Exploring data interaction and nucleotide alignment in a multiple gene analysis of Ips (Coleoptera: Scolytinae)

Body size and sequence of host colonisation predict the presence of acoustic signalling in beetles

Acoustic communication is widespread in beetles, is often sexually dimorphic, and plays a significant role in behaviours such as premating recognition, courtship, and copulation. However, the factors that determine the presence or absence of acoustic signalling in a given species remain unclear. We examined acoustic communication in bark beetles (Scolytinae) and pinhole borers (Platypodinae), which are two speciose groups with widespread sound production capabilities. We show that body size along with the sequence of host colonisation predict the presence of acoustic communication, and report, for the first time in the animal kingdom, a size limit-1.9 mm-below which acoustic signalling ceases to be present.

First complete mitochondrial genome of the tribe Coccini (Hemiptera, Coccomorpha, Coccidae) and its phylogenetic implications

Soft scale insects (Hemiptera, Coccidae) are important pests of various agricultural and horticultural crops and ornamental plants. They have negative impacts on agriculture and forestry. The tribe Coccini represents one of the most ancient evolutionary lineages of soft scale insects. However, no complete Coccini mitochondrial genome (mitogenome) is available in public databases. Here, we described the complete mitogenome of Coccushesperidum L., 1758. The 15,566 bp mitogenome of C.hesperidum had a high A+T content (83.4%) and contained a typical set of 37 genes, with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes (rRNAs). Only seven tRNAs had the typical clover-leaf secondary structure and the remaining tRNAs lacked the DHU arm, TψC arm or both. Moreover, a comparative analysis of all reported scale insect mitogenomes from GenBank database was performed. The mitogenomes of scale insects showed high similarities in base composition and A+T content. Additionally, our phylogenetic analysis confirmed the monophyly of Coccomorpha and revealed that the archaeococcoids were the most basal lineage within Coccomorpha, while Ericeruspela and Didesmococcuskoreanus, belonging to Coccidae, were often mixed with Aclerdidae, making Coccidae a paraphyletic group. These findings expand the mitogenome database of scale insects and provide new insights on mitogenome evolution for future studies across different insect groups.

The phylogenetic structure and coalescent species delimitation of an endemic trapdoor spider genus, Stasimopus (Araneae, Mygalomorphae, Stasimopidae) in the Karoo region of South Africa

The Karoo region of South Africa is a unique and sensitive ecosystem which is facing pressure for development due to economic incentives such as mining, farming and shale gas exploration. The species diversity of many taxa in the area is largely unknown. A phylogenetic analysis of the cork-lid trapdoor spider genus, Stasimopus (Stasimopidae) was undertaken in order to gain insight into the relationships between the species that may be present in the area. The species within Stasimopus are challenging to identify and define using traditional morphological methods due to a high degree of morphological conservatism within the genus. For this reason, multiple coalescent based species delimitation methods were used to attempt to determine the species present for Stasimopus in the region which was tested against the morphological identifications and genetic clades (based on CO1, 16S and EF-1ɣ). We tested single-locus methods Automatic Barcode Gap Discovery (ABGD), Bayesian implementation of Poisson Tree Processes (bPTP) and General Mixed Yule- Coalescent (GMYC), as well as multi-locus Brownie. The phylogenetic analysis of Stasimopus in the Karoo showed that there is a high degree of genetic diversity within the genus. The species delimitation results proved unfruitful for the genus, as they appear to delimit population structure rather than species for most methods. Alternative methods should be investigated to aid in the identification of the species in order truly understand the species diversity of the genus.

Multi-gene phylogeny of North American clear-winged moths (Lepidoptera: Sesiidae): a foundation for future evolutionary study of a speciose mimicry complex

Sesiids are a diverse group of predominantly diurnal moths, many of which are Batesian mimics of Hymenoptera. However, their diversity and relationships are poorly understood. A multi-gene phylogenetic analysis of 48 North American sesiid species confirmed the traditional taxonomic tribal ranks, demonstrated the paraphyly of Carmenta and Synanthedon with respect to several other genera and ultimately provided minimal phylogenetic resolution within and between North American and European groups. Character support from each gene suggested inconsistency between the phylogenetic signal of the CAD gene and that of the other four genes. However, removal of CAD from subsequent phylogenetic analyses did not substantially change the initial phylogenetic results or return Carmenta and Synanthedon as reciprocally monophyletic, suggesting that it was not impacting the overall phylogenetic signal. The lack of resolution using genes that are typically informative at the species level for other lepidopterans suggests a surprisingly rapid radiation of species in Carmenta/Synanthedon. This group also exhibits a wide range of mimicry strategies and hostplant usage, which could be fertile ground for future study.

Resurrection of the genus Subulo Smith, 1827 for the gray brocket deer, with designation of a neotype

The gray brocket deer, Mazama gouazoubiraG. Fischer, 1814, occurs in South America and presents an extensive degree of morphological and genetic variability. Previous phylogenetic research showed that the genus Mazama is polyphyletic and imposed the designation of a different genus-group name for M. gouazoubira. We aimed to review and clarify the taxonomy of M. gouazoubira through the proposal of updating the nomenclature for this taxon and by the characterization of specimens collected close to the original type locality (topotypes). The topotypes were characterized by morphological (general characterization and morphometry), cytogenetic (conventional staining, Ag-NOR, G- and C-banding, and fluorescence in situ hybridization), and phylogenetic (mitogenomes) approaches. We revealed chromosome homologies between cattle and M. gouazoubira using an entire set of cattle whole chromosome painting probes and propose an updated G-band idiogram for the species. The morphometric analysis did not discriminate the individuals of M. gouazoubira, including the topotypes, from other small brocket deer species. However, the phylogenetic analysis, based on a Bayesian inference tree of the mitogenomes, confirmed the polyphyly of the genus Mazama and supported the need to change the gray brocket deer genus-group name. Based on our revision, we validated the genus SubuloSmith, 1827, and fixed a type species for the genus. In the absence of the holotype, we denominated a neotype described by the collection of a male topotype in Paraguay. The nomenclature rearrangement presented here is a starting point that will assist in the taxonomic resolution of Neotropical deer.

Three new species of the genus Biasticus Stål, 1867 (Insecta, Heteroptera, Reduviidae, Harpactorinae) from Central Highlands, Vietnam

Three new assassin bug species of the genus Biasticus Stål, 1867 are recognized in Vietnam based on morphological examination, morphometric and molecular phylogenetic analyses, and described as Biasticustaynguyenensis Ha, Truong & Ishikawa, sp. nov., Biasticusgriseocapillus Ha, Truong & Ishikawa, sp. nov., and Biasticusluteicollis Ha, Truong & Ishikawa, sp. nov. The conspecific male and female associations of the new species were confirmed by phylogenetic analyses and DNA barcoding of the mitochondrial 16S rDNA and COI genes. All three new species are presently restricted to the Central Highlands, Vietnam (Kon Chu Rang NR, Gia Lai Province, and Chu Yang Sin NP, Dak Lak Province).

The bark and ambrosia beetles of Bhutan (Coleoptera: Curculionidae: Scolytinae and Platypodinae): a synopsis with three new species of Scolytinae

The present state of knowledge of the bark and ambrosia beetles of Bhutan is summarised as a basis for future studies of the fauna, and its economic importance in forestry, timber production and crop tree plantations. We describe three new species of Scolytinae: Cyclorhipidion druk Smith & Beaver, Euwallacea insolitus Smith & Beaver, and Xylosandrus geduensis Smith & Beaver. Thirty-four species of Scolytinae, and 13 species of Platypodinae are now known to occur in Bhutan, of which 14 species of Scolytinae, including the three new species, and four species of Platypodinae, are recorded for the first time. A checklist of the fauna is provided, with information on local and world distribution, host trees and biology, and taxonomy.  

Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better

DNA metabarcoding can accelerate research on insect diversity, as it is cheap and fast compared to manual sorting and identification. Most metabarcoding protocols require homogenisation of the sample, preventing further work on the specimens. Mild digestion of the tissue by incubation in a lysis buffer has been proposed as an alternative, and, although some mild lysis protocols have already been presented, they have so far not been evaluated against each other. Here, we analyse how two mild lysis buffers (one more aggressive, one gentler in terms of tissue degradation), two different incubation times, and two DNA purification methods (a manual precipitation and an automated protocol) affect the accuracy of retrieving the true composition of mock communities using two mitochondrial markers (COI and 16S). We found that protocol-specific variation in concentration and purity of the DNA extracts produced had little effect on the recovery of species. However, the two lysis treatments differed in quantification of species abundances. Digestion in the gentler buffer and for a shorter time yielded better representation of original sample composition. Digestion in a more aggressive buffer or longer incubation time yielded lower alpha diversity values and increased differences between metabarcoding results and the true species-abundance distribution. We conclude that the details of non-destructive protocols can have a significant effect on metabarcoding performance. A short and mild lysis treatment appears the best choice for recovering the true composition of the sample. This not only improves accuracy, but also comes with a faster processing time than the other treatments.

Two New Species of the Genus Eucorydia (Blattodea: Corydiidae) from the Nansei Islands in Southwest Japan

Two new species of the cockroach genus Eucorydia Hebard, 1929 from the Nansei Islands in Southwest Japan were compared to two closely related congeners, Eucorydia yasumatsui Asahina, 1971 and Eucorydia dasytoides (Walker, 1868). Eucorydia donanensis Yanagisawa, Sakamaki, and Shimano sp. nov. from Yonaguni-jima Island was characterized by an overall length of 12.5-14.5 mm in males. The dorsal side of the male abdomen was entirely dark purple and there was an obscure orange band running down the middle of the tegmen. Eucorydia tokaraensis Yanagisawa, Sakamaki, and Shimano sp. nov. was characterized by an overall length of 12.0-13.0 mm in males and a distinct orange band running down the middle of the tegmen. Eucorydia yasumatsui, E. donanensis, E. tokaraensis and the zonata population of E. dasytoides were divided into four lineages in a maximum-likelihood tree generated from a dataset concatenated from five (two nuclear, 28S rRNA, histone H3, and three mitochondrial, COII, 12S rRNA, 16S rRNA) genes. We recognized the three Japanese lineages E. yasumatsui, E. donanensis, and E. tokaraensis as distinct species, which were also supported by the pairwise genetic distances (5.4-7.8%, K2P) of the COI sequences. Morphometric analysis was performed on the genitalia. A principal component analysis plot revealed that the sizes of the genitalia in the three Japanese species were similar to each other and smaller than that of the zonata population of E. dasytoides. The analysis also revealed that the three Japanese species were distinguished from each other by combinations of the sizes of L3 and L7 sclerites and the shape of R2 sclerite, with some overlapping exceptions.

Exploring the relationship of Homalosilpha and Mimosilpha (Blattodea, Blattidae, Blattinae) from a morphological and molecular perspective, including a description of four new species

This study utilized six genes (12S, 16S, 18S, 28S, COII and H3) from a total of 40 samples to construct maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees in order to infer the relationships between the morphologically similar genera Homalosilpha Stål, 1874 and Mimosilpha Bey-Bienko, 1957. The phylogenetic analysis showed the two genera have a close relationship and were recovered as sister groups based on ML and BI analyses. Four new species are described among these samples, i.e., Homalosilpha obtusangula sp. nov., Homalosilpha recta sp. nov., Homalosilpha alba sp. nov. and Homalosilpha clavellata sp. nov. based on morphological and COI data. A key to the worldwide Homalosilpha is provided.

Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model

Relaxed clock models enable estimation of molecular substitution rates across lineages and are widely used in phylogenetics for dating evolutionary divergence times. Under the (uncorrelated) relaxed clock model, tree branches are associated with molecular substitution rates which are independently and identically distributed. In this article we delved into the internal complexities of the relaxed clock model in order to develop efficient MCMC operators for Bayesian phylogenetic inference. We compared three substitution rate parameterisations, introduced an adaptive operator which learns the weights of other operators during MCMC, and we explored how relaxed clock model estimation can benefit from two cutting-edge proposal kernels: the AVMVN and Bactrian kernels. This work has produced an operator scheme that is up to 65 times more efficient at exploring continuous relaxed clock parameters compared with previous setups, depending on the dataset. Finally, we explored variants of the standard narrow exchange operator which are specifically designed for the relaxed clock model. In the most extreme case, this new operator traversed tree space 40% more efficiently than narrow exchange. The methodologies introduced are adaptive and highly effective on short as well as long alignments. The results are available via the open source optimised relaxed clock (ORC) package for BEAST 2 under a GNU licence (https://github.com/jordandouglas/ORC).

The Prevalence and Impact of Model Violations in Phylogenetic Analysis

In phylogenetic inference, we commonly use models of substitution which assume that sequence evolution is stationary, reversible, and homogeneous (SRH). Although the use of such models is often criticized, the extent of SRH violations and their effects on phylogenetic inference of tree topologies and edge lengths are not well understood. Here, we introduce and apply the maximal matched-pairs tests of homogeneity to assess the scale and impact of SRH model violations on 3,572 partitions from 35 published phylogenetic data sets. We show that roughly one-quarter of all the partitions we analyzed (23.5%) reject the SRH assumptions, and that for 25% of data sets, tree topologies inferred from all partitions differ significantly from topologies inferred using the subset of partitions that do not reject the SRH assumptions. This proportion increases when comparing trees inferred using the subset of partitions that rejects the SRH assumptions, to those inferred from partitions that do not reject the SRH assumptions. These results suggest that the extent and effects of model violation in phylogenetics may be substantial. They highlight the importance of testing for model violations and possibly excluding partitions that violate models prior to tree reconstruction. Our results also suggest that further effort in developing models that do not require SRH assumptions could lead to large improvements in the accuracy of phylogenomic inference. The scripts necessary to perform the analysis are available in https://github.com/roblanf/SRHtests, and the new tests we describe are available as a new option in IQ-TREE (http://www.iqtree.org).

Hidden and cryptic species reflect parallel and correlated evolution in the phylogeny of the genus Callyntra (Coleoptera: Tenebrionidae) of Central Chile

The origin of cryptic species has traditionally been associated with events of recent speciation, genetic constraints, selection of an adaptive character, sexual selection and/or convergent evolution. Species of the genus Callyntra inhabit coastal terraces, mountain slopes, and peaks; their elytral designs are associated with each of these habitats. However, cryptic species have been described within each of these habitats; the taxonomy of this group has been problematic, thus establishing the phylogenetic relationships in this group is fundamental to clarify the systematics and evolutionary patterns of Callyntra. We reconstructed the phylogeny of this group using two mitochondrial genes (COI, 16S) and one nuclear gene (Mp20). We also performed species delimitation using PTP based methods (PTP, mlPTP, bPTP) and GMYC, and evaluated the evolution of the elytral design related to habitat preference. The results showed a tree with five clades, that together with the different methods of species delimitation recovered the described species and suggested at least five new species. The elytral design and habitat preference showed phylogenetic signals. We propose a new classification based on monophyletic groups recovered by phylogenetic analyses. We also suggest that parallel evolution in different habitats and later stasis in the elytral design would be the cause of the origin of cryptic species in this group from central Chile.

Choosing and Using Introns in Molecular Phylogenetics

Introns are now commonly used in molecular phylogenetics in an attempt to recover gene trees that are concordant with species trees, but there are a range of genomic, logistical and analytical considerations that are infrequently discussed in empirical studies that utilize intron data. This review outlines expedient approaches for locus selection, overcoming paralogy problems, recombination detection methods and the identification and incorporation of LVHs in molecular systematics. A range of parsimony and Bayesian analytical approaches are also described in order to highlight the methods that can currently be employed to align sequences and treat indels in subsequent analyses. By covering the main points associated with the generation and analysis of intron data, this review aims to provide a comprehensive introduction to using introns (or any non-coding nuclear data partition) in contemporary phylogenetics.

Reconstructing the phylogeny of Blattodea: robust support for interfamilial relationships and major clades

Cockroaches are among the most recognizable of all insects. In addition to their role as pests, they play a key ecological role as decomposers. Despite numerous studies of cockroach phylogeny in recent decades, relationships among most major lineages are yet to be resolved. Here we examine phylogenetic relationships among cockroaches based on five genes (mitochondrial 12S rRNA, 16S rRNA, COII; nuclear 28S rRNA and histone H3), and infer divergence times on the basis of 8 fossils. We included in our analyses sequences from 52 new species collected in China, representing 7 families. These were combined with data from a recent study that examined these same genes from 49 species, resulting in a significant increase in taxa analysed. Three major lineages, Corydioidea, Blaberoidea, and Blattoidea were recovered, the latter comprising Blattidae, Tryonicidae, Lamproblattidae, Anaplectidae, Cryptocercidae and Isoptera. The estimated age of the split between Mantodea and Blattodea ranged from 204.3 Ma to 289.1 Ma. Corydioidea was estimated to have diverged 209.7 Ma (180.5-244.3 Ma 95% confidence interval [CI]) from the remaining Blattodea. The clade Blattoidea diverged from their sister group, Blaberoidea, around 198.3 Ma (173.1-229.1 Ma). The addition of the extra taxa in this study has resulted in significantly higher levels of support for a number of previously recognized groupings.

Chemical Ecology of Cave-Dwelling Millipedes: Defensive Secretions of the Typhloiulini (Diplopoda, Julida, Julidae)

Cave animals live under highly constant ecological conditions and in permanent darkness, and many evolutionary adaptations of cave-dwellers have been triggered by their specific environment. A similar "cave effect" leading to pronounced chemical interactions under such conditions may be assumed, but the chemoecology of troglobionts is mostly unknown. We investigated the defensive chemistry of a largely cave-dwelling julid group, the controversial tribe "Typhloiulini", and we included some cave-dwelling and some endogean representatives. While chemical defense in juliform diplopods is known to be highly uniform, and mainly based on methyl- and methoxy-substituted benzoquinones, the defensive secretions of typhloiulines contained ethyl-benzoquinones and related compounds. Interestingly, ethyl-benzoquinones were found in some, but not all cave-dwelling typhloiulines, and some non-cave dwellers also contained these compounds. On the other hand, ethyl-benzoquinones were not detected in troglobiont nor in endogean typhloiuline outgroups. In order to explain the taxonomic pattern of ethyl-benzoquinone occurrence, and to unravel whether a cave-effect triggered ethyl-benzoquinone evolution, we classed the "Typhloiulini" investigated here within a phylogenetic framework of julid taxa, and traced the evolutionary history of ethyl-benzoquinones in typhloiulines in relation to cave-dwelling. The results indicated a cave-independent evolution of ethyl-substituted benzoquinones, indicating the absence of a "cave effect" on the secretions of troglobiont Typhloiulini. Ethyl-benzoquinones probably evolved early in an epi- or endogean ancestor of a clade including several, but not all Typhloiulus (basically comprising a taxonomic entity known as "Typhloiulus sensu stricto") and Serboiulus. Ethyl-benzoquinones are proposed as novel and valuable chemical characters for julid systematics.

Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates

BACKGROUND

Model selection is a vital part of most phylogenetic analyses, and accounting for the heterogeneity in evolutionary patterns across sites is particularly important. Mixture models and partitioning are commonly used to account for this variation, and partitioning is the most popular approach. Most current partitioning methods require some a priori partitioning scheme to be defined, typically guided by known structural features of the sequences, such as gene boundaries or codon positions. Recent evidence suggests that these a priori boundaries often fail to adequately account for variation in rates and patterns of evolution among sites. Furthermore, new phylogenomic datasets such as those assembled from ultra-conserved elements lack obvious structural features on which to define a priori partitioning schemes. The upshot is that, for many phylogenetic datasets, partitioned models of molecular evolution may be inadequate, thus limiting the accuracy of downstream phylogenetic analyses.

RESULTS

We present a new algorithm that automatically selects a partitioning scheme via the iterative division of the alignment into subsets of similar sites based on their rates of evolution. We compare this method to existing approaches using a wide range of empirical datasets, and show that it consistently leads to large increases in the fit of partitioned models of molecular evolution when measured using AICc and BIC scores. In doing so, we demonstrate that some related approaches to solving this problem may have been associated with a small but important bias.

CONCLUSIONS

Our method provides an alternative to traditional approaches to partitioning, such as dividing alignments by gene and codon position. Because our method is data-driven, it can be used to estimate partitioned models for all types of alignments, including those that are not amenable to traditional approaches to partitioning.

The effects of partitioning on phylogenetic inference

Partitioning is a commonly used method in phylogenetics that aims to accommodate variation in substitution patterns among sites. Despite its popularity, there have been few systematic studies of its effects on phylogenetic inference, and there have been no studies that compare the effects of different approaches to partitioning across many empirical data sets. In this study, we applied four commonly used approaches to partitioning to each of 34 empirical data sets, and then compared the resulting tree topologies, branch-lengths, and bootstrap support estimated using each approach. We find that the choice of partitioning scheme often affects tree topology, particularly when partitioning is omitted. Most notably, we find occasional instances where the use of a suboptimal partitioning scheme produces highly supported but incorrect nodes in the tree. Branch-lengths and bootstrap support are also affected by the choice of partitioning scheme, sometimes dramatically so. We discuss the reasons for these effects and make some suggestions for best practice.

A multilocus phylogeny of the world Sycoecinae fig wasps (Chalcidoidea: Pteromalidae)

The Sycoecinae is one of five chalcid subfamilies of fig wasps that are mostly dependent on Ficus inflorescences for reproduction. Here, we analysed two mitochondrial (COI, Cytb) and four nuclear genes (ITS2, EF-1α, RpL27a, mago nashi) from a worldwide sample of 56 sycoecine species. Various alignment and partitioning strategies were used to test the stability of major clades. All topologies estimated using maximum likelihood and Bayesian methods were similar and well resolved but did not support the existing classification. A high degree of morphological convergence was highlighted and several species appeared best described as species complexes. We therefore proposed a new classification for the subfamily. Our analyses revealed several cases of probable speciation on the same host trees (up to 8 closely related species on one single tree of F. sumatrana), which raises the question of how resource partitioning occurs to avoid competitive exclusion. Comparisons of our results with fig phylogenies showed that, despite sycoecines being internally ovipositing wasps host-switches are common incidents in their evolutionary history. Finally, by studying the evolutionary properties of the markers we used and profiling their phylogenetic informativeness, we predicted their utility for resolving phylogenetic relationships of Chalcidoidea at various taxonomic levels.

The aberrant millipede genus Pteridoiulus and its position in a revised molecular phylogeny of the family Julidae (Diplopoda : Julida)

A phylogenetic analysis of 62 species (32 genera) of the Palaearctic millipede family Julidae, including the aberrant alpine genus Pteridoiulus Verhoeff, 1913, was made based on partial sequences of the mitochondrial 16S rRNA (16S) gene and the nuclear 28S rRNA (28S) gene, respectively. The two datasets (16S rDNA and 28S rDNA) were analysed in combination but treated as different partitions using direct optimisation as implemented in POY. The 16S rDNA and the 28S rDNA sequences vary from 410 to 449 bp and from 467 to 525 bp in length, respectively. All searches were performed under six different gap opening costs, an extension gap cost of 1, and a substitution cost of 2. Based on previous investigations the optimal gap opening cost was set to 4, and the robustness of different gap opening costs ranging from 1 to 6 investigated. Additionally, the two data partitions were aligned individually using MAFTT and run in TNT both with gaps treated as a fifth state, and as missing, and finally the alignments were used as input in a maximum likelihood (ML) analysis. The order Julida and the family Julidae were recovered as monophyletic under all weight sets in POY, as well as in the TNT and ML analyses. Likewise, in all analyses Pteridoiulus was found to be sister to another monotypic alpine genus, Heteroiulus Verhoeff, 1897. The Pteridoiulus + Heteroiulus clade is robust to parameter changes but lacks morphological support. The distribution pattern of the clade, Pteridoiulus in the eastern Alps (mainly Austria), Heteroiulus in the southern Alps (Italy) seems unique, since similar patterns all involve very similar, closely related species pairs.

Phylogeny and biogeography of southern African spoon-winged lacewings (Neuroptera: Nemopteridae: Nemopterinae)

Nemopteridae are a charismatic family of lacewings characterised by uniquely extended hind wings. They are an ancient widespread group in the drier regions of the world. The family comprises two subfamilies, Crocinae (thread-wings) and Nemopterinae (spoon- and ribbon-wings). The present distribution of the family has been largely influenced by the vicariant events of plate tectonics, resulting in relict populations in some parts of the world and extensive evolutionary radiations in others, particularly southern Africa where the vast majority of the species are endemic to the Western and Northern Cape Provinces of South Africa. This study aimed to establish the validity of the 11 currently recognised genera and infer their biogeographic history using molecular sequence data from four gene regions. The hypothesis that the Cape nemopterines co-evolved with certain taxa in the Cape Floristic Region was also tested. Phylogenetic analysis supports seven of the 11 currently recognised genera. The crown age of the Nemopterinae is estimated to be at ca. 145.6 Mya, indicating that the group has been present since the late Jurassic. Most of the genera appear to have diversified during the middle Eocene and into the middle Miocene (ca. 44-11 Mya) with recent rapid radiation of several of the genera occurring during the late Miocene (ca. 6-4.5 Mya). While these data support an initial radiation with the Rushioideae (Aizoaceae) it is recommended that further study including observations and gut content be carried out.

A molecular phylogeny of the pan-tropical pond skater genus Limnogonus Stål 1868 (Hemiptera-Heteroptera: Gerromorpha-Gerridae)

We investigated phylogenetic relationships among pond skaters (Heteroptera: Gerridae) of the genus Limnogonus Stål 1868 by performing separate and combined parsimony analyses of DNA sequences from three mitochondrial (COI+II, 16SrRNA) and one nuclear (28SrRNA) gene(s). The taxon sample represented almost two thirds of the known diversity, and with most taxa represented by two or more individuals. A simultaneous analysis of all data showed that L. luctuosus Montrousier 1865 was paraphyletic and suggests that "L. luctuosus" from Australia and possibly also a population from the Society Islands (Moorea) each represents unrecognized species. L. fossarum F. 1775 was strongly supported, but the two subspecies L. f. fossarum F. 1775 and L. f. gilguy Andersen and Weir 1997 were paraphyletic. The two currently recognized subgenera Limnogonus (s. str.) Stål 1868 and L. (Limnogonoides)Andersen 1975 were paraphyletic, and were accordingly broken up in several monophyletic groups, each containing one or more species. From Limnogonus (s. str.) we delimited five clades: I (comprising L. aduncus Drake & Harris 1933, L. recens Drake and Harris 1934, L. profugus Drake & Harris 1930 and L. ignotus Drake and Harris 1934, all from the Neotropical Region), II (comprising L. nitidus Mayr 1865 from the Oriental Region), III (comprising L. franciscanus (Stål 1859) from the New World and L. cereiventris (Signoret 1862) from the Afrotropical Region), IV (comprising L. hungerfordi Andersen 1975 and L. luctuosus Montrousier 1865 from the Oriental and Australasian Regions) and V (comprising L. fossarum F. 1775 from the Oriental and Australasian Regions). From L. (Limnogonoides) we delimited two clades: VI (comprising L. intermedius Poisson 1941 from the Afrotropical Region and L. pectoralis (Mayr 1865) from the Oriental Region) and VII (comprising L. hypoleucus (Gerstaecker 1873), L. nigrescens Poisson 1941, L. poissoni Andersen 1975, and L. capensis China 1925 from the Afrotropical Region). Finally, L. (s. str.) windi Hungerford & Matsuda 1961 from Australia was placed as sister to clades I-VI. A manual optimization of geographical distribution onto the strict consensus tree suggests that Limnogonus is primarily an Old World group with independent transitions to the New World in L. franciscanus and in the common ancestor of Clade I.

DNA-based taxonomy of larval stages reveals huge unknown species diversity in neotropical seed weevils (genus Conotrachelus): relevance to evolutionary ecology

High diversity in tropical phytophagous insects may be linked to narrow host specificity and host shifts, but tests are complicated by incomplete taxonomy and difficulties in food source identification. Specimens of the highly diverse New World genus Conotrachelus (Coleoptera: Curculionoidea) were reared from >17,500 fruits (seeds) at six Central American rain forests. Interception traps were used for comparison with assemblages flying in the forest. Mitochondrial cox1 and the nuclear 28S genes were sequenced for 483 larval and adult specimens. A Yule-Coalescent technique was used to group cox1 sequences into putative species (17 from traps, 48 from rearing). Cox1 sequences of 24 species from museum collections provided matches for three species from traps and no match for the reared species. Inga (Fabaceae) was the predominant host among 15 other genera and 67% of the weevils were monophagous. A three gene tree (cox1, rrnL, 28S) recovered four well-supported clades feeding on Inga confirmed by phylogenetic community analyzes that showed phylogenetic conservation of host plant utilization. This suggests that host shifts are not directly involved in speciation, while the broad taxonomic host range and the evolutionary repeated shifts still contribute to the high species richness in Conotrachelus. The DNA-based approach combining species delimitation and phylogenetic analysis elucidated the evolutionary diversification of this lineage, despite insufficient taxonomic knowledge. Conotrachelus is an example of the diverse tropical groups that require DNA-based taxonomy to study their evolutionary ecology.

Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration

Phylogenetic trees in insects are frequently dated by applying a "standard" mitochondrial DNA (mtDNA) clock estimated at 2.3% My(-1), but despite its wide use reliable calibration points have been lacking. Here, we used a well-established biogeographic barrier, the mid-Aegean trench separating the western and eastern Aegean archipelago, to estimate substitution rates in tenebrionid beetles. Cytochrome oxidase I (cox1) for six codistributed genera across 28 islands (444 individuals) on both sides of the mid-Aegean trench revealed 60 independently coalescing entities delimited with a mixed Yule-coalescent model. One representative per entity was used for phylogenetic analysis of mitochondrial (cox1, 16S rRNA) and nuclear (Mp20, 28S rRNA) genes. Six nodes marked geographically congruent east-west splits whose separation was largely contemporaneous and likely to reflect the formation of the mid-Aegean trench at 9-12 Mya. Based on these "known" dates, a divergence rate of 3.54% My(-1) for the cox1 gene (2.69% when combined with the 16S rRNA gene) was obtained under the preferred partitioning scheme and substitution model selected using Bayes factors. An extensive survey suggests that discrepancies in mtDNA substitution rates in the entomological literature can be attributed to the use of different substitution models, the use of different mitochondrial gene regions, mixing of intraspecific with interspecific data, and not accounting for variance in coalescent times or postseparation gene flow. Different treatments of these factors in the literature confound estimates of mtDNA substitution rates in opposing directions and obscure lineage-specific differences in rates when comparing data from various sources.

Polyphyly of Xylosandrus Reitter inferred from nuclear and mitochondrial genes (Coleoptera: Curculionidae: Scolytinae)

The Xyleborina ambrosia beetle genus Xylosandrus contains 54 species, several of which are of economic importance. The monophyly of the genus was tested using a data set comprised of multiple gene loci: 28S rDNA; the mitochondrial gene cytochrome oxidase I (COI); and the nuclear genes arginine kinase (ArgK), rudimentary (CAD), and Elongation Factor 1alpha (EF-1alpha). The nuclear protein-coding genes CAD and ArgK were used for the first time in phylogenetics of Scolytinae. Analyses were performed using Parsimony and Bayesian optimality criteria. Our analyses included 43 specimens representing 15 Xylosandrus species and 20 species from Amasa, Anisandrus, Cnestus, Euwallacea and Xyleborus, and two species from the outgroup genus Coccotrypes. All analyses recovered a polyphyletic Xylosandrus. Several species of Xylosandrus were consistently placed in clades with the genera Anisandrus and Cnestus with high support values (100% bootstrap support). Among these, was the economically important invasive species X. mutilatus, which was consistently recovered as part of the "Cnestus" clade. In our analyses, both CAD and ArgK demonstrated phylogenetic utility across varying nodal depths. Despite the selection of genes with signals at complementary phylogenetic depths, the data set used herein did not resolve the phylogeny of Xylosandrus and related genera. Since the taxon sample available for molecular work represents only a fraction of Xylosandrus species, a complete revision that combines molecular and morphological data in a total evidence approach is recommended for the genus.

Molecular phylogeny and Holarctic diversification of the subtribe Calathina (Coleoptera: Carabidae: Sphodrini)

A molecular phylogeny of the subtribe Calathina was inferred from DNA sequence data from the mitochondrial cox1-cox2 region and the nuclear genes 28S and EF-1alpha. All lineages within Calathina from the Holarctic region were represented except for the monotypic subgenus Tachalus. Maximum Parsimony and Bayesian analyses of the combined data set showed that the subtribe is a monophyletic lineage that includes a single genus Calathus, where other taxa currently ranked as independent genera (Lindrothius, Synuchidius, Thermoscelis and Acalathus) are nested within this genus.Neocalathus and Lauricalathus, both subgenera of Calathus, were found to be polyphyletic and in need of taxonomic revision. The subtribe appears to have originated in the Mediterranean Basin and thereafter expanded into most parts of the Palearctic region, the Macaronesian archipelagos (at least five independent colonisation events), the Ethiopian highlands and the Nearctic region (at least two independent events).

Two regulatory mechanisms of monoterpenoid pheromone production in Ips spp. of bark beetles

Bark beetles use aggregation pheromones to coordinate host colonization and mating. These monoterpenoid chemical signals are produced de novo in midgut cells via the mevalonate pathway, and pheromone production is induced when an adult beetle feeds on phloem of a host tree. In Ips pini, juvenile hormone (JH) III influences key regulatory enzymes along the mevalonate pathway that leads to pheromone production. In fact, topically applied JH III is sufficient to stimulate pheromone production in unfed males. In this study, we explore the influence of feeding and JH III treatment on pheromone production in male Ips confusus, the pinyon Ips. We also characterize the influence of feeding and JH III treatment on transcript levels and activity of three key enzymes involved in pheromone biosynthesis: 3-hydroxy-3-methylglutaryl-CoA (HMG) synthase (HMGS), HMG-CoA reductase (HMGR) and geranyl diphosphate synthase (GPPS). We also extend the current understanding of the regulation of pheromone biosynthesis in I. pini, by measuring the influence of feeding and JHIII treatment on enzymatic activity of HMGS and GPPS. Feeding on host phloem alone strongly induces pheromone production in male I. confusus, while JH III treatment has no effect. However, feeding and JH III both significantly up-regulate mRNA levels of key mevalonate pathway genes. Feeding up-regulates these genes to a maximum at 32 h, whereas with JH III-treatment, they are up-regulated at 4, 8, and 16 h, but return near to non-treatment levels at 32 h. Feeding, but not JH III treatment, also increases the activity of all three enzymes in I. confusus, while both feeding or treatment with JH III increase HMGS and GPPS activity in I. pini. Our data suggest that pheromone production in Ips is not uniformly controlled by JH III and feeding may stimulate the release of some other regulatory factor, perhaps a brain hormone, required for pheromone production.

Evidence for low-titre infections in insect symbiosis: Wolbachia in the bark beetle Pityogenes chalcographus (Coleoptera, Scolytinae)

Wolbachia are obligatory endosymbiotic alpha-proteobacteria found in many insect species. They are maternally transmitted and often exhibit reproductive phenotypes like cytoplasmic incompatibility. Pityogenes chalcographus is a bark beetle causing severe damage in spruce stands. Its European populations are divided into several mitochondrial clades separated by partial crossing barriers. In this study, we tested a large sample set covering the natural range of the beetle in Europe for the presence of Wolbachia and associations between infection pattern and mitotypes using a highly sensitive nested PCR technique. 35.5% of the individuals were infected with the endosymbiont and two distinct strains were identified. Both strains occur in low titre not accessible by conventional detection methods. The infections are present all over Europe, unlikely to cause the partial crossing barriers in this host and uncoupled from mitochondrial clades. This pattern is indicative for populations evolving towards endosymbiont loss and for repeated intraspecific horizontal transfer of Wolbachia. Alternatively, the low-titre infections found in P. chalcographus are yet another example for Wolbachia that can persist in host species at low densities and frequencies.

Phylogenetic relationships among families of Gadiformes (Teleostei, Paracanthopterygii) based on nuclear and mitochondrial data

Phylogenetic hypotheses among Gadiformes fishes at the suborder, family, and subfamily levels are controversial. To address this problem, we analyze nuclear and mitochondrial DNA (mtDNA) sequences for the most extensive taxonomic sampling compiled to date, representing all of the recognized families and subfamilies in the order (except the monotypic family Lyconidae). Our study sampled 117 species from 46 genera, comprising around 20% of the species described for the order (more than 60% of all genera in the order) and produced 2740 bp of DNA sequence data for each species. Our analysis was successful in confirming the monophyly of Gadiformes and most of the proposed families for the order, but alternative hypotheses of sister-group relationships among families were poorly resolved. Our results are consistent with dividing Gadiformes into 12 families in three suborders, Muraenolepidoidei, Macrouroidei, and Gadoidei. Muraenolepidoidei contains the single family Muraenolepididae. The suborder Macrouroidei includes at least three families: Macrouridae, Macruronidae and Steindachneriidae. Macrouridae is deeply divided into two well-supported subfamilies: Macrourinae and Bathygadinae, suggesting that Bathygadinae may be ranked at the family level. The suborder Gadoidei includes the families: Merlucciidae, Melanonidae, Euclichthyidae, Gadidae, Ranicipitidae, and Bregmacerotidae. Additionally, Trachyrincinae could be ranked at family level including two subfamilies: Trachyrincinae and Macrouroidinae within Gadoidei. Further taxonomic sampling and sequencing efforts are needed in order to corroborate these relationships.

Evidence of repeated and independent saltational evolution in a peculiar genus of sphinx moths (Proserpinus: Sphingidae)

BACKGROUND

Saltational evolution in which a particular lineage undergoes relatively rapid, significant, and unparalleled change as compared with its closest relatives is rarely invoked as an alternative model to the dominant paradigm of gradualistic evolution. Identifying saltational events is an important first-step in assessing the importance of this discontinuous model in generating evolutionary novelty. We offer evidence for three independent instances of saltational evolution in a charismatic moth genus with only eight species.

METHODOLOGY/PRINCIPAL FINDINGS

Maximum parsimony, maximum likelihood and Bayesian search criteria offered congruent, well supported phylogenies based on 1,965 base pairs of DNA sequence using the mitochondrial gene cytochrome oxidase subunit I, and the nuclear genes elongation factor-1 alpha and wingless. Using a comparative methods approach, we examined three taxa exhibiting novelty in the form of Batesian mimicry, host plant shift, and dramatic physiological differences in light of the phylogenetic data. All three traits appear to have evolved relatively rapidly and independently in three different species of Proserpinus. Each saltational species exhibits a markedly different and discrete example of discontinuous trait evolution while remaining canalized for other typical traits shared by the rest of the genus. All three saltational taxa show insignificantly different levels of overall genetic change as compared with their congeners, implying that their divergence is targeted to particular traits and not genome-wide.

CONCLUSIONS/SIGNIFICANCE

Such rapid evolution of novel traits in individual species suggests that the pace of evolution can be quick, dramatic, and isolated--even on the species level. These results may be applicable to other groups in which specific taxa have generated pronounced evolutionary novelty. Genetic mechanisms and methods for assessing such relatively rapid changes are postulated.

DNA based cladograms augment the discovery of a new Ips species from China (Coleoptera: Curculionidae: Scolytinae)

The implementation of DNA in taxonomic study is in its infancy because the association of the amount and type of nucleotide change with species boundaries has not been fully examined for most taxa. Mitochondrial cytochrome c oxidase I (COI) nucleotide data is currently the most popular molecular marker for delimiting species boundaries and a standard pair-wise nucleotide divergence between groups of individuals has been suggested for the recognition of new species. It is unlikely that such a standard would be applicable across animal species, but the association of the amount and type of nucleotide change with species boundaries could help with the establishment of a taxon-specific DNA taxonomy. This study utilizes DNA data from nuclear and mitochondrial genes to improve the taxonomy of an important forest beetle pest, Ips. Amount and type of nucleotide difference are associated with monophyletic species based on a cladistic analysis of these data. As a result, a new species from China is described for a clade of beetles whose nucleotide differences exceeded the amount of evolutionary change observed within currently recognized species. The COI data are analyzed independently with an expanded taxon data set, including pair-wise nucleotide differences between recognized sister species. The wide range of average intraspecific pair-wise nucleotide difference (0-10.0%) suggests limitations to the application of a standard percent nucleotide difference as a means to identify species boundaries. At most, average COI nucleotide intraspecific difference provides an informal guide to identify potential clades that may warrant further systematic investigation.

Multi-locus phylogeny of dolphins in the subfamily Lissodelphininae: character synergy improves phylogenetic resolution

BACKGROUND

Dolphins of the genus Lagenorhynchus are anti-tropically distributed in temperate to cool waters. Phylogenetic analyses of cytochrome b sequences have suggested that the genus is polyphyletic; however, many relationships were poorly resolved. In this study, we present a combined-analysis phylogenetic hypothesis for Lagenorhynchus and members of the subfamily Lissodelphininae, which is derived from two nuclear and two mitochondrial data sets and the addition of 34 individuals representing 9 species. In addition, we characterize with parsimony and Bayesian analyses the phylogenetic utility and interaction of characters with statistical measures, including the utility of highly consistent (non-homoplasious) characters as a conservative measure of phylogenetic robustness. We also explore the effects of removing sources of character conflict on phylogenetic resolution.

RESULTS

Overall, our study provides strong support for the monophyly of the subfamily Lissodelphininae and the polyphyly of the genus Lagenorhynchus. In addition, the simultaneous parsimony analysis resolved and/or improved resolution for 12 nodes including: (1) L. albirostris, L. acutus; (2) L. obscurus and L. obliquidens; and (3) L. cruciger and L. australis. In addition, the Bayesian analysis supported the monophyly of the Cephalorhynchus, and resolved ambiguities regarding the relationship of L. australis/L. cruciger to other members of the genus Lagenorhynchus. The frequency of highly consistent characters varied among data partitions, but the rate of evolution was consistent within data partitions. Although the control region was the greatest source of character conflict, removal of this data partition impeded phylogenetic resolution.

CONCLUSION

The simultaneous analysis approach produced a more robust phylogenetic hypothesis for Lagenorhynchus than previous studies, thus supporting a phylogenetic approach employing multiple data partitions that vary in overall rate of evolution. Even in cases where there was apparent conflict among characters, our data suggest a synergistic interaction in the simultaneous analysis, and speak against a priori exclusion of data because of potential conflicts, primarily because phylogenetic results can be less robust. For example, the removal of the control region, the putative source of character conflict, produced spurious results with inconsistencies among and within topologies from parsimony and Bayesian analyses.