Molecular Clades Research Articles

Diatom Genus Hyalosira (Rhabdonematales emend.) and Resolution of its Polyphyly in Grammatophoraceae and Rhabdonemataceae with a New Genus, Placosira, and Five New Hyalosira Species

Hyalosira gene sequences are divided into two clades within different families. We examined authentic material of Hyalosira (isotype material of H. obtusangula, synonymous with H. delicatula) and voucher specimens of published sequences, and pooled our observations of Hyalosira-like taxa from benthic and epizoic habitats in several parts of the globe. The two molecular clades corresponded to two morphological groups, with Hyalosira obtusangula associated with Grammatophoraceae. We emend the description and provide lectotypification for Hyalosira and propose Placosira to encompass the taxa in the other clade, associated with Rhabdonemataceae. We propose that Hyalosira has uniseriate to triseriate striae, sometimes different on valve face and mantle. Copulae in most species had shallow septa, though in one they were moderately deep. All species had girdle bands bearing two rows of areolae separated by a midrib. We name five new species of Hyalosira. Morphologies of taxa in the Placosira clade were superficially similar to Hyalosira but differed in having areolae with ricae, a single row of areolae on the girdle bands, and tubular rimoportulae on the valve-face-mantle junction. Hyalosira hustedtiana Patrick should revert to its original position in Striatella until the appropriate genus can be determined. We emend Rhabdonematales to encompass Rhabdonemataceae, Grammatophoraceae and Tabellariaceae.

Polyphyletic Trachyspermum (Umbelliferae) revisited: a contribution of molecular and carpological data

Trachyspermum is an economically important genus widely distributed in the Old World. A modern monographic survey is absent, so the number of species and their affinities are treated in the regional Floras extremely contradictorily. In this study, all species names available in the genus Trachyspermum were revised, and 19 validly published names are kept in the genus. To investigate the species relationships in Trachyspermum, which was shown in previous studies to be polyphyletic, nrDNA ITS sequence data were determined for additional taxa, accompanied with study of fruit morphology, micromorphology and anatomy. Our molecular analysis indicates that Trachyspermum is an aggregate of at least seven distant lineages, and that T. ammi (generitype) does not group with other Trachyspermum species. Many carpological characters do not agree with these groups, being rather homoplastic, but we identify that types of hairs in fruit indumentum and microsculpture of hair cuticle are consistent with molecular clades within Trachyspermum. Our investigation provides one more step towards to the taxonomic revision of the genus, and the possibility of splitting of the current Trachyspermum into monophyletic genera is discussed.

Biodiversity hotspot in cold waters: a review of the genus Cuthonella with descriptions of seven new species (Mollusca, Nudibranchia)

Abstract Cuthonella Bergh, 1884 is of one of the most neglected nudibranch groups, with a long history of taxonomic confusion with other aeolidacean genera. Owing to its predominantly Arctic distribution with cold water, its species are difficult to find and to collect, and thus to describe. In this study we revise the genus by presenting molecular and morphological data for a majority of the species, including the type, C. abyssicola Bergh, 1884. The material is based on a broad geographic sampling throughout the Northern Hemisphere. Particular emphasis is placed on the Kuril Islands, a diversity hotspot for the genus. Seven new species and two subspecies of Cuthonella are described from the Arctic and North Pacific regions. The number of species of Cuthonella is thus increased over threefold and now comprises 15 species plus two subspecies instead of five species. This work is the most substantial update of the genus Cuthonella since its description in 1884. To delineate taxonomic and phylogenetic limits of Cuthonella-like aeolidaceans, the molecular phylogeny of the wider traditional “tergipedids” is presented and shows that Cuthonella-like aeolidaceans form a distinct molecular clade as the family Cuthonellidae Miller, 1977, corroborated by reliable morphological apomorphies.

Phylogenetic reconstruction of early diverging tapeworms (Cestoda: Caryophyllidea) reveals ancient radiations in vertebrate hosts and biogeographic regions

Tapeworms of the order Caryophyllidea are the earliest diverging ‘true’ tapeworms (Eucestoda) and parasitise cypriniform and siluriform fishes almost exclusively. They are typified by a monozoic (non-proglottised) body plan, which is a characteristic shared with early diverging ‘cestodarians’ Gyrocotylidea and Amphilinidea. Here we present the most comprehensive multi-gene molecular phylogeny of this group, to date. Specimens of 63 species from 32 genera (~50% and ~75% of known species and genus diversity, respectively) were gathered during an intense and targeted 15-year collecting effort. Phylogenetic reconstructions provide high nodal support for three major lineages, which only partly correspond to currently recognised families. The three well-supported clades were as follows: Clade A was in an unsupported position at the base of the tree and was almost exclusively comprised of parasites of catfishes (Siluriformes) from the Afrotropical and Indomalayan regions, including the type genus of the Lytocestidae (Lytocestus). Clade B formed the sister group to the remaining taxa (Clade C) and was composed of species that parasitise cyprinids and loaches (Cypriniformes: Cyprinoidei and Cobitoidei) from the Palaearctic Region. This clade included the type genus of the Caryophyllaeidae (Caryophyllaeus). Clade C comprised Nearctic species from suckers and minnows (Cypriniformes: Catostomidae and Cyprinoidei), which were previously accommodated in two families, i.e. Capingentidae and Caryophyllaeidae. This clade included the type genus of the Capingentidae (Capingens). In addition to Clades A–C, Balanotaenia bancrofti from the monotypic Balanotaeniidae, which parasitises plotosid catfishes in Australia, and Lytocestoides tanganyikae, which parasitises African cichlids, formed a poorly supported clade at the base of the tree. Whereas morphological characteristics traditionally used to differentiate caryophyllidean families do not characterise molecular lineages, host association and biogeographical distribution play a key role in the circumscription of the three well-supported clades revealed by molecular data. Thus, the taxonomic rearrangement proposed herein was guided by the molecular clades. The names of all four extant families were preserved and family affinity was determined by topological clustering with the type genera of the families. The family diagnoses of the Lytocestidae, Caryophyllaeidae and Capingentidae are amended. Biogeographic patterns are indicative of separate Gondwanan and Laurasian radiations having taken place. Regarding the Gondwanan radiation in the Siluriformes, the topology in Clade A indicates an Asian origin with a subsequent African colonisation. Concerning Laurasia, separate radiations appear to have taken place in the Cypriniformes in the temperate zones of North America and Eurasia. Complete absence of caryophyllideans in the Neotropical Region, where numerous catfishes occur, may be due to the Gondwanan radiation having taken place after the continental separation of Africa and South America.

Molecular phylogeny of the phytoparasitic mite family Phytoptidae (Acariformes: Eriophyoidea) identified the female genitalic anatomy as a major macroevolutionary factor and revealed multiple origins of gall induction.

Phytoptidae s.str. is a lineage of eriophyoid mites associated with angiosperms. Based on representative taxon sampling and four gene markers (COI, HSP70, 18S, and 28S), we inferred the molecular phylogeny of this group and performed comparative analyses of cuticle-lined female internal genitalia. Although basal relationships were unclear, several well supported clades were recovered. These clades were supported by geography, host associations, and female genital anatomy, but contradicted the current morphology-based systematics. The monophyly of each of five conventional supraspecific groupings (Fragariocoptes, Phytoptus, Phytoptinae, Sierraphytoptinae, and Sierraphytoptini) is rejected based on a series of statistical tests. Additionally, four morphological characters (the absence of tibial solenidion φ and opisthosomal seta c1, presence of telosomal pseudotagma, and 'morphotype') were found to be homoplasies that cannot be used to confidently delimit supraspecific lineages of phytoptids. However, our molecular topology was highly congruent with female genital characters. Eight molecular clades were unambiguously supported by the shapes and topography of the spermathecal apparatus and genital apodemes. This suggests that the female genital anatomy could be an important factor affecting cladogenesis in Phytoptidae, a conclusion contrasting with the general expectation that host characteristics should be a major macroevolutionary force influencing the evolution of host-specific symbionts. Indeed, despite the high host-specificity, there were no apparent cophylogenetic patterns. Furthermore, we show that gall-inducing ability evolved multiple times in phytoptids. Because gall formation creates nearly instantaneous niche partitioning and the potential loss or reduction of gene flow, we hypothesize that it could be an important evolutionary factor affecting speciation within different host-associated clades of phytoptid mites.

Four Entities, Three Theories and Four Scenarios Under the Umbrella of the Second Infection for the SARS-COV-2- Virus in Man

The four entities that were overlapped in the sense with post recovery second sars-cov-2 infection in man were as; Re-infection ,co-infection, reactivation infection and stealth infections Three theories tempts to explain the case. Together with a trial to delineate in between them. The infection course may be ;Asymptomatic ,mild, and moderate and severe. The tissue tropism of the virus is lung, then to renal and nervous tissues. The virus genome variate in to six molecular genetic clades, two biotypes as Asian and European, and six patho-types. The co-infectents are: Herps ,adeno ,measles viruses ,S. aureus, N. cattrahalis and Klebsiella. The virus immune-dominant epitopes can induce effector B, memory B, effector auto-reacting B, memory auto-reacting T , effector T and memory T and mucosal invariant T cells. The resulting immune responses are humeral, cellular ,mucosal invariant T cell responses in addition to autoantibody responses. The net results of these responses may terminated by by production of specific antibodies and cytokine and may accompanied by humeral and /or cellular enhancement of the disease. The apparent duration of post-infection immunity seems to be short and the protection efficacy still a matter of debate and four post-recovery immunity scenarios were suggested as sterilizing ,functional ,waning ,and lost immunities. Keywords: Co-Infection ,infection, re-infection ,reactivation infection ,scenarios. DOI: 10.7176/JHMN/82-01 Publication date: November 30 th 2020

New taxonomic and evolutionary insights relevant to the cat flea, Ctenocephalides felis: A geographic perspective

The cat flea, Ctenocephalides felis, is an obligate haematophagous ectoparasite of wildlife and domestic cats and dogs worldwide. Since cat fleas can affect the health of humans and their pets, an uncertain taxonomy of this taxon can greatly inhibit pest and disease management. To address the evolution and taxonomy of the cat flea, we set out to determine 1) how many genetically distinct taxa exist, 2) whether there is morphological support for the genetically distinct taxa, and 3) the role of host range and paleoclimatic events in speciation. We collected a total of 3352 fleas sampled from 576 domestic cats and dogs as well as 10 wildlife species across 30 localities in South Africa. A total of three flea genera, five species, and three of the currently recognized cat flea subspecies, C. f. damarensis, C. f. strongylus and C. f. felis were obtained. Geometric morphometric analyses on head shape were performed on 68 female and 107 male cat flea individuals. Principal component analysis demonstrated large overlap in head shape variation between C. f. strongylus and C. f. felis, rendering this character not useful for phylogenetic inferences. DNA was extracted from 188 Ctenocephalides spp. and mitochondrial COII and nuclear EF1-α sequences were generated. Bayesian and Maximum Likelihood analyses as well as a TCS parsimony haplotype network of the mitochondrial DNA confirmed the presence of three well supported monophyletic clades. These assemblages did not fully corroborate the existence of the three C. felis subspecies. A single well-supported molecular clade included only C. f. damarensis morphotypes that were mostly collected from wildlife. The recognition of this subspecies as a distinct taxon was further corroborated by sequence distances and also the number of plantar spiniform bristles on fore-tarsi V in males. Despite the overall lack of support for the recognition of C. f. damarensis and C. f. strongylus, a geographic trend was visible whereby one genetic lineage corresponded to the western dryer hot subregion, whereas the other was found throughout the region. Bayesian dating suggested that these two clades diverged during the early Pliocene (4.18 mya), a date that corresponds well with the establishment of a dry hot climate in the west of southern Africa. If so, the off-host environment, particularly temperature and humidity, are important factors to consider in the evolution of the cat flea. The present study rejects recent assertions that the three cat flea subspecies are valid entities and rather point to a situation where more sampling is required before the taxonomic status of C. f. damarensis can be resolved.

On the Occurrence of Metadiaptomus chevreuxi (Calanoida, Diaptomidae, Paradiaptominae) in the Iberian Peninsula, With Notes on the Ecology and Distribution of its European Populations

Temporary ponds are one of the most peculiar ecosystems in the world, being characterized by an extraordinarily rich crustacean fauna, with a high degree of endemism. Among them, diaptomid copepods are among the most biogeographically interesting taxa. However, the present knowledge on diaptomid distribution is still far from being exhaustive, even in the relatively well-studied western European countries. In this study, we report the first record of the diaptomid calanoid copepod Metadiaptomus chevreuxi for the Iberian Peninsula, where it was collected in five temporary ponds in Andalusia (Spain). The characteristics of the new sites are described, the literature dealing with the European localities of the species is reviewed, and a molecular phylogenetic tree has been built, based on new and previously available mitochondrial DNA sequences, thus expanding the knowledge on the ecology and phylogeography of this rare species. The species mainly occupies small isolated temporary ponds in (semi-)arid regions, suggesting adaptations to unpredictable aquatic habitats. The existence of two molecular clades separating the Iberian from the Sicilian and Tunisian populations supports the existence of a longitudinal long-term disjunction, whereas the north-south flow is probably facilitated by migrating birds. Further research on the biota of the small water bodies of the western Mediterranean area may help to expand our knowledge on rare aquatic species, such as M. chevreuxi, and to better interpret their natural history.

Integrative redescription of Hypsibius pallidoides Pilato et al., 2011 (Eutardigrada: Hypsibioidea) with the erection of a new genus and discussion on the phylogeny of Hypsibiidae

An integrative redescription of Hypsibius pallidoides Pilato, Kiosya, Lisi, Inshina & Biserov, 2011 was undertaken following a reexamination of the type material and new material using high-quality light microscopy, scanning electron microscopy and methods of molecular taxonomy. Detailed morphological investigations revealed a unique complex of characters that precluded the attribution of this species to the genus Hypsibius Ehrenberg, 1848. Furthermore, phylogenetic analyses indicated the affinity of this species within the subfamily Pilatobiinae (Hypsibiidae). Notahypsibius gen. nov. is erected for H. pallidoides and two putatively related species: H. scaber Maucci, 1987 and Ramazzottius arcticus (Murray, 1907). An emended diagnosis for the genus Pilatobius is given, while the subfamily Pilatobiinae lacks a cohesive morphological diagnosis despite representing, at the same time, a well-supported molecular clade. Obvious controversy between the results of the morphological and molecular analyses of the phylogeny of Hypsibioidea is discussed. The distribution of morphological characters such as the claw type, organization of the bucco-pharyngeal apparatus, and egg shell sculpture type within Eutardigrada is analyzed and their phylogenetic significance discussed.

First steps to restructuring the problematic genus Lasiotocus Looss, 1907 (Digenea: Monorchiidae) with the proposal of four new genera.

Lasiotocus Looss, 1907 is the largest genus within the Monorchiidae Odhner, 1911, with 52 species currently considered valid. Species belonging to this genus exhibit wide morphological variation and it is likely that many of them belong in other genera; however, testing the validity of the group has been hampered by a lack of molecular sequence data, especially for the type-species. Here, we report the first DNA sequences for Lasiotocus mulli (Stossich, 1883) Odhner, 1911, the type-species of the genus, and only the sixth Lasiotocus species to be sequenced. Sequences were generated for three ribosomal DNA markers, the ITS2, 18S and 28S regions, and for one mitochondrial DNA marker, the cox1 region. Phylogenetic analyses show that the six sequenced species form four clearly distinct clades, each of which we argue require separate genera. On the basis of these relationships and review of the morphology of all species in the genus, we propose a system of six genera. Four genera, Lasiotocus, the resurrected concept of Ancylocoelium Nicoll, 1912, Infundiburictus n. gen., and Sinistroporomonorchis n. gen., represent the four molecular clades. Two genera, Paralasiotocus n. gen. and Alloinfundiburictus n. gen., are proposed on the basis of morphology only. Ancylocoelium is resurrected for Ancylocoelium typicum Nicoll, 1912, Infundiburictus is erected for Lasiotocus arrhichostoma Searle, Cutmore & Cribb, 2014, Sinistroporomonorchis is erected for Lasiotocus glebulentus Overstreet, 1971and Lasiotocus lizae Liu, 2002, Paralasiotocus is erected for Lasiotocus okinawaensis Machida, 2011, and Alloinfundiburictus is erected for Lasiotocus cacuminatus Nicoll, 1915. Of the 52 species presently recognised in Lasiotocus, 43 are distributed among these genera; nine are considered species inquirendae or are transferred to other genera. We think it likely that more genera will be required for the species reviewed here but more sequence data are essential to further refine the classification.

Molecular phylogenetic analyses reveal a deep dichotomy in the conifer-inhabiting genus Trisetacus (Eriophyoidea: Nalepellidae), with the two lineages differing in their female genital morphology and host associations.

We analyzed the phylogenetic relationships of the genus Trisetacus using two genes [cytochrome c oxidase subunit I (COI) and D1-D2 region of 28S rDNA (D1-D2 28S)], a representive taxon sampling (nearly 40% of known diversity), and a large set of close and distant outgroups. Our analyses suggest the presence of a dichotomy between Trisetacus associated with Cupressaceae and Pinaceae. The following smaller molecular clades were found: Pin-1 (bud mites, twig sheath mites, bark gall mites, and endoparasitic mites from pinaceans), Pin-2 (needle sheath mites from pines), Pin-2a (putative Nearctic group of needle sheath mites), Pin-2b (putative Palearctic group of needle sheath mites), Cup-1 and 2 (bud, cone, seed mites and mites living under bark scales from cupressaceans). The monophyly of the recently proposed subgenus Brevithecus nested within clade Cup-2 was confirmed. Ancestral character reconstruction analyses recovered: (1) Pinaceae as the ancestral hosts of Nalepellidae and Trisetacus, (2) repetitive reductions of the spermathecal tube independently occurred in two lineages of Trisetacus from Cupressaceae, and (3) several mite habitats on host (galls, cones, twig sheaths, seeds, inside leaves, and under scales) are evolutionarily derived states, whereas living in buds or needle sheaths are ancestral states for Trisetacus clades Cup and Pin. Using confocal microscopy, we identified six basic types of the female internal genitalia of Trisetacus based on shapes of the spermatheca and spermathecal tube. These genitalic types are strongly correlated with lineages recovered by molecular phylogenetic analyses, suggesting that the female genital morphology is both evolutionarily conserved and is a factor influencing macroevolutionary patterns in this group of mites.

Integrative taxonomy of Guinean Lemniscomys species (Rodentia, Mammalia)

In the Republic of Guinea (West Africa), the diversity and distribution of striped grass mice of the genus Lemniscomys is poorly known. In the course of long-term field surveys from 2003 to 2011, we collected 97 specimens from various regions of Guinea with the aim of characterizing the morphological and genetic diversity of the genus in the country. We performed an integrative study that allowed us to detect the existence of at least two species in the collected specimens. Two molecular clades, corresponding to different karyotypes, were recovered. By comparison with type specimens and using classical morphometric analyses, we are able to confirm the presence of L. linulus and L. striatus in Guinea. We redescribe the skull and dental characters of the poorly known L. linulus and report its standard karyotype formula (2N = 56, NFa = 66). We did not collect any L. zebra in Guinea despite its presence in South Mali. In conclusion, the distributions of L. striatus and L. linulus described for Guinea and, including the previously reported L. bellieri, three species are now known to occur in this country. We recognise these three species as valid pending further revision of the genus at a pan-African scale.

Hypothetical evolutionary models of the variable lymphocyte receptor genes in jawless vertebrates

Abstract Both humoral and cellular arms of an adaptive immune system are common to jawed and jawless vertebrates. However, whereas antigen recognition in the jawed vertebrates is mediated by immunoglobulin domain-based B cell receptors and T cell receptors, antigen recognition in jawless vertebrates is mediated by leucine-rich repeat (LRR) sequences in variable lymphocyte receptors (VLRs). Three types of VLR genes (VLRA, VLRB and VLRC) have been characterized in the extant jawless vertebrates, lampreys and hagfishes. VLRA- and VLRC-producing cells are T cell-like, while VLRB-producing cells are B cell-like. The VLRs are assembled by copying neighboring LRR sequences into the incomplete germline genes. In searching for the evolutionary origin of the VLRs we identified hypothetical VLR-like progenitors in amphioxus and tunicates (VLRPs). Molecular cladistics markers and phylogenetic analysis suggest the VLRPs are structurally more similar than other ancestral candidates to assembled VLRs. Based on our further analysis we propose alternative models for the origin of VLRs: (A) Among the VLRs, VLRB is most similar to the ancestral state and two subsequent duplication events gave rise to VLRC and VLRA-like genes; each of the three ancestral VLR genes in a common jawless vertebrate ancestor was then modified by cut and paste transposition of the internal DNA region encoding multiple LRR modules. (B) A cut and paste transposition event in an ancestral VLRB-like gene was followed by sequential duplication events which gave rise to VLRC and VLRA. In both models, subsequent duplications and fragmentations have generated a large array of genomic donor cassettes. Thus, after the emergence of the three VLR loci, each has undergone independent evolution.

Morphological and molecular evidence support the intertidal barnacle Octomeris intermedia Nilsson-Cantell, 1921 (Thoracica, Chthamalidae) as a valid species in Indo-Pacific waters.

Octomeris is a chthamalid intertidal barnacle with eight shell plates. There are currently two species of such barnacles: O. brunnea Darwin, 1854 (type locality in the Philippines), common in the Indo-Pacific region, and O. angulosa Sowerby, 1825, only recorded in South Africa. Octomeris intermedia Nilsson-Cantell, 1921, identified from the Mergui Archipelago in Myanmar, was considered to be conspecific with O. brunnea by Hiro (1939) based on samples collected in Taiwan. The morphological differences in shell and opercular plates between O. brunnea and O. intermedia are believed to be intra-specific variations due to different degrees of shell erosion. In the present study, the genetic and morphological differentiations of Octomeris in the Indo-Pacific region were examined. This study found two molecular clades (with inter-specific differences) based on the divergence in the COI genes, and the species also have distinct geographical distributions. The Octomeris brunnea clade covers samples collected from the Philippines and Taiwan waters and the other clade, which we argue is O. intermedia, is distributed in Phuket and Krabi, Thailand and Langkawi, Malaysia. Phuket and Krabi are located approximately 300 km south of the Mergui Archipelago, the type locality of O. intermedia. The morphology of samples collected from Thailand fits the type description of O. intermedia in Nilsson-Cantell (1921). Our study concludes that O. intermedia is a valid species based on morphological and molecular evidence.

Description of a new species of Phoxinus from the upper Krka River (Adriatic Basin) in Croatia (Actinopterygii: Leuciscidae), first discovered as a molecular clade.

Using morphometric, meristic and qualitative characters, we confirmed a specific status of a clade discovered based on molecular data only. The newly described species Phoxinus krkae has a very local distribution in the upper Krka River but is easily morphologically distinguished from geographically neighbouring species with much wider ranges: Phoxinus lumaireul, Phoxinus marsilii and Phoxinus csikii. Phoxinus krkae is well differentiated in statistical analyses and differs from other species of Phoxinus in northern Adriatic Sea drainages and right-bank tributaries of the middle and lower River Danube by a combination of characters, none of them unique: caudal peduncle length 1.9-2.2 times minimum depth of caudal peduncle; upper lip not projecting beyond lower lip; rostral fold absent; total number of scales in lateral series 74-84; lateral line incomplete and interrupted, commonly 17-49 (< 60% of total number of scales in lateral series) with no or few canal segments on posterior body and caudal peduncle; scales on belly extending forward to over middle of distance between pelvic-fin base and pectoral-fin origin; patches of breast scales commonly connected by scattered scales or forming 1-3 regular rows of scales; total vertebrae commonly 38-39 (22 + 17, 22 + 16 or 21 + 17). The study reveals unrecognised morphological diversity within the group and provides the groundwork for future taxonomic study in Phoxinus in the Adriatic region and the Danube Basin.

Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships.

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).

Evolution of the Caribbean subfamily Mussinae (Anthozoa: Scleractinia: Faviidae): transitions between solitary and colonial forms

Understanding evolutionary transitions in scleractinian corals is fundamental to predicting responses of coral reefs to climate change. We examine transitions between solitary and colonial corals in the fossil record, focusing on the Caribbean solitary reef coral Scolymia and members of the subfamily Mussinae. Fossil specimens are selected from a large well-documented collection of Neogene Caribbean corals, and a total of 23 species are distinguished using 15 morphological features. Ten of the 23 species are extant Caribbean species, seven are previously described extinct Neogene species, and six other extinct species are formally described as new. The 7 + 6 extinct species are added to a morphological data set consisting of 30 extant molecularly characterized species plus seven additional extinct (five Eocene, two Neogene) species. In addition to the Caribbean subfamily Mussinae, the extant species include the Indo-Pacific families Merulinidae and Lobophylliidae, and the Caribbean subfamily Faviinae. Phylogenetic analysis was performed on the data using maximum parsimony, and the results reveal four clades, which correspond with previously reported molecular clades. Solitary corals group most closely with Caribbean Mussinae and Indo-Pacific Lobophylliidae, whereas colonial corals are present in all four clades. Within Caribbean Mussinae, members of the colonial genera Mycetophyllia and Isophyllia form distinct subclades, as do the extinct solitary genera Antillia and Antillophyllia. The relationships within Scolymia are less well defined but its members appear more closely related to extinct solitary genera dating back to the Eocene. These results indicate that evolutionary transitions between solitary and colonial corals have been rare within the Mussinae. Except Antillophyllia, most Mussinae genera are restricted to the Caribbean. During the late Miocene, Mycetophyllia diversified and three other modern Mussinae genera (Mussa, Scolymia, Isophyllia) originated in association with increased Caribbean productivity. Mussinae that were more likely to survive Plio–Pleistocene extinction may have taken refuge in deep forereef habitats.

Diversity and phylogeny of Sargassum (Fucales, Phaeophyceae) in Singapore

Sargassum species play key ecological roles on coral reefs, yet their diversity remains poorly known. Precise identification of Sargassum species, however, is improving with molecular genetic tools, though these have yet to be applied rigorously in Singapore. Historical records list 41 species, but no more than ten were verified based on herbarium vouchers, and even fewer (five species) were confirmed in the field based on a single nuclear gene marker in a previous study. Here, we revised the diversity of Sargassum in Singapore by examining all the morphologically distinct forms collected from the local coral reef environment. A total of six morphotypes, Sargassum aquifolium (Turner) C.Argardh (1820), S. cf. granuliferum C.Argardh (1820), S. ilicifolium (Turner) C.Argardh (1820), S. swartzii C.Argardh (1820), S. polycystum C.Argardh (1824), and an undescribed taxon ‘Sargassum sp.’ (Mattio and Payri 2009), were delineated based on morphological characteristics. The morphotypes were placed in five molecular clades based on phylogenetic analyses of the nuclear ITS-2, chloroplastic partial RuBisCO operon rbcLS, and mitochondrial cox3. Sargassum cf. granuliferum, though morphologically distinct from all other species, is not phylogenetically distinct from S. polycystum. Our results provide a species list for Singapore that will be valuable for future studies on macroalgal biogeography and species-specific ecological relationships with other reef organisms, particularly corals.

A New Classification of the Dictyostelids

Traditional morphology-based taxonomy of dictyostelids is rejected by molecular phylogeny. A new classification is presented based on monophyletic entities with consistent and strong molecular phylogenetic support and that are, as far as possible, morphologically recognizable. All newly named clades are diagnosed with small subunit ribosomal RNA (18S rRNA) sequence signatures plus morphological synapomorphies where possible. The two major molecular clades are given the rank of order, as Acytosteliales ord. nov. and Dictyosteliales. The two major clades within each of these orders are recognized and given the rank of family as, respectively, Acytosteliaceae and Cavenderiaceae fam. nov. in Acytosteliales, and Dictyosteliaceae and Raperosteliaceae fam. nov. in Dictyosteliales. Twelve genera are recognized: Cavenderia gen. nov. in Cavenderiaceae, Acytostelium, Rostrostelium gen. nov. and Heterostelium gen. nov. in Acytosteliaceae, Tieghemostelium gen. nov., Hagiwaraea gen. nov., Raperostelium gen. nov. and Speleostelium gen. nov. in Raperosteliaceae, and Dictyostelium and Polysphondylium in Dictyosteliaceae. The "polycephalum" complex is treated as Coremiostelium gen. nov. (not assigned to family) and the "polycarpum" complex as Synstelium gen. nov. (not assigned to order and family). Coenonia, which may not be a dictyostelid, is treated as a genus incertae sedis. Eighty-eight new combinations are made at species and variety level, and Dictyostelium ammophilum is validated.

Ancestrular morphology in cyclostome bryozoans and the quest for phylogenetically informative skeletal characters

ABSTRACTCyclostomes are an ancient order of bryozoans with more than 500 living species. Traditionally, cyclostome taxonomy has depended almost entirely on characters of the calcareous skeletons of mature colonies. However, the taxonomic distribution of these characters is largely incongruent with well-supported molecular phylogenetic trees, implying the need for major revisions if cyclostome taxonomy is to reflect phylogeny. While far more taxa must be sequenced to ascertain their molecular relationships, there is also a need to discover morphological characters that can be used to support molecular clades, not least to allow these clades to be inferred among fossil cyclostomes for which molecular data will never be available. Here we survey the skeletal morphology of the first-formed part of the skeleton – the protoecium of the founding zooid (ancestrula) – in a variety of Recent and well-preserved fossil cyclostomes, motivated by the recent discovery of a morphologically disparate molecular clade that can be distinguished by protoecial characters. The distribution of pseudopores on the protoecium is shown to vary between species, with eight patterns recognizable, offering a new source of skeletal characters in both living and fossil taxa. However, the patterns seem not to be fully congruent with the cyclostome molecular tree and more data and analyses are required before these patterns can be used to recognize cyclostome clades.