Higher level molecular phylogeny of darkling beetles (Coleoptera: Tenebrionidae)

Insect diversity represents about 60% of the estimated million‐and‐a‐half described eukaryotic species worldwide, yet comprehensive and well‐resolved intra‐ordinal phylogenies are still lacking for the majority of insect groups. This is the case especially for the most species‐rich insect group, the beetles (Coleoptera), a group for which less than 4% of the known species have had their DNA sequenced. In this study, we reconstruct the first higher level phylogeny based on DNA sequence data for the species‐rich darkling beetles, a family comprising at least 20 000 species. Although amongst all families of beetles Tenebrionidae ranks seventh in terms of species diversity, the lack of knowledge on the phylogeny and systematics of the group is such that its monophyly has been questioned (not to mention those of the subfamilies and tribes contained within it). We investigate the evolutionary history of Tenebrionidae using multiple phylogenetic inference methods (Bayesian inference, maximum likelihood and parsimony) to analyse a dataset consisting of eight gene fragments across 404 taxa (including 250 tenebrionid species). Although the resulting phylogenetic framework only encompasses a fraction of the known tenebrionid diversity, it provides important information on their systematics and evolution. Whatever the methods used, our results provide strong support for the monophyly of the family, and highlight the likely paraphyletic or polyphyletic nature of several important tenebrionid subfamilies and tribes, notably the polyphyletic subfamilies Diaperinae and Tenebrioninae that clearly require substantial revision in the future. Some interesting associations in several groups are also revealed by the phylogenetic analyses, such as the pairing of Aphtora Bates with Phrenapatinae. Furthermore this study advances our knowledge of the evolution of the group, providing novel insights into much‐debated theories, such as the apparent relict distribution of the tribe Elenophorini.     

Molecular and morphological phylogenetics of weevils (coleoptera,curculionoidea): do niche shifts accompany diversification?

The main goals of this study were to provide a robust phylogeny for the families of the superfamily Curculionoidea, to discover relationships and major natural groups within the family Curculionidae, and to clarify the evolution of larval habits and host-plant associations in weevils to analyze their role in weevil diversification. Phylogenetic relationships among the weevils (Curculionoidea) were inferred from analysis of nucleotide sequences of 18S ribosomal DNA (rDNA; approximately 2,000 bases) and 115 morphological characters of larval and adult stages. A worldwide sample of 100 species was compiled to maximize representation of weevil morphological and ecological diversity. All families and the main subfamilies of Curculionoidea were represented. The family Curculionidae sensu lato was represented by about 80 species in 30 "subfamilies" of traditional classifications. Phylogenetic reconstruction was accomplished by parsimony analysis of separate and combined molecular and morphological data matrices and Bayesian analysis of the molecular data; tree topology support was evaluated. Results of the combined analysis of 18S rDNA and morphological data indicate that monophyly of and relationships among each of the weevil families are well supported with the topology ((Nemonychidae, Anthribidae) (Belidae (Attelabidae (Caridae (Brentidae, Curculionidae))))). Within the clade Curculionidae sensu lato, the basal positions are occupied by mostly monocot-associated taxa with the primitive type of male genitalia followed by the Curculionidae sensu stricto, which is made up of groups with the derived type of male genitalia. High support values were found for the monophyly of some distinct curculionid groups such as Dryophthorinae (several tribes represented) and Platypodinae (Tesserocerini plus Platypodini), among others. However, the subfamilial relationships in Curculionidae are unresolved or weakly supported. The phylogeny estimate based on combined 18S rDNA and morphological data suggests that diversification in weevils was accompanied by niche shifts in host-plant associations and larval habits. Pronounced conservatism is evident in larval feeding habits, particularly in the host tissue consumed. Multiple shifts to use of angiosperms in Curculionoidea were identified, each time associated with increases in weevil diversity and subsequent shifts back to gymnosperms, particularly in the Curculionidae.     

Morphological innovation,ecological opportunity,and the radiation of a major vascular epiphyte lineage

The emergence of angiosperm‐dominated tropical forests in the Cretaceous led to major shifts in the composition of biodiversity on Earth. Among these was the rise to prominence of epiphytic plant lineages, which today comprise an estimated one‐quarter of tropical vascular plant diversity. Among the most successful epiphytic groups is the Polypodiaceae, which comprises an estimated 1500 species and displays a remarkable breadth of morphological and ecological diversity. Using a time‐calibrated phylogeny for 417 species, we characterized macroevolutionary patterns in the family, identified shifts in diversification rate, and identified traits that are potential drivers of diversification. We find high diversification rates throughout the family, evidence for a radiation in a large clade of Paleotropical species, and support for increased rates of diversification associated with traits including chlorophyllous spores and noncordiform gametophytes. Contrary to previous hypotheses, our results indicate epiphytic species and groups with humus‐collecting leaves diversify at lower rates than the family as a whole. We find that diversification rates in the Polypodiaceae are positively correlated with changes in elevation. Repeated successful exploration of novel habitat types, rather than morphological innovation, appears to be the primary driver of diversification in this group.     

Recurrent genome duplication events likely contributed to both the ancient and recent rise of ferns

Ferns, the second largest group of vascular plants, originated ～400 mil ion years ago(Mya). They became dominant in the ancient Earth landscape before the angiosperms and are stil important in current ecosystems.Many ferns have exceptional y high chromosome numbers,possibly resulting from whole-genome duplications(WGDs).However, WGDs have not been investigated molecularly across fern diversity. Here we detected and dated fern WGDs using a phylogenomic approach and by calculating synonymous substitution rates(Ks). We also investigated a possible correlation between proposed WGDs and shifts in species diversification rates. We identified 19 WGDs: three ancient events along the fern phylogenetic backbone that are shared by 66%–97% of extant ferns, with additional lineage-specific WGDs for eight orders, providing strongevidence for recurring genome duplications across fern evolutionary history. We also observed similar Ks peak values for more than half of these WGDs, with multiple WGDs occurring close to the Cretaceous(～145–66 Mya). Despite the repeated WGD events, the biodiversity of ferns declined during the Cretaceous, implying that other factors probably contributed to the floristic turnover from ferns to angiosperms. This study provides molecular evidence for recurring WGDs in ferns and offers important clues to the genomic evolutionary history of ferns.     

A morphological supermatrix‐based phylogeny for the Neotropical fish superfamily Anostomoidea (Ostariophysi: Characiformes): phylogeny,missing data and homoplasy

Although 11 studies have addressed the systematics of the four families and 281 fish species of the ecomorphologically diverse Anostomoidea, none has proposed a global hypothesis of relationships. We synthesized these studies to yield a supermatrix with 463 morphological characters among 174 ingroup species, and inferred phylogeny with parsimony and Bayesian optimization. We evaluated the applicability of the supermatrix approach to morphological datasets, tested its sensitivity to missing data, determined the impact of homoplastic characters on phylogenetic resolution, and determined the distribution of homologies and homoplasies on the topology. Despite more than 60% missing data, analyses supported the monophyly of all families, and phylogenetic structure degraded only with inclusion of species with high percentages of missing data and in analyses limited to homoplasies. The latter differs modestly from the full matrix indicating phylogenetic signal in homoplastic characters. Character distributions differ across the phylogeny, with a greater prevalence of homologies at deeper nodes and homoplasies nearer the tips than expected by chance. This may suggest early diversification into distinct bauplans with subsequent diversification of faster evolving character systems. The morphological supermatrix approach is powerful and allows integration of classical data with modern methods to examine the evolution of multiple character systems.     

The value of sampling anomalous taxa in phylogenetic studies: major clades of the Asteraceae revealed

The largest family of flowering plants Asteraceae (Compositae) is found to contain 12 major lineages rather than five as previously suggested. Five of these lineages heretofore had been circumscribed in tribe Mutisieae (Cichorioideae), a taxon shown by earlier molecular studies to be paraphyletic and to include some of the deepest divergences of the family. Combined analyses of 10 chloroplast DNA loci by different phylogenetic methods yielded highly congruent well-resolved trees with 95% of the branches receiving moderate to strong statistical support. Our strategy of sampling genera identified by morphological studies as anomalous, supported by broader character sampling than previous studies, resulted in identification of several novel clades. The generic compositions of subfamilies Carduoideae, Gochnatioideae, Hecastocleidoideae, Mutisioideae, Pertyoideae, Stifftioideae, and Wunderlichioideae are novel in Asteraceae systematics and the taxonomy of the family has been revised to reflect only monophyletic groups. Our results contradict earlier hypotheses that early divergences in the family took place on and spread from the Guayana Highlands (Pantepui Province of northern South America) and raise new hypotheses about how Asteraceae dispersed out of the continent of their origin. Several nodes of this new phylogeny illustrate the vast differential in success of sister lineages suggesting focal points for future study of species diversification. Our results also provide a backbone exemplar of Asteraceae for supertree construction.     

Ecological diversification and phylogeny of emydid turtles

Ecological diversification is a central topic in ecology and evolutionary biology. We undertook the first comprehensive species-level phylogenetic analysis of Emydidae (an ecologically diverse group of turtles), and used the resulting phylogeny to test four general hypotheses about ecological diversification. Phylogenetic analyses were based on data from morphology (237 parsimony-informative characters) and mitochondrial DNA sequences (547 parsimony-informative characters) and included 39 of the 40 currently recognized emydid species. Combined analyses of all data provide a well-supported hypothesis for intergeneric relationships, and support monophyly of the two subfamilies (Emydinae and Deirochelyinae) and most genera (with the notable exception of Clemmys and Trachemys ). Habitat and diet were mapped onto the combined-data tree to test fundamental hypotheses about ecological diversification. Using continuous coding of ecological characters showed that lineages changed in habitat before diet, ecological change was most frequently from generalist to specialist, and habitat and diet rarely changed on the same branch of the phylogeny. However, we also demonstrate that the results of ancestral trait reconstructions can be highly sensitive to character coding method (i.e. continuous vs. discrete). Finally, we propose a simple model to describe the pattern of ecological diversification in emydid turtles and other lineages, which may reconcile the (seemingly) conflicting conclusions of our study and two recent reviews of ecological diversification.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79, 577–610.     

Molecular phylogeny of the fungus gnat subfamilies Gnoristinae and Mycomyinae,and their position within Mycetophilidae (Diptera)

The phylogeny of the fungus gnat family Mycetophilidae (Diptera) is reconstructed with a focus on the species‐rich and taxonomically difficult subfamilies Gnoristinae and Mycomyinae. The multigene phylogenetic analyses are based on five nuclear (18S, 28S, CAD, MCS, ITS2) and four mitochondrial (12S, 16S, COI, CytB) gene markers. The analyses strongly support the monophyly of Mycetophilidae and the subfamilies Manotinae, Sciophilinae, Leiinae, and Mycomyinae, although Gnoristinae is paraphyletic with respect to Mycetophilinae. All the genera and groups of genera included are supported as monophyletic, except for Acomoptera Vockeroth, Boletina Staeger, Dziedzickia Johannsen, Ectrepesthoneura Enderlein, and Neoempheria Osten Sacken. Ancestral character state reconstructions were applied to two morphological features present in Gnoristinae and Mycomyinae (i.e. presence of setae on wing membrane and wing vein R₄) in order to assess their evolution. The wing vein R₄ appears as an unstable character, spread throughout different clades. A dated phylogeny of the family Mycetophilidae showed that most of the subfamilies of Mycetophilidae originated and diversified during the Cretaceous. The youngest subfamilies, originated in the Paleogene, appear to be Mycomyinae and Mycetophilinae.     

Molecular phylogeny of hipposiderid bats from Southeast Asia and evidence of cryptic diversity

Old World leaf-nosed bats (Hipposideridae) are among the most widespread and ecologically diverse groups of insectivorous bats in the Old World tropics. However, phylogenetic relationships in Hipposideridae are poorly resolved at both the generic and species levels, and deep genetic divergence within several Southeast Asian species suggests that current taxonomy underestimates hipposiderid diversity in this region. We used mitochondrial and nuclear sequence data to conduct the first extensive molecular phylogenetic analysis of Southeast Asian hipposiderid bats. Inclusion of multiple samples per taxon allowed testing for evidence of evolutionarily distinct lineages within taxa currently defined as single species. In contrast to earlier phylogenies based on morphometrics, molecular data support monophyly of Hipposideros, but are ambiguous regarding the monophyly of Hipposideridae. With a few exceptions, molecular data also support currently recognized species groups classified by qualitative morphological characters. Widespread paraphyly and polyphyly within many currently recognized species of Hipposideros indicates that evolutionary diversity in the genus is underrepresented by current nomenclature. Comparison of available morphological and echolocation data suggest that both geographic isolation and ecological selection have contributed to the diversification of Southeast Asian hipposiderid bats.     

Molecular phylogeny and biogeography of tribe anthemideae (Asteraceae), based on chloroplast gene ndhF

Anthemideae (Asteraceae) is primarily a north temperate, Old World tribe of 109 genera and approximately 1740 species. We sequenced a 1200-bp portion of chloroplast gene ndhF for representative genera and subtribes and constructed a phylogeny for the tribe. There is support for monophyly of subtribes Chrysantheminae and Gonosperminae and for portions of some subtribes. However, our molecular phylogeny differs significantly from traditional classifications and from previously published morphological phylogenies of the tribe. Many South African genera from several different subtribes form a basal grade, indicating multiple, relictual lineages. Eurasian genera form a recently derived clade that includes the Mediterranean genera of the Iberian Peninsula and North Africa. There is little resolution or support for the placement of eastern Asian genera. Apparently, the tribe originated in the Southern Hemisphere, presumably in Africa, with the Eurasian and Mediterranean members being derived from a common ancestor.     

A review of the phylogeny and classification of the Asteraceae

The Asteraceae are commonly divided into two large subfamilies, the Cichorioideae (syn. Lactucoideae; Mutisieae, Cardueae, Lactuceae, Vernonieae, Liabeae, Arctoteae) and the Asteroideae (Inuleae, Astereae, Anthemideae, Senecioneae, Calenduleae, Heliantheae, Eupatorieae). Recent phylogenetic analyses based on morphological and chloroplast DNA data conclusively show that the Mutisieae-Barnadesiinae are the sister group to the rest of the family and that the Asteroideae tribes form a monophyletic group. The Vernonieae and Liabeae are sister tribes and the Eupatorieae are nested within a paraphyletic Heliantheae; otherwise tribal interrelationships are still largely uncertain. The Mutisieae-Barnadesiinae are excluded from the Mutisieae and elevated to the new subfamily Barnadesioideae. The two subfamilies Barnadesioideae and Asteroideae are monophyletic, whereas the status of the Cichorioideae remains uncertain. Analyses of chloroplast DNA data support the monophyly of the Cichorioideae; however, morphological data indicate that the subfamily is paraphyletic. Further studies are needed to test the monophyly of the Cichorioideae, as well as to further resolve tribal interrelationships in the two larger subfamilies.     

Searching for natural lineages within the Cerylonid Series (Coleoptera: Cucujoidea)

Phylogenetic relationships within the diverse beetle superfamily Cucujoidea are poorly known. The Cerylonid Series (C.S.) is the largest of all proposed superfamilial cucujoid groups, comprising eight families and representing most of the known cucujoid species diversity. The monophyly of the C.S., however, has never been formally tested and the higher-level relationships among and within the constituent families remain equivocal. Here we present a phylogenetic study based on 18S and 28S rDNA for 16 outgroup taxa and 61 C.S. ingroup taxa, representing seven of the eight C.S. families and 20 of 39 subfamilies. We test the monophyly of the C.S., investigate the relationships among the C.S. families, and test the monophyly of the constituent families and subfamilies. Phylogenetic reconstruction of the combined data was achieved via standard static alignment parsimony analyses, Direct Optimization using parsimony, and partitioned Bayesian analysis. All three analyses support the paraphyly of Cucujoidea with respect to Tenebrionoidea and confirm the monophyly of the C.S. The C.S. families Bothrideridae, Cerylonidae, Discolomatidae, Coccinellidae and Corylophidae are supported as monophyletic in all analyses. Only the Bayesian analysis recovers a monophyletic Latridiidae. Endomychidae is recovered as polyphyletic in all analyses. Of the 14 subfamilies with multiple terminals in this study, 11 were supported as monophyletic. The corylophid subfamily Corylophinae and the coccinellid subfamilies Chilocorinae and Scymninae are recovered as paraphyletic. A sister grouping of Anamorphinae+Corylophidae is supported in all analyses. Other taxonomic implications are discussed in light of our results.     

基于18S基因序列的姬小蜂分子系统发育

本文基于18S rDNA部分序列,用MP和Baysian方法研究了姬小蜂科的系统发育,对姬小蜂科的单系性及其与其它小蜂科间的关系进行了讨论。姬小蜂亚科、灿姬小蜂亚科和啮姬小蜂亚科形成三个独立的支系,研究结果支持它们各自的单系性,但本结果没有明确姬小蜂科的单系性。研究结果同时还支持瑟姬小蜂族、扁股姬小蜂族和狭面姬小蜂族三个族的地位,但不支持姬小蜂族的地位。姬小蜂科的单系性及其与其它小蜂间的关系还需更多的形态学数据和更多的基因序列来进一步研究[动物学报52 (2) : 288 -301 , 2006]。     

Phylogenetic relationships of the Suidae (Mammalia,Cetartiodactyla): new insights on the relationships within Suoidea

Orliac, M. J., Antoine, P. ‐O., Ducrocq, S. (2010). Phylogenetic relationships of the Suidae (Mammalia, Cetartiodactyla): new insights on the relationships within Suoidea. —Zoologica Scripta, 39, 315–330. In most analyses, both molecular and morphological phylogenies of the Cetartiodactyla support the monophyly of Suoidea. However, the evolutionary history of this superfamily remains poorly known primarily due to long‐lasting debates about the taxonomic content and relationships of the suoid families and subfamilies. Despite their crucial position in the reconstruction of the phylogeny of Cetartiodactyla, Suoidea themselves have received little attention in those phylogenies, and no extensive analysis of the group has been performed so far. We therefore examine the phylogeny of the Suidae through the first phylogenetic analysis of Suoidea, including recent and fossil representatives of all four putative families. The results support the monophyly of the traditional suid subfamilies and indicate the Sanitheriidae as sister taxon to the Suidae clade. The evolutionary history within Suidae reveals its complexity, with major convergences involving important morphological structures such as the auditory region or the upper male canine. Divergent signals gathered from either dental or cranio‐mandibular features are responsible for two long‐lasting unresolved issues within Suoidea: the question of the relationships between ‘Old World’ and ‘New World’ peccaries remaining unsolved, as well as the position and familial status of the mid‐Tertiary tayassuid Perchoerus.     

A molecular approach to arthrotardigrade phylogeny (Heterotardigrada,Tardigrada)

The marine order Arthrotardigrada (class Heterotardigrada, phylum Tardigrada) is known for its conspicuously high morphological diversity and has been traditionally recognized as the most ancestral group within the phylum. Despite its potential importance in understanding the evolution of the phylum, the phylogenetic relationships of Arthrotardigrada have not been clarified. This study conducted molecular phylogenetic analyses of the order encompassing all families except Neoarctidae using nuclear 18S and 28S rRNA fragments. Data from two rare families, Coronarctidae and Renaudarctidae, were included for the first time. The analyses confirmed the monophyly of Heterotardigrada and inferred Coronarctidae as the sister group to all other heterotardigrade taxa. Furthermore, the results support a monophyletic Renaudarctidae + Stygarctidae clade, which has been previously suggested on morphology. Our data indicated that two subfamilies currently placed in Halechiniscidae are only distantly related to this family. We propose that these taxa are each elevated to family level (Styraconyxidae (new rank) and Tanarctidae (new rank)). The morphology of tardigrades is discussed in the context of the inferred phylogeny.     

Cladistic analysis of Aradidae (Insecta,Heteroptera) based on morphological and molecular characters

In this study, we present for the first time a cladistic analysis of the subfamilies of Aradidae, using molecular and morphological characters. Eighty‐three taxa, including 79 species representing eight subfamilies, are treated. The analyses were performed using 72 morphological characters and approximately 1650 bp corresponding to three molecular loci (CO1, 16S and 28S). Characters were analysed using parsimony and Bayesian methods. Based on the combined analyses, we find support for the monophyly of Aradidae, including the subfamilies Aradinae, Aneurinae, Calisiinae, Isoderminae, and Mezirinae and the paraphyly of Prosympiestinae and Chinamyersiinae. In all analyses, Prosympiestinae includes Isoderminae. The Termitaphididae were not found sister to the Aradidae in the Aradoidea.     

A comprehensive generic-level phylogeny of the sunflower family: Implications for the systematics of Chinese Asteraceae

The sunflower family (Asteraceae) is the largest and the most diverse flowering plant family, comprising 24 000–30 000 species and 1600–1700 genera. In China, Asteraceae are also the largest family, with approximately 2336 indigenous species in 248 genera. In the past two decades, molecular phylogenetic analyses has contributed greatly to our understanding of the systematics of Asteraceae. Nevertheless, the large-scale analyses and knowledge about the relationships of Chinese Asteraceae at the generic level as a whole are far from complete due to difficulties in sampling. In this study, we presented a three-marker (rbcL, ndhF, and matK) phylogeny of Asteraceae, including 506 genera (i.e., approximately one-third of Asteraceae genera). The study sampled 200 Chinese genera (i.e., approximately 80% of Chinese Asteraceae genera). The backbones of the new phylogeny were largely congruent with earlier studies, with 13 subfamilies and 45 tribes recognized. Chinese Asteraceae were distributed in 7 subfamilies (Mutisioideae, Wunderlichioideae, Carduoideae, Pertyoideae, Gymnarrhenoideae, Cichorioideae, and Asteroideae) and 22 tribes (Mutiseae, Hyalideae, Cardueae, Pertyeae, Gymnarrheneae, Vernonieae, Cichorieae, Doroniceae, Senecioneae, Astereae, Anthemideae, Gnaphalieae, Calenduleae, Inuleae, Athroismeae, Helenieae, Coreopsideae, Neurolaeneae, Tageteae, Millieae, Eupatorieae, and Heliantheae). Chinese Asteraceae lacked 6 basal subfamilies and 23 tribes. Several previously ambiguous relationships were clarified. Our analyses also resolved some unplaced genera within Chinese Asteraceae. Finally, our phylogenetic tree was used to revise the classification for all genera of Chinese Asteraceae. In total, 255 genera, 22 tribes, and 7 subfamilies in China are recognized.     

Phylogeny of haplo–diploid,fungus‐growing ambrosia beetles (Curculionidae: Scolytinae: Xyleborini) inferred from molecular and morphological data

Cognato, A. I., Hulcr, J., Dole, S. A. & Jordal, B. H. (2010). Phylogeny of haplo‐diploid, fungus‐growing ambrosia beetles (Curculionidae: Scolytinae: Xyleborini) inferred from molecular and morphological data. —Zoologica Scripta, 40, 174–186. The ambrosia beetle tribe Xyleborini currently contains 30 genera and approximately 1200 species which are distributed throughout worldwide forests with most diversity located in the tropics. They also represent the most invasive scolytines in North America. Despite economic concerns and biological curiosity with this group, a comprehensive understanding of generic boundaries and the evolutionary relationship among species is lacking. In this study, we include 155 xyleborine species representing 23 genera in parsimony and Bayesian analyses using 3925 nucleotides from mitochondrial (COI) and nuclear genomes (28S, ArgK, CAD, EF‐1α) and 39 morphological characters. The phylogenies resulting from the parsimony analyses, which treated gap positions either as missing or fifth character states, and the Bayesian analysis were generally similar. Clades with high support or posterior probabilities were found in all trees, while those with low support were not recovered by all analyses. Fourteen of the 23 genera were monophyletic although not all relationships among the genera were resolved. We show monophyly of several species groups associated with particular morphological and biological characters and suggest recognition of these groups as genera. Most interesting was the monophyly of South and Central American species representing several genera. This finding suggests recent and fast radiation of xyleborines in the New World accompanied by morphological and biological diversification.