Description of two new taxa of the ceratobatrachid genus Platymantis from western New Guinea (Amphibia, Anura)

Reappraising adaptive radiation

A new species of the genus Ganesella Blanford, 1863 is reported for the first time from Yapen Island, Papua Province, Indonesia, a region renowned for its endemic flora and fauna. A comprehensive comparison with established species of Ganesella and related genera from Southeast Asia, and especially New Guinea, is conducted to highlight the unique characteristics of this new species, which has remained unobserved since its initial discovery in 1953.

Mountain Pygmies of Western New Guinea: A Morphological and Molecular Approach

Mountain Pygmies of Western New Guinea: A Morphological and Molecular Approach

A major challenge in the post-genomics era will be to integrate molecular sequence data from extant organisms with morphological data from fossil and extant taxa into a single, coherent picture of phylogenetic relationships; only then will these phylogenetic hypotheses be effectively applied to the study of morphological character evolution. At least two analytical approaches to solving this problem have been utilized: (1) simultaneous analysis of molecular sequence and morphological data with fossil taxa included as terminals in the analysis, and (2) the molecular scaffold approach, in which morphological data are analyzed over a molecular backbone (with constraints that force extant taxa into positions suggested by sequence data). The perceived obstacles to including fossil taxa directly in simultaneous analyses of morphological and molecular sequence data with extant taxa include: (1) that fossil taxa are missing the molecular sequence portion of the character data; (2) that morphological characters might be misleading due to convergence; and (3) character weighting, specifically how and whether to weight characters in the morphological partition relative to characters in the molecular sequence data partition. The molecular scaffold has been put forward as a potential solution to at least some of these problems. Using examples of simultaneous analyses from the literature, as well as new analyses of previously published morphological and molecular sequence data matrices for extant and fossil Chiroptera (bats), we argue that the simultaneous analysis approach is superior to the molecular scaffold approach, specifically addressing the problems to which the molecular scaffold has been suggested as a solution. Finally, the application of phylogenetic hypotheses including fossil taxa (whatever their derivation) to the study of morphological character evolution is discussed, with special emphasis on scenarios in which fossil taxa are likely to be most enlightening: (1) in determining the sequence of character evolution; (2) in determining the timing of character evolution; and (3) in making inferences about the presence or absence of characteristics in fossil taxa that may not be directly observable in the fossil record.

The first morphological study concerning the endocrine heart was published by Kisch (12) who had detected a peculiar cytoplasmic inclusion body in muscle cells of the guinea-pig atrium. Only a few years later, Jamieson and Palade (11) described that these structures were specific granules occuring in all mammalian species investigated, including man. Twelve years later, Marie et al. (13) analysed morphometrically the interference between the number of atrial granules and changes in salt and water balance. Recently, DeBold et al. (4) proved the natriuretic and diuretic properties of atrial extracts and postulated a new class of hormones, which are now known as the atrial natriuretic polypeptides (ANP). Further biological activities were detected, namely the vasorelaxant effect of atrial extracts (3,6). This vasorelaxant function is based on the polypeptide hormone, atriopeptin or cardiodilatin (CDD). It is now well known that the different polypeptides characterized in 1983 and 1984 are all expressed from the same gene and present as posttranslational or artificial cleavage products (2,7). In contrast to the large number of biochemical, physiological investigations, and morphological studies on cardiac hormones published so far, combined morphometric and biochemical studies are not available. Exact data based on both stereological-ultrastructural and radio-immunological examination of the endocrine heart, however, is of major importance for the understanding of the secretory activity of myoendocrine cells.

Simple SummaryDue to their potential entomopathogenicity, nematodes of the genus Oscheius have been in the spotlight of the scientific interest in recent years. Unfortunately, some of these species are poorly described and have inadequate or no molecular support. This fact complicates the systematics of the group, and a revision of these species is necessary to elucidate their taxonomic status. In the present study, we provide a detailed description based on the morphological, morphometrical, and molecular characteristics of Oscheius siddiqii from Uttar Pradesh, India, including the first scanning electron microscopy (SEM) studies of the species. Furthermore, based on morphological and molecular data, the status of some Oscheius species is discussed, and several synonymisations are proposed.An insect parasitic nematode belonging to the genus Oscheius was recovered from the agricultural soils from the Hapur district in western Uttar Pradesh, India. Morphological studies on this species exhibited its high resemblance with two Pakistani species: Oscheius siddiqii and O. niazii. No molecular data are available for these taxa but, morphologically, both species do not differ significantly from our strains and each other. Hence, these nematodes can be considered conspecific, and the correct name for this taxon is O. siddiqii, the first described species. The phylogenetic analyses of the ITS-, 18S-, and the 28S rDNA sequences showed that O. siddiqii is a sister taxon to the group formed by Oscheius microvilli, O. myriophilus, O. safricanus, and several unidentified Oscheius species. Additionally, our analyses show that based on molecular and morphological data, the species Oscheius rugaoensis and O. microvilli cannot be distinguished from O. chongmingensis and O. myriophilus, respectively, and are thus considered junior synonyms of these taxa. Furthermore, the available data are not sufficient to evaluate the status of Oscheius basothovii and O. safricanus, which are, in consequence, considered species inquirendae. These findings highlight the necessity of the proper morphological and molecular characterisation of the described Oscheius species.

BackgroundMatrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference.ResultsWe systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur as some intermediate nodes may show large time differences between these two types of data.ConclusionsOur findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before any dating analysis using combined datasets.

A phylogenetic analysis for the Cimicomorpha was conducted using 92 taxa, including eight outgroups and six species of Thaumastocoridae. Density of taxon sampling allows for tests of relationships at the family level for most taxa, whereas in the Miridae denser sampling allows for doing so on the tribal level. This level of sampling also corresponds with the availability of testable published hypotheses of relationships. Morphological data for 73 characters are coded for all taxa. Approximately 3500 base pairs of DNA were sequenced for the following gene regions for 83 taxa: 16S rDNA, 18S rDNA, 28S rDNA and COI. Results are presented for analysis of morphological data, individual molecular partitions, combined molecular data, combined morphological and molecular data for 83 taxa and combined morphological and molecular data for 92 taxa. Analyses of morphological data were performed using the parsimony programs nona and piwe : molecular and combined data were analysed using direct optimization with the program poy . Major conclusions of the present study include recognition of the following monophyletic groups: The Geocorisae is a monophyletic group. The monophyly of the Cimicomorpha – including Thaumastocoridae – is not supported in most analyses. The Reduviidae is monophyletic, with the Phymatinae Complex being the sister‐group of the remaining subfamilies. The circumscription of the Cimiciformes is altered from the prior conception of Schuh and Štys to also include the Joppeicidae, Microphysidae and Velocipedidae, as well as the recently described family Curaliidae; the monophyly of the Cimiciformes is supported in most analyses; the Cimiciformes is treated as the sister‐group of the Miroidea in most analyses. The monophyly of the Cimicoidea, including Curaliidae, is supported in all analyses including molecular data, whereas Curaliidae is treated as a more basal cimiciform in all other analyses. The monophyly and placement of the Thaumastocoridae is ambiguous across the range of analyses, and the monophyly of the Miroidea sensu Schuh and Štys receives limited support in the combined analyses of morphology + molecular data. The Tingidae and Miridae are each monophyletic and together almost invariably form a monophyletic group. Within the Miridae, several inclusive monophyletic groups at the subfamily/tribal level are more or less consistently recognized when molecular data are included; however, the interrelationships of the subfamilies vary substantially across the range of analyses. Of the individual molecular partitions, only 18S rDNA shows significant congruence with combined analyses of morphological, combined molecular or combined morphological and molecular data. Scenarios are discussed for the evolution of the metathoracic scent‐efferent system and the origin of the fossula spongiosa.

Strains of the diatoms Attheya ussurensis, A. decora and A. longicornis, isolated from the northwestern Sea of Japan, were studied to infer their phylogeny and determine their systematic position. Morphological studies were conducted using light and transmission electron microscopy, and molecular analyses were based on nuclear-encoded small-subunit (18S) ribosomal DNA (rDNA) and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) of the plastid gene. The strains studied, as well as sequences of A. longicornis and A. septentrionalis accessed from GenBank, belong to the class Mediophyceae. Molecular data confirmed that Attheya holds a basal position relative to the genera Biddulphia and Chaetoceros (Chaetocerotales). Thus, Attheya is a member of this lineage and not sister to Bacillariophyceae. Strains of Attheya belong to two clearly distinct lineages, differing in morphology and ecology. One lineage included strains of the type species of the genus, A. decora and the species A. ussurensis (psammophytes); the second lineage included the strains A. longicornis and A. septentrionalis (epiphytes or sea-ice diatoms). Morphologically, the two lineages differed in ratio of horn length to valve diameter, shape and number of plastids, presence/absence of girdle band perforation and presence/absence of rimoportula on the valve. Based on morphological and molecular data, we propose Attheya subgenus Attheya, to include A. decora, A. ussurensis, A.arenicola; and Attheya subgenus Dolichoceratia, to include A. longicornis, A. septentrionalis, A. flexuosa, A. gaussii and A. armata.

Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, the number of lineages through time, based on molecular sequence data. In the fields of epidemiology and macroevolution, these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of “total-evidence” analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, that is, lacking morphological and molecular data, which we call occurrences, provide invaluable information to estimate the past number of lineages. Here, we present new methodological developments around the fossilized birth–death process enabling us to (i) incorporate occurrence data in the likelihood function; (ii) consider piecewise-constant birth, death, and sampling rates; and (iii) estimate the past number of lineages, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions. We finally illustrate our new implementation using two empirical data sets stemming from the fields of epidemiology and macroevolution. In epidemiology, we infer the prevalence of the coronavirus disease 2019 outbreak on the Diamond Princess ship, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we infer the diversity trajectory of cetaceans using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. The joint modeling of occurrences and trees holds the promise to further bridge the gap between traditional epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics. [Birth–death model; epidemiology; fossils; macroevolution; occurrences; phylogenetics; skyline.]

Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade

Dataset supporting the use of nematodes as bioindicators of polluted sediments

Bayesian inference of the metazoan phylogeny; a combined molecular and morphological approach.

Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological data sets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and some studies have merged morphological and molecular data to estimate combined evidence phylogenies containing both extinct and extant taxa. However, few, if any, studies have attempted to estimate divergence times using phylogenies containing both fossil and living taxa sampled for both molecular and morphological data. Here, I infer both the phylogeny and the time of origin for Lissamphibia and a number of stem tetrapods using Bayesian methods based on a data set containing morphological data for extinct taxa, molecular data for extant taxa, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post hoc age constraints on internal nodes and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined evidence analyses whenever possible.