Phenotypic evolution and hidden speciation in Candidula unifasciata ssp. (Helicellinae, Gastropoda) inferred by 16S variation and quantitative shell traits

In an effort to link quantitative morphometric information with molecular data on the population level, we have analysed 19 populations of the conchologically variable land snail Candidula unifasciata from across the species range for variation in quantitative shell traits and at the mitochondrial 16S ribosomal (r)DNA locus. In genetic analysis, including 21 additional populations, we observed two fundamental haplotype clades with an average pairwise sequence divergence of 0.209 +/- 0.009 between clades compared to 0.017 +/- 0.012 within clades, suggesting the presence of two different evolutionary lineages. Integrating additional shell material from the Senckenberg Malacological Collection, a highly significant discriminant analysis on the morphological shell traits with fundamental haplotype clades as grouping variable suggested that the less frequent haplotype corresponds to the described subspecies C. u. rugosiuscula, which we propose to regard as a distinct species. Both taxa were highly subdivided genetically (FST = 0.648 and 0.777 P < 0.001). This was contrasted by the partition of morphological variance, where only 29.6% and 21.9% of the variance were distributed among populations, respectively. In C. unifasciata, no significant association between population pairwise FST estimates and corresponding morphological fixation indices could be detected, indicating independent evolution of the two character sets. Partial least square analysis of environmental factors against shell trait variables in C. u. unifasciata revealed significant correlations between environmental factors and certain quantitative shell traits, whose potential adaptational values are discussed.     

Evolutionary conservatism and convergence both lead to striking similarity in ecology,morphology and performance across continents in frogs

Many clades contain ecologically and phenotypically similar species across continents, yet the processes generating this similarity are largely unstudied, leaving fundamental questions unanswered. Is similarity in morphology and performance across assemblages caused by evolutionary convergence or by biogeographic dispersal of evolutionarily conserved ecotypes? Does convergence to new ecological conditions erase evidence of past adaptation? Here, we analyse ecology, morphology and performance in frog assemblages from three continents (Asia, Australia and South America), assessing the importance of dispersal and convergent evolution in explaining similarity across regions. We find three striking results. First, species using the same microhabitat type are highly similar in morphology and performance across both clades and continents. Second, some species on different continents owe their similarity to dispersal and evolutionary conservatism (rather than evolutionary convergence), even over vast temporal and spatial scales. Third, in one case, an ecologically specialized ancestor radiated into diverse ecotypes that have converged with those on other continents, largely erasing traces of past adaptation to their ancestral ecology. Overall, our study highlights the roles of both evolutionary conservatism and convergence in explaining similarity in species traits over large spatial and temporal scales and demonstrates a statistical framework for addressing these questions in other systems.     

Ecological Adaptations of Mandibular Form in Fissiped Carnivora

Among mammals, Carnivora presents an ideal group for investigating the complex interplay between functional adaptation and phylogenetic history. Here we explore mandibular form and its relationship to ecology and phylogeny using geometric morphometrics applied to mandibles of extant Carnivora. Both mandibular size and shape discriminate carnivoran ecological adaptations (diet, membership to small or large predatory guilds), but the interplay of morphology with phylogenetic history is profound. In general, families do not overlap in mandible shape; however, Viverridae, Herpestidae, Canidae, and Mustelidae exhibit functional and morphological convergence. Mandibular allometric trajectories are distinct among families and ecological categories. Our findings suggest that variability in mandibular form among Carnivora is primarily influenced by major evolutionary changes occurring at the family level and less, but significantly so, by ecological adaptations. Small generalist feeders (insectivores, omnivores) exhibit stronger convergence in mandibular shape than highly specialized predators; bigger taxa, such as bears, evolved unique morphologies constrained by allometric scaling. Thus, the findings of this study serve to demonstrate how ecological factors mold anatomical structures in similar ways to serve similar functions. As such, carnivoran species can be usefully grouped into functional ‘guilds’ in eco-morphological studies irrespective of their phylogenetic history.     

Morphological parallelism of sympatric cave-dwelling microsnails of the genus Georissa at Mount Silabur,Borneo (Gastropoda,Neritimorpha, Hydrocenidae)

Parallel evolution in phenotype may result when closely related taxa are adapting in the face of similar ecological pressures. Here, we discuss possible parallelism in shell morphology in the context of the microgeographic phylogeography of two conchologically distinct sympatric hydrocenid snails inhabiting a limestone outcrop and its cave system, Georissa pyrrhoderma and Georissa silaburensis, respectively, at Mount Silabur in Sarawak, Malaysian Borneo. Our results show a certain degree of morphological parallelism of a third, possibly new, cryptic Georissa species within the same cave that strongly diverged from its above-ground sister species, G. pyrrhoderma. We found that both sympatric cave species have shifted from a more sculptured, conical shell toward a broader, less sculptured form.     

Philometrids of the southern flounder Paralichthys lethostigma: a multidimensional approach to determine their diversity

Two species of philometrid nematode, Philometra overstreeti and Philometroides paralichthydis, infect the southern flounder, Paralichthys lethostigma. Individuals of P. overstreeti are located between the teeth and inside the bony part of the branchial arches of the fish. Individuals of P. paralichthydis are associated with the bones of the buccal cavity and among muscles that control the dorsal and anal fins. Sequencing of part of the cytochrome oxidase I gene revealed 4 distinct genetic clades, each corresponding exactly to the 4 respective locations of the parasites in the host, suggesting the need for taxonomic revision. We hypothesized that each clade represented a separate species and, because the worms are morphologically indistinguishable, compared population level parameters of the clades comprising each currently recognized species. For each currently recognized species, the presence of worms from 1 clade was negatively correlated with the presence of worms from the other. Results also indicated significant differences between the clades in prevalences relative to both biotic and abiotic factors. Results clearly indicated major differences in the ecology of the philometrids constituting each clade. Taken as a whole, molecular and ecological data support the contention that the 4 genetic clades are likely 4 distinct species.     

Phylogeographic analysis of Anatolian bats highlights the importance of the region for preserving the Chiropteran mitochondrial genetic diversity in the Western Palaearctic

Identification of intraspecific conservation units and incorporating the distribution of genetic diversity into management plans are crucial requirements for assessing effective protection strategies. This study investigates the phylogeographic structures of 33 bat species present in the Near East in order to evaluate the conservation implications of their intraspecific genetic diversity both at regional and large-scale levels. To compare Anatolian populations with the European ones, we utilized two commonly used mitochondrial markers, Cytb and ND1, and analysed them together with the available sequences from GenBank. The management requirements of the identified clades and their taxonomical relations were evaluated by analysing their distributions and the levels of their genetic differentiations. In 12 species and the large Myotis complex, we identified a total of 15 genetically distinct populations found in the Near East, some of which might represent biologically distinct taxa. Comparing the phylogeographic patterns of different taxa indicates that three regions, the Balkans, the Caucasus, and the southern Anatolia, harbour genetically divergent populations and should have higher priority in conservation practices. Considering that Turkey has one of the richest bat fauna in the Mediterranean region and the Anatolian populations of various species are genetically distinct, protecting populations in Turkey is critically important for preserving the genetic diversity of the bats in the Western Palaearctic. Both regional and large-scale conservation strategies, which incorporate the distribution of genetic diversity, should be assessed and further ecological studies are needed to clarify the taxonomic relations of the identified clades.     

Two undescribed species of Phylloporia from Mexico based on morphological and phylogenetic evidence

Phylloporia rzedowskii and Phylloporia ulloai, both collected in tropical forests of the Sierra of the Huasteca Potosina, San Luis Potosi, Mexico, are described as new species. The main critical morphological features that characterize them are the pileus shape, the pore diameter, the basidiospores shape and size, and, possibly, their ecology, such as the host relationships (specificity/preference). Both species also form distinct clades in phylogenetic analysis based on partial DNA sequences data from the nuclear ribosomal LSU. An identification key for 10 species reported from the Americas is proposed.     

Conservation genetics of three flightless beetle species in southern California

Regional scale conservation decisions can be aided by information on the distribution of intraspecific diversity, especially the extent to which patterns are common to multiple species. We compare patterns of intraspecific mitochondrial cytochrome oxidase I (COI) variation among three flightless beetles (Coleoptera: Tenebrionidae: Nyctoporis carinata LeConte; Staphylinidae: Sepedophilus castaneus (Horn); Carabidae: Calathus ruficollis Dejean) in the southern part of the California Floristic Province biodiversity hotspot. All species exhibit moderate to high levels of total variation, ranging from 2% to 10% (maximum uncorrected distance). Most populations of all species exhibit unique haplotypes, but few populations’ haplotypes constitute exclusive clades. Many adjacent pairs of populations show indications of some, though limited, genetic connectedness, due either to gene flow or ancestral polymorphism. However, in most cases this diminishes sharply over greater distances. By both statistical and phylogenetic measures, Sierra Nevadan populations are highly distinct from those in the coast and transverse ranges. Among the latter, the eastern transverse ranges are generally most unique and isolated, with diversity in the western parts of these ranges showing fewer barriers. Otherwise, few measures agree on areas of highest conservation value, and overall patterns tend to be species-specific.     

Convergent evolution across the Australian continent: ecotype diversification drives morphological convergence in two distantly related clades of Australian frogs

Animals from different clades but subject to similar environments often evolve similar body shapes and physiological adaptations due to convergent evolution, but this has been rarely tested at the transcontinental level and across entire classes of animal. Australia's biome diversity, isolation and aridification history provide excellent opportunities for comparative analyses on broad‐scale macroevolutionary patterns. We collected morphological and environmental data on eighty‐four (98%) Australian hylid frog species and categorized them into ecotypes. Using a phylogenetic framework, we tested the hypothesis that frogs from the same ecotype display similar body shape patterns: (i) across all the Australian hylids, and (ii) through comparison with a similar previous study on 127 (97%) Australian myobatrachid species. Body size and shape variation did not follow a strong phylogenetic pattern and was not tightly correlated with environment, but there was a stronger association between morphotype and ecotype. Both arboreal and aquatic frogs had long limbs, whereas limbs of fossorial species were shorter. Other terrestrial species were convergent on the more typical frog body shape. We quantified the strength of morphological convergence at two levels: (i) between fossorial myobatrachid and hylid frogs, and (ii) in each ecomorph within the hylids. We found strong convergence within ecotypes, especially in fossorial species. Ecotypes were also reflected in physiological adaptations: both arboreal and cocooned fossorial frogs tend to have higher rates of evaporative water loss. Our results illustrate how adaptation to different ecological niches plays a crucial role in morphological evolution, boosting phenotypic diversity within a clade. Despite phylogenetic conservatism, morphological adaptation to repeatedly emerging new environments can erase the signature of ancestral morphotypes, resulting in phenotypic diversification and convergence both within and between diverse clades.     

Developmental dynamics of ecomorphological convergence in a transcontinental lizard radiation

Phenotypic convergence has confounded evolutionary biologists for centuries, explained as adaptations to shared selective pressures, or alternatively, the result of limited developmental pathways. We tested the relative roles of adaptation and constraint in generating convergent cranial morphologies across a large lizard radiation, the Lacertidae, whose members inhabit diverse environments throughout the Old World and display high amounts of homoplasy associated with ecological niche. Using 3D X‐ray computed tomography, we quantified cranial shape variation associated with ontogeny, allometry, and ecology, covering all lacertid genera and one‐third of species diversity. Landmark‐based geometric morphometrics showed that cranial shape varied significantly among biomes, with substantial convergence among arid‐dwelling lineages. Comparisons of species cranial growth trajectories between biomes revealed that allometric postdisplacement, as evidenced by decreased elevation of a constant ontogenetic slope, drives the convergent paedomorphic appearance of independent arid‐dwelling forms. We hypothesize that observed heterochronic changes reflect temporal compression of ancestral life history in response to extreme environments, with associated phenotypes occurring as by‐products of adaptive shifts in reproductive investment. Although allometry has long been considered a developmental constraint, our results demonstrate that allometric flexibility during early ontogeny produces convergent ecomorphologies over vast temporal and spatial scales, thus dramatically obscuring underlying phylogenetic signals.     

Genetic diversity, recombination and cryptic clades in Pseudomonas viridiflava infecting natural populations of Arabidopsis thaliana

Species-level genetic diversity and recombination in bacterial pathogens of wild plant populations have been nearly unexplored. Pseudomonas viridiflava is a common natural bacterial pathogen of Arabidopsis thaliana, for which pathogen defense genes and mechanisms are becoming increasing well known. The genetic variation contained within a worldwide sample of P. viridiflava collected from wild populations of A. thaliana was investigated using five genomic sequence fragments totaling 2.3 kb. Two distinct and deeply diverged clades were found within the P. viridiflava sample and in close proximity in multiple populations, each genetically diverse with synonymous variation as high as 9.3% in one of these clades. Within clades, there is evidence of frequent recombination within and between each sequenced locus and little geographic differentiation. Isolates from both clades were also found in a small sample of other herbaceous species in Midwest populations, indicating a possibly broad host range for P. viridiflava. The high levels of genetic variation and recombination together with a lack of geographic differentiation in this pathogen distinguish it from other bacterial plant pathogens for which intraspecific variation has been examined.     

Rare ecomorphological convergence on a complex adaptive landscape: Body size and diet mediate evolution of jaw shape in squirrels (Sciuridae)

Convergence is widely regarded as compelling evidence for adaptation, often being portrayed as evidence that phenotypic outcomes are predictable from ecology, overriding contingencies of history. However, repeated outcomes may be very rare unless adaptive landscapes are simple, structured by strong ecological and functional constraints. One such constraint may be a limitation on body size because performance often scales with size, allowing species to adapt to challenging functions by modifying only size. When size is constrained, species might adapt by changing shape; convergent shapes may therefore be common when size is limiting and functions are challenging. We examine the roles of size and diet as determinants of jaw shape in Sciuridae. As expected, size and diet have significant interdependent effects on jaw shape and ecomorphological convergence is rare, typically involving demanding diets and limiting sizes. More surprising is morphological without ecological convergence, which is equally common between and within dietary classes. Those cases, like rare ecomorphological convergence, may be consequences of evolving on an adaptive landscape shaped by many‐to‐many relationships between ecology and function, many‐to‐one relationships between form and performance, and one‐to‐many relationships between functionally versatile morphologies and ecology. On complex adaptive landscapes, ecological selection can yield different outcomes.     

The causes of species richness patterns across space, time, and clades and the role of "ecological limits"

A major goal of research in ecology and evolution is to explain why species richness varies across habitats, regions, and clades. Recent reviews have argued that species richness patterns among regions and clades may be explained by "ecological limits" on diversity over time, which are said to offer an alternative explanation to those invoking speciation and extinction (diversification) and time. Further, it has been proposed that this hypothesis is best supported by failure to find a positive relationship between time (e.g., clade age) and species richness. Here, I critically review the evidence for these claims, and propose how we might better study the ecological and evolutionary origins of species richness patterns. In fact, ecological limits can only influence species richness in clades by influencing speciation and extinction, and so this new "alternative paradigm" is simply one facet of the traditional idea that ecology influences diversification. The only direct evidence for strict ecological limits on richness (i.e., constant diversity over time) is from the fossil record, but many studies cited as supporting this pattern do not, and there is evidence for increasing richness over time. Negative evidence for a relationship between clade age and richness among extant clades is not positive evidence for constant diversity over time, and many recent analyses finding no age-diversity relationship were biased to reach this conclusion. More comprehensive analyses strongly support a positive age-richness relationship. There is abundant evidence that both time and ecological influences on diversification rates are important drivers of both large-scale and small-scale species richness patterns. The major challenge for future studies is to understand the ecological and evolutionary mechanisms underpinning the relationships between time, dispersal, diversification, and species richness patterns.     

Resource partitioning and competition for shells in a subtidal hermit crab species assemblage

Summary Shell and habitat utilization are quantified for 12 hermit crab species occurring subtidally in the San Juan Archipelago, Washington. The mechanism of competition for shells between these species is investigated using laboratory experiments to determine shell preferences, shell acquisition rates, and rates of exchange of shells via shell fighting. This information is used to estimate relative intensities of inter- and intra-specific competition for shells between the species in this assemblage. In contrast to earlier findings on intertidal hermit crab assemblages, a significant number (5) of the species in this assemblage appear to experience a greater reduction in their shell supply due to members of other species than due to other members of their own species. The relative amounts of inter- and intra-specific competition differ greatly for different species in the community. The high average figures for interspecific/intraspecific competition are largely a result of the presence of three abundant and very generalized species. In spite of the large number of species and relatively high ratios of interspecific to intraspecific competition, the species in this group are not close to a limiting similarity in resource use. There is suggestive evidence that greater selection pressures for divergence in habitat use may have resulted in the lower amounts of overlap observed in intertidal hermit crab assemblages in previous studies.     

What explains patterns of species richness? The relative importance of climatic‐niche evolution,morphological evolution,and ecological limits in salamanders

A major goal of evolutionary biology and ecology is to understand why species richness varies among clades. Previous studies have suggested that variation in richness among clades might be related to variation in rates of morphological evolution among clades (e.g., body size and shape). Other studies have suggested that richness patterns might be related to variation in rates of climatic‐niche evolution. However, few studies, if any, have tested the relative importance of these variables in explaining patterns of richness among clades. Here, we test their relative importance among major clades of Plethodontidae, the most species‐rich family of salamanders. Earlier studies have suggested that climatic‐niche evolution explains patterns of diversification among plethodontid clades, whereas rates of morphological evolution do not. A subsequent study stated that rates of morphological evolution instead explained patterns of species richness among plethodontid clades (along with “ecological limits” on richness of clades, leading to saturation of clades with species, given limited resources). However, they did not consider climatic‐niche evolution. Using phylogenetic multiple regression, we show that rates of climatic‐niche evolution explain most variation in richness among plethodontid clades, whereas rates of morphological evolution do not. We find little evidence that ecological limits explain patterns of richness among plethodontid clades. We also test whether rates of morphological and climatic‐niche evolution are correlated, and find that they are not. Overall, our results help explain richness patterns in a major amphibian group and provide possibly the first test of the relative importance of climatic niches and morphological evolution in explaining diversity patterns.     

Functional morphology and palaeontological significance of the conchiolin layers in corbulid pelecypods

The Corbulidae, which today are slow, cumbersome, very shallow burrowers, developed special morphological features by which they obtained an outstanding capability to withstand the physical and biological stresses characteristic of their preferred habitat. These features are: an inequivalve, globose shape, thick shells, and conchiolin layers (at least one) embedded within their valves in a unique way. These features enable the corbulids to close their valves tightly during the unfavourable environmental conditions (e.g. low salinity, low oxygen content) which may prevail in the marginal marine regions inhabited by several corbulid species. The conchiolin layers act as a barrier preventing all chemically boring organisms from penetrating into the bivalve shell, or shell dissolution by sea water undersaturated with respect to calcium carbonate. The layered conchiolin weakens the shell mechanically, however, especially during fossilization, when the conchiolin is decomposed. The valve splits apart into two shells so completely different in appearance that they may be attributed to different taxa. The conchiolin layers are therefore of great ecological and palaeontological significance. The nature of these conchiolin layers in Corbula (Varicorbula) gibba (Olivi) is described and illustrated and their functional significance discussed in relation to other living and fossil corbulid species.     

Trophic novelty is linked to exceptional rates of morphological diversification in two adaptive radiations of Cyprinodon pupfish

Adaptive radiations are known for rapid morphological and species diversification in response to ecological opportunity, but it remains unclear if distinct mechanisms drive this pattern. Here, we show that rapid rates of morphological diversification are linked to the evolution of novel ecological niches in two independent Cyprinodon radiations nested within a wide-ranging group repeatedly isolated in extreme environments. We constructed a molecular phylogeny for the Cyprinodontidae, measured 16 functional traits across this group, and compared the likelihoods of single or multiple rates of morphological diversification. We found that rates of morphological diversification within two sympatric Cyprinodon clades containing unique trophic specialists are not part of an adaptive continuum with other clades, but are instead extreme outliers with rates up to 131 times faster than other Cyprinodontidae. High rates were not explained by clade age, but were instead linked to unique trophic niches within Cyprinodon, including scale-eating, zooplanktivory, and piscivory. Furthermore, although both radiations occur in similar environments and have similar sister species, they each evolved unique trophic specialists and high rates of morphological diversification in different sets of traits. We propose that the invasion of novel ecological niches may be a key mechanism driving many classic examples of adaptive radiation.     

A phylogenetic test for adaptive convergence in rock-dwelling lizards

Phenotypic similarity of species occupying similar habitats has long been taken as strong evidence of adaptation, but this approach implicitly assumes that similarity is evolutionarily derived. However, even derived similarities may not represent convergent adaptation if the similarities did not evolve as a result of the same selection pressures; an alternative possibility is that the similar features evolved for different reasons, but subsequently allowed the species to occupy the same habitat, in which case the convergent evolution of the same feature by species occupying similar habitats would be the result of exaptation. Many lizard lineages have evolved to occupy vertical rock surfaces, a habitat that places strong functional and ecological demands on lizards. We examined four clades in which species that use vertical rock surfaces exhibit long hindlimbs and flattened bodies. Morphological change on the phylogenetic branches leading to the rock-dwelling species in the four clades differed from change on other branches of the phylogeny; evolutionary transitions to rock-dwelling generally were associated with increases in limb length and decreases in head depth. Examination of particular characters revealed several different patterns of evolutionary change. Rock-dwelling lizards exhibited similarities in head depth as a result of both adaptation and exaptation. Moreover, even though rock-dwelling species generally had longer limbs than their close relatives, clade-level differences in limb length led to an overall lack of difference between rock- and non-rock-dwelling lizards. These results indicate that evolutionary change in the same direction in independent lineages does not necessarily produce convergence, and that the existence of similar advantageous structures among species independently occupying the same environment may not indicate adaptation.     

Molecular Evidence for Cryptic Speciation in the Cyclophorus fulguratus (Pfeiffer, 1854) Species Complex (Caenogastropoda: Cyclophoridae) with Description of New Species

A high degree of intraspecific variation, both genetic and in shell morphology, of the operculate land snail Cyclophorus fulguratus (Pfeiffer, 1854) suggests that its classification as a single species warrants reconsideration. We sequenced two nuclear (18S and 28S) and two mitochondrial (16S and COI) genes of 46 C. fulguratus specimens and used them to estimate the phylogeny and to determine the validity of species boundaries. Molecular phylogenetic analyses revealed the presence of three lineages corresponding to three geographically disjunctive populations of C. fulguratus in Thailand. Likelihood tests of topologies significantly supported the non-monophyly of the C. fulguratus–complex and Bayesian species delimitation analysis significantly supported the potential representation as distinct species of these three lineages. Discriminant function analysis based on geometric-morphometrics of shell shape allowed for significant distinction of these three candidate species, although they revealed a considerable degree of overlap of shell shape reflecting their crypsis morphologically. The diagnostic characters are provided by color pattern, pattern of protoconch and pattern of jaw. In conclusion, the results support that the C. fulguratus s.l., as currently recognized, consists of three distinct species in Thailand: C. fulguratus s.s., C. rangunensis and C. abditus sp.nov., which are described herein.