Data partitions and complex models in Bayesian analysis: the phylogeny of Gymnophthalmid lizards

Phylogenetic studies incorporating multiple loci, and multiple genomes, are becoming increasingly common. Coincident with this trend in genetic sampling, model-based likelihood techniques including Bayesian phylogenetic methods continue to gain popularity. Few studies, however, have examined model fit and sensitivity to such potentially heterogeneous data partitions within combined data analyses using empirical data. Here we investigate the relative model fit and sensitivity of Bayesian phylogenetic methods when alternative site-specific partitions of among-site rate variation (with and without autocorrelated rates) are considered. Our primary goal in choosing a best-fit model was to employ the simplest model that was a good fit to the data while optimizing topology and/or Bayesian posterior probabilities. Thus, we were not interested in complex models that did not practically affect our interpretation of the topology under study. We applied these alternative models to a four-gene data set including one protein-coding nuclear gene (c-mos), one protein-coding mitochondrial gene (ND4), and two mitochondrial rRNA genes (12S and 16S) for the diverse yet poorly known lizard family Gymnophthalmidae. Our results suggest that the best-fit model partitioned among-site rate variation separately among the c-mos, ND4, and 12S + 16S gene regions. We found this model yielded identical topologies to those from analyses based on the GTR+I+G model, but significantly changed posterior probability estimates of clade support. This partitioned model also produced more precise (less variable) estimates of posterior probabilities across generations of long Bayesian runs, compared to runs employing a GTR+I+G model estimated for the combined data. We use this three-way gamma partitioning in Bayesian analyses to reconstruct a robust phylogenetic hypothesis for the relationships of genera within the lizard family Gymnophthalmidae. We then reevaluate the higher-level taxonomic arrangement of the Gymnophthalmidae. Based on our findings, we discuss the utility of nontraditional parameters for modeling among-site rate variation and the implications and future directions for complex model building and testing.     

The phylogeny of varanoid lizards and the affinities of snakes

Evidence that platynotan squamates (living varanoid lizards, snakes and their fossil relatives) are monophyletic is presented. Evolutionary relationships within this group are then ascertained through a cladistic analysis of 144 osteological characters. Mosasauroids (aigialosaurs and mosasaurs), a group of large marine lizards, are identified as the nearest relatives of snakes, thus resolving the long-standing problem of snake affinities. The mosasauroid–snake clade (Pythonomorpha) is corroborated by 40 derived characters, including recumbent replacement teeth, thecodonty, four or fewer premaxillary teeth, supratemporal–prootic contact, free mandibular tips, crista circumfenestralis, straight vertical splenio-angular joint, loss of posterior ramus of the coronoid, reduced basipterygoid processes, reduced interpterygoid vacuity, zygosphene–zygantral articulations, and absence of epiphyses on the axial skeleton and skull. After mosasauroids, the next closest relatives of snakes are varanids (Varanus, Saniwa and Saniwides) and lanthanotids (Lanthanotus and Cherminotus). Derived features uniting varanids and lanthanotids include nine cervical vertebrae and three or fewer pairs of sternal ribs. The varanid–lanthanotid–pythonomorph clade, here termed Thecoglossa, is supported by features such as the anteriorly positioned basal tubera, and the loss of the second epibranchial. Successive outgroups to thecoglossans are Telmasaurus, an unresolved polytomy (Estesia, Gobidermatidae and Helodermatidae), Paravaranus and Proplatynota. The ''necrosaurs'' are demonstrated to be an artificial (polyphyletic) assemblage of primitive platynotans that are not particularly closely related to each other.Snakes are presumed to have evolved from small, limbless, burrowing lizards and the inability of previous analyses to resolve the affinities of snakes has been attributed to extensive convergence among the numerous lineages of such lizards. The present study contradicts this claim, demonstrating that the problem is due instead to omission of critical fossil taxa. No modern phylogenetic analysis of squamate relationships has simultaneously included both mosasauroids and snakes: previous studies have therefore failed to identify the mosasauroid–snake association and the suite of derived characters supporting it. Mosasauroids are large aquatic animals with well-developed appendages, and none of the derived characters uniting mosasauroids and snakes is obviously correlated with miniaturization, limb reduction or fossoriality. Recognition that mosasauroids, followed by varanids and lanthanotids, are the nearest relatives of snakes will also facilitate studies of relationships within snakes, which until now have been hampered by uncertainty over the most appropriate (closely-related) lizard outgroups.     

Xantusiid "night" lizards: a puzzling phylogenetic problem revisited using likelihood-based Bayesian methods on mtDNA sequences

Contentious issues in Night Lizard (Xantusiidae) evolution are revisited using Maximum Likelihood-based Bayesian methods and compared with results from Neighbor-Joining and Maximum Parsimony analyses. Fragments of three mitochondrial genes, the 12S and 16S ribosomal genes, and the cytochrome b gene, are sampled across an ingroup composed of seven xantusiid species and a 12-species outgroup chosen to bracket ancestral states for six additional clades of scleroglossan lizards. Our phylogenetic analyses afford robust support for the following conclusions: Xantusiidae is part of Scincomorpha, rather than being allied with Gekkota; Lepidophyma is sister to Xantusia, rather than to Cricosaura; Xantusia riversiana is imbedded within, rather than being sister to, other Xantusia species; and rock-morph Xantusia are not closely related to one another. Convergence related to retarded rates of growth and development, or to physical constraints imposed by living in rock crevices, may be responsible for much of the character discordance underlying conflicts in xantusiid phylogeny. Fossil-calibrated Maximum Likelihood-based divergence time estimates suggest that although the xantusiid stem may have originated in the Mesozoic, the crown clade is exclusively Tertiary in age. Thus, the clade including extant Cricosaura does not appear to have been extant during the K-T boundary bolide impact, as has been suggested. Moreover, our divergence-time estimates indicate that the xantusiid island endemics, Cricosaura typica on Cuba and Xantusia riversiana on the California Channel Islands, arrived via dispersal rather than vicariance, as previously proposed.     

Lygosomine phylogeny and the origins of Australian scincid lizards

Aim Australian scincid lizards represent three distinct groups within the cosmopolitan clade Lygosominae, the Egernia, Eugongylus and Sphenomorphus groups. This paper presents a time‐calibrated phylogeny for Lygosominae that provides the necessary temporal framework for assessing the contributions of immigration from Asia and of Gondwanan inheritance in the derivation of the Australian scincid fauna. Location Australasia, Asia, Africa. Methods Phylogenetic relationships and divergence times were inferred from novel BDNF, c‐mos and PTPN12 sequences (2408 aligned sites). Results Lygosomine monophyly is well supported, and there is strong support for monophyly of the Egernia, Eugongylus and Sphenomorphus groups. A sister‐group relationship of Tribolonotus (distributed in Melanesia and the Papuan Region) and the Egernia group is strongly supported in both Bayesian and maximum likelihood analyses. Australian representatives of the Sphenomorphus group compose a significantly supported clade estimated to have originated c. 25 Ma. An age of c. 18 Ma is inferred for a strongly supported clade comprising Australian representatives of the Egernia group; this clade diverged from Corucia zebrata (confined to the Solomon Islands) c. 25 Ma and from Tribolonotus c. 54 Ma. A well‐supported clade including all Australian Eugongylus group taxa sampled is estimated to have arisen c. 20 Ma. Main conclusions The Australian Sphenomorphus group is nested within the more inclusive Sphenomorphus group (distributed primarily in Asia and Australasia), suggesting comparatively recent descent from a colonizing Asian ancestor; the divergence times inferred here indicate that colonization occurred during the mid Cenozoic, subsequent to the rifting of Australia from Antarctica. An Oligocene origin of the extant Eugongylus group fauna of Australasia (the basal members of which are distributed in the Southwest Pacific) indicates that Eugongylus group lygosomines also dispersed to Australia relatively recently. The Egernia group diverged from Tribolonotus in the Early Eocene; however, extant Egernia group lygosomines originated only during the Late Oligocene, implying extensive pruning of stem taxa (i.e. extinction). As a result, inferences of the timing of dispersal into Australia are associated with substantial uncertainty, although independent palaeontological evidence suggests that the Egernia group entered Australia prior to the Oligocene, immediately after (or perhaps before) the separation of Australia and Antarctica.     

The phylogeny of the subgroups within the melanogaster species group: likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny

The relationships among the majority of the subgroups in the Drosophila melanogaster species group remain unresolved. We present a 2223basepair dataset for mitochondrial cytochrome oxidase I and cytochrome oxidase II for 43 species (including new data from 11 species), sampled to include the major subgroups. After a brief review of competing hypotheses for the ananassae, montium, suzukii, and takahashii subgroups, we combine the two genes based on a new use of the SH test and present KH and SH likelihood comparisons (Kishino and Hasegawa, 1989. J. Mol. Evol. 29, 170-179; Shimodaira and Hasegawa, 1999) to test the monophyly and placement of these subgroups within the larger species group. Although we find insignificant differences between the two suggested placements for the ananassae subgroup, the ananassae is sister to the rest of the subgroups in the melanogaster species group in every investigation. For the takahashii subgroup, although we cannot reject monophyly, the species are so closely related to the suzukii subgroup for these data that the two subgroups often form one clade. Finally, we present a Bayesian estimate of the phylogeny for both genes combined, utilizing a recently published method that allows for different models of evolution for different sites.     

Shifting sands and shifty lizards: molecular phylogeny and biogeography of African flat lizards (Platysaurus)

The African flat lizard genus Platysaurus is widely distributed on rock outcrops in southern Africa and is found both east and west of the Kalahari Desert and between major river drainage systems. We assembled a molecular phylogeny for the genus in order to test several biogeographic hypotheses. Sequence data were obtained from 29 specimens representing 14 taxa of Platysaurus that span the geographic range of the genus. We targeted a fragment of the mitochondrial genome comprising the 3' half of the ND4 gene and most of the flanking tRNA-HSL cluster. The edited alignment comprised 864 characters, of which 479 (55%) were variable and 461 (96%) parsimony informative. Overall, the phylogeny was well resolved and supported by high bootstrap values. Four major clades were identified comprising two to seven species: P. mitchelli and P. maculatus maculatus from the north-eastern range of the genus; P. broadleyi and P. capensis from the western range; P. imperator, P. torquatus, and P. intermedius rhodesianus; P. i. intermedius, P. monotropis, P. minor, P. i. nigrescens, P. lebomboensis, P. i. wilhelmi, and P. o. orientalis. Platysaurus has been suggested to represent a recent adaptive radiation where rapid speciation was fuelled by population fragmentation brought on by vicariant events and possibly divergent sexual selection. The traditional explanation for the radiation of the genus is that the eastern migration of the Kalahari sands fragmented populations in the Plio-Pleistocene, resulting in conditions favorable for speciation. Our genetic data strongly suggests that many of the speciation events in Platysaurus already had occurred prior to the Plio-Pleistocene. Moreover, vicariant events associated with the formation of the major river systems played an additional role in the evolution and distribution of Platysaurus species. Our topology displays long internodes and long terminal branches, suggesting that the radiation is much older than previously believed.     

Parthenogenetic activation of mouse oocytes by strontium chloride: a search for the best conditions

Strontium has been successfully used to induce activation of mouse oocytes in nuclear transfer and other experiments, but the optimum treatment conditions have not been studied systematically. When cumulus-free oocytes were treated with 10mM SrCl(2) for 0.5-5h, activation rates (88.4+/-4.1 to 91.2+/-2.7%) did not differ (mean+/-S.E.; P>0.2), but rate of blastulation (57.3+/-3.5%) and cell number per blastocyst (45.0+/-2.4) were the highest after treatment for 2.5h. When treated with 1-20mM SrCl(2) for 2.5h, the activation rate and cell number per blastocyst were higher (P<0.02) after 10mM SrCl(2) treatment than other treatments. The best activation and development were obtained with Ca(2+)-free Sr(2+) medium, but the activation rate was low (37.7+/-1.6%) in Ca(2+)-containing medium. Activation rates were the same, regardless of the presence or absence of cytochalasin B (CB) in the activating medium, but the blastulation rate was higher (P<0.001) in the presence of CB. Only 70% of the cumulus-enclosed oocytes were activated and 10% blastulated after a 10 min exposure to 1.6mM SrCl(2), and many lysed, with increased intensity of Sr(2+) treatment. The presence of CB in SrCl(2) medium markedly reduced lysis of cumulus-enclosed oocytes. Media M16 and CZB did not differ when used as activating media. Only 10.5% of the oocytes collected 13 h post hCG were activated by Sr(2+) treatment alone, with 34% blastulating, but rates of activation and blastulation increased (P<0.001) to 94 and 60%, respectively, when they were further treated with 6-dimethylaminopurine (6-DMAP). The total and ICM cell numbers were less (P<0.001) in parthenotes than in the in vivo fertilized embryos. In conclusion, the concentration and duration of SrCl(2) treatment and the presence or absence of CB in activating medium and cumulus cells had marked effects on mouse oocyte activation and development. To obtain the best activation and development, cumulus-free oocytes collected 18 h post hCG should be treated for 2.5h with 10mM SrCl(2) in Ca(2+)-free medium supplemented with 5 microg/mL of CB.     

Evolution of a centromeric satellite DNA and phylogeny of lacertid lizards.

1. The composition and phyletic distribution of a highly repetitive satellite DNA, isolated from Podarcis sicula, was studied. 2. This DNA was rich in adenine and thymine and displayed frequent adenine stretches. It was always located on the centromeric heterochromatin even in quite taxonomically distant species. 3. Southern blot hybridization of the Taq I satellite on various species of lacertid families showed a close affinity among Podarcis, Algyroides and Lacerta dugesii. 4. All the other taxa investigated did not seem to possess this repeated sequence.     

Hitch-hiking: a parallel heuristic search strategy, applied to the phylogeny problem.

The article introduces a parallel heuristic search strategy ("Hitch-hiking") which can be used in conjunction with other random-walk heuristic search strategies. It is applied to an artificial phylogeny problem, in which character sequences are evolved using pseudo-random numbers from a hypothetical ancestral sequence. The objective function to be minimized is the minimum number of character-state changes required on a binary tree that could account for the sequences observed at the tips (leaves) of the tree -- the Maximum Parsimony criterion. The Hitch-hiking strategy is shown to be useful in that it is robust and that on average the solutions found using the strategy are better than those found without. Also the strategy can dynamically provide information on the characteristics of the landscape of the problem. I argue that Hitch-hiking as a scheme for parallelization of existing heuristic search strategies is of potentially very general use, in many areas of combinatorial optimization.     

Learning foraging thresholds for lizards: an analysis of a simple learning algorithm

This paper gives proof of convergence for a learning algorithm that describes how anoles (lizards found in the Caribbean) learn foraging threshold distance. An anole will pursue a prey if and only if it is within this threshold of the anole's perch. The learning algorithm was proposed by Roughgarden and his colleagues. They experimentally determined that this algorithm quickly converges to the foraging threshold that is predicted by optimal foraging theory. We provide analytic confirmation that the optimal foraging behavior as predicted by Roughgarden's model can be attained by a lizard that follows this simple and zoologically plausible rule of thumb. Copyright 1999 Academic Press.     

Molecular phylogeny of the scincid lizards of New Caledonia and adjacent areas: evidence for a single origin of the endemic skinks of Tasmantis

We use approximately 1900bp of mitochondrial (ND2) and nuclear (c-mos and Rag-1) DNA sequence data to recover phylogenetic relationships among 58 species and 26 genera of Eugongylus group scincid lizards from New Caledonia, Lord Howe Island, New Zealand, Australia and New Guinea. Taxon sampling for New Caledonian forms was nearly complete. We find that the endemic skink genera occurring on New Caledonia, New Zealand and Lord Howe Island, which make up the Gondwanan continental block Tasmantis, form a monophyletic group. Within this group New Zealand and New Zealand+Lord Howe Island form monophyletic clades. These clades are nested within the radiation of skinks in New Caledonia. All of the New Caledonian genera are monophyletic, except Lioscincus. The Australian and New Guinean species form a largely unresolved polytomy with the Tasmantis clade. New Caledonian representatives of the more widespread genera Emoia and Cryptoblepharus are more closely related to the non-Tasmantis taxa than to the endemic New Caledonian genera. Using ND2 sequences and the calibration estimated for the agamid Laudakia, we estimate that the diversification of the Tasmantis lineage began at least 12.7 million years ago. However, using combined ND2 and c-mos data and the calibration estimated for pygopod lizards suggests the lineage is 35.4-40.74 million years old. Our results support the hypothesis that skinks colonized Tasmantis by over-water dispersal initially to New Caledonia, then to Lord Howe Island, and finally to New Zealand.     

The phylogeny of the hominoid primates: a statistical analysis of the DNA-DNA hybridization data

Sibley and Ahlquist compared the single-copy nuclear DNA sequences of the hominoid primates using DNA-DNA hybridization. From this data set they estimated a phylogeny that clusters man and chimpanzees using a distance Wagner procedure. However, no assessment of statistical confidence in this estimated phylogeny was made, despite the fact that their data set contains internal inconsistencies concerning the correct branching order. This paper presents a modification of Pielou's Q- statistic that allows one to make nonparametric tests of phylogenetic relationship from distance data. The results of this analysis indicate that the estimated phylogeny of Sibley and Ahlquist is without statistical significance owing to the internal inconsistencies of the data set. A survey and additional analyses of other types of molecular data indicate that the phylogeny that clusters chimpanzees and gorillas and has the human lineage splitting off earlier is statistically consistent with all the molecular data (including the DNA-DNA hybridization data), whereas the phylogeny estimated by Sibley and Ahlquist can be rejected at the 5% level using the data on restriction- endonuclease sites in the mitochondrial genome.      

Saltatory search: a theoretical analysis

Many animal search in a saltatory fashion: they move forward,pause briefly, and move forward again. Although many optimal-foragingmodels have been developed, most do not address how an animalsearches for food. We view search strategies as "time-distance"functions to allow not only for the possibility of oscillationsin body speed, as implied by saltatory search, but other movementpatterns as well, including cruise search. The key feature ofour models is distinguishing between the body position and thescan position (where the forager is looking). We see the varyingmovement of saltatory search as a consequence of the curvaturein the functions that relate body speed to benefits (Jensen'sinequality)     

In search of the best correlates for local organismal biodiversity in cultivated areas

Based on a transect consisting of 19 identical trap stations in cultivated areas and seminatural habitats, the correlation of species numbers of higher taxonomic groups with total species numbers of flowering plants and arthropods per trap site was calculated. A total of 191214 invertebrate specimens and 2221 species of plants and animals were analysed. Considering the value of the correlation coefficient R2 as well as the effort for sorting and identification, a top twenty list of indicator groups favours Heteroptera, flowering plants, Symphyta and aculeate Hymenoptera as the best choice for biodiversity evaluation. In general, flight traps rated better than pitfall traps. In most taxonomic groups, diversity indices such as the Shannon and the Simpson index were only weakly correlated with local species diversity.     

Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial data,and a revised phylogeny for Sceloporus

Phrynosomatid lizards are among the most common and diverse groups of reptiles in western North America, Mexico, and Central America. Phrynosomatidae includes 136 species in 10 genera. Phrynosomatids are used as model systems in many research programs in evolution and ecology, and much of this research has been undertaken in a comparative phylogenetic framework. However, relationships among many phrynosomatid genera are poorly supported and in conflict between recent studies. Further, previous studies based on mitochondrial DNA sequences suggested that the most species-rich genus (Sceloporus) is possibly paraphyletic with respect to as many as four other genera (Petrosaurus, Sator, Urosaurus, and Uta). Here, we collect new sequence data from five nuclear genes and combine them with published data from one additional nuclear gene and five mitochondrial gene regions. We compare trees from nuclear and mitochondrial data from 37 phrynosomatid taxa, including a “species tree” (from BEST) for the nuclear data. We also present a phylogeny for 122 phrynosomatid species based on maximum likelihood analysis of the combined data, which provides a strongly-supported hypothesis for relationships among most phrynosomatid genera and includes most phrynosomatid species. Our results strongly support the monophyly of Sceloporus (including Sator) and many of the relationships within it. We present a new classification for phrynosomatid lizards and the genus Sceloporus, and offer a new tree with branch lengths for use in comparative studies.     

Ontogeny and phylogeny in temnospondyls: a new method of analysis

A new method has been devised to compare the ontogeny and phylogeny of some of the better documented tetrapods from the Stephanian to the Trias. This approach is based on global parsimony analysis of several temnospondyl amphibians, in which some ontogenetic sequences have been highlighted. Forty-one homologous morphoanatomical character states have been separated into larval, juvenile and adult stages of each of six tetrapod species. The taxonomic congruence (TC) approach involves comparing trees based on larval, juvenile and adult character states. These so-called 'ontotrees' are not congruent, either in their topologies or in the distribution of the character states. The total evidence (TE) approach involves a combined analysis of all the character states observed in the various growth stages of the taxa, and is secondarily used in order to test this taxonomic incongruence. In this case, the TE result corroborates the TC analysis: the TE tree is robust and reveals a few homoplasies which cause the taxonomic incongruence. This is interpreted as either the result of heterochronic events in temnospondyl evolution, or as the product of inaccurate identification of larval and metamorphic fossil forms.     

Toward the phylogeny of Caucasian rock lizards: implications from mitochondrial DNA gene sequences (Reptilia: Lacertidae)

A maximum parsimony phylogeny of 14 Caucasian species of rock lizards, genus Ijicerta , subgenus Archaeolacerta , was constructed from mitochondrial cytochrome b and ATPase 6 partial gene sequences. Congruence analyses were carried out between the two genes. A synthesis of the data sets reveals three well supported monophyletic groups: (1) the caucasica group including ( Lacerta derjugini (( Lalpina, L. clarkorum ) ( L. caucasica, L. daghestanica ))); (2) the rudis group including ( L. parvula ( L. portschinskii ( L. vakntini, L. rudis ))); and (3) the saxicola group including ( L. mixta ( L. nairensis ( L. saxicola, L. raddeijj ). Despite the diagnosis of three groups, the placement of L. praticola as a basal taxon is uncertain, as are the relationships among the three groups. The mitochondrial DNA sequence data suggested prior hybridization between L. mixta and L. alpina and possibly between L. saxicola and L. nairensis. Lacerta raddei was resolved as a paraphyletic species on the mtDNA tree; this may result from either hybridization or random gene sorting.