Elucidating the systematics of Eopachylus and Yraguara (Opiliones: Gonyleptidae) with morphological phylogeny

Phylogenies based on morphology vary considerably in their quality: some are robust and explicit with little conflict in the data set, whereas others are far more tenuous, with much conflict and many possible alternatives. The main primary reasons for untrue or inexplicit morphological phylogenies are: not enough characters developed between branching points, uncertain character polarity, poorly differentiated character states, homoplasy caused by parallelism or reversal, and extinction, which may remove species entirely from consideration and can make originally conflicting data sets misleadingly compatible, increasing congruence at the expense of truth. Extinction differs from other confounding factors in not being apparent either in the data set or in subsequent analysis. One possibility is that variation in the quality of morphological phylogenies has resulted from exposure to different ecological situations. To investigate this, it is necessary to compare the histories of the clades concerned. In the case of explicit morphological phylogenies, ecological and behavioural data can be integrated with them and it may then be possible to decide whether morphological characters are likely to have been elicited by the environments through which the clade has passed. The credibility of such results depends not only on the phylogeny being robust but also on its detailed topology: a pectinate phylogeny will often allow more certain and more explicit statements to be made about historical events. In the case of poor phylogenies, it is not possible to produce detailed histories, but they can be compared with robust phylogenies in the range of ecological situations occupied, and whether they occupy novel situations in comparison with their outgroups. LeQuesne testing can give information about niche homoplasy, and it may also be possible to see if morphological features are functionally associated with ecological parameters, even if the direction of change is unknown. Examination of the robust and explicit phylogeny of the semaphore geckoes (Pristurus) suggests that its quality does stem from a variety of environmental factors. The group has progressed along an ecological continuum, passing through a series of increasingly severe niches that appear to have elicited many morphological changes. The fact that niches are progressively filled reduces the likelihood of species reinvading a previous one with related character reversal. Because the niches of advanced Pristurus are virtually unique within the Gekkonidae the morphological changes produced are also very rare and therefore easy to polarize. Ecological changes on the main stem of the phylogeny are abrupt and associated character states consequently well differentiated.(ABSTRACT TRUNCATED AT 400 WORDS)

We investigate the evolution of sperm ultrastructure of three species of Boidae (Epicrates cenchria, Boa constrictor amarali, and Corallus hortulanus). Spermatozoa of these species are filiform consisting of a head region, containing the nucleus and acrosome complex, a midpiece, and a tail region subdivided into principal piece and endpiece. Multilaminar membranes and extracellular microtubules were observed next to the plasma membrane of the spermatozoa. The following differences were observed among the species: ridge on acrosome surface in Boa constrictor amarali (absent in Epicrates cenchria and Corallus hortulanus), stopper-like perforatorium base plate in Boa constrictor amarali and Epicrates cenchria (absent in Corallus hortulanus), rounded mitochondria in transverse section in Epicrates cenchria and Corallus hortulanus (irregular in Boa constrictor amarali). We mapped sperm characters onto two phylogenies based on morphological (Kluge in Misc Publ Mus Zool Univ Michigan 178:1–58, 1991) and molecular (Austin in Copeia 2:341–352, 2000) data, using a number of squamate species as outgroups. We identified 31 unambiguous character transformations in the morphological phylogeny and 30 in the molecular phylogeny, but only 13 and 12 transformations, respectively, are possible synapomorphies. We identified novel sperm synapomorphies, which were common between the morphological and molecular phylogenies: absence of perforatorium base plate and mitochondria arranged as sinuous tubes in oblique section (Serpentes), acrosome vesicle not subdivided and fibers 3 and 8 at the anteriormost region of principal piece (Boidae), and absence of an electron dense structure inside the proximal centriole (Elapidae + Colubridae). Our results suggest greater agreement between sperm ultrastructure and gross anatomical characters. In addition, we found no tendency for more homoplasies in the sperm head than in the flagellum, as recorded in previous studies.

Recent molecular studies in gerbils found multiple instances of discordance between molecular and morphological phylogenies. In this study, we analyse the largest molecular data set to date of gerbils and their sister group the deomyines to estimate their phylogenetic relationships. Maximum-likelihood and Bayesian analyses were largely concordant, and both generally had high levels of node support. For gerbils, the results were generally concordant with previous molecular phylogenies based on allozymes, chromosomes, DNA/DNA hybridization and DNA sequences, and discordant with morphological phylogenies. None of the traditional gerbil tribes and subtribes were monophyletic. In addition, paraphyly was found in the genera Gerbillus, Gerbilliscus and Meriones as well as in five subgenera within Dipodillus, Gerbillurus and Meriones. Short branches separating taxa in small clusters within Dipodillus and Meriones suggest synonymy. Within deomyines, all genera and subgenera were monophyletic; however, two species groups within Acomys appear to contain synonymous taxa. We also find support for the discordance between molecular and morphological phylogenies in gerbils being partly due to convergent adaptations to arid environments, primarily in the suite of traits associated with inflation of the tympanic bullae. Relative bullar size does appear to be a desert adaptation and is correlated with aridity independent of phylogeny. Further, it varies more strongly along bioclimatic clines than between binary habitat classifications (desert versus mesic).

Phylogeny of the Paracalanidae Giesbrecht, 1888 (Crustacea: Copepoda: Calanoida)

In this study, eight different shells from different species were examined by looking at the physical features of the shells. The purpose of the study was to identify evolutionary links between species with shells. From these physical features, a morphological phylogeny was compiled. And from the morphological phylogeny, it was shown that their the family of the shells was the first trait defined specific clades and that each synapomorphic trait after this was a physical feature of the shells. From the experiment, the following conclusions were discovered: 1) That Scallops and Cockles are the most morphologic clay similar. 2) For taxa A, trait III is an apomorphy because this trait is a single trait that defines this taxa separately from the other taxa. 3) For taxa A, trait I is a plesiomorphy because it is a trait that is ancestral to trait III which defines taxa A (Fig. 2). From the data, these conclusions could introduce a new topic, new ideas, and new information to existing researches.The influx of new ideas would either become helpful, or build off the research of other researchers. This would help the scientific community in increasing its knowledge of the evolutionary background of more species.

BackgroundPorous species boundaries can be a source of conflicting hypotheses, particularly when coupled with variable data and/or methodological approaches. Their impacts can often be magnified when non-model organisms with complex histories of reticulation are investigated. One such example is the genus Catostomus (Osteichthys, Catostomidae), a freshwater fish clade with conflicting morphological and mitochondrial phylogenies. The former is hypothesized as reflecting the presence of admixed genotypes within morphologically distinct lineages, whereas the latter is interpreted as the presence of distinct morphologies that emerged multiple times through convergent evolution. We tested these hypotheses using multiple methods, to including multispecies coalescent and concatenated approaches. Patterson’s D-statistic was applied to resolve potential discord, examine introgression, and test the putative hybrid origin of two species. We also applied naïve binning to explore potential effects of concatenation.ResultsWe employed 14,007 loci generated from ddRAD sequencing of 184 individuals to derive the first highly supported nuclear phylogeny for Catostomus. Our phylogenomic analyses largely agreed with a morphological interpretation,with the exception of the placement of Xyrauchen texanus, which differs from both morphological and mitochondrial phylogenies. Additionally, our evaluation of the putative hybrid species C. columbianus revealed a lack introgression and instead matched the mitochondrial phylogeny. Furthermore, D-statistic tests clarified all discrepancies based solely on mitochondrial data, with agreement among topologies derived from concatenation and multispecies coalescent approaches. Extensive historic introgression was detected across six species-pairs. Potential endemism in the Virgin and Little Colorado Rivers was also apparent, and the former genus Pantosteus was derived as monophyletic, save for C. columbianus.ConclusionsComplex reticulated histories detected herein support the hypothesis that introgression was responsible for conflicts that occurred within the mitochondrial phylogeny, and explains discrepancies found between it and previous morphological phylogenies. Additionally, the hybrid origin of C. columbianus was refuted, but with the caveat that more fine-grain sampling is still needed. Our diverse phylogenomic approaches provided largely concordant results, with naïve binning useful in exploring the single conflict. Considerable diversity was found within Catostomus across southwestern North America, with two drainages [Virgin River (UT) and Little Colorado River (AZ)] reflecting unique composition.

Back to the roots: Reducing evolutionary rate heterogeneity among sequences gives support for the early morphological hypothesis of the root of Siluriformes (Teleostei: Ostariophysi)

Estimations of phylogenies from morphological and molecular data often show contrasting results. We compared morphological and molecular phylogenies in an ancient family of woody dicots, the Betulaceae (birch family). The phylogeny of the family was estimated from parsimony analysis of morphological characters in the genera Alnus, Betula, Carpinus, Corylus, Ostrya, and Ostryopsis and from parsimony and distance-matrix analyses of DNA sequences of the chloroplast gene encoding the large subunit of ribulose-1,5-biphosphate carboxylase (rbcL) in the genera Alnus, Betula, Carpinus, Corylus, and Ostrya and in two outgroups, Quercus and Liquidambar. The topologies obtained by the different methods were completely congruent, and bootstrapping strongly supported the division of the family Betulaceae into two major clades, Betuleae (Alnus and Betula) and Coryleae (other members). Only slightly more homoplasy was present in the rbcL sequence data set than in the morphological set. Relative-rate tests indicated that the Coryleae clade had a faster rate of rbcL evolution than did the Betuleae clade. Heterogeneity of rates of morphological evolution also paralleled those for rbcL.

Established methods of exploratory data analysis reveal conflicts in morphological data from rhynchonellide brachiopods, conflicts that result in mismatches between morphological, combined, and molecular phylogenies. Consideration of the mismatches uncovers several findings of general applicability: causes of conflict include the inherent genealogical deficit of comparative morphology, and genetic signal erosion caused by genome remodelling. Because of genetic signal erosion, cladistic analysis cannot be used safely on taxa whose remote ancestors diverged in deep time. In theory, if not practice, morphological-molecular conflict may be avoided by use of genetically validated characters. The preliminary (prior) classification of the organisms concerned is a hitherto-overlooked first step of cladistic analysis; its integral roles are to enable homology hypotheses, and at least partly to determine cladistic results through classification bias. Thus hitherto, cladistics has been misunderstood and misrepresented; many reported taxon relationships may have been determined more by the prior classification than by the supporting characters. If the prior classification is artificial and does not accurately mirror evolutionary history, morphological and molecular phylogeny mismatches will register as spurious homoplasy. To avoid logical circularity in cladistic analysis there must be clear separation of input (taxon descriptions) from output (clades). This requirement rules out PhyloCode-like approaches to systematics if they allow (named) output of cladistic analysis to serve as the input to further such analyses.

A phylogeny of the nudibranch Halgerda Bergh, 1880 is presented based on mitochondrial CO1 and compared with a previously published morphology-based phylogeny. Incongruence length difference (ILD) tests indicated possibly conflicting phylogenetic signals. Both separate and combined analyses resulted in trees that were very similar in topology, both to each other and to the morphology-based tree (albeit with lower consistency and retention indices). Some differences are noted in the topology based on the optimality criteria used: parsimony and maximum likelihood. Results of this study indicate that the CO1 gene contains sufficient phylogenetic signal for inferring species-level phylogeny in the Nudibranchia and also supports many of the clades in the morphological phylogeny. Specifically, the more basal clades of the morphology-based phylogeny are supported with differences noted at the most terminal taxa.

The genus Isostenosmylus Krüger, 1913 (Neuroptera: Osmylidae) is the most species-rich genus of lance lacewings in the Neotropical region. Seven species are newly described here (Isostenosmylus angustipennis, sp. nov., Isostenosmylus apaapensis sp. nov., Isostenosmylus barbatus, sp. nov., Isostenosmylus inca, sp. nov., Isostenosmylus jaguar, sp. nov., Isostenosmylus penai, sp. nov., Isostenosmylus triangulatus, sp. nov.). A neotype of Oedosmylus morenoi Navás, 1928 is proposed, the male of Isostenosmylus irroratus Ardila-Camacho et al., 2016 is newly described, and identification keys to males and females of Isostenosmylus species are provided. A morphological phylogeny and biogeographical analysis of the genus are also presented. Isostenosmylus is recovered as a monophyletic genus and species are divided in two main clades (named here as ‘bifurcatus’ and ‘pulverulentus’ clades); the greatest diversity of this genus is located in the Andean mountain range, where new studies should be focused on. http://zoobank.org/urn:lsid:zoobank.org:pub:7AA1CED6-D30D-4DE5-A45A-86C2F038B915

SYNOPSIS. Traditional views on the interrelationships of the major animal groups are based on morphological characters, but molecular data of various types have in the last decade given indications of new and sometimes quite puzzling phylogenies. This should be an incentive not only to reevaluation of the available morphological characters but also to new studies to fill the voids in our knowledge. Modern morphology is not concerned only with traditional studies of structure and ontogeny of organ systems, but also with newer methods, such as SEM, TEM, immunocytochemistry, and cell marking. This has given morphology new dimensions, but it also has shown that vast areas of the animal kingdom remain very poorly known even through traditional studies. Phylogenetic trees built on morphology (and molecular trees with morphological characters added) demonstrate morphological characters that are in conflict with the phylogeny, and therefore should be reinvestigated; they also indicate areas where new research can contribute significantly to our understanding of the pathways of the evolution. Morphological phylogeny has the distinct advantage that characters of ancestors can be inferred and the evolutionary changes checked in terms of functional continuity and hypotheses of adaptation.

CELL LINEAGE DATA AND SPIRALIAN EVOLUTION: A REPLY TO NIELSEN AND MEIER

The phylogenetic placement of the red panda (Ailurus fulgens) and the giant panda (Ailuropoda melanoleuca) has been an evolutionary enigma since their original descriptions in the nineteenth century. A series of recent molecular analyses led to a consensus that the giant panda's ancestors were derived from early bears (Ursidae), but left unsettled the phylogenetic relationship of the red panda. Previous molecular and morphological phylogenies were inconclusive and varied among placement of the red panda within the raccoon family (Procyonidae), within the bear family (Ursidae), or in a separate family of carnivores equidistant between the two. To examine a relatively ancient (circa 20-30 million years before the present, MYBP) phylogenetic divergence, we used two slowly evolving genetic markers: mitochondrial 12S rRNA sequence and 592 fibroblast proteins resolved by two dimensional gel electrophoresis. Four different carnivore outgroup species, including dog (Canidae: Canis familiaris), cat (Felidae: Felis catus), fanaloka (Viverridae: Fossa fossa), and mongoose (Herpestidae: Galidia elegans), were selected to identify the root of the phylogenetic topologies. Phylogenetic reconstruction by distance-based methods, maximum parsimony, and maximum likelihood clearly indicate a distinct bifurcation forming the Ursidae and the Procyonidae. Further, our data consistently place the red panda as an early divergence within the Procyonidae radiation and confirm the inclusion of giant panda in the Ursidae lineage.

Morphological phylogeny and biogeography of the Pterostichus raptor species group (Coleoptera: Carabidae) of ground beetles, endemic to the Korean Peninsula and adjacent islands