An Eocene army ant.

Among social insects, army ants are exceptional in their voracious coordinated predation, nomadic life history and highly specialized wingless queens: the synthesis of these remarkable traits is referred to as the army ant syndrome. Despite molecular evidence that the army ant syndrome evolved twice during the mid-Cenozoic, once in the Neotropics and once in the Afrotropics, fossil army ants are markedly scarce, comprising a single known species from the Caribbean 16 Ma. Here we report the oldest army ant fossil and the first from the Eastern Hemisphere (EH), Dissimulodorylus perseus, preserved in Baltic amber dated to the Eocene. Using a combined morphological and molecular ultra conserved elements dataset spanning doryline lineages, we find that D. perseus is nested among extant EH army ants with affinities to Dorylus. Army ants are characterized by limited extant diversification throughout most of the Cenozoic; the discovery of D. perseus suggests an unexpected diversity of now-extinct army ant lineages in the Cenozoic, some of which were present in Continental Europe.

Ant phylogenomics reveals a natural selection hotspot preceding the origin of complex eusociality.

The evolution of eusociality has allowed ants to become one of the most conspicuous and ecologically dominant groups of organisms in the world. A large majority of the current ∼14,000 ant species belong to the formicoids,1 a clade of nine subfamilies that exhibit the most extreme forms of reproductive division of labor, large colony size,2 worker polymorphism,3 and extended queen longevity.4 The eight remaining non-formicoid subfamilies are less well studied, with few genomes having been sequenced so far and unclear phylogenetic relationships.5 By sequencing 65 genomes, we provide a robust phylogeny of the 17 ant subfamilies, retrieving high support to the controversial leptanillomorph clade (Leptanillinae and Martialinae) as the sister group to all other extant ants. Moreover, our genomic analyses revealed that the emergence of the formicoids was accompanied by an elevated number of positive selection events. Importantly, the top three gene functions under selection are linked to key features of complex eusociality, with histone acetylation being implicated in caste differentiation, gene silencing by RNA in worker sterility, and autophagy in longevity. These results show that the key pathways associated with eusociality have been under strong selection during the Cretaceous, suggesting that the molecular foundations of complex eusociality may have evolved rapidly in less than 20 Ma.

A taxonomic revision and a review of the biology of the North American seed-harvester ant genus Veromessor (Hymenoptera: Formicidae: Myrmicinae).

This paper provides a taxonomic revision and a review of the biology for the 10 species of North American seed-harvester ants in the genus Veromessor. Two new synonomies are proposed: V. julianus subsp. clarior W.M. Wheeler and Creighton 1934 new synonym and V. julianus subsp. manni W.M. Wheeler and Creighton 1934 new synonym are synonomized under V. julianus (Pergande, 1894). One new species is described: V. pseudolariversi new species (worker, queen, male), as a result of splitting V. lariversi Smith into two species based on morphological and genetic differences. We also diagnose previously undescribed queens and males for the following species: V. andrei (male), V. chamberlini (queen, male), V. chicoensis (queen, male), V. julianus (queen, male), and V. stoddardi (queen, male). Information on biology of each species is summarized, along with distribution maps and keys to workers, queens, and males. We then discuss the biology for species of Veromessor, focusing on several morphological and ecological traits that display strong variation across the relatively low number of species (10) in the genus. Morphological traits include degree of psammophore development, propodeal spine length, eye size and structure, and worker polymorphism and worker body size, while ecological traits include colony size and foraging method, seasonality of mating flights, mating frequency, and queen size and colony founding strategy.

The maintenance of polymorphism in an ancient social supergene.

Supergenes, regions of the genome with suppressed recombination between sets of functional mutations, contribute to the evolution of complex phenotypes in diverse systems. Excluding sex chromosomes, most supergenes discovered so far appear to be young, being found in one species or a few closely related species. Here, we investigate how a chromosome harbouring an ancient supergene has evolved over about 30 million years (Ma). The Formica supergene underlies variation in colony queen number in at least five species. We expand previous analyses of sequence divergence on this chromosome to encompass about 90 species spanning the Formica phylogeny. Within the nonrecombining region, the gene knockout contains 22 single nucleotide polymorphisms (SNPs) that are consistently differentiated between two alternative supergene haplotypes in divergent European Formica species, and we show that these same SNPs are present in most Formica clades. In these clades, including an early diverging Nearctic Formica clade, individuals with alternative genotypes at knockout also have higher differentiation in other portions of this chromosome. We identify hotspots of SNPs along this chromosome that are present in multiple Formica clades to detect genes that may have contributed to the emergence and maintenance of the genetic polymorphism. Finally, we infer three gene duplications on one haplotype, based on apparent heterozygosity within these genes in the genomes of haploid males. This study strengthens the evidence that this supergene originated early in the evolution of Formica and that just a few loci in this large region of suppressed recombination retain strongly differentiated alleles across contemporary Formica lineages.

The evolution of social parasitism in Formica ants revealed by a global phylogeny.

Studying the behavioral and life history transitions from a cooperative, eusocial life history to exploitative social parasitism allows for deciphering the conditions under which changes in behavior and social organization lead to diversification. The Holarctic ant genus Formica is ideally suited for studying the evolution of social parasitism because half of its 172 species are confirmed or suspected social parasites, which includes all three major classes of social parasitism known in ants. However, the life history transitions associated with the evolution of social parasitism in this genus are largely unexplored. To test competing hypotheses regarding the origins and evolution of social parasitism, we reconstructed a global phylogeny of Formica ants. The genus originated in the Old World ∼30 Ma ago and dispersed multiple times to the New World and back. Within Formica, obligate dependent colony-founding behavior arose once from a facultatively polygynous common ancestor practicing independent and facultative dependent colony foundation. Temporary social parasitism likely preceded or arose concurrently with obligate dependent colony founding, and dulotic social parasitism evolved once within the obligate dependent colony-founding clade. Permanent social parasitism evolved twice from temporary social parasitic ancestors that rarely practiced colony budding, demonstrating that obligate social parasitism can originate from a facultative parasitic background in socially polymorphic organisms. In contrast to permanently socially parasitic ants in other genera, the high parasite diversity in Formica likely originated via allopatric speciation, highlighting the diversity of convergent evolutionary trajectories resulting in nearly identical parasitic life history syndromes.

The biogeographic history of eelpouts and related fishes: Linking phylogeny, environmental change, and patterns of dispersal in a globally distributed fish group.

Modern genetic data sets present unprecedented opportunities to understand the evolutionary origins of diverse taxonomic groups. When the timing of key events is known, it is possible to investigate biogeographic history in the context of major phenomena (e.g., cooling of a major ocean). In this study, we investigated the biogeographic history of the suborder Zoarcoidei, a globally distributed fish group that includes species inhabiting both poles that produce antifreeze proteins to survive chronic subfreezing temperatures. We first generated a multi-locus, time-calibrated phylogeny for the group. We then used biogeographic modeling to reconstruct ancestral ranges across the tree and to quantify the type and frequency of biogeographic events (e.g., founder, dispersal). With these results, we considered how the cooling of the Southern and Arctic Oceans, which reached their present-day subfreezing temperatures 10-15 million years ago (Mya) and 2-3 Mya, respectively, may have shaped the group's evolutionary history, with an emphasis on the most speciose and widely distributed family, eelpouts (family Zoarcidae). Our phylogenetic results clarified the Zoarcoidei taxonomy and showed that the group began to diversify in the Oligocene ~31-32 Mya, with the center of origin for all families in north temperate waters. Within-area speciation was the most common biogeographic event in the group's history (80% of all events) followed by dispersal (20%). Finally, we only found evidence, albeit limited, for ocean cooling underpinning diversification of eelpouts living in the high Antarctic over the last 10 million years.

Ants of the Palouse Prairie: diversity and species composition in an endangered grassland.

Grasslands are globally imperilled ecosystems due to widespread conversion to agriculture and there is a concerted effort to catalogue arthropod diversity in grasslands to guide conservation decisions. The Palouse Prairie is one such endangered grassland; a mid-elevation habitat found in Washington and Idaho, United States. Ants (Formicidae) are useful indicators of biodiversity and historical ecological disturbance, but there has been no structured sampling of ants in the Palouse Prairie. To fill this gap, we employed a rapid inventory sampling approach using pitfall traps to capture peak ant activity in five habitat fragments. We complemented our survey with a systemic review of field studies for the ant species found in Palouse Prairie. Our field inventory yielded 17 ant species across 10 genera and our models estimate the total ant species pool to be 27. The highest ant diversity was found in an actively-managed ecological trust in Latah County, Idaho, suggesting that restoration efforts may increase biodiversity. We also report two rarely-collected ants in the Pacific Northwest and a microgyne that may represent an undescribed species related to Brachymyrmex depilis. Our score-counting review revealed that grassland ants in Palouse Prairie have rarely been studied previously and that more ant surveys in temperate grasslands have lagged behind sampling efforts of other global biomes.

Insect morphometry is reproducible under average investigation standards.

Morphometric research is being applied to a growing number and variety of organisms. Discoveries achieved via morphometric approaches are often considered highly transferable, in contrast to the tacit and idiosyncratic interpretation of discrete character states. The reliability of morphometric workflows in insect systematics has never been a subject of focused research, but such studies are sorely needed. In this paper, we assess the reproducibility of morphometric studies of ants where the mode of data collection is a shared routine.We compared datasets generated by eleven independent gaugers, that is, collaborators, who measured 21 continuous morphometric traits on the same pool of individuals according to the same protocol. The gaugers possessed a wide range of morphometric skills, had varying expertise among insect groups, and differed in their facility with measuring equipment. We used intraclass correlation coefficients (ICC) to calculate repeatability and reproducibility values (i.e., intra- and intergauger agreements), and we performed a multivariate permutational multivariate analysis of variance (PERMANOVA) using the Morosita index of dissimilarity with 9,999 iterations.The calculated average measure of intraclass correlation coefficients of different gaugers ranged from R = 0.784 to R = 0.9897 and a significant correlation was found between the repeatability and the morphometric skills of gaugers (p = 0.016). There was no significant association with the magnification of the equipment in the case of these rather small ants. The intergauger agreement, that is the reproducibility, varied between R = 0.872 and R = 0.471 (mean R = 0.690), but all gaugers arrived at the same two-species conclusion. A PERMANOVA test revealed no significant gauger effect on species identity (R 2 = 0.69, p = 0.58).Our findings show that morphometric studies are reproducible when observers follow the standard protocol; hence, morphometric findings are widely transferable and will remain a valuable data source for alpha taxonomy.

Comprehensive phylogeny of Myrmecocystus honey ants highlights cryptic diversity and infers evolution during aridification of the American Southwest.

The New World ant genus Myrmecocystus Wesmael, 1838 (Formicidae: Formicinae: Lasiini) is endemic to arid and semi-arid habitats of the western United States and Mexico. Several intriguing life history traits have been described for the genus, the best-known of which are replete workers, that store liquified food in their largely expanded crops and are colloquially referred to as "honeypots". Despite their interesting biology and ecological importance for arid ecosystems, the evolutionary history of Myrmecocystus ants is largely unknown and the current taxonomy presents an unsatisfactory systematic framework. We use ultraconserved elements to infer the evolutionary history of Myrmecocystus ants and provide a comprehensive, dated phylogenetic framework that clarifies the molecular systematics within the genus with high statistical support, reveals cryptic diversity, and reconstructs ancestral foraging activity. Using maximum likelihood, Bayesian and species tree approaches on a data set of 134 ingroup specimens (including samples from natural history collections and type material), we recover largely identical topologies that leave the position of only few clades uncertain and cover the intra- and interspecific variation of 28 of the 29 described and six undescribed species. In addition to traditional support values, such as bootstrap and posterior probability, we quantify genealogical concordance to estimate the effects of conflicting evolutionary histories on phylogenetic inference. Our analyses reveal that the current taxonomic classification of the genus is inconsistent with the molecular phylogenetic inference, and we identify cryptic diversity in seven species. Divergence dating suggests that the split between Myrmecocystus and its sister taxon Lasius occurred in the early Miocene. Crown group Myrmecocystus started diversifying about 14.08 Ma ago when the gradual aridification of the southwestern United States and northern Mexico led to formation of the American deserts and to adaptive radiations of many desert taxa.

Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants.

Knowledge of the internal phylogeny and evolutionary history of ants (Formicidae), the world's most species-rich clade of eusocial organisms, has dramatically improved since the advent of molecular phylogenetics. A number of relationships at the subfamily level, however, remain uncertain. Key unresolved issues include placement of the root of the ant tree of life and the relationships among the so-called poneroid subfamilies. Here we assemble a new data set to attempt a resolution of these two problems and carry out divergence dating, focusing on the age of the root node of crown Formicidae. For the phylogenetic analyses we included data from 110 ant species, including the key species Martialis heureka. We focused taxon sampling on non-formicoid lineages of ants to gain insight about deep nodes in the ant phylogeny. For divergence dating we retained a subset of 62 extant taxa and 42 fossils in order to approximate diversified sampling in the context of the fossilized birth-death process. We sequenced 11 nuclear gene fragments for a total of ∼7.5 kb and investigated the DNA sequence data for the presence of among-taxon compositional heterogeneity, a property known to mislead phylogenetic inference, and for its potential to affect the rooting of the ant phylogeny. We found sequences of the Leptanillinae and several outgroup taxa to be rich in adenine and thymine (51% average AT content) compared to the remaining ants (45% average). To investigate whether this heterogeneity could bias phylogenetic inference we performed outgroup removal experiments, analysis of compositionally homogeneous sites, and a simulation study. We found that compositional heterogeneity indeed appears to affect the placement of the root of the ant tree but has limited impact on more recent nodes. Our findings have implications for outgroup choice in phylogenetics, which should be made not only on the basis of close relationship to the ingroup, but should also take into account sequence divergence and other properties relative to the ingroup. We put forward a hypothesis regarding the rooting of the ant phylogeny, in which Martialis and the Leptanillinae together constitute a clade that is sister to all other ants. After correcting for compositional heterogeneity this emerges as the best-supported hypothesis of relationships at deep nodes in the ant tree. The results of our divergence dating under the fossilized birth-death process and diversified sampling suggest that the crown Formicidae originated during the Albian or Aptian ages of the Lower Cretaceous (103-124 Ma). In addition, we found support for monophyletic poneroids comprising the subfamilies Agroecomyrmecinae, Amblyoponinae, Apomyrminae, Paraponerinae, Ponerinae, and Proceratiinae, and well-supported relationships among these subfamilies except for the placement of Proceratiinae and (Amblyoponinae + Apomyrminae). Our phylogeny also highlights the non-monophyly of several ant genera, including Protanilla and Leptanilla in the Leptanillinae, Proceratium in the Proceratiinae, and Cryptopone, Euponera, and Mesoponera within the Ponerinae.

Convergent Evolution of the Army Ant Syndrome and Congruence in Big-Data Phylogenetics.

Army ants are a charismatic group of organisms characterized by a suite of morphological and behavioral adaptations that includes obligate collective foraging, frequent colony relocation, and highly specialized wingless queens. This army ant syndrome underlies the ecological success of army ants and its evolution has been the subject of considerable debate. It has been argued to have arisen once or multiple times within the ant subfamily Dorylinae. To address this question in a phylogenetic framework I generated data from 2166 loci and a comprehensive taxon sampling representing all 27 genera and 155 or approximately 22% of doryline species. Most analyses show strong support for convergent evolution of the army ant syndrome in the Old and New World but certain relationships are sensitive to analytics. I examine the signal present in this data set and find that conflict is diminished when only loci less likely to violate common phylogenetic model assumptions are considered. I also provide a temporal and spatial context for doryline evolution with time-calibrated, biogeographic, and diversification rate shift analyses. This study shows that the army ant syndrome is both an example of remarkable convergence of a complex set of traits and a case of long-term evolutionary stasis. The sensitivity of some of the phylogenetic results underscores the need for cautious analysis of phylogenomic data and calls for more efficient algorithms employing better-fitting models of molecular evolution. Congruence among results obtained using different analytics may be used to assess robustness in phylogenomics.

Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids.

The onset of phylogenomics has contributed to the resolution of numerous challenging evolutionary questions while offering new perspectives regarding biodiversity. However, in some instances, analyses of large genomic datasets can also result in conflicting estimates of phylogeny. Here, we present the first phylogenomic scale study of a dipteran parasitoid family, built upon anchored hybrid enrichment and transcriptomic data of 240 loci of 43 ingroup acrocerid taxa. A new hypothesis for the timing of spider fly evolution is proposed, wielding recent advances in divergence time dating, including the fossilized birth-death process to show that the origin of Acroceridae is younger than previously proposed. To test the robustness of our phylogenetic inferences, we analyzed our datasets using different phylogenetic estimation criteria, including supermatrix and coalescent-based approaches, maximum-likelihood and Bayesian methods, combined with other approaches such as permutations of the data, homogeneous versus heterogeneous models, and alternative data and taxon sets. Resulting topologies based on amino acids and nucleotides are both strongly supported but critically discordant, primarily in terms of the monophyly of Panopinae. Conflict was not resolved by controlling for compositional heterogeneity and saturation in third codon positions, which highlights the need for a better understanding of how different biases affect different data sources. In our study, results based on nucleotides were both more robust to alterations of the data and different analytical methods and more compatible with our current understanding of acrocerid morphology and patterns of host usage.

Advances using molecular data in insect systematics.

The size of molecular datasets has been growing exponentially since the mid 1980s, and new technologies have now dramatically increased the slope of this increase. New datasets include genomes, transcriptomes, and hybrid capture data, producing hundreds or thousands of loci. With these datasets, we are approaching a consensus on the higher level insect phylogeny. Huge datasets can produce new challenges in interpreting branch support, and new opportunities in developing better models and more sophisticated partitioning schemes. Dating analyses are improving as we recognize the importance of careful fossil calibration selection. With thousands of genes now available, coalescent methods have come of age. Barcode libraries continue to expand, and new methods are being developed for incorporating them into phylogenies with tens of thousands of individuals.

Generic revision of the ant subfamily Dorylinae (Hymenoptera, Formicidae).

The generic classification of the ant subfamily Dorylinae is revised, with the aim of facilitating identification of easily-diagnosable monophyletic genera. The new classification is based on recent molecular phylogenetic evidence and a critical reappraisal of doryline morphology. New keys and diagnoses based on workers and males are provided, along with reviews of natural history and phylogenetic relationships, distribution maps, and a list of valid species for each lineage. Twenty-eight genera (27 extant and 1 extinct) are recognized within the subfamily, an increase from 20 in the previous classification scheme. Species classified in the polyphyletic Cerapachys and Sphinctomyrmex prior to this publication are here distributed among 9 and 3 different genera, respectively. Amyrmex and Asphinctanilloides are synonymized under Leptanilloides and the currently recognized subgenera are synonymized for Dorylus. No tribal classification is proposed for the subfamily, but several apparently monophyletic genus-groups are discussed. Valid generic names recognized here include: Acanthostichus (= Ctenopyga), Aenictogiton, Aenictus (= Paraenictus, Typhlatta), Cerapachys (= Ceratopachys), Cheliomyrmex, Chrysapace gen. rev., Cylindromyrmex (= Holcoponera, Hypocylindromyrmex, Metacylindromyrmex), Dorylus (= Alaopone syn. n., Anomma syn. n., Cosmaecetes, Dichthadia syn. n., Rhogmus syn. n., Shuckardia, Sphecomyrmex, Sphegomyrmex, Typhlopone syn. n.), Eburopone gen. n., Eciton (= Camptognatha, Holopone, Mayromyrmex), Eusphinctus gen. rev., Labidus (= Nycteresia, Pseudodichthadia), Leptanilloides (= Amyrmex syn. n., Asphinctanilloides syn. n.), Lioponera gen. rev. (= Neophyracaces syn. n., Phyracaces syn. n.), Lividopone, Neivamyrmex (= Acamatus, Woitkowskia), Neocerapachys gen. n., Nomamyrmex, Ooceraea gen. rev. (= Cysias syn. n.), Parasyscia gen. rev., †Procerapachys, Simopone, Sphinctomyrmex, Syscia gen. rev., Tanipone, Vicinopone, Yunodorylus gen. rev., Zasphinctus gen. rev. (= Aethiopopone syn. n., Nothosphinctus syn. n.).

AMAS: a fast tool for alignment manipulation and computing of summary statistics.

The amount of data used in phylogenetics has grown explosively in the recent years and many phylogenies are inferred with hundreds or even thousands of loci and many taxa. These modern phylogenomic studies often entail separate analyses of each of the loci in addition to multiple analyses of subsets of genes or concatenated sequences. Computationally efficient tools for handling and computing properties of thousands of single-locus or large concatenated alignments are needed. Here I present AMAS (Alignment Manipulation And Summary), a tool that can be used either as a stand-alone command-line utility or as a Python package. AMAS works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. The manipulation functions include conversions among popular formats, concatenation, extracting sites and splitting according to a pre-defined partitioning scheme, creation of replicate data sets, and removal of taxa. The statistics calculated include the number of taxa, alignment length, total count of matrix cells, overall number of undetermined characters, percent of missing data, AT and GC contents (for DNA alignments), count and proportion of variable sites, count and proportion of parsimony informative sites, and counts of all characters relevant for a nucleotide or amino acid alphabet. AMAS is particularly suitable for very large alignments with hundreds of taxa and thousands of loci. It is computationally efficient, utilizes parallel processing, and performs better at concatenation than other popular tools. AMAS is a Python 3 program that relies solely on Python's core modules and needs no additional dependencies. AMAS source code and manual can be downloaded from http://github.com/marekborowiec/AMAS/ under GNU General Public License.

Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa.

BACKGROUND: Understanding the phylogenetic relationships among major lineages of multicellular animals (the Metazoa) is a prerequisite for studying the evolution of complex traits such as nervous systems, muscle tissue, or sensory organs. Transcriptome-based phylogenies have dramatically improved our understanding of metazoan relationships in recent years, although several important questions remain. The branching order near the base of the tree, in particular the placement of the poriferan (sponges, phylum Porifera) and ctenophore (comb jellies, phylum Ctenophora) lineages is one outstanding issue. Recent analyses have suggested that the comb jellies are sister to all remaining metazoan phyla including sponges. This finding is surprising because it suggests that neurons and other complex traits, present in ctenophores and eumetazoans but absent in sponges or placozoans, either evolved twice in Metazoa or were independently, secondarily lost in the lineages leading to sponges and placozoans. RESULTS: To address the question of basal metazoan relationships we assembled a novel dataset comprised of 1080 orthologous loci derived from 36 publicly available genomes representing major lineages of animals. From this large dataset we procured an optimized set of partitions with high phylogenetic signal for resolving metazoan relationships. This optimized data set is amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. Our analyses strongly support the Ctenophora as the sister lineage to other Metazoa. We find no support for the traditional view uniting the ctenophores and Cnidaria. Our findings are supported by Bayesian comparisons of topological hypotheses and we find no evidence that they are biased by long-branch attraction. CONCLUSIONS: Our study further clarifies relationships among early branching metazoan lineages. Our phylogeny supports the still-controversial position of ctenophores as sister group to all other metazoans. This study also provides a workflow and computational tools for minimizing systematic bias in genome-based phylogenetic analyses. Future studies of metazoan phylogeny will benefit from ongoing efforts to sequence the genomes of additional invertebrate taxa that will continue to inform our view of the relationships among the major lineages of animals.

Studies on California ants: a review of the genus Temnothorax (Hymenoptera, Formicidae).

The following ten new species of the ant genus Temnothorax are described and illustrated: T. anaphalantus (California, Baja California), T. arboreus (California), T. caguatan (Oregon, California, Baja California), T. morongo (California, Baja California), T. myrmiciformis (California, Baja California), T. nuwuvi (Nevada), T. paiute (California, Nevada), T. pseudandrei (Arizona, California), T. quasimodo (California) and T. wardi (California). A key to workers of the twenty-two Temnothorax species known or expected to occur in California is provided.