Phylogenetic signal in the song of crests and kinglets (Aves: Regulus)

Territorial song structures are often the most prominent characters for distinguishing closely related taxa among songbirds. Learning processes may cause convergent evolution of passerine songs, but phylogenetic information of acoustic traits can be investigated with the help of molecular phylogenies, which are not affected by cultural evolutionary processes. We used a phylogeny based on cytochrome b sequences to trace the evolution of territorial song within the genus Regulus. Five discrete song units are defined as basic components of regulid song via sonagraphic measurements. Traits of each unit are traced on a molecular tree and a mean acoustic character difference between taxon pairs is calculated. Acoustic divergence between regulid taxa correlates strongly with genetic distances. Syntax features of complete songs and of single units are most consistent with the molecular data, whereas the abundance of certain element types is not. Whether song characters are innate or learned was interpreted using hand-reared birds in aviary experiments. We found that convergent character evolution seems to be most probable for learned acoustic traits. We conclude that syntax traits of whole verses or subunits of territorial song, especially innate song structures, are the most reliable acoustic traits for phylogenetic reconstructions in Regulus.     

Testing concordance in species boundaries using acoustic,morphological, and molecular data in the field cricket genus Itaropsis (Orthoptera: Grylloidea,Gryllidae: Gryllinae)

In most taxa, species boundaries are inferred based on differences in morphology or DNA sequences revealed by taxonomic or phylogenetic analyses. In crickets, acoustic mating signals or calling songs have species‐specific structures and provide a third data set to infer species boundaries. We examined the concordance in species boundaries obtained using acoustic, morphological, and molecular data sets in the field cricket genus Itaropsis. This genus is currently described by only one valid species, Itaropsis tenella, with a broad distribution in western peninsular India and Sri Lanka. Calling songs of males sampled from four sites in peninsular India exhibited significant differences in a number of call features, suggesting the existence of multiple species. Cluster analysis of the acoustic data, molecular phylogenetic analyses, and phylogenetic analyses combining all data sets suggested the existence of three clades. Whatever the differences in calling signals, no full congruence was obtained between all the data sets, even though the resultant lineages were largely concordant with the acoustic clusters. The genus Itaropsis could thus be represented by three morphologically cryptic incipient species in peninsular India; their distributions are congruent with usual patterns of endemism in the Western Ghats, India. Song evolution is analysed through the divergence in syllable period, syllable and call duration, and dominant frequency. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 285–303.     

Evolution of advertisement signals in North American hylid frogs: vocalizations as end-products of calling behavior

We studied the advertisement signals in two clades of North American hylid frogs in order to characterize the relationships between signal acoustic structure and underlying behavior. A mismatch was found between the acoustic structure and the mechanism of sound production. Two separate sets of phylogenetic characters were coded following acoustic versus mechanistic criteria, and exploratory treatments were made to compare their respective phylogenetic content in comparison with the molecular phylogeny ( Faivovich et al., 2005 ). We discuss the consequences of the acoustic/mechanistic mismatch in terms of significance of acoustic characters for phylogenetic and comparative studies; and the evolution of vocalizations in North American treefrogs. Considering only the acoustic structure of frog vocalizations can lead to misleading results in terms of both phylogenetic signal and evolution of vocalizations. In contrast, interpreting the acoustic signals with regard to the mechanism of sound production results in consistent phylogenetic information. The mechanistic coding also provides strong homologies for use in comparative studies of frog vocalizations, and to derive and test evolutionary hypotheses. © The Willi Hennig Society 2005.     

On the selection of phylogenetic eigenvectors for ecological analyses

Among the statistical methods available to control for phylogenetic autocorrelation in ecological data, those based on eigenfunction analysis of the phylogenetic distance matrix among the species are becoming increasingly important tools. Here, we evaluate a range of criteria to select eigenvectors extracted from a phylogenetic distance matrix (using phylogenetic eigenvector regression, PVR) that can be used to measure the level of phylogenetic signal in ecological data and to study correlated evolution. We used a principal coordinate analysis to represent the phylogenetic relationships among 209 species of Carnivora by a series of eigenvectors, which were then used to model log‐transformed body size. We first conducted a series of PVRs in which we increased the number of eigenvectors from 1 to 70, following the sequence of their associated eigenvalues. Second, we also investigated three non‐sequential approaches based on the selection of 1) eigenvectors significantly correlated with body size, 2) eigenvectors selected by a standard stepwise algorithm, and 3) the combination of eigenvectors that minimizes the residual phylogenetic autocorrelation. We mapped the mean specific component of body size to evaluate how these selection criteria affect the interpretation of non‐phylogenetic signal in Bergmann's rule. For comparison, the same patterns were analyzed using autoregressive model (ARM) and phylogenetic generalized least‐squares (PGLS). Despite the robustness of PVR to the specific approaches used to select eigenvectors, using a relatively small number of eigenvectors may be insufficient to control phylogenetic autocorrelation, leading to flawed conclusions about patterns and processes. The method that minimizes residual autocorrelation seems to be the best choice according to different criteria. Thus, our analyses show that, when the best criterion is used to control phylogenetic structure, PVR can be a valuable tool for testing hypotheses related to heritability at the species level, phylogenetic niche conservatism and correlated evolution between ecological traits.     

Phylogeny and the evolution of acoustic communication in extant Ensifera (Insecta, Orthoptera)

Ensifera present an appropriate and interesting model for the study of acoustic communication, because of their diverse signal and communication modalities, and due to their accessibility for field and laboratory studies. Several hypotheses have been proposed to explain the acoustic evolution of Ensifera, but they were elaborated without any reference to a falsifiable phylogeny, and were consequently highly speculative. Similarly, phylogenetic relationships between ensiferan clades have not hitherto been studied using modern standard methodology, and the sole cladistic analysis by Gwynne in 1995 was methodologically flawed. No sound hypothesis therefore currently exists for ensiferan phylogeny, which precludes historical analysis of their communication modalities. In the present paper, the phylogeny is established on the basis of morpho‐anatomical characters and used to analyse the evolution of acoustic communication in this clade by mapping the characters related to auditory and stridulatory structures onto the resultant trees. Cladistic analyses resulted in two equi‐parsimonious cladograms (length 154, C 64, CI 58, RI 61) with the following topologies: (1) [(Grylloidea–Gryllotalpidae) (Rhaphidophoridae (Schizodactylidae (Gryllacrididae ((Stenopelmatidae–Cooloola) (Anostostomatidae (Prophalangopsis (Cyphoderris (Tettigoniidae–Lezina))))))))] (2) [(Grylloidea–Gryllotalpidae)(Rhaphidophoridae (Schizodactylidae (Gryllacrididae–Cooloola–(Stenopelmatidae (Anostostomatidae (Prophalangopsis (Cyphoderris (Tettigoniidae–Lezina))))))))]. According to these topologies, Ensifera were ancestrally devoid of acoustic and hearing systems. An acoustic (tegminal or femoro‐abdominal) apparatus appeared a number of times independently with convergent structures. Similarly, tibial tympana developed several times independently. Moreover, four hypotheses (each according to a definite pattern of character transformation) can be proposed to explain the evolution of acoustic communication in the different ensiferan clades and relate it to a definite communicatory context. These hypotheses do not apply equally to ensiferan subclades. Grylloidea and Gryllotalpoidea could have experienced convergently a direct development of an intraspecific acoustic communication. Acoustic communication in Tettigoniidea has evolved more ambiguously, and may either have resulted from a direct evolution analogous to that having occurred in Gryllidea, or have developed in a completely different behavioural context. Future studies of acoustic communication in the different ensiferan clades will have to take into account the fact that the involved structures most often are not homologous and that their evolution may not have taken place in similar conditions. Different hypotheses of acoustic communication evolution may apply to different clades, and there may be no single explanation for acoustic communication in Ensifera.     

Testing drivers of acoustic divergence in cicadas (Cicadidae: Tettigettalna)

Divergence in acoustic signals may have a crucial role in the speciation process of animals that rely on sound for intra-specific recognition and mate attraction. The acoustic adaptation hypothesis (AAH) postulates that signals should diverge according to the physical properties of the signalling environment. To be efficient, signals should maximize transmission and decrease degradation. To test which drivers of divergence exert the most influence in a speciose group of insects, we used a phylogenetic approach to the evolution of acoustic signals in the cicada genus Tettigettalna, investigating the relationship between acoustic traits (and their mode of evolution) and body size, climate and micro-/macro-habitat usage. Different traits showed different evolutionary paths. While acoustic divergence was generally independent of phylogenetic history, some temporal variables’ divergence was associated with genetic drift. We found support for ecological adaptation at the temporal but not the spectral level. Temporal patterns are correlated with micro- and macro-habitat usage and temperature stochasticity in ways that run against the AAH predictions, degrading signals more easily. These traits are likely to have evolved as an anti-predator strategy in conspicuous environments and low-density populations. Our results support a role of ecological selection, not excluding a likely role of sexual selection in the evolution of Tettigettalna calling songs, which should be further investigated in an integrative approach.     

Bayesian model adequacy and choice in phylogenetics

Bayesian inference is becoming a common statistical approach to phylogenetic estimation because, among other reasons, it allows for rapid analysis of large data sets with complex evolutionary models. Conveniently, Bayesian phylogenetic methods use currently available stochastic models of sequence evolution. However, as with other model-based approaches, the results of Bayesian inference are conditional on the assumed model of evolution: inadequate models (models that poorly fit the data) may result in erroneous inferences. In this article, I present a Bayesian phylogenetic method that evaluates the adequacy of evolutionary models using posterior predictive distributions. By evaluating a model's posterior predictive performance, an adequate model can be selected for a Bayesian phylogenetic study. Although I present a single test statistic that assesses the overall (global) performance of a phylogenetic model, a variety of test statistics can be tailored to evaluate specific features (local performance) of evolutionary models to identify sources failure. The method presented here, unlike the likelihood-ratio test and parametric bootstrap, accounts for uncertainty in the phylogeny and model parameters.     

Neotropical frogs and mating songs: The evolution of advertisement calls in glassfrogs

Anurans emit advertisement calls with the purpose of attracting mates and repelling conspecific competitors. The evolution of call traits is expected to be associated with the evolution of anatomical and behavioural traits due to the physics of call emission and transmission. The evolution of vocalizations might imply trade‐offs with other energetically costly behaviours, such as parental care. Here, we investigated the association between body size, calling site, parental care and call properties (call duration, number of notes, peak frequency, frequency bandwidth and call structure) of the advertisement calls of glassfrogs (Centrolenidae)—a family of Neotropical, leaf‐dwelling anurans—using phylogenetic comparative methods. We also explored the tempo and mode of evolution of these traits and compared them with those of three morphological traits associated with body size, locomotion and feeding. We generated and compiled acoustic data for 72 glassfrog species (46% of total species richness), including representatives of all genera. We found that almost all acoustic traits have significant, but generally modest, phylogenetic signal. Peak frequency of calls is significantly associated with body size, whereas call structure is significantly associated with calling site and paternal care. Thus, the evolution of body size, calling site and paternal care could constrain call evolution. The estimated disparity of acoustic traits was larger than that of morphological traits and the peak in disparity of acoustic traits generally occurred later in the evolution of glassfrogs, indicating a historically recent outset of the acoustic divergence in this clade.     

Abiotic noise,call frequency and stream-breeding anuran assemblages

Environmental noise can be an important selective force modulating signal evolution in species with acoustic communication. Many anuran species breed alongside streams; hence, the sound produced by the flowing water is an important source of noise for acoustic communication. Since calling is physiologically very expensive in anurans, and communication is essential for reproduction, we expected adaptations that reduce environmental masking effects and allow acoustic communication in streamside breeders. This basic assumption of the acoustic adaptation hypothesis has not been yet evaluated at a large phylogenetic scale. We combined ahistorical and phylogenetic methods to test whether anuran species that breed alongside streams call at higher frequencies than species that breed away from streams. We compiled primary and secondary data on body size, breeding habitat, and the dominant frequency of the advertisement call for 110 species; 40 of them breed alongside streams and 70 away from streams. Call frequency was slightly higher and body size was significantly smaller in streamside breeding species. After controlling for the effects of body size and phylogenetic signal, only differences in body size persisted between species breeding at both kinds of habitats. Our data suggest that habitat filtering rather than acoustic adaptation explains the high call frequency of stream breeders. Species with large body size, pleiotropically constrained to utter low-frequency calls, would have succeeded less often in establishing viable populations alongside streams, due to the masking effect of low-frequency noise. Thus, small species calling at relatively high frequencies would be more common there. Although our data do not preclude adaptations to noisy habitats in some anuran species, they do not provide support for the acoustic adaptation hypothesis at a wider phylogenetic scale.     

Combined molecular phylogenetic analysis of the Orthoptera (Arthropoda,Insecta) and implications for their higher systematics

A phylogenetic analysis of mitochondrial and nuclear rDNA sequences from species of all the superfamilies of the insect order Orthoptera (grasshoppers, crickets, and relatives) confirmed that although mitochondrial sequences provided good resolution of the youngest superfamilies, nuclear rDNA sequences were necessary to separate the basal groups. To try to reconcile these data sets into a single, fully resolved orthopteran phylogeny, we adopted consensus and combined data strategies. The consensus analysis produced a partially resolved tree that lacked several well-supported features of the individual analyses. However, this lack of resolution was explained by an examination of resampled data sets, which identified the likely source of error as the relatively short length of the individual mitochondrial data partitions. In a subsequent comparison in which the mitochondrial sequences were initially combined, we observed less conflict. We then used two approaches to examine the validity of combining all of the data in a single analysis: comparative analysis of trees recovered from resampled data sets, and the application of a randomization test. Because the results did not point to significant levels of heterogeneity in phylogenetic signal between the mitochondrial and nuclear data sets, we therefore proceeded with a combined analysis. Reconstructing phylogenies under the minimum evolution and maximum likelihood optimality criteria, we examined monophyly of the major orthopteran groups, using nonparametric and parametric bootstrap analysis and Kishino-Hasegawa tests. Our analysis suggests that phylogeny reconstruction under the maximum likelihood criteria is the most discriminating approach for the combined sequences. The results indicate, moreover, that the caeliferan Pneumoroidea and Pamphagoidea, as previously suggested, are polyphyletic. The Acridoidea is redefined to include all pamphagoid families other than the Pyrgomorphidae, which we propose should be accorded superfamily status.     

Rapid radiation and cryptic speciation in squat lobsters of the genus Munida (Crustacea, Decapoda) and related genera in the South West Pacific: molecular and morphological evidence

Squat lobsters (genus Munida and related genera) are among the most diverse taxa of western Pacific crustaceans, though several features of their biology and phylogenetic relationships are unknown. This paper reports an extensive phylogenetic analysis based on mitochondrial DNA sequences (cytochrome c oxidase subunit I and 16S rRNA) and the morphology of 72 species of 12 genera of western Pacific squat lobsters. Our phylogenetic reconstruction using molecular data supports the recent taxonomic splitting of the genus Munida into several genera. Excluding one species (M. callista), the monophyly of the genus Munida was supported by Bayesian analysis of the molecular data. Three moderately diverse genera (Onconida, Paramunida, and Raymunida) also appeared monophyletic, both according to morphological and molecular data, always with high support. However, other genera (Crosnierita and Agononida) seem to be para- or polyphyletic. Three new cryptic species were identified in the course of this study. It would appear that the evolution of this group was marked by rapid speciation and stasis, or certain constraints, in its morphological evolution.     

The evolution of vocalisations in the genus Corvus: effects of phylogeny, morphology and habitat

In this study we investigated the phylogenetic, morphological and ecological factors affecting the caw calls of 28 species of the genus Corvus, spanning the worldwide range of the taxon. The three phylogeographic groups identified by Goodwin (1986, Crows of the World, British Museum (Natural History), St Edmudsbury Press, Bury St Edmunds), i.e. the American stock, the Palearctic-African stock and the Oriental-Australian stock, were differentiated by some of the acoustic features of their calls, suggesting that historical factors may have played an important role in the evolution of vocalisations in this group. To assess the effects of morphology (body size and bill length) and environment (open vs. closed habitat) and to simultaneously take into account the phylogenetic effects, we used the phylogenetically independent contrast method. This manner of analysis revealed that body size was important in shaping the acoustic attributes of the caw call, as it influenced two temporal and two spectral variables, whereas the effect of bill length was far weaker. Notably, our results did not confirm the negative correlation between call frequency and body size that resulted in a phylogeny-free analysis of the same data in many studies on passerines. Larger Corvus species, in fact, utter calls with higher fundamental frequency than those of smaller species. Hence, these results show that incorporating phylogeny in analyses can substantially alter the conclusions reached by studies carried out with non-phylogenetic approaches. The acoustic environment, considered one of the most important forces driving the evolution of vocalisations in passerines, slightly influenced only two acoustic parameters in the Corvusgenus, call fundamental frequency and duration of pulsed units, both of which increased in the calls of forest species.     

How the environment shapes animal signals: a test of the acoustic adaptation hypothesis in frogs

Long‐distance acoustic signals are widely used in animal communication systems and, in many cases, are essential for reproduction. The acoustic adaptation hypothesis (AAH) implies that acoustic signals should be selected for further transmission and better content integrity under the acoustic constraints of the habitat in which they are produced. In this study, we test predictions derived from the AAH in frogs. Specifically, we focus on the difference between torrent frogs and frogs calling in less noisy habitats. Torrents produce sounds that can mask frog vocalizations and constitute a major acoustic constraint on call evolution. We combine data collected in the field, material from scientific collections and the literature for a total of 79 primarily Asian species, of the families Ranidae, Rhacophoridae, Dicroglossidae and Microhylidae. Using phylogenetic comparative methods and including morphological and environmental potential confounding factors, we investigate putatively adaptive call features in torrent frogs. We use broad habitat categories as well as fine‐scale habitat measurements and test their correlation with six call characteristics. We find mixed support for the AAH. Spectral features of torrent frog calls are different from those of frogs calling in other habitats and are related to ambient noise levels, as predicted by the AAH. However, temporal call features do not seem to be shaped by the frogs’ calling habitats. Our results underline both the complexity of call evolution and the need to consider multiple factors when investigating this issue.     

PHYLOGENIES,SPATIAL AUTOREGRESSION,AND THE COMPARATIVE METHOD: A COMPUTER SIMULATION TEST

Brownian motion computer simulation was used to test the statistical properties of a spatial autoregressive method in estimating evolutionary correlations between two traits using interspecific comparative data. When applied with a phylogeny of 42 species, the method exhibited reasonable Type I and II error rates. Estimation abilities were comparable to those of independent contrasts and minimum evolution (parsimony) methods, and generally superior to a traditional nonphylogenetic approach (not taking phylogenies into account at all). However, the autoregressive method performed extremely poorly with a smaller phylogeny (15 species) and with nearly independent (“star”) phylogenies. In both of these situations, any phylogenetic autocorrelation present in the data was not detected by the method. Results show how diagnostic techniques (e.g., Moran's I) can be useful in detecting and avoiding such situations, but that such techniques should not be used as definitive evidence that phylogenetic correlation is not present in a set of comparative data. The correction factor (α) proposed by Gittleman and Kot (1990) for use in weighting phylogenetic information had little effect in most analyses of 15 or 42 species with incorrect phylogenetic information, and may require much larger sample sizes before significant improvement is shown. With the sample sizes tested in this study, however, the autoregressive method implemented with this correction factor and correct phylogenetic information led to downwardly biased estimates of the absolute magnitude of the evolutionary correlation between two traits. Cautions and recommendations for implemention of the spatial autoregressive method are given; computer programs to conduct the analyses are available on request.     

Phylogeny and the modalities of acoustic diversification in extant Eneopterinae (Insecta, Orthoptera, Grylloidea, Eneopteridae)

Calling with a tegminal stridulatory apparatus is widespread in crickets. However, the evolution of cricket stridulums has been poorly studied and then only on the basis of prephylogenetic models, which are unable to account for the huge diversity recently documented for acoustic features in crickets. The present paper focuses on the evolution of acoustic devices in the subfamily Eneopterinae. This is the first attempt to reconstruct the phylogeny of a large and diverse cricket clade in order to analyze the evolution of emitting structures using precise homology statements. In the first step, we reconstruct the phylogeny of this clade using a morphological data set of 193 characters and 45 taxa. The resultant phylogeny supports the monophyly of the subfamily and that of the 13 genera represented by at least two species in our taxonomic sample. Phylogenetic relationships within the subfamily also support the definition of five tribes: Eurepini, Eneopterini, Nisitrini, Xenogryllini and Lebinthini. In the second step, the evolution of acoustic devices is studied by optimization of venation characters defined on precise homology statements. As hypothesized by previous authors, losses of acoustic communication occur independently in the course of eneopterine evolution; however, they happen abruptly with no intermediate state. Our results also document for the first time the modalities of forewing evolution: the diversification of male forewing venation originates from two processes, a continuous and regular modification process, responsible for slight venation change; and an irregular, more intense punctuated process, allowing the emergence of different venations. This diversification process with sudden changes could be related to the occurrence of acoustic novelties in advertisement calls.     

Phylogenetic and ecological effects on interspecific variation in structurally simple avian vocalizations

Flight calls are structurally simple avian vocalizations largely associated with sustained migratory flight. We used a multilocus phylogeny of 47 North American wood warblers (Aves: Parulidae) to quantify the extent of phylogenetic signal in flight-call spectrographic characteristics and to remove phylogenetic effects when testing for associations among flight-call attributes, behavioural characters related to migration strategies and ecological habitat variables. We also employed a quantile regression and null model approach to compare a matrix of interspecific phylogenetic divergence with indices of the corresponding acoustic differences derived from spectrographic measurements of flight calls. Nearly half of the measurements of flight-call properties exhibited significant associations with phylogeny. Controlling for phylogenetic effects, high-frequency flight calls were associated with species occupying taller and more open forest canopies. Ecological properties associated with migratory and winter distributions did not correlate with flight-call characteristics. Differences among the evolutionary histories of structural vs. signal properties of flightcalls suggest that phylogenetic and ecological effects are present. The evolution of flight-call syllable structure may involve selection for species recognition, whereas adaptation to the acoustic environment likely has influenced evolution of their spectral and temporal properties. More generally, the historical contribution to variation in behavioural characters is a long-standing source of debate; these results suggest that substantial phylogenetic effects may be present even in vocal traits that may be highly labile. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 155–173.     

Phylogeny of Ensifera (Hexapoda: Orthoptera) using three ribosomal loci, with implications for the evolution of acoustic communication

Representatives of the Orthopteran suborder Ensifera (crickets, katydids, and related insects) are well known for acoustic signals produced in the contexts of courtship and mate recognition. We present a phylogenetic estimate of Ensifera for a sample of 51 taxonomically diverse exemplars, using sequences from 18S, 28S, and 16S rRNA. The results support a monophyletic Ensifera, monophyly of most ensiferan families, and the superfamily Gryllacridoidea which would include Stenopelmatidae, Anostostomatidae, Gryllacrididae, and Lezina. Schizodactylidae was recovered as the sister lineage to Grylloidea, and both Rhaphidophoridae and Tettigoniidae were found to be more closely related to Grylloidea than has been suggested by prior studies. The ambidextrously stridulating haglid Cyphoderris was found to be basal (or sister) to a clade that contains both Grylloidea and Tettigoniidae. Tree comparison tests with the concatenated molecular data found our phylogeny to be significantly better at explaining our data than three recent phylogenetic hypotheses based on morphological characters. A high degree of conflict exists between the molecular and morphological data, possibly indicating that much homoplasy is present in Ensifera, particularly in acoustic structures. In contrast to prior evolutionary hypotheses based on most parsimonious ancestral state reconstructions, we propose that tegminal stridulation and tibial tympana are ancestral to Ensifera and were lost multiple times, especially within the Gryllidae.     

Increased taxon sampling greatly reduces phylogenetic error

Several authors have argued recently that extensive taxon sampling has a positive and important effect on the accuracy of phylogenetic estimates. However, other authors have argued that there is little benefit of extensive taxon sampling, and so phylogenetic problems can or should be reduced to a few exemplar taxa as a means of reducing the computational complexity of the phylogenetic analysis. In this paper we examined five aspects of study design that may have led to these different perspectives. First, we considered the measurement of phylogenetic error across a wide range of taxon sample sizes, and conclude that the expected error based on randomly selecting trees (which varies by taxon sample size) must be considered in evaluating error in studies of the effects of taxon sampling. Second, we addressed the scope of the phylogenetic problems defined by different samples of taxa, and argue that phylogenetic scope needs to be considered in evaluating the importance of taxon-sampling strategies. Third, we examined the claim that fast and simple tree searches are as effective as more thorough searches at finding near-optimal trees that minimize error. We show that a more complete search of tree space reduces phylogenetic error, especially as the taxon sample size increases. Fourth, we examined the effects of simple versus complex simulation models on taxonomic sampling studies. Although benefits of taxon sampling are apparent for all models, data generated under more complex models of evolution produce higher overall levels of error and show greater positive effects of increased taxon sampling. Fifth, we asked if different phylogenetic optimality criteria show different effects of taxon sampling. Although we found strong differences in effectiveness of different optimality criteria as a function of taxon sample size, increased taxon sampling improved the results from all the common optimality criteria. Nonetheless, the method that showed the lowest overall performance (minimum evolution) also showed the least improvement from increased taxon sampling. Taking each of these results into account re-enforces the conclusion that increased sampling of taxa is one of the most important ways to increase overall phylogenetic accuracy.     

Insufficient resolving power of mitogenome data in deciphering deep phylogeny of Holometabola

The mitochondrial genome (mitogenome) is one of the most widely used markers for phylogenetic analysis. Compared with whole-genome data, mitogenome data are less expensive to obtain and easier to manipulate. However, compositional bias and accelerated evolutionary rate reduce the effectiveness of the mitogenome in determining insect phylogeny. This study shows that mitogenome data are not suitable to reconstruct deep holometabolan evolution, even with a most comprehensive data coding scheme and the more realistic CAT model. For the deep levels of divergence within Holometabola, protein-coding genes only retain weak phylogenetic signals, leading to peculiar interordinal relationships. Consensus relationships in the Holometabola phylogeny, such as the monophyly of Holometabola, the most basal position of Hymenoptera, and the sister group relationship between the Strepsiptera and Coleoptera were rarely resolved in our analyses. The relationships of the holometabolan groups as inferred by mitogenomes are highly vulnerable to gene types, data coding regimes, model choice, and optimality criteria, and no consistent alternative hypothesis of Holometabola's relationships is supported. Thus, we suggest that the slowly evolving nuclear genes or genome-scale approaches may be better options for resolving deep-level phylogeny of Holometabola.