The discovery of Neotropical Lepidosira (Collembola,Entomobryidae) and its systematic position

We herein present the first reliable record of Lepidosira from Neotropical Region. Lepidosira neotropicalis sp. n. from Brazil is described and illustrated in detail, including its complete mitochondrial genome. We perform a Bayesian phylogenetic analysis to place the new species within the Entomobryidae, and at the same time to test previous contrasting hypotheses on Lepidosira position within the Entomobryinae versus Seirinae for the first time. Phylogenetic analyses were based on one mitochondrial and two nuclear genes, Cytochrome Oxidase subunit I, 18S ribosomal RNA and 28S ribosomal RNA, respectively. Lepidosira neotropicalis sp. n. resembles L. sundana Yoshii and Suhardjono and L. nigropunctata (Nguyen) in dorsal chaetotaxy of abdominal segments I and II, but differs from all other species by the combination of head (dorsally and ventrally) and dorsal trunk chaetotaxy, plus empodial complex morphology. Our phylogenetic analyses support the placement of Lepidosira within Entomobryinae, as the sister group of Lepidocyrtoides. Overall, our revision enables a more objective diagnosis to Lepidosira and suggests that the genus is in need of a full revision due to its variable morphology, and lack of data needed to evaluate its monophyly. Finally, we provide an identification key for Neotropical genera of Entomobryinae.     

Phylogeny of Veneridae (Bivalvia) based on mitochondrial genomes

Veneridae is one of the most diverse families of bivalve molluscs. However, their phylogenetic relationships among subfamilies have been debated for years. To explore phylogenetic relationships of Veneridae, we sequenced 13 complete mitochondrial genome sequences from eight subfamilies and compared with available complete mitochondrial genome of other Veneridae taxa (18 previously reported sequences). Phylogenetic analyses using probabilistic methods recovered two highly supported clades. In addition, the protein‐coding gene order revealed a highly conserved pattern among the same subclade lineages. According to our molecular analyses, Tapetinae should be recognized as a valid subfamily, but the genera formed para‐polyphyletic clades. Chioninae was recovered not monophyletic that differs from a previously molecular phylogeny. Furthermore, the reconstructed chronogram calibrated with fossils recovered the Veneridae have originated during the early Permian (about 290 million years ago). Noticeably, programmed frameshift was found in the nad4 gene of Leukoma jedoensis, Anomalodiscus squamosus and Antigona lamellaris and cob gene of L. jedoensis. This is the first time that the presence of the programmed frameshift has been found in the protein‐coding genes of Heterodonta species. Our results improved the phylogenetic resolution within Veneridae, and a more taxonomic sampling analysis of the subfamily Chioninae is supposed to construct.     

Avian mitochondrial genomes retrieved from museum eggshell

Avian eggshell is a bio‐ceramic material with exceptional properties for preserving DNA within its crystalline structure, presenting an opportunity to retrieve genomic information from extinct or historical populations of birds. However, intracrystalline DNA has only been recovered from the large, thick eggshell of palaeognaths; members of their more‐diverse sister group (neognaths) lay smaller, thinner eggs that may not exhibit the same propensity for DNA preservation. Here, we use three 40–60‐year‐old museum eggshell specimens of Australian neognath birds to determine the minimum mass of eggshell from which intracrystalline DNA can be retrieved, and to characterize the yield and quality of such DNA. In doing so, we describe the first protocol for successful extraction of intracrystalline DNA from neognath eggshells, with the view to unlocking the potential of vast museum egg collections for genetic research. We were able to retrieve DNA fragments over 200 bp in length from 10 mg of eggshell powder from all three specimens, and demonstrate that expanding the existing blow‐hole can allow sufficient material to be collected for DNA extraction while minimizing damage to the appearance and structural integrity of the egg. Furthermore, we were able to reconstruct near‐complete mitochondrial genomes at a coverage of 40‐83X through shotgun sequencing of these extracts on three NextSeq lanes. Given the current extinction and extirpation rates of many avian species world‐wide, genetic data from eggshell could provide a rapid and cost‐effective approach to examining temporal changes in avian diversity, which is not only becoming crucial for conservation management, but also serve to deepen our understanding of genome‐wide evolutionary processes.     

Phylogeny of African fruit bats (Chiroptera,Pteropodidae) based on complete mitochondrial genomes

Members of the family Pteropodidae, also known as Old World fruit bats, are represented in Africa by 14 genera and 44 species. Here, we sequenced 67 complete mitochondrial genomes from African and Asian pteropodids to better understand the evolutionary history of the subfamily Rousettinae, which includes most of the African species. An increased frequency of guanine to adenine transitions is detected in the mtDNA genomes of Macroglossus sobrinus and all species of Casinycteris and Scotonycteris. Our phylogenetic and molecular dating analyses based on 126 taxa and 15,448 characters indicate a low signal for deep relationships within the family, suggesting a rapid diversification during the Late Oligocene period of “warming.” Within the subfamily Rousettinae, most nodes are highly supported by our different analyses (all nucleotide sites, SuperTRI analyses of a sliding window, transversions only, coding genes only, and amino acid sequences). The results indicate the existence of four tribes: Rousettini—distributed from Africa through Mediterranean region and South Asia to South-East Asia; Eonycterini—found in Asia; and Epomophorini and Scotonycterini—restricted to sub-Saharan Africa. Although most interspecies relationships are highly supported, three parts of the Rousettinae mitochondrial tree are still unresolved, suggesting rapid diversification: (a) among the three subtribes Epomophorina (Epomophorus sensu lato, i.e., including Micropteropus, Epomops, Hypsignathus, Nanonycteris), Plerotina (Plerotes), and Myonycterina (Myonycteris, Megaloglossus) in the Late Miocene; (b) among Epomops, Hypsignathus, and other species of Epomophorina at the Pliocene–Pleistocene boundary; and (c) among Myonycteris species in the Early Pleistocene. Within the Epomophorini, Stenonycteris lanosus emerged first, suggesting that lingual echolocation may have appeared in the common ancestor of Epomophorini and Rousettini. Our analyses suggest that multiple events of mtDNA introgression occurred within the Epomophorus species complex during the Pleistocene.     

Phylogeny and species diversity of the genus Herichthys (Teleostei: Cichlidae)

We provide a review of the systematics of Herichthys by evaluating the usefulness of several mitochondrial and nuclear genetic markers together with morphological data. The nDNA next‐generation sequencing ddRAD analysis together with the mtDNA cytochrome b gene provided well‐resolved and well‐supported phylogenies of Herichthys. On the other hand, the nDNA S7 introns have limited resolution and support and the COI barcoding analysis completely failed to recover all but one species of Herichthys as monophyletic. The COI barcoding as currently implemented is thus insufficient to distinguish clearly distinct species in the genus Herichthys that are supported by other molecular markers and by morphological characters. Based on our results, Herichthys is composed of 11 species and includes two main clades (the H. labridens and H. cyanoguttatus species groups). Herichthys bartoni is in many respects the most plesiomorphic species in the genus and has a conflicting phylogenetic position between mtDNA and nDNA markers, where the robust nDNA ddRAD data place it as a rather distant basal member of the H. labridens species group. The mtDNA of H. bartoni is on the other hand only slightly divergent from the sympatric and syntopic H. labridens, and the species thus probably have hybridized in the relatively recent past. The sympatric and syntopic Herichthys steindachneri and H. pame are supported as sister species. The Herichthys cyanoguttatus species group shows two well‐separated basal species (the northernmost H. minckleyi and the southernmost H. deppii) followed by the closely related and centrally distributed species H. cyanoguttatus, H. tepehua, H. carpintis, and H. tamasopoensis whose relationships differ between analyses and show likely hybridizations between themselves and the two basal species as suggested by conflicts between DNA analyses. Several instances of introgressions/hybridizations have also been found between the two main clades of Herichthys.     

Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

There has been much recent interest and progress in the characterization of community structure and community assembly processes through the application of phylogenetic methods. To date most focus has been on groups of taxa for which some relevant detail of their ecology is known, for which community composition is reasonably easily quantified and where the temporal scale is such that speciation is not likely to feature. Here, we explore how we might apply a molecular genetic approach to investigate community structure and assembly at broad taxonomic and geographical scales, where we have little knowledge of species ecology, where community composition is not easily quantified, and where speciation is likely to be of some importance. We explore these ideas using the class Collembola as a focal group. Gathering molecular evidence for cryptic diversity suggests that the ubiquity of many species of Collembola across the landscape may belie greater community complexity than would otherwise be assumed. However, this morphologically cryptic species-level diversity poses a challenge for attempts to characterize diversity both within and among local species assemblages. Recent developments in high throughput parallel sequencing technology, combined with mtDNA barcoding, provide an advance that can bring together the fields of phylogenetic and phylogeographic analysis to bear on this problem. Such an approach could be standardized for analyses at any geographical scale for a range of taxonomic groups to quantify the formation and composition of species assemblages.     

Phylogeny of Neotropical Lepidocyrtus (Collembola: Entomobryidae): first assessment of patterns of speciation in Puerto Rico and phylogenetic relevance of some subgeneric diagnostic characters

A phylogenetic analysis of the Neotropical members of genus Lepidocyrtus was conducted to assess the pattern of speciation in Puerto Rico while testing the phylogenetic information content of two characters used to diagnose subgenera. The analysis included twenty‐two species of Lepidocyrtus from the Neotropical Region for which information on the tergal chaetotaxy of the trunk was available, two species of Holarctic Lepidocyrtus, three species of Pseudosinella, two species of Metasinella used in outgroup analysis and ninety‐two informative characters. The results do not support a monophyletic origin for the Puerto Rican Lepidocyrtus, suggesting the current fauna originated through repeated invasions from abroad. Three instances of endemic speciation can be inferred from the cladograms. The geographical distribution and diversity of colour forms suggest that L. caprilesi and L. paracaprilesi speciated sympatrically, whereas vicariance can explain speciation for L. lepargus and L. maldonadoi. The mode of speciation for L. dispar and L. biphasis remains unclear because the proportion of morphological variation between these species does not fit the proportions expected under the sympatric model suggested by their geographical distribution. The results support an early conclusion regarding appendicular scale distribution as a poor indicator of phylogenetic relationships. Taxa defined using this character are likely to be polyphyletic. The results disagree with a previous study in documenting low levels of homoplasy for the dental tubercle, implying that this character contains phylogenetic information useful in defining subgenera. However, the presence or absence of a dental tubercle is not diagnostic and should be used in combination with other characters. Comparisons of levels of homoplasy in Neotropical and Hawaiian Lepidocyrtus suggest that the relative position of two setae on the second abdominal tergum may be a better subgeneric character than other characters currently in use.     

Analysis of ancient human genomes

High‐capacity sequencing technologies have dramatically reduced both the cost and time required to generate complete human genome sequences. Besides expanding our knowledge about existing diversity, the nature of these technologies makes it possible to extend knowledge in yet another dimension: time. Recently, the complete genome sequence of a 4,000‐year‐old human from the Saqqaq culture of Greenland was determined to 20‐fold coverage. These data make it possible to investigate the population affinities of this enigmatic culture and, by identifying several phenotypic traits of this individual, provide a limited glimpse into how these people may have looked. While undoubtedly a milestone in ancient DNA research, the cost to generate an ancient genome, even from such an exceptionally preserved specimen, remains out of reach for most. Nonetheless, recently developed DNA capture methods, already applied to Neanderthal and fossil human mitochondrial DNA, may soon make large‐scale genome‐wide analysis of ancient human diversity a reality, providing a fresh look at human population history.     

Phylogeny and evolution of Cervidae based on complete mitochondrial genomes

Mitochondrial DNA sequences can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We made phylogenetic analyses of 19 species of Cervidae, with Bos taurus as the outgroup. We used neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods on whole mitochondrial genome sequences. The consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Plesiometacarpalia and Telemetacarpalia, and four tribes, Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. The divergence times in these families were estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock method; the results were consistent with those of previous studies. We concluded that the evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; this method could be used broadly in phylogenetic evolutionary analysis of animal taxa.     

Australian species of Sinella (Sinella) Brook (Collembola: Entomobryidae)

Abstract  The Australian subgenus Sinella ( Sinella ) Brook is revised. Two species are recognised. A new species from New South Wales and South Australia, Sinella ( Sinella ) samueli , is described and the widely distributed species Sinella ( Sinella ) termitum Schött is redescribed based on examination of a specimen from the type series and fresh collections from a wide range of localities in south-eastern Australia. New patterns of chaetotaxy for the genus are described from these species.     

Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1

We determined the complete nucleotide sequence of the mitochondrial (mt) genome of five individual caecilians (Amphibia: Gymnophiona) representing five of the six recognized families: Rhinatrema bivittatum (Rhinatrematidae), Ichthyophis glutinosus (Ichthyophiidae), Uraeotyphlus cf. oxyurus (Uraeotyphlidae), Scolecomorphus vittatus (Scolecomorphidae), and Gegeneophis ramaswamii (Caeciliidae). The organization and size of these newly determined mitogenomes are similar to those previously reported for the caecilian Typhlonectes natans (Typhlonectidae), and for other vertebrates. Nucleotide sequences of the nuclear RAG1 gene were also determined for these six species of caecilians, and the salamander Mertensiella luschani atifi. RAG1 (both at the amino acid and nucleotide level) shows slower rates of evolution than almost all mt protein-coding genes (at the amino acid level). The new mt and nuclear sequences were compared with data for other amphibians and subjected to separate and combined phylogenetic analyses (Maximum Parsimony, Minimum Evolution, Maximum Likelihood, and Bayesian Inference). All analyses strongly support the monophyly of the three amphibian Orders. The Batrachia hypothesis (Gymnophiona, (Anura, Caudata) receives moderate or good support depending on the method of analysis. Within Gymnophiona, the optimal tree (Rhinatrema, (Ichthyophis, Uraeotyphlus), (Scolecomorphus, (Gegeneophis Typhlonectes) agrees with the most recent morphological and molecular studies. The sister group relationship between Rhinatrematidae and all other caecilians, that between Ichthyophiidae and Uraeotyphlidae, and the monophyly of the higher caecilians Scolecomorphidae+Caeciliidae+Typhlonectidae, are strongly supported, whereas the relationships among the higher caecilians are less unambiguously resolved. Analysis of RAG1 is affected by a spurious local rooting problem and associated low support that is ameliorated when outgroups are excluded. Comparisons of trees using the non-parametric Templeton, Kishino-Hasegawa, Approximately Unbiased, and Shimodaira-Hasegawa tests suggest that the latter may be too conservative.     

Description of a new Homidia species (Collembola,Entomobryidae) from Korea

A new species, Homidia pseudoformosana from Korea is described in the present paper. The new species is characterized by labral papillae, ciliated labial seta L₁ and dorsal chaetotaxy of abdominal segment IV. The detailed differences between similar Homidia species are provided.     

Phylogeny and comparative genomic analysis of Pteriomorphia (Mollusca: Bivalvia) based on complete mitochondrial genomes

The subclass Pteriomorphia is a morphologically diverse and economically important group of Mollusca. We retrieved 42 mitochondrial genomes (mtGenomes) of Pteriomorphia and concatenated protein-coding genes, rRNAs and tRNAs to assess phylogenetic relationships and divergence times among the families with maximum likelihood (ML) and Bayesian inference (BI) analyses. Both ML and BI analyses strongly support the same topology except for the position of Atrina pectinata. Our study confirms the monophyly of the families Arcidae, Mytilidae, Pteriidae, Ostreidae and Pectinidae. Within Pteriomorphia, we recovered two clusters, one comprising Mytilidae, Arcidae and Pectinidae, the other consisting of Ostreidae, Pteriidae and Pinnidae, but we did not confirm a basal position for any family. The phylogenetic trees suggest that Ostreidae, Pteriidae and Pinnidae should be grouped as the order Ostreoida. Divergence times of major families are estimated as follows: Arcidae, 315.9 Ma; Pectinidae, 384.4 Ma; Ostreidae, 240.8 Ma; Mytilidae, 390.8 Ma. Comparative analysis indicates a low-level codon usage bias (with an average of 50.29) in mtGenomes of Pteriomorphia. In Mytilidae and Ostreidae, the codon usage bias was under mutation pressure rather than selection. Contrastingly, mutation is not the main factor in defining the codon usage in Pectinidae and Pteriidae. Among Ostreidae, Pectinidae and Mytilidae, Ka/Ks ratios range from 0.00 to 1.22 and most values (89.11%) are less than 0.20, indicating that most genes are under strong negative or purifying selection. The protein-coding gene orders show dramatically different patterns in Pteriomorphia. There is no gene block even consisting of two genes that is shared by five families.     

Report of Akabosia matsudoensis Kinoshita (Collembola; Paronellidae) from Korea,with notes on the Korean aquatic springtail fauna

A hygrophilous collembolan species, Akabosia matsudoensis is redescribed and illustrated with a list and key to other aquatic fauna belonging to Entomobryoidea from Korea. Specimens inhabiting the damp area near a creek were collected with hand net and aspirator. This species is characterized by the absence of scale, having 2 + 2 macrosetae on the vertex of the head, 2 feathered prelabial setae, dens crenulated and the base of mucro with bladder like appendage. Genus Akabosia reported only one species, A. matsudoensis, that was originally recorded in Japan; Korea is the second recorded country and it is the only Paronellidae from Korea.     

Distribution pattern and radiation of the European subterranean genus Verhoeffiella (Collembola,Entomobryidae)

One of the most striking features of obligate subterranean species is their narrow distribution ranges. These prevail not only at specific, but often also at generic level. However, some subterranean genera have continental scale and disjunct distribution, which challenges their monophyly and questions the scenarios of their origin and colonization. In our study, we investigated the subterranean collembolan genus Verhoeffiella, currently known from five remote karst regions of Europe. Four nuclear and one mitochondrial genes were assembled to reveal the evolutionary history of the genus. We tested the monophyly of the genus, explored its relationship with putative surface relatives, and its temporal patterns of molecular diversification. The phylogeny revealed a complex relationship of Verhoeffiella with surface species Heteromurus nitidus and partially disentangled the biogeographical question of its disjunct distribution. Further on, several lineages of Verhoeffiella were recognized in the Dinarides, showing highly underestimated diversity and, compared with the number of described species, a sevenfold increase in the number of MOTUs. The radiation is relatively recent, with the events triggering the diversification linked to the Messinian salinity crisis and Pleistocene climatic shifts. The combination of this extensive subterranean radiation and close evolutionary links with epigean relatives makes Verhoeffiella an exceptional case within the subterranean fauna of temperate areas, which significantly contributes to our understanding of subterranean colonization and diversification patterns.     

浙江省洞头拟裸长角虫兆属一新种（长角虫兆科：弹尾纲）

记述浙江省洞头岛拟祼长角虫兆属1无眼新种,岛屿拟裸长角虫兆Coecobrya islandica Shi&Pan sp.nov.。此新种的鉴定特征为无眼,弹器基具"光滑"刚毛,胫胕节内侧无"光滑"刚毛,下唇MREL1L2为光滑刚毛,X和X4为光滑刺状小刚毛,上唇基刚毛,腹部第II–IV节的感觉毛以及背部毛序。该新种与短毛拟裸长角虫兆Coecobrya brevis Xu et al.,2012最相似。本文给出了该新种的特征图及与相似种的详细特征比较。模式标本保存于台州学院生命科学学院和南京农业大学植保学院昆虫系。