Egg shape and size allometry in geckos (Squamata: Gekkota), lizards with contrasting eggshell structure: why lay spherical eggs?

Hard, highly calcified eggshells evolved several independent times during the history of amniotes. Because of phylogenetic conservatism of this trait, lineages in which closely related taxa differ in eggshell structure are rare. Four gekkotan families (Carphodactylidae, Diplodactylidae, Eublepharidae and Pygopodidae) have eggs with soft shells, while their close relatives (Gekkonidae) lay eggs with hard shells. Geckos thus offer a rare opportunity to compare the impact of the emergence of a hard eggshell on the economy of egg architecture. Because a sphere has the smallest surface area of all three‐dimensional solids of a given volume, spherical eggs in geckos with hard eggshells reduce calcium investment and should therefore be advantageous. Here, we document that hard‐shelled gekkonid eggs are indeed more spherical than those of the other gecko lineages. However, within gekkonids, small species lay more elongated eggs than larger species. We speculate that miniature gekkonid females, which lay larger eggs relative to body size compared with large gekkonids, produce elongate eggs in order to pass the egg through a limited pelvic opening.     

The structure of the skull and jaw adductor musculature in the Gekkota, with comments on the phylogenetic relationships of the Xantusiidae (Reptilia: Lacertilia)

The skull and trigeminal jaw adductor musculature of the lizard families Gekkonidae, Pygopodidae and Xantusiidae are described. The external jaw adductor shows a different structure in the Gekkonidae and Pygopodidae than is observed in other lizards, approached only by the Xantusiidae and Feyliniidae. Paedomorphosis seems to be involved in the differentiation of the jaw adductor musculature in the Gekkonidae. The Gekkonidae and Pygopodidae may be hypothesized to form a monophyletic group, the Gekkota, on the basis of numerous synapomorphies. Within the Gekkota, the Pygopodidae are the sister-group of the Gekkonidae and retain some plesiomorphous features which are absent in the latter. The Xantusiidae share few synapomorphies with the Gekkota on the one hand, and some with scincomorph lizards on the other, especially with the Lacertidae.     

Interrelationships among gekkonid geckos inferred from mitochondrial and nuclear gene sequences

Gekkonid geckos, representing more than 85 percent of the gekkotan genera, are found on all major land masses and almost all oceanic islands in the tropics and subtropics. Intergeneric relationships of the Gekkonidae have been far more difficult to resolve than those among other gekkotan families. Our data set consists of a large number of complete mitochondrial 12S rRNA gene sequences and partial nuclear C-mos gene sequences for 33 genera of geckos, two genera of pygopods and two genera of eublepharids. Maximum parsimony (MP) and maximum likelihood (ML) trees were generated based on unweighted analysis using PAUP 4.0b10. Bayesian inference (BI) analyses trees were generated by MrBayes 3.0B4. All phylogenetic trees supported the monophyly of Gekkonidae with great confidence. The 12S data and combined data (12S and C-mos) place Sphaerodactylus deeply within gekkonine geckos, whereas Teratoscincus+Pristurus are the sister group of the remaining gekkonids. However, it is known that 12S may be positively misleading when dealing with older divergences. Therefore, the conflict between the results in this study and the latest conclusions based on C-mos points to the need for future focus on the phylogenetic position of both Sphaerodactylus and Teratoscincus.     

Molecular phylogenetic and dating analyses using mitochondrial DNA sequences of eyelid geckos (Squamata: Eublepharidae)

Mitochondrial DNA sequences of approximately 2.3 kbp including the complete NADH dehydrogenase subunit 2 gene and its flanking genes, as well as parts of 12S and 16S rRNA genes were determined from major species of the eyelid gecko family Eublepharidae sensu [Kluge, A.G. 1987. Cladistic relationships in the Gekkonoidea (Squamata, Sauria). Misc. Publ. Mus. Zool. Univ. Michigan 173, 1-54.]. In contrast to previous morphological studies, phylogenetic analyses based on these sequences supported that Eublepharidae and Gekkonidae form a sister group with Pygopodidae, raising the possibility of homoplasious character change in some key features of geckos, such as reduction of movable eyelids and innovation of climbing toe pads. The phylogenetic analyses also provided a well-resolved tree for relationships between the eublepharid species. The Bayesian estimation of divergence times without assuming the molecular clock suggested the Jurassic divergence of Eublepharidae from Gekkonidae and radiations of most eublepharid genera around the Cretaceous. These dating results appeared to be robust against some conditional changes for time estimation, such as gene regions used, taxon representation, and data partitioning. Taken together with geological evidence, these results support the vicariant divergence of Eublepharidae and Gekkonidae by the breakup of Pangea into Laurasia and Gondwanaland, and recent dispersal of two African eublepharid genera from Eurasia to Africa after these landmasses were connected in the Early Miocene.     

Molecular evidence for Gondwanan origins of multiple lineages within a diverse Australasian gecko radiation

Aim Gondwanan lineages are a prominent component of the Australian terrestrial biota. However, most squamate (lizard and snake) lineages in Australia appear to be derived from relatively recent dispersal from Asia (< 30 Ma) and in situ diversification, subsequent to the isolation of Australia from other Gondwanan landmasses. We test the hypothesis that the Australian radiation of diplodactyloid geckos (families Carphodactylidae, Diplodactylidae and Pygopodidae), in contrast to other endemic squamate groups, has a Gondwanan origin and comprises multiple lineages that originated before the separation of Australia from Antarctica. Location Australasia. Methods Bayesian (beast ) and penalized likelihood rate smoothing (PLRS) (r 8s ) molecular dating methods and two long nuclear DNA sequences (RAG‐1 and c‐mos) were used to estimate a timeframe for divergence events among 18 genera and 30 species of Australian diplodactyloids. Results At least five lineages of Australian diplodactyloid geckos are estimated to have originated > 34 Ma (pre‐Oligocene) and basal splits among the Australian diplodactyloids occurred c. 70 Ma. However, most extant generic and intergeneric diversity within diplodactyloid lineages appears to post‐date the late Oligocene (< 30 Ma). Main conclusions Basal divergences within the diplodactyloids significantly pre‐date the final break‐up of East Gondwana, indicating that the group is one of the most ancient extant endemic vertebrate radiations east of Wallace’s Line. At least five Australian lineages of diplodactyloid gecko are each as old or older than other well‐dated Australian squamate radiations (e.g. elapid snakes and agamids). The limbless Pygopodidae (morphologically the most aberrant living geckos) appears to have radiated before Australia was occupied by potential ecological analogues. However, in spite of the great age of the diplodactyloid radiation, most extant diversity appears to be of relatively recent origin, a pattern that is shared with other Australian squamate lineages.     

Intercontinental distribution of Plagiochila corrugata (Plagiochilaceae, Hepaticae) inferred from nrDNA ITS sequences and morphology

Plagiochila sect. Vagae is a large pantropical clade that is characterized morphologically by frequent terminal branching, vegetative distribution by propagules on the ventral surface of the leaves and a capsule wall with thickenings in all layers. Plagiochila corrugata from Brazil is characterized by strongly undulate, toothed leaf margins and represents the only known neotropical species of sect. Vagae with unispiral elaters. Plagiochila cambuena from Madagascar is distinguished by the same features. Maximum likelihood and parsimony analyses of 38 nrDNA ITS sequences of Plagiochila reveal P. corrugata and P. cambuena in a weakly (ML) to well (MP) supported monophyletic lineage within P.  sect.  Vagae . As an outcome of the morphological and molecular investigation, P. cambuena is relegated to the synonymy of P. corrugata. Plagiochila corrugata is placed in a Vagae -subclade with 11 further American species. The range of P. corrugata can be ascribed to long-range dispersal from the Neotropics rather than a Gondwanan distribution. Species from tropical Asia and Africa are placed at the base of the Vagae clade. Branch length within P.  sect.  Vagae points to a sudden radiation.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 146 , 469–481.     

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.     

Phylogenetic relationships of the north-eastern Atlantic and Mediterranean blenniids

The phylogenetic relationships of 27 north-eastern Atlantic and Mediterranean blennioids are analysed based on a total of 1001 bp from a combined fragment of the 12S and 16S mitochondrial rDNA. The most relevant results with implications in current blenniid taxonomy are: (1) Lipophrys pholis and Lipophrys (=  Paralipophrys ) trigloides are included in a well-supported clade that by the rule of precedence must be named Lipophrys ; (2) the sister species of this clade are not the remaining species of the genus Lipophrys but instead a monotypic genus comprising Coryphoblennius galerita ; (3) the smaller species of Lipophrys were recovered in another well-supported and independent clade, which we propose to be recognized as Microlipophrys ; (4) although some authors included the genera Salaria and Lipophrys in a single group we have never recovered such a relationship. Instead, Salaria is more closely related to the genera Scartella and Parablennius ; (5) the genus Parablennius , which was never recovered as a monophyletic clade, is very diverse and may include several distinct lineages; (6) the relative position of Aidablennius sphynx casts some doubts on the currently recognized relationships between the different blenniid tribes. Meristic, morphological, behavioural and ecological characters support our results and are also discussed. The possible roles of the tropical West African coast and the Mediterranean in the diversification of blenniids are discussed.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 86 , 283–295.     

Multiple levels of allopatric divergence in the endemic Philippine fruit bat Haplonycteris fischeri (Pteropodidae)

As part of a larger comparative phylogeographical study of Philippine fruit bats, I used fragments of the mitochondrial genes cytochrome  b and ND2 to investigate phylogeography and diversification in Haplonycteris fischeri , a pteropodid bat endemic to the Philippines but widespread within the archipelago. Genetic diversity in H. fischeri was extremely high in these commonly studied genes, with 101 unique haplotypes in 123 sequenced individuals, although small, continuously isolated islands had less diversity than had large island complexes. Seven monophyletic groups and one paraphyletic group were restricted to individual islands, groups of islands, or parts of islands. Each Pleistocene island complex had a single resident monophyletic lineage; these five groups were separated by approximately 6–8% sequence divergence and apparently have been diverging for 4–6 Myr. Within island groups, monophyletic lineages on some individual islands suggest that current ocean channels have also been barriers to gene flow; in some cases, multiple allopatric clades were present on single islands. Basal divergence dates were estimated to be in the early Pliocene, and most diversification was apparently connected to the ongoing geological evolution of the Philippines. Geological history and current geography interact with ecology to cause substantial genetic differentiation within this primary forest-specialist species.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 329–349.     

Cladistic analysis and a revised classification of fossil and recent mysticetes

A cladistic analysis that includes representatives of all recent genera of mysticetes and several fossil species that were previously referred to the family Cetotheriidae, with tooth-bearing mysticetes and an archaeocete as an outgroup, is presented here. The result of this analysis forms the base of a revised classification of Mysticeti. Cetotheriidae is redefined as a monophyletic family, which includes the genera Cetotherium , Piscobalaena , and a new subfamily Herpetocetinae, including Herpetocetus , Nannocetus , Metopocetus , and Cephalotropis . Eschrichtiidae is the closest sister taxon to Cetotheriidae. A few species are referred to Eomysticetoidea, whereas the remaining species that were previously referred to Cetotheriidae appear in four clades that branch off from the lineage leading to Balaenopteridae. These are a Mauicetus clade and three clades that are named as new families Aglaocetidae, Pelocetidae, and Diorocetidae.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 875–894.     

Speciation mirrors geomorphology and palaeoclimatic history in African laminate-toothed rats (Muridae: Otomyini) of the Otomys denti and Otomys lacustris species-complexes in the 'Montane Circle' of East Africa

We adopted an integrated systematic approach to delimit evolutionary species and describe phylogeographic, morphometric and ecological relationships in Otomys denti (from the Albertine Rift, Southern Rift in Malawi and the northern Eastern Arc Mountains) and Otomys lacustris (from the Southern Rift in Tanzania and Zambia, and the southern Eastern Arc Mountains). Molecular [cytochrome (cyt) b sequences, 1143 bp, N  = 18], craniometric (classical, N  = 100 and geometric, N  = 60) and ecological (Partial Least Squares regression of shape and ecogeographic variables) approaches show a profound, parallel disjunction between two groups: (1) Eastern Arc and Southern Rift (including the Malawi Rift) ( O. lacustris and Otomys denti sungae ) and (2) Albertine Rift ( Otomys denti denti and Otomys denti kempi ) taxa. Within both groups, cyt b sequences or craniometric analysis provided evidence for the differentiation of both southern and northern Eastern Arc from Southern Rift lineages (across the so-called Makambako Gap). Within the Albertine Rift ( denti – kempi ) lineage, populations from individual mountain ranges differed significantly in skull shape (but not size), but were similar genetically. Over-reliance in the past on very few morphological characters (e.g. number of molar laminae) and a polytypic species concept has obscured phylogenetic relationships and species discrimination in this group. We recognize at least three species in this group, and distinct lineages within two of these species. Each species or lineage was endemic to one of three regions: the Albertine Rift, the Malawi Rift or the Eastern Arc. Our result echo conclusions of recent studies of other mammalian and bird taxa and reflect the geomorphology and palaeoclimatic history of the region.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 913–941.     

On the monophyly of Dactylorhiza Necker ex Nevski (Orchidaceae): is Coeloglossum viride (L.) Hartman a Dactylorhiza?

Previous phylogenetic analyses of Orchidaceae subtribe Orchidinae resulted in the proposal to classify Coeloglossum viride (L.) Hartman within the genus Dactylorhiza in order to maintain its monophyly. In this paper, we report some results that contradict previous studies regarding the monophyly of the traditional Dactylorhiza and its phylogenetic relationship with Coeloglossum. Our results, which combine sequences of the internal and external transcribed spacers of the nuclear ribosomal DNA, support the monophyly of Dactylorhiza , with Coeloglossum being a sister clade. The position of C. viride in the phylogenetic tree, and the considerable morphological differences with respect to Dactylorhiza , incline us to retain both lineages as distinct genera.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 152 , 261–269.     

Pollen morphology of the Swertiinae (Gentianaceae): phylogenetic implications

Recent molecular surveys of the Swertiinae (Gentianaceae–Gentianeae) revealed unexpected phylogenetic relationships, including polyphyly of the genera Gentianella , Jaeschkea , Lomatogonium and Swertia . To find new non-molecular characters supporting the phylogeny, we examined the exine variation of 73 species of all major lineages of subtribe Swertiinae using environmental scanning electron miscroscopy supplementing older, mainly light microscopical, studies. In contrast to previous studies, we were able to pick out taxa from phylogenetic key positions with particular focus on Swertia . Many distantly related taxa such as parts of Frasera , Gentianopsis , Halenia , Gentianella , Megacodon and several lineages of Swertia share a striate–reticulate or reticulate exine pattern. This is interpreted as the plesiomorphic character state of Swertiinae. There is also considerable variation of derived patterns; for example, different types of microechinate or almost smooth pollen was repeatedly observed in distantly related groups. Another extreme was the ring-shaped reticulation found in a North American species of Gentianopsis . Unfortunately, major relationships as revealed by molecular analyses were rarely supported because of the abundance of the plesiomorphic type and homoplasy even on low taxonomic levels; for example, within Lomatogonium . Exine variation was particularly useful in characterizing independent lineages of Swertia . For example, according to pollen characters and in agreement with other data, the Asian Swertia cuneata is a sister group of a strongly diversified African lineage and Swertia yunnanensis , which is rather aberrant in flower morphology, seems close to parts of Lomatogonium .  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 323–341.     

Rapid diversification of mating systems in ciliates

Ciliates are a diverse group of microbial eukaryotes that exhibit tremendous variety in several aspects of their mating systems. To understand the evolutionary forces driving mating system diversification in ciliates, we use a comparative approach synthesizing data from many ciliate species in light of recent phylogenetic analyses. Specifically, we investigate the evolution of number of mating types, mode of mating type inheritance, and the molecular determinants of mating types across the taxonomic diversity of ciliates, with an emphasis on three well-studied genera: Tetrahymena , Paramecium , and Euplotes . We find that there have been many transitions in the number of mating types, and that the requirement of nuclear reorganization may be a more important factor than genetic exchange in determining the optimum number of mating types in a species. We also find that the molecular determinants of mating types and mode of inheritance are evolving under different constraints in different lineages of ciliates. Our results emphasize the need for further detailed examination of mating systems in understudied ciliate lineages.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 187–197.     

Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome <Emphasis Type="Italic">b</Emphasis> sequences

Complete mitochondrial cytochrome b sequences of 54 species, including 18 newly sequenced, were analyzed to infer the phylogenetic relationships within the family Cyprinidae in East Asia. Phylogenetic trees were generated using various tree-building methods, including Neighbor-joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods, with Myxocyprinus asiaticus (family Catostomidae) as the designated outgroup. The results from NJ and ML methods were mostly similar, supporting some existing subfamilies within Cyprinidae as monophyletic, such as Cultrinae, Xenocyprinae and Gobioninae (including Gobiobotinae). However, genera within the subfamily “Danioninae” did not form a monophyletic group. The subfamily Leuciscinae was divided into two unrelated groups: the “Leuciscinae” in East Asia forming as a monophyletic group together with Cultrinae and Xenocyprinae, while the Leuciscinae in Europe, Siberia, and North America as another monophyletic group. The monophyly of subfamily Cyprininae sensu Howes was supported by NJ and ML trees and is basal in the tree. The position of Acheilognathinae, a widely accepted monophyletic group represented by Rhodeus sericeus, was not resolved.     

Python phylogenetics: inference from morphology and mitochondrial DNA

We used nucleotide sequences from four mitochondrial genes and structural features of the mitochondrial control region, combined with a revised, previously published, morphological data set to infer phylogenetic relationships among the pythons. We aimed to determine which of two competing hypotheses of relationships of the genera Aspidites and Python best explains the evolutionary and bioegeographical history of the family. All analyses of the combined data recover a set of relationships in which (1) the genus Python is paraphyletic with the two east Asian species, P. reticulatus and P. timoriensis , as the sister lineage to the seven Australo-Papuan python genera. We support recognition of a distinct genus for the P. reticulatus  +  P. timoriensis clade; (2) the remaining species of the genus Python form a clade which is the sister lineage to the remainder of the family; (3) the genus Aspidites is embedded among the Australo-Papuan genera. The seemingly primitive characteristics of Aspidites may be better interpreted as reversals or specializations that have accompanied a switch to burrowing in this genus. Resolution of the relationships among the Australo-Papuan lineages is weak, possibly because of rapid diversification early in the history of the radiation. We assessed the tempo of the Indo-Australian python radiation using a maximum likelihood framework based on the birth–death process. We find strong support for elevated speciation rates during the period when Australia collided with the proto-Indonesian archipelago. The data support an origin for pythons outside Australia, followed by a radiation into Australia during the mid-Tertiary.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 603–619.     

Karyotype Reorganization in the Hokou Gecko (Gekko hokouensis,Gekkonidae): The Process of Microchromosome Disappearance in Gekkota

The Hokou gecko (Gekko hokouensis: Gekkonidae, Gekkota, Squamata) has the chromosome number 2n = 38, with no microchromosomes. For molecular cytogenetic characterization of the gekkotan karyotype, we constructed a cytogenetic map for G. hokouensis, which retains the ancestral karyotype of Gekkota, with 86 functional genes, and compared it with cytogenetic maps for four Toxicofera species that have many microchromosomes (Elaphe quadrivirgata, Varanus salvator macromaculatus, Leiolepis reevesii rubritaeniata, and Anolis carolinensis) and that for a lacertid species (Lacerta agilis) with only one pair of autosomal microchromosomes. Ten pairs of G. hokouensis chromosomes [GHO1, 2, 3, Z(4), 6, 7, 8, 13, 14, and 15] showed highly conserved linkage homology with macrochromosomes and/or macrochromosome arms of the four Toxicofera species and corresponded to eight L. agilis macrochromosomes (LAG). However, GHO5, GHO9, GHO10, GHO11, and LAG6 were composed of chromosome segments that have a homology with Toxicofera microchromosomes, and no homology was found in the chromosomes between G. hokouensis and L. agilis. These results suggest that repeated fusions of microchromosomes may have occurred independently in each lineage of Gekkota and Lacertidae, leading to the disappearance of microchromosomes and appearance of small-sized macrochromosomes.