Phylogeny and biogeography of dolichoderine ants: effects of data partitioning and relict taxa on historical inference

A Fine Morphological Study of the Rare Anillidris bruchi Santschi (Hymenoptera: Formicidae: Dolichoderinae) Male and Queen

Using optical and scanning electron microscopy, we describe the following new morphologically distinctive characters of the rare Neotropical ant Anillidris bruchi Santschi, 1936, male and queen: scattered setae inter-ommatidia, semicircular hypostomal notch, antennal cleaning, metatibial spurs, and the remnant of the M2 vein in the hindwings. In males, we show for the first time the morphology of maxillary and labial palpi, the absence of metapleural glands, and, in external genitalia, for the first time in ants, a new mechano-sensory area on the volsella that we called "volsella sensorium", composed of several spine-like sensilla. Additionally, we give an updated morphological diagnosis of the alate caste, which will be useful for future studies to clarify the phylogeny of the genus Anillidris.

Characterization and Phylogenetic Implication of Complete Mitochondrial Genome of the Medicinal Ant Formica sinae (Hymenoptera: Formicidae): Genomic Comparisons in Formicidae

Ants (Hymenoptera: Formicidae) are among the largest and most widespread families of terrestrial insects and are valuable to medical and ecological investigations. The mitochondrial genome has been widely used as a reliable genetic marker for species identification and phylogenetic analyses. To further understand the mitogenome-level characteristics of the congeneric Formicidae species, the complete mitogenome of Formica sinae (Hymenoptera: Formicidae) was sequenced, annotated, and compared with other 48 Formicidae species. The results showed that gene composition, content, and codon usage were conserved. The complete mitochondrial genome of F. sinae was 17,432 bp, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one control region located between rrnS and trnM, which was 1,256 bp long, the longest of all sequenced species. Gene rearrangement was not detected in Formica species (Hymenoptera: Formicidae). All PCGs of F. sinae were initiated with ATN codons and terminated with the TAA codon. The overall nucleotide composition of F. sinae was AT-biased (83.51%), being 80.58% in PCGs, 86.68% in tRNAs, 87.10% in rRNAs, and 88.70% in the control region. Phylogenetic analyses indicated that each subfamily formed a strongly monophyletic group. Furthermore, F. sinae clustered with Formica fusca (Hymenoptera: Formicidae) and Formica selysi (Hymenoptera: Formicidae). This work enhances the genetic data of Formicidae and contributes to our understanding of their phylogenic relationship, evolution, and utilization.

Complete Nucleotide Sequence of the Mitogenome of Tapinoma ibericum (Hymenoptera: Formicidae: Dolichoderinae), Gene Organization and Phylogenetics Implications for the Dolichoderinae Subfamily

The ant Tapinoma ibericum Santschi, 1925 is native to the Iberian Peninsula. This species, as well as other species from the Tapinoma nigerrimum complex, could form supercolonies that make these species potentially invasive and could give rise to pests. Recently a mature colony from this species has been found in the Isle of Wight (United Kingdom). Mitogenomes have been used to study the taxonomy, biogeography and genetics of species, improving the development of strategies against pest invasion. However, the number of available mitogenomes from the subfamily Dolichoderinae is still scarce and only two of these mitogenomes belong to Tapinoma species. Herein, the complete mitogenome of T. ibericum is presented in order to increase the molecular information of the genus. The T. ibericum mitogenome, retrieved by Next-Generation Sequencing data, is 15,715 bp in length. It contains the typical set of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs and the A + T-rich control region. Comparisons of the T. ibericum mitogenome with other dolichoderine mitogenomes revealed the existence of four gene rearrangements in relation with the ancestral insect mitogenome. One of these rearrangements, involving the tRNA-Ile, tRNA-Gln and tRNA-Met genes, was found in most of the analyzed ant mitogenomes. Probably this rearrangement was an ancestral or plesiomorphic character in Formicidae. Interestingly, another rearrangement that affects to tRNA-Trp, tRNA-Cys and tRNA-Tyr genes was found only in Tapinoma species. This change could be a synapomorphic character for the genus Tapinoma, and could be used as a phylogenetic marker. Additionally, a phylogenetic analysis was performed using the protein-coding gene sequences from available Dolichoderinae mitogenomes, as well as mitogenomes from representative species from other Formicidae subfamilies. Results support the monophyletic nature of the genus Tapinoma placing it within the same clade as the rest of Dolichoderinae species.

Ants (Hymenoptera: Formicidae) from Miocene Ethiopian amber: filling gaps in the geological record of African terrestrial biota

The Early Miocene (16–23 Mya) amber of Ethiopia constitutes a new source of fossil ants for Africa, where they are otherwise poorly documented. Here we report a diversified assemblage of six subfamilies and at least 19 genera that are still predominantly alive in the Afrotropics today. In this first account, a particular reference is made to the subfamily Dolichoderinae, with the description of two new species: Technomyrmex svojtkai Perrichot & Engel sp. nov. and Ravavy goldmani Boudinot & Perrichot sp. nov. The first is illustrated and described based on synchrotron-radiation microcomputed tomography, and the second represents the first fossil record for the tribe Bothriomyrmecini and Ravavy, a Malagasy and Afrotropical genus that was hitherto monotypic. The ant composition in Ethiopian amber is congruent with the global pattern emerging across ants and showing a Neogene diversification almost exclusively within extant genera.

Olfactory System Morphology Suggests Colony Size Drives Trait Evolution in Odorous Ants (Formicidae: Dolichoderinae)

In social insects colony fitness is determined in part by individual worker phenotypes. Across ant species, colony size varies greatly and is thought to affect worker trait variation in both proximate and ultimate ways. Little is known about the relationship between colony size and worker trait evolution, but hypotheses addressing the role of social structure in brain evolution suggest workers of small-colony species may have larger brains or larger brain regions necessary for complex behaviors. In previous work on odorous ants (Formicidae: Dolichoderinae) we found no correlation between colony size and these brain properties, but found that relative antennal lobe size scaled negatively with colony size. Therefore, we now test whether sensory systems scale with colony size, with particular attention to olfactory components thought to be involved in nestmate recognition. Across three species of odorous ants, Forelius mccooki, Dorymyrmex insanus, and D. bicolor, which overlap in habitat and foraging ecology but vary in colony size, we compare olfactory sensory structures, comparing those thought to be involved in nestmate recognition. We use the visual system, a sensory modality not as important in social communication in ants, as a control comparison. We find that body size scaling largely explains differences in eye size, antennal length, antennal sensilla density, and total number of olfactory glomeruli across these species. However, sensilla basiconica and olfactory glomeruli in the T6 cluster of the antennal lobe, structures known to be involved in nestmate recognition, do not follow body size scaling observed for other structures. Instead, we find evidence from the closely related Dorymyrmex species that the larger colony species, D. bicolor, invests more in structures implicated in nestmate recognition. To test for functional consequences, we compare nestmate and non-nestmate interactions between these two species and find D. bicolor pairs of either type engage in more interactions than D. insaus pairs. Thus, we do not find evidence supporting a universal pattern of sensory system scaling associated with changes in colony size, but hypothesize that observed differences in the olfactory components in two closely related Dorymyrmex species are evidence of a link between colony size and sensory trait evolution.

Total evidence and sensitivity phylogenetic analyses of egg-brooding frogs (Anura: Hemiphractidae)

We study the phylogenetic relationships of egg-brooding frogs, a group of 118 neotropical species, unique among anurans by having embryos with large bell-shaped gills and females carrying their eggs on the dorsum, exposed or inside a pouch. We assembled a total evidence dataset of published and newly generated data containing 51 phenotypic characters and DNA sequences of 20 loci for 143 hemiphractids and 127 outgroup terminals. We performed six analytical strategies combining different optimality criteria (parsimony and maximum likelihood), alignment methods (tree- and similarity-alignment), and three different indel coding schemes (fifth character state, unknown nucleotide, and presence/absence characters matrix). Furthermore, we analyzed a subset of the total evidence dataset to evaluate the impact of phenotypic characters on hemiphractid phylogenetic relationships. Our main results include: (i) monophyly of Hemiphractidae and its six genera for all our analyses, novel relationships among hemiphractid genera, and non-monophyly of Hemiphractinae according to our preferred phylogenetic hypothesis; (ii) non-monophyly of current supraspecific taxonomies of Gastrotheca, an updated taxonomy is provided; (iii) previous differences among studies were mainly caused by differences in analytical factors, not by differences in character/taxon sampling; (iv) optimality criteria, alignment method, and indel coding caused differences among optimal topologies, in that order of degree; (v) in most cases, parsimony analyses are more sensitive to the addition of phenotypic data than maximum likelihood analyses; (vi) adding phenotypic data resulted in an increase of shared clades for most analyses.

Complete mitochondrial genome of the H3 haplotype Argentine ant Linepithema humile (Mayr, 1868) (Formicidae; Hymenoptera)

The argentine ant, Linepithema humile (Mayr, 1867), is an invasive ant species that has spread across the world. We have determined the mitochondrial genome of L. humile collected in South Korea, which is 15,934 bp containing 10 SNPs and 5 INDELs compared to the previous mitogenome. Most SNPs were found in cox3, followed by cytb. From SNPs our mitogenome was identified as a H3 haplotype, which was previously recorded in Japan and the U.S. while the previous mitogenome was H1 haplotype. Phylogenetic analysis was congruent to previous study within the tribe Leptomyrmecini but not between other tribes of subfamily Dolichoderinae.

Biogeography of Iberian Ants (Hymenoptera: Formicidae)

Ants are highly diverse in the Iberian Peninsula (IP), both in species richness (299 cited species) and in number of endemic species (72). The Iberian ant fauna is one of the richest in the broader Mediterranean region, it is similar to the Balkan Peninsula but lower than Greece or Israel, when species richness is controlled by the surface area. In this first general study on the biogeography of Iberian ants, we propose seven chorological categories for grouping thems. Moreover, we also propose eight biogeographic refugium areas, based on the criteria of “refugia-within-refugium” in the IP. We analysed species richness, occurrence and endemism in all these refugium areas, which we found to be significantly different as far as ant similarity was concerned. Finally, we collected published evidence of biological traits, molecular phylogenies, fossil deposits and geological processes to be able to infer the most probable centre of origin and dispersal routes followed for the most noteworthy ants in the IP. As a result, we have divided the Iberian myrmecofauna into four biogeographical groups: relict, Asian-IP disjunct, Baetic-Rifan and Alpine. To sum up, our results support biogeography as being a significant factor for determining the current structure of ant communities, especially in the very complex and heterogenous IP. Moreover, the taxonomic diversity and distribution patterns we describe in this study highlight the utility of Iberian ants for understanding the complex evolutionary history and biogeography of the Iberian Peninsula.

Synonymisation of the male-based ant genus Phaulomyrma (Hymenoptera:Formicidae) with Leptanilla based upon Bayesian total-evidence phylogenetic inference

Although molecular data have proven indispensable in confidently resolving the phylogeny of many clades across the tree of life, these data may be inaccessible for certain taxa. The resolution of taxonomy in the ant subfamily Leptanillinae is made problematic by the absence of DNA sequence data for leptanilline taxa that are known only from male specimens, including the monotypic genus Phaulomyrma Wheeler & Wheeler. Focusing upon the considerable diversity of undescribed male leptanilline morphospecies, the phylogeny of 35 putative morphospecies sampled from across the Leptanillinae, plus an outgroup, is inferred from 11 nuclear loci and 41 discrete male morphological characters using a Bayesian total-evidence framework, with Phaulomyrma represented by morphological data only. Based upon the results of this analysis Phaulomyrma is synonymised with Leptanilla Emery, and male-based diagnoses for Leptanilla that are grounded in phylogeny are provided, under both broad and narrow circumscriptions of that genus. This demonstrates the potential utility of a total-evidence approach in inferring the phylogeny of rare extant taxa for which molecular data are unavailable and begins a long-overdue systematic revision of the Leptanillinae that is focused on male material.

Diversity and Distribution of the Dominant Ant Genus Anonychomyrma (Hymenoptera: Formicidae) in the Australian Wet Tropics

Anonychomyrma is a dolichoderine ant genus of cool-temperate Gondwanan origin with a current distribution that extends from the north of southern Australia into the Australasian tropics. Despite its abundance and ecological dominance, little is known of its species diversity and distribution throughout its range. Here, we describe the diversity and distribution of Anonychomyrma in the Australian Wet Tropics bioregion, where only two of the many putative species are described. We hypothesise that the genus in tropical Australia retains a preference for cool wet rainforests reminiscent of the Gondwanan forests that once dominated Australia, but now only exist in upland habitats of the Wet Tropics. Our study was based on extensive recent surveys across five subregions and along elevation and vertical (arboreal) gradients. We integrated genetic (CO1) data with morphology to recognise 22 species among our samples, 20 of which appeared to be undescribed. As predicted, diversity and endemism were concentrated in uplands above 900 m a.s.l. Distribution modelling of the nine commonest species identified maximum temperature of the warmest month, rainfall seasonality, and rainfall of the wettest month as correlates of distributional patterns across subregions. Our study supported the notion that Anonychomyrma radiated from a southern temperate origin into the tropical zone, with a preference for areas of montane rainforest that were stably cool and wet over the late quaternary.

Plastome comparative genomics in maples resolves the infrageneric backbone relationships

Maples (Acer) are among the most diverse and ecologically important tree genera of the north-temperate forests. They include species highly valued as ornamentals and as a source of timber and sugar products. Previous phylogenetic studies employing plastid markers have not provided sufficient resolution, particularly at deeper nodes, leaving the backbone of the maple plastid tree essentially unresolved. We provide the plastid genome sequences of 16 species of maples spanning the sectional diversity of the genus and explore the utility of these sequences as a source of information for genetic and phylogenetic studies in this group. We analyzed the distribution of different types of repeated sequences and the pattern of codon usage, and identified variable regions across the plastome. Maximum likelihood and Bayesian analyses using two partitioning strategies were performed with these and previously published sequences. The plastomes ranged in size from 155,212 to 157,023 bp and had structure and gene content except for Acer palmatum (sect. Palmata), which had longer inverted repeats and an additional copy of the rps19 gene. Two genes, rps2 and rpl22, were found to be truncated at different positions and might be non-functional in several species. Most dispersed repeats, SSRs, and overall variation were detected in the non-coding sequences of the LSC and SSC regions. Fifteen loci, most of which have not been used before in the genus, were identified as the most variable and potentially useful as molecular markers for barcoding and genetic studies. Both ML and Bayesian analyses produced similar results irrespective of the partitioning strategy used. The plastome-based tree largely supported the topology inferred in previous studies using cp markers while providing resolution to the backbone relationships but was highly incongruous with a recently published nuclear tree presenting an opportunity for further research to investigate the causes of discordance, and particularly the role of hybridization in the diversification of the genus. Plastome sequences are valuable tools to resolve deep-level relationships within Acer. The variable loci and SSRs identified in this study will facilitate the development of markers for ecological and evolutionary studies in the genus. This study underscores the potential of plastid genome sequences to improve our understanding of the evolution of maples.

A review of amber and copal occurrences in Africa and their paleontological significance

The paleontological interest for fossil plant resins (amber and copal) has greatly increased in the last decades, as field studies have resulted in the discovery of various new deposits worldwide. Yet, amber-rich deposits remain particularly scarce on continents from former Gondwana. Here we review the known occurrences of copal and amber from Africa, with a state-of-the-art regarding the age dating, the putative plant sources, the fossil content, as well as the paleoenvironmental settings. The first African ambers known to yield arthropods and other organismal inclusions, found recently from the early Cretaceous of Congo and the Miocene of Ethiopia, are briefly overviewed.

Linking Colony Size with Foraging Behavior and Brain Investment in Odorous Ants (Formicidae: Dolichoderinae)

Superorganisms represent a unique level of biological organization in which the phenotype of the reproductive unit, the colony, results from traits expressed at the level of individual workers. Because body size scaling has important consequences for cell diversity and system complexity in solitary organisms, colony size is a trait of particular interest in superorganism evolution. In some instances, division of labor and worker polymorphism scale with colony size, but in general little is known about how colony size drives differences in individual-level behavior or neural traits. Ants represent the greatest diversity of superorganisms and provide a manner of natural experiment to test trends in trait evolution across multiple instances of colony size expansion. In this study, we control for environmental differences and worker size polymorphism to test if colony size correlates with measures of foraging behavior and brain size in dolichoderine ants. We present data from 3 species ranked by colony size. Our results suggest colony size correlates with measures of exploratory behavior and brain investment, with small-colony ants showing higher exploratory drive and faster exploration rate than the larger colony species, and greater relative investment in the primary olfactory brain region, the antennal lobe, than the larger colony species.

The complete mitochondrial genome of Ochetellus glaber (Mayr, 1862) (Hymenoptera:Formicidae)

Ochetellus glaber (Mayr, 1867) is a dolichoderine ant found in the warm regions of Asia and Australia. We have determined the mitochondrial genome of O. glaber whose length is 16,259 bp including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a single large control region. The base composition was AT-biased (GC ratio is 17.8%). Gene order of O. glaber is identical to other species of the subfamily Dolichoderinae. Phylogenetic trees show that O. glaber is nested in other mitochondrial genomes of tribe Leptomyrmecini, implying the neotropical genera are ancestral to Australian genera such as Ochetellus.

Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus Asteropyrum (Ranunculaceae)

Two complete chloroplast genome sequences of Asteropyrum, as well as those of 25 other species from Ranunculaceae, were assembled using both Illumina and Sanger sequencing methods to address the structural variation of the cp genome and the controversial systematic position of the genus. Synteny and plastome structure were compared across the family. The cp genomes of the only two subspecies of Asteropyrum were found to be differentiated with marked sequence variation and different inverted repeat-single copy (IR-SC) borders. The plastomes of both subspecies contains 112 genes. However, the IR region of subspecies peltatum carries 27 genes, whereas that of subspecies cavaleriei has only 25 genes. Gene inversions, transpositions, and IR expansion-contraction were very commonly detected in Ranunculaceae. The plastome of Asteropyrum has the longest IR regions in the family, but has no gene inversions or transpositions. Non-coding regions of the cp genome were not ideal markers for inferring the generic relationships of the family, but they may be applied to interpret species relationship within the genus. Plastid phylogenomic analysis using complete cp genome with Bayesian method and partitioned modeling obtained a fully resolved phylogenetic framework for Ranunculaceae. Asteropyrum was detected to be sister to Caltha, and diverged early from subfamily Ranunculoideae.

Limited female dispersal predicts the incidence of Wolbachia across ants (Hymenoptera: Formicidae)

The endosymbiotic bacterium Wolbachia is perhaps the greatest panzootic in the history of life on Earth, yet remarkably little is known regarding the factors that determine its incidence across species. One possibility is that Wolbachia more easily invades species with structured populations, due to the increased strength of genetic drift and higher initial frequency of infection. This should enable strains that induce mating incompatibilities to more easily cross the threshold prevalence above which they spread to either fixation or a stable equilibrium infection prevalence. Here, we provide empirical support for this hypothesis by analysing the relationship between female dispersal (as a proxy for population structure) and the incidence of Wolbachia across 250 species of ants. We show that species in which the dispersal of reproductive females is limited are significantly more likely to be infected with Wolbachia than species whose reproductive ecology is consistent with significant dispersal of females, and that this relationship remains after controlling for host phylogeny. We suggest that structured host populations, in this case resulting from limited female dispersal, may be an important feature determining how easily Wolbachia becomes successfully established in a novel host, and thus its occurrence across a wide diversity of invertebrate hosts.

A Mesozoic clown beetle myrmecophile (Coleoptera: Histeridae)

Complex interspecies relationships are widespread among metazoans, but the evolutionary history of these lifestyles is poorly understood. We describe a fossil beetle in 99-million-year-old Burmese amber that we infer to have been a social impostor of the earliest-known ant colonies. Promyrmister kistneri gen. et sp. nov. belongs to the haeteriine clown beetles (Coleoptera: Histeridae), a major clade of 'myrmecophiles'-specialized nest intruders with dramatic anatomical, chemical and behavioral adaptations for colony infiltration. Promyrmister reveals that myrmecophiles evolved close to the emergence of ant eusociality, in colonies of stem-group ants that predominate Burmese amber, or with cryptic crown-group ants that remain largely unknown at this time. The clown beetle-ant relationship has been maintained ever since by the beetles host-switching to numerous modern ant genera, ultimately diversifying into one of the largest radiations of symbiotic animals. We infer that obligate behavioral symbioses can evolve relatively rapidly, and be sustained over deep time.

The cephalic anatomy of workers of the ant species Wasmannia affinis (Formicidae, Hymenoptera, Insecta) and its evolutionary implications

Despite the ecological significance of ants and the intensive research attention they have received, thorough treatments of the anatomy and functional morphology are still scarce. In this study we document the head morphology of workers of the myrmicine Wasmannia affinis with optical microscopy, μ-computed tomography, scanning electron microscopy, and 3D reconstruction, providing the first complete anatomical treatment of an ant head with a broad array of modern techniques. We discuss the potential of the applied methods to generate detailed and well-documented morphological data sets with increased efficiency. We also address homology problems, particularly in the context of the cephalic digestive tract. According to our analyses the "pharynx" of previous ant studies is homologous to the prepharynx of other insects. We also discuss the phylogenetic potential and functional significance of the observed characters, with internal features such as tentorium and musculature discussed for the first time. Our investigation underlines that detailed anatomical data for Formicidae are still very fragmentary, which in turn limits our understanding of the major design elements underlying the ant bauplan. We attempt to provide a template for further anatomical studies, which will help to understand the evolution of this fascinating group on the phenotypic level.

The proteome map of the escamolera ant (Liometopum apiculatum Mayr) larvae reveals immunogenic proteins and several hexamerin proteoforms

The larvae of escamolera ant (Liometopum apiculatum Mayr) have been considered a delicacy since Pre-Hispanic times. The increased demand for this stew has led to massive collection of ant nests. Yet biological aspects of L. apiculatum larvae remain unknown, and mapping the proteome of this species is important for understanding its biological characteristics. Two-dimensional gel electrophoresis (2-DE) followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was used to characterize the larvae proteome profile. From 380 protein spots analyzed, 174 were identified by LC-MS/MS and homology search against the Hymenoptera subset of the NCBInr protein database using the Mascot search engine. Peptide de novo sequencing and homology-based alignment allowed the identification of 36 additional protein spots. Identified proteins were classified by cellular location, molecular function, and biological process according to the Gene Ontology annotation. Immunity- and defense-related proteins were identified including PPIases, FK506, PEBP, and chitinases. Several hexamerin proteoforms were identified and the cDNA of the most abundant protein detected in the 2-DE map was isolated and characterized. L. apiculatum hexamerin (LaHEX, GeneBank accession no. MH256667) contains an open reading frame of 2199 bp encoding a polypeptide of 733 amino acid residues with a calculated molecular mass of 82.41 kDa. LaHEX protein is more similar to HEX110 than HEX70 from Apis mellifera. Down-regulation of LaHEX was observed throughout ant development. This work represents the first proteome map as well as the first hexamerin characterized from L. apiculatum larvae.

A simple method for data partitioning based on relative evolutionary rates

BACKGROUND

Multiple studies have demonstrated that partitioning of molecular datasets is important in model-based phylogenetic analyses. Commonly, partitioning is done a priori based on some known properties of sequence evolution, e.g. differences in rate of evolution among codon positions of a protein-coding gene. Here we propose a new method for data partitioning based on relative evolutionary rates of the sites in the alignment of the dataset being analysed. The rates are inferred using the previously published Tree Independent Generation of Evolutionary Rates (TIGER), and the partitioning is conducted using our novel python script RatePartitions. We conducted simulations to assess the performance of our new method, and we applied it to eight published multi-locus phylogenetic datasets, representing different taxonomic ranks within the insect order Lepidoptera (butterflies and moths) and one phylogenomic dataset, which included ultra-conserved elements as well as introns.

METHODS

We used TIGER-rates to generate relative evolutionary rates for all sites in the alignments. Then, using RatePartitions, we partitioned the data into partitions based on their relative evolutionary rate. RatePartitions applies a simple formula that ensures a distribution of sites into partitions following the distribution of rates of the characters from the full dataset. This ensures that the invariable sites are placed in a partition with slowly evolving sites, avoiding the pitfalls of previously used methods, such as k-means. Different partitioning strategies were evaluated using BIC scores as calculated by PartitionFinder.

RESULTS

Simulations did not highlight any misbehaviour of our partitioning approach, even under difficult parameter conditions or missing data. In all eight phylogenetic datasets, partitioning using TIGER-rates and RatePartitions was significantly better as measured by the BIC scores than other partitioning strategies, such as the commonly used partitioning by gene and codon position. We compared the resulting topologies and node support for these eight datasets as well as for the phylogenomic dataset.

DISCUSSION

We developed a new method of partitioning phylogenetic datasets without using any prior knowledge (e.g. DNA sequence evolution). This method is entirely based on the properties of the data being analysed and can be applied to DNA sequences (protein-coding, introns, ultra-conserved elements), protein sequences, as well as morphological characters. A likely explanation for why our method performs better than other tested partitioning strategies is that it accounts for the heterogeneity in the data to a much greater extent than when data are simply subdivided based on prior knowledge.

Macroecology and macroevolution of the latitudinal diversity gradient in ants

The latitudinal diversity gradient—the tendency for more species to occur toward the equator—is the dominant pattern of life on Earth, yet the mechanisms responsible for it remain largely unexplained. Recently, the analysis of global data has led to advances in understanding, but these advances have been mostly limited to vertebrates and trees and have not provided consensus answers. Here we synthesize large-scale geographic, phylogenetic, and fossil data for an exemplar invertebrate group—ants—and investigate whether the latitudinal diversity gradient arose due to higher rates of net diversification in the tropics, or due to a longer time period to accumulate diversity due to Earth’s climatic history. We find that latitudinal affinity is highly conserved, temperate clades are young and clustered within tropical clades, and diversification rate shows no systematic variation with latitude. These results indicate that diversification time—and not rate—is the main driver of the diversity gradient in ants.

Multiple hypotheses have been proposed for the declining biodiversity gradient between the tropics and poles. Here, the authors compile and analyze geographic data for all ant species and large-scale phylogenies, suggesting that diversification time drives the latitudinal diversity gradient in ants.

Colobopsis explodens sp. n., model species for studies on "exploding ants" (Hymenoptera, Formicidae), with biological notes and first illustrations of males of the Colobopsis cylindrica group

A taxonomic description of all castes of Colobopsisexplodens Laciny & Zettel, sp. n. from Borneo, Thailand, and Malaysia is provided, which serves as a model species for biological studies on “exploding ants” in Southeast Asia. The new species is a member of the Colobopsiscylindrica (COCY) group and falls into a species complex that has been repeatedly summarized under the name Colobopsissaundersi (Emery, 1889) (formerly Camponotussaundersi). The COCY species group is known under its vernacular name “exploding ants” for a unique behaviour: during territorial combat, workers of some species sacrifice themselves by rupturing their gaster and releasing sticky and irritant contents of their hypertrophied mandibular gland reservoirs to kill or repel rivals. This study includes first illustrations and morphometric characterizations of males of the COCY group: Colobopsisexplodens Laciny & Zettel, sp. n. and Colobopsisbadia (Smith, 1857). Characters of male genitalia and external morphology are compared with other selected taxa of Camponotini. Preliminary notes on the biology of C.explodens Laciny & Zettel, sp. n. are provided. To fix the species identity of the closely related C.badia, a lectotype from Singapore is designated. The following taxonomic changes within the C.saundersi complex are proposed: Colobopsissolenobia (Menozzi, 1926), syn. n. and Colobopsistrieterica (Menozzi, 1926), syn. n. are synonymized with Colobopsiscorallina Roger, 1863, a common endemic species of the Philippines. Colobopsissaginata Stitz, 1925, stat. n., hitherto a subspecies of C.badia, is raised to species level.

The assembly of ant-farmed gardens: mutualism specialization following host broadening

Ant-gardens (AGs) are ant/plant mutualisms in which ants farm epiphytes in return for nest space and food rewards. They occur in the Neotropics and Australasia, but not in Africa, and their evolutionary assembly remains unclear. We here use phylogenetic frameworks for important AG lineages in Australasia, namely the ant genus Philidris and domatium-bearing ferns (Lecanopteris) and flowering plants in the Apocynaceae (Hoya and Dischidia) and Rubiaceae (Myrmecodia, Hydnophytum, Anthorrhiza, Myrmephytum and Squamellaria). Our analyses revealed that in these clades, diaspore dispersal by ants evolved at least 13 times, five times in the Late Miocene and Pliocene in Australasia and seven times during the Pliocene in Southeast Asia, after Philidris ants had arrived there, with subsequent dispersal between these two areas. A uniquely specialized AG system evolved in Fiji at the onset of the Quaternary. The farming in the same AG of epiphytes that do not offer nest spaces suggests that a broadening of the ants' plant host spectrum drove the evolution of additional domatium-bearing AG-epiphytes by selecting on pre-adapted morphological traits. Consistent with this, we found a statistical correlation between the evolution of diaspore dispersal by ants and domatia in all three lineages. Our study highlights how host broadening by a symbiont has led to new farming mutualisms.

Insights into the evolution, biogeography and natural history of the acorn ants, genus Temnothorax Mayr (hymenoptera: Formicidae)

BACKGROUND

Temnothorax (Formicidae: Myrmicinae) is a diverse genus of ants found in a broad spectrum of ecosystems across the northern hemisphere. These diminutive ants have long served as models for social insect behavior, leading to discoveries about social learning and inspiring hypotheses about the process of speciation and the evolution of social parasitism. This genus is highly morphologically and behaviorally diverse, and this has caused a great deal of taxonomic confusion in recent years. Past efforts to estimate the phylogeny of this genus have been limited in taxonomic scope, leaving the broader evolutionary patterns in Temnothorax unclear. To establish the monophyly of Temnothorax, resolve the evolutionary relationships, reconstruct the historical biogeography and investigate trends in the evolution of key traits, I generated, assembled, and analyzed two molecular datasets: a traditional multi-locus Sanger sequencing dataset, and an ultra-conserved element (UCE) dataset. Using maximum likelihood, Bayesian, and summary-coalescent based approaches, I analyzed 22 data subsets consisting of 103 ingroup taxa and a maximum of 1.8 million base pairs in 2485 loci.

RESULTS

The results of this study suggest an origin of Temnothorax at the Eocene-Oligocene transition, concerted transitions to arboreal nesting habits in several clades during the Oligocene, coinciding with ancient global cooling, and several convergent origins of social parasitism in the Miocene and Pliocene. As with other Holarctic taxa, Temnothorax has a history of migration across Beringia during the Miocene.

CONCLUSIONS

Temnothorax is corroborated as a natural group, and the notion that many of the historical subgeneric and species group concepts are artificial is reinforced. The strict form of Emery's Rule, in which a socially parasitic species is sister to its host species, is not well supported in Temnothorax.

Rediscovery of the enigmatic fungus-farming ant "Mycetosoritis" asper Mayr (Hymenoptera: Formicidae): Implications for taxonomy, phylogeny, and the evolution of agriculture in ants

We report the rediscovery of the exceedingly rarely collected and enigmatic fungus-farming ant species Mycetosoritis asper. Since the description of the type specimen in 1887, only four additional specimens are known to have been added to the world's insect collections. Its biology is entirely unknown and its phylogenetic position within the fungus-farming ants has remained puzzling due to its aberrant morphology. In 2014 we excavated and collected twenty-one colonies of M. asper in the Floresta Nacional de Chapecó in Santa Catarina, Brazil. We describe here for the first time the male and larva of the species and complement the previous descriptions of both the queen and the worker. We describe, also for the first time, M. asper biology, nest architecture, and colony demographics, and identify its fungal cultivar. Molecular phylogenetic analyses indicate that both M. asper and M. clorindae are members of the genus Cyphomyrmex, which we show to be paraphyletic as currently defined. More precisely, M. asper is a member of the Cyphomyrmex strigatus group, which we also show to be paraphyletic with respect to the genus Mycetophylax. Based on these results, and in the interest of taxonomic stability, we transfer the species M. asper, M. clorindae, and all members of the C. strigatus group to the genus Mycetophylax, the oldest available name for this clade. Based on ITS sequence data, Mycetophylax asper practices lower agriculture, cultivating a fungal species that belongs to lower-attine fungal Clade 2, subclade F.

Model selection in statistical historical biogeography of Neotropical insects-The Exophthalmus genus complex (Curculionidae: Entiminae)

Statistical historical biogeographic methods rely on models that represent various biogeographic processes. Until recently model selection in this domain was not widely used, and the impact of differential model selection on inferring biogeographic scenarios was not well understood. Focusing on Neotropical weevils in the Exophthalmus genus complex (EGC) (Insecta: Curculionidae: Entiminae), we compare three commonly used biogeographic models - DIVA (Dispersal-Vicariance Analysis), DEC (Dispersal-Extinction-Cladogenesis) and BayArea (Bayesian Analysis of Biogeography), and examine the impact of modeling founder-event jump dispersal on historical biogeographic reconstructions. We also investigate the biogeographic events that have shaped patterns of distribution, diversification, and endemism in this weevil lineage. We sample representatives of 65 species of the EGC and 26 outgroup terminals from the Neotropics, including Caribbean islands and the mainland. We reconstruct a molecular phylogeny based on six genes and apply molecular dating using a relaxed clock with three fossil calibration points. Historical biogeographic estimations and alternative biogeographic models are computed and compared with the R package BioGeoBEARS. Model selection strongly favors biogeographic models that include founder-event jump dispersal. Without modeling jump dispersal, estimations based on the three biogeographic models are dramatically different, especially for early-diverging nodes. When jump dispersal is included, the three biogeographic models perform similarly. Accordingly, we show that the Neotropical mainland was colonized by Caribbean species in the early Miocene, and that in situ diversification accounts for a majority (∼75%) of the biogeographic events in the EGC. Our study highlights the need to assess wide-ranging historical biogeographic processes - including founder-event jump dispersal - for best-fitting statistical Caribbean biogeographic reconstructions. Moreover, colonization of the Neotropical mainland from the Caribbean reinforces the notion that islands can be an important source of continental diversity.

Where Fossils Dare and Males Matter: combined morphological and molecular analysis untangles the evolutionary history of the spider ant genus Leptomyrmex Mayr (Hymenoptera : Dolichoderinae)

The distinctive ant genus Leptomyrmex Mayr, 1862 had been thought to be endemic to Australasia for over 150 years, but enigmatic Neotropical fossils have challenged this view for decades. The present study responds to a recent and surprising discovery of extant Leptomyrmex species in Brazil with a thorough evaluation of the Dominican Republic fossil material, which dates to the Miocene. In the first case study of direct fossil inclusion within Formicidae Latreille, 1809, we incorporated both living and the extinct Leptomyrmex species. Through simultaneous analysis of molecular and morphological characters in both Bayesian and parsimony frameworks, we recovered the fossil taxon as sister-group to extant Leptomyrmex in Brazil while considering the influence of taxonomic and character sampling on inferred hypotheses relating to tree topology, biogeography and morphological evolution. We also identified potential loss of signal in the binning of morphological characters and tested the impact of parameterisation on divergence date estimation. Our results highlight the importance of securing sufficient taxon sampling for extant lineages when incorporating fossils and underscore the utility of diverse character sources in accurate placement of fossil terminals. Specifically, we find that fossil placement in this group is influenced by the inclusion of male-based characters and the newly discovered Neotropical ‘Lazarus taxon’.

Fitness and physiology of Adelges tsugae (Hemiptera: Adelgidae) in relation to the health of the eastern hemlock

The hemlock woolly adelgid, Adelges tsugae Annand is an invasive insect that frequently causes hemlock (Tsuga spp.) mortality in the eastern United States. Studies have shown that once healthy hemlocks become infested by the adelgid, nutrients are depleted from the tree, leading to both tree decline and a reduction of the adelgid population. Since A. tsugae is dependent on hemlock for nutrients, feeding on trees in poor health may affect the ability of the insect to obtain necessary nutrients and may consequently affect their physiological and population health. Trees were categorized as lightly or moderately impacted by A. tsugae based on quantitative and qualitative tree health measurements. Population health of A. tsugae on each tree was determined by measuring insect density and peak mean fecundity; A. tsugae physiological health was determined by measuring insect biomass, total carbon, carbohydrate, total nitrogen, and amino nitrogen levels. Adelges tsugae from moderately impacted trees exhibited significantly greater fecundity than from lightly impacted trees. However, A. tsugae from lightly impacted hemlocks contained significantly greater levels of carbohydrates, total nitrogen, and amino nitrogen. While the results of the physiological analysis generally support our hypothesis that A. tsugae on lightly impacted trees are healthier than those on moderately impacted trees, this was not reflected in the population health measurements. Adelges tsugae egg health in response to tree health should be verified. This study provides the first examination of A. tsugae physiological health in relation to standard A. tsugae population health measures on hemlocks of different health levels.

Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles

Deep level insect relationships are generally difficult to resolve, especially within taxa of the most diverse and species rich holometabolous orders. In beetles, the major diversity occurs in the Phytophaga, including charismatic groups such as leaf beetles, longhorn beetles and weevils. Bark and ambrosia beetles are wood boring weevils that contribute 12 percent of the diversity encountered in Curculionidae, one of the largest families of beetles with more than 50000 described species. Phylogenetic resolution in groups of Cretaceous age has proven particularly difficult and requires large quantity of data. In this study, we investigated 100 nuclear genes in order to select a number of markers with low evolutionary rates and high phylogenetic signal. A PCR screening using degenerate primers was applied to 26 different weevil species. We obtained sequences from 57 of the 100 targeted genes. Sequences from each nuclear marker were aligned and examined for detecting multiple copies, pseudogenes and introns. Phylogenetic informativeness (PI) and the capacity for reconstruction of previously established phylogenetic relationships were used as proxies for selecting a subset of the 57 amplified genes. Finally, we selected 16 markers suitable for large-scale phylogenetics of Scolytinae and related weevil taxa.

Combined hybridization and mitochondrial capture shape complex phylogeographic patterns in hybridogenetic Cataglyphis desert ants

Some species of Cataglyphis desert ants have evolved a hybridogenetic mode of reproduction at the social scale. In hybridogenetic populations, two distinct genetic lineages coexist. Non-reproductive offspring (workers) are hybrids of the two lineages, whereas sexual offspring (males and new queens) are produced by parthenogenesis and belong to the mother queen lineage. How this unusual reproductive system affects phylogeographic patterns and speciation processes remains completely unknown to date. Using one mitochondrial and four nuclear genes, we examined the phylogenetic relationships between three species of Cataglyphis (C. hispanica, C. humeya and C. velox) where complex DNA inheritance through social hybridogenesis may challenge phylogenetic inference. Our results bring two important insights. First, our data confirm a hybridogenetic mode of reproduction across the whole distribution range of the species C. hispanica. In contrast, they do not provide support for hybridogenesis in the populations sampled of C. humeya and C. velox. This suggests that these populations are not hybridogenetic, or that hybridogenesis is too recent to result in reciprocally monophyletic lineages on nuclear genes. Second, due to mitochondrial introgression between lineages (Darras and Aron, 2015), the faster-evolving COI marker is not lineage specific, hence, unsuitable to further investigate the segregation of lineages in the species studied. Different mitochondrial haplotypes occur in each locality sampled, resulting in strongly structured populations. This micro-allopatric structure leads to over-splitting species delimitation on mitochondrial gene, as every locality could potentially be considered a putative species; haploweb analyses of nuclear markers, however, yield species delimitations that are consistent with morphology. Overall, this study highlights how social hybridogenesis varies across species and shapes complex phylogeographic patterns.

Leaf beetles are ant-nest beetles: the curious life of the juvenile stages of case-bearers (Coleoptera, Chrysomelidae, Cryptocephalinae)

Although some species of Cryptocephalinae (Coleoptera: Chrysomelidae) have been documented with ants (Hymenoptera: Formicidae) for almost 200 years, information on this association is fragmentary. This contribution synthesizes extant literature and analysizes the data for biological patterns. Myrmecophily is more common in the tribe Clytrini than in Cryptocephalini, but not documented for Fulcidacini or the closely-related Lamprosomatinae. Myrmecophilous cryptocephalines (34 species in 14 genera) primarily live among formicine and myrmecines ants as hosts. These two ant lineages are putative sister-groups, with their root-node dated to between 77–90 mya. In the New World tropics, the relatively recent radiation of ants from moist forests to more xeric ecosystems might have propelled the association of cryptocephalines and ant nests. Literature records suggest that the defensive behavioral profile or chemical profile (or both) of these ants has been exploited by cryptocephalines. Another pattern appears to be that specialized natural enemies, especially parasitoid Hymenoptera, exploit cryptocephaline beetles inside the ant nests. With the extant data at hand, based on the minimum age of a fossil larva dated to 45 mya, we can infer that the origin of cryptocephaline myrmecophily could have arisen within the Upper Cretaceous or later. It remains unknown how many times myrmecophily has appeared, or how old is the behavior. This uncertainty is compounded by incongruent hypotheses about the origins of Chrysomelidae and angiosperm-associated lineages of cryptocephalines. Living with ants offers multiple advantages that might have aided the colonization of xeric environments by some cryptocephaline species.

Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

BACKGROUND

Ultraconserved elements (UCEs) have been successfully used in phylogenomics for a variety of taxa, but their power in phylogenetic inference has yet to be extensively compared with that of traditional Sanger sequencing data sets. Moreover, UCE data on invertebrates, including insects, are sparse. We compared the phylogenetic informativeness of 959 UCE loci with a multi-locus data set of ten nuclear markers obtained via Sanger sequencing, testing the ability of these two types of data to resolve and date the evolutionary history of the second most species-rich subfamily of ants in the world, the Formicinae.

RESULTS

Phylogenetic analyses show that UCEs are superior in resolving ancient and shallow relationships in formicine ants, demonstrated by increased node support and a more resolved phylogeny. Phylogenetic informativeness metrics indicate a twofold improvement relative to the 10-gene data matrix generated from the identical set of taxa. We were able to significantly improve formicine classification based on our comprehensive UCE phylogeny. Our divergence age estimations, using both UCE and Sanger data, indicate that crown-group Formicinae are older (104-117 Ma) than previously suggested. Biogeographic analyses infer that the diversification of the subfamily has occurred on all continents with no particular hub of cladogenesis.

CONCLUSIONS

We found UCEs to be far superior to the multi-locus data set in estimating formicine relationships. The early history of the clade remains uncertain due to ancient rapid divergence events that are unresolvable even with our genomic-scale data, although this might be largely an effect of several problematic taxa subtended by long branches. Our comparison of divergence ages from both Sanger and UCE data demonstrates the effectiveness of UCEs for dating analyses. This comparative study highlights both the promise and limitations of UCEs for insect phylogenomics, and will prove useful to the growing number of evolutionary biologists considering the transition from Sanger to next-generation sequencing approaches.

Phylogenetic tests reject Emery's rule in the evolution of social parasitism in yellowjackets and hornets (Hymenoptera: Vespidae, Vespinae)

Social parasites exploit the brood-care behaviour and social structure of one or more host species. Within the social Hymenoptera there are different types of social parasitism. In its extreme form, species of obligate social parasites, or inquilines, do not have the worker caste and depend entirely on the workers of a host species to raise their reproductive offspring. The strict form of Emery's rule states that social parasites share immediate common ancestry with their hosts. Moreover, this rule has been linked with a sympatric origin of inquilines from their hosts. Here, we conduct phylogenetic analyses of yellowjackets and hornets based on 12 gene fragments and evaluate competing evolutionary scenarios to test Emery's rule. We find that inquilines, as well as facultative social parasites, are not the closest relatives of their hosts. Therefore, Emery's rule in its strict sense is rejected, suggesting that social parasites have not evolved sympatrically from their hosts in yellowjackets and hornets. However, the relaxed version of the rule is supported, as inquilines and their hosts belong to the same Dolichovespula clade. Furthermore, inquilinism has evolved only once in Dolichovespula.

Global phylogenetic structure of the hyperdiverse ant genus Pheidole reveals the repeated evolution of macroecological patterns

Adaptive radiations are of particular interest owing to what they reveal about the ecological and evolutionary regulation of biodiversity. This applies to localized island radiations such as Darwin's finches, and also to rapid radiations occurring on a global scale. Here we analyse the macroevolution and macroecology of Pheidole, a famously hyperdiverse and ecologically dominant ant genus. We generate and analyse four novel datasets: (i) a robust global phylogeny including 285 Pheidole species, (ii) a global database on regional Pheidole richness in 365 political areas summarizing over 97 000 individual records from more than 6500 studies, (iii) a global database of Pheidole richness from 3796 local communities and (iv) a database of Pheidole body sizes across species. Analysis of the potential climate drivers of richness revealed that the patterns are statistically very similar across different biogeographic regions, with both regional and local richness associated with the same coefficients of temperature and precipitation. This similarity occurs even though phylogenetic analysis shows that Pheidole reached dominance in communities through serial localized radiations into different biomes within different continents and islands. Pheidole body size distributions have likewise converged across geographical regions. We propose these cases of convergence indicate that the global radiation of Pheidole is structured by deterministic factors regulating diversification and diversity.

Resolving the phylogeny of a speciose spider group, the family Linyphiidae (Araneae)

For high-level molecular phylogenies, a comprehensive sampling design is a key factor for not only improving inferential accuracy, but also for maximizing the explanatory power of the resulting phylogeny. Two standing problems in molecular phylogenies are the unstable placements of some deep and long branches, and the phylogenetic relationships shown by robust supported clades conflict with recognized knowledge. Empirical and theoretical studies suggest that increasing taxon sampling is expected to ameliorate, if not resolve, both problems; however, sometimes neither the current taxonomic system nor the established phylogeny can provide sufficient information to guide additional sampling design. We examined the phylogeny of the spider family Linyphiidae, and selected ingroup species based on epigynal morphology, which can be reconstructed in a phylogenetic context. Our analyses resulted in seven robustly supported clades within linyphiids. The placements of four deep and long branches are sensitive to variations in both outgroup and ingroup sampling, suggesting the possibility of long branch attraction artifacts. Results of ancestral state reconstruction indicate that successive state transformations of the epigynal plate are associated with early cladogenetic events in linyphiid diversification. Representatives of different subfamilies were mixed together within well supported clades and examination revealed that their defining characters, as per traditional taxonomy, are homoplastic. Furthermore, our results demonstrated that increasing taxon sampling produced a more informative framework, which in turn helps to study character evolution and interpret the relationships among linyphiid lineages. Additional defining characters are needed to revise the linyphiid taxonomic system based on our phylogenetic hypothesis.

The effects of partitioning on phylogenetic inference

Partitioning is a commonly used method in phylogenetics that aims to accommodate variation in substitution patterns among sites. Despite its popularity, there have been few systematic studies of its effects on phylogenetic inference, and there have been no studies that compare the effects of different approaches to partitioning across many empirical data sets. In this study, we applied four commonly used approaches to partitioning to each of 34 empirical data sets, and then compared the resulting tree topologies, branch-lengths, and bootstrap support estimated using each approach. We find that the choice of partitioning scheme often affects tree topology, particularly when partitioning is omitted. Most notably, we find occasional instances where the use of a suboptimal partitioning scheme produces highly supported but incorrect nodes in the tree. Branch-lengths and bootstrap support are also affected by the choice of partitioning scheme, sometimes dramatically so. We discuss the reasons for these effects and make some suggestions for best practice.