Arie van der Meijden

Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians

BackgroundIdentifying species of organisms by short sequences of DNA has been in the center of ongoing discussions under the terms DNA barcoding or DNA taxonomy. A C-terminal fragment of the mitochondrial gene for cytochrome oxidase subunit I (COI) has been proposed as universal marker for this purpose among animals.ResultsHerein we present experimental evidence that the mitochondrial 16S rRNA gene fulfills the requirements for a universal DNA barcoding marker in amphibians. In terms of universality of priming sites and identification of major vertebrate clades the studied 16S fragment is superior to COI. Amplification success was 100% for 16S in a subset of fresh and well-preserved samples of Madagascan frogs, while various combination of COI primers had lower success rates.COI priming sites showed high variability among amphibians both at the level of groups and closely related species, whereas 16S priming sites were highly conserved among vertebrates. Interspecific pairwise 16S divergences in a test group of Madagascan frogs were at a level suitable for assignment of larval stages to species (1–17%), with low degrees of pairwise haplotype divergence within populations (0–1%).ConclusionWe strongly advocate the use of 16S rRNA as standard DNA barcoding marker for vertebrates to complement COI, especially if samples a priori could belong to various phylogenetically distant taxa and false negatives would constitute a major problem.

Patterns of Endemism and Species Richness in Malagasy Cophyline Frogs Support a Key Role of Mountainous Areas for Speciation

Abstract Cophyline narrow-mouthed frogs (Anura: Microhylidae) are a diverse endemic radiation of Madagascar. Cophylines contain a high proportion of range restricted species and constitute a good model system to understand patterns of evolutionary diversification in tropical ecosystems. We combine spatial and phylogenetic analyses for a near-complete taxon sample to test competing explanations for patterns of species richness (SR) and endemism. Our reconstruction of the phylogeny of cophylines indicates the presence of 22 new species and several instances of nonmonophyly. We found a strong historical signal in current cophyline ranges indicating a high degree of spatial niche conservatism in clade diversification, with clades occurring in the North of Madagascar constituting the most derived in the phylogeny. We identified six positively correlated centers of SR and endemism that can neither be explained by stochastic models such as elevational or latitudinal mid-domain effect, nor by low-elevation river catchments. Instead, the locations of these centers in areas spanning a high altitudinal range in combination with specific climatic parameters support a key role of mountainous areas for speciation of these anurans, although we cannot exclude an influence of habitat loss due to human impact. High conservation priority is ascribed to these areas.

Relationships between head morphology, bite performance and ecology in two species of Podarcis wall lizards

Understanding the relationship between form and function is central to our comprehension of how phenotypic diversity evolves. Traits involved in multiple activities, such as social interactions and ecological resource use, are under the influence of different evolutionary forces potentially acting in opposite directions. Such systems provide the opportunity of understanding how potential constraints on morphological variation may influence whole-organism performance. In this study we examined morphology and bite performance in two closely related species of Podarcis wall lizards with divergent microhabitat preferences, to investigate how natural and sexual selection interact to shape the evolution of head traits. Our results show that although head morphology is markedly different between species and sexes, only sexes differ in bite force, indicating that the ecological differentiation between species is reflected in their morphology but does not constrain performance. Rather, the modification of the relative size of head components between species and a shift in the form-function relationship provide a potential explanation of how equal performance is attained by different morphological configurations. Geometric morphometrics provide a clear, biomechanically meaningful image of how this is achieved and show a bisexual pattern of head shape-bite force association in both species. This, together with a strong allometry of head size on body size and head shape on head size, provides indirect morphological evidence for the importance of sexual selection in shaping morphological and functional patterns. Finally, our findings suggest that the differences observed between species and sexes in head traits and bite performance are not reflected in their dietary ecology, implying that if trophic niche segregation between groups occurs, the reasons behind it are not primarily related to head morphology and functional variation.

Phylogeography of Sardinian cave salamanders (genus Hydromantes) is mainly determined by geomorphology.

Detecting the factors that determine the interruption of gene flow between populations is key to understanding how speciation occurs. In this context, caves are an excellent system for studying processes of colonization, differentiation and speciation, since they represent discrete geographical units often with known geological histories. Here, we asked whether discontinuous calcareous areas and cave systems represent major barriers to gene flow within and among the five species of Sardinian cave salamanders (genus Hydromantes) and whether intraspecific genetic structure parallels geographic distance within and among caves. We generated mitochondrial cytochrome b gene sequences from 184 individuals representing 48 populations, and used a Bayesian phylogeographic approach to infer possible areas of cladogenesis for these species and reconstruct historical and current dispersal routes among distinct populations. Our results show deep genetic divergence within and among all Sardinian cave salamander species, which can mostly be attributed to the effects of mountains and discontinuities in major calcareous areas and cave systems acting as barriers to gene flow. While these salamander species can also occur outside caves, our results indicate that there is a very poor dispersal of these species between separate cave systems.

Choose Your Weapon: Defensive Behavior Is Associated with Morphology and Performance in Scorpions

Morphology can be adaptive through its effect on performance of an organism. The effect of performance may, however, be modulated by behavior; an organism may choose a behavioral option that does not fully utilize its maximum performance. Behavior may therefore be decoupled from morphology and performance. To gain insight into the relationships between these levels of organization, we combined morphological data on defensive structures with measures of defensive performance, and their utilization in defensive behavior. Scorpion species show significant variation in the morphology and performance of their main defensive structures; their chelae (pincers) and the metasoma (“tail”) carrying the stinger. Our data show that size-corrected pinch force varies to almost two orders of magnitude among species, and is correlated with chela morphology. Chela and metasoma morphology are also correlated to the LD50 of the venom, corroborating the anecdotal rule that dangerously venomous scorpions can be recognized by their chelae and metasoma. Analyses of phylogenetic independent contrasts show that correlations between several aspects of chela and metasoma morphology, performance and behavior are present. These correlations suggest co-evolution of behavior with morphology and performance. Path analysis found a performance variable (pinch force) to partially mediate the relationship between morphology (chela aspect ratio) and behavior (defensive stinger usage). We also found a correlation between two aspects of morphology: pincer finger length correlates with the relative “thickness” (aspect ratio) of the metasoma. This suggests scorpions show a trade-off between their two main weapon complexes: the metasoma carrying the stinger, and the pedipalps carrying the chelae.

Packing a pinch: functional implications of chela shapes in scorpions using finite element analysis.

Scorpions depend on their pedipalps for prey capture, defense, mating and sensing their environment. Some species additionally use their pedipalps for burrowing or climbing. Because the pincers or chelae at the end of the pedipalps vary widely in shape, they have been used as part of a suite of characters to delimit ecomorphotypes. We here evaluate the influence of the different chela cuticular shapes on their performance under natural loading conditions. Chelae of 20 species, representing seven families and spanning most of the range of chela morphologies, were assigned to clusters based on chela shape parameters using hierarchical cluster analysis. Several clusters were identified corresponding approximately to described scorpion ecomorphotypes. Finite element models of the chela cuticulae were constructed from CT scans and loaded with estimated pinch forces based on in vivo force measurements. Chela shape clusters differed significantly in mean Von Mises stress and strain energy. Normalized FEA showed that chela shape significantly influenced Von Mises stress and strain energy in the chela cuticula, with Von Mises stress varying up to an order of magnitude and strain energy up to two orders of magnitude. More elongate, high‐aspect ratio chela forms showed significantly higher mean stress compared with more robust low‐aspect ratio forms. This suggests that elongate chelae are at a higher risk of failure when operating near the maximum pinch force. Phylogenetic independent contrasts (PIC) were calculated based on a partly resolved phylogram with branch lengths based on an alignment of the 12S, 16S and CO1 mitochondrial genes. PIC showed that cuticular stress and strain in the chela were correlated with several shape parameters, such as aspect ratio, movable finger length, and chela height, independently of phylogenetic history. Our results indicate that slender chela morphologies may be less suitable for high‐force functions such as burrowing and defense. Further implications of these findings for the ecology and evolution of the different chela morphologies are discussed.

Genetic Diversity of Maghrebian Hottentotta (Scorpiones: Buthidae) Scorpions Based on CO1: New Insights on the Genus Phylogeny and Distribution

ABSTRACT The medically important scorpion genus Hottentotta Birula, 1908 has long been a taxonomical challenge. This species-rich scorpion genus contains three lineages spread over most of Africa and part of Asia. The Maghrebian Hottentotta was historically recognised as a single species, H. franzwerneri (Birula, 1914), divided in two subspecies with disjunct distributions. A recent morphological study raised both Maghreb subspecies to species level, H. franzwerneri and H. gentili (Pallary, 1924). In this study we assess the phylogenetic relationships between specimens of the genus Hottentotta from Morocco using cytochrome oxidase 1 (CO1) mitochondrial DNA sequences. Our finding of H. gentili in the eastern portion of Morocco increases the known range of this taxon and significantly reduces the geographic distance that separates it from H. franzwerneri. Furthermore, we found four well supported clades in the Maghrebian Hottentotta. All H. franzwerneri specimens group in the franzwerneri clade, but H. gentili specimens group in three different clades. The Ziz valley clade form a sister group to the franzwerneri clade, specimens from the core range of H. gentili group in the central clade, while specimens from the southern distribution of the species group in the Low Draa valley clade, basal in our tree. These findings challenge current Hottentotta taxonomy because they imply paraphyly of H. gentili, although mitochondrial introgression cannot be excluded. Further studies are needed to fully comprehend the taxonomy of Hottentotta from this region and the role that colour characters play in scorpion species diagnoses.

Assessing the molecular phylogeny of a near extinct group of vertebrates: the Neotropical harlequin frogs (Bufonidae; Atelopus)

Neotropical harlequin frogs, Atelopus, are a species-rich bufonid group. Atelopus monophyly has been suggested but intergeneric, interspecific and intraspecific relationships are poorly understood. One reason is that morphological characters of harlequin frogs are often difficult to interpret, making species delimitations difficult. Molecular analyses (DNA barcoding, phylogeny) may be helpful but sampling is hampered as most of the more than 100 Atelopus species have undergone severe population declines and many are possibly extinct. We processed mitochondrial DNA (12S and 16S rRNA) of 28 available ingroup samples from a large portion of the genus’ geographic range (Bayesian Inference, Maximum Likelihood). Our samples constitute a monophyletic unit, which is sister to other bufonid genera studied including the Andean genus Osornophryne. In contrast to previous morphological studies, our results suggest that Osornophryne is neither sister to Atelopus nor nested within it. Within Atelopus, we note two major clades with well supported subclades, one Amazonian–Guianan Clade (Flavescens-spumarius Clade plus Tricolor Clade) and an Andean–Chocó–Central American Clade (Varius Clade plus all other Atelopus). The first mentioned includes all species that possess a middle ear (i.e. stapes) except for A. seminiferus lacking it (like all remaining Atelopus). Previously proposed species groups based on frog-like versus toad-like overall appearance (i.e. Longirostris and Ignescens Groups) or phalangeal reduction in the thumb (i.e. Flavescens Group) are not monophyletic in our phylogeny, thus characters used to define them are not considered synapomorphies. We show that genetic divergence can be high between species belonging to different clades, in spite of their phenetic similarity (e.g. A. pulcher, Atelopus sp. 2). On the other hand, within the same clade, colour can vary tremendously, while genetic divergence is low (e.g. A. flavescens and allies). These observations demonstrate that Atelopus taxonomy is complicated and that an integrative approach is required before ‘splitting’ or ‘lumping’ nominal species.

Reinforcing and expanding the predictions of the disturbance vicariance hypothesis in Amazonian harlequin frogs: a molecular phylogenetic and climate envelope modelling approach

The disturbance vicariance hypothesis (DV) has been proposed to explain speciation in Amazonia, especially its edge regions, e.g. in eastern Guiana Shield harlequin frogs (Atelopus) which are suggested to have derived from a cool-adapted Andean ancestor. In concordance with DV predictions we studied that (i) these amphibians display a natural distribution gap in central Amazonia; (ii) east of this gap they constitute a monophyletic lineage which is nested within a pre-Andean/western clade; (iii) climate envelopes of Atelopus west and east of the distribution gap show some macroclimatic divergence due to a regional climate envelope shift; (iv) geographic distributions of climate envelopes of western and eastern Atelopus range into central Amazonia but with limited spatial overlap. We tested if presence and apparent absence data points of Atelopus were homogenously distributed with Ripley’s K function. A molecular phylogeny (mitochondrial 16S rRNA gene) was reconstructed using Maximum Likelihood and Bayesian Inference to study if Guianan Atelopus constitute a clade nested within a larger genus phylogeny. We focused on climate envelope divergence and geographic distribution by computing climatic envelope models with MaxEnt based on macroscale bioclimatic parameters and testing them by using Schoener’s index and modified Hellinger distance. We corroborated existing DV predictions and, for the first time, formulated new DV predictions aiming on species’ climate envelope change. Our results suggest that cool-adapted Andean Atelopus ancestors had dispersed into the Amazon basin and further onto the eastern Guiana Shield where, under warm conditions, they were forced to change climate envelopes.

Phylogenetic relationships of Sardinian cave salamanders, genus Hydromantes, based on mitochondrial and nuclear DNA sequence data

The Tyrrhenian island of Sardinia is known for its high level of endemism. Beside the importance of this island as a refuge during the last glaciations, little is known about the origin and relationships of Sardinian species. Therefore, in an effort to resolve these relationships, in the current study we extended the existing dataset considerably by adding two nuclear genes and additional mitochondrial sequence data, as well as greatly extend the number of Sardinian populations represented in the dataset from eight to 16 populations.