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Host-microbe interactions are intimately linked to eukaryotic evolution, particularly in sap-sucking insects that often rely on obligate microbial symbionts for nutrient provisioning. Cicadas (Cicadidae: Auchenorrhyncha) specialize on xylem fluid and derive many essential amino acids and vitamins from intracellular bacteria or fungi (Hodgkinia, Sulcia, and Ophiocordyceps) that are propagated via transmission from mothers to offspring. Despite the beneficial role of these non-gut symbionts in nutrient provisioning, the role of beneficial microbiota within the gut remains unclear. Here, we investigate the relative abundance and impact of host phylogeny and ecology on gut microbial diversity in cicadas using 16S ribosomal RNA gene amplicon sequencing data from 197 wild-collected cicadas and new mitochondrial genomes across 38 New Zealand cicada species, including natural hybrids between one pair of two species. We find low abundance and a lack of phylogenetic structure and hybrid effects but a significant role of elevation in explaining variation in gut microbiota.

In vicariant species formation, divergence results primarily from periods of allopatry and restricted gene flow. Widespread species harboring differentiated, geographically distinct sublineages offer a window into what may be a common mode of species formation, whereby a species originates, spreads across the landscape, then fragments into multiple units. However, incipient lineages usually lack reproductive barriers that prevent their fusion upon secondary contact, blurring the boundaries between a single, large metapopulation-level lineage and multiple independent species. Here, we explore this model of species formation in the Eastern Red-backed Salamander (Plethodon cinereus), a widespread terrestrial vertebrate with at least 6 divergent mitochondrial clades throughout its range. Using anchored hybrid enrichment data, we applied phylogenomic and population genomic approaches to investigate patterns of divergence, gene flow, and secondary contact. Genomic data broadly match most mitochondrial groups but reveal mitochondrial introgression and extensive admixture at several contact zones. While species delimitation analyses in Bayesian Phylogenetics and Phylogeography supported 5 lineages of P. cinereus , genealogical divergence indices (gdi) were highly sensitive to the inclusion of admixed samples and the geographic representation of candidate species, with increasing support for multiple species when removing admixed samples or limiting sampling to a single locality per group. An analysis of morphometric data revealed differences in body size and limb proportions among groups, with a reduction of forelimb length among warmer and drier localities consistent with increased fossoriality. We conclude that P. cinereus is a single species, but one with highly structured component lineages of various degrees of independence. [ABSTRACT FROM AUTHOR]

A comprehensive phylogeny of north European Geometridae is reconstructed using a two‐step analytical pipeline. First, a phylogenomic backbone tree was inferred using a 117‐species subset of geometrid moths and a 35‐species set of outgroup taxa from eight other macroheteroceran families. The data matrix totalled 209,499 bp from 648 protein‐coding loci obtained using anchored hybrid enrichment technique for sequencing. This backbone was used for constructing a larger phylogeny of Geometridae based on up to 11 'traditional' protein‐coding genes which were obtained for all 376 species of north European geometrids, complemented by 98 species from taxonomic key groups of Geometridae from other parts of the world. Our results largely corroborate earlier findings about higher classification of Geometridae, but new evidence nevertheless allows us to suggest several changes to the taxonomy. Lampropterygini Õunap & Nedumpally tribus nova and Pelurgini Õunap & Nedumpally tribus nova (both Larentiinae) are described. Epirranthini are regarded as a junior subjective synonym of Rumiini syn. n. Triphosini and Macariini are shown to be paraphyletic within their current limits. Costaconvexa Agenjo is transferred from Xanthorhoini to Epirrhoini new tribe association, Artiora Meyrick from Ennomini incertae sedis to Boarmiini new tribe association, Selenia Hübner from Ennominae incertae sedis to Epionini new tribe association and Epirranthis Hübner from Epirranthini to Rumiini new tribe association. Ochyria Hübner stat. rev. is revived from synonym of Xanthorhoe Hübner as a valid genus and Epelis Hulst stat. rev. and Speranza Curtis stat. rev. from synonyms of Macaria Curtis as valid genera, leading to the following new or revised combinations: Ochyria quadrifasiata (Clerck) rev. comb., Epelis carbonaria (Clerck) comb. n., Speranza fusca (Thunberg) comb. n., Speranza artesiaria (Denis & Schiffermüller) rev. comb., Speranza brunneata (Thunberg) rev. comb., Speranza wauaria (Linnaeus) rev. comb., Speranza loricaria (Eversmann) rev. comb.Perizoma saxicola Tikhonov rev. comb. is transferred back to its original genus from Gagitodes Warren. Hydrelia Hübner, Xanthorhoe and Heliomata Grote & Robinson are shown to be paraphyletic within their current limits. [ABSTRACT FROM AUTHOR]

AIM: Rump plumage coloration of the Eastern Yellow Robin (Eopsaltria australis), a widespread Australian songbird, varies from bright yellow in the tropical north to oliveâgreen in the temperate south. Here, we test whether colour variation: (1) correlates most strongly with neutral genetic variation and so is best explained by historical processes, (2) reflects selection associated with different visual environments (dense versus open habitats) and/or (3) reflects selection associated with climatic variation. LOCATION: Eastern Australia. METHODS: We quantified colour variation using reflectance spectrometry and visual models. We performed geographical cline analysis of colour and neutral genetic variation (genomeâwide single nucleotide polymorphisms). We tested for correlations of colour variation with climate, vegetation density, geographical location and genetic variation. We accounted for covariation and spatial autocorrelation, and conducted analyses at continental and regional spatial scales. RESULTS: Clinal variation of colour traits and neutral genetic markers were largely concordant. At the continental scale, colour variation was strongly associated with neutral genetic structure and geography, and to a lesser extent with environment. At the regional scale, environmental variation was a better predictor of colour variation than it was at the larger scale. MAIN CONCLUSION: At the continental scale, colour variation is strongly associated with largeâscale population history. In contrast, at the regional scale, where the influence of history and geography is weaker, environmental variation has a role in facilitating the maintenance of colour variation. Our results highlight the need to assess selective and neutral alternatives at multiple spatial scales when studying geographical variation.

We present the first genome-wide molecular phylogeny of jumping spiders (Araneae: Salticidae), inferred from Anchored Hybrid Enrichment (AHE) sequence data. From 12 outgroups plus 34 salticid taxa representing all but one subfamily and most major groups recognized in previous work, we obtained 447 loci totalling 96,946 aligned nucleotide sites. Our analyses using concatenated likelihood, parsimony, and coalescent methods (ASTRAL and SVDQuartets) strongly confirm most previous results, resolving as monophyletic the Spartaeinae, Salticinae (with the hisponines sister), Salticoida, Amycoida, Saltafresia, and Simonida. The agoriines, previously difficult to place beyond subfamily, are finally placed confidently within the saltafresians as relatives of the chrysillines and hasariines. Relationships among the baviines, astioids, marpissoids, and saltafresians remain uncertain, though our analyses tentatively conclude the first three form a clade together. Deep relationships, among the seven subfamilies, appear to be largely resolved, with spartaeines, lyssomanines, and asemoneines forming a clade. In most analyses, Onomastus (representing the onomastines) is strongly supported as sister to the hisponines plus salticines. Overall, the much-improved resolution of many deep relationships despite a relatively sparse taxon sample suggests AHE is a promising technique for salticid phylogenetics.

BackgroundDespite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae.ResultsOur aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma.ConclusionsThe Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.

BackgroundThe past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes at the base of the Ovalentaria tree with confidence. Here we test whether a phylogenomic approach will provide better support for these nodes, and if not, why this may be.ResultsAfter using a novel method to account for paralogous loci, we estimated phylogenies with maximum likelihood and species tree methods using DNA sequence alignments of over 80,000 base pairs. Several key relationships within Ovalentaria are well resolved, including 1) the sister taxon relationship between Cichlidae and Pholidichthys, 2) a clade containing blennies, grammas, clingfishes, and jawfishes, and 3) monophyly of Atherinomorpha (topminnows, flyingfishes, and silversides). However, many nodes in the phylogeny associated with the early diversification of Ovalentaria are poorly resolved in several analyses. Through the use of rarefaction curves we show that limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny does not appear to be due to a deficiency of data, as average global node support ceases to increase when only 1/3rd of the sampled loci are used in analyses. Instead this lack of resolution may be driven by model misspecification as a Bayesian mixed model analysis of the amino acid dataset provided good support for parts of the base of the Ovalentaria tree.ConclusionsAlthough it does not appear that the limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny is due to a deficiency of data, it may be that both stochastic and systematic error resulting from model misspecification play a role in the poor resolution at the base of the Ovalentaria tree as a Bayesian approach was able to resolve some of the deeper nodes, where the other methods failed.

The Cumberland Plateau Salamander, Plethodon kentucki, is a cryptic species with respect to the sympatric Northern Slimy Salamander, Plethodon glutinosus. It was first described by Highton and MacGregor (1983) by using allozyme data. In that description, the authors reported extreme levels of genetic differentiation for a single species with a narrow distribution; however, follow-up studies found patterns of genetic variation that were discordant with the allozyme data. In this paper, we describe patterns of genetic variation within P. kentucki by using an anchored hybrid enrichment dataset of 21 individuals sampled from across its known range. We identified four genetic groups with extensive admixture and isolation by distance. We constructed a population tree by using TreeMix and inferred gene flow between two of the four genetic groups. Finally, we used Bayesian phylogenetics and phylogeography (BPP) in conjunction with the genealogical divergence index (gdi) to test species boundaries within P. kentucki. Although BPP suggested that P. kentucki could be four species, gdi indicated that none of the groups were sufficiently independent to constitute separate species. We conclude that P. kentucki is best recognized as a single species with substantial genetic structure within its limited distribution. [ABSTRACT FROM AUTHOR]

Species are the fundamental unit of biodiversity studies. However, many species complexes are difficult to delimit, especially those characterized by complicated patterns of population structure. Salamanders in the family Plethodontidae often form species by slowly fragmenting across a landscape over space and time. They thus provide many examples of species complexes in which gradual Darwinian evolution has resulted in multiple units of varying degrees of differentiation, including incompletely separated lineages. Herein, we report on a molecular systematic investigation of woodland salamanders in the Plethodon wehrlei group, a group that has recently been split from two species into five species. To quantify patterns of genetic variation, we collected genetic samples from 24 individuals from 20 populations, including all species and representing a carefully selected subset of previous work. From these samples, we obtained genomic data by using anchored hybrid enrichment, resulting in 319 loci averaging 1300 bp in length. Biallelic single-nucleotide polymorphisms were randomly selected from 316 of these loci for some analyses. We examined patterns of genetic structure by using a combination of multivariate statistics and methods based on evolutionary models (such as the Bayesian program STRUCTURE) and found that all of the recognized species formed genetic clusters; however, P. wehrlei and P. punctatus were relatively weakly differentiated and STRUCTURE identified three separate clusters within P. jacksoni. Species trees inferred using the weighted accurate species tree algorithm (wASTRAL), Bayesian phylogenetics and phylogeography (BPP), and TreeMix all recovered the same topology, with P. dixi sister to the other taxa, which included a northern clade (P. wehrlei, P. punctatus, P. pauleyi) and a southern clade (P. jacksoni, with three separate groups). TreeMix only inferred one gene flow event. We evaluated the candidate species by using BPP and the genealogical divergence index (gdi). Although BPP delimited all candidate species with strong support (all posterior probabilities = 1.0), the gdi only strongly supported P. dixi and P. pauleyi, both of which have only been recently described. We discuss the difficult problem of species delimitation in groups that form species via range fragmentation. We also provide a vision for future research, with the aim of better testing and diagnosing the species diversity within the P. wehrlei group. [ABSTRACT FROM AUTHOR]