Variation in the circumtesticular Leydig cell tunic of teiid lizards (Cnemidophorus and Ameiva)

Testicular structure in bisexual teiid lizards (Cnemidophorus and Ameiva) is apparently unique among vertebrates in having a circumtesticular subtunic band of Leydig (interstitial) cells, that varies in species of Cnemidophorus from 1.2 to 42.1 cells in thickness (transverse cross-section), between the outer tunic (tunica albuginea) and the seminiferous tubules. The regression on body size, ontogenetic change, seasonal periodicity, and other aspects of structure and function of this subtunic Leydig cell structure are discussed.     

Historical biogeography and cryptic diversity in the Callichthyinae (Siluriformes,Callichthyidae)

The family Callichthyidae, divided into the subfamilies Corydoradinae and Callichthyinae, contains more than 200 species of armoured catfishes distributed throughout the Neotropics, as well as fossil species dating from the Palaeocene. Both subfamilies are very widely distributed throughout the continent, with some species ranges extending across multiple hypothesized biogeographical barriers. Species with such vast geographical ranges could be made up of multiple cryptic populations that are genetically distinct and have diverged over time. Although relationships among Callichthyinae genera have been thoroughly investigated, the historical biogeography of the Callichthyinae and the presence of species complexes have yet to be examined. Furthermore, there is a lack of fossil‐calibrated molecular phylogenies providing a time frame for the evolution of the Callichthyinae. Here, we present a novel molecular data set for all Callichthyinae genera composed of partial sequences of mitochondrial and nuclear markers. These data were used to construct a fossil‐calibrated tree for the Callichthyinae and to reconstruct patterns of spatiotemporal evolution. All phylogenetic analyses [Bayesian, maximum likelihood and maximum parsimony (MP)] resulted in a single fully resolved and well‐supported hypothesis for the Callichthyinae, where Dianema is the sister group of all the remaining genera. Results suggest that the ancestry of most Callichthyinae genera originated in the Amazonas basin, with a number of subsequent ancestral dispersal events between adjacent basins. High divergences in sequences and time were observed for several samples of Hoplosternum littorale, Megalechis picta and Callichthys callichthys, suggesting that these species may contain cryptic diversity. The results highlight the need for a taxonomic revision of species complexes within the Callichthyinae, which may reveal more diversity within this relatively species‐poor lineage.     

Combined phylogenetic analysis of the subclass Marchantiidae (Marchantiophyta): towards a robustly diagnosed classification

The most extensive combined phylogenetic analyses of the subclass Marchantiidae yet undertaken was conducted on the basis of morphological and molecular data. The morphological data comprised 126 characters and 56 species. Taxonomic sampling included 35 ingroup species with all genera and orders of Marchantiidae sampled, and 21 outgroup species with two genera of Blasiidae (Marchantiopsida), 15 species of Jungermanniopsida (the three subclasses represented) and the three genera of Haplomitriopsida. Takakia ceratophylla (Bryophyta) was employed to root the trees. Character sampling involved 92 gametophytic and 34 sporophytic traits, supplemented with ten continuous characters. Molecular data included 11 molecular markers: one nuclear ribosomal (26S), three mitochondrial genes (nad1, nad5, rps3) and seven chloroplast regions (atpB, psbT‐psbH, rbcL, ITS, rpoC1, rps4, psbA). Searches were performed under extended implied weighting, weighting the character blocks against the average homoplasy. Clade stability was assessed across three additional weighting schemes (implied weighting corrected for missing entries, standard implied weighting and equal weighting) in three datasets (molecular, morphological and combined). The contribution from different biological phases regarding node recovery and diagnosis was evaluated. Our results agree with many of the previous studies but cast doubt on some relationships, mainly at the family and interfamily level. The combined analyses underlined the fact that, by combining data, taxonomic enhancements could be achieved regarding taxon delimitation and quality of diagnosis. Support values for many clades of previous molecular studies were improved by the addition of morphological data. The long‐held assumption that morphology may render spurious or low‐quality results in this taxonomic group is challenged. The morphological trends previously proposed are re‐evaluated in light of the new phylogenetic scheme.     

Phylogeny, biogeography and evolution of clutch size in South American lizards of the genus Kentropyx (Squamata: Teiidae)

The lizard genus Kentropyx (Squamata: Teiidae) comprises nine species, which have been placed in three species groups (calcarata group, associated to forests ecosystems; paulensis and striata groups, associated to open ecosystems). We reconstructed phylogenetic relationships of Kentropyx based on morphology (pholidosis and coloration) and mitochondrial DNA data (12S and 16S), using maximum parsimony and Bayesian methods, and evaluated biogeographic scenarios based on ancestral areas analyses and molecular dating by Bayesian methods. Additionally, we tested the life‐history hypothesis that species of Kentropyx inhabiting open ecosystems (under seasonal environments) produce larger clutches with smaller eggs and that species inhabiting forest ecosystems (under aseasonal conditions) produce clutches with fewer and larger eggs, using Stearns’ phylogenetic‐subtraction method and canonical phylogenetic ordination to take in to account the effects of phylogeny. Our results showed that Kentropyx comprises three monophyletic groups, with K. striata occupying a basal position in opposition to previous suggestions of relationships. Additionally, Bayesian analysis of divergence time showed that Kentropyx may have originated at the Tertiary (Eocene/Oligocene) and the ‘Pleistocene Refuge Hypothesis’ may not explain the species diversification. Based on ancestral reconstruction and molecular dating, we argued that a savanna ancestor is more likely and that historical events during the Tertiary of South America promoted the differentiation of the genus, coupled with recent Quaternary events that were important as dispersion routes and for the diversification at populational levels. Clutch size and egg volume were not significantly different between major clades and ecosystems of occurrence, even accounting for the phylogenetic effects. Finally, we argue that phylogenetic constraints and phylogenetic inertia might be playing essential roles in life history evolution of Kentropyx.     

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.     

Evolution of blindness in scolopendromorph centipedes (Chilopoda: Scolopendromorpha): insight from an expanded sampling of molecular data

Relative to its diversity (34 genera, 700 species), Scolopendromorpha has been undersampled in molecular phylogenetic analyses compared with the other chilopod orders. Previous analyses based on morphology have not resolved several key controversies in systematics and evolutionary morphology unambiguously. Here we apply new molecular and morphological data to scolopendromorph phylogenetics, with a focus on the evolution of blindness. The taxonomic sample includes 19 genera, many lacking previous molecular data, and diverse, cosmopolitan genera of Scolopendridae are sampled by multiple species. Phylogenetic analysis with Direct Optimization used 94 morphological characters and ca. 4.5 kb of sequence data from two nuclear (18S and 28S rRNA) and two mitochondrial (16S rRNA and COI) loci. A single most‐parsimonious cladogram selected after sensitivity analyses resolves Scolopendromorpha as monophyletic, and divides it into a blind clade of three families (Plutoniumidae, Cryptopidae, Scolopocryptopidae) and its ocellate sister group, Scolopendridae. Some species‐rich, cosmopolitan genera (Cormocephalus, Otostigmus, Scolopendra) in Scolopendridae are non‐monophyletic, and in several instances (e.g. New and Old World Scolopendra) relationships are more congruent with geographical distributions than with traditional classifications. The tribe Asanadini is particularly subject to parameter‐sensitivity, nesting in the combined analysis within Scolopendrini but as sister to all other Scolopendrinae for molecular data alone. The total‐evidence tree unambiguously optimizes trunk segmentation: a 23‐segmented trunk has a single origin in the blind clade. © The Willi Hennig Society 2011.     

Molecular phylogeny of Entomobrya (Collembola: Entomobryidae) from China: Color pattern groups and multiple origins

Highly diversified colorations among springtails (Collembola) have been widely used for species diagnosis, but their phylogenetic significance is poorly known. We addressed this issue in the largest Entomobryinae genus Entomobrya, which possesses variable color patterns among species. The relationships within the genus and to other genera have also rarely been studied. Based on material mainly from China, we have conducted a multilocus phylogeny and topology tests with likelihood and Bayesian algorithms, and accordingly demonstrated the non-monophyly of Chinese Entomobrya. The division of five clades, including Entomobrya and several related genera, coincided well with five types of colorations, respectively. Further analyses of divergence time and historical biogeography revealed that Chinese Entomobrya originated mainly from Palearctic (northern and western) China in the Paleocene and Eocene. This study highlights the great phylo? genetic values as well as taxonomic uses of coloration in Chinese Entomobrya. Multiple phylogenetic and biogeographic origins of Entomobrya imply its complicated relationships with both scaled and unsealed genera of Entomobryinae.     

Phylogenetic analysis of the genus Hexachlamys (Myrtaceae) based on plastid and nuclear DNA sequences and their taxonomic implications

Myrtaceae are one of the most species‐rich families of flowering plants in the Neotropics. They include several complex genera and species; Hexachlamys is one of the complex genera. It has not been recognized as a distinct genus and has been included in Eugenia, based on morphological grounds. Therefore, molecular systematic studies may be useful to understand and to help to solve these relationships. Here, we performed a molecular phylogenetic analysis using plastid and nuclear data in order to check the inclusion of Hexachlamys in Eugenia. Plastid (accD, rpoB, rpoC1, trnH‐psbA) and nuclear (ITS2) sequence data were analysed using Bayesian and maximum parsimony methods. The trees constructed using ITS2 and trnH‐psbA were the best able to resolve the relationships between species and genera, revealing the non‐monophyly of Hexachlamys. The molecular phylogenetic analyses were in agreement with previous morphological revisions that have included Hexachlamys in Eugenia. These results reinforce the importance of uniting knowledge and strategies to understand better issues of delimitation of genera and species in groups of plants with taxonomic problems. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 532–543.     

Ecological release in lizard assemblages of neotropical savannas

We compare lizard assemblages of Cerrado and Amazonian savannas to test the ecological release hypothesis, which predicts that niche dimensions and abundance should be greater in species inhabiting isolated habitat patches with low species richness (Amazonian savannas and isolated Cerrado patches) when compared with nonisolated areas in central Cerrado with greater species richness. We calculated microhabitat and diet niche breadths with data from 14 isolated Cerrado patches and Amazon savanna areas and six central Cerrado populations. Morphological data were compared using average Euclidean distances, and lizard abundance was estimated using the number of lizards captured in pitfall traps over an extended time period. We found no evidence of ecological release with respect to microhabitat use, suggesting that historical factors are better microhabitat predictors than ecological factors. However, data from individual stomachs indicate that ecological release occurs in these areas for one species (Tropidurus) but not others (Ameiva ameiva, Anolis, Cnemidophorus, and Micrablepharus), suggesting that evolutionary lineages respond differently to environmental pressures, with tropidurids being more affected by ecological factors than polychrotids, teiids, and gymnophthalmids. We found no evidence that ecological release occurs in these areas using morphological data. Based on abundance data, our results indicate that the ecological release (density compensation) hypothesis is not supported: lizard species are not more abundant in isolated areas than in nonisolated areas. The ecology of species is highly conservative, varying little from assemblage to assemblage. Nevertheless, increases in niche breadth for some species indicate that ecological release occurs as well. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Species concept and nomenclatural changes within the genera Elliptochloris and Pseudochlorella (Trebouxiophyceae) based on an integrative approach

The genera Elliptochloris and Pseudochlorella were erected for Chlorella‐like green algae producing two types of autospores and cell packages, respectively. Both genera are widely distributed in different soil habitats, either as free living or as photobionts of lichens. The species of these genera are often difficult to identify because of the high phenotypic plasticity and occasional lack of characteristic features. The taxonomic and nomenclatural status of these species, therefore, remains unclear. In this study, 34 strains were investigated using an integrative approach. Phylogenetic analyses demonstrated that the isolates belong to two independent lineages of the Trebouxiophyceae (Elliptochloris and Prasiola clades) and confirmed that the genera are not closely related. The comparison of morphology, molecular phylogeny, and analyses of secondary structures of SSU and ITS rDNA sequences revealed that all of the strains belong to three genera: Elliptochloris, Pseudochlorella, and Edaphochlorella. As a consequence of the taxonomic revisions, we propose two new combinations (Elliptochloris antarctica and Pseudochlorella signiensis) and validate Elliptochloris reniformis, which is invalidly described according to the International Code for Nomenclature (ICN), by designating a holotype. To reflect the high phenotypic plasticity of P. signiensis, two new varieties were described: P. signiensis var. magna and P. signiensis var. communis. Chlorella mirabilis was not closely related to any of these genera and was, therefore, transferred to the new genus Edaphochlorella. All of the taxonomic changes were highly supported by all phylogenetic analyses and were confirmed by the ITS‐2 Barcodes using the ITS‐2/CBC approach.     

Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification

Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty‐six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB‐rbcL and trnL‐F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum‐parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three‐colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well‐supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.     

An integrative approach to the evolution of shrimps of the genus Palaemon (Decapoda,Palaemonidae)

Shrimps of the genus Palaemon Weber, 1795 comprise of 86 species with a wide morphological and ecological variability along the tropical and temperate regions. Studies based on molecular data have indicated that despite a recent taxonomic rearrangement, it may remain not monophyletic. On the other hand, cladistic, morphological analyses have suggested the presence of synapomorphies, implying a natural status for the genus. In this work, a broad taxonomic and molecular sampling is applied to verify whether Palaemon is a monophyletic taxon and, based on the recovered phylogeny, identify geographical and morphological patterns related to the lineages. Partial sequences of 16S rRNA, histone H3 and 18S rRNA from 60 species of Palaemon and 15 species from other genera of Palaemonidae were analysed. In addition, previously used characters as well as novel diagnostic characters were scrutinized. The present phylogeny indicates that the species of Palaemon fall into three distinct lineages and that the colonization of America and Europe likely occurred multiple times. Morphological characters allow for the identification of at least four monophyletic groups in Palaemon; two of which are monospecific at the moment. Based on the present results, it may become necessary to establish two new genera (to accommodate Palaemon concinnus and Palaemon mercedae, respectively), as well as re‐erect the genus Alaocaris Holthuis, 1949 for Palaemon antrorum, potentially including a further six American species.     

Revisiting Ross and Sims (1971): toward a molecular phylogeny of the Biddulphiaceae and Eupodiscaceae (Bacillariophyceae)

The ocellate and pseudocellate diatoms in the Eupodiscaceae and Biddulphiaceae (respectively) are common inhabitants of the marine littoral (and plankton zone) with a rich fossil history making them important components of marine stratigraphic studies and good candidates for molecular dating work. These diatoms are important for un‐derstanding the phylogeny of the diatoms as a whole, as molecular phylogenies have blurred the traditional distinction between the pennate and multipolar non‐pennate diatoms. However, the convoluted taxonomic history of these groups has the potential to disrupt both stratigraphic and molecular dating studies. Although efforts have been made to examine frustule morphology of several ocellate and pseudocellate diatoms and develop a morphological scheme to define genera, very little work has been done to determine how these groups are interrelated. In this study, we use nuclear and chloroplast molecular markers to construct a phylogeny of a diverse sampling of Eupodiscaceae and Biddulphiaceae taxa. The ocellus‐bearing taxa (Eupodiscaceae) are monophyletic, and thus the ocellus may be a useful character in delimiting the Eupodiscaceae, the Biddulphiaceae are polyphyletic and scattered across a number of lineages of multipolar non‐pennate diatoms. Hypothesis testing aimed at assessing the likeliness of several morphology based hypotheses against the molecular data highlights uncertainty in both types of data. We present evidence that there are monophyletic genera within both the Biddulphiaceae and Eupodiscaceae, and recommend the taxa within the Odontella mobilensis/sinensis/regia clade be transferred to a new genus: Trieres Ashworth & Theriot.     

A reconsideration of Sphaerodactylus dommeli Böhme, 1984 (Squamata: Gekkota: Sphaerodactylidae), a Miocene lizard in amber

The Miocene gecko in amber, Sphaerodactylus dommeli, is one of the best‐preserved fossil gekkotan species; nonetheless, its identity has been questioned and it has been insinuated to be an iguanian referable to the mega‐diverse genus Anolis. In this paper, we provide digital X‐rays and new osteological evidence that include 11 characters that reaffirms its placement within the infraorder Gekkota and eight characters that specifically place this fossil within the species‐rich genus Sphaerodactylus, in which it was originally described. This contribution seeks to eliminate remaining scepticism about the generic allocation of this species, and to provide a reliable calibration point for ongoing research in squamate phylogenetics, especially for biogeographical studies and molecular dating inference. This contribution also reviews many diagnostic characters for the two genera in question, which is critical for the correct identification of amber‐embedded specimens representing the rich Hispaniolan lizard paleocommunity.     

Species delimitation of the white‐tailed rubythroat Calliope pectoralis complex (Aves,Muscicapidae) using an integrative taxonomic approach

Our knowledge of the systematics and taxonomy of Asian birds has improved much in the last two decades, and the number of recognised species has increased significantly as a result of in‐depth studies using an integrative taxonomic approach. The Sino‐Himalayan mountains harbor a high level of passerine diversity. Several allopatric or parapatric taxa that are currently treated as subspecies of polytypic species within that region are likely to deserve full species status, and thus their taxonomic status needs to be revisited. Based on analyses of multilocus data, vocalizations and morphology, we propose that the white‐tailed rubythroat Calliope pectoralis should be treated as two species, the Himalayan rubythroat C. pectoralis sensu stricto in the Tian Shan and Himalayan mountains, and the Chinese rubythroat C. tschebaiewi in the mountains of southwestern and north‐central China. According to our dating analyses based on mitochondrial loci, these two species diverged approximately 2.2 million yr ago. We further found that C. tschebaiewi was paraphyletic to C. pectoralis sensu stricto in nuclear data, which demonstrates a state of mitonuclear discordance that warrants further work. Our results suggest that geographic changes and glacial cycles in the Pleistocene may have caused allopatric divergence in the C. pectoralis complex. Our study stresses the importance of applying an integrative taxonomy approach to fully unravel the true avian diversity in the Sino‐Himalayan Mountains.     

THE EVOLUTIONARY HISTORY OF PARTHENOGENETIC CNEMIDOPHORUS LEMNISCATUS (SAURIA,TEIIDAE). I. EVIDENCE FOR A HYBRID ORIGIN

Chromosomes and allozymes were studied from chromosomally distinct unisexual (races B and C) and bisexual (races D and E) populations of the teiid lizard Cnemidophorus lemniscatus, and from selected outgroup taxa (C. murinus, C. nigricolor, Ameiva ameiva, and A. auberi). Karyotyping confirmed the racial identity of individuals and showed that the chromosomal composition of populations at specific localities has remained the same for 20 years. All individuals of both unisexual populations were heterozygous for a pericentric inversion that distinguishes D and E bisexuals. Also, the unisexuals were all heterozygous for 8 of 11 protein loci for which D and E were fixed or nearly fixed for different alleles. Most of these alleles represent derived states relative to the other Cnemidophorus and Ameiva analyzed, and the fixed heterozygote condition at these nine markers provides unequivocal support for the hypothesis that the unisexual C. lemniscatus arose by hybridization between ancestors genetically similar to extant D and E populations. At the remaining three loci for which D and E show fixed differences, the unisexuals were homozygous rather than heterozygous. This suggests that either (1) allozymes have been lost by mutations to null, silent, or convergent mobility states, (2) ancestral genotypes were similar to but not identical with the extant D and E races, and/or (3) limited recombination may occur between unisexual genomes. Allozyme-based genetic distances between D and E were large, suggesting that bisexual races D and E are genetically isolated; each race should be accorded full species status. This conclusion is supported by the absence of any clear biochemical evidence for their monophyly with respect to the other Cnemidophorus examined. Cladistic analyses of 17 phylogenetically informative loci revealed two equally parsimonious shortest trees, one supporting monophyly and the other paraphyly of the C. lemniscatus complex. Further testing of the monophyly of C. lemniscatus requires additional data. With the present study, the evidence that all parthenogenetic Cnemidophorus are of hybrid origin is complete.