Multilocus phylogeny, species age and biogeography of the Lesser Antillean anoles.

Lesser Antillean anoles provide classic examples of island radiations. A detailed knowledge of their phylogeny and biogeography, in particular how the age of species relate to the ages of their respective islands and the age of their radiation, is essential to elucidate the tempo and mechanisms of these radiations. We conduct a large-scale phylogenetic and phylogeographic investigation of the Lesser Antillean anoles using multiple genetic markers and comprehensive geographic sampling of most species.

Predictability in evolution: Adaptation of the Bonaire anole (Anolis bonairensis) to an extreme environment.

The extent to which evolution is deterministic (predictable), or random, is a fundamental question in evolution. This case study attempts to determine the extent to which interspecific divergence can be predicted from intraspecific trends related species. The mountainous Lesser Antilles are occupied by one or two anole species with very substantial intraspecific differences in the quantitative traits between xeric and rainforest habitats.

The importance of being genomic: Non-coding and coding sequences suggest different models of toxin multi-gene family evolution.

Studies of multi-gene protein families, including many toxins, are crucial for understanding the role of gene duplication in generating protein diversity in general. However, many evolutionary analyses of gene families are based on coding sequences, and do not take into account many potentially confounding evolutionary factors, such as recombination and convergence due to selection. We illustrate this using snake venom gene sequences from the Phospholipase A2 (PLA2) subfamily.

Convergence of multiple markers and analysis methods defines the genetic distinctiveness of cryptic pitvipers.

Using multiple markers and multiple analytical approaches is critical for establishing species boundaries reliably, especially so in the case of cryptic species. Despite development of new and powerful analytical methods, most studies continue to adopt a few, with the choice often being subjective. One such example is routine analysis of Amplified Fragment Length Polymorphism (AFLP) data using population genetic models despite disparity between method assumptions and data properties.

Phylogeography of the endangered Lesser Antillean iguana, Iguana delicatissima: a recent diaspora in an archipelago known for ancient herpetological endemism.

Iguana delicatissima is an endangered endemic of the Lesser Antilles in the Caribbean. Phylogeographic analyses for many terrestrial vertebrate species in the Caribbean, particularly lizards, suggest ancient divergence times. Often, the closest relatives of species are found on the same island, indicating that colonization rates are so low that speciation on islands is often more likely to generate biodiversity than subsequent colonization events.

Widespread parallel population adaptation to climate variation across a radiation: implications for adaptation to climate change.

Global warming will impact species in a number of ways, and it is important to know the extent to which natural populations can adapt to anthropogenic climate change by natural selection. Parallel microevolution within separate species can demonstrate natural selection, but several studies of homoplasy have not yet revealed examples of widespread parallel evolution in a generic radiation. Taking into account primary phylogeographic divisions, we investigate numerous quantitative traits (size, shape, scalation, colour pattern and hue) in anole radiations from the mountainous Lesser Antillean islands.

Predicting function from sequence in a large multifunctional toxin family.

Venoms contain active substances with highly specific physiological effects and are increasingly being used as sources of novel diagnostic, research and treatment tools for human disease. Experimental characterisation of individual toxin activities is a severe rate-limiting step in the discovery process, and in-silico tools which allow function to be predicted from sequence information are essential. Toxins are typically members of large multifunctional families of structurally similar proteins that can have different biological activities, and minor sequence divergence can have significant consequences.

Quantitative traits and mode of speciation in Martinique anoles.

We investigate extensive quantitative trait variation (dewlap hue, colour pattern, dorsum hue, body proportions and scalation) in the Martinique anole across eight transects representing nascent parapatric ecological speciation, nascent allopatric speciation and allopatric divergence without sufficient genetic structure to suggest speciation. Quantitative trait divergence can be extremely large between adjacent sets of populations, but with one exception that this is associated with difference in habitat rather than past allopatry. Nascent ecological speciation shows the greatest level of quantitative trait divergence across all character sets including those implicated in natural, as well as sexual selection.

Phylogenetic structure and species boundaries in the mountain pitviper Ovophis monticola (Serpentes: Viperidae: Crotalinae) in Asia.

We investigated phylogenetic structure and morphological variation in Asian mountain pitvipers of the genus Ovophis (comprising 3-4 species some of which are considered polytypic) by sequencing four mitochondrial markers (cytochrome b, NADH dehydrogenase subunit 4, 12S and 16S rRNA) from 72 specimens, and analysed them in a Bayesian framework together with another 26 sequences from closely related genera. We reconstructed the region of origin and direction of dispersal of the major clades, and of Ovophis as a whole, using likelihood framework analysis. We also defined morphogroups from 280 specimens from across the range of Ovophis to allow the geographic extent of the major clades to be determined, as well as to allow inclusion of specimens lacking sequence data.

Estimating genetic variability in non-model taxa: a general procedure for discriminating sequence errors from actual variation.

Genetic variation is the driving force of evolution and as such is of central interest for biologists. However, inadequate discrimination of errors from true genetic variation could lead to incorrect estimates of gene copy number, population genetic parameters, phylogenetic relationships and the deposition of gene and protein sequences in databases that are not actually present in any organism. Misincorporation errors in multi-template PCR cloning methods, still commonly used for obtaining novel gene sequences in non-model species, are difficult to detect, as no previous information may be available about the number of expected copies of genes belonging to multi-gene families.

Genetic tests for ecological and allopatric speciation in anoles on an island archipelago.

From Darwin's study of the Galapagos and Wallace's study of Indonesia, islands have played an important role in evolutionary investigations, and radiations within archipelagos are readily interpreted as supporting the conventional view of allopatric speciation. Even during the ongoing paradigm shift towards other modes of speciation, island radiations, such as the Lesser Antillean anoles, are thought to exemplify this process. Geological and molecular phylogenetic evidence show that, in this archipelago, Martinique anoles provide several examples of secondary contact of island species.

Inclusion of nuclear intron sequence data helps to identify the Asian sister group of New World pitvipers.

Despite much effort towards resolving the molecular phylogenetic tree for pitvipers, some aspects remain unresolved. In particular, the sister group of the diverse New World radiation has remained impossible to identify with any certainty. In this study, which for the first time includes nuclear intron data from all major groups of Asian pitvipers as well as representatives of the New World radiation, Bayesian inference allows Gloydius to be identified as the most likely sister group to the New World radiation and sheds light on other ambiguous relationships among the Old World pitvipers.

Genetic data from 28 STR loci for forensic individual identification and parentage analyses in 6 bird of prey species.

Twenty-eight STR loci were screened in wild populations of six bird of prey species providing allele frequencies and population genetic parameters necessary for the application of STRs in wildlife forensic genetic casework. Individual STR loci were validated according to forensic recommendations in specimens of golden eagle (Aquila chrysaetos), goshawk (Accipiter gentilis), merlin (Falco columbarius), peregrine falcon (Falco peregrinus), gyr falcon (Falco rusticolus) and saker falcon (Falco cherrug). Deviations from Hardy-Weinberg expectations and linkage disequilibrium between locus pairs were examined.

The roles of allopatric divergence and natural selection in quantitative trait variation across a secondary contact zone in the lizard Anolis roquet.

Populations of the Caribbean lizard, Anolis roquet, are thought to have experienced long periods of allopatry before recent secondary contact. To elucidate the effects of past allopatry on population divergence in A. roquet, we surveyed parallel transects across a secondary contact zone in northeastern Martinique.

A forensic STR profiling system for the Eurasian badger: a framework for developing profiling systems for wildlife species.

Developing short tandem repeat (STR) profiling systems for forensic identification is complicated in animal species. Obtaining a representative number of individuals from populations, limited access to family groups and a lack of developed STR markers can make adhering to human forensic guidelines difficult. Furthermore, a lack of animal specific guidelines may explain why many wildlife forensic STR profiling systems developed to date have not appropriately addressed areas such as marker validation or the publication and analysis of population data necessary for the application of these tools to forensic science.

Development of microsatellite markers in the St Lucia anole, Anolis luciae.

Anolis lizards are important models in studies of ecology and evolution. Here we describe 13 polymorphic microsatellites for use in population screening in the St Lucia anole, Anolis luciae, that can be used as a natural replicate to Anolis roquet on Martinique to study processes involved in population differentiation and speciation. Genotyping of 32 individuals using M13 tails and FAM-labelled universal M13 primers showed that all loci were polymorphic with high genetic diversity, averaging at 16.

Microsatellite data show evidence for male-biased dispersal in the Caribbean lizard Anolis roquet.

Dispersal is a key component of an organism's life history and differences in dispersal between sexes appear to be widespread in vertebrates. However, most predictions of sex-biased dispersal have been based on observations of social structure in birds and mammals and more data are needed on other taxa to test whether these predictions apply in other organisms. Caribbean anole lizards are important model organisms in various biological disciplines, including evolutionary biology.

The relative importance of ecology and geographic isolation for speciation in anoles.

The biogeographic patterns in sexually reproducing animals in island archipelagos may be interpreted as reflecting the importance of allopatric speciation. However, as the forms are allopatric, their reproductive isolation is largely untestable. A historical perspective integrating geology and molecular phylogeny reveals specific cases where ancient precursor islands coalesce, which allows the application of population genetics to critically test genetic isolation.

Validation of the barcoding gene COI for use in forensic genetic species identification.

The application of forensics to wildlife crime investigation routinely involves genetic species identification based on DNA sequence similarity. This work can be hindered by a lack of authenticated reference DNA sequence data resulting in weak matches between evidence and reference samples. The introduction of DNA barcoding has highlighted the expanding use of the mtDNA gene, cytochrome c oxidase I (COI), as a genetic marker for species identification.

Optimal intron analyses in the trimeresurus radiation of Asian pitvipers.

Nuclear introns are commonly used as phylogenetic markers, but a number of issues related to alignment strategies, indel treatments, and the incorporation of length-variant heterozygotes (LVHs) are not routinely addressed when generating phylogenetic hypotheses. Topological congruence in relation to an extensive mitochondrial DNA multigene phylogeny (derived from 2,423 bp of 12S, 16S, ND4, and CYTB genes) of the Asian pitviper Trimeresurus radiation was used to compare combinations of "by eye" and edited and unedited ClustalX 1.8 alignments of two nuclear introns.

Targeting optimal introns for phylogenetic analyses in non-model taxa: experimental results in Asian pitvipers.

Nuclear introns are increasingly used as phylogenetic markers. Here, we present a multidisciplinary approach towards optimal locus selection and amplification using Asian pitvipers as an example of a non-model taxon, and raise the profile of length variant heterozygotes (LVHs) in intron loci. Taxon-specific primers were identified using a bioinformatic approach, and also designed from existing exon primed, intron crossing (EPIC) primer amplifications.

The dynamics of genetic and morphological variation on volcanic islands.

Oceanic archipelagos of volcanic origin have been important in the study of evolution because they provide repeated natural experiments allowing rigorous tests of evolutionary hypotheses. Ongoing volcanism on these islands may, however, affect the evolutionary diversification of species. Analysis of population structure and phylogeographic patterns in island populations can provide insight into evolutionary dynamics on volcanic islands.