described here, which yielded a single most parsimonious tree that is similar to a previously published hypothesis (Pyrellina marsya (Pyrellina distincta (Deltotus facetus ((Polietina steini (Polietina ponti sp. nov., P. prima (P. bicolor, P. minor, P. univittata)(P. flavithorax, P. major)))(P. flavidicincta (P. rubella (P. concinna (P. orbitalis, P. wulpi)))))))). The identity of Polietina vouchers with nucleotide sequences registered in the GenBank were also verified and corrected.

Building a Twig Phylogeny

In this classroom activity, students build a phylogeny for woody plant species based on the morphology of their twigs. Using any available twigs, students can practice the process of cladistics to test evolutionary hypotheses for real organisms. They identify homologous characters, determine polarity through outgroup comparison, and construct a parsimonious tree based on synapomorphies (shared derived characters). This activity efficiently demonstrates many systematics concepts, including homology, homoplasy (convergence and reversal), polarity, synapomorphy, symplesiomorphy, autapomorphy, polytomy, and parsimony. It also engages students in inquiry, promotes student collaboration, raises awareness of plant structure, and exposes students to the diversity of common local trees.

Phylogeny, biogeography and description of Ameripassalus, a new Mesoamerican genus of Passalidae (Coleoptera)

Ameripassalus, gen. nov., is described as the first genus of Passalini with a distribution restricted to Mesoamerica. The species include A. guatemalensis (Kaup, 1869), comb. nov. from Passalus Fabricius, A. difficilis, sp. nov. and A. tamaulipensis, sp. nov. from Mexico, and A. jacki, sp. nov. and A. nigritus, sp. nov. from Guatemala. A matrix of 46 morphological characters, including the species from Ameripassalus, gen. nov. and 13 species of the genera Paxillus MacLeay, Ptichopus Kaup, Heliscus Zang, Veturius Kaup, Spasalus Kaup, Passipassalus Fonseca & Reyes-Castillo, Passalus Fabricius and Leptaulax Kaup were analysed. Only a single most parsimonious tree was found; in this Ameripassalus is retrieved as a monophyletic group. Ameripassalus difficilis, sp. nov. is shown as the sister group of the rest of the species in the genus. The species with the southernmost distribution (A. guatemalensis (A. nigritus, sp. nov. + A. jacki, sp. nov.)) form a nested clade within the species with the northernmost distribution. Keys to identify adults of the genera of Passalini and to the species of Ameripassalus are provided.