Phylogenetic divergences of the true bugs (Insecta: Hemiptera: Heteroptera), with emphasis on the aquatic lineages: the last piece of the aquatic insect jigsaw originated in the Late Permian/Early Triassic

Heteroptera are among the most diverse hemimetabolous insects. Seven infraorders have been recognized within this suborder of Hemiptera. Apart from the well‐established sister‐group relationship between Cimicomorpha and Pentatomomorpha (= Terheteroptera), the two terminal lineages, the relationships among the other five infraorders are still controversial, of which three (Gerromorpha, Nepomorpha and Leptopodomorpha) are intimately connected to aquatic environments. However, the various and often conflicting available phylogeny hypotheses do not offer a clear background for a connection between diversification and palaeoenvironments. In this study, a molecular data set representing 79 taxa and 10 149 homologous sites is used to infer the phylogenetic relationships within Heteroptera. Bayesian inference, maximum‐likelihood and maximum parsimony analyses were employed. The results of phylogenetic inferences largely confirm the widely accepted phylogenetic context. Estimation of the divergence time based on the phylogenetic results revealed that Gerromorpha, Nepomorpha and Leptopodomorpha originated successively during the period from the Late Permian to Early Triassic (269–246 Ma). This timescale is consistent with the origin and radiation time of various aquatic holometabolans. Our results indicate that the aquatic and semi‐aquatic true bugs evolved under environmental conditions of high air temperature and humidity in an evolutionary scenario similar to that of the aquatic holometabolans.     

Phylogenetic analysis of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha): evidence from mitochondrial genomes

Background  

The true water bugs are grouped in infraorder Nepomorpha (Insecta: Hemiptera: Heteroptera) and are of great economic importance. The phylogenetic relationships within Nepomorpha and the taxonomic hierarchies of Pleoidea and Aphelocheiroidea are uncertain. Most of the previous studies were based on morphological characters without algorithmic assessment. In the latest study, the molecular markers employed in phylogenetic analyses were partial sequences of 16S rDNA and 18S rDNA with a total length about 1 kb. Up to now, no mitochondrial genome of the true water bugs has been sequenced, which is one of the largest data sets that could be compared across animal taxa. In this study we analyzed the unresolved problems in Nepomorpha using evidence from mitochondrial genomes.     

Divergence Times and Phylogenetic Patterns of Sebacinales,a Highly Diverse and Widespread Fungal Lineage

Patterns of geographic distribution and composition of fungal communities are still poorly understood. Widespread occurrence in terrestrial ecosystems and the unique richness of interactions of Sebacinales with plants make them a target group to study evolutionary events in the light of nutritional lifestyle. We inferred diversity patterns, phylogenetic structures and divergence times of Sebacinales with respect to their nutritional lifestyles by integrating data from fossil-calibrated phylogenetic analyses. Relaxed molecular clock analyses indicated that Sebacinales originated late Permian within Basidiomycota, and their split into Sebacinaceae and Serendipitaceae nom. prov. likely occurred during the late Jurassic and the early Cretaceous, coinciding with major diversifications of land plants. In Sebacinaceae, diversification of species with ectomycorrhizal lifestyle presumably started during the Paleocene. Lineage radiations of the core group of ericoid and cavendishioid mycorrhizal Sebacinales started probably in the Eocene, coinciding with diversification events of their hosts. The diversification of Sebacinales with jungermannioid interactions started during the Oligocene, and occurred much later than the diversification of their hosts. Sebacinales communities associated either with ectomycorrhizal plants, achlorophyllous orchids, ericoid and cavendishioid Ericaceae or liverworts were phylogenetically clustered and globally distributed. Major Sebacinales lineage diversifications started after the continents had drifted apart. We also briefly discuss dispersal patterns of extant Sebacinales.     

Higher level phylogeny and the first divergence time estimation of Heteroptera (Insecta: Hemiptera) based on multiple genes

Heteroptera, or true bugs, are the largest, morphologically diverse and economically important group of insects with incomplete metamorphosis. However, the phylogenetic relationships within Heteroptera are still in dispute and most of the previous studies were based on morphological characters or with single gene (partial or whole 18S rDNA). Besides, so far, divergence time estimates for Heteroptera totally rely on the fossil record, while no studies have been performed on molecular divergence rates. Here, for the first time, we used maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) with multiple genes (18S rDNA, 28S rDNA, 16S rDNA and COI) to estimate phylogenetic relationships among the infraorders, and meanwhile, the Penalized Likelihood (r8s) and Bayesian (BEAST) molecular dating methods were employed to estimate divergence time of higher taxa of this suborder. Major results of the present study included: Nepomorpha was placed as the most basal clade in all six trees (MP trees, ML trees and Bayesian trees of nuclear gene data and four-gene combined data, respectively) with full support values. The sister-group relationship of Cimicomorpha and Pentatomomorpha was also strongly supported. Nepomorpha originated in early Triassic and the other six infraorders originated in a very short period of time in middle Triassic. Cimicomorpha and Pentatomomorpha underwent a radiation at family level in Cretaceous, paralleling the proliferation of the flowering plants. Our results indicated that the higher-group radiations within hemimetabolous Heteroptera were simultaneously with those of holometabolous Coleoptera and Diptera which took place in the Triassic. While the aquatic habitat was colonized by Nepomorpha already in the Triassic, the Gerromorpha independently adapted to the semi-aquatic habitat in the Early Jurassic.     

Revisiting habitat and lifestyle transitions in Heteroptera (Insecta: Hemiptera): insights from a combined morphological and molecular phylogeny

Heteroptera, the true bugs, are part of the largest clade of non-holometabolous insects, the Hemiptera, and include > 42 000 described species in about 90 families. Despite progress in resolving phylogenetic relationships between and within infraorders since the first combined morphological and molecular analysis published in 1993 (29 taxa, 669 bp, 31 morphological characters), recent hypotheses have relied entirely on molecular data. Weakly supported nodes along the backbone of Heteroptera made these published phylogenies unsuitable for investigations into the evolution of habitats and lifestyles across true bugs. Here we present the first combined morphological and molecular analyses of Heteroptera since 1993, using 135 taxa in 60 families, 4018 aligned bp of ribosomal DNA and 81 morphological characters, and various analytical approaches. The sister-group relationship of the predominantly aquatic Nepomorpha with all remaining Heteroptera is supported in all analyses, and a clade formed by Enicocephalomorpha, Dipsocoromorpha and Gerromorpha in some. All analyses recover Leptopodomorpha + (Cimicomorpha + Pentatomomorpha), mostly with high support. Parsimony- and likelihood-based ancestral state reconstructions of habitats and lifestyles on the combined likelihood phylogeny provide new insights into the evolution of true bugs. The results indicate that aquatic and semi-aquatic true bugs invaded these habitats three times independently from terrestrial habitats in contrast to a recent hypothesis. They further suggest that the most recent common ancestor of Heteroptera was predacious, and that the two large predominantly phytophagous clades (Trichophora and Miroidea) are likely to have derived independently from predatory ancestors. We conclude that by combining morphological and molecular data and employing various analytical methods our analyses have converged on a relatively well-supported hypothesis of heteropteran infraordinal relationships that now requires further testing using phylogenomic and more extensive morphological datasets.     

Distribution of water bugs (Heteroptera: Nepomorpha, Gerromorpha) over latitudinal zones in the northeast of European Russia

Data on the taxonomic composition of water bugs (Heteroptera: Nepomorpha, Gerromorpha) in the northeast of European Russia are given. A total of 34 water-bug species, which belong to 16 genera and 8 families, are recorded. The species diversity of Nepomorpha and Gerromorpha changes northwards: 33 occur in the taiga zone and only 8 species occur in the tundra zone. The bulk of the fauna consists of Eurosiberian (29%) and trans-Eurasian (26%) species; in latitude-related terms, the temperate group is most richly represented (64%). The species composition of the aquatic and semiaquatic heteropteran fauna of the region is especially similar to that of the tundra and taiga zones of Western Siberia.     

Multilocus analyses of an Antarctic fish species flock (Teleostei, Notothenioidei, Trematominae): phylogenetic approach and test of the early-radiation event

Clades that have undergone episodes of rapid cladogenesis are challenging from a phylogenetic point of view. They are generally characterised by short or missing internal branches in phylogenetic trees and by conflicting topologies among individual gene trees. This may be the case of the subfamily Trematominae, a group of marine teleosts of coastal Antarctic waters, which is considered to have passed through a period of rapid diversification. Despite much phylogenetic attention, the relationships among Trematominae species remain unclear. In contrast to previous studies that were mostly based on concatenated datasets of mitochondrial and/or single nuclear loci, we applied various single-locus and multilocus phylogenetic approaches to sequences from 11 loci (eight nuclear) and we also used several methods to assess the hypothesis of a radiation event in Trematominae evolution. Diversification rate analyses support the hypothesis of a period of rapid diversification during Trematominae history and only a few nodes in the hypothetical species tree were consistently resolved with various phylogenetic methods. We detected significant discrepancies among trees from individual genes of these species, most probably resulting from incomplete lineage sorting, suggesting that concatenation of loci is not the most appropriate way to investigate Trematominae species interrelationships. These data also provide information about the possible effects of historic climate changes on the diversification rate of this group of fish.     

DO FRESHWATER FISHES DIVERSIFY FASTER THAN MARINE FISHES? A TEST USING STATE‐DEPENDENT DIVERSIFICATION ANALYSES AND MOLECULAR PHYLOGENETICS OF NEW WORLD SILVERSIDES (ATHERINOPSIDAE)

Freshwater habitats make up only ～0.01% of available aquatic habitat and yet harbor 40% of all fish species, whereas marine habitats comprise >99% of available aquatic habitat and have only 60% of fish species. One possible explanation for this pattern is that diversification rates are higher in freshwater habitats than in marine habitats. We investigated diversification in marine and freshwater lineages in the New World silverside fish clade Menidiinae (Teleostei, Atherinopsidae). Using a time‐calibrated phylogeny and a state‐dependent speciation–extinction framework, we determined the frequency and timing of habitat transitions in Menidiinae and tested for differences in diversification parameters between marine and freshwater lineages. We found that Menidiinae is an ancestrally marine lineage that independently colonized freshwater habitats four times followed by three reversals to the marine environment. Our state‐dependent diversification analyses showed that freshwater lineages have higher speciation and extinction rates than marine lineages. Net diversification rates were higher (but not significant) in freshwater than marine environments. The marine lineage‐through time (LTT) plot shows constant accumulation, suggesting that ecological limits to clade growth have not slowed diversification in marine lineages. Freshwater lineages exhibited an upturn near the recent in their LTT plot, which is consistent with our estimates of high background extinction rates. All sequence data are currently being archived on Genbank and phylogenetic trees archived on Treebase.     

Patterns of mammalian diversification in recent evolutionary times: global tendencies and methodological issues

Changes in diversification patterns estimated from phylogenetic trees are an important source of information about the dynamics of evolution. To study the diversification of mammals, we reconstructed phylogenetic trees of 29 families and fitted both constant-rate and variable-rate models of diversification. In addition, we investigated the effect of clock models and phylogenetic reconstruction problems on diversification analyses. We observed, first, that none of the families increased its diversification rate during the last few million years, including the Pleistocene. Furthermore, we detected a decrease in diversification that, after application of different tests, was significant only for a minority of families. However, when diversification variation was analysed in a combined tree of all families, a global decline in diversification became significant. Therefore, although distorted by some methodological artefacts, we found an underlying signal of gradually decreasing diversification that suggests that ecological factors may have shaped the recent diversification of mammals.     

Keys to families and genera of gerromorpha and nepomorpha (Insecta: Heteroptera) in the central Amazonia, Brazil

Few studies have been done in Brazil on aquatic and semi-aquatic Gerromorpha and Nepomorpha (Heteroptera), Minas Gerais being the state where these insects have been studied the most. The present study presents keys for identification of Gerromorpha and Nepomorpha adults, thus providing a tool for ecological studies on aquatic insects in Central Amazonia. The specimens used to elaborate the taxonomic keys were collected in Presidente Figueiredo county in streams and artificial lakes and in Manaus county in streams, white-water floodplain (várzea) lakes and Rio Negro black-water flooded forest (igapó). Specimens from the invertebrate collection of the Instituto Nacional de Pesquisas da Amazonia (INPA) were also examined and included in the keys. Thirty one genera from 13 families of the infra-orders mentioned.     

Evolution of freshwater crab diversity in the Aegean region (Crustacea: Brachyura: Potamidae)

The aim of this study was to estimate the influence of the palaeogeographic and climatic history of the Aegean region on the diversity of freshwater crabs of the genus Potamon and to test whether this area served as source or reservoir in species diversity. Necessary species delimitation was accomplished by phylogenetic analyses of the mitochondrial markers COX1 and ND1, partial 16S rRNA gene and the tRNALeu gene. We found 14 genetic lineages of which nine could be assigned to previously recognised species. Temporal estimates of the splitting pattern in the phylogeny of Potamon indicated that a combination of geological and climatic events influenced their diversification. Within Potamon, the lineages separated into a western group and an eastern group. This first split in the genus occurred approximately 8.3-5.5 Mya, thus possibly correlated with the Messinian salinity crisis. A likelihood approach to geographic range evolution suggested for most species, occurring in the Aegean area, an origin in the Middle East. Moreover, there were no insular endemics in the central Aegean archipelago, therefore low sea-levels during the Pleistocene glacial periods possibly enabled dispersal to these islands, but subsequent rise in sea-level did not cause speciation. Nevertheless, the diversification of most lineages occurred during the Pleistocene epoch thus coinciding with Quaternary fluctuations of the climate.     

Phylogenetic analysis of ecomorphological divergence, community structure, and diversification rates in dusky salamanders (Plethodontidae: Desmognathus)

An important dimension of adaptive radiation is the degree to which diversification rates fluctuate or remain constant through time. Focusing on plethodontid salamanders of the genus Desmognathus, we present a novel synthetic analysis of phylogeographic history, rates of ecomorphological evolution and species accumulation, and community assembly in an adaptive radiation. Dusky salamanders are highly variable in life history, body size, and ecology, with many endemic lineages in the southern Appalachian Highlands of eastern North America. Our results show that life-history evolution had important consequences for the buildup of plethodontid-salamander species richness and phenotypic disparity in eastern North America, a global hot spot of salamander biodiversity. The origin of Desmognathus species with aquatic larvae was followed by a high rate of lineage accumulation, which then gradually decreased toward the present time. The peak period of lineage accumulation in the group coincides with evolutionary partitioning of lineages with aquatic larvae into seepage, stream-edge, and stream microhabitats. Phylogenetic simulations demonstrate a strong correlation between morphology and microhabitat ecology independent of phylogenetic effects and suggest that ecomorphological changes are concentrated early in the radiation of Desmognathus. Deep phylogeographic fragmentation within many codistributed ecomorph clades suggests long-term persistence of ecomorphological features and stability of endemic lineages and communities through multiple climatic cycles. Phylogenetic analyses of community structure show that ecomorphological divergence promotes the coexistence of lineages and that repeated, independent evolution of microhabitat-associated ecomorphs has a limited role in the evolutionary assembly of Desmognathus communities. Comparing and contrasting our results to other adaptive radiations having different biogeographic histories, our results suggest that rates of diversification during adaptive radiation are intimately linked to the degree to which community structure persists over evolutionary time.     

水盾草科系统位置评述

水盾草科(Cabombaceae)是双子叶植物。水盾草科包括2属: 水盾草属(Cabomba Aublet.)和莼菜属(Brasenia Schreb.)。形态学研究显示水盾草科具有许多原始性状, 而且在其适应水生环境的过程中经历了性状退化。水盾草科又被称为“古草本”。最新的分子系统发育研究显示, 水盾草科是现存被子植物系统树基部ANITA类群的成员之一。但有关水盾草科的系统位置存在争议。被子植物的起源与早期分化一直是植物学家关注的热点。本文对该科系统位置的研究历史与现状进行评述。     

Renewed diversification is associated with new ecological opportunity in the Neotropical turtle ants

Ecological opportunity, defined as access to new resources free from competitors, is thought to be a catalyst for the process of adaptive radiation. Much of what we know about ecological opportunity, and the larger process of adaptive radiation, is derived from vertebrate diversification on islands. Here, we examine lineage diversification in the turtle ants (Cephalotes), a species‐rich group of ants that has diversified throughout the Neotropics. We show that crown group turtle ants originated during the Eocene (around 46 mya), coincident with global warming and the origin of many other clades. We also show a marked lineage‐wide slowdown in diversification rates in the Miocene. Contrasting this overall pattern, a species group associated with the young and seasonally harsh Chacoan biogeographic region underwent a recent burst of diversification. Subsequent analyses also indicated that there is significant phylogenetic clustering within the Chacoan region and that speciation rates are highest there. Together, these findings suggest that recent ecological opportunity, from successful colonization of novel habitat, may have facilitated renewed turtle ant diversification. Our findings highlight a central role of ecological opportunity within a successful continental radiation.     

水盾草科系统位置评述

水盾草科（Cabombaceae）是双子叶植物。水盾草科包括2属：水盾草属（Cabomba Aublet．）和莼菜属（Brasenia Schreb．）。形态学研究显示水盾草科具有许多原始性状,而且在其适应水生环境的过程中经历了性状退化。水盾草科又被称为“古草本”。最新的分子系统发育研究显示,水盾草科是现存被子植物系统树基部ANITA类群的成员之一。但有关水盾草科的系统位置存在争议。被子植物的起源与早期分化一直是植物学家关注的热点。本文对该科系统位置的研究历史与现状进行评述。     

The adipokinetic hormones of Heteroptera: a comparative study

The adipokinetic hormones (AKHs) from 15 species of heteropteran Hemiptera (encompassing eight families, six superfamilies and three infraorders) have been isolated and structurally identified using liquid chromatography coupled with mass spectrometry. None of the structures are novel and all are octapeptides. These peptide sequence data are used, together with the previously available AKH sequence data on Heteroptera, to create a larger dataset for comparative analyses. This results, in total, in AKH sequences from 30 species (spanning 13 families), which are used in a matrix confronted with the current hypotheses on the phylogeny of Heteroptera. The expanded dataset shows that all heteropterans have octapeptide AKHs; three species have two AKHs, whereas the overwhelming majority have only one AKH. From a total of 11 different AKH peptides known from Heteroptera to date, three AKHs occur frequently: Panbo‐red pigment‐concentrating hormone (RPCH) (×10), Schgr‐AKH‐II (×6) and Anaim‐AKH (×4). The heteropteran database also suggests that particular AKH variants are family‐specific. The AKHs of Heteroptera: Pentatomomorpha (all terrestrial) are not present in Nepomorpha (aquatic) and Gerromorpha: Gerridae (semiaquatic); AKHs with a Val in position 2 are absent in the Pentatomomorpha (only AKHs with Leu² are present), whereas Val² predominates in the nonterrestrial species. An unexpected diversity of AKH sequences is found in Nepomorpha, Nepoidea, Nepidae and Nepinae, whereas Panbo‐RPCH (which has been identified in all infraorders of decapod crustaceans) is present in all analysed species of Pentatomidae and also in the only species of Tessaratomidae investigated. The molecular evolution of Heteroptera with respect to other insect groups and to crustaceans is discussed     

Global dispersal and ancient cryptic species in the smallest marine eukaryotes

Small eukaryotic species (<1 mm) are thought to behave as prokaryotes in that, lacking geographical barriers to their dispersal due to their tiny size, they are ubiquitous. Accordingly, the absence of geographical insulation would imply the existence of a relatively small number of microeukaryotic species. To test these ideas, we sequenced and compared several nuclear, mitochondrial, and chloroplast genes from the isolates of a marine picoeukaryotic alga (approximately 2 microm), Micromonas pusilla, collected worldwide. Independent and combined phylogenetic analyses demonstrate that this traditional single morphospecies actually comprises several independent lineages, some of which are shown to be ubiquitous in oceans. However, while some lineages group closely related strains, others form distant clusters, revealing the existence of cryptic species. Moreover, molecular dating using a relaxed clock suggests that their first diversification may have started as early as during the Late Cretaceous (approximately 65 MYA), implying that "M. pusilla" is the oldest group of cryptic species known to date. Our results illustrate that global dispersal of a picoeukaryote is possible in oceans, but this does not imply a reduced species number. On the contrary, we show that the morphospecies concept is untenable because it overlooks a large genetic and species diversity and may lead to incorrect biological assumptions.     

Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases

Background  

Cytosolic glutathione transferases (cGST) are a large group of ubiquitous enzymes involved in detoxification and are well known for their undesired side effects during chemotherapy. In this work we have performed thorough phylogenetic analyses to understand the various aspects of the evolution and functional diversification of cGSTs. Furthermore, we assessed plausible correlations between gene duplication and substrate specificity of gene paralogs in humans and selected species, notably in mammalian enzymes and their natural substrates.     

Towards a global perspective for Salvia L.: Phylogeny,diversification and floral evolution

Salvia is the most species-rich genus in Lamiaceae, encompassing approximately 1000 species distributed all over the world. We sought a new evolutionary perspective for Salvia by employing macroevolutionary analyses to address the tempo and mode of diversification. To study the association of floral traits with speciation and extinction, we modelled and explored the evolution of corolla length and the lever-mechanism pollination system across our Salvia phylogeny. We reconstructed a multigene phylogeny for 366 species of Salvia in the broad sense including all major recognized lineages and 50 species from Iran, a region previously overlooked in studies of the genus. Our comprehensive sampling of Iranian species of Salvia provides higher phylogenetic resolution for southwestern Asian species than obtained in previous studies. Our phylogenetic data in combination with divergence time estimates were used to examine the evolution of corolla length, woody versus herbaceous habit, and presence versus absence of a lever mechanism. We investigated the timing and dependence of Salvia diversification related to corolla length evolution through a disparity test and BAMM analysis. A HiSSE model was used to evaluate the dependency of diversification on the lever-mechanism pollination system in Salvia. A medium corolla length (15–18 mm) was reconstructed as the ancestral state for Salvia with multiple shifts to shorter and longer corollas. Macroevolutionary model analyses indicate that corolla length disparity is high throughout Salvia evolution, significantly different from expectations under a Brownian motion model during the last 28 million years of evolution. Our analyses show evidence of a higher diversification rate of corolla length for some Andean species of Salvia compared to other members of the genus. Based on our tests of diversification models, we reject the hypothesis of a direct effect of the lever mechanism on Salvia diversification. Therefore, we suggest caution in considering the lever-mechanism pollination system as one of the main drivers of speciation in Salvia.