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1.  Large-scale phylogeny of chameleons suggests African origins and Eocene diversification 
Oceanic dispersal has emerged as an important factor contributing to biogeographic patterns in numerous taxa. Chameleons are a clear example of this, as they are primarily found in Africa and Madagascar, but the age of the family is post-Gondwanan break-up. A Malagasy origin for the family has been suggested, yet this hypothesis has not been tested using modern biogeographic methods with a dated phylogeny. To examine competing hypotheses of African and Malagasy origins, we generated a dated phylogeny using between six and 13 genetic markers, for up to 174 taxa representing greater than 90 per cent of all named species. Using three different ancestral-state reconstruction methods (Bayesian and likelihood approaches), we show that the family most probably originated in Africa, with two separate oceanic dispersals to Madagascar during the Palaeocene and the Oligocene, when prevailing oceanic currents would have favoured eastward dispersal. Diversification of genus-level clades took place in the Eocene, and species-level diversification occurred primarily in the Oligocene. Plio-Pleistocene speciation is rare, resulting in a phylogeny dominated by palaeo-endemic species. We suggest that contraction and fragmentation of the Pan-African forest coupled to an increase in open habitats (savannah, grassland, heathland), since the Oligocene played a key role in diversification of this group through vicariance.
doi:10.1098/rspb.2013.0184
PMCID: PMC3619509  PMID: 23536596
dispersal; vicariance; colonization; Gondwana; Chamaeleonidae; reptiles
2.  Sexual Dimorphism in Bite Performance Drives Morphological Variation in Chameleons 
PLoS ONE  2014;9(1):e86846.
Phenotypic performance in different environments is central to understanding the evolutionary and ecological processes that drive adaptive divergence and, ultimately, speciation. Because habitat structure can affect an animal’s foraging behaviour, anti-predator defences, and communication behaviour, it can influence both natural and sexual selection pressures. These selective pressures, in turn, act upon morphological traits to maximize an animal’s performance. For performance traits involved in both social and ecological activities, such as bite force, natural and sexual selection often interact in complex ways, providing an opportunity to understand the adaptive significance of morphological variation with respect to habitat. Dwarf chameleons within the Bradypodion melanocephalum-Bradypodion thamnobates species complex have multiple phenotypic forms, each with a specific head morphology that could reflect its use of either open- or closed-canopy habitats. To determine whether these morphological differences represent adaptations to their habitats, we tested for differences in both absolute and relative bite performance. Only absolute differences were found between forms, with the closed-canopy forms biting harder than their open-canopy counterparts. In contrast, sexual dimorphism was found for both absolute and relative bite force, but the relative differences were limited to the closed-canopy forms. These results indicate that both natural and sexual selection are acting within both habitat types, but to varying degrees. Sexual selection seems to be the predominant force within the closed-canopy habitats, which are more protected from aerial predators, enabling chameleons to invest more in ornamentation for communication. In contrast, natural selection is likely to be the predominant force in the open-canopy habitats, inhibiting the development of conspicuous secondary sexual characteristics and, ultimately, enforcing their overall diminutive body size and constraining performance.
doi:10.1371/journal.pone.0086846
PMCID: PMC3903609  PMID: 24475183
3.  A Multilocus Phylogeny of the World Sycoecinae Fig Wasps (Chalcidoidea: Pteromalidae) 
PLoS ONE  2013;8(11):e79291.
The Sycoecinae is one of five chalcid subfamilies of fig wasps that are mostly dependent on Ficus inflorescences for reproduction. Here, we analysed two mitochondrial (COI, Cytb) and four nuclear genes (ITS2, EF-1α, RpL27a, mago nashi) from a worldwide sample of 56 sycoecine species. Various alignment and partitioning strategies were used to test the stability of major clades. All topologies estimated using maximum likelihood and Bayesian methods were similar and well resolved but did not support the existing classification. A high degree of morphological convergence was highlighted and several species appeared best described as species complexes. We therefore proposed a new classification for the subfamily. Our analyses revealed several cases of probable speciation on the same host trees (up to 8 closely related species on one single tree of F. sumatrana), which raises the question of how resource partitioning occurs to avoid competitive exclusion. Comparisons of our results with fig phylogenies showed that, despite sycoecines being internally ovipositing wasps host-switches are common incidents in their evolutionary history. Finally, by studying the evolutionary properties of the markers we used and profiling their phylogenetic informativeness, we predicted their utility for resolving phylogenetic relationships of Chalcidoidea at various taxonomic levels.
doi:10.1371/journal.pone.0079291
PMCID: PMC3818460  PMID: 24223925
4.  Mind the gaps: investigating the cause of the current range disjunction in the Cape Platanna, Xenopus gilli (Anura: Pipidae) 
PeerJ  2013;1:e166.
Low-lying areas of the Cape at Africa’s south-westernmost tip have undergone dramatic marine-remodelling, with regular changes in sea-level following glacial cycles. Species for which marine barriers are impenetrable underwent concomitant radical distribution changes which may account for current range disjunctions. The Cape platanna, Xenopus gilli, is a frog distributed in only three disjunt areas within low-lying regions of the southwestern Cape. We determined the relationship between frogs from these three disjunct areas, by using a combination of morphometric analysis and mtDNA (ND2 and 16S fragments) sequences of 130 frogs from eight ponds. Coalescent analyses on molecular data dated the divergence in two major clades to around 4.6 Mya, a period during which major uplifting on the eastern side of the subcontinent caused climate changes throughout southern Africa. Principal components analysis showed significant morphometric differences between each clade on head and limb measurements. Consistent differences in ventral colouration and patterning were also observed. We report on increased levels of hybridisation with X. laevis throughout the range of X. gilli, which reaches at least 27% hybrids in some ponds. Urgent conservation actions are required to control habitat loss from alien invasive vegetation, and prevent introgression with the domestic-exotic, X. laevis.
doi:10.7717/peerj.166
PMCID: PMC3792190  PMID: 24109551
Hybridization; mtDNA; Morphometrics; Population genetics; Range disjunction; Xenopus laevis
5.  Convergent Evolution Associated with Habitat Decouples Phenotype from Phylogeny in a Clade of Lizards 
PLoS ONE  2012;7(12):e51636.
Convergent evolution can explain similarity in morphology between species, due to selection on a fitness-enhancing phenotype in response to local environmental conditions. As selective pressures on body morphology may be strong, these have confounded our understanding of the evolutionary relationships between species. Within the speciose African radiation of lacertid lizards (Eremiadini), some species occupy a narrow habitat range (e.g. open habitat, cluttered habitat, strictly rupicolous, or strictly psammophilic), which may exert strong selective pressures on lizard body morphology. Here we show that the overall body plan is unrelated to shared ancestry in the African radiation of Eremiadini, but is instead coupled to habitat use. Comprehensive Bayesian and likelihood phylogenies using multiple representatives from all genera (2 nuclear, 2 mitochondrial markers) show that morphologically convergent species thought to represent sister taxa within the same genus are distantly related evolutionary lineages (Ichnotropis squamulosa and Ichnotropis spp.; Australolacerta rupicola and A. australis). Hierarchical clustering and multivariate analysis of morphological characters suggest that body, and head, width and height (stockiness), all of which are ecologically relevant with respect to movement through habitat, are similar between the genetically distant species. Our data show that convergence in morphology, due to adaptation to similar environments, has confounded the assignment of species leading to misidentification of the taxonomic position of I. squamulosa and the Australolacerta species.
doi:10.1371/journal.pone.0051636
PMCID: PMC3520956  PMID: 23251601
6.  Hiding deep in the trees: discovery of divergent mitochondrial lineages in Malagasy chameleons of the Calumma nasutum group 
Ecology and Evolution  2012;2(7):1468-1479.
We conducted a comprehensive molecular phylogenetic study for a group of chameleons from Madagascar (Chamaeleonidae: Calumma nasutum group, comprising seven nominal species) to examine the genetic and species diversity in this widespread genus. Based on DNA sequences of the mitochondrial gene (ND2) from 215 specimens, we reconstructed the phylogeny using a Bayesian approach. Our results show deep divergences among several unnamed mitochondrial lineages that are difficult to identify morphologically. We evaluated lineage diversification using a number of statistical phylogenetic methods (general mixed Yule-coalescent model; SpeciesIdentifier; net p-distances) to objectively delimit lineages that we here consider as operational taxonomic units (OTUs), and for which the taxonomic status remains largely unknown. In addition, we compared molecular and morphological differentiation in detail for one particularly diverse clade (the C. boettgeri complex) from northern Madagascar. To assess the species boundaries within this group we used an integrative taxonomic approach, combining evidence from two independent molecular markers (ND2 and CMOS), together with genital and other external morphological characters, and conclude that some of the newly discovered OTUs are separate species (confirmed candidate species, CCS), while others should best be considered as deep conspecific lineages (DCLs). Our analysis supports a total of 33 OTUs, of which seven correspond to described species, suggesting that the taxonomy of the C. nasutum group is in need of revision.
doi:10.1002/ece3.269
PMCID: PMC3434913  PMID: 22957155
Calumma nasutum group; Chamaeleonidae; genital morphology; Madagascar; molecular diversity; snout appendage scales
7.  Eastward from Africa: palaeocurrent-mediated chameleon dispersal to the Seychelles islands 
Biology Letters  2010;7(2):225-228.
Madagascar and the Seychelles are Gondwanan remnants currently isolated in the Indian Ocean. In the Late Cretaceous, these islands were joined with India to form the Indigascar landmass, which itself then split into its three component parts around the start of the Tertiary. This history is reflected in the biota of the Seychelles, which appears to contain examples of both vicariance- and dispersal-mediated divergence from Malagasy or Indian sister taxa. One lineage for which this has been assumed but never thoroughly tested is the Seychellean tiger chameleon, a species assigned to the otherwise Madagascar-endemic genus Calumma. We present a multi-locus phylogenetic study of chameleons, and find that the Seychellean species is actually the sister taxon of a southern African clade and requires accomodation in its own genus as Archaius tigris. Divergence dating and biogeographic analyses indicate an origin by transoceanic dispersal from Africa to the Seychelles in the Eocene–Oligocene, providing, to our knowledge, the first such well-documented example and supporting novel palaeocurrent reconstructions.
doi:10.1098/rsbl.2010.0701
PMCID: PMC3061160  PMID: 20826471
biogeography; overseas dispersal; Indian Ocean; Chamaeleonidae; Archaius
8.  Sequential Fragmentation of Pleistocene Forests in an East Africa Biodiversity Hotspot: Chameleons as a Model to Track Forest History 
PLoS ONE  2011;6(10):e26606.
Background
The Eastern Arc Mountains (EAM) is an example of naturally fragmented tropical forests, which contain one of the highest known concentrations of endemic plants and vertebrates. Numerous paleo-climatic studies have not provided direct evidence for ancient presence of Pleistocene forests, particularly in the regions in which savannah presently occurs. Knowledge of the last period when forests connected EAM would provide a sound basis for hypothesis testing of vicariance and dispersal models of speciation. Dated phylogenies have revealed complex patterns throughout EAM, so we investigated divergence times of forest fauna on four montane isolates in close proximity to determine whether forest break-up was most likely to have been simultaneous or sequential, using population genetics of a forest restricted arboreal chameleon, Kinyongia boehmei.
Methodology/Principal Findings
We used mitochondrial and nuclear genetic sequence data and mutation rates from a fossil-calibrated phylogeny to estimate divergence times between montane isolates using a coalescent approach. We found that chameleons on all mountains are most likely to have diverged sequentially within the Pleistocene from 0.93–0.59 Ma (95% HPD 0.22–1.84 Ma). In addition, post-hoc tests on chameleons on the largest montane isolate suggest a population expansion ∼182 Ka.
Conclusions/Significance
Sequential divergence is most likely to have occurred after the last of three wet periods within the arid Plio-Pleistocene era, but was not correlated with inter-montane distance. We speculate that forest connection persisted due to riparian corridors regardless of proximity, highlighting their importance in the region's historic dispersal events. The population expansion coincides with nearby volcanic activity, which may also explain the relative paucity of the Taita's endemic fauna. Our study shows that forest chameleons are an apposite group to track forest fragmentation, with the inference that forest extended between some EAM during the Pleistocene 1.1–0.9 Ma.
doi:10.1371/journal.pone.0026606
PMCID: PMC3203880  PMID: 22053198
9.  Genetic and historic evidence for climate-driven population fragmentation in a top cetacean predator: the harbour porpoises in European water 
Recent climate change has triggered profound reorganization in northeast Atlantic ecosystems, with substantial impact on the distribution of marine assemblages from plankton to fishes. However, assessing the repercussions on apex marine predators remains a challenging issue, especially for pelagic species. In this study, we use Bayesian coalescent modelling of microsatellite variation to track the population demographic history of one of the smallest temperate cetaceans, the harbour porpoise (Phocoena phocoena) in European waters. Combining genetic inferences with palaeo-oceanographic and historical records provides strong evidence that populations of harbour porpoises have responded markedly to the recent climate-driven reorganization in the eastern North Atlantic food web. This response includes the isolation of porpoises in Iberian waters from those further north only approximately 300 years ago with a predominant northward migration, contemporaneous with the warming trend underway since the ‘Little Ice Age’ period and with the ongoing retreat of cold-water fishes from the Bay of Biscay. The extinction or exodus of harbour porpoises from the Mediterranean Sea (leaving an isolated relict population in the Black Sea) has lacked a coherent explanation. The present results suggest that the fragmentation of harbour distribution range in the Mediterranean Sea was triggered during the warm ‘Mid-Holocene Optimum’ period (approx. 5000 years ago), by the end of the post-glacial nutrient-rich ‘Sapropel’ conditions that prevailed before that time.
doi:10.1098/rspb.2010.0412
PMCID: PMC2981983  PMID: 20444724
cetacean; climate change; habitat fragmentation; population genetics; coalescence
10.  Rise of oceanographic barriers in continuous populations of a cetacean: the genetic structure of harbour porpoises in Old World waters 
BMC Biology  2007;5:30.
Background
Understanding the role of seascape in shaping genetic and demographic population structure is highly challenging for marine pelagic species such as cetaceans for which there is generally little evidence of what could effectively restrict their dispersal. In the present work, we applied a combination of recent individual-based landscape genetic approaches to investigate the population genetic structure of a highly mobile extensive range cetacean, the harbour porpoise in the eastern North Atlantic, with regards to oceanographic characteristics that could constrain its dispersal.
Results
Analyses of 10 microsatellite loci for 752 individuals revealed that most of the sampled range in the eastern North Atlantic behaves as a 'continuous' population that widely extends over thousands of kilometres with significant isolation by distance (IBD). However, strong barriers to gene flow were detected in the south-eastern part of the range. These barriers coincided with profound changes in environmental characteristics and isolated, on a relatively small scale, porpoises from Iberian waters and on a larger scale porpoises from the Black Sea.
Conclusion
The presence of these barriers to gene flow that coincide with profound changes in oceanographic features, together with the spatial variation in IBD strength, provide for the first time strong evidence that physical processes have a major impact on the demographic and genetic structure of a cetacean. This genetic pattern further suggests habitat-related fragmentation of the porpoise range that is likely to intensify with predicted surface ocean warming.
doi:10.1186/1741-7007-5-30
PMCID: PMC1971045  PMID: 17651495
11.  Long-term feeding ecology and habitat use in harbour porpoises Phocoena phocoena from Scandinavian waters inferred from trace elements and stable isotopes 
BMC Ecology  2007;7:1.
Background
We investigated the feeding ecology and habitat use of 32 harbour porpoises by-caught in 4 localities along the Scandinavian coast from the North Sea to the Barents Sea using time-integrative markers: stable isotopes (δ13C, δ15N) and trace elements (Zn, Cu, Fe, Se, total Hg and Cd), in relation to habitat characteristics (bathymetry) and geographic position (latitude).
Results
Among the trace elements analysed, only Cd, with an oceanic specific food origin, was found to be useful as an ecological tracer. All other trace elements studied were not useful, most likely because of physiological regulation and/or few specific sources in the food web. The δ13C, δ15N signatures and Cd levels were highly correlated with each other, as well as with local bathymetry and geographic position (latitude). Variation in the isotopic ratios indicated a shift in harbour porpoise's feeding habits from pelagic prey species in deep northern waters to more coastal and/or demersal prey in the relatively shallow North Sea and Skagerrak waters. This result is consistent with stomach content analyses found in the literature. This shift was associated with a northward Cd-enrichment which provides further support to the Cd 'anomaly' previously reported in polar waters and suggests that porpoises in deep northern waters include Cd-contaminated prey in their diet, such as oceanic cephalopods.
Conclusion
As stable isotopes and Cd provide information in the medium and the long term respectively, the spatial variation found, shows that harbour porpoises experience different ecological regimes during the year along the Scandinavian coasts, adapting their feeding habits to local oceanographic conditions, without performing extensive migration.
doi:10.1186/1472-6785-7-1
PMCID: PMC1781931  PMID: 17229317

Results 1-11 (11)