Evolutionary relationships of Eastern Palearctic Brown Frogs, genus Rana: paraphyly of the 24-chromosome species group and the significance of chromosome number change

The Eurasian 'brown frogs' are a morphologically conservative assemblage consisting of the European Rana temporaria and a large number of similar species considered to be related. Although the chromosome number of the great majority of Rana species is 26, there are several species of brown frogs (including R. arvalis, R. chensinensis, R. omativentris and R. dybowskii ) which instead have 24 chromosomes. Yet comparative study of isozyme variation at 25 gene loci from these and seven other European, Caucasian, and east Asian species indicates that the 24-chromosome brown frogs are not a monophyletic group. To the exclusion of R. arvalis , the east Asian 24-chromosome species form a distinct clade related to the 26-chromosome species R. temporaria, R. dalmatina, R. japonica , and R. tagai more closely than to R. arvalis. This result is reinforced by the comparative position of the nucleolar organizer region (NOR) in the karyotypes of these frogs, as shown by NOR-banding of metaphase chromosomes. The NOR is on chromosome No. 2 in R. arvalis but on chromosome No. 10 in the other three 24-chromosome species. The systematic positions of the Causasian species A. camerani and R. macrocnemis relative to the other species are unclear except that these frogs are distinct enough to be considered part of an outgroup clade. However, in general, the systematics of the entire brown frog group remains unresolved due to great genetic divergences between species and the evident homoplasy of the brown frog morphotype. The parallel origins of reduced karyotypes among the brown frogs demonstrate that caution should be exercised when judging systematic relationships based upon gross karyology in the absence of more detailed information.     

Molecular phylogenetics of Uvaria (Annonaceae): relationships with Balonga,Dasoclema and Australian species of Melodorum

An extended molecular phylogenetic analysis of Uvaria (Annonaceae) is presented, using maximum parsimony, maximum likelihood and Bayesian methods, based on sequences of four plastid DNA regions (matK, psbA‐trnH spacer, rbcL and trnL‐F). The additional taxa include the monotypic West African genus Balonga, the monotypic South‐East Asian genus Dasoclema and seven Australian representatives of the genus Melodorum. The results indicate that all of these taxa are nested within a well‐supported clade otherwise consisting of Uvaria species, indicating that their taxonomic treatment needs to be reassessed. The distinguishing morphological characteristics of the taxa are re‐evaluated and interpreted as specialized adaptations of the basic Uvaria structure. The genus Uvaria is accordingly extended following the transfer of these species, necessitating six new nomenclatural combinations and two replacement names. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 33–43.     

Age estimates of Frullania (Frullaniaceae,Porellales) main lineages: another example of rapid and recent diversification in liverwort evolution

Frullania Raddi is an extant genus of liverworts (Bryophytes) widespread around the world. It belongs to the family Frullaniaceae Lorch., with a large number of species distributed into several subgenera, sections and subsections according with different morphological classifications. As shown in previous studies, most Frullania sub-generic classifications are supported by molecular data, indicating that morphological characters appear well suitable to discriminate species. However, deep among-clade relationships remain unclear, probably due to the rapid diversification of main clades, paralleling other plant lineages. In this study, we reconstruct Frullania phylogeny based on available molecular data used in previous studies, and we present time estimates for the origin of its main branches. Results supported the monophyly of most subgenera as demonstrated in previous studies and supported a rapid diversification of these main lineages. Time estimates under a relaxed molecular clock and with integrated fossil evidence and nucleotide mutation rates further suggested a Jurassic origin of the genus and a rapid diversification during Palaeogene and Neogene. This may have been influenced by geographical and climate changes during these periods as predicted for most leafy liverworts.     

Taxonomy and phenotypic relationships of the Anastrepha fraterculus complex in the Mesoamerican and Pacific Neotropical dominions (Diptera,Tephritidae)

Previous morphometric studies based on linear measurements of female structures of the aculeus, mesonotum, and wing revealed the existence of seven morphotypes within the Anastrepha fraterculus cryptic species complex along the Neotropical Region. The current research followed linear and geometric morphometric approaches in 40 population samples of the nominal species Anastrepha fraterculus (Wiedemann) spread throughout the Meso-American and Pacific Neotropical dominions (including Mexico, Central America, Venezuela, Colombia, Ecuador, and Peru). The goals were to explore the phenotypic relationships of the morphotypes in these biogeographical areas; evaluate the reliability of procedures used for delimitation of morphotypes; and describe their current distribution. Findings determined that morphotypes previously recognized via the linear morphometrics were also supported by geometric morphometrics of the wing shape. In addition, we found an eighth morphotype inhabiting the highlands of Ecuador and Peru. Morphotypes are related into three natural phenotypic groups nominated as Mesoamerican-Caribbean lineage, Andean lineage, and Brazilian lineage. The hypothesis that lineages are not directly related to each other is discussed, supported by their large morphological divergence and endemicity in these three well-defined biogeographic areas. In addition, this hypothesis of the non-monophyly of the Anastrepha fraterculus complex is also supported by evidence from other authors based on molecular studies and the strong reproductive isolation between morphs from different lineages.     

Skull shapes of the Lissodelphininae: radiation,adaptation and asymmetry

Within Delphinidae, the sub‐family Lissodelphininae consists of 8 Southern Ocean species and 2 North Pacific species. Lissodelphininae is a result of recent phylogenetic revisions based on molecular methods. Thus, morphological radiation within the taxon has not been investigated previously. The sub‐family consists of ecologically diverse groups such as (1) the Cephalorhynchus genus of 4 small species inhabiting coastal and shelf waters, (2) the robust species in the Lagenorhynchus genus with the coastal La. australis, the offshore La. cruciger, the pelagic species La. obscurus and La. obliquidens, and (3) the morphologically aberrant genus Lissodelphis. Here, the shapes of 164 skulls from adults of all 10 species were compared using 3‐dimensional geometric morphometrics. The Lissodelphininae skulls were supplemented by samples of Lagenorhynchus albirostris and Delphinus delphis to obtain a context for the variation found within the subfamily. Principal components analysis was used to map the most important components of shape variation on phylogeny. The first component of shape variation described an elongation of the rostrum, lateral and dorsoventral compression of the neurocranium and smaller temporal fossa. The two Lissodelphis species were on the high extreme of this spectrum, while Lagenorhynchus australis, La. cruciger and Cephalorhynchus heavisidii were at the low extreme. Along the second component, La. cruciger was isolated from the other species by its expanded neurocranium and concave facial profile. Shape variation supports the gross phylogenetic relationships proposed by recent molecular studies. However, despite the great diversity of ecology and external morphology within the subfamily, shape variation of the feeding apparatus was modest, indicating a similar mode of feeding across the subfamily. All 10 species were similar in their pattern of skull asymmetry, but interestingly, two species using narrowband high frequency clicks (La. cruciger and C. hectori) were among the most asymmetric species, contradicting previous interpretations of odontocete skull asymmetry. J. Morphol. 277:776–785, 2016. © 2016 Wiley Periodicals, Inc.     

Phylogenetic relationships in the Sceloporus variabilis (Squamata: Phrynosomatidae) complex based on three molecular markers,continuous characters and geometric morphometric data

The monophyly of the Sceloporus variabilis group is well established with five species and two species complexes, but phylogenetic relationships within species complexes are still uncertain. We studied 278 specimens in 20 terminals to sample all taxa in the “variabilis group,” including three subspecies in the “variabilis complex,” and two outgroups (Sceloporus grammicus and Sceloporus megalepidurus). We assembled an extensive morphological data set with discrete and continuous characters (distances and scale counts), including geometric morphometric data (landmark coordinates of three shapes), and a three‐marker molecular data set as well (ND4, 12S and RAG1). We conducted parsimony and Bayesian phylogenetic inferences on these data, including several partitioning and weighting schemes. We suggest elevating three subspecies to full species status. Therefore, we recommend recognition of nine species in the “variabilis group.” First, S. variabilis is sister to Sceloporus teapensis. In turn, Sceloporus cozumelae is sister to Sceloporus olloporus. These four species are a monophyletic group, which is sister to Sceloporus smithi. Finally, Sceloporus marmoratus is sister of the clade of five species. The other species in the “variabilis group” (Sceloporus chrysostictus, Sceloporus couchii and Sceloporus parvus) are a paraphyletic grade at the base of the tree. Our analyses reject the existence of the “variabilis complex.” We conducted a parsimony‐based ancestral reconstruction on body size (snout–vent length), femoral pores and dorsal scales and related morphological changes to geographic distribution of the species. Our phylogenetic hypothesis will allow best designs of comparative studies with species in the “variabilis group,” one of the earliest divergent lineages in the genus.     

The taxonomy, distribution and origins of two species of Phaulacridium (Orthoptera: Acrididae) in the South Island of New Zealand

Extensive collecting of grasshoppers of the genus Phaulacridium in New Zealand has indicated the presence of a new species, P. otagoense Ritchie & Westerman, distributed parapatrically with respect to the common and widespread species, P. marginale (Walker) in the Mackenzie Plains and Central Otago regions of South Island. Phaulacridium otagoense occurs on exposed hillsides with bare patches caused by rabbit grazing while P. marginale is found in adjoining areas with lusher vegetation and less severe erosion. A key to the two species and a differential diagnosis are provided. Statistically significant differences in morphology and in nuclear DNA content and chiasma frequency confirm the separate species status of the two taxa. The present-day distribution and probable allopatric origin of P. otagoense from P. marginale is discussed in the light of past and present vegetational and climatic factors and their recent disruption by human agencies. The holotype and some paratypes of P. otagoense are deposited in the Canterbury Museum, Christchurch, New Zealand and further paratypes are deposited in the Australian National Insect Collection, Canberra and the British Museum (Natural History), London     

The complex history of the genus Ilex L. (Aquifoliaceae): evidence from the comparison of plastid and nuclear DNA sequences and from fossil data

 A plastid phylogeny of the genus Ilex based on three different loci (the atpB-rbcL spacer, trnL-trnF and rbcL) is compared with its nuclear phylogeny based on two different loci (the ribosomal ITS and the 5S RNA spacer). These two sets of molecular data are then compared to geographical and temporal data from the fossil record. The plastid phylogeny is strongly correlated with the geographic distribution of extant species. However, the nuclear phylogeny is strongly incongruent with the plastid phylogeny, suggesting frequent interlineage hybridizations. Moreover, the comparison of the ribosomal ITS tree and the 5S RNA spacer tree indicates also possible lineage sorting. Particularly interesting is the finding of two different Ilex lineages in the plastid American clade showing different biogeographic patterns in South America. One of them has a simple North American/South American biogeographical relationship. The other has complex biogeographical relationships, some species showing direct Asian/South American biogeographical relationships. During its history, the genus Ilex probably experienced frequent lineage sorting and interlineage hybridization with subsequent nuclear or cytoplasmic introgression, making the study of its history very complex. Received September 24, 2001; accepted August 19, 2002 Published online: November 28, 2002 Addresses of the authors: Jean-Fran?ois Manen (e-mail: manen@cjb.ville-ge.ch), Yamama Naciri-Graven, Conservatoire et Jardin Botaniques, Impératrice 1, CH-1292 Chambésy/Genève, Switzerland. Michael C. Boulter, Palaeobiology Research Unit, University of East London, Romford Road, London E15 4LZ, UK.     

Standing and flowing: the complex origins of adaptive variation

A population faced with a new selection pressure can only adapt if appropriate genetic variation is available. This genetic variation might come from new mutations or from gene exchange with other populations or species, or it might already segregate in the population as standing genetic variation (which might itself have arisen from either mutation or gene flow). Understanding the relative importance of these sources of adaptive variation is a fundamental issue in evolutionary genetics (Orr & Betancourt 2001 ; Barrett & Schluter 2008 ; Gladyshev et al. 2008 ) and has practical implications for conservation, plant and animal breeding, biological control and infectious disease prevention (e.g. Robertson 1960 ; Soulé & Wilcox 1980 ; Prentis et al. 2008 ; Pennings 2012 ). In this issue of Molecular Ecology, Roesti et al. ( 2014 ) make an important contribution to this longstanding debate.     

New choristoderes (Reptilia: Diapsida) from the Upper Cretaceous and Palaeocene, Alberta and Saskatchewan, Canada, and phylogenetic relationships of Choristodera

New choristoderan fossils from the Late Cretaceous and Palaeocene of Alberta and Saskatchewan, Canada, are described: incomplete maxillae and dentaries from the Upper Cretaceous Oldman Formation, Alberta, extend the range of the primitive Cteniogenys from the Jurassic in the North American Western Interior; an incomplete dentary from the Palaeocene Ravenscrag Formation, Saskatchewan, comprises the first occurrence of the crocodile-like Simoedosaurus in Canada and the earliest record of the genus; well-preserved skulls and mandibles from the Oldman and Horseshoe Canyon formations, Alberta, document a new species of Champsosaurus and clarify the status of previously known species of the genus. New information about Asian choristoderes supports a Tchoiria- ( Ikechosaurus + Simoedosaurus ) relationship, contrary to previous work. Choristoderes share no convincing synapomorphies with either Lepidosauromorpha or Archosauromorpha, but occupy a more basal position within Diapsida, possibly as a sister-taxon with Neodiapsida (Younginiformes + Sauria).     

Phylogenetic relationships within the tribe Janieae (Corallinales,Rhodophyta) based on molecular and morphological data: a reappraisal of Jania1

Generic boundaries among the genera Cheilosporum, Haliptilon, and Jania—currently referred to the tribe Janieae (Corallinaceae, Corallinales, Rhodophyta)—were reassessed. Phylogenetic relationships among 42 corallinoidean taxa were determined based on 26 anatomical characters and nuclear SSU rDNA sequence data for 11 species (with two duplicate plants) referred to the tribe Corallineae and 15 species referred to the tribe Janieae (two species of Cheilosporum, seven of Haliptilon, and six of Jania, with five duplicate plants). Results from our approach were consistent with the hypothesis that the tribe Janieae is monophyletic. Our data indicate, however, that Jania and Haliptilon as currently delimited are not monophyletic, and that Cheilosporum should not be recognized as an independent genus within the Janieae. Our data resolved two well‐supported biogeographic clades for the included Janieae, an Indian‐Pacific clade and a temperate North Atlantic clade. Among anatomical characters, reproductive structures reflected the evolution of the Janieae. Based on our results, three genera, Cheilosporum, Haliptilon, and Jania, should be merged into a single genus, with Jania having nomenclatural priority. We therefore propose new combinations where necessary of some species previously included in Cheilosporum and Haliptilon.     

Mitochondrial relationships and divergence dates of the African colobines: evidence of Miocene origins for the living colobus monkeys

The African colobines represent a neglected area of cercopithecid systematics. Resolving the phylogenetic relationships and estimating divergence dates among the living forms will provide insight into the evolution of this group and may shed light upon the evolution of other African primates as well. This is the first molecular assessment of the evolutionary relationships among the modern colobus monkeys, which are comprised of the black-and-white, olive, and red colobus groups. Over 4,000 base pairs of mitochondrial DNA were amplified and sequenced in over 40 colobus monkey individuals incorporating representatives from all commonly recognized species. Gene trees were inferred using maximum likelihood and Bayesian inference, and penalized likelihood was employed to estimate mitochondrial divergence dates among the sampled taxa. The results are congruent with some aspects of previous phylogenetic hypotheses based on morphology and vocalizations, although the relationships among several West and Central African taxa differ to some degree. The divergence date analysis suggests that the black-and-white, olive, and red colobus had diverged from one another by the end of the Miocene, and that by the Plio-Pleistocene many of the species lineages were already present. This demonstrates that the initial extant colobus monkey diversification occurred much earlier than previously thought and was likely part of the same adaptive radiation that produced the diverse colobine taxa seen in the African Plio-Pleistocene fossil record. The lack of early members from the modern lineages in fossiliferous deposits suggests that they resided in part in the forests of Central and West Africa, which also currently harbor the highest levels of colobus monkey diversity. These forests should not be ignored in models of Plio-Pleistocene human and nonhuman primate evolution.     

Untangling the contribution of characters to evolutionary relationships: a case study using fossils,morphology, and Genes

Given the importance of phylogenetic trees to understanding common ancestry and evolution, they are a necessary part of the undergraduate biology curriculum. However, a number of common misconceptions, such as reading across branch tips and understanding homoplasy, can pose difficulties in student understanding. Students also may take phylogenetic trees to be fact, instead of hypotheses. Below we outline a case study that we have used in upper-level undergraduate evolution and ichthyology courses that utilizes shark teeth (representing fossils), body characters, and mitochondrial genes. Students construct their own trees using freely available software, and are prompted to compare their trees with a series of questions. Finally, students explore homoplasy, polytomies, and trees as hypotheses during a class discussion period. This case study gives students practice with tree-thinking, as well as demonstrating that tree topology is reliant on which characters and tree-building algorithms are used.     

Taxonomy of the genus Megacyclops (Crustacea,Copepoda): morphometry and the use of enzyme electrophoresis

Morphometric investigations on the populations of Megacyclops in Lake Constance showed, that in a sublittoral region from about 20 to 50 m depth an intermediate type between the two species M. viridis (littoral) and M. gigas (benthal) could be distinguished. Using enzyme electrophoresis it was evident, that these specimens belonged to M. viridis.The annual range of water temperatures in the sub-littoral region corresponds to that found in the shallow areas of the lake or in ponds during winter and early spring, when the adults of M. viridis are markedly larger than in summer and fall (seasonal variation). Nevertheless the sublittoral population represents a different local type with special characteristics in morphometric details.     

Evolution and biogeography of the woody Hawaiian violets (Viola, Violaceae): arctic origins, herbaceous ancestry and bird dispersal

Specialists studying the genus Viola have consistently allied the Hawaiian violets comprising section Nosphinium--most of which are subshrubs or treelets--with putatively primitive subshrubs in certain South American violet groups. Hawaiian violets also possess inflorescences, a floral disposition otherwise found only in other genera of the Violaceae, thus strengthening the hypothesis of a very ancient origin for the Hawaiian species. A survey of phylogenetic relationships among infrageneric groups of Viola worldwide using nuclear rDNA internal transcribed spacer (ITS) sequences revealed a dramatically different biogeographic origin for the Hawaiian violets: A monophyletic Hawaiian clade was placed in a close sister relationship with the amphi-Beringian tundra violet, V. langsdorffii s. 1., in a highly derived position. This remarkable and unforeseen relationship received strong clade support values across analyses, and monophyly of the Hawaiian lineage was further indicated by a unique 26-base-pair deletion in section Nosphinium. The high polyploid base chromosome number (n approximately equal to 40) in the Hawaiian violets relates them to Alaskan and eastern Siberian populations in the polyploid V. langsdorffii complex. More than 50 species of the 260 allochthonous birds wintering in the Hawaiian Islands are found to breed in the Arctic, occupying habitats in which individual birds might have encountered ancestral V. langsdorffii populations and served as dispersers to the central Pacific region. Acquisition of derived morphological traits (e.g., arborescence and inflorescences), significance of a confirmed Arctic origin for a component of the Hawaiian flora, and the likelihood of other "cryptic" Arctic elements in the Hawaiian flora deserving independent molecular phylogenetic corroboration are discussed.     

Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree

The biggest unsolved problems in chloroplast evolution are the origins of dinoflagellate and euglenoid chloroplasts,which have envelopes of three membranes not two like plants and chromists, and of the sporozoan plastid, bounded by four smooth membranes. I review evidence that all three of these protozoan plastid types originated by secondary symbiogenesis from eukaryotic symbionts. Instead of separate symbiogenetic events, I argue that dinoflagellate and sporozoan plastids are directly related and that the common ancestor of dinoflagellates and Sporozoa was photosynthetic. I suggest that the last common ancestor of all Alveolata was photosynthetic and acquired its chlorophyll c-containing plastids in the same endosymbiogenetic event as those of Chromista. Chromistaand Alveolata are postulated to be a clade designated chrornalveolates. I propose that euglenoids obtained their plastids from the same(possibly ulvophycean) green alga as chlorarachneans and that Discicristata (Euglenozoa plus Percolozoa) and Cercozoa (the group including chlorarachneans) form a clade designated cabozoa (protozoa with chlorophyll a + b). If both theories are correct, there were only two secondary symbiogenetic events (witnessed by the chlorarachnean and cryptomonad nucleormorphs) in the history of life, not seven as commonly assumed. This greatly reduces the postulated number of independent origins of chloroplast protein-targeting machinery and of gene transfers from endosymbiont to host nuclei. I discuss the membrane and plastid losses and innovations in protein targeting implied by these theories, the comparative evidence for them, and their implications for eukaryote megaphylogeny. The principle of evolutionary conservatism leads to a novel theory for the function of periplastid vesicles in membrane biogenesis ofchlorarachneans and chromists and of the key steps in secondary symbiogenesis. Protozoan classification is also slightly revised by abandoning the probably polyphyletic infrakingdom Actinopoda, grouping Foraminifera and Radiolaria as a new infrakingdom Retaria,placing Heliozoa within a revised infrakingdom Sarcomastigota, establishing a new flagellate phylum Loukozoa for Jakobea plus Anaeromonadea within an emended subkingdom Eozoa, and ranking Archezoa as an infrakingdom within Eozoa.     

Taxonomic revision of the genus Galictis (Carnivora: Mustelidae): species delimitation,morphological diagnosis,and refined mapping of geographical distribution

Although critical for enabling in‐depth evolutionary, ecological, or conservation‐orientated studies, taxonomic knowledge is still scarce for many groups of organisms, including mammals of the order Carnivora. For some of these taxa, even basic aspects such as species limits and geographical distribution are still uncertain. This is the case for the Neotropical mustelid genus Galictis, considered one of the least studied carnivoran genera in the Americas. To address this issue, we performed a comprehensive assessment of morphological and molecular characters to test the number of species within Galictis, and to characterize their distinctiveness and evolutionary history. In addition, we reviewed and consolidated the available information on the taxonomy of this genus, so as to provide a historical framework upon which we could interpret our data. Our analyses demonstrated that two Galictis species can be clearly delimited and diagnosed using metric and nonmetric morphological characters as well as DNA sequences from mitochondrial and nuclear gene segments. On the basis of this clarified species‐level delimitation, we reassessed the geographical range of each Galictis taxon, identifying possible areas of sympatry between them. These results provide a solid taxonomic framework for Galictis, enabling the development of additional studies focusing on this poorly known taxon. © 2013 The Linnean Society of London, Zoological Journal of the Linnean Society, 2013, 167 , 449–472.     

Two new species in the Chaetoceros socialis complex (Bacillariophyta): C. sporotruncatus and C. dichatoensis,and characterization of its relatives,C. radicans and C. cinctus

The diatom genus Chaetoceros is one of the most abundant and diverse phytoplankton in marine and brackish waters worldwide. Within this genus, Chaetoceros socialis has been cited as one of the most common species. However, recent studies from different geographic areas have shown the presence of pseudo‐cryptic diversity within the C. socialis complex. Members of this complex are characterized by curved chains (primary colonies) aggregating into globular clusters, where one of the four setae of each cell curves toward the center of the cluster and the other three orient outwards. New light and electron microscopy observations as well as molecular data on marine planktonic diatoms from the coastal waters off Chile revealed the presence of two new species, Chaetoceros sporotruncatus sp. nov. and C. dichatoensis. sp. nov. belonging to the C. socialis complex. The two new species are similar to other members of the complex (i.e., C. socialis and C. gelidus) in the primary and secondary structure of the colony, the orientation pattern of the setae, and the valve ultrastructure. The only morphological characters that can be used to differentiate the species of this complex are aspects related to resting spore morphology. The two newly described species are closely related to each other and form a sister clade to C. gelidus in molecular phylogenies. We also provide a phylogenetic status along with the morphological characterization of C. radicans and C. cintus, which are genetically related to the C. socialis complex.