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The subgenus Aeschyntelus includes six species that show variations in body color and shape, thus making it difficult to identify them based on morphological identification alone. To date, no genetic study has evaluated species within this genus. Herein, we collected 171 individuals from 90 localities of Rhopalus and employed an integrative taxonomic approach that incorporated morphological data, mitochondrial genomic data (COI, whole mitochondrial data) and nuclear genomic data (18S + 28S rRNAs, nuclear genome-wide SNPs) to delineate species boundaries. Our analyses confirmed the status of nine described species of Rhopalus and proposed the recognition of one new species known as Rhopalus qinlinganus sp. nov., which is classified within the subgenus Aeschyntelus. Discrepancies arising from nuclear and mitochondrial data suggest the presence of mito-nuclear discordance. Specifically, mitochondrial data indicated admixture within Clade A, comprising R. kerzhneri and R. latus, whereas genome-wide SNPs unambiguously identified two separate species, aligning with morphological classification. Conversely, mitochondrial data clearly distinguished Clade B- consisting of R. sapporensis into two lineages, whereas genome-wide SNPs unequivocally identified a single species. Our study also provides insights into the evolutionary history of Aeschyntelus, thus indicating that it likely originated in East Asia during the middle Miocene. The development of Aeschyntelus biodiversity in the southwestern mountains of China occurred via an uplift-driven diversification process. Our findings highlight the necessity of integrating both morphological and multiple molecular datasets for precise species identification, particularly when delineating closely related species. Additionally, it reveals the important role of mountain orogenesis on speciation within the southwestern mountains of China., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Inc.)

Ciliophora, an exceptionally diverse lineage of unicellular eukaryotes, exhibits a remarkable range of species richness across classes in the ciliate Tree of Life. In this study, we have acquired transcriptome and genome data from 40 representative species in seven ciliate classes. Utilizing 247 genes and 105 taxa, we devised a comprehensive phylogenomic tree for Ciliophora, encompassing over 60 % of orders and constituting the most extensive dataset of ciliate species to date. We established a robust phylogenetic framework that encompasses ambiguous taxa and the major classes within the phylum. Our findings support the monophyly of each of two subphyla (Postciliodesmatophora and Intramacronucleata), along with three subclades (Protocruzia, CONTHREEP, and SAPML) nested within Intramacronucleata, and elucidate evolutionary positions among the major classes within the phylum. Drawing on the robust ciliate Tree of Life and three constraints, we estimated the radiation of Ciliophora around 1175 Ma during the middle of the Proterozoic Eon, and most of the ciliate classes diverged from their sister lineage during the latter half of this period. Additionally, based on the time-calibrated tree and species richness pattern, we investigated net diversification rates of Ciliophora and its classes. The global net diversification rate for Ciliophora was estimated at 0.004979 species/Ma. Heterogeneity in net diversification rates was evident at the class level, with faster rates observed in Oligohymenophorea and Spirotrichea than other classes within the subclades CONTHREEP and SAPML, respectively. Notably, our analysis suggests that variations in net diversification rates, rather than clade ages, appear to contribute to the differences in species richness in Ciliophora at the class level., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Inc.)

Peritrichs are one of the largest groups within the class Oligohymenophorea. They have a worldwide distribution and a high degree of species diversity. Using the single-cell genome sequencing technique, we obtained the genomes of five sessilid peritrichs. Combining both genomic and transcriptomic data of other publicly available oligohymenophorean ciliates (including the genomes of three sessilid peritrichs from our team's previous study), we conducted a comparative genomics study. Our phylogenomic analyses using both maximum likelihood and Bayesian inference methods recovered the subclass Peritrichia and each of its two orders (Sessilida and Mobilida) as being monophyletic. The non-monophyly of two families (Vorticellidae and Zoothamniidae) was also well supported in both trees. Molecular clock analysis showed that the origin of the subclass Peritrichia was estimated to be during the late Proterozoic. We also analyzed the stop codon usage of 44 oligohymenophoreans. The results showed that most of these species used TGA as the biased stop codon and reassigned the other two stop codons (TAA and TAG) to code amino acids. In addition, we found that the presence of a typical peritrich lorica is a plesiomorphic character of the family Vaginicolidae. Through GO enrichment analysis for group-specific orthogroups of Vaginicolidae, we successfully identified the biological process and molecular function GO terms that were linked with the typical peritrich lorica, including three glycosaminoglycan-related and two chitin-related GO terms. Finally, our enrichment analyses of significantly expanded gene families in Peritrichia found that sessilids were more tolerant to environmental stress (mainly organic matter) than mobilids, suggesting that peritrich lineages (especially sessilids) may have the potential for application in environmental pollution control and bioremediation. Together, the results presented in this study will facilitate wider genome-scale phylogenetic analyses of Peritrichia and deepen the understanding of their unique advantages for environmental pollution control bioremediation., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Inc.)

Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA and overall cost of the library construction, sequencing and assembly was conducted on mixtures of specimens, which raises the problem of chimera formation of mitogenomes. We present a novel chimera detection test based on gene tree incongruence, but identified only a single mitogenome of chimeric origin. Together with existing data for a final set of 127 taxa, phylogenetic analysis on nucleotide and amino acid sequences using Maximum Likelihood and Bayesian Inference revealed a basal split of Microdontinae from all other syrphids. The remainder consists of several deep clades assigned to the subfamily Eristalinae in the current classification, including a clade comprising the subfamily Syrphinae (plus Pipizinae). These findings call for a re-definition of subfamilies, but basal nodes had insufficient support to fully justify such action. Molecular-clock dating placed the origin of the Syrphidae crown group in the mid-Cretaceous while the Eristalinae-Syrphinae clade likely originated near the K/Pg boundary. Transformation of larval life history characters on the tree suggests that Syrphidae initially had sap feeding larvae, which diversified greatly in diet and habitat association during the Eocene and Oligocene, coinciding with the diversification of angiosperms and the evolution of various insect groups used as larval host, prey, or mimicry models. Mitogenomes proved to be a powerful phylogenetic marker for studies of Syrphidae at subfamily and tribe levels, allowing dense taxon sampling that provided insight into the great ecological diversity and rapid evolution of larval life history traits of the hoverflies., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Inc.)

The stylommatophoran land-snail genus Corilla is endemic to Sri Lanka and India's Western Ghats. On the basis of habitat distribution and shell morphology, the 10 extant Sri Lankan species fall into two distinct groups, lowland and montane. Here, we use phylogenetic analyses of restriction-site-associated DNA sequencing (RADseq) data and ancestral-state reconstructions of habitat association and shell morphology to clarify the systematics and evolution of Sri Lankan Corilla. Our dataset consists of 9 species of Corilla. Phylogenetic analyses were based on 88 assemblies (9,604-4,132,850 bp) generated by the RADseq assembler ipyrad, using four parameter combinations and different levels of missing data. Trees were inferred using a maximum likelihood (ML) approach. Ancestral states were reconstructed using maximum parsimony (MP) and ML approaches, with 1 binary state character analysed for habitat association (lowland vs montane) and 6 binary state characters analysed for shell morphology (shape, colour, lip width, length of upper palatal folds, orientation of upper palatal folds and collabral sculpture). Over a wide range of missing data (40-87 % missing individuals per locus) and assembly sizes (62,279-4,132,850 bp), nearly all trees conformed to one of two topologies (A and B), most relationships were strongly supported and total branch support approached the maximal value. Apart from the position of Corilla odontophora 'south', topologies A and B showed similar, well-resolved relationships at and above the species level. Our study agrees with the shell-based taxonomy of C. adamsi, C. beddomeae, C. carabinata, C. colletti and C. humberti (all maximally supported as monophyletic species). It shows that C. erronea and C. fryae constitute a single relatively widespread species (for which the valid name is C. erronea) and that the names C. gudei and C. odontophora each apply to at least two distinct, yet conchologically-cryptic species. The MP and ML ancestral-state reconstructions yielded broadly similar results and provide firm evidence that diversification in Sri Lankan Corilla has involved evolutionary convergence in the shell morphology of lowland lineages, with a pale shell and wide lip having evolved on at least two separate occasions (in C. carabinata and C. colletti) from montane ancestors having a dark, narrow-lipped shell., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Hitherto, the phylogeny of ciliated protists, an important group of model organisms in many fields, has been mainly based on a single marker gene (SSU rDNA, nuclear small subunit ribosomal RNA gene). However, there is increasing evidence showing this is insufficient to provide robust phylogenies and has resulted in confusing systematics in many ciliates groups. Among these, the phylogenies within family Deviatidae (Spirotrichea, Hypotrichia) are ambiguous due to the dependence on SSU rDNA and undersampling. Here, we provide eight new sequences and conduct phylogenetic analyses based on both multi-gene and single-gene to clarify evolutionary relationships among all deviatids for which gene sequence are available. The results reveal that: (1) the monophyly of Deviatidae is well-supported by both single-gene and concatenated data; (2) the presence of fine cirri and relatively wide spacing of these cirri within all rows are plesiomorphies of Deviatidae; (3) Pseudosincirra longicirrata is closely related to Deviata rositae, which is supported by their shared possession of dorsomarginal kineties; (4) phylogenetic analyses and approximately unbiased test based on multi-gene support a close relationship among taxa lacking dorsomarginal kineties (D. parabacilliformis, D. multilineae nov. spec., D. abbrevescens, D. brasiliensis and Perisincirra paucicirrata); (5) Deviatidae shows a close relationship with Dorsomarginalia and Strongylidium-Hemiamphisiella-Pseudouroleptus assemblage, suggesting the presence/absence of dorsomarginal kineties is phylogenetically informative in this family and presence of them may be a plesiomorphy. Based on the morphological, morphogenetic and phylogenetic data, the evolutionary relationships within Deviatidae are hypothesized, and a new ciliate, Deviata multilineae nov. spec., collected from China, is investigated., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Diseases of bivalve molluscs caused by paramyxid parasites of the genus Marteilia have been linked to mass mortalities and the collapse of commercially important shellfish populations. Until recently, no Marteilia spp. have been detected in common cockle (Cerastoderma edule) populations in the British Isles. Molecular screening of cockles from ten sites on the Welsh coast indicates that a Marteilia parasite is widespread in Welsh C. edule populations, including major fisheries. Phylogenetic analysis of ribosomal DNA (rDNA) gene sequences from this parasite indicates that it is a closely related but different species to Marteilia cochillia, a parasite linked to mass mortality of C. edule fisheries in Spain, and that both are related to Marteilia octospora, for which we provide new rDNA sequence data. Preliminary light and transmission electron microscope (TEM) observations support this conclusion, indicating that the parasite from Wales is located primarily within areas of inflammation in the gills and the connective tissue of the digestive gland, whereas M. cochillia is found mainly within the epithelium of the digestive gland. The impact of infection by the new species, here described as Marteilia cocosarum n. sp., upon Welsh fisheries is currently unknown., (Copyright © 2022. Published by Elsevier Inc.)

Broad tapeworms (Diphyllobothriidea) are parasites whose adults are capable of infecting a wide range of freshwater, marine and terrestrial tetrapods including humans. Previous works examining the evolution of habitat and host use in this group have been hampered by the lack of a well-resolved phylogeny. In order to produce a robust phylogenetic framework for diphyllobothriideans, we sequenced the complete mitochondrial genome of 13 representatives, carefully chosen to cover the major clades, and two outgroup species representing the Spathebothriidea and Haplobothriidea. In addition, complementary data from the nuclear ribosomal operon was sequenced for 10 representative taxa. Mitogenomes and ssrDNA and lsrDNA were used towards elucidating the phylogenetic framework for the Diphyllobothriidea. The Cephalochlamydidae is confirmed as the earliest diverging diphyllobothriidean lineage, and Solenophoridae and Diphyllobothriidae are sister groups. We infer a probable freshwater origin of the diphyllobothriideans. The ancestral condition for life cycle complexity could not be unambiguously resolved. However, we infer exclusive use of a three-host life cycle following the origin of the Solenophoridae + Diphyllobothriidae. Regarding definitive host use, although we infer reptiles as the most likely ancestral condition, this result should be revisited with a more densely sampled phylogeny in future studies. Freshwater habitat is used by the early diverging lineages within the Solenophoridae + Diphyllobothriidae clade. For the latter, habitat use shifts between freshwater and marine environments, and definitive host use includes marine and terrestrial mammals and birds. We use mitochondrial genomes to distinguish Schistocephalus species occurring in different species of sticklebacks and demonstrate conspecificity of Ligula cf. intestinalis specimens collected from two Fennoscandian ringed seal subspecies., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Phylogenetic relationships of sub-Saharan African natricine snakes are understudied and poorly understood, which in turn has precluded analyses of the historical biogeography of the Seychelles endemic Lycognathophis seychellensis. We inferred the phylogenetic relationships of Seychelles and mainland sub-Saharan natricines by analysing a multilocus DNA sequence dataset for three mitochondrial (mt) and four nuclear (nu) genes. The mainland sub-Saharan natricines and L. seychellensis comprise a well-supported clade. Two maximally supported sets of relationships within this clade are (Limnophis,Natriciteres) and (Afronatrix,(Hydraethiops,Helophis)). The relationships of L. seychellensis with respect to these two lineages are not clearly resolved by analysing concatenated mt and nu data. Analysed separately, nu data best support a sister relationship of L. seychellensis with (Afronatrix,(Hydraethiops,Helophis)) and mt data best support a sister relationship with all mainland sub-Saharan natricines. Methods designed to cope with incomplete lineage sorting strongly favour the former hypothesis. Genetic variation among up to 33 L. seychellensis from five Seychelles islands is low. Fossil calibrated divergence time estimates support an overseas dispersal of the L. seychellensis lineage to the Seychelles from mainland Africa ca. 43-25 million years before present (Ma), rather than this taxon being a Gondwanan relic., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Members of the gastropod superfamily Stromboidea (Littorinimorpha) are characterised by their elaborate shell morphologies, distinctive mode of locomotion, and often large and colourful eyes. This iconic group comprises over 130 species, including many large and charismatic species. The family Strombidae is of particular interest, largely due to its commercial importance and wide distribution in tropical and subtropical waters. Although a few strombid mitochondrial genomes have been sequenced, data for the other four Recent families in Stromboidea are lacking. In this study we report seven new stromboid mitogenomes obtained from transcriptomic and genomic data, with taxonomic representation from each Recent stromboid family, including the first mitogenomes for Aporrhaidae, Rostellariidae, Seraphsidae and Struthiolariidae. We also report a new mitogenome for the family Xenophoridae. We use these data, along with published sequences, to investigate the relationships among these and other caenogastropod groups. All analyses undertaken in this study support monophyly of Stromboidea as redefined here to include Xenophoridae, a finding consistent with morphological and behavioural data. Consistent with previous morphological and molecular analyses, including those based on mitogenomes, monophyly of Hypsogastropoda is confirmed but monophyly of Littorinimorpha is again rejected., (Crown Copyright © 2021. Published by Elsevier Inc. All rights reserved.)

Old World orioles (Oriolidae) are medium-sized passerine birds confined largely to forested areas of Africa, Eurasia and Australasia. We present a new complete molecular (mtDNA) subspecies level phylogeny of the Oriolidae including all 113 taxa (35 species) together with a backbone phylogeny of 19 taxa from the main Oriolus clades based on (i) 21 nuclear genes, (ii) whole mito-genomes, and (iii) genome-wide ultraconserved elements. We use this phylogeny to assess systematic relationships and the biogeographical history of this avian family. Furthermore, we use morphological measurements to investigate the relationship between size and shape axes and upstream or back-colonization of this extensive island region from Asia. We show that several subspecies or groups of subspecies may warrant species rank and we find a continental example of two morphologically distinct species (O. mellianus/O. traillii) being genetically (mtDNA) very similar. Biogeographically, we confirm previous findings that members of the Oriolidae originated in Australo-Papua. Dispersal out of this area took place around 15 Mya to southeast Asia and Africa, and from Africa to the Palearctic followed by recolonization of the Indonesian and Philippine island region during the Plio-Pleistocene. Recolonisation of the Indonesian and Philippine islands coincided with an increase in body size, which may have facilitated the ability to co-exist with other congenerics., (Copyright © 2019 Elsevier Inc. All rights reserved.)

The Sima de los Huesos (SH) endocranial sample includes 16 complete or partial endocasts corresponding to European Middle Pleistocene hominins. Different anatomical and molecular studies have demonstrated that these hominins are phylogenetically related to Neanderthals, thus making them the earliest unquestionable representatives of the Neanderthal lineage. The description of endocranial variation in this population is fundamental to shedding light on the evolution of the Neanderthal brain. In this contribution, we analyze and describe endocranial variation in this sample, including aspects related to brain size (endocranial volume and encephalization) and brain organization (through qualitative descriptions and quantitative analyses). Our results indicate that the SH hominins show a transitional state between a primitive hominin endocranial configuration (which is found in Homo erectus and non-SH Middle Pleistocene Homo) and the derived configurations found in Neanderthals and modern humans, without a clear anticipation of classic Neanderthal endocranial traits. In comparison with other cranial and postcranial traits that show a fully Neanderthal or clear pre-Neanderthal condition in the SH collection, endocranial variation in these hominins is surprisingly primitive and shows no Neanderthal affinity. These results and the comparison with other cranial traits confirm that Neanderthals evolved in a mosaic fashion. Traits related to mastication (dental, facial and mandibular anatomy) led the Neanderthalization process, whereas neurocranial anatomy must have acquired a fully Neanderthal condition considerably later., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Peritrichia is a large and distinctive assemblage of ciliated protists that was first observed by Antonie van Leeuwenhoek over 340 years ago. In the last two decades the evolutionary relationships of this subclass have been increasingly debated as morphological and molecular analyses have generated contrasting conclusions. In this study, we provide genomic-scale data from 12 typical representatives. We combine taxon- and gene-rich phylogenomic analyses, with up to 151 genes (43,956 amino acid residues) from 18 freshwater, brackish and marine isolates in order to assess the systematics and evolutionary history of the Peritrichia. The main findings were: (1) the subclass Peritrichia originates from the end of the Proterozoic to the Cambrian; (2) the monophyletic Peritrichia is sister to the Peniculia (represented by Paramecium) within the class Oligohymenophorea; (3) spasmin plays a significant role in peritrich evolution: we detected the spasmin gene in target ciliates and traced the molecular evolution of spasmin, a key spasmoneme component, together with phylogenetic relationships and morphology of the peritrichs. These findings provide evidence that spasmin is an important molecule to illustrate the phylogenetic position of Peritrichia within the class Oligohymenophorea, the monophyly of Peritrichia, and the diverse and rapid evolution of sessilid peritrichs., (Copyright © 2018 Elsevier Inc. All rights reserved.)

The insect order Hymenoptera presents marvelous morphological and ecological diversity. Higher-level hymenopteran relationships remain controversial, even after recent phylogenomic analyses, as their taxon sampling was limited. To shed light on the origin and diversification of Hymenoptera, in particular the poorly studied Parasitica, we undertook phylogenetic analyses of 40 newly and 43 previously sequenced mitochondrial genomes representing all major clades of Hymenoptera. Various Bayesian inferences using different data partitions and phylogenetic methods recovered similar phylogenetic trees with strong statistical support for almost all nodes. Novel findings of the mitogenomic phylogeny mainly affected the three infraorders Ichneumonomorpha, Proctotrupomorpha and Evaniomorpha, the latter of which was split into three clades. Basal relationships of Parasitica recovered Stephanoidea + (Gasteruptiidae + Aulacidae) as the sister group to Ichneumonomorpha + (Trigonalyoidea + Megalyroidea). This entire clade is sister to Proctotrupomorpha, and Ceraphronoidea + Evaniidae is sister to Aculeata (stinging wasps). Our divergence time analysis indicates that major hymenopteran lineages originated in the Mesozoic. The radiation of early apocritans may have been triggered by the Triassic-Jurassic mass extinction; all extant families were present by the Cretaceous., (Copyright © 2018 Elsevier Inc. All rights reserved.)

The phylogenetic relationships of the nymphalid butterfly tribe Limenitidini are best known for the genera Limenitis and Adelpha, model taxa for evolutionary processes such as Batesian mimicry and rapid adaptive radiations. Whereas these American limenitidines have received the most attention, phylogenetic relationships of their Asian relatives are still controversial and largely unexplored. Even one of the largest genera in Asia, Athyma, is polyphyletic. To clarify the phylogenetic relationships of these Asian Limenitidini, a total of 53 representatives were sampled; 37 have their mitogenomes sequenced for the first time. Our phylogenetic results confirm that mitogenomic data provides well-resolved relationships at most major levels of the phylogeny, even using different partition schemes or different inference methods. Interestingly, our results show that some Athyma taxa are embedded within the genus Limenitis, whereas the genus Tacola, previously considered to be a synonym of Athyma, needs to be recognized as a valid clade. Additionally, the other Limenitidini genera in Asia (namely Tarattia, Litinga, Sumalia, Pandita and Patsuia) are now grouped either within Athyma or Limenitis, so these genera need to be sunk. Importantly, we also show that the mainly Old World Limenitis and entirely New World Adelpha are sister groups, confirming the relevance of Asian lineages to global studies of Limenitis evolution., (Copyright © 2018 Elsevier Inc. All rights reserved.)

A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes., (Copyright © 2018 Elsevier Inc. All rights reserved.)

This paper discusses the problem of whether creating a matrix with all the character state combinations that have a fixed number of steps (or extra steps) on a given tree T, produces the same tree T when analyzed with maximum parsimony or maximum likelihood. Exhaustive enumeration of cases up to 20 taxa for binary characters, and up to 12 taxa for 4-state characters, shows that the same tree is recovered (as unique most likely or most parsimonious tree) as long as the number of extra steps is within 1/4 of the number of taxa. This dependence, 1/4 of the number of taxa, is discussed with a general argumentation, in terms of the spread of the character changes on the tree used to select character state distributions. The present finding allows creating matrices which have as much homoplasy as possible for the most parsimonious or likely tree to be predictable, and examination of these matrices with hill-climbing search algorithms provides additional evidence on the (lack of a) necessary relationship between homoplasy and the ability of search methods to find optimal trees., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Assessing the relative contributions of immigration and diversification into the buildup of species diversity is key to understanding the role of historical processes in driving biogeographical and diversification patterns in species-rich regions. Here, we investigated how colonization, in situ speciation, and extinction history may have generated the present-day distribution and diversity of Goura crowned pigeons (Columbidae), a group of large forest-dwelling pigeons comprising four recognized species that are all endemic to New Guinea. We used a comprehensive geographical and taxonomic sampling based mostly on historical museum samples, and shallow shotgun sequencing, to generate complete mitogenomes, nuclear ribosomal clusters and independent nuclear conserved DNA elements. We used these datasets independently to reconstruct molecular phylogenies. Divergence time estimates were obtained using mitochondrial data only. All analyses revealed similar genetic divisions within the genus Goura and recovered as monophyletic groups the four species currently recognized, providing support for recent taxonomic changes based on differences in plumage characters. These four species are grouped into two pairs of strongly supported sister species, which were previously not recognized as close relatives: Goura sclaterii with Goura cristata, and Goura victoria with Goura scheepmakeri. While the geographical origin of the Goura lineage remains elusive, the crown age of 5.73 Ma is consistent with present-day species diversity being the result of a recent diversification within New Guinea. Although the orogeny of New Guinea's central cordillera must have played a role in driving diversification in Goura, cross-barrier dispersal seems more likely than vicariance to explain the speciation events having led to the four current species. Our results also have important conservation implications. Future assessments of the conservation status of Goura species should consider threat levels following the taxonomic revision proposed by del Hoyo and Collar (HBW and BirdLife International illustrated checklist of the birds of the world 1: non-passerines, 2014), which we show to be fully supported by genomic data. In particular, distinguishing G. sclaterii from G. scheepmakeri seems to be particularly relevant., (Copyright © 2017 Elsevier Inc. All rights reserved.)

The beetle suborder Adephaga consists of several aquatic ('Hydradephaga') and terrestrial ('Geadephaga') families whose relationships remain poorly known. In particular, the position of Cicindelidae (tiger beetles) appears problematic, as recent studies have found them either within the Hydradephaga based on mitogenomes, or together with several unlikely relatives in Geadephaga based on 18S rRNA genes. We newly sequenced nine mitogenomes of representatives of Cicindelidae and three ground beetles (Carabidae), and conducted phylogenetic analyses together with 29 existing mitogenomes of Adephaga. Our results support a basal split of Geadephaga and Hydradephaga, and reveal Cicindelidae, together with Trachypachidae, as sister to all other Geadephaga, supporting their status as Family. We show that alternative arrangements of basal adephagan relationships coincide with increased rates of evolutionary change and with nucleotide compositional bias, but these confounding factors were overcome by the CAT-Poisson model of PhyloBayes. The mitogenome + 18S rRNA combined matrix supports the same topology only after removal of the hypervariable expansion segments. Densely sampled mitogenomes, analyzed with site heterogeneous mixture models, support a plausible hypothesis of basal relationships in the Adephaga., (Copyright © 2017 Elsevier Inc. All rights reserved.)

The diverse and pantropical genus Ctenitis, in the Dryopteridaceae, has been largely ignored in phylogenetic studies until now. In this study, we fill in this gap by reconstructing the first comprehensive phylogeny of the genus including 53 species currently recognized in the genus Ctenitis, among which seven species formerly were assigned to the genus Pseudotectaria and one to Heterogonium. Special emphasis was given to the sampling of species occurring in the African-Indian Ocean region. The presented results include reconstruction of a biogeographic scenario based on estimated divergence times and ancestral area reconstruction. Our findings confirm the inclusion, within Ctenitis, of the Indian Ocean species formerly placed in Pseudotectaria and Heterogonium. The crown group divergence was estimated to date back to the Oligocene or Early Miocene. The biogeographical scenario indicates an initial divergence of the Asian-Pacific ranges and the neotropical ranges, and a subsequent colonization of the Afro-Madagascan region by a lineage with neotropical ancestors. The Afro-Madagascan lineage splits into a lineage endemic to the Mascarene islands and a lineage occurring in Madagascar, the Comoros and Africa. The range expansion towards Africa and Madagascar was estimated to date back to the late Miocene, whereas the estimated ages for the onset of the diversification of the Mascarene diversity is consistent with the ages of these young, volcanic islands. The absence of any extant species of Ctenitis with a multi-continental distribution range and the rarity of inter-island dispersal and speciation in the Indian Ocean region suggest a limited contribution of long distance dispersal to the biogeographical history of this fern genus, versus a high contribution of local speciation., (Copyright © 2017. Published by Elsevier Inc.)

Syllis gracilis is an emblematic member of the subfamily Syllinae (Syllidae, Annelida), which inhabits shallow, temperate coastal waters and can be found on algae, coral rubble, and sponges. Their distinctive ypsiloid chaetae, usually found in specimens from populations all around the world, led to the consideration of the species as cosmopolitan, even though four other species have similar chaetae: Syllis magellanica, S. picta, S. mayeri and S. ypsiloides. The discovery of deeply divergent lineages in the Mediterranean Sea, that were morphologically similar, questioned the cosmopolitanism of S. gracilis and suggested the possibility of it being a species complex. In order to assess the speciation patterns within the putative S. gracilis complex, we undertook species delimitation and phylogenetic analyses on 61 specimens morphologically ascribed to Syllis gracilis and closely related species using a multilocus molecular dataset (two mitochondrial and two nuclear markers). Our results suggest high levels of genetic differentiation between the S. gracilis populations analyzed, some of which have morphologically distinctive features. Five to eight distinct lineages (depending on the analysis) were identified, all with geographically restricted distributions. Although the presence of ypsiloid chaetae has been traditionally considered the main character to identify S. gracilis, we conclude that this feature is homoplastic. Instead, we propose that characters such as the degree of fusion of blades and shafts in chaetae, the morphology of the posterior chaetae or the animal color pattern should be considered to differentiate lineages within the S. gracilis species complex. Our study does not support the cosmopolitanism of S. gracilis, and instead provides morphological and molecular evidence of the existence of a complex of pseudo-cryptic species., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Many recent studies discuss the influence of climatic and geological events in the evolution of Neotropical biota by correlating these events with dated phylogenetic hypotheses. Myrtaceae is one of the most diverse Neotropical groups and it therefore a good proxy of plant diversity in the region. However, biogeographic studies on Neotropical Myrtaceae are still very limited. Myrcia s.l. is an informal group comprising three accepted genera (Calyptranthes, Marlierea and Myrcia) making up the second largest Neotropical group of Myrtaceae, totalling about 700 species distributed in nine subgroups. Exclusively Neotropical, the group occurs along the whole of the Neotropics with diversity centres in the Caribbean, the Guiana Highlands and the central-eastern Brazil. This study aims to identify the time and place of divergence of Myrcia s.l. lineages, to examine the correlation in light of geological and climatic events in the Neotropics, and to explore relationships among Neotropical biogeographic areas. A dated phylogenetic hypothesis was produced using BEAST and calibrated by placing Paleomyrtinaea princetonensis (56Ma) at the root of the tree; biogeographic analysis used the DEC model with dispersal probabilities between areas based on distance and floristic affinities. Myrcia s.l. originated in the Montane Atlantic Forest between the end of Eocene and early Miocene and this region acted as a secondary cradle for several lineages during the evolution of this group. The Caribbean region was important in the diversification of the Calyptranthes clade while the Guayana shield appears as ancestral area for an older subgroup of Myrcia s.l. The Amazon Forest has relatively low diversity of Myrcia s.l. species but appears to have been important in the initial biogeographic history of old lineages. Lowland Atlantic Forest has high species diversity but species rich lineages did not originate in the area. Diversification of most subgroups of Myrcia s.l. occurred throughout the Miocene, as reported for other Neotropical taxa. During the Miocene, geological events may have influenced the evolution of the Caribbean and Amazon forest lineages, but other regions were geological stable and climate changes were the most likely drivers of diversification. The evolution of many lineages in montane areas suggests that Myrcia s.l. may be particularly adapted to such environments., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Parahepatospora carcini n. gen. n. sp., is a novel microsporidian parasite discovered infecting the cytoplasm of epithelial cells of the hepatopancreas of a single Carcinus maenas specimen. The crab was sampled from within its invasive range in Atlantic Canada (Nova Scotia). Histopathology and transmission electron microscopy were used to show the development of the parasite within a simple interfacial membrane, culminating in the formation of unikaryotic spores with 5-6 turns of an isofilar polar filament. Formation of a multinucleate meront (>12 nuclei observed) preceded thickening and invagination of the plasmodial membrane, and in many cases, formation of spore extrusion precursors (polar filaments, anchoring disk) prior to complete separation of pre-sporoblasts from the sporogonial plasmodium. This developmental feature is intermediate between the Enterocytozoonidae (formation of spore extrusion precursors within the sporont plasmodium) and all other Microsporidia (formation of spore extrusion precursors after separation of sporont from the sporont plasmodium). SSU rRNA-based gene phylogenies place P. carcini within microsporidian Clade IV, between the Enterocytozoonidae and the so-called Enterocytospora-clade, which includes Enterocytospora artemiae and Globulispora mitoportans. Both of these groups contain gut-infecting microsporidians of aquatic invertebrates, fish and humans. According to morphological and phylogenetic characters, we propose that P. carcini occupies a basal position to the Enterocytozoonidae. We discuss the discovery of this parasite from a taxonomic perspective and consider its origins and presence within a high profile invasive host on the Atlantic Canadian coastline., (Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.)

The subfamily Cantharidinae Gray, 1857 (Trochoidea: Trochidae) includes 23 recognized genera and over 200 known living species. These marine top shell snails are microphagous grazers that generally live in shallow rocky shores and in macroalgae and seagrass beds of sub-tropical and temperate waters from the Central and Western Indo-Pacific biogeographic regions to the Mediterranean Sea and the Eastern Atlantic Ocean. Recent molecular phylogenetic studies revising the family Trochidae supported the monophyly of the subfamily Cantharidinae and its sister group relationship to the subfamily Stomatellinae. These studies and others has thus far mostly focused on Indo-Pacific members of the subfamily Cantharidinae whereas here, we investigated phylogenetic relationships among their counterparts from the Mediterranean Sea and the North-eastern (NE) Atlantic Ocean including 33 species of genera Gibbula, Jujubinus, Phorcus, Clelandella, and Callumbonella. The Mediterranean and NE Atlantic taxa were supplemented with 30 Indo-Pacific Cantharidinae species plus 19 members of the sister group subfamily Stomatellinae. Phylogenetic trees were constructed using Bayesian inference and maximum likelihood with two datasets comprised of partial sequences of four or six mitochondrial (cox1, rrnL, rrnS, and cob) and nuclear (28S rRNA and histone H3) genes. A clade comprised of all Mediterranean and NE Atlantic taxa was recovered with high support, but its sister group among the Indo-Pacific lineages could not be determined with confidence (although the assignment of "Trochus" kotschyi to Priotrochus could be rejected). Within the Mediterranean and NE Atlantic clade, genera Phorcus and Jujubinus were recovered as reciprocally monophyletic, and the deep-sea genera Clelandella and Callumbonella were placed with high support as sister to Jujubinus. However, the genus Gibbula as currently defined was not monophyletic and constituent species were divided into three major clades and two independent lineages. Phylogenetic relationships among Phorcus, Jujubinus (plus Clelandella and Callumbonella), and the different clades of Gibbula were not fully resolved but received higher support in the phylogenetic analyses based on six genes. A first approach to resolve phylogenetic relationships within Stomatellinae was conducted showing that the diversity of the subfamily is highly underestimated at present, and that Calliotrochus is possibly a member of this subfamily. A chronogram was reconstructed using an uncorrelated relaxed lognormal molecular clock and the origin of the Mediterranean and NE Atlantic clade was dated right after the Azolla phase in the Middle Eocene about 48 million years ago whereas diversification of major clades (genera) followed the eastern closure of the Tethys Ocean in the Middle Miocene about 14 million years ago., (Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.)

Phylogenetic relationships of dung beetles in the tribe Onthophagini, including the species-rich, cosmopolitan genus Onthophagus, were inferred using whole mitochondrial genomes. Data were generated by shotgun sequencing of mixed genomic DNA from >100 individuals on 50% of an Illumina MiSeq flow cell. Genome assembly of the mixed reads produced contigs of 74 (nearly) complete mitogenomes. The final dataset included representatives of Onthophagus from all biogeographic regions, closely related genera of Onthophagini, and the related tribes Onitini and Oniticellini. The analysis defined four major clades of Onthophagini, which was paraphyletic for Oniticellini, with Onitini as sister group to all others. Several (sub)genera considered as members of Onthophagus in the older literature formed separate deep lineages. All New World species of Onthophagus formed a monophyletic group, and the Australian taxa are confined to a single or two closely related clades, one of which forms the sister group of the New World species. Dating the tree by constraining the basal splits with existing calibrations of Scarabaeoidea suggests an origin of Onthophagini sensu lato in the Eocene and a rapid spread from an African ancestral stock into the Oriental region, and secondarily to Australia and the Americas at about 20-24 Mya. The successful assembly of mitogenomes and the well-supported tree obtained from these sequences demonstrates the power of shotgun sequencing from total genomic DNA of species pools as an efficient tool in genus-level phylogenetics., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Phylogenetic analyses of ciliated protists are frequently based on single molecular markers, usually the small subunit ribosomal RNA gene (SSU rDNA), despite the well-known limitations of this approach. Here, 78 new sequences of three linked genes (SSU rDNA, ITS1-5.8S rDNA-ITS2, LSU rDNA) were characterized and applied to phylogenetic analyses of oligotrichs (s. str.). It was found that: (1) three taxa, that is tontoniids, pelagostrombidiids and cyrtostrombidiids should be split from the family Strombidiidae (s. l.), which supports Agatha's classification based on morphological characters; (2) the families Tontoniidae and Cyrtostrombidiidae are both monophyletic whereas Strombidiidae is polyphyletic; (3) the positions of the families Cyrtostrombidiidae and Pelagostrombidiidae varied in different trees although with low support values; (4) the close relationship between Varistrombidium and Apostrombidium is confirmed, which updates the evolutionary hypothesis for oligotrichs based on ciliary patterns; and (5) two relatively stable clades were found in the family Strombidiidae., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Anillini are a tribe of minute, euedaphic ground beetles (Carabidae) characterized by the loss of eyes, loss of wings and high levels of local endemism. Despite their presumed low dispersal, they have a nearly cosmopolitan distribution, including isolated islands such as New Zealand and New Caledonia. We used a time calibrated molecular phylogeny to test, first, if the tribe as currently understood is monophyletic and, second, whether the time of divergence is compatible with an early vicariant diversification after the breakup of Gondwana. We sequenced portions of 6 mitochondrial and 3 nuclear genes for 66 specimens in 17 genera of Anillini plus 39 outgroups. The resulting phylogenetic tree was used to estimate the time of diversification using two independent calibration schemes, by applying molecular rates for the related genus Carabus or by dating the tree with fossil and geological information. Rates of molecular evolution and lineage ages were mostly concordant between both calibration schemes. The monophyly of Anillini was well-supported, and its age was consistent with a Gondwanian origin of the main lineages and an initial diversification at ca. 100Ma representing the split between the eyed Nesamblyops (New Zealand) and the remaining Anillini. The subsequent diversification, including the split of the Nearctic Anillinus and the subsequent splits of Palaearctic lineages, was dated to between 80 and 100Ma and thus was also compatible with a tectonic vicariant origin. On the contrary, the estimated age of the New Caledonian blind Orthotyphlus at ca. 30±20Ma was incompatible with a vicariant origin, suggesting the possibility of trans-oceanic dispersal in these endogean beetles., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Afrotropical Acraeini butterflies provide a fascinating potential model system to contrast with the Neotropical Heliconiini, yet their phylogeny remains largely unexplored by molecular methods and their generic level nomenclature is still contentious. To test the potential of mitogenomes in a simultaneous analysis of the radiation, we sequenced the full mitochondrial genomes of 19 African species. Analyses show the potential of mitogenomic phylogeny reconstruction in this group. Inferred relationships are largely congruent with a previous multilocus study. We confirm a monophyletic Telchinia to include the Asiatic Pareba with a complicated paraphylum, traditional (sub)genus Acraea, toward the base. The results suggest that several proposed subgenera and some species groups within Telchinia are not monophyletic, while two other (sub)genera could possibly be combined. Telchinia was recovered without strong support as sister to the potentially interesting system of distasteful model butterflies known as Bematistes, a name that is suppressed in some treatments. Surprisingly, we find that this taxon has remarkably divergent mitogenomes and unexpected synapomorphic tRNA rearrangements. These gene order changes, combined with evidence for deviating dN/dS ratios and evidence for episodal diversifying selection, suggest that the ancestral Bematistes mitogenome has had a turbulent past. Our study adds genetic support for treating this clade as a distinct genus, while the alternative option, adopted by some authors, of Acraea being equivalent to Acraeini merely promotes redundancy. We pave the way for more detailed mitogenomic and multi-locus molecular analyses which can determine how many genera are needed (possibly at least six) to divide Acraeini into monophyletic groups that also facilitate communication about their biology., (Copyright © 2016 Elsevier Inc. All rights reserved.)

This study presents the most complete generic phylogenetic framework to date for the tribe Coleeae (Bignoniaceae), which is endemic to Madagascar and the other smaller islands in the western part of the Indian Ocean. The study is based on plastid and nuclear DNA regions and includes 47 species representing the five currently recognized genera (including all the species occurring in the western Indian Ocean region). Bayesian and maximum likelihood analyses supported (i) the monophyly of the tribe, (ii) the monophyly of Phylloctenium, Phyllarthron and Rhodocolea and (iii) the paraphyly of Colea due to the inclusion of species of Ophiocolea. The latter genus was also recovered paraphyletic due to the inclusion of two species of Colea (C. decora and C. labatii). The taxonomic implications of the mutual paraphyly of these two genera are discussed in light of morphological evidence, and it is concluded that the two genera should be merged, and the necessary new nomenclatural combinations are provided. The phylogenetic framework shows Phylloctenium, which is endemic to Madagascar and restricted to dry ecosystems, as basal and sister to the rest of the tribe, suggesting Madagascar to be the centre of origin of this clade. The remaining genera are diversified mostly in humid ecosystems, with evidence of multiple dispersals to the neighboring islands, including at least two to the Comoros, one to Mauritius and one to the Seychelles. Finally, we hypothesize that the ecological success of this tribe might have been triggered by a shift of fruit-dispersal mode from wind to lemur., (Copyright © 2015 Elsevier Inc. All rights reserved.)

To fully understand macroevolutionary patterns and processes, we need to include both extant and extinct species in our models. This requires phylogenetic trees with both living and fossil taxa at the tips. One way to infer such phylogenies is the Total Evidence approach which uses molecular data from living taxa and morphological data from living and fossil taxa. Although the Total Evidence approach is very promising, it requires a great deal of data that can be hard to collect. Therefore this method is likely to suffer from missing data issues that may affect its ability to infer correct phylogenies. Here we use simulations to assess the effects of missing data on tree topologies inferred from Total Evidence matrices. We investigate three major factors that directly affect the completeness and the size of the morphological part of the matrix: the proportion of living taxa with no morphological data, the amount of missing data in the fossil record, and the overall number of morphological characters in the matrix. We infer phylogenies from complete matrices and from matrices with various amounts of missing data, and then compare missing data topologies to the "best" tree topology inferred using the complete matrix. We find that the number of living taxa with morphological characters and the overall number of morphological characters in the matrix, are more important than the amount of missing data in the fossil record for recovering the "best" tree topology. Therefore, we suggest that sampling effort should be focused on morphological data collection for living species to increase the accuracy of topological inference in a Total Evidence framework. Additionally, we find that Bayesian methods consistently outperform other tree inference methods. We therefore recommend using Bayesian consensus trees to fix the tree topology prior to further analyses., (Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.)

Thelypteridaceae is one of the largest fern families, having about 950 species and a cosmopolitan distribution but with most species occurring in tropical and subtropical regions. Its generic classification remains controversial, with different authors recognizing from one up to 32 genera. Phylogenetic relationships within the family have not been exhaustively studied, but previous studies have confirmed the monophyly of the lineage. Thus far, sampling has been inadequate for establishing a robust hypothesis of infrafamilial relationships within the family. In order to understand phylogenetic relationships within Thelypteridaceae and thus to improve generic reclassification, we expand the molecular sampling, including new samples of Old World taxa and, especially, many additional neotropical representatives. We also explore the monophyly of exclusively or mostly neotropical genera Amauropelta, Goniopteris, Meniscium, and Steiropteris. Our sampling includes 68 taxa and 134 newly generated sequences from two plastid genomic regions (rps4-trnS and trnL-trnF), plus 73 rps4 and 72 trnL-trnF sequences from GenBank. These data resulted in a concatenated matrix of 1980 molecular characters for 149 taxa. The combined data set was analyzed using maximum parsimony and bayesian inference of phylogeny. Our results are consistent with the general topological structure found in previous studies, including two main lineages within the family: phegopteroid and thelypteroid. The thelypteroid lineage comprises two clades; one of these included the segregates Metathelypteris, Coryphopteris, and Amauropelta (including part of Parathelypteris), whereas the other comprises all segregates of Cyclosorus s.l., such as Goniopteris, Meniscium, and Steiropteris (including Thelypteris polypodioides, previously incertae sedis). The three mainly neotropical segregates were found to be monophyletic but nested in a broadly defined Cyclosorus. The fourth mainly neotropical segregate, Amauropelta, was found to include species considered to be part of Parathelypteris. In Old World thelypteroids, which correspond to nearly half the diversity in the family, an increase in sampling is still needed to resolve relationships and circumscription of genera, particularly in the christelloid clade (i.e., Amphineuron, Chingia, Christella, Pneumatopteris, Pronephrium, and Sphaerostephanos). Based on currently available knowledge, we propose the recognition of 16 genera in the family., (Copyright © 2015 Elsevier Inc. All rights reserved.)

The Corvides (previously referred to as the core Corvoidea) are a morphologically diverse clade of passerine birds comprising nearly 800 species. The group originated some 30 million years ago in the proto-Papuan archipelago, to the north of Australia, from where lineages have dispersed and colonized all of the world's major continental and insular landmasses (except Antarctica). During the last decade multiple species-level phylogenies have been generated for individual corvoid families and more recently the inter-familial relationships have been resolved, based on phylogenetic analyses using multiple nuclear loci. In the current study we analyse eight nuclear and four mitochondrial loci to generate a dated phylogeny for the majority of corvoid species. This phylogeny includes 667 out of 780 species (85.5%), 141 out of 143 genera (98.6%) and all 31 currently recognized families, thus providing a baseline for comprehensive macroecological, macroevolutionary and biogeographical analyses. Using this phylogeny we assess the temporal consistency of the current taxonomic classification of families and genera. By adopting an approach that enforces temporal consistency by causing the fewest possible taxonomic changes to currently recognized families and genera, we find the current familial classification to be largely temporally consistent, whereas that of genera is not., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Scuticociliates and hymenostomes are two groups of the ciliate class Oligohymenophorea, a diverse clade that includes two model genera, Tetrahymena and Paramecium, which have been intensively studied due to their ease of culture and their amenability to a wide range of biochemical and genetic investigations. However, phylogenetic relationships among the subclasses of the Oligohymenophorea, and especially between the Scuticociliatia and Hymenostomatia, are not clearly resolved. Here, we investigate the phylogenetic relationship between the subclasses Scuticociliatia and Hymenostomatia based on omics data. The transcriptomes of five species, comprising four oligohymenophoreans and one colpodean, were sequenced. A supermatrix was constructed for phylogenomic analyses based on 113 genes encoding 43,528 amino acid residues from 26 taxa, including ten representatives of the class Oligohymenophorea. Our phylogenomic analyses revealed that the monophyletic Scuticociliatia is sister to the monophyletic Hymenostomatia, which together form the terminal branch within the monophyletic class Oligohymenophorea. Competing hypotheses for this relationship were rejected by topological tests. Our results provide corroborative evidence for the close relationship between the subclasses Scuticociliatia and Hymenostomatia, justifying the possible use of the model hymenostome T. thermophila as an effective experimental system to study the molecular and cellular biology of the scuticociliates., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Termites (Isoptera) offer an alternative model for the development of eusociality which is not dependent on a high degree of relatedness as found between sisters in hymenopterans (bees, wasps, ants). Recent phylogenetic studies have established that termites belong within the cockroaches as sister to the subsocial Cryptocercidae. Cryptocercidae shares several important traits with termites, thus we need to understand the phylogenetic position of Cryptocercidae+Isoptera to determine how these traits evolved. However, placement of Cryptocercidae+Isoptera is still uncertain. We used both molecular (12S, 16S, COII, 18S, 28S, H3) and morphological characters to reconstruct the phylogeny of Dictyoptera. We included all previously suggested sister groups of Cryptocercidae+Isoptera as well as taxa which might represent additional major cockroach lineages. We used Bayes factors to test different sister groups for Cryptocercidae+Isoptera and assessed character support for the consensus tree based on morphological characters and COII amino acid data. We used the molecular data and fossil calibration to estimate divergence times. We found the most likely sister groups of Cryptocercidae+Isoptera to be Tryonicidae, Anaplecta or Tryonicidae+Anaplecta. Anaplecta has never previously been suggested as sister group or even close to Cryptocercidae+Isoptera, but was formerly placed in Blaberoidea as sister to the remaining taxa. Topological tests firmly supported our new placement of Anaplecta. We discuss the morphological characters (e.g. retractable genitalic hook) that have contributed to the previous placement of Anaplecta in Blaberoidea as well as the factors that might have contributed to a parallel development of genitalic features in Anaplecta and Blaberoidea. Cryptocercidae+Isoptera is placed in a clade with Tryonicidae, Anaplecta and possibly Lamproblattidae. Based on this, we suggest that wood-feeding, and the resultant need to conserve nitrogen, may have been an important factor in the development of termite eusociality. Nocticolidae was placed as sister group to Latindia+Paralatindia (both Corydiidae), this clade was in turn placed as sister group to the remaining Corydiidae. The Nocticolidae+Corydiidae clade is supported by both morphological and COII amino acid changes. Our divergence time estimates placed the split between Mantodea and Blattodea at 273mya (middle Permian) and the splits between the major blattodean lineages no later than 200mya (end of Triassic)., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Knowledge concerning the diversity of parasitism and its reach across our current understanding of the tree of life has benefitted considerably from novel molecular phylogenetic methods. However, the timing of events and the resolution of the nature of the intimate relationships between parasites and their hosts in deep time remain problematic. Despite its vagaries, the fossil record provides the only direct evidence of parasites and parasitism in the fossil record of extant and extinct lineages. Here, we demonstrate the potential of the fossil record and other lines of geological evidence to calibrate the origin and evolution of parasitism by combining different kinds of dating evidence with novel molecular clock methodologies. Other novel methods promise to provide additional evidence for the presence or the life habit of pathogens and their vectors, including the discovery and analysis of ancient DNA and other biomolecules, as well as computed tomographic methods., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Numerous crustacean lineages have independently moved into parasitism as a mode of life. In modern marine ecosystems, parasitic crustaceans use representatives from many metazoan phyla as hosts. Crustaceans also serve as hosts to a rich diversity of parasites, including other crustaceans. Here, we show that the fossil record of such parasitic interactions is sparse, with only 11 examples, one dating back to the Cambrian. This may be due to the limited preservation potential and small size of parasites, as well as to problems with ascribing traces to parasitism with certainty, and to a lack of targeted research. Although the confirmed stratigraphic ranges are limited for nearly every example, evidence of parasitism related to crustaceans has become increasingly more complete for isopod-induced swellings in decapods so that quantitative analyses can be carried out. Little attention has yet been paid to the origin of parasitism in deep time, but insight can be generated by integrating data on fossils with molecular studies on modern parasites. In addition, there are other traces left by parasites that could fossilize, but have not yet been recognized in the fossil record., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

The backbone phylogeny of Lepidoptera remains unresolved, despite strenuous recent morphological and molecular efforts. Molecular studies have focused on nuclear protein coding genes, sometimes adding a single mitochondrial gene. Recent advances in sequencing technology have, however, made acquisition of entire mitochondrial genomes both practical and economically viable. Prior phylogenetic studies utilised just eight of 43 currently recognised lepidopteran superfamilies. Here, we add 23 full and six partial mitochondrial genomes (comprising 22 superfamilies of which 16 are newly represented) to those publically available for a total of 24 superfamilies and ask whether such a sample can resolve deeper lepidopteran phylogeny. Using recoded datasets we obtain topologies that are highly congruent with prior nuclear and/or morphological studies. Our study shows support for an expanded Obtectomera including Gelechioidea, Thyridoidea, plume moths (Alucitoidea and Pterophoroidea; possibly along with Epermenioidea), Papilionoidea, Pyraloidea, Mimallonoidea and Macroheterocera. Regarding other controversially positioned higher taxa, Doidae is supported within the new concept of Drepanoidea and Mimallonidae sister to (or part of) Macroheterocera, while among Nymphalidae butterflies, Danainae and not Libytheinae are sister to the remainder of the family. At the deepest level, we suggest that a tRNA rearrangement occurred at a node between Adeloidea and Ditrysia+Palaephatidae+Tischeriidae., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Novel flaviviruses that are genetically related to pathogenic mosquito-borne flaviviruses (MBFV) have been isolated from mosquitoes in various geographical locations, including Finland. We isolated and characterized another novel virus of this group from Finnish mosquitoes collected in 2007, designated as Ilomantsi virus (ILOV). Unlike the MBFV that infect both vertebrates and mosquitoes, the MBFV-related viruses appear to be specific to mosquitoes similar to the insect-specific flaviviruses (ISFs). In this overview of MBFV-related viruses we conclude that they differ from the ISFs genetically and antigenically. Phylogenetic analyses separated the MBFV-related viruses isolated in Africa, the Middle East and South America from those isolated in Europe and Asia. Serological cross-reactions of MBFV-related viruses with other flaviviruses and their potential for vector-borne transmission require further characterization. The divergent MBFV-related viruses are probably significantly under sampled to date and provide new information on the variety, properties and evolution of vector-borne flaviviruses., (Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.)

The weevils and their relatives (superfamily Curculionoidea) constitute a huge radiation of beetles, but basal relationships in this group remain controversial, in particular within the largest family, Curculionidae. We used next-generation sequencing to generate mitochondrial genome data comprising 12 protein coding genes for 27 taxa. Together with two published ingroup sequences, (sub)family relationships were assessed with Bayesian and ML searches under various models and partitioning schemes. Forward and reverse strands of the mitochondrial genome differed in nucleotide skew. Consequently synonymous codon usage differed substantially on either strand for each amino acid, whereby codons ending in AT and GC were favored on the forward and reverse strands, respectively. Data partitioning by forward/reverse strand and codon position greatly improved likelihood scores and nodal support, whereas the tree topology was largely stable. The analysis generally supports the basal position of several 'orthocerus' lineages with straight antennae and male genitalia of an ancestral type; a paraphyletic mixed group of Heteromorphi exhibiting mixed ancestral and derived antennal and genitalic characters; and the derived 'gonathocerous' lineages with kinked antennae corresponding to the strongly supported Curculionidae. The latter did not include the wood boring Platypodinae that was recovered as sister to Dryophthoridae, while the Scolytinae and Cossoninae formed two independent lineages of wood borers within Curculionidae. A basal split in Curculionidae placed the Entiminae and Hyperinae as sister to all other subfamilies with high support, which provides a new ecological concept for structuring the Curculionidae according to the ectophagous larval life style in the former versus endophagous larvae in all others. This basal split is also supported by gene order rearrangements in a tRNA cluster. Recent studies supporting the monophyly of wood boring weevils may be attributable to long-branch attraction, as molecular rates in their mitochondrial genomes were found to be higher than in other lineages, but this did not confound tree searches under combined analysis of mitochondrial protein coding genes., (Copyright © 2013 Elsevier Inc. All rights reserved.)