Showing papers in "Zoologica Scripta in 2007"
TL;DR: A new molecular phylogeny is presented for the highly diverse, bivalve molluscan subclass Heterodonta, indicating that the basal clades of Crassatelloidea, Anomalodesmata and Lucinoidea diverged very early in the Lower Palaeozoic.
Abstract: A new molecular phylogeny is presented for the highly diverse, bivalve molluscan subclass Heterodonta. The study, the most comprehensive for heterodonts to date, used new sequences of 18S and 28S rRNA genes for 103 species from 49 family groups with species of Palaeoheterodonta (Trigoniidae, Margaritiferidae and Unionidae) as outgroups. Results confirm previous analyses that the Carditidae/Astartidae/Crassatellidae clade is basal to all other heterodonts including Anomalodesmata (often classified as a separate subclass or order). Thyasiroidea occupy a near basal position between the Crassatelloidea and Anomalodesmata. Lucinidae form a well-supported monophyletic group distinct from Thyasiridae and Ungulinidae. The Solenoidea and Hiatelloidea link as sister groups distant from the Tellinoidea and Myoidea, respectively, where they had been previously associated. The position of the Gastrochaenidae is unstable but does not group with myoidean taxa. Species of four families of Galeommatoidea form a clade that also includes Sportellidae of the Cyamioidea. The Cardioidea and Tellinoidea form highly supported, long branched, individual clades but group as sister taxa. A major clade including Veneroidea, Mactroidea, Myoidea and other families is given the unranked name Neoheterodontei. There is no support for a separate order Myoida (Myoidea and Pholadoidea). Dreissenidae group within the clade including Myidae, Corbulidae, Pholadidae and Teredinidae. The Corbiculoidea is confirmed as polyphyletic with the Sphaeriidae and Corbiculidae forming separate clades within the Neoheterodontei; Corbiculidae grouping with the Glauconomidae. Hemidonacidae are unrelated to the Cardiidae, as previously proposed, but nest within the Neoheterodontei. The Gaimardiidae group near to the Ungulinidae and not with Cyamioidea where most recently classified. The family Ungulinidae, previously classified in the Lucinoidea, forms a well-supported clade within the Neoheterodontei and is elevated to superfamily rank — Ungulinoidea. The monophyletic status of Glossoidea, Arcticoidea and Veneroidea is unconfirmed. A brief review of the fossil record of the heterodonts indicates that the basal clades of Crassatelloidea, Anomalodesmata and Lucinoidea diverged very early in the Lower Palaeozoic. Other groups such as the Hiatelloidea, Solenoidea, Gastrochaenidae probably were of late Palaeozoic origins. The Cardioidea and Tellinoidea originated in the Triassic while major groups of Neoheterodontei radiated in the Late Mesozoic. The phylogenetic position of the Thyasiroidea and Galeommatoidea suggests a longer fossil history than has so far been recognized.
143 citations
TL;DR: The mitochondrial 16S rRNA proved to be a useful DNA ‘barcode’ gene for hydroids, not only allowing discrimination of species, but also in some cases of populations, genera and families, and their intra‐ or interphylogenetic associations.
Abstract: Fifty-six sequences of the mitochondrial 16S RNA gene were generated for hydroids, belonging to six nominal families — Eudendriidae, Lafoeidae, Haleciidae, Sertulariidae, Plumulariidae and Aglaopheniidae — collected from bathyal environments of the Gulf of Cadiz (22 haplotypes), Greenland (1 haplotype), Azores (1 haplotype), the shallow waters of the UK (17 haplotypes) and Portugal (2 haplotypes). When combined and analysed with 68 additional sequences published in GenBank, corresponding to 63 nominal species of these families (nine species in common between the GenBank sequences and those presented by the authors), cryptic species were detected (e.g. two species of Nemertesia and other of Lafoea), as well as apparent cases of conspecificity (e.g. Nemertesia antennina and N. perrieri and Aglaophenia octodonta, A. pluma and A. tubiformis). Other taxonomic inconsistencies were found in the data including cases where species from different genera clustered together (e.g. Sertularia cupressina, Thuiaria thuja, Abietinaria abietina and Ab. filicula). The mitochondrial 16S rRNA proved to be a useful DNA ‘barcode’ gene for hydroids, not only allowing discrimination of species, but also in some cases of populations, genera and families, and their intra- or interphylogenetic associations. Although still under-represented in public data bases, the 16S rRNA gene is starting to be used frequently in the study of hydroids. These data provide powerful complementary evidence for advancing our understanding of hydrozoan systematics.
112 citations
TL;DR: Bayesian and maximum‐likelihood phylogenies of Vetigastropoda were reconstructed by separate and combined analyses of one mitochondrial, one nuclear and two nuclear gene sequences, with an emphasis on dense taxonomic sampling.
Abstract: Bayesian and maximum-likelihood phylogenies of Vetigastropoda (Mollusca: Gastropoda) were reconstructed by separate and combined analyses of one mitochondrial (cytochrome oxidase I, COI) and two nuclear (histone H3 and 18S rRNA) gene sequences, with an emphasis on dense taxonomic sampling. More than 70 vetigastropod species belonging to 13 families and 25 subfamilies constituted a robust clade against the two outgroup clades Neomphalina and Cocculinoidea. The phylogenetically controversial family Seguenziidae appeared as a derived Vetigastropoda and constituted a highly supported clade with eucycline and cataegine trochids, and three skeneimorphs (Adeuomphalus, Ventsia and Xyloskenea). These taxa herein treated as the superfamily Seguenzioidea are morphologically very diverse and grouped only by the combination of symplesiomorphies in the shell, radular and head-foot characters. Anatomical peculiarities of Seguenziidae, including the presence of the penis and seminal receptacle, are all apomorphic conditions independently derived from those in higher gastropod clades, as a consequence of the small size and in response to deep-sea habitats, where sperm storage seems to be especially beneficial with low numerical density of individuals and limited periodic cues for gametogenesis. Indeed, internal or semi-internal fertilization has been evolved at least six times in Vetigastropoda, essentially in deep-sea lineages, with weak phylogenetic constraints. Other new vetigastropod clades with high support values include: Turbinidae + Tegulinae (Trochidae) + Skeneidae s.s., Clypeosectidae + Lepetodrilidae, Anatominae (Scissurellidae) + Bathyxylophila (Skeneidae) and Lepetodriloidea + Scissurellidae +Bathyxylophila.
106 citations
TL;DR: The present study found that Ancylidae as traditionally understood, i.e. covering most freshwater limpet gastropods, is paraphyletic, as the genera of Burnupia and Protancylus have been shown to lie phylogenetically outside the Ancylini.
Abstract: Planorbid gastropods are the most diverse group of limnic pulmonates, with both discoidal and highspired taxa. Phylogenetic relationships among these genera are confused and controversial. In particular, the monophyly of the limpet-like taxa (traditionally Ancylidae) is disputed. Even recent molecular studies have concluded that substantially more work is necessary to solve the remaining issues concerning intergeneric phylogenetic relationships and higher taxa systematics. Planorbid snails are of great significance for humans as several members of this group are intermediate hosts of blood flukes (schistosomes) causing a chronic disease, schistosomiasis. We used the two independent molecular markers COI and 18S (concatenated dataset of 2837 nucleotide bp) to infer phylogenetic relationships of 26 genera (27 species) of Planorboidea, represented mostly by type species from mainly topotypical populations. With the majority of the taxa discussed not having been studied previously, this study attempted to test several hypotheses on planorbid phylogenetic relationships using Bayesian inference techniques. The monophyly of Planorboidea (= ‘Ancyloplanorbidae’) is strongly suggested on the basis of our extensive molecular analysis. Besides a distinct Burnupia clade, two major clades were recovered that correspond to family level taxa (traditional Bulinidae and Planorbidae). Considerable rearrangements of suprageneric taxa are evident from the phylogeny inferred. Therefore, the only clades recognized by current classifications and supported by our analysis are Planorbini and Segmentinini. The present study found that Ancylidae as traditionally understood, i.e. covering most freshwater limpet gastropods, is paraphyletic, as the genera of Burnupia and Protancylus have been shown to lie phylogenetically outside the Ancylini. Chromosome numbers and levels of polyploidy are discussed in the light of the new phylogeny. An earlier theory of shell shape evolution, i.e. that of patelliform taxa being most advanced, was not supported by this study; a limpet-shaped taxon is most basal within Planorboidea. Although many taxa still remain to be studied, our results will hopefully contribute towards a better understanding of this very important group of freshwater organisms. Some taxonomic implications are discussed.
81 citations
TL;DR: Results indicate that the Hawaiian Islands were colonised by two independent Theridiinae lineages, one of which originated in the Americas and both lineages have undergone local diversification in the archipelago and have convergently evolved similar bizarre morphs.
Abstract: The Hawaiian happy face spider (Theridion grallator Simon, 1900), named for a remarkable abdominal colour pattern resembling a smiling face, has served as a model organism for understanding the generation of genetic diversity. Theridion grallator is one of 11 endemic Hawaiian species of the genus reported to date. Asserting the origin of island endemics informs on the evolutionary context of diversification, and how diversity has arisen on the islands. Studies on the genus Theridion in Hawaii, as elsewhere, have long been hampered by its large size (> 600 species) and poor definition. Here we report results of phylogenetic analyses based on DNA sequences of five genes conducted on five diverse species of Hawaiian Theridion, along with the most intensive sampling of Theridiinae analysed to date. Results indicate that the Hawaiian Islands were colonised by two independent Theridiinae lineages, one of which originated in the Americas. Both lineages have undergone local diversification in the archipelago and have convergently evolved similar bizarre morphs. Our findings confirm para- or polyphyletic status of the largest Theridiinae genera: Theridion, Achaearanea and Chrysso. Convergent simplification of the palpal organ has occurred in the Hawaiian Islands and in two continental lineages. The results confirm the convergent evolution of social behaviour and web structure, both already documented within the Theridiidae. Greater understanding of phylogenetic relationships within the Theridiinae is key to understanding of behavioural and morphological evolution in this highly diverse group.
80 citations
TL;DR: The phylogenetic analyses revealed that the Javan and Small Indian mongooses grouped in two separate clades with their range limits located in Myanmar.
Abstract: 1Veron, G., Patou, M.-L., Pothet, G., Simberloff, D. & Jennings, A. P. (2007). Systematicstatus and biogeography of the Javan and small Indian mongooses (Herpestidae, Carnivora).— Zoologica Scripta, 36, 1–10.The Javan and small Indian mongooses, ranging from the Middle East to South-east Asia,are considered as two species or as a single species, varying in size and colour from west toeast. In order to clarify their systematic status and to define the limits of their ranges,Cytochrome b sequences were obtained from 27 specimens, and localities of 392 specimensfrom museum collections were determined. The phylogenetic analyses revealed that theJavan and Small Indian mongooses grouped in two separate clades with their range limitslocated in Myanmar. The Javan mongoose is in fact closer to the grey mongoose than to thesmall Indian mongoose.
78 citations
TL;DR: It is suggested that the west Balkan lineage represents an early offshoot of L. bilineata that was isolated during a previous Pleistocene glacial from the more western L. v. viridis, arguing for two distinct refuges there, and a low genetic diversity in the northern part of the range.
Abstract: It is well known that the current genetic pattern of many European species has been highly influenced by climatic changes during the Pleistocene. While there are many well known vertebrate examples, knowledge about squamate reptiles is sparse. To obtain more data, a range-wide sampling of Lacerta viridis was conducted and phylogenetic relations within the L. viridis complex were analysed using an mtDNA fragment encompassing part of cytochrome b, the adjacent tRNA genes and the noncoding control region. Most genetic divergence was found in the south of the distribution range. The Carpathian Basin and the regions north of the Carpathians and Alps are inhabited by the same mitochondrial lineage, corresponding to Lacerta viridis viridis. Three distinct lineages occurred in the south-eastern Balkans — corresponding to L. v. viridis, L. v. meridionalis, L. v. guentherpetersi— as well as a fourth lineage for which no subspecies name is available. This distribution pattern suggests a rapid range expansion of L. v. viridis after the Holocene warming, leading to a colonization of the northern part of the species range. An unexpected finding was that a highly distinct genetic lineage occurs along the western Balkan coast. Phylogenetic analyses (Bayesian, maximum likelihood, maximum parsimony) suggested that this west Balkan lineage could represent the sister taxon of Lacerta bilineata. Due to the morphological similarity of taxa within the L. viridis complex this cryptic taxon was previously assigned to L. v. viridis. The distribution pattern of several parapatric, in part highly, distinct genetic lineages suggested the existence of several refuges in close proximity on the southern Balkans. Within L. bilineata sensu stricto a generally similar pattern emerged, with a high genetic diversity on the Apennine peninsula, arguing for two distinct refuges there, and a low genetic diversity in the northern part of the range. Close to the south-eastern Alps, three distinct lineages (L. b. bilineata, L. v. viridis, west Balkan taxon) occurred within close proximity. We suggest that the west Balkan lineage represents an early offshoot of L. bilineata that was isolated during a previous Pleistocene glacial from the more western L. bilineata populations, which survived in refuges on the Apennine peninsula.
78 citations
TL;DR: The results support the conclusion that the two forms of Tetraclita squamosa are genetically differentiated species and are comparable to values for other congeneric barnacle species.
Abstract: The common intertidal barnacle Tetraclita squamosa occurs in two morphologically and genetically distinct forms in East Asia. The north-western Pacific form (Japan, Okinawa and Taiwan) has green parietes and the tergo-scutal flaps are black without any patterns. The south China form (Xiamen, Hong Kong) also has green parietes but the tergo-scutal flaps are black with two white spots on the tergal and scutal margin. Compared to the NW Pacific form, the south China form has a beaked tergum, a sharper tergal spur and cirrus I lacks serrulate type setae that have four rows of setules. The two forms differ by 15–16% in COI divergence, which is comparable to values for other congeneric barnacle species. The 12S rRNA and ITS1 sequences are also distinct between the two forms. Our results support the conclusion that the two forms are genetically differentiated species. We describe the NW Pacific form as a new species, Tetraclita pacifica. We are treating the other species as Tetraclita squamosa based on the fact that Pilsbry, in 1916, redescribed T. squamosa squamosa using samples collected from south China and the Philippines. Further studies are needed to confirm the identity and geographical distribution of the ‘widely distributed’T. squamosa in the Indo-West Pacific.
78 citations
TL;DR: New 18S and 28S rRNA sequences analysed with parsimony, maximum likelihood and Bayesian methods of phylogenetic reconstruction show that Nemertodermatida, generally classified as the sister group of Acoela within the recently proposed Phylum Acoelomorpha, are a separate basal bilaterian lineage.
Abstract: We used new 18S and 28S rRNA sequences analysed with parsimony, maximum likelihood and Bayesian methods of phylogenetic reconstruction to show that Nemertodermatida, generally classified as the sis ...
66 citations
TL;DR: The insufficiency of blast searches in GenBank to assign many of the obtained sequences to correct phylum was noted and clearly demonstrates the need for better search strategies specifically targeted at identification using DNA barcodes.
Abstract: Divergence in cytochrome c oxidase 1 (COI), the genetic marker proposed for DNA barcoding, was investigated in marine bivalves from the genera Ennucula, Nucula, Yoldiella and Thyasira. No overlap in levels of intra- and interspecific variation was found. The levels of divergence found suggest that barcodes from COI will be useful in distinguishing between the species investigated in this study. The insufficiency of blast searches in GenBank to assign many of the obtained sequences to correct phylum was noted and clearly demonstrates the need for better search strategies specifically targeted at identification using DNA barcodes.
63 citations
TL;DR: The radiation of the murine rodents is investigated and the size and shape of the mandible, a morphological character involved in the feeding process, was quantified and compared with an estimate of molecular divergence based on interphotoreceptor retinoid binding protein sequences.
Abstract: What actually is the expected pattern relating to molecular and morphological divergence? A phylogenetic correlation is expected; however, natural selection may force morphological evolution away from this expected correlation. To assess this relationship and the way it is modulated by selection, we investigated the radiation of the murine rodents, also called as Old World rats and mice. Regarding their diet, they are diversified as they include many omnivorous as well as specialist taxa. The size and shape of the mandible, a morphological character involved in the feeding process, was quantified and compared with an estimate of molecular divergence based on interphotoreceptor retinoid binding protein (IRBP) sequences. Size and shape of the mandible appeared to be related by an allometric relationship whatever the ecology of the taxa. Small size characterizes most murines, causing a dominance of low size distances; still, the frequency of important size differentiation increases with molecular distances. Regarding shape changes, the pattern is much contrasted between omnivores and specialists. A pattern of phenotypic drift characterizes the mandible evolution of taxa sharing an omnivorous diet. Little saturation occurs over more than 10 million years with regard to the shape of the mandible that appears as a valuable marker of phylogenetic history in this context. In contrast, important morphological distances can occur when specialist taxa are involved, even when the molecular divergence is small. Ecological specialization thus triggers an uncoupling of molecular and phenotypic evolution, and the departure from a phenotypic drift pattern.
TL;DR: Using DNA sequences of the mitochondrial cytochrome b gene, phylogeny and taxonomy of South and South‐east Asian turtles of all species and subspecies of the genera Batagur, CallagUR, Hardella, Kachuga and Pangshura is investigated.
Abstract: Using DNA sequences of the mitochondrial cytochrome b gene, we investigated phylogeny and taxonomy of South and South-east Asian turtles of all species and subspecies of the genera Batagur, Callagur, Hardella, Kachuga and Pangshura. We found three major clades: (i) a moderately to well-supported clade containing all large riverine species assigned so far to Batagur, Callagur and Kachuga; (ii) a well-supported monophylum comprising the four Pangshura species; and (iii) Hardella that could constitute either the sister-taxon of Pangshura or of a clade comprising Batagur, Callagur, Kachuga and Pangshura. The genus Kachuga is clearly polyphyletic. Therefore, we recommend placing all Batagur, Callagur and Kachuga species in one genus. According to the International Code of Zoological Nomenclature Batagur Gray, 1856, being originally erected at higher rank, takes precedence over the simultaneously published name Kachuga Gray, 1856, and the younger name Callagur Gray, 1870, resulting in an expanded genus Batagur. Indonesian and Malaysian Batagur baska proved to be highly distinct from our sequences of this species from the Sundarbans (Bangladesh, adjacent India), suggesting that a previously unidentified species is involved. This finding is of high conservation relevance in the critically endangered B. baska. The currently recognized subspecies within Hardella thurjii, Pangshura smithii and P. tentoria do not correspond well with mtDNA clades. Considering that the two subspecies of H. thurjii are likely to be based only on individual ontogenetic differences, we propose abandoning the usage of subspecies within H. thurjii. In the Ghaghra River, Uttar Pradesh (India) we detected shared haplotypes in P. smithii and P. tentoria, implying that the unusual morphological characters of the Ghaghra River population of P. tentoria could be the result of interspecific hybridization.
TL;DR: Maximum likelihood, neighbor‐joining, maximum parsimony, and Bayesian phylogenetic analyses show that the genus Alticola does not appear to be a monophyletic group since the representatives of Aschizomys branch within Clethrionomys, whereas two other subgenera (Alticola and Platycranius) form a separate monophylettic clade.
Abstract: Central Asian mountain voles Alticola is one of the least known groups of voles both in evolution and life history. This genus includes three subgenera Alticola s.str., Aschizomys and Platycranius, and belongs to the tribe Clethrionomyini comprising also red-backed voles Clethrionomys and oriental voles Eothenomys. In order to elucidate the phylogenetic relationships within Alticola and to examine its position within the tribe, mitochondrial cytochrome b (cyt b) gene variation was estimated, and the results were compared with morphological and palaeontological data. Maximum likelihood (ML), neighbor-joining (NJ), maximum parsimony (MP) and Bayesian phylogenetic analyses show that the genus Alticola does not appear to be a monophyletic group since the representatives of Aschizomys branch within Clethrionomys, whereas two other subgenera (Alticola and Platycranius) form a separate monophyletic clade. Flat-headed vole Alticola (Platycranius) strelzowi is nested within the nominative subgenus showing close association with A. (Alticola) semicanus. Surprisingly, the two species of Aschizomys do not form a monophyletic group. The results of the relaxed-clock analysis suggest that the Alticola clade splits from the Clethrionomys stem in early Middle Pliocene while basal cladogenetic events within Alticola s.str. dates back to the late Middle to early Late Pliocene. A scenario of evolution in Clethrionomyini is put forward implying rapid parallel morphological changes in different lineages leading to the formation of Alticola-like biomorphs adapted to mountain and arid petrophilous habitats.
Corresponding author: Vladimir S. Lebedev, Zoological Museum, Moscow State University, B. Nikitskaya 6, 125009 Moscow, Russia. E-mail: wslebedev@hotmail.com
Anna A. Bannikova, Lomonosov Moscow State University, Vorobievy Gory, 119992 Moscow, Russia. E-mail: hylomys@mail.ru
Alexey S. Tesakov, Geological Institute RAS, Pyzhevsky 7, 119017 Moscow, Russia. E-mail: tesak@ginras.ru
Natalia I. Abramson, Zoological Institute RAS, Universitetskaya nab. 1, 199034 St Petersburg, Russia. E-mail: lemmus@zin.ru
TL;DR: The nested clade analyses reveal that a common pattern of climatic and geological history over long‐term glacial habitat fragmentation has determined the geographic and haplotype distributions found for D. klovstadi.
Abstract: We carried out a phylogeographic study using mtDNA (COII) for the endemic springtail Desoria klovstadi (formerly Isotoma klovstadi) from northern Victoria Land, Antarctica. Low levels of sequence divergence (≤ 1.6%) across 26 unique haplotypes (from 69 individuals) were distributed according to geographic location. Cape Hallett and Daniell Peninsula contained the highest nucleotide (both > 0.004) and haplotype (both > 0.9) diversity with 10 (of 16) and 8 (of 12) unique haplotypes, respectively. All other populations (Football Saddle, Crater Cirque, Cape Jones) had lower diversity with 2–4 unique haplotypes. Across the 69 individuals from five populations there was only a single haplotype shared between two populations (Daniell Peninsula and Football Saddle). Furthermore, nested clade analyses revealed that some of the Daniell Peninsula haplotypes were more closely related to Football Saddle haplotypes than to any other population. Such discrete haplotype groupings suggest historical (rare) dispersal across the Pleistocene (1.8 mya−11 kya) and Holocene (11 kya–present), coupled with repeated extinction, range contraction and expansion events, and/or incomplete sampling across the species range. The nested clade analyses reveal that a common pattern of climatic and geological history over long-term glacial habitat fragmentation has determined the geographic and haplotype distributions found for D. klovstadi.
TL;DR: Comparing genetic and morphological data of Fijian Rhantus and Copelatus diving beetles, it is shown that even in island radiations it is not per se possible to know if mitochondrial DNA barcoding would perform well and that fixed cutoff values, as sometimes used to discriminate between barcodes, thus species, might be meaningless.
Abstract: We present a molecular phylogeny and taxonomic review of the Pacific island colymbetine diving beetles, focusing on the Fijian and New Caledonian faunas. Four new species are described: Rhantus monteithi and R. poellerbauerae from New Caledonia, and R. kini and R. bula from Fiji. We also describe the 3rd instar larvae of R. monteithi and R. poellerbauerae spp. nov., assigned to adults using mtDNA sequence data and discuss larval characters in the light of phylogeny. The phylogenetic hypotheses derived from both parsimony and Bayesian inference based on 3508 aligned nucleotides from a combination of mitochondrial (cox1, cob and rrnL-tRNALeu-Nad1) and nuclear genes (18S rRNA and H3) reveal a clade comprising R. novaecaledoniae, R. alutaceus, R. pseudopacificus, R. monteithi sp. nov. and R. poellerbauerae sp. nov., which agrees with the R. pacificus group sensu Balke (1993). Carabdytes upin was included within this clade, possibly indicating paraphyly of the genus Rhantus. Rhantus annectens, R. bacchusi, R. supranubicus, R. suturalis, R. simulans, and the Palearctic R. exsoletus, R. latitans and R. bistriatus formed a clade corresponding to the R. suturalis group sensu Balke (2001). Rhantus vitiensis, previously assigned to the R. pacificus group, was included in the R. suturalis clade. We find some support for a scenario where the Pacific was colonized out of the Northern hemisphere only during the past c. 12 million years, rejecting a Gondwanan origin of the morphologically isolated endemics. The new species are all characterized by mtDNA haplotype clusters, the degree of divergence between sister species pairs ranging from 1.3 to 7%, while R. novaecaledoniae individuals from all over New Caledonia apparently form one morphospecies, with moderate genetic diversity (up to 2.3% mtDNA divergence between populations). The sisters R. pollerbauerae sp. nov. + R. monteithi sp. nov. occur sympatrically on Mont Panie but appear ecologically segregated, while the sisters R. vitiensis + R. bula sp. nov. were encountered syntopically on Viti Levu. Comparing genetic and morphological data of Fijian Rhantus and Copelatus diving beetles, we here show that even in island radiations it is not per se possible to know if mitochondrial DNA barcoding would perform well (Rhantus: YES, Copelatus: NO). At the same time we show that fixed cutoff values, as sometimes used to discriminate between barcodes, thus species, might be meaningless. We underpin the importance of morphology for sustainable exploration of global diversity.
TL;DR: The estimates of colonization times of South America predate the closure of the Panama Isthmus and support the hypothesis of a short‐lived, terrestrial corridor at the end of the Miocene, 5.7 Myr BP.
Abstract: Synchronous intercontinental splits between assemblages of woodpeckers suggested by molecular data
TL;DR: The Charipinae are a major group of hyperparasitoids of Hemiptera and the first cladistic analysis of this subfamily's internal relationships is presented, based on 96 morphological characters of adults, which points to the need for a world revision of the basal genus Phaenoglyphis.
Abstract: The Charipinae are a major group of hyperparasitoids of Hemiptera. Here, we present the first cladistic analysis of this subfamily's internal relationships, based on 96 morphological characters of adults. The data matrix was analysed using uniformly weighted parsimony. The effects of using alternative weighting schemes were explored by performing additional searches employing implied weights criteria. One of the caveats of implied weights analysis is that it lacks an objective criterion for selecting the value of the concavity function. In the present study, differential weighting was used to explore the sensitivity of our results to the alternative assumptions made in the analysis and to select one of the most parsimonious trees under equal weights, which we regard as being the hypothesis that minimizes the amount of ad hoc assumptions. The validity of the two existing tribes and the monophyly of all the genera of Charipinae were tested, in particular the cosmopolitan and highly species-rich Alloxysta and Phaenoglyphis, which appear repeatedly in ecological and biochemical studies of host–parasitoid associations. The evolution of several major characters and the relationships between genera are discussed. On the basis of the phylogenetic results, we discuss a number of taxonomic issues. A new classification of the subfamily is proposed in which no tribes are maintained, Carvercharips is synonymyzed with Alloxysta, and the creation of a new genus from Nepal is justified. Our analysis points to the need for a world revision of the basal genus Phaenoglyphis, which is shown as paraphyletic.
TL;DR: The definition of genetic and morphologic boundaries among three currently recognized branching morpho‐species, Psammocora stellata, Pslammocora contigua and Psammoora obtusangula, is addressed through a joint morphometric and molecular study using corallite and branch measurements, and a portion of the β‐tubulin gene as a marker.
Abstract: The Indo-Pacific coral genus Psammocora Dana (1846) has never been formally revised, and its phylogeny has only been partially explored. Several synonymies have been proposed for the 11 nominal species which have highly plastic branching growth forms. In the present study, the definition of genetic and morphologic boundaries among three currently recognized branching morpho-species, Psammocora stellata, Psammocora contigua and Psammocora obtusangula, is addressed through a joint morphometric and molecular study using corallite and branch measurements, and a portion of the β-tubulin gene as a marker. The results show a morphological and partial phylogenetic distinction between P. stellata specimens and a complex composed of P. contigua and P. obtusangula, which is interpreted as a synonym species of P. contigua. Among the factors that could be responsible for the lack of reciprocal monophyly of the three species, hybridization is considered the most likely, due to the presence of interspecific recombinant sequences. Type material of nominal species of branching Psammocora is examined and classified based on genetically defined groups, and compared with synonym in the literature. Among the morphological characters used, corallite variables were best for discriminating between the two lineages and allow recognition of putative hybrid specimens. Psammocora stellata is reported for the first time in the western Indian Ocean (Mayotte), thus greatly extending its known distribution range. Finally, a hybrid swarm is identified in the Arabo-Persian Gulf, while no genetic structure is detected elsewhere in the Indo-Pacific region.
TL;DR: A new procedure for defining taxa upon a single character state is developed centred on the designation of two specimens, belonging to two distinct species, exhibiting the same given character state, as type material, and referred to as ‘cladotypes’.
Abstract: A new procedure for defining taxa upon a single character state is developed. It is centred on the designation of two specimens, belonging to two distinct species, exhibiting the same given character state, as type material, and referred to as ‘cladotypes’. A taxon name/definition designates a monophyletic group until one of the following assumptions is falsified: (1) the character state typified by cladotypes is homologous in individuals that are designated as cladotypes, and (2) cohesion mechanisms isolated individuals exhibiting the type-character-state from those that do not. A taxon defined by a character state that is found to be a combination of several character states is to be redefined upon a character state shared by its cladotypes. If several character states are available, the character state that makes the taxon the least inclusive taxon including cladotypic species (i.e., species to which belong cladotypes) is to be preferred. Taxon names designate obsolete phylogenetic hypotheses if the first assumption is falsified (such names are to be kept for this purpose, i.e., they are not to be recycled in another definition). Rules governing adaptation of previously erected names are proposed. Main cases of taxa synonymy involve definitions based on different pairs of cladotypes but referring to the same type-character-state; and definitions based on the same character-state initially hypothesised as acquired by convergence in cladotypic species pairs, but later demonstrated as originating from a unique ancestor. Taxa could be synonyms if a permanent splitting event did not segregate individuals exhibiting a new character state, qualified as type-character-state, from individuals already assigned to a previously erected taxon. This procedure accommodates potentially any species concept, but is not tied to any; it is an extension of the composite species concept. Species are treated in a different way than other taxa: they are defined as sets of individuals belonging to the same evolving (segments of) metapopulation lineages as a holotype specimen, and do not need a defining character state.
TL;DR: This study highlights multiple morphological simplifications of the colonial organisation during the evolution of Plumularioidea and the convergence of the defensive polyps — the dactylozooids — of plumularioid families with those of others Leptothecata (Hydrodendron) or AnthoathecATA (Hydractinia).
Abstract: The Plumularioidea (Cnidaria, Hydrozoa, Leptothecata) are the most species rich superfamily of the class Hydrozoa. They display a complex and diversified colonial organisation and their life cycle comprises either a reduced free-living, pelagic generation (medusoid), alternating with the benthic colonial form or in most species, no pelagic generation. In order to understand the evolution of colonial and life cycle characters among Plumularioidea, we have reconstructed their phylogeny. Partial mitochondrial 16S rRNA sequences and 64 morphological characters were analysed separately and in combination. The morphological data included not only characters of the individual polyps and medusae, but also characters describing the organisation of colonies, for which we propose general principles applying to character coding in modular organisms. The phylogenetic analyses supported the monophyly of Plumularioidea and of the four plumularioid families (Aglaopheniidae, Halopterididae, Kirchenpaueriidae and Plumulariidae). Most genera were paraphyletic or polyphyletic. This study highlights multiple morphological simplifications of the colonial organisation during the evolution of Plumularioidea and the convergence of the defensive polyps — the dactylozooids — of Plumularioidea with those of others Leptothecata (Hydrodendron) or Anthoathecata (Hydractinia). Concerning the evolution of the life cycle, the phylogeny supports a provocative scenario, where the medusa was lost in an ancestor of the Plumularioidea, and then re-acquired four times independently within this group, in the form of simple medusoids.
TL;DR: The most parsimonious tree obtained from analysis of dataset 2 is used in a dispersal‐vicariance analysis to infer ancestral areas and major biogeographical events and is generally congruent with each other, as well as with previously published hypotheses.
Abstract: With 61 species occurring mostly in the Andes and adjacent lowland areas, Stenocercus lizards represent one of the most widespread and well-represented Andean vertebrate groups. Phylogenetic relationships among species of Stenocercus are inferred using different datasets based on mitochondrial DNA sequence data of 35 species and morphological data of 59 species. Among morphological data, polymorphic and meristic/morphometric characters are coded under the frequency parsimony and gap-weighting methods, respectively, and the accuracy of these methods is tested. When both types of characters are included, the resulting tree topology is more similar to the topologies obtained from analyses of DNA sequence data than those topologies obtained after exclusion of one or both types of characters. The phylogenetic hypotheses inferred including 59 species of Stenocercus (dataset 1) and excluding those species for which DNA data were not available (dataset 2) are generally congruent with each other, as well as with previously published hypotheses. The most parsimonious tree obtained from analysis of dataset 2 is used in a dispersal-vicariance analysis to infer ancestral areas and major biogeographical events. Species of Stenocercus are divided into two major clades. Clade A has diversified mostly in the central Andes, with a few species in the northern Andes and one species in the southern Andes. Clade B is more widespread, with species in the northern, central, and southern Andes, as well as in the Atlantic lowlands and Amazon basin. The most recent common ancestor of Stenocercus is inferred to have occurred in the eastern cordillera of the central Andes. Given morphological similarity and altitudinal distribution of some species nested in a northern-Andes clade, as well as the relatively recent uplift of this Andean region, it is possible that species in this clade have diverged as recently as the mid-Pliocene.
TL;DR: The phylogenetic relationships within the African clade is investigated, which with the exclusion of Pycnonotus contains approximately 50 species, of which the majority are placed in three large genera Andropadus, Phyllastrephus and Chlorocichla, and indicates that none of the three largest currently recognized genera are monophyletic.
Abstract: The Pycnonotidae (bulbuls and greenbuls) comprise approximately 130 species and are widely distributed across Africa and Asia, mainly in evergreen thickets and forest. Recent molecular findings suggest a basal split between the African and the Asian species, although the three African Pycnonotus species are part of the Asian radiation and represent a relative recent immigration to Africa. In this study we investigate the phylogenetic relationships within the African clade, which with the exclusion of Pycnonotus contains approximately 50 species, of which the majority are placed in three large genera Andropadus, Phyllastrephus and Chlorocichla. We use three nuclear markers (myoglobin intron 2, ODC introns 6 and 7 along with intervening exon 7, and β-fibrinogen intron 5), together encompassing 2072 aligned positions, to infer the relationships within the African clade. The resulting tree is generally well supported and indicates that none of the three largest currently recognized genera are monophyletic. For instance, the species included in Andropadus represent three different clades that are not each other's closest relatives. The montane species currently placed in that genus form a strongly supported clade, which is sister to Ixonotus, Thescelocichla, Baeopogon and Chlorocichla, although within this clade the genus Chlorocichla is polyphyletic. The remaining Andropadus species fall into two groups, one of these with A. importunus and A. gracilirostris, which along with Calyptocichla serina form a basal branch in the African greenbul radiation. In support of some previous studies the Leaf-love (Pyrrhurus scandens) is placed within Phyllastrephus. We also propose a new classification that reflects the phylogenetic relationships among African greenbuls.
TL;DR: Johora is shown to be monophyletic and composed of three clades that correspond with the topography of the Malay Peninsula and one of which evolved semiterrestrial habits, possibly in response to competition by the second.
Abstract: The phylogeny and biogeography of the Malayan freshwater crab genus Johora was studied using two mitochondrial genes, 16S rRNA (560 bp) and cytochrome oxidase subunit I (COI) (616 bp), and one nuclear gene, histone 3 (H3) (328 bp). Johora is shown to be monophyletic and composed of three clades that correspond with the topography of the Malay Peninsula. The three clades were estimated to be of similar age (c. 11 million years ago (mya)). The Malayan island of Pulau Tioman (with five species) was determined to have been colonised independently by two separate clades (at c. 11 and 5 mya, respectively), one of which evolved semiterrestrial habits, possibly in response to competition by the second. A partitioned Bremer support (PBS) analysis reveals that most of the support for the phylogenetic tree comes from the COI gene fragment and that the nuclear protein-encoding genes H3 is useful for reconstructing the relationships of Johora.
TL;DR: Evidence of paraphyly or polyphyly in all of the widespread genera examined (Hypselodoris, Mexichromis, Chromodoris and Glossodoris) was recovered, and controversy surrounding the placement of the three most basal genera was only partially resolved.
Abstract: Turner, L. M. & Wilson, N. G. (2008). Polyphyly across oceans: a molecular phylogeny of the Chromodorididae (Mollusca, Nudibranchia). — Zoologica Scripta, 37, 23–42. The Chromodorididae is a large and colourful family of nudibranch sea slugs distributed across the world’s oceans. Most diversity is centred in the Indo-Pacific, but several genera are present in multiple ocean basins, or across regions separated by biogeographical barriers. The monophyly of these widespread genera had not been tested previously. We used 18S rDNA, 16S rDNA and COI sequence data to generate a molecular phylogeny for this group. We recovered evidence of paraphyly or polyphyly in all of the widespread genera examined (Hypselodoris, Mexichromis, Chromodoris and Glossodoris). East Atlantic Hypselodoris and west Atlantic + east Pacific Mexichromis species were more closely related to each other than they were to their Indo-Pacific congeners. The addition of Southern Ocean species of Digidentis demonstrated an interesting alternative to this relationship, becoming the sister group for the east Atlantic Hypselodoris on the basis of 16S and 18S data, but not COI data. Sister group relationships were recovered for most monotypic or enigmatic genera. Ardeadoris is linked to Glossodoris, as is Diversidoris; Pectenodoris is sister to the Indo-Pacific Mexichromis clade, and Verconia is the sister to Noumea haliclona. Controversy surrounding the placement of the three most basal genera was only partially resolved. Using Actinocyclus to root the mitochondrial trees, Cadlinella was the unsupported sister to the Chromodorididae (excluding Cadlina), and Tyrinna occupied a relatively basal position, although this also did not receive significant statistical support. Adding nuclear 18S data gave support for Cadlina as the sister group to the rest of the Chromodorididae s.s. Otherwise, like previous molecular studies, mitochondrial genes supported an alternative position for Cadlina (with other dorid genera).
TL;DR: The results showed that each lineage of Graphiurus, Glis, Glirulus and Muscardinus dates from the Late Oligocene to the Early Miocene period, which is mostly in agreement with fossil records.
Abstract: We examined phylogenetic relationships among six species representing three subfamilies, Glirinae, Graphiurinae and Leithiinae with sequences from three nuclear protein-coding genes (apolipoprotein B, APOB; interphotoreceptor retinoid-binding protein, IRBP; recombination-activating gene 1, RAG1). Phylogenetic trees reconstructed from maximum-parsimony (MP), maximum-likelihood (ML) and Bayesian-inference (BI) analyses showed the monophyly of Glirinae (Glis and Glirulus) and Leithiinae (Dryomys, Eliomys and Muscardinus) with strong support, although the branch length maintaining this relationship was very short, implying rapid diversification among the three subfamilies. Divergence time estimates were calculated from ML (local clock model) and Bayesian-dating method using a calibration point of 25 Myr (million years) ago for the divergence between Glis and Glirulus, and 55 Myr ago for the split between lineages of Gliridae and Sciuridae on the basis of fossil records. The results showed that each lineage of Graphiurus, Glis, Glirulus and Muscardinus dates from the Late Oligocene to the Early Miocene period, which is mostly in agreement with fossil records. Taking into account that warm climate harbouring a glirid-favoured forest dominated from Europe to Asia during this period, it is considered that this warm environment triggered the prosperity of the glirid species through the rapid diversification. Glirulus japonicus is suggested to be a relict of this ancient diversification during the warm period.
TL;DR: The beachflea is a trans‐Atlantic amphipod inhabiting the littoral fringe of Iceland, and in the cooler north‐west, several small populations inhabit isolated warm springs.
Abstract: The beachflea [Orchestia gammarellus (Pallas)] is a trans-Atlantic amphipod inhabiting the littoral fringe. In Iceland, its distribution is temperature-limited; it has recently colonized Iceland's relatively warm south-western coast, and in the cooler north-west, several small populations inhabit isolated warm springs. We address two questions: (i) Do the warm spring populations show evidence of long-term residence in Iceland, or of recent colonization? (ii) For the new south-western Icelandic populations, can the source population be determined? We sequenced COI for 22 populations in Iceland, Nova Scotia, the Faroe Islands, the British Isles, Norway and Sweden. Morphometric analysis of a subset of populations assessed 16 continuous and five discrete characters. Genetically, we found a star phylogeny: a common haplotype was found at all sites except two neighbouring warm spring populations, and all haplotypes were within two base pairs of this common haplotype. Morphometrically, almost all populations examined differed significantly in some characters; however, the warm spring populations differed slightly more from each other than did other populations. Although the origins of the Icelandic populations could not be well resolved, our data are consistent with a recent European origin.
TL;DR: Preliminary phylogenetic analyses indicated that the nearest sister lineage to S. serpulae was S. vivax, a bizarre tape‐like gregarine found in the intestines of sipunculids, which helped to illustrate that the diversification and biogeographical distribution of archigregarine parasites is probably more extensive than usually assumed.
Abstract: Archigregarines are dynamic single-celled parasites that inhabit the intestinal systems of marine invertebrates, especially suspension feeding and deposit feeding polychaetes Certain archigregarines in the genus Selenidium have retained several plesiomorphic characters, and improved knowledge of these species is expected to shed considerable light onto the earliest stages in apicomplexan evolution Although archigregarines are related to some of the most notorious parasites known (eg, Cryptosporidium and Plasmodium), current knowledge of the group is meagre In an attempt to improve our understanding of archigregarine diversity and evolution, I have characterised the general ultrastructure and molecular phylogenetic position of Selenidium serpulae (Lankester) Caullery and Mesnil The parasites were isolated from the intestines of the calcareous tubeworm Serpula vermicularis (Polychaeta) collected in the eastern Pacific Ocean The trophozoites (extracellular feeding stages) were spindle-shaped and capable of slow and continuous bending, and coiling, especially when dislodged from the host epithelium The trophozoite surface was composed of 19–23 longitudinal folds, prominent transverse folds and a robust, trilayered pellicle subtended by a single row of microtubules, each surrounded by an electron transparent sheath Putative mitochondria were observed, but they were inconspicuous and apparently highly reduced, a condition that is indicative of anaerobic metabolism The small subunit (SSU) rDNA sequence from S serpulae was very closely related to two (short) sequences derived from an environmental PCR survey of an oxygen-depleted hydrothermal vent system in the Gulf of California, namely C1-E017 (AY046619) and C2-E016 (AY046806) This result suggested that archigregarines with a morphology and lifecycle much like that in S serpulae are thriving in this oxygen poor ecosystem In addition, phylogenetic analyses of a larger SSU rDNA dataset (excluding the shorter environmental sequences) indicated that the nearest sister lineage to S serpulae was S vivax, a bizarre tape-like gregarine found in the intestines of sipunculids This relationship was bolstered by comparative ultrastructural data and helped to illustrate that the diversification and biogeographical distribution of archigregarine parasites is probably more extensive than usually assumed
TL;DR: Phylogenetic relationships among members of the diving beetle tribe Cybistrini were inferred from analysis of 47 adult and larval morphological characters and sequences from portions of the genes cytochrome oxidase I and II, histone III (H3) and wingless.
Abstract: Miller, K. B., Bergsten, J. & Whiting, M. F. (2007). Phylogeny and classificaiton of diving beetles in the tribe Cybistrini (Coleoptera, Dytiscidae, Dytiscinae). — Zoologica Scripta, 36 , 41–59. Phylogenetic relationships among members of the diving beetle tribe Cybistrini (Coleoptera: Dytiscidae) were inferred from analysis of 47 adult and larval morphological characters and sequences from portions of the genes cytochrome oxidase I (COI) and II (COII), histone III (H3) and wingless . Thirty-three species of Cybistrini were included, representing all genus-groups except Regimbartina Chatanay and Megadytes ( Bifurcitus ) Brinck, and most historically recognized species groups and subgenera used in the tribe. Outgroups include six species from other tribes within Dytiscinae and Lancetinae. Analyses included parsimony analysis of the combined data, likelihood analysis of combined molecular data and partitioned Bayesian analysis of the combined data. Results indicate that Cybistrini is well supported as a monophyletic group. Within the tribe, all currently recognized genus groups were found to be monophyletic with the exception of Onychohydrus Schaum, which is paraphyletic with respect to Austrodytes Watts in the parsimony analysis, but monophyletic in the likelihood and Bayesian analyses, and Cybister sensu stricto , which is paraphyletic with respect to C. ( Melanectes ) Brinck and C. ( Scaphinectes ) Adam in the parsimony analysis or only the latter in the likelihood and Bayesian analyses. Results also suggest that some, but not all, historically recognized species groups or subgenera in the large genus Cybister Curtis are monophyletic, and this is discussed and compared. To improve the classification, the name Sternhydrus Brinck is elevated from subgenus to genus rank ( new status ). Four subgenera in the genus Cybister are recognized: C. ( Melanectes ) Brinck, C. ( Megadytoides ) Brinck ( resurrected ), C. ( Neocybister ) Miller, Bergsten and Whiting ( new subgenus ) and C. ( Cybister ) Curtis. The following new synonyms are established: Trochalus Dejean ( new synonym ), and Scaphinectes Adam = Cybister ( Cybister ) ( new synonym ). The Neotropical species Cybister parvus Tremouilles (not examined) apparently does not fit any historical or currently recognized genus-group diagnosis in Cybistrini, so it is retained in Cybister but incertae sedis with respect to subgenus. In addition to classification, the evolution of the unique character combinations present in cybistrines are discussed. A key to the adults of genera and subgenera is presented.
TL;DR: It was found that Micracini formed the sister group to Cactopinus, a group of mainly cactus feeding scolytine beetles, and Ipini was monophyletic with Pseudips and Acanthotomicus subtending to the most basal node of that clade.
Abstract: Phylogenetic relationships in Scolytinae were reconstructed from 107 DNA sequences that spanned the D2 and D3 expansion segments, and related core regions of the nuclear large ribosomal subunit (28S). Sequences were analysed by parsimony and Bayesian analyses of aligned sequences aided by a new secondary structure model for the D2–D3 domains. Direct optimization was performed on ambiguous alignment regions in combination with fixed states optimization of unambiguous regions, but performed poorly compared to the Bayesian and parsimony analyses. Generally, the phylogenetic signal mainly resolved relationships within tribes, while deeper divergences were either not resolved or received marginal support. In addition to confirming several previously established clades, we found that Micracini formed the sister group to Cactopinus, a group of mainly cactus feeding scolytine beetles. Furthermore, Ipini was monophyletic with Pseudips and Acanthotomicus subtending to the most basal node of that clade. The monophyly of Corthylini, which consists of the bark and cone feeding Pityophtorina and the ambrosia fungus-feeding Corthylina, was supported in some of the analyses. A close relationship was found between Phloeotribus and the two Phloeosinini genera Chramesus and Pseudochramesus, suggesting an evolutionary trajectory for the origin of a lamellate antennal club in Phloeotribus.
TL;DR: The results indicate high levels of homoplasy in traditionally used morphological characters in the Hesioninae, Gyptini and Gyptis are nonmonophyletic, and that Hesionini is probably the sister to all other hesionids.
Abstract: We assess phylogenetic relationships within the polychaete family Hesionidae from morphological data combined with nucleotide data from 18S rDNA, 28S rDNA, 16S rDNA and COI. Parsimony and Bayesian analyses were performed on two data sets; the first was based on a more restricted set of terminals with both morphological and molecular data (17 ingroup terminals), while the second included additional taxa with morphological data only (25 ingroup terminals). The different sets of terminals yielded fully congruent results, as did the parsimony and the Bayesian analyses. Our results indicate high levels of homoplasy in traditionally used morphological characters in the group, and that Hesioninae, Gyptini and Gyptis are nonmonophyletic. Hesionini (mainly Hesione and Leocrates), Psamathini (mainly Hesiospina, Micropodarke, Nereimyra, Psamathe and Syllidia), Ophiodrominae (Gyptini and Ophiodromini) and Ophiodromini (mainly Heteropodarke, Ophiodromus and Podarkeopsis) are monophyletic and agree with previous classifications, and Hesionini is probably the sister to all other hesionids. The placements of the small hesionids capricornia and Lizardia, the hydrothermal vent taxa Hesiodeira and Hesiolyra, and the newly described Hesiobranchia, remain uncertain.