Genome Survey Sequencing of the Mole Cricket Gryllotalpa orientalis.

The mole cricket Gryllotalpa orientalis is an evolutionarily, medicinal, and agriculturally significant insect that inhabits underground environments and is distributed globally. This study measured genome size by flow cytometry and k-mer based on low-coverage sequencing, and nuclear repetitive elements were also identified. The haploid genome size estimate is 3.14 Gb by flow cytometry, 3.17 Gb, and 3.77 Gb-based two k-mer methods, respectively, which is well within the range previously reported for other species of the suborder Ensifera. 56% of repetitive elements were found in G. orientalis, similar to 56.83% in Locusta migratoria. However, the great size of repetitive sequences could not be annotated to specific repeat element families. For the repetitive elements that were annotated, Class I-LINE retrotransposon elements were the most common families and more abundant than satellite and Class I-LTR. These results based on the newly developed genome survey could be used in the taxonomic study and whole genome sequencing to improve the understanding of the biology of G. orientalis.

De Novo Assembly and Characterization of the Transcriptome of an Omnivorous Camel Cricket (Tachycines meditationis).

Tachycines meditationis (Orthoptera: Rhaphidophoridae: Tachycines) is a widely distributed insect in eastern Asia. This species is common in urban environments, and its unique omnivorous diet may contribute to its success in various habitats. However, molecular studies on the species are scarce. Here, we obtained the first transcriptome sequence of T. meditationis and performed preliminary analyses to test whether the evolution of coding sequences fits the expectations based on the species' ecology. We retrieved 476,495 effective transcripts and annotated 46,593 coding sequences (CDS). We analysed the codon usage and found that directional mutation pressure was the leading cause of codon usage bias in this species. This genome-wide relaxed codon usage pattern in T. meditationis is surprising, given the potentially large population size of this species. Moreover, despite the omnivorous diet, the chemosensory genes of this species do not exhibit codon usage deviating significantly from the genome-level pattern. They also do not seem to experience more gene family expansion than other cave cricket species do. A thorough search for rapidly evolved genes using the dN/dS value showed that genes associated with substance synthesis and metabolic pathways, such as retinol metabolism, aminoacyl-tRNA biosynthesis, and fatty acid metabolism, underwent species-specific positive selection. While some results seem to contradict the species ecology, our transcriptome assembly provides a valuable molecular resource for future studies on camel cricket evolution and molecular genetics for feeding ecology in insects, in general.

Redescription of two species and a new distribution record for China of the genus MelanogryllusChopard, 1961 and a report of one new species of the genus Velarifictorus Randell, 1964 (Orthoptera: Gryllidae; Gryllinae).

Dark body color is very common among crickets, and this article discusses four species of black field crickets with distinct distributions. There are three species of the genus Melanogryllus Chopard, 1961 and one species of the genus Velarifictorus Randell, 1964. Of them, Melanogryllus chopardi Bey-Bienko, 1968 was discovered in Southwest Xizang, on the border between China and Nepal; Melanogryllus desertus (Pallas, 1771) was primarily found in arid regions of northwestern China; Melanogryllus bilineatus Yang & Yang, 1994 was often collected from the Southeast China coastal region; and the last species, Velarifictorus yuanilandrevus sp. nov., is a new species that was collected in Yunnan, a province in Southwest China. In addition, the new species could be distinguished from the others by its black body coloration and the absence of yellow stripes on the head. Here, we describe these species in detail, with photographs of the genitalia, and provide a distribution map for them and keys for Chinese Melanogryllus species.

Two new species of ground crickets (Orthoptera: Trigonidiidae; Nemobiinae) from China.

Here we describe two new species of ground crickets from Yunnan Province, China (Homonemobius brevipennis sp. nov. and Pteronemobius osuviridis sp. nov.). Descriptions, illustrations, and distributions of these new species are provided.

The intraspecific variation of morphology and coloration of field crickets: a taxonomic revision of Chinese Gymnogryllus Saussure, 1877 and Phonarellus Gorochov, 1983 (Orthoptera, Gryllidae, Gryllini).

After extensive sampling of specimens from species found in China, we examined the intraspecific morphological variation of several characters used for species delimitation in two closely related cricket genera, Gymnogryllus Saussure, 1877 and Phonarellus Gorochov, 1983. We found that the characters (male genitalia in Gymnogryllusodonopetalus Xie & Zheng, 2003 and Phonarellusritsemae (Saussure, 1877), and coloration of the hind leg in Phonarellusminor (Chopard, 1959)) exhibit considerable amounts of variation within species, and are thus not reliable characters for species differentiation. Therefore, we revised the taxonomy of these two genera. Five synonyms are proposed: G.yunnanensis (= G.odonopetalus) syn. nov., G.striatus (= G.odonopetalus) syn. nov., G.longus (= G.odonopetalus) syn. nov., G.tumidulus (= G.odonopetalus) syn. nov., and P.flavipes (= P.minor) syn. nov. All species mentioned above are described and illustrated. Keys and a distribution map are provided.

Description of three new species of Gomphomastacinae (Orthoptera: Eumastacoidea) from the east of Qinghai-Tibet plateau, China.

The grasshopper Subfamily Gomphomastacinae (Orthoptera: Acridoidea: Eumastacidae) is widely distributed in the Qinghai-Tibetan Plateau and Central Asia. This paper describes three new species: Ptygomastax nihilsulcus Ge, sp. nov. Phytomastax pentaspinula Ge, sp. nov. and Pentaspinula unispinula Ge, sp. nov. of the subfamily from the eastern Qinghai-Tibetan Plateau, along with an updated identification key of species of the related genera. Detail figures of the body and genitalia of the new species are also provided.

A synoptic review of Gomphomastacinae (Orthoptera: Eumastacoidea) from the Qinghai-Tibet plateau with a description of new species.

With unique climate, topography, and vegetation, the Qinghai-Tibet plateau is a special biogeographic region with richness of endemic species. However, the taxonomy and distribution of many insect groups on this plateau are still poorly known. Here, we synthesized a species checklist of subfamily Gomphomastacinae (Orthoptera: Acridoidea: Eumastacidae) for this region, while describing a new species: Myrmeleomastax wideis Qiu, sp. nov.. Images of the new species and the distribution map of all the known species are provided. Type specimens for the new species are deposited in the Zoological and Botanical Museum, Shaanxi Normal University, Xi'an, China (SNNU).

Differences in Quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species.

The mountains of southwest China (MSWC) is a biodiversity hotspot with highly complex and unusual terrain. However, with the majority of studies focusing on the biogeographic consequences of massive mountain building, the Quaternary legacy of biodiversity for the MSWC has long been overlooked. Here, we took a statistical comparative phylogeography approach to examine factors that shaped community-wide diversification. With data from 30 vertebrate species, the results reveal spatially concordant genetic structure, and temporally clustered co-divergence events associated with river barriers during severe glacial cycles. This indicates the importance of riverine barriers in the phylogeographic history of the MSWC vertebrate community. We conclude that the repeated glacial cycles are associated with co-divergences that are themselves structured by the heterogeneity of the montane landscape of the MSWC. This orderly process of diversification has profound implications for conservation by highlighting the relative independence of different geographical areas in which some, but not all species in communities have responded similarly to climate change and calls for further comparative phylogeographic investigations to reveal the connection between biological traits and divergence pulses in this biodiversity hotspot.

Draft Genome of a Blister Beetle Mylabris aulica.

Mylabris aulica is a widely distributed blister beetle of the Meloidae family. It has the ability to synthesize a potent defensive secretion that includes cantharidin, a toxic compound used to treat many major illnesses. However, owing to the lack of genetic studies on cantharidin biosynthesis in M. aulica, the commercial use of this species is less extensive than that of other blister beetle species in China. This study reports a draft assembly and possible genes and pathways related to cantharidin biosynthesis for the M. aulica blister beetle using nanopore sequencing data. The draft genome assembly size was 288.5 Mb with a 467.8 Kb N50, and a repeat content of 50.62%. An integrated gene finding pipeline performed for assembly obtained 16,500 protein coding genes. Benchmarking universal single-copy orthologs assessment showed that this gene set included 94.4% complete Insecta universal single-copy orthologs. Over 99% of these genes were assigned functional annotations in the gene ontology, Kyoto Encyclopedia of Genes and Genomes, or Genbank non-redundant databases. Comparative genomic analysis showed that the completeness and continuity of our assembly was better than those of Hycleus cichorii and Hycleus phaleratus blister beetle genomes. The analysis of homologous orthologous genes and inference from evolutionary history imply that the Mylabris and Hycleus genera are genetically close, have a similar genetic background, and have differentiated within one million years. This M. aulica genome assembly provides a valuable resource for future blister beetle studies and will contribute to cantharidin biosynthesis.

A Checklist of Short-horned Grasshopper Species (Orthoptera: Caelifera) from Littoral Region of Cameroon with description of a new species of the genus Hemierianthus Saussure, 1903 (Orthoptera: Chorotypidae).

The Littoral Region of Cameroon is one of the most highly disturbed regions in Cameroon that remain poorly studied and where no investigation regarding the grasshopper fauna has been conducted. Hence a survey was conducted from August 2015 to November 2018 in 11 localities of this region. In each locality, grasshoppers were sampled in three vegetation types (forests, fallows and cultivated farms) using sweep nets sampling method. We collected in total 51 short-horned grasshopper species belonging to the families Acrididae, Chorotypidae, Euschmidtiidae, Pyrgomorphidae and Thericleidae. Among these species, 43 belong to Acrididae, 5 to Pyrgomorphidae and only one belongs to the Chorotypidae, Euschmidtiidae and Thericleidae respectively. The Chorotypidae species Hemierianthus mbongueensis Yetchom Xu sp.nov. is also described in this study. Twelve grasshopper species were widely distributed as they occurred in all study sites and 11 were recorded exclusively from one study site. This study showed that there is high species richness of short-horned grasshoppers in the Littoral Region of Cameroon. However, more sampling effort in different ecosystems of this region and other regions of Cameroon will certainly improve our understanding on grasshopper taxonomy, ecology and biogeography.

Does Population Structure Predict the Rate of Speciation? A Comparative Test across Australia's Most Diverse Vertebrate Radiation.

Population divergence is the first step in allopatric speciation, as has long been recognized in both theoretical models of speciation and empirical explorations of natural systems. All else being equal, lineages with substantial population differentiation should form new species more quickly than lineages that maintain range-wide genetic cohesion through high levels of gene flow. However, there have been few direct tests of the extent to which population differentiation predicts speciation rates as measured on phylogenetic trees. Here, we explicitly test the links between organismal traits, population-level processes, and phylogenetic speciation rates across a diverse clade of Australian lizards that shows remarkable variation in speciation rate. Using genome-wide double digest restriction site-associated DNA data from 892 individuals, we generated a comparative data set on isolation by distance and population differentiation across 104 putative species-level lineages (operational taxonomic units). We find that species show substantial variation in the extent of population differentiation, and this variation is predicted by organismal traits that are thought to be proxies for dispersal and deme size. However, variation in population structure does not predict variation in speciation rate. Our results suggest that population differentiation is not the rate-limiting step in species formation and that other ecological and historical factors are primary determinants of speciation rates at macroevolutionary scales.

A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories.

PREMISE OF THE STUDY: Discordant gene trees are commonly encountered when sequences from thousands of loci are applied to estimate phylogenetic relationships. Several processes contribute to this discord. Yet, we have no methods that jointly model different sources of conflict when estimating phylogenies. An alternative to analyzing entire genomes or all the sequenced loci is to identify a subset of loci for phylogenetic analysis. If we can identify data partitions that are most likely to reflect descent from a common ancestor (i.e., discordant loci that indeed reflect incomplete lineage sorting [ILS], as opposed to some other process, such as lateral gene transfer [LGT]), we can analyze this subset using powerful coalescent-based species-tree approaches. METHODS: Test data sets were simulated where discord among loci could arise from ILS and LGT. Data sets where analyzed using the newly developed program CLASSIPHY (Huang et al., ) to assess whether our ability to distinguish the cause of discord among loci varied when ILS and LGT occurred in the recent versus deep past and whether the accuracy of these inferences were affected by the mutational process. KEY RESULTS: We show that accuracy of probabilistic classification of individual loci by the cause of discord differed when ILS and LGT events occurred more recently compared with the distant past and that the signal-to-noise ratio arising from the mutational process contributes to difficulties in inferring LGT data partitions. CONCLUSIONS: We discuss our findings in terms of the promise and limitations of identifying subsets of loci for species-tree inference that will not violate the underlying coalescent model (i.e., data partitions in which ILS, and not LGT, contributes to discord). We also discuss the empirical implications of our work given the many recalcitrant nodes in the tree of life (e.g., origins of angiosperms, amniotes, or Neoaves), and recent arguments for concatenating loci.

Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards.

Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based species delimitation to delineate 83 species-level lineages within the genus for downstream analyses. We then used these genetic data to infer levels of within-population genetic diversity. Using a phylogenetically informed approach, we tested whether variation in genetic diversity could be explained by population size, environmental heterogeneity or historical demography. We find that the strongest predictor of genetic diversity is a novel proxy for census population size: the number of vouchered occurrences in museum databases. However, museum occurrences only explain a limited proportion of the variance in genetic diversity, suggesting that genetic diversity might be difficult to predict at shallower phylogenetic scales.

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences.

There is a lack of consensus on how next-generation sequence (NGS) data should be considered for phylogenetic and phylogeographic estimates, with some studies excluding loci with missing data, whereas others include them, even when sequences are missing from a large number of individuals. Here, we use simulations, focusing specifically on RAD (Restriction site Associated DNA) sequences, to highlight some of the unforeseen consequence of excluding missing data from next-generation sequencing. Specifically, we show that in addition to the obvious effects associated with reducing the amount of data used to make historical inferences, the decisions we make about missing data (such as the minimum number of individuals with a sequence for a locus to be included in the study) also impact the types of loci sampled for a study. In particular, as the tolerance for missing data becomes more stringent, the mutational spectrum represented in the sampled loci becomes truncated such that loci with the highest mutation rates are disproportionately excluded. This effect is exacerbated further by factors involved in the preparation of the genomic library (i.e., the use of reduced representation libraries, as well as the coverage) and the taxonomic diversity represented in the library (i.e., the level of divergence among the individuals). We demonstrate that the intuitive appeals about being conservative by removing loci may be misguided. [Next-generation sequencing; phylogenetic; phylogeography; RADseq; RADtags; species delimitation.].

A Robust Semi-Parametric Test for Detecting Trait-Dependent Diversification.

Rates of species diversification vary widely across the tree of life and there is considerable interest in identifying organismal traits that correlate with rates of speciation and extinction. However, it has been challenging to develop methodological frameworks for testing hypotheses about trait-dependent diversification that are robust to phylogenetic pseudoreplication and to directionally biased rates of character change. We describe a semi-parametric test for trait-dependent diversification that explicitly requires replicated associations between character states and diversification rates to detect effects. To use the method, diversification rates are reconstructed across a phylogenetic tree with no consideration of character states. A test statistic is then computed to measure the association between species-level traits and the corresponding diversification rate estimates at the tips of the tree. The empirical value of the test statistic is compared to a null distribution that is generated by structured permutations of evolutionary rates across the phylogeny. The test is applicable to binary discrete characters as well as continuous-valued traits and can accommodate extremely sparse sampling of character states at the tips of the tree. We apply the test to several empirical data sets and demonstrate that the method has acceptable Type I error rates.

Sex-linked genomic variation and its relationship to avian plumage dichromatism and sexual selection.

BACKGROUND: Sexual dichromatism is the tendency for sexes to differ in color pattern and represents a striking form of within-species morphological variation. Conspicuous intersexual differences in avian plumage are generally thought to result from Darwinian sexual selection, to the extent that dichromatism is often treated as a surrogate for the intensity of sexual selection in phylogenetic comparative studies. Intense sexual selection is predicted to leave a footprint on genetic evolution by reducing the relative genetic diversity on sex chromosome to that on the autosomes. RESULTS: In this study, we test the association between plumage dichromatism and sex-linked genetic diversity using eight species pairs with contrasting levels of dichromatism. We estimated Z-linked and autosomal genetic diversity for these non-model avian species using restriction-site associated (RAD) loci that covered ~3 % of the genome. We find that monochromatic birds consistently have reduced sex-linked genomic variation relative to phylogenetically-paired dichromatic species and this pattern is robust to mutational biases. CONCLUSIONS: Our results are consistent with several interpretations. If present-day sexual selection is stronger in dichromatic birds, our results suggest that its impact on sex-linked genomic variation is offset by other processes that lead to proportionately lower Z-linked variation in monochromatic species. We discuss possible factors that may contribute to this discrepancy between phenotypes and genomic variation. Conversely, it is possible that present-day sexual selection -- as measured by the variance in male reproductive success -- is stronger in the set of monochromatic taxa we have examined, potentially reflecting the importance of song, behavior and other non-plumage associated traits as targets of sexual selection. This counterintuitive finding suggests that the relationship between genomic variation and sexual selection is complex and highlights the need for a more comprehensive survey of genomic variation in avian taxa that vary markedly in social and genetic mating systems.

Genome-Wide Association and Trans-ethnic Meta-Analysis for Advanced Diabetic Kidney Disease: Family Investigation of Nephropathy and Diabetes (FIND).

Diabetic kidney disease (DKD) is the most common etiology of chronic kidney disease (CKD) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus. Approximately 45% of U.S. patients with incident end-stage kidney disease (ESKD) have DKD. Independent of glycemic control, DKD aggregates in families and has higher incidence rates in African, Mexican, and American Indian ancestral groups relative to European populations. The Family Investigation of Nephropathy and Diabetes (FIND) performed a genome-wide association study (GWAS) contrasting 6,197 unrelated individuals with advanced DKD with healthy and diabetic individuals lacking nephropathy of European American, African American, Mexican American, or American Indian ancestry. A large-scale replication and trans-ethnic meta-analysis included 7,539 additional European American, African American and American Indian DKD cases and non-nephropathy controls. Within ethnic group meta-analysis of discovery GWAS and replication set results identified genome-wide significant evidence for association between DKD and rs12523822 on chromosome 6q25.2 in American Indians (P = 5.74x10-9). The strongest signal of association in the trans-ethnic meta-analysis was with a SNP in strong linkage disequilibrium with rs12523822 (rs955333; P = 1.31x10-8), with directionally consistent results across ethnic groups. These 6q25.2 SNPs are located between the SCAF8 and CNKSR3 genes, a region with DKD relevant changes in gene expression and an eQTL with IPCEF1, a gene co-translated with CNKSR3. Several other SNPs demonstrated suggestive evidence of association with DKD, within and across populations. These data identify a novel DKD susceptibility locus with consistent directions of effect across diverse ancestral groups and provide insight into the genetic architecture of DKD.

Minimal effects of latitude on present-day speciation rates in New World birds.

The tropics contain far greater numbers of species than temperate regions, suggesting that rates of species formation might differ systematically between tropical and non-tropical areas. We tested this hypothesis by reconstructing the history of speciation in New World (NW) land birds using BAMM, a Bayesian framework for modelling complex evolutionary dynamics on phylogenetic trees. We estimated marginal distributions of present-day speciation rates for each of 2571 species of birds. The present-day rate of speciation varies approximately 30-fold across NW birds, but there is no difference in the rate distributions for tropical and temperate taxa. Using macroevolutionary cohort analysis, we demonstrate that clades with high tropical membership do not produce species more rapidly than temperate clades. For nearly any value of present-day speciation rate, there are far more species in the tropics than the temperate zone. Any effects of latitude on speciation rate are marginal in comparison to the dramatic variation in rates among clades.

Sexual selection and diversification: reexamining the correlation between dichromatism and speciation rate in birds.

Theory predicts that sexual selection can serve as an important driver of speciation, but phylogenetic comparative analyses have failed to demonstrate a consistent effect of sexual selection on species richness at macroevolutionary scales. Sexual dichromatism in birds is an example of a phenotypic trait that is hypothesized to reflect the intensity of sexual selection, yet previous studies have reached ambiguous conclusions regarding its role in promoting species diversification. Here, we revisit this problem by pairing published spectrophotometer estimates of plumage dichromatism in the bird-visible range with a newly developed method for modeling speciation rates on phylogenetic trees that explicitly accounts for diversification rate variation through time and among clades. We find little evidence linking dichromatism to speciation across birds, using several measures of dichromatism and macroevolutionary diversification. These results suggest that sexual dichromatism plays a limited role in determining speciation rates at macroevolutionary scales in birds.

Do estimated and actual species phylogenies match? Evaluation of East African cichlid radiations.

A large number of published phylogenetic estimates are based on a single locus or the concatenation of multiple loci, even though genealogies of single or concatenated loci may not accurately reflect the true history of species diversification (i.e., the species tree). The increased availability of genomic data, coupled with new computational methods, improves resolution of species relationships beyond what was possible in the past. Such developments will no doubt benefit future phylogenetic studies. It remains unclear how robust phylogenies that predate these developments (i.e., the bulk of phylogenetic studies) are to departures from the assumption of strict gene tree-species tree concordance. Here, we present a parametric bootstrap (PBST) approach that assesses the reliability of past phylogenetic estimates in which gene tree-species tree discord was ignored. We focus on a universal cause of discord-the random loss of gene lineages from genetic drift-and apply the method in a meta-analysis of East African cichlids, a group encompassing historical scenarios that are particularly challenging for phylogenetic estimation. Although we identify some evolutionary relationships that are robust to gene tree discord, many past phylogenetic estimates of cichlids are not. We discuss the utility of the PBST method for evaluating the robustness of gene tree-based phylogenetic estimations in general as well as for testing the clade-specific performance of species tree estimation methods and designing sampling strategies that increase the accuracy of estimated species relationships.