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R S Thorpe

Publications and source records attributed to R S Thorpe.

At least 19 recordsLinked to original sources
PubMed2006

Evidence for a Müllerian mimetic radiation in Asian pitvipers.

Müllerian mimicry, in which toxic species gain mutual protection from shared warning signals, is poorly understood in vertebrates, reflecting a paucity of examples. Indirect evidence for mimicry is found if monophyletic species or clades show parallel geographic variation in warning patterns. Here, we evaluate a hypothesis of Müllerian mimicry for the pitvipers in Southeast Asia using a phylogeny derived from DNA sequences from four combined mitochondrial regions. Mantel matrix correlation tests show that conspicuous red colour pattern elements are significantly associated with sympatric and parapatric populations in four genera. To our knowledge, this represents the first evidence of a Müllerian mimetic radiation in vipers. The putative mimetic patterns are rarely found in females. This appears paradoxical in light of the Müllerian prediction of monomorphism, but may be explained by divergent selection pressures on the sexes, which have different behaviours. We suggest that biased predation on active males causes selection for protective warning coloration, whereas crypsis is favoured in relatively sedentary females.

Animals↗
PubMed2005

Molecular clocks and geological dates: cytochrome b of Anolis extremus substantially contradicts dating of Barbados emergence.

Even though molecular clocks vary in rate to some extent, they are widely used and very important in a range of evolutionary studies, not least in interpreting cause and colonization in phylogeography. Evolutionists may use island age and emergence to give the earliest possible date for colonization by a species and hence give the lower limit in a molecular clock calibration. The geology of the Lesser Antilles is well studied and Barbados, although composed of some ancient rocks, is thought to have emerged only about 1 million years ago (Ma). The cytochrome b mitochondrial gene is the most widely used gene in vertebrate phylogeography, and generally evolves at a rate of 1-2% per million years (Myr) for poikilothermic vertebrates. Divergence measured across almost all of this gene in the endemic anole (Anolis extremus) reveals a mean patristic distance of approximately 8.3% between this clade and its sister, together with distinct divergence and phylogeographical structure within Barbados. The divergence time, estimated by a range of procedures using four calibration points, is not in the least compatible with the proposed geological time of emergence of Barbados. Hence, either the molecular clock rate does not apply to the Barbadian anole population, or the geological dating of the emergence of Barbados is erroneous. The compatibility of geological times and molecular divergence of this complex on Martinique, together with relative rates tests comparing the rates on Barbados and Martinique, do not suggest atypical clock rates. The question of whether Barbados emerged much earlier than is currently thought, or whether the molecular clock assumptions are inappropriate, remains open.

Animals↗
PubMed2004

The utility of AFLPs for supporting mitochondrial DNA phylogeographical analyses in the Taiwanese bamboo viper, Trimeresurus stejnegeri.

An amplified fragment length polymorphism (AFLP) assay was performed on individuals representing discrete haplotypes from two genetically distinct mtDNA lineages of the bamboo viper, Trimeresurus stejnegeri (Schmidt), within Taiwan. AFLP (525 polymorphic markers from five primer pairs) and mtDNA genetic distances were highly correlated and an analysis of molecular variance, and a Bayesian approach similarly partitioned estimates of genetic similarity according to the mtDNA phylogeographical pattern. These results are discussed in relation to biogeographical hypotheses, comparative rates of mtDNA molecular evolution, and in the identification of evolutionary significant units of Taiwanese T. stejnegeri. In spite of the high degree of congruence between the genetic datasets, the AFLP phylogenetic analysis did not support the mtDNA tree, suggesting that no contemporary barriers to gene flow exist between individuals from the two mtDNA lineages.

Analysis of Variance↗
PubMed2004

Ecological diversification in a group of Indomalayan pitvipers (Trimeresurus): convergence in taxonomically important traits has implications for species identification.

We analyse molecular and phenotypic evolution in a group of taxonomically problematic Indomalayan pitvipers, the Trimeresurus sumatranus group. Mitochondrial DNA sequencing provides a well-resolved phylogeny, with each species representing a distinct lineage. Multivariate morphological analysis reveals a high level of phenotypic differentiation, which is congruent between the sexes but does not reflect phylogenetic history. An adaptive explanation for the observed pattern of differentiation is supported by independent contrasts analysis, which shows significant correlations between current ecology and the characters that most account for the variation between taxa, including those that are presently used to identify the species. Reduced precipitation and altitude, and increased temperature, are correlated with higher numbers of scales on the head, body and tail. It is hypothesized that scale number plays an important role in heat and water exchange by influencing the area of exposed of interstitial skin, and that colour pattern variation reflects selection pressures involving camouflage and thermoregulation. Ecological convergence in traits used for classification is found to have important implications for species identification where taxa are distributed over varying environments.

Animals↗
PubMed2003

Phylogeny, paraphyly and ecological adaptation of the colour and pattern in the Anolis roquet complex on Martinique.

Martinique is an environmentally heterogeneous island with a complex geological history. It is occupied by a solitary anole, Anolis roquet, showing marked geographical variation in colour and other features. Phylogenetic analysis of a segment (1 kb) of the mitochondrial cytochrome b gene across the Anolis roquet series in the southern Lesser Antilles and at 63 localities of Anolis roquet in Martinique indicate that A. roquet is paraphyletic as A. extremus (Barbados) is nested within the Martinique populations. Moreover, divergent phylogenetic lineages exist within Martinique (max. 10.6% uncorrected pairwise), and these lineages are closely associated with the geological history of this complex island. However, objective quantification of the spectroradiometric analysis of hue by delta analysis, together with analysis of the colour pattern, indicate that they are primarily determined by adaptation to environmental conditions, irrespective of these phylogenetic lineages. There is remarkable convergence in hue and pattern in both extreme xeric (dark chevrons on a dull, generally grey/brown, background), and montane conditions (black reticulation and non-UV white spots on a bright, saturated green background). Moreover, parallel trends occur between Martinique and other Lesser Antillean anoles, which further argues for adaptation (increase in green saturation in montane areas and higher levels of UV on the dewlap of some Atlantic forms). As an exception, there are two specific situations where anoles from different lineages look different. These are (i). in the low-altitude regions of the northwest where the northwestern and central lineages make contact, and (ii). in the far south of the island where the southern and central lineages meet.

Adaptation, Biological↗
PubMed2002

The usefulness of amplified fragment length polymorphism markers for taxon discrimination across graduated fine evolutionary levels in Caribbean Anolis lizards.

Fine-level taxon discrimination is important in biodiversity assessment and ecogeographical research. Genomic markers are often required for studies on closely related taxa, however, most existing mitochondrial and nuclear markers require prior knowledge of the genome and are impractical for use in small conservation projects. This study describes the application of amplified fragment length polymorphism (AFLP) to discriminate at four progressively finer evolutionary levels of Caribbean Anolis lizards from the central Lesser Antilles. AFLP is shown to be a rapid and effective method for discriminating between species. Separation increases with primer pair number and choice of primer combination appears to be noncritical. Initial population-level results show markedly less discriminatory power. A screening technique for the identification of population informative markers combining principal component and principal coordinate analyses is presented and assessed. Subsequent results show selected conspecific AFLP data to be remarkably congruent with those of mitochondrial DNA, microsatellite and morphological markers. The use of AFLP as a low-cost nuclear marker in species-level taxon discrimination is supported, whereas population level application demands further consideration.

Animals↗
PubMed2001

Evidence that ultraviolet markings are associated with patterns of molecular gene flow.

Recent studies have shown UV vision and markings to be important in vertebrates, particularly birds, where behavioral experiments have demonstrated its potential importance in sexual selection. However, there has been no genetic evidence that UV markings determine patterns of evolution among natural populations. Here we report molecular evidence that UV markings are associated with the pattern of gene flow in the Tenerife lizard (Gallotia galloti). This species has vicariance-induced, approximate east--west lineages in Tenerife closely congruent with the primary lineages of the sympatric gecko species. Against expectations, these molecular phylogeographic lineages (representing geological history) and isolation-by-distance do not appear to influence gene flow. Sexually mature males from populations either side of a latitudinal ecotone have different UV markings and gene flow appears to be linked to this difference in UV markings. It may be that these groups with different UV sexual markings mate assortatively, restricting the gene flow between them. This has implications for debate on the relative importance of vicariance and biotopes in influencing biodiversity, with this evidence supporting the latter.

Animals↗
PubMed2001

Intraspecific phylogeography of Lacerta vivipara and the evolution of viviparity.

The lacertid lizard Lacerta vivipara is one of the few squamate species with two reproductive modes. We present the intraspecific phylogeny obtained from neighbor-joining and maximum-parsimony analyses of the mtDNA cytochrome b sequences for 15 individuals from Slovenian oviparous populations, 34 individuals from western oviparous populations of southern France and northern Spain, 92 specimens from European and Russian viviparous populations, and 3 specimens of the viviparous subspecies L. v. pannonica. The phylogeny indicates that the evolutionary transition from oviparity to viviparity probably occurred once in L. vivipara. The western oviparous group from Spain and southern France is phylogenetically most closely related to the viviparous clade. However, the biarmed W chromosome characterizing the western viviparous populations is an apomorphic character, whereas the uniarmed W chromosome, existing both in the western oviparous populations and in the geographically distant eastern viviparous populations, is a plesiomorphic character. This suggests an eastern origin of viviparity. Various estimates suggest that the oviparous and viviparous clades of L. vivipara split during the Pleistocene. Our results are discussed in the framework of general evolutionary models: the concept of an oviparity-viviparity continuum in squamates, the cold climate model of selection for viviparity in squamates, and the contraction-expansion of ranges in the Pleistocene resulting in allopatric differentiation.

Animals↗
PubMed2001

Nuclear and mtDNA phylogenies of the Trimeresurus complex: implications for the gene versus species tree debate.

Phylogenies based on mitochondrial DNA (mtDNA) may represent gene trees that may not be congruent with the equivalent species tree. One solution to this problem is to include additional, independent loci from the nuclear genome. Sequence data from the seventh intron of the beta-fibrinogen gene were generated for 25 specimens of vipers, including 8 nominal species of the Trimeresurus complex of Asian pit vipers. Phylogenetic trees were generated using maximum-parsimony and maximum-likelihood methods. The taxonomic level at which the intron provided significant phylogenetic information was examined and the trees were compared to those produced from previously obtained mtDNA cytochrome b sequences. A variety of different approaches (separate analyses, conditional data combination, and consensus) were used in an attempt to provide a sound organismal phylogeny based on both nuclear and mtDNA data sets. We discuss the implications for the gene tree-species tree debate and its particular relevance to medically important organisms.

Animals↗
PubMed2001

Can microsatellites be used to infer phylogenies? Evidence from population affinities of the Western Canary Island lizard (Gallotia galloti).

Population phylogeographic studies are generally based solely on mtDNA without corroboration, from an independent segregating unit (i.e., nuclear genes), that the mtDNA gene tree represents the organismal phylogeny. This paper attempts to evaluate the utility of microsatellites for this process by use of the Western Canary Island lacertid (Gallotia galloti) as a model. The geological times of island eruptions are known, and well-supported mtDNA phylogenies exist (corroborated as the organismal phylogeny rather than just a gene tree by nuclear random amplified polymorphic DNAs (RAPDs)). The allelic variation in 12 populations from four islands (representing five haplotype lineages) was investigated in five unlinked microsatellite loci. Analysis of molecular variance showed this data to be highly structured. A series of genetic distances among populations was computed based on both the variance in allele frequency (i.e., F(st) related) and the variance in repeat numbers (i.e., R(st) related). The genetic distances based on the former were more highly correlated with the mtDNA genetic distances than those based on the latter. All trees based on both models supported the primary division shown by mtDNA and RAPDs, which is dated at ca. 2.8 to 5.6 mybp (depending on calibration of the mtDNA clock) and which could, under the evolutionary species concept, be regarded separate species. This was achieved despite theoretical problems posed by the use of few loci, suspected bottlenecks, and large population sizes. The finer details were less consistently represented. Nevertheless, this study demonstrates that even a small number of microsatellites can be useful in corroborating the deeper divisions of a population phylogeny.

Alleles↗
PubMed2001

Multiple causation of phylogeographical pattern as revealed by nested clade analysis of the bamboo viper (Trimeresurus stejnegeri) within Taiwan.

In order to assess the utility of nested clade analysis, both standard phylogenetic algorithms and nested clade analysis were performed on a geographically widespread survey of mitochondrial DNA haplotypes of the bamboo viper, Trimeresurus stejnegeri, within Taiwan. Gross tree topologies were congruent for all analyses and indicated the presence of two geographically overlapping clades within Taiwan. The smaller lineage was restricted to the north and east coasts, whereas the larger lineage occupied all but the northern range of the species within Taiwan including the Pacific offshore populations of Green and Orchid Islands. The phylogeographical pattern supports the existence of at least one colonization event from the continent since the initial isolation of Taiwan from the mainland in the Pliocene. However, determining the exact number of colonization events was not possible due to the simultaneous vicariant forces of hypothesized continental landbridge connections and the occurrence of dramatic in situ orogenesis throughout the Pleistocene. Nested clade analysis provided multiple temporal and spatial population historical inferences that are not possible with standard analyses and therefore should become widely applied to future phylogeographical studies.

Animals↗
PubMed2001

The use of amplified fragment length polymorphism in determining species trees at fine taxonomic levels: analysis of a medically important snake, Trimeresurus albolabris.

There are a huge number of phylogenetic studies based on mitochondrial DNA (mtDNA); however, these may represent gene trees that may not be congruent with the species tree. A solution to this problem is to include additional, independent, loci from the nuclear genome. At fine taxonomic levels, i.e. between populations and closely related species, previously suggested nuclear markers such as intron sequence data may not be appropriate. In this study we investigate the use of amplified fragment length polymorphisms (AFLP) to aid determination of the species tree for 24 specimens of a medically important snake, Trimeresurus albolabris. This is of particular importance for many venomous snakes as venom often varies intraspecifically. Five different primer combinations produced 434 bands and were analysed by constructing a phylogenetic tree using neighbour joining and principal component analysis. Results were similar across all methods and found distinct groupings. The results were compared with mtDNA data and a reconciled tree was constructed in order to determine the species tree for T. albolabris. We found that T. albolabris (sensu lato) is not monophyletic. Specimens from the Indonesian islands (except West Java) form a distinct clade and we propose elevation to species level. A specimen from Nepal is also distinct and suggests that this population also deserves specific status. We suggest that AFLPs may prove a valuable aid in determining species trees as opposed to gene trees at fine taxonomic levels and this should facilitate the incorporation of molecular data into such activities as antivenom production and conservation management.

Animals↗
PubMed2000

Pre-pleistocene refugia and differentiation between populations of the caucasian salamander (Mertensiella caucasica).

A 350-bp fragment of the mitochondrial cytochrome-b gene was sequenced in the Caucasian salamander, Mertensiella caucasica, representing 10 populations from across its range along the Black Sea coast. Five haplotypes were discovered among 65 fragments analyzed, differing at 2-50 positions. The highest differentiation between haplotypes was observed in animals from the eastern part of the species' range (Borjomi) compared to those from the remainder of the species' range. Randomly amplified nuclear DNA revealed a pattern of spatial genetic variation similar to that of the mitochondrial genome. M. caucasica, as currently known, represents two evolutionary lineages that evolved independently, perhaps since the lower Pliocene. These lineages represent taxa, possibly to be described as species, distributed in the Borjomi area in central Georgia and in southwestern Georgia and northeastern Turkey. The multivariate analysis of morphological data did not reveal significant differences between the taxa. However, substantial morphological differentiation was observed within both lineages, showing parallel patterns in body proportions and coloration patterns. This variation is possibly associated with extant ecological conditions. Salamanders with reduced pigmentation from southwestern Georgia were not genetically distinguishable from neighboring populations.

Animals↗
PubMed2000

Historical biogeography of the Western Rattlesnake (Serpentes: viperidae: Crotalus viridis), inferred from mitochondrial DNA sequence information.

We infer the phylogeography of the Western Rattlesnake (Crotalus viridis) using phylogenetic analysis of mitochondrial DNA sequences from 1345 bp of the genes for cytochrome b and NADH dehydrogenase subunit 4. Two main clades are revealed: one includes populations from east and south of the Rocky Mountains (conventionally referred to as Crotalus viridis viridis and C. v. nuntius), and the other consists of populations west of the Rocky Mountains. Within the western clade, a population from southern Arizona (C. v. cerberus) represents the sister taxon to the remaining western populations. The conventional subspecies recognized in this species do not fully correspond to the phylogenetic pattern, and a review of the systematic status of several populations is needed. Our data allow the inferences that small body size evolved twice and that the ability of one population (C. v. concolor) to secrete highly lethal toxins related to Mojave toxin arose within the complex. Our phylogeny should represent the basis for further studies on the causes of geographical variation in this complex.

Animals↗
PubMed2000

A phylogeny of the trimeresurus group of pit vipers: new evidence from a mitochondrial gene tree.

The Trimeresurus group is an important radiation of over 40 Asian pit viper species. Once considered congeneric, four genera are generally currently recognized (Trimeresurus sensu stricto, Ovophis, Protobothrops, and Tropidolaemus) but relationships within and between these are still unclear. This study, based on mitochondrial cytochrome b sequences, is the first to include a large number of species (21) and demonstrates that the current taxonomy does not adequately represent either the relationships or the genetic diversity present in the complex. Although many deeper nodes are not strongly supported, the following novel conclusions are all well supported: (1) the paraphyly of Trimeresurus sensu stricto, (2) the presence of several divergent clades within Trimeresurus sensu stricto, (3) the paraphyly of some widespread, medically significant, species, (4) the nonmonophyly of Ovophis, and (5) the monophyly of Protobothrops. Mapping of morphological characters onto the mitochondrial tree further supports the four groups proposed for Trimeresurus sensu stricto.

Animals↗
PubMed2000

A phylogenetic analysis of body size evolution in the Anolis roquet group (Sauria: Iguanidae): character displacement or size assortment?

The important role that competition plays in structuring communities is well documented; however, the role of competition in an evolutionary context remains unclear. Evolutionary investigations into the role of competition have often focused on the process of character displacement, and a good example of this is the evolution of body size in the Anolis lizards of the Caribbean islands. Previous work on the A. roquet species group has taken a phylogenetic approach and concluded that patterns of body size differences are not caused by character displacement but are a result of size assortment. Using a phylogenetic reconstruction based on the sequence of the cytochrome b gene (cyt-b) and ancestral character-state reconstruction methods, we investigated the roles of character displacement and size assortment. Our results indicated that size assortment alone was insufficient to explain the observed patterns of body size differences. Furthermore, we found that change in body size was associated with a change in allopatry/sympatry, thus supporting the character-displacement hypothesis. We conclude that patterns of body size differences in the A. roquet species group appear to be the result of a combination of character displacement and size assortment because character displacement was only found to be possible on three occasions.

Animals↗
PubMed2000

Phylogeography and natural selection in the Tenerife gecko Tarentola delalandii: testing historical and adaptive hypotheses.

Combining phylogeographic and matrix correspondence approaches in the analysis of geographical variation provides a fruitful approach to inferring the causes of molecular and morphological evolution within species. Here we present a study on the gecko Tarentola delalandii on the island of Tenerife, Canary Islands, which provides an outstanding model of an exceptionally high degree of phylogeographic differentiation in magnitude and pattern on a small spatial scale. We reconstruct the population history of T. delalandii using phylogeographic information, matrix correspondence tests and estimates of divergence times in conjunction with geological data. It appears that populations differentiated on three precursor islands and secondary contact followed the junction of these islands. The cytochrome b sequence appears to be evolving at least at approximately 1% per million years in this species. Matrix correspondence tests indicate that morphological character systems may reflect ecological selection regimes (colour pattern), history (body dimensions) or both (scalation). The results imply that natural selection can override a historical legacy, but also underline the potential relevance of molecular phylogenetic data for the interpretation of geographical variation in morphology.

Animals↗