Verrucaria madida (Verrucariaceae, Ascomycota) new to Asia and Russia from the Sakhalin Region

Reappraising adaptive radiation

Data on species composition of ciliates in the small rivers at Khabarovsk and in southern Sakhalin Island are presented. Modified method of sampling was applied with using of samplers and “glass fouling” on the shallows of the rivers. More than 230 samples were collected in the small rivers at Khabarovsk and about 200 samples in the southern Sakhalin. Species composition of the ciliates was determined immediately after the sampling and repeatedly on nutrient media. In total, 86 species of ciliates are identified, mostly belonged to the classes Oligohymenophorea and Spirotrichea. Six eurybionts were found: Coleps hirtus, Paramecium caudatum, Dexiostoma campylum, Colpidium colpoda, Uronema nigricans, and Vorticella convallaria сomplex . The classes Armophorea and Phyllopharyngea were more diverse by species in the area at Khabarovsk but the class Spirotrichea - in southern Sakhalin. In general, faunas of ciliates in two surveyed regions are similar. The highest inter-regional similarity of the species composition is registered between the rivers at Khabarovsk and the Susuya River in Sakhalin (25-33 %, by Jackaroo) that is probably associated with a heightened level of pollution in the Susuya. Most of the species adapt to habitat rapidly, so they are found in different environments: among benthos, plankton, periphyton. Some patterns of the ciliocommunities are discussed.

Strisores is a clade of neoavian birds that include diurnal aerial specialists such as swifts and hummingbirds, as well as several predominantly nocturnal lineages such as nightjars and potoos. Despite the use of genome-scale molecular datasets, the phylogenetic interrelationships among major strisorean groups remain controversial. Given the availability of next-generation sequence data for Strisores and the clade’s rich fossil record, we reassessed the phylogeny of Strisores by incorporating a large-scale sequence dataset with anatomical data from living and fossil strisoreans within a Bayesian total-evidence framework. Combined analyses of molecular and morphological data resulted in a phylogenetic topology for Strisores that is congruent with the findings of two recent molecular phylogenomic studies, supporting nightjars (Caprimulgidae) as the extant sister group of the remainder of Strisores. This total-evidence framework allowed us to identify morphological synapomorphies for strisorean clades previously recovered using molecular-only datasets. However, a combined analysis of molecular and morphological data highlighted strong signal conflict between sequence and anatomical data in Strisores. Furthermore, simultaneous analysis of molecular and morphological data recovered differing placements for some fossil taxa compared with analyses of morphological data under a molecular scaffold, highlighting the importance of analytical decisions when conducting morphological phylogenetic analyses of taxa with molecular phylogenetic data. We suggest that multiple strisorean lineages have experienced convergent evolution across the skeleton, obfuscating the phylogenetic position of certain fossils, and that many distinctive specializations of strisorean subclades were acquired early in their evolutionary history. Despite this apparent complexity in the evolutionary history of Strisores, our results provide fossil support for aerial foraging as the ancestral ecological strategy of Strisores, as implied by recent phylogenetic topologies derived from molecular data.

The paper provides an overview of the concordance between molecular (nuclear ribosomal DNA ITS) and morphological data in the group of geophilic Umbelliferae of Middle Asia, which includes the genera Elwendia, Elaeosticta, Hyalolaena, Galagania, Oedibasis, Mogoltavia and Gongylotaxis. In general, a good consistency of data of different types can be observed. At the same time, at some levels of the taxonomic hierarchy, the consistency between morphological and molecular data looks much higher than at others. The identification of the group of geophilic Umbelliferae agrees much better with molecular data than the boundaries between genera within it and the proposed intrageneric groupings. Some observed cases of inconsistency, such as the position of Hyalolaena melanorrhiza among the species of the genus Elaeosticta and the polyphyly of the genera Hyalolaena and Oedibasis, are rather difficult to explain from a morphological point of view, only from a biogeography.

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.

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.

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.]

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.

The systematics of Leptotyphlopidae is historically controversial mostly due to their conserved external morphology in comparison with other snakes. However, recent studies have stressed that anatomical data might be informative for clarifying the leptotyphlopid taxonomy and evolution. We erect a new genus to accommodate Leptotyphlops collaris based on evidence from osteology, hemipenial morphology, and molecular data. We also provide expanded data regarding the intraspecific variation based on additional specimens collected in field trips and literature data, performing detailed comparisons among the new genus and all other New World leptotyphlopids. The new genus is distinguished from other leptotyphlopids by its unique hemipenial morphology and its exclusive combination of osteological and external morphology characters, with molecular data also supporting the new generic arrangement. We also provide a comprehensive discussion of the hemipenial morphology for the subfamily Epictinae based on literature and novel data gathered herein.

Chapter Six - Morphological and molecular data in the study of the evolution, population genetics and taxonomy of Rhizostomeae

The relationships within the Bryaceae, with emphasis on the genus Bryum, were studied based on morphological and anatomical characters and using cladistic methods. The analysis was performed with thirty-six species representing the different parts of the family, and with Funaria hygrometrica Hedw., Mnium hornum (Dicks.) Lindb., and Tayloria lingulata Hedw. as outgroups. The Bryaceae, and the subfamilies Bryoideae, Mielichhoferioideae, and Pohlioideae, as defined by several earlier authors appear to be paraphyletic. The genus Bryum seems to be paraphyletic, because Leptobryum pyriforme (Hedw.) Wils., Osculatia columbica De Not., and Rhodobryum giganteum (Schwaegr.) Paris, appear as ingroups within this genus when the tree is rooted with Funaria. Mnium hornum came out as the sister taxon of a clade including Pohlia cruda (Hedw.) Lindb. and P. longicollis (Hedw.) Lindb., whereas P. drummondii (Müll. Hall.) A.L. Andrews, appears not to be closely related to the other two Pohlia species studied here, making this genus paraphyletic. Mielichhoferia mielichhoferiana (Funck.) Loeske, appears as the sister taxon of Schizymenium bryoides Harv., suggesting that both these genera are paraphyletic. Overall, the stabilities of the clades are low and it is suggested that combined analyses of morphological, anatomical, and molecular data are needed to get better resolved and more stable trees.

Gracilaria parvispora is reported for the first time as an invasive species in northwestern Mexico based on morphological, anatomical and molecular data. The species is widely distributed in the region, where it colonizes sandy and rocky habitats from intertidal areas down to a depth of 1.5 m. The morphological and anatomical data from the Mexican specimens matched the circumscription of the species in Hawaiian waters. Two molecular markers (rbcL and cox1) showed that the Mexican populations were closer to the Hawaiian populations than the Korean populations, which may relate to a similarity in seawater temperatures between Hawaii and Baja California. Gracilaria parvispora formed extensive mats together with Gracilaria vermiculophylla. It was found in stomach samples from a green turtle (Chelonia mydas) in the coastal lagoons of Baja California Sur. The ecological impacts of the two alien Gracialria species on other native species and communities have yet to be determined. This is the first demonstration of a second invasive Gracilaria species, following the introduction of G. vermiculophylla into the northwestern Mexico region.