Cladistics最新文献

Inocelliidae is one of the two extant families of the holometabolan order Raphidioptera (snakeflies), with the modern fauna represented by seven genera and 44 species. The evolutionary history of the family is little-known. Here we present the first phylogenetic and biogeographical analyses based on a worldwide sampling of taxa and datasets combined with morphological characters and mitochondrial genomes, aiming to investigate the intergeneric phylogeny and historical biogeography of Inocelliidae. The phylogenetic inference from the combined analysis of morphological and molecular data recovered the sister-group relationship between a clade of (Negha + Indianoinocellia) + Sininocellia and a clade of Fibla + the Inocellia clade (interiorly nested by Amurinocellia and Parainocellia). Amurinocellia stat.r. and Parainocellia stat.r. et emend.n. are relegated to subgeneric status within Inocellia, whereas a newly erected subgenus of Inocellia, Epinocellia subgen.n., accommodates the former Parainocellia burmana (U. Aspöck and H. Aspöck, 1968) plus a new species Inocellia (Epinocellia) weii sp.n. Further, the Inocellia crassicornis group constitutes the nominotypical subgenus Inocellia stat.n., but the Inocellia fulvostigmata group is paraphyletic. Diversification within Inocelliidae is distinguished by an Eocene divergence leading to extant genera and a Miocene radiation of species. A biogeographical scenario depicts how the diverse inocelliid fauna from East Asia could have originated from western North America via dispersal across the Beringia during the early Tertiary, and how the Miocene ancestors of Inocellia could have accomplished long-distance dispersals via the Tibet–Himalayan corridor or eastern Palaearctic to western Palaearctic. Our results shed new light specifically on the evolution of Inocelliidae and, in general, the Raphidioptera.

Triatominae, commonly known as kissing bugs, are a group of approximately 150 species of hematophagous reduviids, some of which are vectors of Trypanosoma cruzi, the etiological agent of the Chagas disease. Distributional patterns of triatomines have been studied based on macroecological and historical biogeographic approaches, but the definition of distributional patterns and areas of endemism are yet to be defined based on objective criteria. We used two methods to identify biogeographic units in the Triatominae: the endemicity analysis based on an optimality criterion (NDM/VNDM software) and a network approach aimed to simplify and highlight the underlying structure in species distributions (Infomap Bioregions). Information on species distributions was obtained from a data paper, comprising 21 815 records for 135 triatomine species occurring in the Americas. The resulting areas of each method were clustered using a meta consensus criterion based on dissimilarities and interpreted as recurrent areas. The NDM areas show a nested structure, presenting greater restrictions to the inclusion of species in a given area, requiring broad sympatry. In contrast, bioregions emphasize spatial patterns with better-delimited areas and species occurrences do not need to be highly congruent. When areas were clustered based on their species composition two clear patterns arose from both methods: (i) areas within the southern Amazon and southeast South America, especially in the Chacoan subregion, formed a cluster, and (ii) areas north of the Amazon, Pacific, Mesoamerica, Mexican transition zone and Nearctic formed another cluster. Moreover, within each of these two clusters, there was a latitudinal gradient of the areas in the Americas showing spatial similarity between the areas found in both methods. Results of both methods show well-bound areas separating the triatomine fauna in the Brazilian subregions, resulting in the recognition of areas corresponding to the biomes Chaco, Pampa, Cerrado, and Caatinga, and, to a lesser extent, the Atlantic Forest.

The Cretaceous–Paleogene (KPg) boundary, one of Earth’s five major extinction events, occurred just before the appearance of Placentalia in the fossil record. The Gobi Desert, Mongolia and the Western Interior of North America have important fossil mammals occurring just before and after the KPg boundary (e.g. Prodiacodon, Deltatheridium) that have yet to be phylogenetically tested in a character-rich context with molecular data. We present here phylogenetic analyses of >6000 newly scored anatomical observations drawn from six untested fossils and added to the largest existing morphological matrix for mammals. These data are combined with sequence data from 27 nuclear genes. Results show the existence of a new eutherian sister clade to Placentalia, which we name and characterize. The extinct clade Leptictidae is part of this placental sister clade, indicating that the sister clade survived the KPg event to co-exist in ancient ecosystems during the Paleogene radiation of placentals. Analysing the Cretaceous metatherian Deltatheridium in this character-rich context reveals it is a member of Marsupialia, a finding that extends the minimum age of Marsupialia before the KPg boundary. Numerous shared-derived features from multiple anatomical systems support the assignment of Deltatheridium to Marsupialia. Computed tomography scans of exquisite new specimens better document the marsupial-like dental replacement pattern of Deltatheridium. The new placental sister clade has both Asian and North American species, and is ancestrally characterized by shared derived features such as a hind limb modified for saltatorial locomotion.

Pselaphinae is a large subfamily, comprising over 10 000 species of the megadiverse Staphylinidae (rove beetles). A remarkable feature of this group is the extreme structural diversity of different body regions, especially the head and its appendages. Within Pselaphinae, Clavigeritae stand out as a clade of highly specialized myrmecophiles. We examined internal and external head structures of the clavigerite species Diartiger kubotai Nomura, using state-of-the-art techniques. The cephalic morphology indicates in a phylogenetic context that the loss of eyes in some Clavigeritae was the latest of major evolutionary changes. We compiled the largest set of morphological data ever scored for the subfamily, comprising 155 characters of the head. Parsimony analyses and Bayesian inference yielded a similar phylogenetic pattern, largely congruent with results published previously. We retrieved Pselaphinae as a clade, and Faronitae as sister to all remaining groups of the subfamily. Faronitae are followed by a “Euplectitae grade” and non-monophyletic Goniaceritae, Batrisitae and Pselaphitae. Clavigeritae are monophyletic, but have evolved within the pselaphite grade. The enigmatic Colilodion Besuchet, recently shifted from Clavigeritae to a paraphyletic Pselaphitae, was placed as sister to extant clavigerites based on an array of cephalic synapomorphies. The current classification of Pselaphinae is unstable and deep changes should be made maintaining only monophyletic units, whereas most of the supertribes are paraphyletic. Characters of the head, with a concentration of mouthparts and sensory structures, and essential parts of the digestive tract and the nervous system, are highly informative phylogenetically. Study of internal structures, presently still at a very preliminary stage, obviously is essential for understanding the evolution of Pselaphinae. Future genetic investigations may reveal mechanisms behind the unique structural megadiversity in this exceptional group of rove beetles.

The genus Pleurodema comprises 15 species distributed through the Neotropical region, from sea level up to 5000 m.a.s.l. A total-evidence analysis of Pleurodema is provided based on the parsimony criterion. The combined dataset included morphometric, phenotypic, and DNA evidence (34 taxa, 4441 characters). The parsimony analysis yielded one most-parsimonious tree. Pleurodema was recovered as a well-supported clade composed of two major subclades. One subclade has an identical topology to that of previous analyses, the P. brachyops Clade (P. alium, P. borellii, P. brachyops, P. cinereum, P. diplolister, and P. tucumanum). The other subclade includes the remaining nine species of the genus, exhibiting a topology different from that of previous studies. According to the present phylogeny, this second lineage is formed by the P. nebulosum Clade (P. guayapae + P. nebulosum), P. marmoratum, the re-defined P. thaul Clade (P. bufoninum, P. somuncurense, P. thaul) and the P. bibroni Clade (P. bibroni, P. cordobae, P. kriegi). The reproductive modes of Pleurodema represent a unique combination of features within Leiuperinae, including three egg-clutch structures, two types of amplexus, and lack of vocalization. Also, some species of Pleurodema have been considered fossorial, because they are capable of digging with their hind-limbs and remaining in self-made burrows during dry seasons. The evolution of characters associated with reproductive biology and fossoriality is discussed in light of the obtained results.

In maximum likelihood (ML), the support for a clade can be calculated directly as the likelihood ratio (LR) or log-likelihood difference (S, LLD) of the best trees with and without the clade of interest. However, bootstrap (BS) clade frequencies are more pervasive in ML phylogenetics and are almost universally interpreted as measuring support. In addition to theoretical arguments against that interpretation, BS has several undesirable attributes for a support measure. For example, it does not vary in proportion to optimality or identify clades that are rejected by the evidence and can be overestimated due to missing data. Nevertheless, if BS is a reliable predictor of S, then it might be an efficient indirect method of measuring support—an attractive possibility, given the speed of many BS implementations. To assess the relationship between S and BS, we analyzed 106 empirical datasets retrieved from TreeBASE. Also, to evaluate the degree to which S and BS are affected by the number of replicates during suboptimal tree searches for S and pseudoreplicates during BS estimation, we randomly selected 5 of the 106 datasets and analyzed them using variable numbers of replicates and pseudoreplicates, respectively. The correlation between S and BS was extremely weak in the datasets we analyzed. Increasing the number of replicates during tree search decreased the estimated values of S for most clades, but the magnitude of change was small. In contrast, although increasing pseudoreplicates affected BS values for only approximately 40% of clades, values both increased and decreased, and they did so at much greater magnitudes. Increasing replicates/pseudoreplicates affected the rank order of clades in each tree for both S and BS. Our findings show decisively that BS is not an efficient indirect method of measuring support and suggest that even quite superficial searches to calculate S provide better estimates of support.

The sequential breakup of the supercontinent Pangaea since the Middle Jurassic is one of the crucial factors that has driven the biogeographical patterns of terrestrial biotas. Despite decades of effort searching for concordant patterns between diversification and continental fragmentation among taxonomic groups, increasing evidence has revealed more complex and idiosyncratic scenarios resulting from a mixture of vicariance, dispersal and extinction. Aquatic insects with discreet ecological requirements, low vagility and disjunct distributions represent a valuable model for testing biogeographical hypotheses by reconstructing their distribution patterns and temporal divergences. Insects of the order Megaloptera have exclusively aquatic larvae, their adults have low vagility, and the group has a highly disjunct geographical distribution. Here we present a comprehensive phylogeny of Megaloptera based on a large-scale mitochondrial genome sequencing of 99 species representing >90% of the world genera from all major biogeographical regions. Molecular dating suggests that the deep divergence within Megaloptera pre-dates the breakup of Pangaea. Subsequently, the intergeneric divergences within Corydalinae (dobsonflies), Chauliodinae (fishflies) and Sialidae (alderflies) might have been driven by both vicariance and dispersal correlated with the shifting continent during the Cretaceous, but with strikingly different and incongruent biogeographical signals. The austral distribution of many corydalids appears to be a result of colonization from Eurasia through southward dispersal across Europe and Africa during the Cretaceous, whereas a nearly contemporaneous dispersal via northward rafting of Gondwanan landmasses may account for the colonization of extant Eurasian alderflies from the south.

Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially among subfamilies, remain uncertain. Genomic data (83 taxa, 589 loci) were integrated with Sanger data (130 taxa, 22 loci), to reconstruct a phylogeny of Gracillariidae. Based on analyses of both datasets combined and analyzed separately, monophyly of Gracillariidae and all its subfamilies, monophyly of the clade “LAMPO” (subfamilies: Lithocolletinae, Acrocercopinae, Marmarinae, Phyllocnistinae, and Oecophyllembiinae) and relationships of its subclade “AMO” (subfamilies: Acrocercopinae, Marmarinae, and Oecophyllembiinae) were strongly supported. A sister-group relationship of Ornixolinae to the remainder of the family, and a monophyletic leaf roller lineage (Callicercops Vári + Parornichinae) + Gracillariinae, as sister to the “LAMPO” clade were supported by the most likely tree. Dating analyses indicate a mid-Cretaceous (105.3 Ma) origin of the family, followed by a rapid diversification into the nine subfamilies predating the Cretaceous–Palaeogene extinction. We hypothesize that advanced larval behaviours, such as making keeled or tentiform blotch mines, rolling leaves and galling, allowed gracillariids to better avoid larval parasitoids allowing them to further diversify. Finally, we stabilize the classification by formally re-establishing the subfamily ranks of Marmarinae stat.rev., Oecophyllembiinae stat.rev. and Parornichinae stat.rev., and erect a new subfamily, Callicercopinae Li, Ohshima and Kawahara to accommodate the enigmatic genus Callicercops.

RAD sequencing yields large amounts of genome-wide data at a relatively low cost and without requiring previous taxon-specific information, making it ideal for evolutionary studies of highly diversified and neglected organisms. However, concerns about information decay with phylogenetic distance have discouraged its use for assessing supraspecific relationships. Here, using Double Digest Restriction Associated DNA (ddRAD) data, we perform the first deep-level approach to the phylogeny of Zodarion, a highly diversified spider genus. We explore the impact of loci and taxon filtering across concatenated and multispecies coalescent reconstruction methods and investigate the patterns of information dropout in reference to both the time of divergence and the mitochondrial divergence between taxa. We found that relaxed loci-filtering and nested taxon-filtering strategies maximized the amount of molecular information and improved phylogenetic inference. As expected, there was a clear pattern of allele dropout towards deeper time and mitochondrial divergences, but the phylogenetic signal remained strong throughout the phylogeny. Therefore, we inferred topologies that were almost fully resolved, highly supported, and noticeably congruent between setups and inference methods, which highlights overall inconsistency in the taxonomy of Zodarion. Because Zodarion appears to be among the oldest and most mitochondrially diversified spider genera, our results suggest that ddRAD data show high potential for inferring intra-generic relationships across spiders and probably also in other taxonomic groups.

The Eastern Asia (EA) – North America (NA) disjunction is a well-known biogeographic pattern of the Tertiary relict flora; however, few studies have investigated the evolutionary history of this disjunction using a phylogenomic approach. Here, we used 2369 single copy nuclear genes and nearly full plastomes to reconstruct the evolutionary history of the small Tertiary relict genus Thuja, which consists of five disjunctly distributed species. The nuclear species tree strongly supported an EA clade Thuja standishii–Thuja sutchuenensis and a “disjunct clade”, where western NA species T. plicata is sister to an EA-eastern NA disjunct Thuja occidentalis–Thuja koraiensis group. Our results suggested that the observed topological discordance among the gene trees as well as the cytonuclear discordance is mainly due to incomplete lineage sorting, probably facilitated by the fast diversification of Thuja around the Early Miocene and the large effective population sizes of ancestral lineages. Furthermore, approximately 20% of the T. sutchuenensis nuclear genome is derived from an unknown ancestral lineage of Thuja, which might explain the close resemblance of its cone morphology to that of an ancient fossil species. Overall, our study demonstrates that single genes may not resolve interspecific relationships for disjunct taxa, and that more reliable results will come from hundreds or thousands of loci, revealing a more complex evolutionary history. This will steadily improve our understanding of their origin and evolution.