Comparing alignment methods for inferring the history of the new world lizard genus Mabuya (Squamata: Scincidae)

The rapid increase in the ability to generate molecular data, and the focus on model-based methods for tree reconstruction have greatly advanced the use of phylogenetics in many fields. The recent flurry of new analytical techniques has focused almost solely on tree reconstruction, whereas alignment issues have received far less attention. In this paper, we use a diverse sampling of gene regions from lizards of the genus Mabuya to compare the impact, on phylogeny estimation, of new maximum likelihood alignment algorithms with more widely used methods. Sequences aligned under different optimality criteria are analyzed using partitioned Bayesian analysis with independent models and parameter settings for each gene region, and the most strongly supported phylogenetic hypothesis is then used to test the hypothesis of two colonizations of the New World by African scincid lizards. Our results show that the consistent use of model-based methods in both alignment and tree reconstruction leads to trees with more optimal likelihood scores than the use of independent criteria in alignment and tree reconstruction. We corroborate and extend earlier evidence for two independent colonizations of South America by scincid lizards. Relationships within South American Mabuya are found to be in need of taxonomic revision, specifically complexes under the names M. heathi, M. agilis, and M. bistriata (sensu, M.T. Rodrigues, Papeis Avulsos de Zoologia 41 (2000) 313).     

Discovery of a diploid population of theHemidactylus garnotii-vietnamensis complex (Reptilia: Gekkonidae)

A diploid member of the parthenogenetic gekkonid species complexHemidactylus garnotii-vietnamensis was discovered for the first time from Thailand. This gecko, seemingly unisexual and parthenogenetic, possesses 2n=2x=38 chromosomes, showing distinct heteromorphisms. The absence of bisexual congeneric species with a combination of karyomorphs to produce this karyotype indicates the occurrence of chromosomal rearrangements after the initial estabilishment of a diploid clonal lineage of hybrid origin. Results of karyotypic comparisons of the present sample and the three known triploid species belonging to theH. garnotii-vietnamensis complex suggest that a triploid karyomorph similar to that ofH. vietnamensis has first emerged through an insemination of the diploid parthenogen's egg by the sperm from a bisexual species having 44 chromosomes (all telocentric), and that the karyomorph subsequently experienced some minor chromosomal aberrations to produce the karyomorphs ofH. vietnamensis andH. garnotii. The origin of theH. stejnegeri karyotype still remains an open question for future studies.     

Chromosomal variability in the genus Primula (Primulaceae)

Chromosome numbers and measurements were recorded in 47 individuals of ten taxa of Primula , representing eight species and two subspecies from ten populations. The basic numbers of chromosomes were x  = 8, 9 or 11, and they were mostly metacentric, medium-long to medium-small, ranging in length from c . 3.6 µm to 1.6 µm. Diploid chromosome numbers of 2 n  = 2 x  = 24 and 22 were scored for the first time in P. loeseneri Kitag. and P. prenantha Balf. & Sm., respectively. A new ploidy level of 2 n  = 4 x  = 44 was found in P. burmanica Balf. & King. The recorded diploid numbers of the remaining species confirmed earlier reports. Interspecific variability in chromosome numbers was correlated with heterogeneity in their mean length. Comparison of the data with those in the literature revealed that the observed variability of chromosomal characters was compatible with the other taxonomic criteria and supports the current taxonomic delimitation. Chromosomal variation at the diploid level is the predominant feature in Primula evolution, and allopatric speciation has played a major role in its specific diversity. Subgen. Aleuritia could represent the main clade from which the other subgenera have evolved. The origin of the chromosome numbers, geographical distribution and evolution of the species were assessed, and the parallel polyphyletic mode of evolution in the genus was confirmed.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 211–219.     

A new phylogenetic classification for the gymnophthalmid genera Cercosaura , Pantodactylus and Prionodactylus (Reptilia: Squamata)

Because of the poor state of knowledge of many of the gymnophthalmid genera, systematic revision is necessary to render the classification consistent with evolutionary history. To that end, I conducted a review of the species of three genera of the Cercosaurinae which appear to form a monophyletic group: Cercosaura , Pantodactylus , and Prionodactylus . Phylogenetic analysis of 61 morphological characters was conducted after specimens of all species were examined to evaluate the composition of each taxon. The phylogenetic reconstruction suggested that the genus Prionodactylus was paraphyletic. A new phylogenetic classification is proposed that synonymizes Pantodactylus and Prionodactylus with Cercosaura. Cercosaura is redefined to include 11 species and seven subspecies. A key is provided to distinguish among species.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 137 , 101−115.     

Chromosomal variation and zoogeography inAteles

Karyotypes are reported from 21 spider monkeys distributed among five taxa of the genus Ateles.G- and C- banding techniques revealed variations between taxa. Two variants were discovered for chromosome 5, for chromosome 7, and for the Y chromosome. Four forms of chromosome 6 were seen. The variations are all probably pericentric inversions. One individual was heteromorphic at position 6. The data are compared with prebanding reports of Ateleschromosomes and reports of five animals studied with banding techniques. The variation in Ateleschromosomes is similar in degree to that found in other ceboid genera. The variants may be related to forest refugia formed during the Plio-Pleistocene. Karyotyping of many New World primates is required to ensure a homogeneous experimental group.     

Ribosomal gene variation in soybean (Glycine) and its relatives

Summary The genes encoding the 18S25S ribosomal RNA gene repeat in soybean (Glycine max) and its relatives in the genus Glycine are surveyed for variation in repeat length and restriction enzyme site locations. Within the wild species of subgenus Glycine, considerable differences in repeat size occur, with a maximum observed in G. falcata. Repeat length and site polymorphisms occur in several species, but within individual plants only single repeat types are observed. The rDNA of the cultivated soybean and its wild progenitor, G. soja are identical at the level of this study, and no variation is found in over 40 accessions of the two species. Data from rDNA mapping studies are congruent with those of previous biosystematic studies, and in some instances give evidence of divergences not seen with other approaches.     

Placental ontogeny of the Tasmanian scincid lizard, Niveoscincus ocellatus (Reptilia: Squamata)

A prominent scenario for the evolution of reptilian placentation infers that placentotrophy arose by gradual modification of a simple vascular chorioallantoic placenta to a complex structure with a specialized region for nutrient transfer. The structure of the chorioallantoic placenta of Niveoscincus ocellatus, apparently described originally from a single embryonic stage, was interpreted as a transitional evolutionary type that provided support for the model. Recently, N. ocellatus has been found to be as placentotrophic as species with complex chorioallantoic placentae containing a specialized region called a placentome. We studied placental development in N. ocellatus and confirmed that the chorioallantoic placenta lacks specializations found in species with a placentome. We also found that this species has a specialized omphaloplacenta. The chorioallantoic placenta is confined to the region adjacent to the embryo by a membrane, similar to that found in some other viviparous skinks, that divides the egg into embryonic and abembryonic hemispheres. We term this structure the "inter-omphalopleuric" membrane. The position of this membrane in N. ocellatus is closer to the embryonic pole of the egg than to the abembryonic pole and thus the surface area of the omphaloplacenta is greater than that of the chorioallantoic placenta. In addition, the omphaloplacenta is regionally diversified and more complex histologically than the chorioallantoic placenta. An impressive and unusual feature of the omphaloplacenta of N. ocellatus is the development of extensive overlapping folds in the embryonic component of mid-gestation embryos. The histological complexity and extensive folding of the omphaloplacenta make this a likely site of placental transfer of nutrients in this species.     

Molecular systematics of racers, whipsnakes and relatives (Reptilia: Colubridae) using mitochondrial and nuclear markers

Four protein-encoding mitochondrial genes (cytochrome b , NADH-dehydrogenase subunits 1, 2 and 4) and one nuclear (c-mos) gene were sequenced to infer phylogenetic relationships among Old and New World representatives of racers and whipsnakes, Coluber (sensu lato). New World Coluber ( Coluber sensu stricto, including Masticophis ) and Salvadora proved to have affinities with the Old World non-racer colubrine genus Ptyas (and possibly Elaphe s.l. and Coronella ), whereas Old World ' Coluber ' form several basally related clades; these are (1) Hemorrhois -( Spalerosophis-Platyceps ); (2) Hierophis , with Eirenis nested within this paraphyletic genus and (3) ' Coluber ' dorri as the sister taxon to Macroprotodon cucullatus . The position of ' Coluber ' zebrinus along with Hemerophis socotrae located at the base of the Old World racer radiation forming the possible sister group to all remaining Palearctic racers and whipsnakes remains less well supported. Nevertheless, inter- and subgeneric relationships among many of the Old World racer groups have been resolved.     

Isoenzyme variation in the wild relatives ofVicia faba (Fabaceae)

Electrophoretic analysis of five enzyme systems, LAP, PGI, SKDH, SOD and 6-PGDH, among 102Vicia accessions representingV. bithynica and seven species of theV. narbonensis complex, namelyV. eristalioides, V. kalakhensis, V. johannis, V. galilaea, V. serratifolia, V. narbonensis andV. hyaeniscyamus, has been performed. The recorded variation was tentatively assigned to 41 allelic genes at eight loci; intraspecific variation was observed in all species except forV. eristalioides. The results obtained were compared with the corresponding data reported earlier forV. faba. Hierarchical grouping of the investigated taxa, includingV. faba, was based onNei's genetic identities calculated from the allozyme frequency data.Vicia faba andV. bithynica were shown to be most distantly related to one another and to the remaining species investigated.Vicia serratifolia appeared to be a peripheral member of theV. narbonensis complex. The results are discussed with reference to genetic diversity and taxonomic relationships of the species under study.     

Phylogenetic taxonomy of the Cercosaurini (Squamata: Gymnophthalmidae), with new genera for species of Neusticurus and Proctoporus

The tribe Cercosaurini is one of the most poorly studied groups of the lizard family Gymnophthalmidae. Recent studies have suggested that two cercosauriine genera, Neusticurus and Proctoporus , are polyphyletic. The aim of the current study was to rectify the polyphyletic relationships and construct a phylogenetic taxonomy of the Cercosaurini that is congruent with evolutionary history. Neusticurus is divided into two genera, one of them new ( Potamites ), based on the clades recovered by molecular studies and previously discussed morphological data. Proctoporus is divided into three genera, one of which is new ( Petracola ), while an older name ( Riama ) is resurrected for another. All five genera are described and defined and taxonomic keys are presented. This study represents an important advance in rectifying the taxonomy of the Cercosaurini. Many other para- and polyphyletic genera remain in the Gymnophthalmidae and much future work on this group is warranted.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 405–416.     

Renal sexual segment of the Cottonmouth snake, Agkistrodon piscivorous (Reptilia, Squamata, Viperidae)

The seasonal variation of the renal sexual segment (RSS) of males of the Cottonmouth snake, Agkistrodon piscivorous, is described using light and electron microscopy. This study is the first to describe the ultrastructure of the RSS of a viper (Viperidae) and only the fourth on a snake. Renal sexual segments from males collected February to May and from August to November are similar in appearance. The cells are eosinophilic and react with periodic acid/Schiff procedure (PAS) for neutral carbohydrates and bromphenol blue (BB) for proteins. At the ultrastructure level, the cells contain large (2 microm diameter), electron-dense secretory granules and smaller vesicles with a diffuse material, and these structures abut against the luminal border and upon clear vacuoles continuous with intercellular canaliculi. Evidence was found for both apocrine and merocrine processes of product release. In June and July, the RSS are significantly smaller in diameter, largely basophilic, and have only scattered granules that are PAS+ and BB+. Cytologically, the RSS from June to July lack electron-dense secretory granules and the smaller vesicles with diffuse material. Numerous condensing vacuoles and abundant rough endoplasmic reticulum, however, indicate that active product synthesis is occurring. This is the first report of significant seasonal variation in the histology and ultrastructure of the RSS of a snake, although such reports exist for lizards. The seasons when the RSS is most highly hypertrophied correspond to the fall and spring mating seasons of A. piscivorous, as determined by other studies.     

Examining the utility of categorical models and alleviating artifacts in phylogenetic reconstruction of the Squamata (Reptilia)

Reconstruction artifacts are a serious hindrance to the elucidation of phylogenetic relationships and a number of methods have been devised to alleviate them. Previous studies have demonstrated a striking disparity in the evolutionary rates of the mitochondrial (mt) genomes of squamate reptiles (lizards, worm lizards and snakes) and the reconstruction artifacts that may arise from this. Here, to examine basal squamate relationships, we have added the mt genome of the blind skink Dibamus novaeguineae to the mitogenomic dataset and applied different models for resolving the squamate tree. Categorical models were found to be less susceptible to artifacts than were the commonly used noncategorical phylogenetic models GTR and mtREV. The application of different treatments to the data showed that the removal of the fastest evolving sites in snakes improved phylogenetic signal in the dataset. Basal divergences remained, nevertheless, poorly resolved. The proportion of both fast-evolving and conserved sites in the squamate mt genomes relative to sites with intermediate rates of evolution suggests rapid early divergences among squamate taxa and at least partly explains the short internal relative to external branches in the squamate tree. Thus, mt and nuclear trees may never reach full agreement because of the short branches characterizing these divergences.     

A new species of Thecadactylus from Sint Maarten, Lesser Antilles (Reptilia, Squamata, Gekkonidae)

We describe a new species of Thecadactylusfrom the Caribbean island of Sint Maarten. The new species differs from all other species in the genus by having a distinct dorsal pattern of numerous irregular but sharply deliminated black spots and blotches on an otherwise almost patternless background.     

Molecular systematics of the genus Allodontichthys (Cyprinodontiformes: Goodeidae)

Phylogenetic analyses of cytochrome c oxidasesubunit I (627bp) and mitochondrial controlregion (338bp aligned) sequences for all knownspecies of Allodontichthys wereperformed. Allodontichthys was recoveredas monophyletic, and A. hubbsi wassupported as the most primitive member of thegenus in all analyses. Combined-data analysessuggest that A. polylepis is sister to aclade comprising A. tamazulae and A. zonistius; however, a strict consensus of COIand control region cladograms results in acollapse of this node. The two species thatare broadly sympatric, A. hubbsi and A. tamazulae, are not sister taxa.Allodontichthys was found the sistergroup of a clade including Ilyodon andXenotaenia. These three genera are theonly goodeids to occupy high-gradient riversystems. Ilyodon and Allodontichthys share similar distributions;however, Allodontichthys exhibits greaterthan an order of magnitude more geneticvariation in COI than Ilyodon incomparisons of individuals from the samelocalities in the Ameca and Armeria drainagesystems. This is interpreted to mean Allodontichthys arrived in some westerndrainages significantly before Ilyodon.The Rio Coahuayana appears to be the center oforigin of the genus Allodontichthys. This river basin contains the most primitivemember of the genus, and appears to haveconnected with the Mesa Central, the center of endemism of the Goodeidae. A calibrated rateof molecular change in COI reveals Allodontichthys began diverging approximately6.2 million years ago (mya). Remainingspeciation in the group appears to haveoccurred about 2.7 to 3.3 mya. The hypothesisthat a hard polytomy comprising A. zonistius, A. polylepis, and A. tamazulae could be explained by speciation ofA. polylepis and A. tamazulae fromdifferent A. zonistius ancestors ispresented. Stream capture is evident but notfrequent in the history of Allodontichthys, and speciation does notclearly correlate with documented geologicactivity of the Mexican Transvolcanic Belt.     

Evidence for parallel ecological speciation in scincid lizards of the Eumeces skiltonianus species group (Squamata: Scincidae)

We identify instances of parallel morphological evolution in North American scincid lizards of the Eumeces skiltonianus species group and provide evidence that this system is consistent with a model of ecological speciation. The group consists of three putative species divided among two morphotypes, the small-bodied and striped E. skiltonianus and E. lagunensis versus the large-bodied and typically uniform-colored E. gilberti. Members of the group pass through markedly similar phenotypic stages during early development, but differ with respect to where terminal morphology occurs along the developmental sequence. The morphotypes also differ in habitat preference, with the large-bodied gilberti form generally inhabiting lower elevations and drier environments than the smaller, striped morphs. We inferred the phylogenetic relationships of 53 skiltonianus group populations using mtDNA sequence data from the ND4 protein-coding gene and three flanking tRNAs (900 bp total). Sampling encompassed nearly the entire geographic range of the group, and all currently recognized species and subspecies were included. Our results provide strong evidence for parallel origins of three clades characterized by the gilberti morphotype, two of which are nested within the more geographically widespread E. skiltonianus. Eumeces lagunensis was also nested among populations of E. skiltonianus. Comparative analyses using independent contrasts show that evolutionary changes in body size are correlated with differences in adult color pattern. The independently derived association of gilberti morphology with warm, arid environments suggests that phenotypic divergence is the result of adaptation to contrasting selection regimes. We provide evidence that body size was likely the target of natural selection, and that divergences in color pattern and mate recognition are probable secondary consequences of evolving large body size.     

Diversification of the arboreal mice of the genus Habromys (Rodentia: Cricetidae: Neotominae) in the Mesoamerican highlands

The arboreal mice of the genus Habromys (Rodentia: Cricetidae: Neotominae) are among the most poorly known Neotropical rodents. We investigated species-level phylogenetic relationships among the seven described Habromys species using 1331 aligned bases from the mitochondrial ND3 and ND4 regions. Sequences were obtained from 30 specimens of the seven known species of Habromys and we performed maximum parsimony, maximum likelihood, and Bayesian probabilities analyses. The monophyly of the genus Habromys within the Neotomines was verified. The northernmost H. simulatus is sister to the remaining species of the group; within the latter, the southernmost clade (Oaxaca to Central America) is sister to the Transmexican Volcanic Belt clade. Four major clades are clearly distinguished: H. simulatus from the Sierra Madre Oriental and the closely associated Sierra Mazateca; H. delicatulus and H. schmidlyi from the Transmexican Volcanic Belt; H. lepturus, H. chinanteco, and H. ixtlani from the northern Oaxacan highlands; and H. lophurus from Nuclear Central America. Within species, the analyses suggest that H. simulatus and H. lophurus are each composed by two different taxa.     

Renal sexual segment of the ground skink, Scincella laterale (Reptilia, Squamata, Scincidae)

Mature squamates possess hypertrophied regions of the distal urinary ducts, the renal sexual segment (RSS). The RSS is believed to provide seminal fluid that mixes with sperm and is released into the female cloaca during coitus. This study is the first to describe ultrastructure of the RSS in a lizard collected throughout the active season. The species examined, Scincella laterale, represents the largest family (Scincidae: 1,200 species) of lizards. Although sperm are present in the posterior ductus deferens of male S. laterale throughout the year, an annual spermatogenic cycle occurs that results in spermiation in spring, coinciding with maximum development of the RSS. Female S. laterale may possess stored sperm in vaginal crypts from March-May and large oviductal eggs April-June. Thus, the correlation between mating and RSS activity observed in other squamates is also found in S. laterale. Cytologically, the active RSS consists of columnar cells with numerous apical, electron-dense secretory vacuoles which are released by an apocrine process. The granules stain positively for proteins with bromphenol blue and react with PAS for neutral carbohydrates. After the mating season the RSS undergoes recrudescence and the electron-dense granules are replaced by a mucoid secretion that characterizes more proximal portions of the nephric tubules throughout the year. Little variation in ultrastructure of the RSS occurs between S. laterale and Cnemidophorus lemniscatus (Teiidae), the only other lizard in which seasonal variation of the RSS has been studied using similar methods. Females exhibit differentiation similar to that of males in the distal urinary tubules, but to a lesser degree. This is only the second such report for female squamates, and the differentiation of the region in females is proposed to result from adrenal androgens.