Systematics of Neotropical freshwater crabs Trichodactylinae based on multi-genes and morphological data: new tribe and new combinations

The Eleutherodactylus subgenus Syrrhophus has a complex taxonomic history. For many years the species were classified into series and groups of species based on morphological and allozyme data. However, most of the species have conservative morphology, and their phylogenetic relationships have not been resolved. Furthermore, recent studies employing molecular tools have shown that Syrrhophus diversity is highly underestimated. Here, we present a near-complete phylogenetic hypothesis based on mitochondrial data (16S rRNA, cytochrome c oxidase subunit I, and cytochrome b) and employing maximum likelihood and Bayesian methods. The Bayesian tree has high support values (posterior probabilities ≥0.95) whereas the maximum likelihood hypothesis has generally low values (bootstrap support <70). Both phylogenetic analyses recovered Syrrhophus as monophyletic and composed of four main, allopatric clades (E. symingtoni clade, E. longipes clade, E. modestus clade, and E. nitidus clade) concordant with geography. Based on the molecular and morphological data, we describe a new species from the state of San Luis Potosí, Mexico. The new species is most closely related to E. campi and E. cystignathoides from which it has a genetic distance >7% in 16S rRNA. Finally, based on the phylogenetic results, we resurrect E. rubrimaculatus from synonymy. Our results increase the number of species in the subgenus Syrrhophus to 41. We highlight the importance of efforts to study this important component of Mexican biodiversity. http://zoobank.org/urn:lsid:zoobank.org:pub:3C2B2315-D5C8-420A-938C-A2B3A75B4248

The spider genus Nops MacLeay is revised, with redescriptions of 22 previously known species and descriptions of 12 new species. A new diagnosis for the genus is provided and keys to separate the species are proposed. After this revision Nops includes 34 extant species, thereof 15 (44%) occur in the Caribbean Islands, four (12%) in Central America and 15 (44%) in South America. Females of Nops meridionalis Keyserling and Nops gertschiChickering are found and described for the first time. Three new synonymies are proposed: Nops virginicus Sánchez-Ruiz with Nops blandus Bryant, Nops craneae Chickering with Nops maculatus Simon and Nops proseni Birabén with Nops farhati Prosen. Four species are considered inquerenda: Nops anisitsi Strand, Nops bellulus Chamberlin, Nops branicki(Taczanowski) and Nops glaucusHasselt. The following new species are described: N. jaragua n. sp., N. navassa n. sp., and N. pallidus n. sp. from the Caribbean region; N. campeche n. sp. and N. tico n. sp. from Central America, and N. alexenriquei n. sp., N. amazonas n. sp., N. bahia n. sp., N. ipojuca n. sp., N. itapetinga n. sp., N. minas n. sp. and N. pocone n. sp. from South America. New geographical records and distribution maps are provided for all species, with illustrations and reviewed diagnoses. The Nops species are restricted to the Neotropical region, from the Caribbean Islands and Mexico to the north of Argentina. The highest species richness is concentrated in the Wider Caribbean Region, including Central America and the north of Colombia and Venezuela where 64.7% of the species occur. Endemism in the Caribbean islands is very high; most of these species are single island endemics. A cladistic analysis, based on morphological data, was executed to test the monophyly of the genus. This is the first cladistic analysis of Caponiidae, and it includes besides the Nops species, 1) the six other species that were transferred from Nops, now in the genera Orthonops, Cubanops, Tarsonops and Medionops, and 2) Nopsides ceralbonus Chamberlin and Nyetnops guarani Platnick Lise. Therefore, representatives of all known Nopinae genera are included in the ingroup. The data matrix comprises 41 taxa scored for 47 morphological characters. The analyses under equal weights resulted in six equally parsimonious trees of 99 steps. All these trees are congruent with a unique hypothesis for Nopinae genera. Thus, all topological differences among the most parsimonious trees were the consequence of different hypotheses of relationships within Nops. The same result was also found under implied weighting with constants of concavity k = 2 to 13, where the topology of all trees was congruent for a single Nopinae genera hypothesis, but relationships within Nops were not resolved. All analysis under equal and implied weights recovered the monophyly of Nops with high support values, but internal clades within the genus showed low branch supports. Our results thus suggest that to resolve the internal relationships of Nops, studies based on molecular evidence are necessary to counteract the deficit of morphological data. The hypothesis obtained for Nopinae showed high branch support values for most of clades, corroborating all the transfers made from Nops. Medionops was recovered as the sister group of Nops with high support values. Nops, Medionops and Nopsides form a closely related, distinct spider group among nopine, supported by five unambiguous synapomorphies. Two of these synapomorphies could be functionally related: the presence of an arolium on the anterior pretarsi and the elongated and dorsally reflexed unpaired claw on the anterior legs. Nopsides appears to be a genus with apomorphic characters, presenting highly modified legs, but lacking the crista and gladius, and gaining a pair of anterior lateral eyes. Nyetnops is sister to all other nopine genera. Our results identified the necessity of further studies on nopine leg structures (arolium, crista, gladius and adesmatic joints) to improve understanding of the phylogenetic relationships of Nopinae genera.

Reappraising adaptive radiation

Although the endosymbiotic evolution of chloroplasts through primary and secondary associations is well established, the evolutionary timing and stability of the secondary endosymbiotic events is less well resolved. Heterokonts include both photosynthetic and nonphotosynthetic members and the nonphotosynthetic lineages branch basally in phylogenetic reconstructions. Molecular and morphological data indicate that heterokont chloroplasts evolved via a secondary endosymbiosis, involving a heterotrophic host cell and a photosynthetic ancestor of the red algae and this endosymbiotic event may have preceded the divergence of heterokonts and alveolates. If photosynthesis evolved early in this lineage, nuclear genomes of the nonphotosynthetic groups may contain genes that are not essential to photosynthesis but were derived from the endosymbiont genome through gene transfer. These genes offer the potential to trace the evolutionary history of chloroplast gains and losses within these lineages. Glutamine synthetase (GS) is essential for ammonium assimilation and glutamine biosynthesis in all organisms. Three paralogous gene families (GSI, GSII, and GSIII) have been identified and are broadly distributed among prokaryotic and eukaryotic lineages. In diatoms (Heterokonta), the nuclear-encoded chloroplast and cytosolic-localized GS isoforms are encoded by members of the GSII and GSIII family, respectively. Here, we explore the evolutionary history of GSII in both photosynthetic and nonphotosynthetic heterokonts, red algae, and other eukaryotes. GSII cDNA sequences were obtained from two species of oomycetes by polymerase chain reaction amplification. Additional GSII sequences from eukaryotes and bacteria were obtained from publicly available databases and genome projects. Bayesian inference and maximum likelihood phylogenetic analyses of GSII provided strong support for the monophyly of heterokonts, rhodophytes, chlorophytes, and plants and strong to moderate support for the Opisthokonts. Although the phylogeny is reflective of the unikont/bikont division of eukaryotes, we propose based on the robustness of the phylogenetic analyses that the heterokont GSII gene evolved via endosymbiotic gene transfer from the nucleus of the red-algal endosymbiont to the nucleus of the host. The lack of GSIII sequences in the oomycetes examined here further suggests that the GSIII gene that functions in the cytosol of photosynthetic heterokonts was replaced by the endosymbiont-derived GSII gene.

The Cerithioidea is an ecologically important superfamily of basal Caenogastropoda with speciose marine, brackish water, and freshwater lineages primarily in tropical, subtropical, and warm temperate regions of the world. They often represent significant components of the communities where they occur and have given rise to several spectacular endemic radiations in rivers and ancient lakes. Earlier attempts to resolve the phylogenetic history of the group have been based on smaller taxon and character subsets with incongruent results. Here the monophyly and phylogeny of the group is evaluated with expanded morphological and molecular (16S, 28S rRNA) data sets. For morphological analyses, 151 characters (shell, operculum, radula, alimentary tract, kidney, nervous system, reproductive anatomy, and sperm ultrastructure) were scored for 47 cerithioideans (representing 17 families) and nine outgroup taxa. To test monophyly of the Cerithioidea, extended molecular data sets of 16S and 28S sequences for 57 and 44 taxa, respectively, were compiled using new and previously published sources. For combined analyses, a pruned molecular data set was combined with the morphological partition. The morphological data were analysed alone using only parsimony; molecular and simultaneous analyses were performed using both parsimony and Bayesian inference. The effect of excluding unconserved regions of the alignments was also explored. All analyses, with the exception of the individual 16S and 28S data sets, support monophyly of the Cerithioidea as currently formulated. Of the 12 families represented by more than one terminal, only two (Planaxidae, Potamididae) are always supported as monophyletic; Batillariidae, Cerithiidae, Pachychilidae, Pleuroceridae, Semisulcospiridae, Thiaridae, and Turritellidae are monophyletic in most but not all topologies. The combination of diverse data sources (morphology, 16S and 28S sequences) and inclusion of unconserved regions of the alignments improved the recovery of monophyletic families. At deeper levels, a consensus is beginning to emerge in the recognition of three main assemblages, but whether these represent clades or grades is still unclear; the resolution of these assemblages and the branching order within them are sensitive to exclusion of unconserved regions and choice of optimality criterion. No clear conclusion is reached with respect to the number of freshwater invasions, with two invasions supported on some topologies and three supported on others. Progress toward a robust and stable resolution of cerithioidean relationships will require (1) strategically coordinated sampling for additional morphological and molecular data; (2) comprehensive anatomical treatments for several poorly documented limnic lineages (e.g. Melanopsidae, Thiaridae) and comparative data for poorly understood organ systems (e.g. renal system); (3) the addition of poorly known, minute, and/or rare marine taxa, to provide novel character combinations, insight into putative homologies, and to help anchor basal nodes and break up long branches. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162, 43–89.

The validity of Pelodiscus parviformis within the genus is still not very clear. In this study, molecular and morphological data were combined to evaluate the validity of P. parviformis. The phylogeny of some species in Pelo- discus was reconstructed by maximum parsimony, maximum likelihood and Bayesian inference analyses based on five mitochondria DNA fragments (5308 bp of 12S rRNA, 16S rRNA, ND4, CO1 and Cyt b). The results of ML, MP and Bayesian analyses suggest that P. parviformis might be paraphyletic to P. sinensis, whereas the partitioned Bayesian analyses support the reciprocal monophyly of P. parviformis and P. sinensis. Considering the advantages of heteroge- nous characteristics of sequence evolution, we choose the result of partitioned Bayesian analyses. Furthermore, the mor- phological data lend support the distinct species status of P. parviformis and P. sinensis, such as tubercles on carapace skin, color of plastron skin, dark spots on plastron, basisphenoid characteristics (ratio of the smallest width to the largest width; the smallest width of basisphenoid is restrained by two holes on each side) and the shape of entoplastron. Com- bining the molecular and morphological data, we inferred that P. parviformis is a valid species. In addition, the results of this study suggest a new record of P. axenaria in Guangxi, China.

The Great Barrier Reef is the largest coral reef ecosystem on the planet and supports a diverse community of marine fishes, as well as the organisms that parasitise them. Although the digenetic trematodes that parasitise fishes of the Great Barrier Reef have been studied for over a century, the species richness and diversity of many trematode lineages is yet to be explored. Trigonocephalotrema, gen. nov. is proposed to accommodate three new species, Trigonocephalotrema euclidi, sp. nov., T. hipparchi, sp. nov. and T. sohcahtoa, sp. nov., parasitic in fishes of Naso Lacepède and Zebrasoma Swainson (Acanthuridae) in the tropical Pacific. Species of Trigonocephalotrema are characterised with morphological and molecular data (18S rRNA, ITS2 and 28S rRNA). Species of Trigonocephalotrema are morphologically distinguished from all other haplosplanchnid lineages by having terminal, triangular, plate-like oral suckers. With the inclusion of the new molecular data, Bayesian inference and maximum likelihood analyses of the Haplosplanchnidae Poche, 1926 recovered identical tree topologies and demonstrated Trigonocephalotrema as a well-supported monophyletic group. Although species of Trigonocephalotrema are differentiated from all other haplosplanchnid lineages on the basis of morphology, species within the genus are morphologically cryptic; thus, accurate species identification will require inclusion of host and molecular data. Species of Trigonocephalotrema cannot be assigned to a recognised subfamily within the Haplosplanchnidae using either morphological or molecular data and would require the erection of a new subfamily to accommodate them. However, we find little value in the use of subfamilies within the Haplosplanchnidae, given that there are so few taxa in the family, and herein propose that their use be avoided.

Gloydius is a widespread pitviper group occurring from Eastern Europe to Korea and Siberia, with only one known species, G. himalayanus (Günther, 1864), found south of the Himalayas. We provide combined genetic and morphological data for G. himalayanus from specimens collected from Himachal Pradesh, India. Bayesian Inference and Maximum Likelihood phylogenetic analysis were performed on four concatenated mitochondrial genes, along with a multi-locus coalescent analysis of these and five additional nuclear genes. Our results indicate that G. himalayanus from the Chamba Valley, in western Himachal Pradesh, are highly distinct from the remaining studied populations. Haplotype networks of each nuclear locus showed that G. himalayanus contains high haplotype diversity with low haplotype sharing between the Chamba Valley population and populations from further west. Principal component analysis and canonical variate analysis conducted on morphological data of live and museum specimens also highlight the morphological distinctiveness of the Chamba population and we herein describe this population as a new species, Gloydius chambensis sp. nov. Recent descriptions of other new species of snakes from this valley underscores its isolation and suggests that further herpetological investigation of the highly dissected landscapes of the western Himalayas is needed to assess the true diversity of the region.

BackgroundLoricifera is an enigmatic metazoan phylum; its morphology appeared to place it with Priapulida and Kinorhyncha in the group Scalidophora which, along with Nematoida (Nematoda and Nematomorpha), comprised the group Cycloneuralia. Scarce molecular data have suggested an alternative phylogenetic hypothesis, that the phylum Loricifera is a sister taxon to Nematomorpha, although the actual phylogenetic position of the phylum remains unclear.MethodsEcdysozoan phylogeny was reconstructed through maximum-likelihood (ML) and Bayesian inference (BI) analyses of nuclear 18S and 28S rRNA gene sequences from 60 species representing all eight ecdysozoan phyla, and including a newly collected loriciferan species.ResultsEcdysozoa comprised two clades with high support values in both the ML and BI trees. One consisted of Priapulida and Kinorhyncha, and the other of Loricifera, Nematoida, and Panarthropoda (Tardigrada, Onychophora, and Arthropoda). The relationships between Loricifera, Nematoida, and Panarthropoda were not well resolved.ConclusionsLoricifera appears to be closely related to Nematoida and Panarthropoda, rather than grouping with Priapulida and Kinorhyncha, as had been suggested by previous studies. Thus, both Scalidophora and Cycloneuralia are a polyphyletic or paraphyletic groups. In addition, Loricifera and Nematomorpha did not emerge as sister groups.Electronic supplementary materialThe online version of this article (doi:10.1186/s40851-015-0017-0) contains supplementary material, which is available to authorized users.

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.

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

Lutzia Theobald was reduced to a subgenus of Culex in 1932 and was treated as such until it was restored to its original generic status in 2003, based mainly on modifications of the larvae for predation. Previous phylogenetic studies based on morphological and molecular data have provided conflicting support for the generic status of Lutzia: analyses of morphological data support the generic status whereas analyses based on DNA sequences do not. Our previous phylogenetic analyses of Culicini (based on 169 morphological characters and 86 species representing the four genera and 26 subgenera of Culicini, most informal group taxa of subgenus Culex and five outgroup species from other tribes) seemed to indicate a conflict between adult and larval morphological data. Hence, we conducted a series of comparative and data exclusion analyses to determine whether the alternative positions of Lutzia are due to conflicting signal or to a lack of strong signal. We found that separate and combined analyses of adult and larval data support different patterns of relationships between Lutzia and other Culicini. However, the majority of conflicting clades are poorly supported and once these are removed from consideration, most of the topological disparity disappears, along with much of the resolution, suggesting that morphology alone does not have sufficiently strong signal to resolve the position of Lutzia. We critically examine the results of other phylogenetic studies of culicinine relationships and conclude that no morphological or molecular data set analysed in any study conducted to date has adequate signal to place Lutzia unequivocally with regard to other taxa in Culicini. Phylogenetic relationships observed thus far suggest that Lutzia is placed within Culex but further data and extended taxon sampling are required to confirm its position relative to Culex.

Bluish Mycena are rare, but constitute a taxonomically complex group. A total of eight bluish species in four sections have previously been reported from North America, Europe, Oceania and Asia. Two species with a blue pileus, collected in China during our taxonomic study of Mycena s.l., are described here as new to science: Mycenacaeruleogrisea sp. nov. and M.caeruleomarginata sp. nov. Detailed descriptions, line drawings and a morphological comparison with closely-related species, especially herbarium specimens of M.subcaerulea from the USA, are provided. The results of Bayesian Inference and Maximum Likelihood phylogenetic analyses of a dataset of 96 nuclear rDNA ITS and 20 nLSU sequences of 43 Mycena species are also presented. The morphological data and the results of the phylogenetic analyses support the introduction of M.caeruleogrisea and M.caeruleomarginata as new species. A taxonomic key to bluish Mycena species of sections Amictae, Cyanocephalae, Sacchariferae and Viscipelles is provided.

The species Phalangium nalanae Kurt, Erdek &amp; Kurt 2023 and Phalangium taylani Kurt, Erdek &amp; Kurt 2023 were previously described from Hakkari, Turkey based on morphological data and no molecular data are presented. In this study, the 28S rRNA gene region of these species belonging to the genus Phalangium was sequenced, and phylogenetic relationships of these species were revealed by performing maximum likelihood (ML) analysis and Bayesian inference (BI) analysis.

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.