Maximizing information in systematic revisions: a combined molecular and morphological analysis of a cryptic green pitviper complex (Trimeresurus stejnegeri)

Although the integration of DNA information in taxonomy has been invaluable, logistical problems relating to sampling can seriously limit its applicability. Here we describe the analysis of a morphologically cryptic species complex, in which we maximize the information present by using both a DNA phylogeny and a multivariate morphometric approach. The green pitviper Trimeresurus stejnegeri s.l. is widespread in Asia, with a number of described subspecies (some of which are considered full species by some workers) and two new species that have recently been described from Thailand. The phylogeny indicates three clades, which can also be discerned in the principal component analyses of morphological variation. Combining molecular and morphological information permits evaluation of the taxonomic position of populations not represented in the phylogeny − in particular, the subspecies T. s. chenbihui and T. s. yunnanensis . We discuss nomenclatural issues raised by this analysis, although these cannot be fully resolved until the holotypes of these subspecies can be examined. Finally, we apply a molecular clock calibrated in New World pitvipers, and discuss some of the palaeoclimatic changes that might have impacted upon diversification in this group.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82 , 219–235.     

Mitochondrial diversification of the Peromyscus mexicanus species group in Nuclear Central America: biogeographic and taxonomic implications

The mountain mice of the Peromyscus mexicanus group currently encompass six known species; however, the limits between species remain uncertain, with two considered monotypic and the other four having multiple associated subspecific names. Based on the most comprehensive sampling of the group throughout its distribution in Nuclear Central America, we used data of the mitochondrial cytochrome b gene to assess its genetic diversity, phylogeny, and main biogeographic and diversification patterns. Our mitochondrial phylogeny only partially reflects the current taxonomy of the group, in agreement with some of the taxonomically recognized species. Specifically, our phylogenetic results show that the group is highly structured, including four main clades with genetic distances ranging from 11 to 8.6%. A remarkable level of differentiation is found at a more local level, defined as 15 different lineages with high nucleotide and haplotype diversity (π = 0.068, h = 0.99), and with divergence and genetic distance values (p‐uncorrected = 9.9–2.4%; K2P = 10.8–3.0%) similar to values observed between species within Peromyscus. Accordingly, we propose that the reference name P. mexicanus is polyphyletic and should be restricted to the mountains of central Mexico west of the Isthmus of Tehuantepec. We suggest to limit the other five recognized specific names to equal number of lineages, as monophyletic, and to revalidate three junior synonyms: Peromyscus salvadorensis, P. nicaraguae and P. tropicalis. The Isthmus of Tehuantepec, the Motagua‐Polochic‐Jocotán fault system, the Maya Highlands and the Honduras Depression are examples of geographic features that are likely associated with the differentiation of main lineages. Some other lineages may represent candidate species, hence the need to review the taxonomic status of the entire P. mexicanus group.     

An evaluation of the systematic value of skull morphology in the Trimeresurus radiation (Serpentes: Viperidae: Crotalinae) of Asian pitvipers

Trimeresurus (in its widest sense) is a very diverse and widespread radiation of Asian pitvipers, which has been subject to numerous taxonomic revisions, some of which have been based on characteristics of the skull. In order to evaluate the taxonomic utility of such characters, we conducted a comparison of the skulls of 57 specimens representing nine genera, and two currently unassigned species that are very closely related to each other. A canonical variate analysis reveals three distinct phenetic groups: the Protobothrops group, a group containing Ovophis monticola , ' Ovophis ' okinavensis , and ' Trimeresurus ' gracilis , and finally a group comprising the remaining species and characterized by considerable overlap between most genera with the exception of the monotypic Peltopelor and Himalayophis . Agreement between phenetic similarity based on skull characteristics and phylogenetic relationships based on molecular evidence varies between different groups: the morphological similarity of the skull of Protobothrops sieversorum to the other Protobothrops species is congruent with their recent synonymization while the phenetic similarity among the species within the second group does not reflect current molecular phylogenetic relationships and indicates that convergent or parallel evolution may be responsible for at least some of the phenetic similarity detected among skulls of the Asian pit vipers examined. A test of phylogenetic independence, however, indicates that there is still a significant phylogenetic signal that can be recovered from several skull characteristics. Thus, we conclude that skull morphology can contribute to an overall understanding of pitviper taxonomy, but that it would be unwise to rely on skull characteristics alone.     

A test of adaptive hypotheses: Mandibular traits,nest construction materials,and feeding habits in neotropical social wasps (Vespidae,Polistinae)

Summary. The success of many behaviors in hymenoptera depends on the shape and structure of their mandibles. Neotropical social wasps exhibit variation in the shape of their mandibles; both the type of material used in the nest construction and the food sources have been proposed as selective forces that explain that variation. These hypotheses were studied using Independent Contrast analyses and combined tests of significance between: nine mandibles traits, the type of nest material and food source types. Necrophagy and short fiber use are derived conditions in the subfamily that have evolved five times each, while the use of long fibers and live prey are primitive conditions. The mandible structures appear related to the nest fiber type but not to necrophagy. Particularly, species that use long fibers have bigger internal dorsal tooth, longer internal ventral tooth, and shorter and more curved mandibles. Similar results were obtained by including plant hairs as a third nest material type. These findings open related questions for groups of social insects where studies on evolution of mandibles have emphasized food sources.Received 23 November 2003; revised 9 March 2004; accepted 21 April 2004.     

Morphological convergence of shell shape in distantly related scallop species (Mollusca: Pectinidae)

Morphological convergence is a central concept in evolutionary biology, but convergent patterns remain under‐studied in nonvertebrate organisms. Some scallop species exhibit long‐distance swimming, a behaviour whose biomechanical requirements probably generate similar selective regimes. We tested the hypothesis that shell shape similarity in long‐distance swimming species is a result of convergent evolution. Using landmark‐based geometric morphometrics, we quantified shell shape in seven species representing major behavioural habits. All species displayed distinct shell shapes, with the exception of the two long‐distance swimmers, whose shells were indistinguishable. These species also displayed reduced morphological variance relative to other taxa. Finally, a phylogenetic simulation revealed that these species were more similar in their shell shape than was expected under Brownian motion, the model of character evolution that best described changes in shell shape. Together, these findings reveal that convergent evolution of shell shape occurs in scallops, and suggest that selection for shell shape and behaviour may be important in the diversification of the group. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 571–584.     

Phenotypic plasticity raises questions for taxonomically important traits: a remarkable new Andean rainfrog (Pristimantis) with the ability to change skin texture

We describe a new frog, Pristimantis mutabilis sp. nov., from the Andes of Ecuador. Individuals of the new species are remarkable for their ability to change skin texture from tuberculate to almost smooth in a few minutes, being the first documented amphibian species to show such dramatic phenotypic plasticity. The new taxon is assigned to the P. myersi group. It differs from other members of its group by body size (adult males 17.2–17.4 mm; adult females 20.9–23.2 mm), arboreal habitat, and red flash coloration in females. We document three call types for the new species, which differ through their number of notes and amplitude peaks. The three types are pulsed calls that share a dominant frequency of 3186.9–3445.3 Hz. Surprisingly, we also document similar skin texture plasticity in species (P. sobetes) from a different species group, suggesting that this ability might be more common than previously thought. The discovery of these variable species poses challenges to amphibian taxonomists and field biologists, who have traditionally used skin texture and presence/absence of tubercles as important discrete traits in diagnosing and identifying species. Reciprocal monophyly and genetic distances also support the validity of the new species, as it has distances of 15.1–16.3% (12S) and 16.4–18.6% (16S) from the most similar species, Pristimantis verecundus. Additionally, each of the two known populations of Pristimantis mutabilis are reciprocally monophyletic and exhibit a high genetic distance between them (5.0–6.5%). This pattern is best explained by the presence of a dry valley (Guayllabamba River) that seems to be acting as a dispersal barrier. © 2015 The Linnean Society of London     

Evidence for speciational change in the evolution of ratites (Aves: Palaeognathae)

To perform a comparative analysis of character associations framed in a phylogenetic context (e.g. independent contrasts), a model of character evolution must be assumed. According to phyletic gradualism, morphological change accumulates gradually over time within lineages, and speciation events do not have a major role. Under speciational models, morphological change is assumed to occur during or just after cladogenesis in both daughter species, and the resulting morphologies do not change over long periods of time (stasis), until the next cladogenetic event. A novel method is presented for comparing these models of character evolution that uses permutational multiple phylogenetic regressions. The addition of divergence times to well-corroborated phylogenetic trees and the utilization of the method developed in this paper allows the estimation of relative frequency of gradual change and speciational change from living organisms. This method is applied to a dataset from ratites with the conclusion that, for a range of morphological features, change tends to have been speciational rather than gradual.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 99–106.     

Life history and allozyme diversification in regional ecomorphs of the Hyalella azteca (Crustacea: Amphipoda) species complex

In North America, several species in the freshwater amphipod genus Hyalella occur as one of two alternative phenotypic types, or 'ecomorphs', each possessing life history traits that allow success in alternative habitats that differ in predation regime. This study documents life history diversification, reproductive isolation and allozyme differentiation of Hyalella ecomorphs in Oklahoma, and compares these results to previously reported patterns of phenotypic and systematic diversification in Michigan. As in Michigan, two ecomorphs are common in Oklahoma, with an early maturing, small sized ecomorph found in habitats containing Lepomis sunfish, which prey on Hyalella , and a late reproducing, large sized ecomorph found in fishless habitats and in very shallow margins of large reservoirs. Allozyme analysis and laboratory interbreeding trials demonstrated that ecomorphs in Oklahoma are reproductively isolated species. Phenotypically, these species are very similar to species of the same ecomorph in Michigan. Large ecomorph species in the two regions differ substantially in allozyme allele composition in a pattern consistent with reproductive isolation, yet these species did not differ in a comparison of phenotype. The small ecomorph in Oklahoma is similar in phenotype to two of three small ecomorph species in Michigan. Overall, this study supports the hypothesis that Hyalella diversification in North America is characterized by the evolution of similar phenotypic solutions to comparable ecological challenges.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 161–175.     

Intricate evolutionary histories in montane species: a phylogenetic window into craniodental discrimination in the Peromyscus mexicanus species group (Mammalia: Rodentia: Cricetidae)

Mountain‐associated species, which exhibit allopatric distributions associated with elevation, endemisms and complex evolutionary histories, pose challenging evolutionary scenarios in which to discern the diversification of species. The Peromyscus mexicanus mice group, distributed along mountains in southern Mexico and Central America, is morphometrically variable, a key rationale for the ongoing controversy regarding its species delimitation. Based on the recognized 15 mitochondrial lineages for the group, we analysed external and craniodental morphometric variables to test whether lineages can be differentiated morphometrically and allow for the delimitation of species. We also aimed to test the prediction that the phylogenetic structure of the morphometric data is concordant with that of the molecular information. Based on 19 craniodental measurements from 521 specimens, multivariate and discriminant analyses showed that lineages are morphometrically discernible, representing distinct phenotypes, and that overall size and mandible measurements are significant features that discriminate lineages, supporting hypotheses about differences in feeding habits between species. Also, a pattern of increasing size with elevation was observed, further supported by specific morphological differences exhibited between highland and lowland lineages inhabiting the same mountain. Our results demonstrate that P. mexicanus is both genetically and morphometrically variable, where most highland montane species are differentiated from lowland species; also, a significant correlation between mitochondrial and morphometric information is indicative of phenetic concordance, altogether in agreement with a recent taxonomic proposal for the group. We suggest that the group's intricate diversification responds to ecological diversification and adaptation to a variety of mountain habitats and Pleistocene biogeographic climatic dynamics.     

Morphological convergence and coexistence in three sympatric North American species of Microtus (Rodentia: Arvicolinae)

Aim  Niche theory predicts that ecologically identical species cannot stably coexist in local communities. My aim was to investigate morphological diversity as a possible factor enabling the coexistence of a species-rich Microtus (Rodentia: Arvicolinae) fauna in a hotspot of North American mammalian diversity, the Greater Yellowstone Ecosystem (GYE).
Location  The Greater Yellowstone Ecosystem, North America.
Methods  Using in-hand morphological measurements of size and shape, I compared the morphologies of three North American vole species ( Microtus spp.), in sympatry in the GYE and in allopatry across their ranges, in order to examine: (1) whether morphologies are fixed or plastic and (2) the degree of morphological character displacement or convergence in sympatric species.
Results  Support was found for plasticity of morphology for all three vole species: M. longicaudus , M. montanus and M. pennsylvanicus. However, Microtus individuals of all species from the GYE area of sympatry were more similar to each other than to allopatric individuals of the same species.
Main conclusions  Competition among these congeners is not manifested in morphological overdispersion. The response of these congeneric species to the same local ecological conditions is convergent. The relative strength of environmental conditions appears to be stronger than the strength of competitive interactions among the study species.     

Molecular identification of schistosome intermediate hosts: case studies of Bulinus forskalii group species (Gastropoda: Planorbidae) from Central and East Africa

African freshwater snails of the genus Bulinus act as intermediate hosts for schistosomes, trematode parasites responsible for medical and veterinary forms of schistosomiasis. The relationship between these snails and their parasites is an intricate one, with particular species of snail susceptible to infection only by certain species of schistosome. In common with other self-fertile hermaphrodite gastropods, Bulinus consists of a number of closely related species complexes with restricted gene flow between populations of each taxon. Consequently, despite their medical and veterinary importance as intermediate hosts, unambiguous identification and differentiation of planorbid snails such as these remains problematic, often confounding attempts to define the distribution and evolutionary relationships of conchologically similar taxa. Here we consider how morphological methods of discrimination can be used in conjunction with molecular based approaches to improve snail identification, thereby achieving a better understanding of the epidemiology of schistosomiasis. Data are presented from Central and East African taxa which illustrate how PCR-based methods have begun to be used in combination with traditional analyses in an integrated approach to characterize the genus Bulinus , specifically the B. forskalii species group. Particular emphasis is given to the analyses of Random Amplified Polymorphic DNA (RAPDs) and the mitochondrial gene cytochrome oxidase I (COI).     

The evolution of ecologically important characters in Heliconius butterflies (Lepidoptera: Nymphalidae): a cladistic review

The biology of Heliconius butterflies has provided a rich source of data to test theories of ecological genetics, coevolution and community ecology. Many putatively adaptive characters have been discussed with reference to a phylogenetic hypothesis based on a variety of morphological and life-history traits interpreted from an evolutionary taxonomic perspective. Here, alternate interpretations of characters on the traditional tree and a more recent mitochondrial DNA cladogram with a substantially different topology are compared and contrasted. It is shown that many characters ostensibly providing support for the traditional phylogenetic hypothesis are almost equally parsimoniously distributed and in some cases more parsimoniously distributed on the mtDNA tree than on the tree inferred from those characters. Discussion of alternate evolutionary scenarios based on the mDNA-based topology is presented for pupal mating, pollen feeding, foodplant coevolution, and other ecologically significant features.     

Combining mitochondrial DNA sequences and morphological data to infer species boundaries: phylogeography of lanceheaded pitvipers in the Brazilian Atlantic forest,and the status of Bothrops pradoi (Squamata: Serpentes: Viperidae)

Phylogeographic studies using mitochondrial DNA sequence information are frequently used as the principal source of evidence to infer species boundaries. However, a critical analysis of further evidence is essential to test whether different haplotype clades identify different species. We demonstrate a hypothesis‐testing approach, using a combination of phylogeographic methods, multivariate morphometrics and matrix association tests, to investigate species boundaries in eastern Brazilian pitvipers conventionally assigned to the species Bothrops leucurus and B. pradoi. Two basal haplotype clades with partly overlapping geographical distributions are identified, which could either represent two partly sympatric species, or multiple haplotypes within one organismal lineage. We use partial Mantel matrix association tests to verify whether generalized morphology, or any of four supposedly diagnostic characters for the two species, show any association with mtDNA variation. Negative results lead to the conclusion that the haplotype clades do not denote independently evolving organismal lineages, and do not constitute separate species under any criterion.     

A molecular identification key for economically important thrips species (Thysanoptera: Thripidae) using direct sequencing and a PCR-RFLP-based approach

Abstract

• 1 Treatments against pathogens or pests are often very specific and, as a fundamental first step, require the ability to identify taxa correctly and unambiguously. We used PCR amplification techniques to successfully establish a molecular identification key for economically important thrips species.
• 2 A PCR amplified 433 bp long fragment of the mitochondrial COI coding gene was analysed by automated direct sequencing and RFLP. Sequencing of 264 individual thrips representing 10 named species detected 17 haplotypes. Variation within species was low, whereas among species variation was high resulting in an average sequence divergence of 18.6% and an average pairwise species differentiation (calculated as F_ST‐value) of 0.9896.
• 3 Two restriction enzymes (AluI, Sau3AI) produced patterns that allowed unambiguous identification of all thrips species.
• 4 Statistical support for the quality of the key was given by (i) a highly significant permutation approach, assigning individual haplotypes to the correct species groups and (ii) a hierarchical NJ cluster analysis in which all conspecific individual sequences clustered together with maximal (100%) bootstrap support.
• 5 This study has shown that the use of genetic markers represents a valuable alternative for situations, such as epidemiological research, in which correct identification with classical morphological methods is either very difficult and time consuming or virtually impossible.

     

Variability of functional traits and their syndromes in a freshwater fish species (Phoxinus phoxinus): The role of adaptive and nonadaptive processes

Functional traits can covary to form “functional syndromes.” Describing and understanding functional syndromes is an important prerequisite for predicting the effects of organisms on ecosystem functioning. At the intraspecific level, functional syndromes have recently been described, but very little is known about their variability among populations and—if they vary—what the ecological and evolutionary drivers of this variation are. Here, we quantified and compared the variability in four functional traits (body mass, metabolic rate, excretion rate, and boldness), their covariations and the subsequent syndromes among thirteen populations of a common freshwater fish (the European minnow, Phoxinus phoxinus). We then tested whether functional traits and their covariations, as well as the subsequent syndromes, were underpinned by the phylogenetic relatedness among populations (historical effects) or the local environment (i.e., temperature and predation pressure), and whether adaptive (selection or plasticity) or nonadaptive (genetic drift) processes sustained among‐population variability. We found substantial among‐population variability in functional traits and trait covariations, and in the emerging syndromes. We further found that adaptive mechanisms (plasticity and/or selection) related to water temperature and predation pressure modulated the covariation between body mass and metabolic rate. Other trait covariations were more likely driven by genetic drift, suggesting that nonadaptive processes can also lead to substantial differences in trait covariations among populations. Overall, we concluded that functional syndromes are population‐specific, and that both adaptive and nonadaptive processes are shaping functional traits. Given the pivotal role of functional traits, differences in functional syndromes within species provide interesting perspectives regarding the role of intraspecific diversity for ecosystem functioning.     

Ecological mechanisms favouring behavioural diversification in the absence of morphological diversification: a theoretical examination using brook charr (Salvelinus fontinalis)

1. Behavioural diversification is thought to be an important initial step in the origin of resource polymorphisms. We developed a model for young brook charr (Salvelinus fontinalis Mitchill) to examine four mechanisms that could generate a U-shaped relationship between growth rate (fitness) and the proportion of time spent moving that would favour alternative foraging tactics in the absence of obvious differences in body size and shape. 2. Recently emerged brook charr of similar size and shape inhabit still-water pools along the sides of streams. Some individuals tend to sit and wait for crustacean prey at the pool substrate near the bank, while others tend to search actively for insect prey at the pool surface away from the bank. 3. The ecological mechanisms modelled were (i) the relationship between the rate of prey capture and the proportion of time spent moving is curvilinear, such that net rate of energy gain is maximized at two different levels of activity; (ii) switching between foraging locations and, hence, tactics involves lost opportunity and travel costs; (iii) switching between prey types and, hence, tactics involves a learning cost; and (iv) foraging success is status-dependent with individuals switching between tactics having a lower status than those specializing at a tactic. 4. Singly, no mechanism predicted the U-shaped relationship between growth rate and the proportion of time spent moving. Together, a U-shaped relationship was obtained, indicating that the behavioural diversification and diversifying selection observed in the field may be a consequence of multiple, subtle mechanisms.     

Sequence analysis of the mitochondrial DNA control region of ciscoes (genus Coregonus): taxonomic implications for the Great Lakes species flock

Sequence variation in the control region (D-loop) of the mitochondrial DNA (mtDNA) was examined to assess the genetic distinctiveness of the shortjaw cisco ( Coregonus zenithicus ). Individuals from within the Great Lakes Basin as well as inland lakes outside the basin were sampled. DNA fragments containing the entire D-loop were amplified by PCR from specimens of C. zenithicus and the related species C. artedi , C. hoyi , C. kiyi , and C. clupeaformis . DNA sequence analysis revealed high similarity within and among species and shared polymorphism for length variants. Based on this analysis, the shortjaw cisco is not genetically distinct from other cisco species.     

Phylogeography of the Patelloida profunda group (Gastropoda: Lottidae): diversification in a dispersal-driven marine system

In the last decade, greater than expected levels of genetic structure have been reported for many marine taxa with high dispersal capabilities. Although little-studied to date, it is predicted that taxa with poor dispersal abilities would exhibit even more genetic differentiation than high dispersal taxa. These systems may track biogeographical processes better than more dispersive taxa and, more critically, function as the 'lowest common denominators' in MPA design initiatives. We investigate phylogeographical patterns in the poorly dispersing, yet widely distributed Patelloida profunda group and related congeners across the Indo-west Pacific region. One hundred and twenty-five individuals were sequenced for COI mtDNA [593 base pairs (bp)] and 44 individuals were sequenced for 16S mtDNA (539 bp). Identified P. profunda group lineages are highly geographically structured, with 12 reciprocally monophyletic lineages reported from 13 localities. Divergences within Indian and Pacific basins range from d = 0.013 to 0.127 and between basins from d = 0.147 to 0.197. The latter split is ancient (> 15 Myr) and cannot be related to Plio-Pleistocene sea-level fluctuations, characteristic of previously reported divergences in the same region. Juxtaposed against this structure is genetic connectivity between two widely separated P. profunda populations that share a common haplotype (phiST = 0.001). This finding contrasts with previous work in the same geographical region and cautions strongly against single taxon indicators for designing conservation priorities or marine protected areas (MPAs). Historical and/or biological factors may play more significant roles than oceanography alone in determining the genetic structuring of taxa. In light of these findings, we discuss the difficulty in deriving biogeographical process or directionality from phylogenetic trees in dispersal-driven systems. Even with a well-resolved, highly supported topology, many equally parsimonious scenarios are possible.