Site-Specific Evolutionary Rate Inference: Taking Phylogenetic Uncertainty into Account

The evolutionary rate at an amino acid site is indicative of how conserved this site is and, in turn, allows evaluating the importance of this site in maintaining the structure/function of the protein. When evolutionary rates are estimated, one must reconstruct the phylogenetic tree describing the evolutionary relationship among the sequences under study. However, if the inferred phylogenetic tree is incorrect, it can lead to erroneous site-specific rate estimates. Here we describe a novel Bayesian method that uses Markov chain Monte Carlo methodology to integrate over the space of all possible trees and model parameters. By doing so, the method considers alternative evolutionary scenarios weighted by their posterior probabilities. We show that this comprehensive evolutionary approach is superior over methods that are based on only a single tree. We illustrate the potential of our algorithm by analyzing the conservation pattern of the potassium channel protein family.Itay Mayrose, Amir Mitchell contributed equal. Reviewing Editor : Dr. Nicolas Galtier     

Ithomiini Butterflies (Lepidoptera: Nymphalidae) of Antioquia, Colombia

Colombia is one of the most biodiverse countries on the planet. However, economic and scientific investment in completing inventories of its biodiversity has been relatively poor in comparison with other Neotropical countries. Butterflies are the best studied group of invertebrates, with the highest proportion of known to expected species. More than 3,200 species of butterflies have been recorded in Colombia, although the study of the still many unexplored areas will presumably increase this number. This work provides a list of Ithomiini butterflies collected in the department of Antioquia and estimates the total number of species present, based on revision of entomological collections, records in the literature and field work performed between 2003 and 2011. The list includes 99 species and 32 genera, representing 27% of all Ithomiini species. We report 50 species of Ithomiini not formerly listed from Antioquia, and found the highest diversity of ithomiine species to be at middle elevations (900–1,800 m). The mean value of the Chao2 estimator for number of species in Antioquia is 115 species, which is close to a predicted total of 109 based on known distributions of other Ithomiini not yet recorded from the department. Nine species are potentially of particular conservation importance because of their restricted distributions, and we present range maps for each species. We also highlight areas in Antioquia with a lack of biodiversity knowledge to be targeted in future studies. This paper contributes to mapping the distribution of the Lepidoptera of Antioquia department in particular and of Colombia in general.     

Wing-Click Sounds of Heliconius cydno alithea (Nymphalidae: Heliconiinae) Butterflies

Field-collected Heliconius cydno Doubleday females were observed producing audible wing clicks during encounters between conspecifics in greenhouses in a large insectary during the day and at roosting time. Occasionally, these females also were observed producing sounds in aggressive encounters with females of a close relative, H. erato (L). However, the wing-clicks were not observed subsequently from first-generation adults born in the greenhouses. The sounds were produced in short trains of 3–10 wing-clicks at the rate of 10 clicks/s. The individual clicks had a mean duration of 1.48 ms and a broad frequency spectrum, with a peak near 1075 Hz. This peak lies near the 1200-Hz frequency of maximal sensitivity measured previously for auditory neurons of H. erato. The production of these previously unreported sounds suggests that wing clicks may play a role in both intra- and interspecific communication among Heliconius species.     

Phylogenetic relationships among Heliconiinae genera based on morphology (Lepidoptera: Nymphalidae)

Abstract.  Phylogenetic relationships among Heliconiinae genera are proposed based on early-stage and adult morphology. Parsimony analyses of forty-nine species in twenty-nine genera indicate that Heliconiinae can be divided into four main groups: (1) Pardopsis , Acraea and Actinote ; (2) Cethosia plus Neotropical genera; (3) Oriental genera and (4) fritillaries. Analyses of adult characters suggested that Oriental genera form a monophyletic group, whereas those of adult plus early-stage characters artificially split this group into three separate lineages. Our character set does not contain enough phylogenetic information to resolve relationships among fritillary genera with confidence, and further studies of this group are needed. The classification of the Heliconiinae is revised based on our results.     

The Impact of Modelling Rate Heterogeneity among Sites on Phylogenetic Estimates of Intraspecific Evolutionary Rates and Timescales

Phylogenetic analyses of DNA sequence data can provide estimates of evolutionary rates and timescales. Nearly all phylogenetic methods rely on accurate models of nucleotide substitution. A key feature of molecular evolution is the heterogeneity of substitution rates among sites, which is often modelled using a discrete gamma distribution. A widely used derivative of this is the gamma-invariable mixture model, which assumes that a proportion of sites in the sequence are completely resistant to change, while substitution rates at the remaining sites are gamma-distributed. For data sampled at the intraspecific level, however, biological assumptions involved in the invariable-sites model are commonly violated. We examined the use of these models in analyses of five intraspecific data sets. We show that using 6–10 rate categories for the discrete gamma distribution of rates among sites is sufficient to provide a good approximation of the marginal likelihood. Increasing the number of gamma rate categories did not have a substantial effect on estimates of the substitution rate or coalescence time, unless rates varied strongly among sites in a non-gamma-distributed manner. The assumption of a proportion of invariable sites provided a better approximation of the asymptotic marginal likelihood when the number of gamma categories was small, but had minimal impact on estimates of rates and coalescence times. However, the estimated proportion of invariable sites was highly susceptible to changes in the number of gamma rate categories. The concurrent use of gamma and invariable-site models for intraspecific data is not biologically meaningful and has been challenged on statistical grounds; here we have found that the assumption of a proportion of invariable sites has no obvious impact on Bayesian estimates of rates and timescales from intraspecific data.     

Quantifying Phylogenetic Beta Diversity: Distinguishing between 'True' Turnover of Lineages and Phylogenetic Diversity Gradients

The evolutionary dissimilarity between communities (phylogenetic beta diversity PBD) has been increasingly explored by ecologists and biogeographers to assess the relative roles of ecological and evolutionary processes in structuring natural communities. Among PBD measures, the PhyloSor and UniFrac indices have been widely used to assess the level of turnover of lineages over geographical and environmental gradients. However, these indices can be considered as 'broad-sense' measures of phylogenetic turnover as they incorporate different aspects of differences in evolutionary history between communities that may be attributable to phylogenetic diversity gradients. In the present study, we extend an additive partitioning framework proposed for compositional beta diversity to PBD. Specifically, we decomposed the PhyloSor and UniFrac indices into two separate components accounting for 'true' phylogenetic turnover and phylogenetic diversity gradients, respectively. We illustrated the relevance of this framework using simple theoretical and archetypal examples, as well as an empirical study based on coral reef fish communities. Overall, our results suggest that using PhyloSor and UniFrac may greatly over-estimate the level of spatial turnover of lineages if the two compared communities show contrasting levels of phylogenetic diversity. We therefore recommend that future studies use the 'true' phylogenetic turnover component of these indices when the studied communities encompass a large phylogenetic diversity gradient.     

Behavioral Adaptations to Pollen-Feeding in Heliconius Butterflies (Nymphalidae, Heliconiinae): An Experiment Using Lantana Flowers

Butterflies in the genera Heliconius and Laparus obtain fitness-related benefits from using amino acids derived from pollen. These butterflies have morphological features of the proboscis that facilitate pollen-feeding. Here we investigate behavioral characteristics potentially involved in pollen-gathering. Analysis of four behavioral characters showed that pollen-feeding species manipulate Lantana flowers faster and more thoroughly compared to non-pollen-feeding relatives. Although this suggests that pollen-feeding species are potentially more efficient in harvesting pollen, every butterfly tested successfully removed pollen from Lantana and non-pollen-feeding butterflies generally extracted larger amounts of pollen than Heliconius and Laparus. Morphological characteristics of the proboscis and the production of abundant fluid exudate help keep pollen attached in the proboscis for long periods of time—possibly key to Heliconius' and Laparus' ability to obtain amino acids from pollen. Our results, in concert with those of previous morphological analysis, indicate that behavioral and structural attributes associated with pollen-feeding in Heliconius and Laparus are subtle modifications of widespread butterfly characteristics and raise the question why other butterflies do not use pollen in their diet.     

陕西延安市区蝶类多样性初探

延安市区有蝶类6科25属36种,其中凤蝶科2属3种;粉蝶科5属8种;眼蝶科3属5种;蛱蝶科7属10种;灰蝶科7属9种;弄蝶科1属1种。陕西省新记录5种。区系分析表明,该地区以广布种为优势种。     

Quantifying the Diversification of Hepatitis C Virus (HCV) during Primary Infection: Estimates of the In Vivo Mutation Rate

Hepatitis C virus (HCV) is present in the host with multiple variants generated by its error prone RNA-dependent RNA polymerase. Little is known about the initial viral diversification and the viral life cycle processes that influence diversity. We studied the diversification of HCV during acute infection in 17 plasma donors, with frequent sampling early in infection. To analyze these data, we developed a new stochastic model of the HCV life cycle. We found that the accumulation of mutations is surprisingly slow: at 30 days, the viral population on average is still 46% identical to its transmitted viral genome. Fitting the model to the sequence data, we estimate the median in vivo viral mutation rate is 2.5×10⁻⁵ mutations per nucleotide per genome replication (range 1.6–6.2×10⁻⁵), about 5-fold lower than previous estimates. To confirm these results we analyzed the frequency of stop codons (N = 10) among all possible non-sense mutation targets (M = 898,335), and found a mutation rate of 2.8–3.2×10⁻⁵, consistent with the estimate from the dynamical model. The slow accumulation of mutations is consistent with slow turnover of infected cells and replication complexes within infected cells. This slow turnover is also inferred from the viral load kinetics. Our estimated mutation rate, which is similar to that of other RNA viruses (e.g., HIV and influenza), is also compatible with the accumulation of substitutions seen in HCV at the population level. Our model identifies the relevant processes (long-lived cells and slow turnover of replication complexes) and parameters involved in determining the rate of HCV diversification.     

Timing and Patterns in the Taxonomic Diversification of Lepidoptera (Butterflies and Moths)

The macroevolutionary history of the megadiverse insect order Lepidoptera remains little-known, yet coevolutionary dynamics with their angiospermous host plants are thought to have influenced their diversification significantly. We estimate the divergence times of all higher-level lineages of Lepidoptera, including most extant families. We find that the diversification of major lineages in Lepidoptera are approximately equal in age to the crown group of angiosperms and that there appear to have been three significant increases in diversification rates among Lepidoptera over evolutionary time: 1) at the origin of the crown group of Ditrysia about 150 million years ago (mya), 2) at the origin of the stem group of Apoditrysia about 120 mya and finally 3) a spectacular increase at the origin of the stem group of the quadrifid noctuoids about 70 mya. In addition, there appears to be a significant increase in diversification rate in multiple lineages around 90 mya, which is concordant with the radiation of angiosperms. Almost all extant families appear to have begun diversifying soon after the Cretaceous/Paleogene event 65.51 mya.     

Morphological Characters Are Compatible with Mitogenomic Data in Resolving the Phylogeny of Nymphalid Butterflies (Lepidoptera: Papilionoidea: Nymphalidae)

Nymphalidae is the largest family of butterflies with their phylogenetic relationships not adequately approached to date. The mitochondrial genomes (mitogenomes) of 11 new nymphalid species were reported and a comparative mitogenomic analysis was conducted together with other 22 available nymphalid mitogenomes. A phylogenetic analysis of the 33 species from all 13 currently recognized nymphalid subfamilies was done based on the mitogenomic data set with three Lycaenidae species as the outgroups. The mitogenome comparison showed that the eleven new mitogenomes were similar with those of other butterflies in gene content and order. The reconstructed phylogenetic trees reveal that the nymphalids are made up of five major clades (the nymphaline, heliconiine, satyrine, danaine and libytheine clades), with sister relationship between subfamilies Cyrestinae and Biblidinae, and most likely between subfamilies Morphinae and Satyrinae. This whole mitogenome-based phylogeny is generally congruent with those of former studies based on nuclear-gene and mitogenomic analyses, but differs considerably from the result of morphological cladistic analysis, such as the basal position of Libytheinae in morpho-phylogeny is not confirmed in molecular studies. However, we found that the mitogenomic phylogeny established herein is compatible with selected morphological characters (including developmental and adult morpho-characters).     

基于线粒体Cyt b基因的线蛱蝶亚科的系统发育

基于线粒体Cytb基因部分序列,以波蛱蝶为外群,采用邻接法、最大简约法和贝叶斯法分别构建了中国线蛱蝶亚科10属25种蝶类的系统发育树,探讨了各主要类群间的系统发育关系。其结果表明,所有线蛱蝶亚科聚为两大枝:第一枝包括环蛱蝶属、菲蛱蝶属、蟠蛱蝶属和缕蛱蝶属,其中缕蛱蝶属与环蛱蝶族亲缘关系较近;第二枝包括丽蛱蝶属、穆蛱蝶属、线蛱蝶属、带蛱蝶属、律蛱蝶属和翠蛱蝶属,其中线蛱蝶属为非单系群,翠蛱蝶属和律蛱蝶属则为单系发生,并构成姐妹群。     

Inferring the Dynamics of Diversification: A Coalescent Approach

Recent analyses of the fossil record and molecular phylogenies suggest that there are fundamental limits to biodiversity, possibly arising from constraints in the availability of space, resources, or ecological niches. Under this hypothesis, speciation rates decay over time and biodiversity eventually saturates, with new species emerging only when others are driven to extinction. This view of macro-evolution contradicts an alternative hypothesis that biodiversity is unbounded, with species ever accumulating as they find new niches to occupy. These contrasting theories of biodiversity dynamics yield fundamentally different explanations for the disparity in species richness across taxa and regions. Here, we test whether speciation rates have decayed or remained constant over time, and whether biodiversity is saturated or still expanding. We first derive a general likelihood expression for internode distances in a phylogeny, based on the well-known coalescent process from population genetics. This expression accounts for either time-constant or time-variable rates, time-constant or time-variable diversity, and completely or incompletely sampled phylogenies. We then compare the performance of different diversification scenarios in explaining a set of 289 phylogenies representing amphibians, arthropods, birds, mammals, mollusks, and flowering plants. Our results indicate that speciation rates typically decay over time, but that diversity is still expanding at present. The evidence for expanding-diversity models suggests that an upper limit to biodiversity has not yet been reached, or that no such limit exists.     

利用线粒体CO II基因序列对中国尾蛱蝶属系统分化的研究

利用线粒体COII基因序列分析法,研究了我国尾蛱蝶属5种蝴蝶的系统分化。结果表明,在尾蛱蝶属5个种的12个样品中,405 bp长的COII片段有11.4%的位点为多态性位点,大部分的碱基改变是转换。各物种内不同个体间的差异明显小于不同物种间的差异,种内个体间的差异一般为0.5%～1.5%,各物种间的差异绝大多数在4%以上。利用最大似然性法构建的尾蛱蝶属聚类关系图显示,尾蛱蝶属蝴蝶分为两大分支,一支包括大二尾蛱蝶、二尾蛱蝶和忘忧尾蛱蝶,另外一个分支包括窄斑凤尾蛱蝶和黑凤尾蛱蝶聚在一起。在大二尾蛱蝶、二尾蛱蝶和忘忧尾蛱蝶这一分支中,大二尾蛱蝶和忘忧尾蛱蝶的亲缘关系较近,而二尾蛱蝶较远。这些分子系统学的结果均与形态学的结果相一致,是对形态分类的有力支持。     

利用线粒体COII基因序列对中国尾蛱蝶属系统分化的研究(鳞翅目:蛱蝶科)

利用线粒体C0II基因序列分析法,研究了我国尾蛱蝶属5种蝴蝶的系统分化.结果表明,在尾蛱蝶属5个种的12个样品中,405 bp长的COII片段有11.4%的位点为多态性位点,大部分的碱基改变是转换.各物种内不同个体间的差异明显小于不同物种间的差异,种内个体间的差异一般为0.5%～1.5%,各物种间的差异绝大多数在4%以上.利用最大似然性法构建的尾蛱蝶属聚类关系图显示,尾蛱蝶属蝴蝶分为两大分支,一支包括大二尾蛱蝶、二尾蛱蝶和忘忧尾蛱蝶,另外一个分支包括窄斑凤尾蛱蝶和黑凤尾蛱蝶聚在一起.在大二尾蛱蝶、二尾蛱蝶和忘忧尾蛱蝶这一分支中,大二尾蛱蝶和忘忧尾蛱蝶的亲缘关系较近,而二尾蛱蝶较远.这些分子系统学的结果均与形态学的结果相一致,是对形态分类的有力支持.     

湖南省万佛山风景区蝴蝶多样性考察初报

2005年6月对湖南省万佛山风景区的蝴蝶进行了调查,记录到蝴蝶10科、41属、84种。通过应用Shannon-Weiner指数、Pielou指数和KA指数,对农田、水域、林地和居民区4种不同生境的调查及多样性分析,表明万佛山风景区是一个良好的蝴蝶生息地,应予以保护。     

The Evolution of Cultural Diversity: A Phylogenetic Approach

The Evolution of Cultural Diversity:. Phylogenetic Approach . Ruth Mace, Clare J. Holden, and Stephen Shennan, eds. Oxford, U.K.: Cavendish Publishing, 2005. 291 pp.     

Using Lifetime Risk Estimates in Personal Genomic Profiles: Estimation of Uncertainty

Personal genome tests are now offered direct-to-consumer (DTC) via genetic variants identified by genome-wide association studies (GWAS) for common diseases. Tests report risk estimates (age-specific and lifetime) for various diseases based on genotypes at multiple loci. However, uncertainty surrounding such risk estimates has not been systematically investigated. With breast cancer as an example, we examined the combined effect of uncertainties in population incidence rates, genotype frequency, effect sizes, and models of joint effects among genetic variants on lifetime risk estimates. We performed simulations to estimate lifetime breast cancer risk for carriers and noncarriers of genetic variants. We derived population-based cancer incidence rates from Surveillance, Epidemiology, and End Results (SEER) Program and comparative international data. We used data for non-Hispanic white women from 2003 to 2005. We derived genotype frequencies and effect sizes from published GWAS and meta-analyses. For a single genetic variant in FGFR2 gene (rs2981582), combination of uncertainty in these parameters produced risk estimates where upper and lower 95% simulation intervals differed by more than 3-fold. Difference in population incidence rates was the largest contributor to variation in risk estimates. For a panel of five genetic variants, estimated lifetime risk of developing breast cancer before age 80 for a woman that carried all risk variants ranged from 6.1% to 21%, depending on assumptions of additive or multiplicative joint effects and breast cancer incidence rates. Epidemiologic parameters involved in computation of disease risk have substantial uncertainty, and cumulative uncertainty should be properly recognized. Reliance on point estimates alone could be seriously misleading.     

Phylogenetic relationships of Hamadryas (Nymphalidae: Biblidinae) based on the combined analysis of morphological and molecular data

A new phylogenetic hypothesis for the Neotropical butterfly genus Hamadryas, based on the combination of a morphological matrix, one mitochondrial (COI) and four nuclear markers (CAD, RpS5, EF1a, and Wingless), is presented. Results from analyses of the molecular evidence are compared with a previously published morphological phylogeny. Molecular data and the analysis of the complete dataset support the monophyly of Hamadryas and most sister groups suggested by morphological data alone. The addition of DNA sequences to the morphological matrix helped define species groups for which no morphological synapomorphies were found. Partitioned Bremer support indicates that COI, CAD, and morphology were consistently in agreement with the combined evidence tree. In contrast, signal from the nuclear markers Rps5, EF1a, and Wingless showed indifference at most levels of the tree, and minor conflict at nodes solving the relationships between species groups. Though resolved, the combined evidence tree shows low resample values, particularly among species groups whose relationships were characterized by short internodes. A reassessment about the pattern of character change for sound production is presented and discussed.     

Phylogenetic relationships and historical biogeography of tribes and genera in the subfamily Nymphalinae (Lepidoptera: Nymphalidae)

We infer for the first time the phylogenetic relationships of genera and tribes in the ecologically and evolutionarily well‐studied subfamily Nymphalinae using DNA sequence data from three genes: 1450 bp of cytochrome oxidase subunit I (COI) (in the mitochondrial genome), 1077 bp of elongation factor 1‐alpha (EF1‐α) and 400–403 bp of wingless (both in the nuclear genome). We explore the influence of each gene region on the support given to each node of the most parsimonious tree derived from a combined analysis of all three genes using Partitioned Bremer Support. We also explore the influence of assuming equal weights for all characters in the combined analysis by investigating the stability of clades to different transition/transversion weighting schemes. We find many strongly supported and stable clades in the Nymphalinae. We are also able to identify ‘rogue’ taxa whose positions are weakly supported (the different gene regions are in conflict with each other) and unstable. Our main conclusions are: (1) the tribe Coeini as currently constituted is untenable, and Smyrna, Colobura and Tigridia are part of Nymphalini; (2) ‘Kallimini’ is paraphyletic with regard to Melitaeini and should be split into three tribes: Kallimini s.s., Junoniini and Victorinini; (3) Junoniini, Victorinini, Melitaeini and the newly circumscribed Nymphalini are strongly supported monophyletic groups, and (4) Precis and Junonia are not synonymous or even sister groups. The species Junonia coenia, a model system in developmental biology, clearly belongs in the genus Junonia. A dispersal‐vicariance analysis suggests that dispersal has had a major effect on the distributions of extant species, and three biotic regions are identified as being centres of diversification of three major clades: the Palaearctic for the Nymphalis‐group, the Afrotropics for Junoniini and the Nearctic for Melitaeini. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 86 , 227–251.