Dataset supporting the use of nematodes as bioindicators of polluted sediments

Reappraising adaptive radiation

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.

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.

Accurate differentiation and identification of flea species are essential for both basic and applied research on fleas, as well as for the diagnosis of flea-borne diseases. However, distinguishing between flea species can be challenging, especially among those with minimal morphological differences. Therefore, some scholars have suggested the necessity of comprehensive revisions to the classification of fleas, incorporating morphological, molecular, and phylogenetic data. In this study, we focused on classifying the rodents’ parasitic fleas in southeastern China and provided molecular and phylogenetic data. We also described a new subspecies Ctenophthalmus breviprojiciens fujiansis n. ssp. A total of 392 fleas were collected from 8 species of rodents in 10 counties. Morphologically, they belonged to 10 species, 9 genera and 5 families. Barcode identification based on COI gene and phylogenetic analysis based on five genetic markers (18S rDNA, 28S rDNA, EF-1a, COI, COII) revealed that the molecular and morphological identification of Xenopsylla cheopis, Aviostivalius klossi bispiniformis, Leptopsylla segnis, Monopsyllus anisus and Ctenocephalides felis felis were consistent. The taxonomic status of Neopsylla specialis minpiensis and Peromyscopsylla himalaica sinica as subspecies is questionable due to significant intraspecific genetic distance, and further morphological and molecular data are required to determine if they should be elevated to species level. The molecular identification of C. breviprojiciens n. ssp., N. dispar fukienensis, and Nosopsyllus nicanus could not be completed at this time due to a lack of sequences for related species in existing GenBank databases. Additionally, phylogenetic relationships of 31 species from 9 genera and 5 families of Siphonaptera were inferred based on five molecular markers (18S rDNA, 28S rDNA, EF-1a, COI and COII) using Maximum Likelihood analyses. The analyses revealed that various taxa of Siphonaptera are monophyletic at the subspecies, species, and genus levels. However, at the family level, Leptopsyllidae, Ceratophyllidae, Pulicidae, and Pygiopsyllidae are all monophyletic, while Ctenophthalmidae is paraphyletic. we support the view of some authors that revising the catchall group Ctenophthalmidae and elevating each of its constituent subfamilies to family status.

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

The phylogeny of spider flies is presented based on an analysis of DNA sequence data combined with morphological characters for both living and fossil species. We sampled 40 extant and extinct genera across all major lineages of Acroceridae, which were compared with outgroup taxa from various lower brachyceran families. In all, 81 morphological characters of 60 extant and 10 extinct ingroup species were combined with 7.1 kb of DNA sequences of two nuclear (CAD and 28S rDNA) and two mitochondrial genes (COI and 16S rDNA). Results strongly support the monophyly of Acroceridae, with major clades contained within classified here in five extant subfamilies (Acrocerinae, Cyrtinae stat. rev. , Ogcodinae stat. rev. , Panopinae and Philopotinae) and one extinct subfamily, Archocyrtinae. The evolution of important spider fly traits is discussed, including genitalia and wing venation. The status of the enigmatic Psilodera Gray and Pterodontia Gray as members of the Panopinae is confirmed based on both molecular and morphological data.

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.]

The integration of morphological and molecular data is essential to understand the affinities of fossil taxa and spatio-temporal evolutionary processes of organisms. However, homoplastic morphological characters can mislead the placement of fossil taxa and impact downstream analyses. Here, we provide an example of how to mitigate effectively the effect of morphological homoplasy on the placement of fossil taxa and biogeographic inferences of Cissampelideae. We assembled three data types, morphological data only, morphological data with a molecular scaffold and combined morphological and molecular data. By removing high-level homoplastic morphological data or reweighting the morphological characters, we conducted 15 parsimony, 12 undated Bayesian and four dated Bayesian analyses. Our results show that the 14 selected Cissampelideae fossil taxa are placed poorly when based only on morphological data, but the addition of molecular scaffold and combination of morphological and molecular data greatly improve the resolution of fossil nodes. We raise the monotypic Stephania subg. Botryodiscia to generic status and discover that three fossils previously assigned to Stephania should be members of Diploclisia. The Bayesian tip-dated tree recovered by removing homoplastic morphological characters with a Rescaled Consistency Index <0.25 has the highest stratigraphic fit and consequently generates more reasonable biogeographic reconstruction for Cissampelideae. Cissampelideae began to diversify in Asia in the latest Cretaceous and subsequently dispersed to South America around the Cretaceous-Palaeogene boundary. Two dispersal events from Asia to Africa occurred in the Early Eocene and the Late Eocene-Late Oligocene, respectively. These findings provide guidelines and practical methods for mitigating the effects of homoplastic morphological characters on fossil placements and Bayesian tip-dating, as well as insights into the past tropical floristic exchanges among different continents.

Cercopithifilaria rugosicauda (Spirurida, Onchocercidae) is a subcutaneous filarial nematode of the European roe deer (Capreolus capreolus) transmitted by Ixodes ricinus (Acari, Ixodidae). At the necropsy of a roe deer from the Parco Regionale di Gallipoli Cognato (Basilicata region, southern Italy), two female nematodes of C. rugosicauda were found. Following the necropsy, seven skin snips were sampled from different body regions and 96 I. ricinus ticks were collected. In addition, 240 ticks were collected by dragging in the enclosure where the roe deer lived. Samples were examined for the presence of C. rugosicauda larvae and assayed by PCR targeting cytochrome c oxidase subunit 1 (cox1, ∼300bp) and 12S rDNA (∼330bp) gene fragments. Female nematodes, microfilariae from skin samples and eight third stage larvae (L3) from ticks were morphologically and molecularly identified as C. rugosicauda. Phylogenetic analyses clustered this species with other sequences of Cercopithifilaria spp. This study represents the first report of C. rugosicauda in a roe deer and ticks from Italy and provides new morphological and molecular data on this little known nematode.

Results of analyses of molecular sequence (COI, 28S-D2) and morphology (21 character states) data, both alone and combined, were used to determine relationships between 18 species of Scirtothrips (Thysanoptera: Thripidae, Thripinae). Two species of Neohydatothrips from Panama were used as the outgroup. Five major pest Scirtothrips were included in these analyses: S. aurantii, S. citri, S. dorsalis, S. kenyensis, and S. perseae. Trees generated from a parsimony analysis of molecular data and Bayesian analysis of molecular and morphology data combined showed high levels of congruence. The morphology-only tree had several differences in species groupings when compared with trees derived using molecular data. Both parsimony and Bayesian analyses using molecular data indicated that Scirtothrips species associated with avocados were monophyletic, a result not observed with morphological analyses. No support was found for a monophyletic S. dorsalis clade when sampled from six different countries. The S. dorsalis complex may be comprised of at least three separable groups identiable at the molecular level, but indistinguishable morphologically. The implications of this nding for S. dorsalis, a thrips pest of global signicance with high invasion potential, are discussed.

Alvarez, B., Crisp, M.D., Driver, F., Hooper, J.N.A. &amp; Van Soest, R.W.M. (2000). Phylogenetic relationships of the family Axinellidae (Porifera: Demospongiae) using morphological and molecular data. —Zoologica Scripta, 29, 169–198.Twenty‐seven species of marine sponges belonging to Axinellidae and related groups (Halichondriidae, Dictyonellidae, Agelasida) were selected to test the monophyly of Axinellidae and investigate their phylogenetic relationships using parsimony and maximum likelihood methods. Partial 28S rDNA sequences, including the D3 domain, and traditional morphological characters (mainly skeletal ones) were used independently to construct phylogenetic trees. Sequences were aligned using the appropriate model of secondary structure of the RNA and compared to that produced by the multiple sequence alignment program, ClustalW. The alignment using secondary structure constraints produced a better estimate of the phylogeny and was demonstrated to be an effective and objective method.Results of the cladistic analyses of the molecular and morphological data sets were not fully congruent; the morphological data suggest that Axinellidae is monophyletic, however, the molecular data suggest that it is nonmonophyletic. The single most‐parsimonious tree derived from the molecular data showed that species ofAxinella(exceptA. polypoides) are united in a clade that is more closely related to members of Agelasida than to other species of Axinellidae; the remaining members of Axinellidae form a monophyletic group that is closely related to the families Dictyonellidae and Halichondriidae. The consensus tree of 20 most‐parsimonious trees from the morphological analysis, on the other hand, showed that all the sampled species of Axinellidae belong to a monophyletic group which is closely related to the species of Dictyonellidae and Halichondriidae. Only two branches were identical in both cladograms, the one uniting the species ofPtilocaulisandReniochalinaand the one with the species of Dictyonellidae.The robustness of the molecular and morphological trees (or parts of the trees), was tested using bootstrap, jack‐knife, PTP and T‐PTP tests. The results of the PTP test were significant indicating significant cladistic structure in both data sets. The bootstrap and jack‐knife values indicate that the molecular tree is in general better supported than the morphological one. The lack of morphological characters and the homoplastic nature of some may explain the weak support of the morphological tree. A T‐PTP test of nonmonophyly showed that the nonmonophyly of Axinellidae, as indicated by the results of the molecular analysis, is not significant; however, a T‐PTP test of monophyly of Axinellidae, as indicated by the morphological tree, produced significant results. This indicates that the monophyly of Axinellidae based on morphological data cannot be rejected; the family however, cannot be defined in terms of a unique diagnostic character common to all members of the ingroup.Tests of heterogeneity (reciprocal T‐PTP and partition homogeneity test) indicated that the data partitions are heterogeneous, which could be due to sampling errors (in either data set) or differences in the underlying phylogenies; therefore data were not combined in a single analysis. Further, both data sets are unequally sized (95 informative molecular characters vs. 16 informative morphological characters), which means that the molecular signal could swamp the morphological signal if the data is combined.Nonmonophyly of Axinellidae is supported by chemical and genetic evidence available in the literature and DNA sequences data of axinellid species from New Zealand. However, this needs to be confirmed using independent evidence from different genes (or gene regions), biochemistry, histology or cell ultrastructure. Therefore, no changes to the taxonomic position of the family in the higher classification are proposed at this stage.

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 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.

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