Phylogeny of the African representatives of the catfish family Clariidae (Teleostei, Siluriformes) based on a combined analysis: independent evolution towards anguilliformity

Clariid catfishes span a broad range of body forms ranging between fusiform and anguilliform morphotypes. Although such variation in body shape has been observed in other families of teleost fishes, amphibians and reptiles, it is rarely as extreme as within the Clariidae. Although the Clariidae were thought to have undergone anagenetic evolution (i.e. progressive evolution within a lineage), more recent studies indicate that anguilliformity evolved several times through a process of cladogenesis (i.e. branching of evolutionary lineages). In this study, it is shown that the phylogenetic analysis of morphological data mainly gives a reflection of the cranial evolution in the Clariidae despite the use of 18 post-cranial characters (out of a total of 53 characters). A combined phylogenetic analysis of both morphological and molecular data rather suggests the derived nature of body elongation. The corresponding morphological changes that co-occur with this elongation can be regarded as an extreme case of convergent evolution at the genus level within the Clariidae.     

Insight into the phylogeny of African Clariidae (Teleostei, Siluriformes): implications for their body shape evolution, biogeography, and taxonomy

The phylogenetic relationships among Clariidae species (Teleostei, Siluriformes) were assessed using 563 nucleotides of the cytochrome b mitochondrial gene. We included 32 Clariidae species representative of seven genera in our analysis. Hetropneustes fossilis (Heteropneustidae) and Clarotes laticeps (Claroteidae) were used as outgroups. The molecular data identified two evolutionary lineages that correspond on one hand to African species and on the other hand to Asian species. Morphological and osteological evolution in Clariidae did not follow an orthogenetic series. Species with robust body, strong ossified head, and large adipose fin were not ancestral ones and eel-like species were not phylogenetically related and represent independent adaptation to life in mud. Adaptation to life in deep water occurred two times independently in lake Tanganyika (with Dinotopterus cunningtoni) and in Lake Malawi (with Bathyclarias species). Molecular dating using a molecular clock of 1% divergence per million years and a comparison with fossils records allowed an estimate of the timing of cladogenesis within the species studied. The Clariidae family originated in Asia 50 MY ago but contemporary African and Asian studied species originated from a common ancestor that was present on the Arabian plate about 15 MY ago. Systematic implications of these results are also discussed.     

Evolutionary constraints in hind wing shape in Chinese dung beetles (Coleoptera: Scarabaeinae)

This study examines the evolution hindwing shape in Chinese dung beetle species using morphometric and phylogenetic analyses. Previous studies have analyzed the evolution of wing shape within a single or very few species, or by comparing only a few wing traits. No study has analyzed wing shape evolution of a large number of species, or quantitatively compared morphological variation of wings with proposed phylogenetic relationships. This study examines the morphological variation of hindwings based on 19 landmarks, 119 morphological characters, and 81 beetle species. Only one most parsimonious tree (MPT) was found based on 119 wing and body characters. To better understand the possible role of the hindwing in the evolution of Scarabaeinae, additional phylogenetic analyses were proposed based on the only body features (106 characters, wing characters excluded). Two MPT were found based on 106 body characters, and five nodes were collapsed in a strict consensus. There was a strong correlation between the morphometric tree and all phylogenetic trees (r>0.5). Reconstructions of the ancestral wing forms suggest that Scarabaeinae hindwing morphology has not changed substantially over time, but the morphological changes that do occur are focused at the base of the wing. These results suggest that flight has been important since the origin of Scarabaeinae, and that variation in hindwing morphology has been limited by functional constraints. Comparison of metric disparity values and relative evolutionary sequences among Scarabaeinae tribes suggest that the primitive dung beetles had relatively diverse hindwing morphologies, while advanced dung beetles have relatively similar wing morphologies. The strong correlation between the morphometric tree and phylogenetic trees suggest that hindwing features reflect the evolution of whole body morphology and that wing characters are suitable for the phylogenetic analyses. By integrating morphometric and cladistic approaches, this paper sheds new light on the evolution of dung beetle hind wings.     

Discrete and morphometric traits reveal contrasting patterns and processes in the macroevolutionary history of a clade of scorpions

Many palaeontological studies have investigated the evolution of entire body plans, generally relying on discrete character‐taxon matrices. In contrast, macroevolutionary studies performed by neontologists have mostly focused on morphometric traits. Although these data types are very different, some studies have suggested that they capture common patterns. Nonetheless, the tests employed to support this claim have not explicitly incorporated a phylogenetic framework and may therefore be susceptible to confounding effects due to the presence of common phylogenetic structure. We address this question using the scorpion genus Brachistosternus Pocock 1893 as case study. We make use of a time‐calibrated multilocus molecular phylogeny, and compile discrete and traditional morphometric data sets, both capturing the overall morphology of the organisms. We find that morphospaces derived from these matrices are significantly different, and that the degree of discordance cannot be replicated by simulations of random character evolution. Moreover, we find strong support for contrasting modes of evolution, with discrete characters being congruent with an ‘early burst’ scenario whereas morphometric traits suggest species‐specific adaptations to have driven morphological evolution. The inferred macroevolutionary dynamics are therefore contingent on the choice of character type. Finally, we confirm that metrics of correlation fail to detect these profound differences given common phylogenetic structure in both data sets, and that methods incorporating a phylogenetic framework and accounting for expected covariance should be favoured.     

Structure and function in the catfish

The catfish (Siluroidei) appear to have evolved from an ancestor which, in most respects other than the form of its teeth, resembled primitive Characinoidei. In the first part of this paper it is shown that most of the numerous and profound anatomical changes which have occurred in the course of their evolution from this ancestor can be related to one or other of three basic changes: depression of the body in adaptation to bottom-feeding habits, sensory modification in adaptation to nocturnal habits, and the evolution of defensive fin spines. Diplomystes is more primitive than other known catfish in the form of its maxilla and pectoral girdle, and in the posterior position of its dorsal fin.
The second part of the paper is concerned with some of the more specialized families of catfish (Mochokidae, Siluridae, Schilbeidae, Malapteruridae, Clariidae, Callichthyidae and Loricariidae). The specializations in each case are described, and related to the habits of the fish.     

Size increase and form allometry during evolution of ciliate species in the genera Colpoda and Tillina (Ciliophora: Colpodida).

With the absence of a fossil record to provide direct evidence of evolutionary relationships, many researchers have inferred by circular reasoning that body size increase and form allometry have occurred during the evolution of ciliated protozoa. This study establishes ancestor-descendant relationships among five species of the related genera Colpoda and Tillina using ultrastructural characteristics which are not apparently dependent on size and form. This independent test suggests that phylogenetic size increase and phylogenetic form allometry have occurred during the evolution of these ciliates. Interrelationships of body size increase, increase in number of cortical organelles, and form allometry are discussed in reference to the divergence of these ciliate species.     

Macroevolution of life‐history traits in passerine birds: adaptation and phylogenetic inertia

We used a recent passerine phylogeny and comparative method to evaluate the macroevolution of body and egg mass, incubation and fledging periods, time to independence and time with parents of the main passerine lineages. We hypothesised that passerine reproductive traits are affected by adaptation to both past and present environmental factors and phenotypic attributes such as body mass. Our results suggest that the evolution of body and egg mass, time to independence, incubation and fledging times are affected by strong phylogenetic inertia and that these breeding traits are all affected by body mass. Time with parents, where major lineages exhibit their own fixed optima and body mass does not have an effect, and clutch size which is affected by body mass and additionally by climate regimes, do not exhibit any phylogenetic inertia.     

从细胞色素b基因序列变异分析中国鲇形目鱼类的系统发育

采用PCR技术获得中国鲇形目鱼类11科24属27个代表种类细胞色素b基因1138bp全序列,比较分析了来自北美洲、非洲的部分鲇形目鱼类同一基因序列,并选取脂鲤目、鲤形目和鲱形目鱼类作外类群,采用Bayesian方法和最大简约法(MP)构建分子系统树。结果表明：(1)鲇形目鱼类细胞色素b基因序列中,与脂鲤目、鲤形目以及鲱形目鱼类相比存在3bp的缺失;(2)鲇形目鱼类各科代表种类形成一单系群;(3)两种建树方法均支持铫科、粒鲇科和钝头鮠科形成一单系群;而胡子鲇科、刀鲇科、海鲇科、鮰科、长臀鮠科、鲢科、鲇科、棘脂鲿科、鲿科形成一大的单系群;但鳗鲇科的系统位置两种建树方法没有取得一致结果;而其中长臀鲍科与北美的鮰科形成姐妹群,胡子鲇、鮰科、鲇科、鲿科和鮡科是较明显的单系群。     

Body Size Evolution in Extant Oryzomyini Rodents: Cope's Rule or Miniaturization?

At the macroevolutionary level, one of the first and most important hypotheses that proposes an evolutionary tendency in the evolution of body sizes is "Cope's rule". This rule has considerable empirical support in the fossil record and predicts that the size of species within a lineage increases over evolutionary time. Nevertheless, there is also a large amount of evidence indicating the opposite pattern of miniaturization over evolutionary time. A recent analysis using a single phylogenetic tree approach and a bayesian based model of evolution found no evidence for Cope's rule in extant mammal species. Here we utilize a likelihood-based phylogenetic method, to test the evolutionary trend in body size, which considers phylogenetic uncertainty, to discern between Cope's rule and miniaturization, using extant Oryzomyini rodents as a study model. We evaluated body size trends using two principal predictions: (a) phylogenetically related species are more similar in their body size, than expected by chance; (b) body size increased (Cope's rule)/decreased (miniaturization) over time. Consequently the distribution of forces and/or constraints that affect the tendency are homogenous and generate this directional process from a small/large sized ancestor. Results showed that body size in the Oryzomyini tribe evolved according to phylogenetic relationships, with a positive trend, from a small sized ancestor. Our results support that the high diversity and specialization currently observed in the Oryzomyini tribe is a consequence of the evolutionary trend of increased body size, following and supporting Cope's rule.     

Correlated evolution of body and fin morphology in the cichlid fishes

Body and fin shapes are chief determinants of swimming performance in fishes. Different configurations of body and fin shapes can suit different locomotor specializations. The success of any configuration is dependent upon the hydrodynamic interactions between body and fins. Despite the importance of body–fin interactions for swimming, there are few data indicating whether body and fin configurations evolve in concert, or whether these structures vary independently. The cichlid fishes are a diverse family whose well‐studied phylogenetic relationships make them ideal for the study of macroevolution of ecomorphology. This study measured body, and caudal and median fin morphology from radiographs of 131 cichlid genera, using morphometrics and phylogenetic comparative methods to determine whether these traits exhibit correlated evolution. Partial least squares canonical analysis revealed that body, caudal fin, dorsal fin, and anal fin shapes all exhibited strong correlated evolution consistent with locomotor ecomorphology. Major patterns included the evolution of deep body profiles with long fins, suggestive of maneuvering specialization; and the evolution of narrow, elongate caudal peduncles with concave tails, a combination that characterizes economical cruisers. These results demonstrate that body shape evolution does not occur independently of other traits, but among a suite of other morphological changes that augment locomotor specialization.     

HOW LIZARDS TURN INTO SNAKES: A PHYLOGENETIC ANALYSIS OF BODY-FORM EVOLUTION IN ANGUID LIZARDS

Abstract One of the most striking morphological transformations in vertebrate evolution is the transition from a lizardlike body form to an elongate, limbless (snakelike) body form. Despite its dramatic nature, this transition has occurred repeatedly among closely related species (especially in squamate reptiles), making it an excellent system for studying macroevolutionary transformations in body plan. In this paper, we examine the evolution of body form in the lizard family Anguidae, a clade in which multiple independent losses of limbs have occurred. We combine a molecular phylogeny for 27 species, our morphometric data, and phylogenetic comparative methods to provide the first statistical phylogenetic tests of several long‐standing hypotheses for the evolution of snakelike body form. Our results confirm the hypothesized relationships between body elongation and limb reduction and between limb reduction and digit reduction. However, we find no support for the hypothesized sequence going from body elongation to limb reduction to digit loss, and we show that a burrowing lifestyle is not a necessary correlate of limb loss. We also show that similar degrees of overall body elongation are achieved in two different ways in anguids, that these different modes of elongation are associated with different habitat preferences, and that this dichotomy in body plan and ecology is widespread in limb‐reduced squamates. Finally, a recent developmental study has proposed that the transition from lizardlike to snakelike body form involves changes in the expression domains of midbody Hox genes, changes that would link elongation and limb loss and might cause sudden transformations in body form. Our results reject this developmental model and suggest that this transition involves gradual changes occurring over relatively long time scales.     

Effect of site-specific heterogeneous evolution on phylogenetic reconstruction: a simple evaluation

Recent studies have shown that heterogeneous evolution may mislead phylogenetic analysis, which has been neglected for a long time. We evaluate the effect of heterogeneous evolution on phylogenetic analysis, using 18 fish mitogenomic coding sequences as an example. Using the software DIVERGE, we identify 198 amino acid sites that have experienced heterogeneous evolution. After removing these sites, the rest of sites are shown to be virtually homogeneous in the evolutionary rate. There are some differences between phylogenetic trees built with heterogeneous sites ("before tree") and without heterogeneous sites ("after tree"). Our study demonstrates that for phylogenetic reconstruction, an effective approach is to identify and remove sites with heterogeneous evolution, and suggests that researchers can use the software DIVERGE to remove the influence of heterogeneous evolution before reconstructing phylogenetic trees.     

Modeling body size evolution in Felidae under alternative phylogenetic hypotheses

The use of phylogenetic comparative methods in ecological research has advanced during the last twenty years, mainly due to accurate phylogenetic reconstructions based on molecular data and computational and statistical advances. We used phylogenetic correlograms and phylogenetic eigenvector regression (PVR) to model body size evolution in 35 worldwide Felidae (Mammalia, Carnivora) species using two alternative phylogenies and published body size data. The purpose was not to contrast the phylogenetic hypotheses but to evaluate how analyses of body size evolution patterns can be affected by the phylogeny used for comparative analyses (CA). Both phylogenies produced a strong phylogenetic pattern, with closely related species having similar body sizes and the similarity decreasing with increasing distances in time. The PVR explained 65% to 67% of body size variation and all Moran's I values for the PVR residuals were non-significant, indicating that both these models explained phylogenetic structures in trait variation. Even though our results did not suggest that any phylogeny can be used for CA with the same power, or that "good" phylogenies are unnecessary for the correct interpretation of the evolutionary dynamics of ecological, biogeographical, physiological or behavioral patterns, it does suggest that developments in CA can, and indeed should, proceed without waiting for perfect and fully resolved phylogenies.     

Phylogenetics of pond and lake lifestyles in Chaoborus midge larvae

Abstract . Aquatic invertebrates experience strong trade-offs between habitats due to the selective effects of different predators. Diel vertical migration and small body size are thought to be effective strategies against fish predation in lakes. In the absence of fish in small ponds, migration is ineffective against invertebrate predators and large body size is an advantage. Although widely discussed, this phenomenon has never been tested in a phylogenetic context. We reconstructed a mitochondrial DNA (mtDNA) tree to investigate the phylogenetic distribution of pond and lake lifestyles among 10 species of northern temperate Chaoborus midge larvae. The mtDNA tree is similar to previous morphological trees for Chaoborus , the only difference being the disruption of the subgenus Chaoborus sensu stricto. At least three shifts have occurred between pond and lake lifestyles, each time associated with evolution of diel vertical migration in the lake taxon. The trend in larval body size with habitat type is sensitive to tree and character reconstruction methods, only weakly consistent with the effects of fish predation. Despite long time periods over which adaptation to each habitat type could have occurred, there remains significant phylogenetic heritability in larval body size. The tree provides a framework for comparative studies of the metapopulation genetic consequences of pond and lake lifestyles.     

No evidence for directional evolution of body mass in herbivorous theropod dinosaurs

The correlation between large body size and digestive efficiency has been hypothesized to have driven trends of increasing mass in herbivorous clades by means of directional selection. Yet, to date, few studies have investigated this relationship from a phylogenetic perspective, and none, to our knowledge, with regard to trophic shifts. Here, we reconstruct body mass in the three major subclades of non-avian theropod dinosaurs whose ecomorphology is correlated with extrinsic evidence of at least facultative herbivory in the fossil record—all of which also achieve relative gigantism (more than 3000 kg). Ordinary least-squares regressions on natural log-transformed mean mass recover significant correlations between increasing mass and geological time. However, tests for directional evolution in body mass find no support for a phylogenetic trend, instead favouring passive models of trait evolution. Cross-correlation of sympatric taxa from five localities in Asia reveals that environmental influences such as differential habitat sampling and/or taphonomic filtering affect the preserved record of dinosaurian body mass in the Cretaceous. Our results are congruent with studies documenting that behavioural and/or ecological factors may mitigate the benefit of increasing mass in extant taxa, and suggest that the hypothesis can be extrapolated to herbivorous lineages across geological time scales.     

The imprint of cenozoic migrations and evolutionary history on the biogeographic gradient of body size in new world mammals

Ecology, evolution, and historical events all contribute to biogeographic patterns, but studies that integrate them are scarce. Here we focus on how biotic exchanges of mammals during the Late Cenozoic have contributed to current geographic body size patterns. We explore differences in the environmental correlates and phylogenetic patterning of body size between groups of mammals participating and not participating in past biotic exchanges. Both the association of body size with environmental predictors and its phylogenetic signal were stronger for groups that immigrated into North or South America than for indigenous groups. This pattern, which held when extinct clades were included in the analyses, can be interpreted on the basis of the length of time that clades have had to diversify and occupy niche space. Moreover, we identify a role for historical events, such as Cenozoic migrations, in configuring contemporary mammal body size patterns and illustrate where these influences have been strongest for New World mammals.     

Differential Evolution of Advertisement Call Traits in Dart-Poison Frogs (Anura: Dendrobatidae)

The ability to recognise and discriminate between heterospecific and conspecific individuals plays an essential role in mate choice, reproductive isolation and thus species diversification. Many animals discriminate based on advertisement calls, whose evolution may be driven by a variety of forces such as natural selection, sexual selection or stochastic processes. The relative importance of stochastic processes acting on a given trait is usually correlated with its phylogenetic signal. Mate-recognition signals are complex traits composed of multiple features that could potentially respond independently to evolutionary forces. The advertisement call of anurans is used in species recognition and mate choice. In this study, we estimate the phylogenetic signal for body size and a suite of traits describing the male advertisement call from dart-poison frogs (Anura: Dendrobatidae). We found a surprisingly high phylogenetic signal for all call traits. In addition, call traits varied in their degree of phylogenetic signal, suggesting that evolutionary forces have been acting differently on different traits. Pulse duration showed the strongest phylogenetic signal. Peak frequency and body size were correlated and presented high phylogenetic signal indicating that the evolution of one trait may be driving or constraining the other. Since most variation in call traits can be explained by the phylogenetic history of the species, we cannot reject the hypothesis that stochastic processes account for significant evolutionary divergence in frog calls.     

A fishy mosasaur: the axial skeleton of Plotosaurus (Reptilia, Squamata) reassessed

The concept of convergence, that is, how unrelated animals independently evolve similar morphological traits, is a fundamental aspect of evolution. Hitherto, the Mesozoic ichthyosaurs were regarded as the sole obligate marine reptiles that achieved a fully streamlined body and a semilunate tail fluke. However, analyses of vertebral centrum morphometrics and process orientation have revealed that a subsequent clade of secondarily aquatic reptiles, the mosasaurs (here exemplified by the advanced, mid-Maastrichtian mosasaurine Plotosaurus ), had developed a deep, fusiform body and a probable pursuit-predatory behaviour by the time of their sudden extinction at the Cretaceous–Paleogene boundary. Stringent physical constraints and selection pressures, imposed by the surrounding water, probably were responsible for this spectacular example of large-scale evolutionary convergence.     

Evidence for repeated acquisition and loss of complex body-form characters in an insular clade of Southeast Asian semi-fossorial skinks

Evolutionary simplification, or loss of complex characters, is a major theme in studies of body-form evolution. The apparently infrequent evolutionary reacquisition of complex characters has led to the assertion (Dollo's Law) that once lost, complex characters may be impossible to re-evolve, at least via the exact same evolutionary process. Here, we provide one of the most comprehensive, fine-scale analyses of squamate body-form evolution to date, introducing a new model system of closely related, morphologically variable, lizards. Our phylogenetic results support independent instances of complete limb loss as well as multiple instances of digit and external ear opening loss and re-acquisition. Even more striking, we find strong statistical support for the re-acquisition of a pentadactyl body form from a digit-reduced ancestor. Our study reveals that species of the genus Brachymeles exemplify regions of morphospace (body plans) previously undocumented in squamates. Our findings have broad, general implications for body-form evolution in burrowing vertebrates: whatever constraints have shaped trends in morphological evolution among other squamate groups (excluding Bipes) have been lost in this one exemplary clade. The results of our study join a nascent body of literature showing strong statistical support for character loss, followed by evolutionary re-acquisition of complex structures associated with a generalized pentadactyl body form.     

Phylogenetic signal,feeding behaviour and brain volume in Neotropical bats

Comparative correlational studies of brain size and ecological traits (e.g. feeding habits and habitat complexity) have increased our knowledge about the selective pressures on brain evolution. Studies conducted in bats as a model system assume that shared evolutionary history has a maximum effect on the traits. However, this effect has not been quantified. In addition, the effect of levels of diet specialization on brain size remains unclear. We examined the role of diet on the evolution of brain size in Mormoopidae and Phyllostomidae using two comparative methods. Body mass explained 89% of the variance in brain volume. The effect of feeding behaviour (either characterized as feeding habits, as levels of specialization on a type of item or as handling behaviour) on brain volume was also significant albeit not consistent after controlling for body mass and the strength of the phylogenetic signal (λ). Although the strength of the phylogenetic signal of brain volume and body mass was high when tested individually, λ values in phylogenetic generalized least squares models were significantly different from 1. This suggests that phylogenetic independent contrasts models are not always the best approach for the study of ecological correlates of brain size in New World bats.