Family-level Relationships Research Articles

Investigating the causal link between gut microbiota and dry age-related macular degeneration: a bidirectional Mendelian randomization study.

To assess the causal link between 211 gut microbiota (GM) taxa and dry age-related macular degeneration (dAMD) risk. Mendelian randomization using instrumental factors taken from a genome-wide association study (GWAS) were used. Inverse variance weighted (IVW) analysis and sensitivity analysis were performed on the FinnGen project, which included 5095 cases and 222 590 controls. The IVW analysis showed substantial genus- and family-level relationships between GM taxa and dAMD risk. Specifically, the family Peptococcaceae (P=0.03), genus Bilophila (P=3.91×10-3), genus Faecalibacterium (P=6.55×10-3), and genus Roseburia (P=0.04) were linked to a higher risk of developing dAMD, while the genus Candidatus Soleaferrea (P=7.75×10-4), genus Desulfovibrio (P=0.04) and genus Eubacterium ventriosum group (P=0.04) exhibited a protective effect against dAMD. No significant causal relationships were observed at higher taxonomic levels. Additionally, in the reverse IVW analysis, no meaningful causal effects of the 7 GM taxa. These findings give support for the gut-retina axis participation in dAMD and shed light on putative underlying processes. Investigations on the connection between GM and dAMD have not yet revealed the underlying mechanism.

Genome-scale approach to reconstructing the phylogenetic tree of psyllids (superfamily Psylloidea) with account of systematic bias

Psyllids (class Insecta: order Hemiptera: superfamily Psylloidea) are a taxonomically and phylogenetically challenging clade. Recent studies have largely advanced the phylogeny of this group, yet the family-level relationships among Aphalaridae, Carsidaridae, and others remain unresolved. Genome-scale phylogenetic analysis is known to provide a finer resolution for problems like that. However, such phylogenomics also introduces new problems: incorrect trees with high confidence yielded due to systematic error (bias). Here we addressed these issues using hundreds of single-copy orthologous (SCO) genes in psyllid transcriptomes and genomes. Our analyses revealed conflicts between the nucleotide-based and amino-acid-based phylogenetic trees. While the nucleotide-based phylogeny strongly supported the (Aphalaridae + Carsidaridae) + Others relationship, the amino-acid-based one recovered Aphalaridae + (Carsidaridae + Others) with 100% support. Further inspection revealed significant compositional heterogeneity in nucleotide sequences for 67% of SCO genes, but not in the corresponding translated amino acid sequences. We then used different strategies to combat this compositional bias, and found that using the RY-coding strategy (coding the standard nucleotides as purines and pyrimidines) the nucleotide-based phylogeny became consistent with the amino-acid-based one. We further applied RY-coding to a published concatenated nucleotide dataset and recovered the Aphalaridae monophyly (which is refuted by the original literature on non-recoded sequences) at the base of psyllid tree. Moreover, it was found that variations in evolutionary rate could lead to errors in nucleotide-based phylogeny. The fast-evolving Heteropsylla cubana (Psyllidae: Ciriacreminae) was incorrectly placed within the subfamily Psyllinae. This bias can be avoided by using data removal or RY-coding strategies. Together, our results strongly support the family relationship of Aphalaridae + (Carsidaridae + Others), and show that the amino-acid-based concatenation analysis is more robust than nucleotide-based one. Future phylogenomic analysis of psyllid nucleotide sequences should take into account methods such as the RY-coding scheme to address potential systematic biases arising from composition and rate heterogeneities.

Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes.

The Charadriiformes provide a good source for researching evolution owing to their diverse distribution, behavior, morphology, and ecology. However, in the Charadrii, family-level relationships remain understudied, and the monophyly of Charadriidae is also a subject of controversy. In the present study, we generated complete mitogenomes for two species, Charadrius leschenaultii and Charadrius mongolus, which were found to be 16,905 bp and 16,844 bp in length, respectively. Among the 13 protein codon genes, we observed variation in the rate of non-synonymous substitution rates, with the slowest rate found in COI and the fastest rate observed in ATP8. The Ka/Ks ratio for all Charadriidae species was significantly lower than one, which inferred that the protein-coding genes underwent purifying selection. Phylogenetic analysis based on the genes of Cyt b, 12S and ND2 revealed that the genus Pluvialis is the sister group of three families (Haematopodidae, Ibidorhynchidae, Recurvirostridae). However, the phylogenetic analysis based on complete mitogenomes indicated that the genus Pluvialis is within the Charadriidae family. This study highlights the importance of carefully selecting the number of genes used to obtain accurate estimates of the species tree. It also suggests that relying on partial mtDNA genes with fast-evolving rates may lead to misleading results when resolving the Pluvialis sister group. Future research should focus on sequencing more mitogenomes at different taxonomic levels to gain a better understanding of the features and phylogenetic relationships within the Charadriiformes order.

Towards a systematic revision of the superfamily Cyrenoidea (Bivalvia: Imparidentia): species delimitation, multi-locus phylogeny and mitochondrial phylogenomics

Cyrenoidea is a superfamily of bivalves (Bivalvia: Imparidentia) currently comprising three families (Cyrenidae, Cyrenoididae and Glauconomidae). The superfamily is widely distributed in marine, brackish and freshwater environments, with an estimated 60 or more living species. Recent phylogenetic results have confirmed the monophyly of Cyrenoidea and placement in Venerida. Nevertheless, a comprehensive phylogenetic analysis of Cyrenoidea remains elusive and the phylogeny is unresolved due to inadequate sampling in previous studies. Moreover, the taxonomy and delimitation of most species, originally based on shell morphology, have not yet been tested with molecular data. Here, we constructed three molecular datasets by sequencing three markers (<i>COI</i>+<i>16S</i> rRNA+<i>28S</i> rRNA) and complete mitogenomes for <i>Geloina coaxans</i> (Gmelin, 1791) and <i>Glauconome virens</i> (Linnaeus, 1767). <i>COI</i> barcoding clarifies the validity of <i>Geloina coaxans</i> and <i>Geloina erosa</i> that have been subject to controversy regarding synonymy. Additionally, the barcoding supports the existence of multiple cryptic species within the <i>Geloina expansa</i> complex. A multi-locus dataset (<i>COI</i>+<i>16S</i> rRNA+<i>28S</i> rRNA) provides the most comprehensive phylogeny of all eight recognised genera of Cyrenoidea to date. Phylogenetic results indicate that the currently recognised family Cyrenidae is polyphyletic. The type species <i>Geloina coaxans</i>, <i>Cyanocyclas limosa</i> (Maton, 1811) and <i>Polymesoda caroliniana</i> (Bosc, 1801) that have long been classified within the family Cyrenidae based on shell morphology, have a closer relationship with <i>Cyrenoida floridana</i> Dall, 1896 than with other Cyrenidae. Therefore we transfer the genera <i>Geloina</i>, <i>Cyanocyclas</i> and <i>Polymesoda</i> from the family Cyrenidae to the family Cyrenoididae. The mitochondrial phylogenomics further support the family-level relationships in Cyrenoidea obtained from the three-gene analyses, confirming that the newly defined Cyrenoididae is closely related to Glauconomidae as the sister group. We observed a novel gene arrangement in <i>Glauconome virens</i>, the first report on the mitogenome of the family Glauconomidae, by comparing gene arrangements. Three patterns of gene rearrangement identified in Cyrenoidea are shared by the families Glauconomidae, Cyrenoididae and Cyrenidae, suggesting that gene arrangements can be a valuable tool for phylogenetic studies.

Detecting Darwinian Shortfalls in the Amazonian Odonata.

Among the oldest winged insects, odonates are a monophyletic order that have become important models for ecological studies because of their highly diverse reproductive behaviors and their role as top predators and bioindicators. However, knowledge on evolutionary relationships within the order is still scarce compared to other taxa, and this situation is even more complicated in areas with high biodiversity, such as in the Amazon. Here, we sought to identify knowledge gaps on Amazonian Odonata regarding three main aspects: (i) how the inclusion of Amazonian taxa affects our interpretation of the evolutionary relationships of Zygoptera and Anisoptera; (ii) the position of Amazonian taxa in the existing supertree of the Odonata; (iii) dating evolutionary divergence between nodes using fossil records; (iv) assessing whether more species-rich basins (e.g., Amazon basin) have a larger phylogenetic gap when compared to basins with lower richness in South and Central America; and (v) in the light of our knowledge, we discuss diversification patterns found in the most predominant clades of Amazonian taxa. We built a supertree from currently available phylogenetic information of Odonata. The results show that there is no genetic information for 85% (n: 503) of the Amazonian species and that family level relationships are unknown for 17 genera. After compiling the data, we observed that clades belonging to Neotropical lineages are the most poorly resolved, with large polytomies. This problem was identified in many Anisoptera genera, such as Macrothemis, Dasythemis, Elasmothemis, and Erythrodiplax. Our results also suggest that not always the richest basins have the greatest phylogenetic gaps. As expected, we found important gaps in the existing Odonata phylogenies, especially in clades that include Amazonian representatives, that are also those less known from ecological and conservation perspectives.

Molecular phylogenetic analysis of the Paguristes tortugae Schmitt, 1933 complex and selected other Paguroidea (Crustacea: Decapoda: Anomura)

Morphological characters, as presently applied to describe members of the Paguristes tortugae Schmitt, 1933 species complex, appear to be of limited value in inferring phylogenetic relationships within the genus, and may have similarly misinformed understanding of relationships between members of this complex and those presently assigned to the related genera Areopaguristes Rahayu McLaughlin, 2010 and Pseudopaguristes McLaughlin, 2002. Previously undocumented observations of similarities and differences in color patterns among populations additionally suggest genetic divergences within some species, or alternatively seem to support phylogenetic groupings of some species. In the present study, a Maximum Likelihood (ML) phylogenetic analysis was undertaken based on the H3, 12S mtDNA, and 16S mtDNA sequences of 148 individuals, primarily representatives of paguroid species from the western Atlantic. This molecular analysis supported a polyphyletic Diogenidae Ortmann, 1892, although incomplete taxonomic sampling among the genera of Diogenidae limits the utility of this finding for resolving family level relationships. Several hypotheses regarding the evolutionary relationships among hermit crab genera were refuted by the Kishino-Hasegawa (KH). Shimodaira-Hasegawa (SH) and Approximately Unbiased (AU) tree topology tests, among them the hypothesis that Areopaguristes is monophyletic. A lack of support for the monophyly of Areopaguristes calls into question the phylogenetic validity of gill number for the differentiation of Paguristes, Areopaguristes, and Pseudopaguristes. The study was inconclusive with regard to the relationships among these three genera, but previously unknown diversity within both Paguristes and Areopaguristes was demonstrated. Existence of an undescribed species confounded under the name Paguristes tortugae Schmitt, 1933 was supported by genetics, morphology, and coloration. A second undescribed species with remarkable similarity to Areopaguristes hummi Wass, 1955 was discovered based on genetics and coloration.

Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes.

Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies. Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees. We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order's classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.

Comparative mitochondrial genome analysis of Eudocima salaminia (Cramer, 1777) (Lepidoptera: Noctuoidea), novel gene rearrangement and phylogenetic relationship within the superfamily Noctuoidea.

The species Eudocima salaminia (Cramer, 1777) commonly known as the fruit-piercing moth belongs to family Erebidae. Its distribution varies from India and across South-east Asia, pacific islands and parts of Australia. The insect is a devastating pest of citrus, longans and lychees. In the present study, complete mitochondrial genome of Eudocima salaminia was sequenced and analyzed using Illumina sequencer. The phylogenetic tree was reconstructed based on nucleotide sequences of 13 PCGs using Maximum likelihood method-General Reversible mitochondrial (mtREV) model. The mitogenome has 15,597 base pairs (bp) in length, comprising of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and A + T-rich region. All protein-coding genes (PCGs) initiate with canonical start codon ATN. The gene order (trnQ-trnI-trnM) of tRNA shows a different rearrangement compared to ancestral insect gene order (trnI-trnQ-trnM). Almost all tRNAs have a typical cloverleaf secondary structure except for trnS1 (AGN) which lacks the dihydrouridine arm. At the beginning of the control region, we observed a conserved polyT", motif "ATTTA" and microsatellite (TA)n element. There are 21 intergenic regions and five overlapping regions ranging from 1 to 73bp and 1 to 8bp, respectively. The phylogenetic relationships based on nucleotide sequences of 13 PCGs using Maximum likelihood method showed the family level relationships as (Notodontidae + (Euteliidae + Noctuidae + (Erebidae + Nolidae))). The present study represents the similarity to phylogenetic analysis of Noctuoidea mitogenome. Moreover, the family Erebidae is the sister to the families of (Euteliidae + Noctuidae + Nolidae).

Two Complete Mitochondrial Genomes From Leuctridae (Plecoptera: Nemouroidea): Implications for the Phylogenetic Relationships Among Stoneflies.

The family-level relationships within Plecoptera have been a focused area of research for a long time. Its higher classification remains unstable, and the phylogenetic relationships within Plecoptera should be re-examined. Here, we sequenced and analyzed two complete mitochondrial genomes (mitogenomes) of Paraleuctra cercia and Perlomyia isobeae of the family Leuctridae. We reconstructed the phylogeny of Plecoptera based on 13 protein-coding genes (PCGs) from published stoneflies. Our results showed that the Bayesian inference and maximum-likelihood tree had similar topological structures except for the positions of two families, Peltoperlidae and Scopuridae. The Plecoptera is divided into two clades, the suborder Antarctoperlaria and the suborder Arctoperlaria. The two suborders subsequently formed two groups, Eusthenioidea and Gripopterygoidea, and Euholognatha and Systellognatha, which is consistent with the results of morphological studies. In addition, the Leuctridae is the earliest branch within the superfamily Nemouroidea. But the monophyly of Perloidea and Pteronarcyoidea are still not well supported.

Phylogenomic re-evaluation of Triaenonychoidea (Opiliones : Laniatores), and systematics of Triaenonychidae, including new families, genera and species

The Opiliones superfamily Triaenonychoidea currently includes two families, the monogeneric New Zealand–endemic Synthetonychiidae Forster, 1954 and Triaenonychidae Sørensen, 1886, a diverse family distributed mostly throughout the temperate Gondwanan terranes, with ~110 genera and ~500 species and subspecies currently described. Traditionally, Triaenonychidae has been divided into subfamilies diagnosed by very few morphological characters largely derived from the troublesome ‘Roewerian system’ of morphology, and classifications based on this system led to many complications. Recent research within Triaenonychoidea using morphology and traditional multilocus data has shown multiple deeply divergent lineages, non-monophyly of Triaenonychidae, and non-monophyly of subfamilies, necessitating a revision based on phylogenomic data. We used sequence capture of ultraconserved elements across 164 samples to create a 50% taxon occupancy matrix with 704 loci. Using phylogenomic and morphological examinations, we explored family-level relationships within Triaenonychoidea, including describing two new families: (1) Lomanellidae Mendes & Derkarabetian, fam. nov., consisting of Lomanella Pocock, 1903, and a newly described genus Abaddon Derkarabetian & Baker, gen. nov. with one species, A. despoliator Derkarabetian, sp. nov.; and (2) the elevation to family of Buemarinoidae Karaman, 2019, consisting of Buemarinoa Roewer, 1956, Fumontana Shear, 1977, Flavonuncia Lawrence, 1959, and a newly described genus Turonychus Derkarabetian, Prieto & Giribet, gen. nov., with one species, T. fadriquei Derkarabetian, Prieto & Giribet, sp. nov. With our dataset we also explored phylogenomic relationships within Triaenonychidae with an extensive taxon set including samples representing ~80% of the genus-level diversity. Based on our results we (1) discuss systematics of this family including the historical use of subfamilies, (2) reassess morphology in the context of our phylogeny, (3) hypothesise placement for all unsampled genera, (4) highlight lineages most in need of taxonomic revision, and (5) provide an updated species-level checklist. Aside from describing new taxa, our study provides the phylogenomic context necessary for future evolutionary and systematic research across this diverse lineage. ZooBank Registration: urn:lsid:zoobank.org:pub:81683834-98AB-43AA-B25A-C28C6A404F41

Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes).

Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large data sets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or incorrect parameter estimates when reconstructing phylogeny by using the gadiform fishes as a model clade. Gadiformes include some of the most economically important fishes in the world (e.g., Cods, Hakes, and Rattails). Despite many attempts, a robust higher-level phylogenetic framework was lacking due to limited character and taxonomic sampling, particularly from several species-poor families that have been recalcitrant to phylogenetic placement. We compiled the first phylogenomic data set, including 14,208 loci (n}{}>2.8 M bp) from 58 species representing all recognized gadiform families, to infer a time-calibrated phylogeny for the group. Data were generated with a gene-capture approach targeting coding DNA sequences from single-copy protein-coding genes. Species-tree and concatenated maximum-likelihood (ML) analyses resolved all family-level relationships within Gadiformes. While there were a few differences between topologies produced by the DNA and the amino acid data sets, most of the historically unresolved relationships among gadiform lineages were consistently well resolved with high support in our analyses regardless of the methodological and biological approaches used. However, at deeper levels, we observed inconsistency in branch support estimates between bootstrap and gene and site coefficient factors (gCF, sCF). Despite numerous short internodes, all relationships received unequivocal bootstrap support while gCF and sCF had very little support, reflecting hidden conflict across loci. Most of the gene-tree and species-tree discordance in our study is a result of short divergence times, and consequent lack of informative characters at deep levels, rather than incomplete lineage sorting. We use this phylogeny to establish a new higher-level classification of Gadiformes as a way of clarifying the evolutionary diversification of the order. We recognize 17 families in five suborders: Bregmacerotoidei, Gadoidei, Ranicipitoidei, Merluccioidei, and Macrouroidei (including two subclades). A time-calibrated analysis using 15 fossil taxa suggests that Gadiformes evolved n}{}sim 79.5 Ma in the late Cretaceous, but that most extant lineages diverged after the Cretaceous–Paleogene (K-Pg) mass extinction (66 Ma). Our results reiterate the importance of examining phylogenomic analyses for evidence of systematic error that can emerge as a result of unsuitable modeling of biological factors and/or methodological issues, even when data sets are large and yield high support for phylogenetic relationships. [Branch length heterogeneity; Codfishes; commercial fish species; Cretaceous-Paleogene (K-Pg); heterotachy; systematic error; target enrichment.]

Defying death: incorporating fossils into the phylogeny of the complex thalloid liverworts (Marchantiidae, Marchantiophyta) confirms high order clades but reveals discrepancies in family-level relationships.

In recent years, the use of extensive molecular and morphological datasets has clarified the phylogenetic relationships among the orders of complex thalloid liverworts (Marchantiidae). However, previous studies excluded extinct taxa; thereby, undersampling the actual taxonomic diversity of the group. Here, we conducted a total-evidence analysis of Marchantiidae incorporating fossils. The combined dataset consisted of 11 genes-sampled from the nuclear, mitochondrial and plastid genomes-and 128 morphological characters. Sixty-two species, representing all classes and orders within Marchantiophyta and genera within Marchantiidae were included in the analyses. Six fossils were scored from literature: two assigned to the outgroup (Metzgeriothallus sharonae and Pallaviciniites sandaolingensis) and four to the ingroup (Marchantites cyathodoides, M.huolinhensis, Ricciopsis ferganica and R.sandaolingensis). Tree searches were conducted using parsimony as the optimality criterion. Clade sensitivity was assessed across a wide range of weighting regimes. Also, we evaluated the influence of fossils on the inferred topologies and branch support. Our results were congruent with previously inferred clades above the order level: Neohodgsoniales was sister to a clade formed by Sphaerocarpales and Marchantiales. However, relationships among families within Marchantiales contradicted recent studies. For instance, a clade consisting of Monosoleniaceae, Wiesnerellaceae and Targioniaceae was sister to the morphologically simple taxa instead of being nested within them as in previous studies. Novel synapomorphies were found for several clades within Marchantiales. Outgroup fossils were more influential than Marchantiidae fossils on overall topologies and branch support values. Except for a single weighting scheme, sampling continuous characters and down-weighting characters improved fossil stability. Ultimately, our results challenge the widespread notion that bryophyte fossils are problematic for phylogenetic inference.

A new genus and species of sabretooth, Oriensmilus liupanensis (Barbourofelinae, Nimravidae, Carnivora), from the middle Miocene of China suggests barbourofelines are nimravids, not felids

Since the early 2000s, a revival of a felid relationship for barbourofeline sabretooths has become popular due to recent discoveries of fragmentary fossils from Africa. According to this view, barbourofelines trace their common ancestor with felids through shared similarities in dental morphology going back to the early Miocene of Africa and Europe. However, whether or not such an idea is represented in the basicranial morphology, a conservative area of high importance in family-level relationships, is yet to be tested. A nearly complete skull of Oriensmilus liupanensis gen. and sp. nov. from the middle Miocene Tongxin Basin of northern China represents the most primitive known barbourofeline with an intact basicranial region, affording an opportunity to re-examine the relationship of felids and nimravines. We also present an update on East Asian records of barbourofelines. The new skull of Oriensmilus possesses a suite of characters shared with nimravines, such as the lack of an ossified (entotympanic) bullar floor, absence of an intrabullar septum, lack of a ventral promontorial process of the petrosal, presence of a small rostral entotympanic on the dorsal side of the caudal entotympanic, and a distinct caudal entry of the internal carotid artery and nerve that pierces the caudal entotympanic at the junction of the ossified and unossified caudal entotympanics. The absence of an ossified bullar floor in O. liupanensis and its presence in those from the middle Miocene of Sansan, France thus help to bracket the transition of this character, which must have happened in the early part of the middle Miocene. Spatial relationships between bullar construction and the middle ear configuration of the carotid artery in Oriensmilus strongly resemble those in nimravines but are distinctly different from felids and other basal feliforms. Despite the attractive notion that early barbourofelines arose from a Miocene ancestor that also gave rise to felids, the basicranial evidence argues against this view.http://zoobank.org/urn:http://lsid:zoobank.org:pub:2DE98DBC-4D02-4E18-9788-0B0D8587E73F

Phylogenomic interrogation resolves the backbone of the Pseudoscorpiones tree of life

Pseudoscorpiones, with nearly 3700 described species, are an ancient and globally distributed group of arachnids with a fossil record dating back to the Middle Devonian. Previous attempts to reconstruct their phylogenetic history have used morphology or a few amplicons, mostly of rRNAs and mitochondrial genes, which have not been able to completely resolve family-level relationships nor the earliest nodes in the pseudoscorpion tree—those which are most informative about the origins of key characters like venoms and silk. Here we undertake a phylogenetic approach using 41 pseudoscorpion transcriptomes and a series of analyses that account for many of the common pitfalls faced in large phylogenomic analyses. All analyses, using concatenation methods and coalescent approaches, supported monophyly of Iocheirata (the venomous pseudoscorpions), which diversified mostly during the Mesozoic, but paraphyly of Epiocheirata, with a sister group relationship of Feaelloidea to Iocheirata, with Chthonioidea as their sister group. These three main lineages were established during the mid-to-late Paleozoic. Our phylogenetic scheme is consistent with the prior hypothesis that the lack of venom in Pseudoscorpiones is plesiomorphic and not a synapomorphy of Epiocheirata. Based on the results of this study, a new classification is proposed for Pseudoscorpiones including the following new nomenclatural and taxonomic acts: the new suborders Palaeosphyronida Harvey and Atoposphyronida Harvey for Dracochelidae and Feaelloidea, respectively; the newly recognized superfamily Garypinoidea for Garypinidae and Larcidae; the revised rank for Lechytiidae and Tridenchthoniidae, which are regarded as subfamilies of Chthoniidae; the revised rank for Tridenchthoniini and Verrucadithini which are regarded as tribes of Tridenchthoniinae; and the elevation of Hesperolpiinae as a distinct family, Hesperolpiidae.

Earth history and the passerine superradiation

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.

The phylogeny and evolutionary timescale of stoneflies (Insecta: Plecoptera) inferred from mitochondrial genomes

Phylogenetic analysis based on mitochondrial genomic data from 25 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera (stoneflies). The monophyly of both currently recognized suborders was strongly supported, concordant with previous molecular analyses of Plecoptera. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae + Diamphipnoidae and Austroperlidae + Gripopterygidae; consistent with relationships proposed based on morphology. The largely northern hemisphere suborder Arctoperlaria also divided into two groups, Euholognatha and Systellognatha, each composed of the five families traditionally assigned to each infraorder (the placement Scopuridae by mt genome data remains untested at this time). Within Euholognatha, strong support for the clade Nemouridae + Notonemouridae confirmed the northern origin of the currently southern hemisphere restricted Notonemouridae. Other family level relationships within the Arctoperlaria differ from those recovered by previous morphology and molecular based analyses. A fossil-calibrated divergence estimation suggests the formation of two suborders dates back to the Jurassic (181 Ma), with subsequent diversification of most stonefly families during the Cretaceous. This result confirms the hypothesis that initial divergence between the suborders was driven by the breakup of the supercontinent Pangaea into Laurasia and Gondwanaland (commencing 200 Ma and complete by 150 Ma).

Persistence of Effects of VLBW/PT Birth Status and Maternal Emotional Availability (EA) on Child EA Trajectories.

Few studies have examined the longitudinal impact of birth status on the infant–mother relationship and on children’s socio-emotional development. In the present study we investigated developmental patterns of such relationships [using the Emotional Availability (EA) Scales] in fullterm and VLBW/PT infants from infancy to emerging school age. Our objectives were to: (a) model the developmental trajectories of EA dimensions (maternal sensitivity, structuring, non-hostility; child responsiveness, involvement) in a VLBW/PT and fullterm sample, (b) identify potential effects of VLBW/PT status on these trajectories, and (c) determine whether the effects of VLBW/PT status on children’s socio-emotional development (child EA) remained after accounting for the effect of maternal EA. Child–mother dyads (n = 109) were observed in home-based interactions (face-to-face and free play) when children were 6, 12, 18, and 57-months-old in fullterm (37–41 weeks, >2500 g; n = 48) and healthy VLBW/PT (26–32 weeks gestation, birth weight 800–1500 g, corrected for gestational age; n = 61) children. Developmental trajectories of maternal and child EA were assessed using multilevel growth modeling in Mplus. Results indicated that, even after controlling for maternal EA, there was a persistent negative effect of VLBW/PT birth status on child EA trajectories. Both initially and over time, VLBW/PT infants lagged behind their fullterm counterparts on levels of responsiveness and involvement with mothers. There was also a persistent positive effect of maternal EA (sensitivity and structuring) on child EA trajectories. Higher average levels of maternal sensitivity and structuring across time were also associated with higher and persistent levels of child responsiveness and involvement of their mothers. Importantly, results held after modeling both effects together, and after controlling for maternal education and child gender. Our results have implications for VLBW/PT children’s development, the parent–child relationship, and integrating family level factors and relationship dimensions in early prevention and intervention programs.

The Complexity of Radicalization and Recruitment in Kwale, Kenya

ABSTRACT Al-Shabaab, the East-African affiliate of Al Qaeda has carried out a number of large-scale devastating attacks in the region and a steady stream of smaller scale ones. In recent years Al-Shabaab’s ongoing strength has relied upon its ability to build local support within Kenya. This work looks at Kwale County on Kenya’s coast and examines some of the factors involved in radicalization and/or recruitment into the group, including economic hardship, historical marginalization, land injustices, drugs, problems at the family level and poor relationships with state security agencies. It highlights the more recent phenomenon of those returning from fighting with Al-Shabaab and the problems of their reintegration. It concludes that there are a number of phenomenon related in complex and sometimes self-perpetuating ways which all need to be considered in the response to radicalization and recruitment.

The extraordinary genus Myja is not a tergipedid, but related to the Facelinidae s. str. with the addition of two new species from Japan (Mollusca, Nudibranchia).

Morphological and molecular data are presented for the first time in an integrative way for the genus Myja Bergh, 1896. In accordance with the new molecular phylogenies, the traditional Facelinidae is paraphyletic. Herein is presented the phylogenetic placement of true Facelinidae s. str., including the first molecular data for F.auriculata (Müller, 1776), type species of the genus Facelina Alder & Hancock, 1855. The taxonomic history of F.auriculata is reviewed. The genus Myja is related to the clade Facelinidae s. str., but shows disparate morphological traits. Two new species of the genus Myja, M.karinsp. n., and M.hyotansp. n., are described from the Pacific waters of Japan (middle Honshu), and M.cf.longicornis Bergh, 1896 is investigated from Thailand. According to molecular analysis and review of available morphological information, the genus Myja contains more hidden diversity. The family-level relationship within aeolidacean nudibranchs with emphasis on the family Facelinidae is outlined. The problem of the relationship between Facelinidae Bergh, 1889 and Glaucidae Gray, 1827 is discussed. The family Glaucidae has precedence over Facelinidae and is phylogenetically related to the core group of Facelinidae s. str., but has a profoundly modified aberrant external morphology, thus making a purely molecular-based approach to the taxonomy an unsatisfactory solution. To accommodate recently discovered hidden diversity within glaucids, the genus Glaucilla Bergh, 1861 is restored. The family Facelinidae s. str. is separate from, and not closely related to, a clade containing the genera Dondice Marcus, 1958, Godiva MacNae 1954, Hermissenda Bergh, 1879, and Phyllodesmium Ehrenberg, 1831 (= Myrrhine Bergh, 1905). The oldest valid available name for the separate ex-facelinid paraphyletic clade that contains several facelinid genera is Myrrhinidae Bergh, 1905, and resurrection of this family name under provision of the ICZN article 40.1 can preliminarily solve the problem of paraphyly of the traditional Facelinidae. “Facelinidae” s. l. needs to be further divided into several separate families, pending further study.

Coronacoccus hengyangensis gen. et sp. nov., a new member of Chlorellaceae (Trebouxiophyceae, Chlorophyta) with radiococcacean morphology

:The Chlorellaceae is a family in the order Chlorellales that includes mostly coccoid algae of minute sizes, and a portion of this family was separated into two sister groups (the Chlorella clade and the Parachlorella clade) according to molecular phylogenetic analyses. To date, the Parachlorella clade comprises 11 genera that exhibit a range of morphological variation. In this study, we discovered from China a strain marked as FACHB-2137; we use a polyphasic approach, including phylogenetic analyses of SSU+ITS rDNA, an ITS2/CBC (compensatory base changes) approach, light microscopy and transmission electron microscopy, to characterise the strain. Molecular analyses revealed that the strain was nested within the Parachlorella clade (Chlorellaceae, Trebouxiophyceae), forming an independent lineage separated from other genera. The new strain's morphology has the characteristic autospores that release by rupturing or splitting of the cell wall into several (two to four) portions; this strain differs from other members of the Parachlorella clade in that the mother cell wall remains rather distinct, and the daughter cells remain as cup-shaped in the colonial mucilage for an extended period. Morphologically, this new strain closely resembles members of the Radiococcaceae. This indicates that inferring family-level relationships based exclusively on morphology can be problematic. We describe this alga as a new genus and species, Coronacoccus hengyangensis gen. et sp. nov. This morphotype is described for the first time in the Parachlorella clade.