The evolutionary history of bees in time and space

Bees are the most significant pollinators of flowering plants. This partnership began ca. 120 million years ago, but the uncertainty of how and when bees spread across the planet has greatly obscured investigations of this key mutualism. We present a novel analysis of bee biogeography using extensive new genomic and fossil data to demonstrate that bees originated in Western Gondwana (Africa and South America). Bees likely originated in the Early Cretaceous, shortly before the breakup of Western Gondwana, and the early evolution of any major bee lineage is associated with either the South American or African land masses. Subsequently, bees colonized northern continents via a complex history of vicariance and dispersal. The notable early absences from large landmasses, particularly in Australia and India, have important implications for understanding the assembly of local floras and diverse modes of pollination. How bees spread around the world from their hypothesized Southern Hemisphere origin parallels the histories of numerous flowering plant clades, providing an essential step to studying the evolution of angiosperm pollination syndromes in space and time.

Novel Microsatellite Markers for Osmia lignaria (Hymenoptera: Megachilidae): A North American Pollinator of Agricultural Crops and Wildland Plants

Comprehensive decisions on the management of commercially produced bees, depend largely on associated knowledge of genetic diversity. In this study, we present novel microsatellite markers to support the breeding, management, and conservation of the blue orchard bee, Osmia lignaria Say (Hymenoptera: Megachilidae). Native to North America, O. lignaria has been trapped from wildlands and propagated on-crop and used to pollinate certain fruit, nut, and berry crops. Harnessing the O. lignaria genome assembly, we identified 59,632 candidate microsatellite loci in silico, of which 22 were tested using molecular techniques. Of the 22 loci, 12 loci were in Hardy-Weinberg equilibrium (HWE), demonstrated no linkage disequilibrium (LD), and achieved low genotyping error in two Intermountain North American wild populations in Idaho and Utah, USA. We found no difference in population genetic diversity between the two populations, but there was evidence for low but significant population differentiation. Also, to determine if these markers amplify in other Osmia, we assessed 23 species across the clades apicata, bicornis, emarginata, and ribifloris. Nine loci amplified in three species/subspecies of apicata, 22 loci amplified in 11 species/subspecies of bicornis, 11 loci amplified in seven species/subspecies of emarginata, and 22 loci amplified in two species/subspecies of ribifloris. Further testing is necessary to determine the capacity of these microsatellite loci to characterize genetic diversity and structure under the assumption of HWE and LD for species beyond O. lignaria. These markers will inform the conservation and commercial use of trapped and managed O. lignaria and other Osmia species for both agricultural and nonagricultural systems.

Phylogenetic relationships and the evolution of host preferences in the largest clade of brood parasitic bees (Apidae: Nomadinae)

Brood parasites (also known as cleptoparasites) represent a substantial fraction of global bee diversity. Rather than constructing their own nests, these species instead invade those of host bees to lay their eggs. Larvae then hatch and consume the food provisions intended for the host's offspring. While this life history strategy has evolved numerous times across the phylogeny of bees, the oldest and most speciose parasitic clade is the subfamily Nomadinae (Apidae). However, the phylogenetic relationships among brood parasitic apids both within and outside the Nomadinae have not been fully resolved. Here, we present new findings on the phylogeny of this diverse group of brood parasites based on ultraconserved element (UCE) sequence data and extensive taxon sampling with 114 nomadine species representing all tribes. We suggest a broader definition of the subfamily Nomadinae to describe a clade that includes almost all parasitic members of the family Apidae. The tribe Melectini forms the sister group to all other Nomadinae, while the remainder of the subfamily is composed of two sister clades: a "nomadine line" representing the former Nomadinae sensu stricto, and an "ericrocidine line" that unites several mostly Neotropical lineages. We find the tribe Osirini Handlirsch to be polyphyletic, and divide it into three lineages, including the newly described Parepeolini trib. nov. In addition to our taxonomic findings, we use our phylogeny to explore the evolution of different modes of parasitism, detecting two independent transitions from closed-cell to open-cell parasitism. Finally, we examine how nomadine host-parasite associations have evolved over time. In support of Emery's rule, which suggests close relationships between hosts and parasites, we confirm that the earliest nomadines were parasites of their close free-living relatives within the family Apidae, but that over time their host range broadened to include more distantly related hosts spanning the diversity of bees. This expanded breadth of host taxa may also be associated with the transition to open-cell parasitism.

Partitioned Gene-Tree Analyses and Gene-Based Topology Testing Help Resolve Incongruence in a Phylogenomic Study of Host-Specialist Bees (Apidae: Eucerinae)

Incongruence among phylogenetic results has become a common occurrence in analyses of genome-scale data sets. Incongruence originates from uncertainty in underlying evolutionary processes (e.g., incomplete lineage sorting) and from difficulties in determining the best analytical approaches for each situation. To overcome these difficulties, more studies are needed that identify incongruences and demonstrate practical ways to confidently resolve them. Here, we present results of a phylogenomic study based on the analysis 197 taxa and 2,526 ultraconserved element (UCE) loci. We investigate evolutionary relationships of Eucerinae, a diverse subfamily of apid bees (relatives of honey bees and bumble bees) with >1,200 species. We sampled representatives of all tribes within the group and >80% of genera, including two mysterious South American genera, Chilimalopsis and Teratognatha. Initial analysis of the UCE data revealed two conflicting hypotheses for relationships among tribes. To resolve the incongruence, we tested concatenation and species tree approaches and used a variety of additional strategies including locus filtering, partitioned gene-trees searches, and gene-based topological tests. We show that within-locus partitioning improves gene tree and subsequent species-tree estimation, and that this approach, confidently resolves the incongruence observed in our data set. After exploring our proposed analytical strategy on eucerine bees, we validated its efficacy to resolve hard phylogenetic problems by implementing it on a published UCE data set of Adephaga (Insecta: Coleoptera). Our results provide a robust phylogenetic hypothesis for Eucerinae and demonstrate a practical strategy for resolving incongruence in other phylogenomic data sets.

Contribution to the knowledge of the bumblebee fauna of Afghanistan (Hymenoptera, Apidae, Bombus Latreille)

Bumblebees (Hymenoptera: Apidae: genus Bombus Latreille, 1802) constitute an important group of pollinators for many wild plants and crops in north temperate regions and South America. Although knowledge of these insects has been increasing over the last decades, some geographic areas remain poorly studied and additions to the knowledge of their faunas are infrequent. Afghanistan is one example of a country that is currently underrepresented in the scientific literature despite its high species diversity. For this study, more than 420 new occurrence records were gathered for 17 bumblebee species belonging to all eight subgenera recorded in the country, including the first record of a species closely related to the Blongipennis group. Additionally, the first standardized database for Afghan bees is launched, which we hope will be enriched in the future to allow further assessments of population trends for the bumblebees of Afghanistan. Finally, the previously published species records for the country are discussed considering the most recent taxonomic revisions of the genus and key perspectives are highlighted for further work in this understudied country and neighboring regions.

Agriculturally dominated landscapes reduce bee phylogenetic diversity and pollination services

Land-use change threatens global biodiversity and may reshape the tree of life by favoring some lineages over others. Whether phylogenetic diversity loss compromises ecosystem service delivery remains unknown. We address this knowledge gap using extensive genomic, community, and crop datasets to examine relationships among land use, pollinator phylogenetic structure, and crop production. Pollinator communities in highly agricultural landscapes contain 230 million fewer years of evolutionary history; this loss was strongly associated with reduced crop yield and quality. Our study links landscape-mediated changes in the phylogenetic structure of natural communities to the disruption of ecosystem services. Measuring conservation success by species counts alone may fail to protect ecosystem functions and the full diversity of life from which they are derived.

Genomes of the Hymenoptera

Hymenoptera is the second-most sequenced arthropod order, with 52 publically archived genomes (71 with ants, reviewed elsewhere), however these genomes do not capture the breadth of this very diverse order (Figure 1, Table 1). These sequenced genomes represent only 15 of the 97 extant families. Although at least 55 other genomes are in progress in an additional 11 families (see Table 2), stinging wasps represent 35 (67%) of the available and 42 (76%) of the in progress genomes. A more comprehensive catalog of hymenopteran genomes is needed for research into the evolutionary processes underlying the expansive diversity in terms of ecology, behavior, and physiological traits within this group. Additional sequencing is needed to generate an assembly for even 0.05% of the estimated 1 million hymenopteran species, and we recommend premier level assemblies for at least 0.1% of the >150,000 named species dispersed across the order. Given the haplodiploid sex determination in Hymenoptera, haploid male sequencing will help minimize genome assembly issues to enable higher quality genome assemblies.

Extensive mitochondrial heteroplasmy in the neotropical ants of the Ectatomma ruidum complex (Formicidae: Ectatomminae)

We assembled mitogenomes from 21 ant workers assigned to four morphospecies (E. ruidum spp. 1-4) and putative hybrids of the Ectatomma ruidum complex (E. ruidum spp. 2x3), and to E. tuberculatum using NGS data. Mitogenomes from specimens of E. ruidum spp. 3, 4 and 2 × 3 had a high proportion of polymorphic sites. We investigated whether polymorphisms in mitogenomes are due to nuclear mt paralogues (numts) or due to the presence of more than one mitogenome within an individual (heteroplasmy). We did not find loss of function signals in polymorphic protein-coding genes, and observed strong evidence for purifying selection in two haplotype-phased genes, which indicate the presence of two functional mitochondrial genomes coexisting within individuals instead of numts. Heteroplasmy due to hybrid paternal leakage is not supported by phylogenetic analyses. Our results reveal the presence of a fast-evolving secondary mitochondrial lineage of uncertain origin in the E. ruidum complex.

The ‘Peripatos' in Eurogondwana? — Lack of evidence that southeast Asian onychophorans walked through Europe

Onychophorans, or velvet worms, are cryptic but extremely charismatic terrestrial invertebrates that have often been the subject of interesting biogeographic debate. Despite great interest, a well resolved and complete phylogeny of the group and a reliable chronogram have been elusive due to their broad geographic distribution, paucity of samples, and challenging molecular composition. Here we present a molecular phylogenetic analysis of Onychophora that includes previously unsampled and undersampled lineages and we analyse the expanded dataset using a series of nested taxon sets designed to increase the amount of information available for particular subclades. These include a dataset with outgroups, one restricted to the ingroup taxa, and three others for Peripatopsidae, Peripatidae and Neopatida (= the Neotropical Peripatidae). To explore competing biogeographic scenarios we generate a new time tree for Onychophora using the few available reliable fossils as calibration points. Comparing our results to those of Cyphophthalmi, we reconsider the hypothesis that velvet worms reached Southeast Asia via Eurogondwana, and conclude that a more likely scenario is that they reached Southeast Asia by rafting on the Sibumasu terrane. Our phylogenetic results support the reciprocal monophyly of both families as well as an early division between East and West Gondwana, also in both families, each beginning to diversify between the Permian and the Jurassic. Peripatopsidae clearly supports paraphyly of South Africa with respect to southern South America (Chile) and a sister group relationship of the Southeast Asian/New Guinean Paraperipatus to the Australian/New Zealand taxa. The latter includes a clade that divides between Western Australia and Eastern Australia and two sister clades of trans-Tasman species (one oviparous and one viviparous). This pattern clearly shows that oviparity is secondarily derived in velvet worms. Peripatidae finds a sister group relationship between the Southeast Asian Eoperipatus and the West Gondwanan clade, which divides into the African Mesoperipatus and Neopatida. The latter shows a well supported split between the Pacific Oroperipatus (although it is unclear whether they form one or two clades) and a sister clade that includes the members of the genera Peripatus, Epiperipatus, Macroperipatus and representatives of the monotypic genera Cerradopatus, Plicatoperipatus and Principapillatus. However, Peripatus, Epiperipatus and Macroperipatus are not monophyletic, and all the species from the monotypic genera are related to geographically close species. The same goes for the type species of Macroperipatus (from Trinidad, and sister group to other Trinidad and Tobago species of Epiperipatus) and Epiperipatus (from French Guiana, and related to other Guyana shield species of Epiperipatus and Peripatus). Geographic structure within Neopatida is largely obscured by an unresolved backbone, but many well supported instances of generic non-monophyly challenge the current taxonomic framework, which has often relied on anatomical characters that are untested phylogenetically.

Dry habitats were crucibles of domestication in the evolution of agriculture in ants

The evolution of ant agriculture, as practised by the fungus-farming 'attine' ants, is thought to have arisen in the wet rainforests of South America about 55-65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in South American rainforests. The 'out-of-the-rainforest' hypothesis, while generally accepted, has never been tested in a phylogenetic context. It also presents a problem for explaining how fungal domestication might have occurred, given that isolation from free-living populations is required. Here, we use phylogenomic data from ultra-conserved element (UCE) loci to reconstruct the evolutionary history of fungus-farming ants, reduce topological uncertainty, and identify the closest non-fungus-growing ant relative. Using the phylogeny we infer the history of attine agricultural systems, habitat preference and biogeography. Our results show that the out-of-the-rainforest hypothesis is correct with regard to the origin of attine ant agriculture; however, contrary to expectation, we find that the transition from lower to higher agriculture is very likely to have occurred in a seasonally dry habitat, inhospitable to the growth of free-living populations of attine fungal cultivars. We suggest that dry habitats favoured the isolation of attine cultivars over the evolutionary time spans necessary for domestication to occur.

The acacia ants revisited: convergent evolution and biogeographic context in an iconic ant/plant mutualism

Phylogenetic and biogeographic analyses can enhance our understanding of multispecies interactions by placing the origin and evolution of such interactions in a temporal and geographical context. We use a phylogenomic approach-ultraconserved element sequence capture-to investigate the evolutionary history of an iconic multispecies mutualism: Neotropical acacia ants (Pseudomyrmex ferrugineus group) and their associated Vachellia hostplants. In this system, the ants receive shelter and food from the host plant, and they aggressively defend the plant against herbivores and competing plants. We confirm the existence of two separate lineages of obligate acacia ants that convergently occupied Vachellia and evolved plant-protecting behaviour, from timid ancestors inhabiting dead twigs in rainforest. The more diverse of the two clades is inferred to have arisen in the Late Miocene in northern Mesoamerica, and subsequently expanded its range throughout much of Central America. The other lineage is estimated to have originated in southern Mesoamerica about 3 Myr later, apparently piggy-backing on the pre-existing mutualism. Initiation of the Pseudomyrmex/Vachellia interaction involved a shift in the ants from closed to open habitats, into an environment with more intense plant herbivory. Comparative studies of the two lineages of mutualists should provide insight into the essential features binding this mutualism.

First record of the genus Leptanilloides (Hymenoptera: Formicidae: Dorylinae) from the United States

We describe a new species of the Neotropical genus Leptanilloides, L. chihuahuaensis sp. n., based on male specimens from the Davis Mountains in western Texas. Known males of species of Leptanilloides are compared with L. chihuahuaensis. This is the first report of the genus from the United States and the Nearctic region. Previously, the Leptanilloides genus-group was only known to occur from southern Mexico to southeastern Brazil; and thus, this record from Texas represents a remarkable extension of the known range of the genus.

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g. exons). However, molecular techniques requiring RNA as a template, including transcriptome sequencing, are limited to using very high-quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n = 1510) of ultraconserved elements (UCEs) shared among the insect order Hymenoptera. We used in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled hymenoptera, and we designed a set of RNA baits (n = 2749) for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We used our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we used these UCE loci to reconstruct phylogenetic relationships spanning very old (≥220 Ma) to very young (≤1 Ma) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support, although this result could be explained by factors such as taxon sampling. We discuss this approach and our results in the context of elucidating the evolutionary history of one of the most diverse and speciose animal orders.

How ants drop out: ant abundance on tropical mountains

In tropical wet forests, ants are a large proportion of the animal biomass, but the factors determining abundance are not well understood. We characterized ant abundance in the litter layer of 41 mature wet forest sites spread throughout Central America (Chiapas, Guatemala, Honduras, Nicaragua, and Costa Rica) and examined the impact of elevation (as a proxy for temperature) and community species richness. Sites were intentionally chosen to minimize variation in precipitation and seasonality. From sea level to 1500 m ant abundance very gradually declined, community richness declined more rapidly than abundance, and the local frequency of the locally most common species increased. These results suggest that within this elevational zone, density compensation is acting, maintaining high ant abundance as richness declines. In contrast, in sites above 1500 m, ant abundance dropped abruptly to much lower levels. Among these high montane sites, community richness explained much more of the variation in abundance than elevation, and there was no evidence of density compensation. The relative stability of abundance below 1500 m may be caused by opposing effects of temperature on productivity and metabolism. Lower temperatures may decrease productivity and thus the amount of food available for consumers, but slower metabolisms of consumers may allow maintenance of higher biomass at lower resource supply rates. Ant communities at these lower elevations may be highly interactive, the result of continuous habitat presence over geological time. High montane sites may be ephemeral in geological time, resulting in non-interactive communities dominated by historical and stochastic processes. Abundance in these sites may be determined by the number of species that manage to colonize and/or avoid extinction on mountaintops.

Revision of the Middle American clade of the ant genus Stenamma Westwood (Hymenoptera, Formicidae, Myrmicinae)

Stenamma is a cryptic “leaf-litter” ant genus that occurs in mesic forest habitats throughout the Holarctic region, Central America, and part of northwestern South America (Colombia and Ecuador). The genus was thought to be restricted primarily to the temperate zone, but recent collecting efforts have uncovered a large radiation of Neotropical forms, which rival the Holarctic species in terms of morphological and behavioral diversity. By inferring a broad-scale molecular phylogeny of Stenamma, Branstetter (2012) showed that all Neotropical species belong to a diverse Middle American clade (MAC), and that this clade is sister to an almost completely geographically separated Holarctic clade (HOC). Here, the Middle American clade of Stenamma is revised to recognize 40 species, of which 33 are described as new. Included in the revision are a key to species based on the worker caste, and for each species where possible, descriptions and images of workers and queens, images of males, information on geographic distribution, descriptions of intraspecific variation, and notes on natural history. Several species groups are defined, but the majority of species remain unassigned due to a lack of diagnostic morphological character states for most molecular clades. The following species are redescribed: Stenamma alas Longino, Stenamma diversum Mann, Stenamma expolitum Smith, Stenamma felixi Mann, Stenamma huachucanum Smith, Stenamma manni Wheeler, and Stenamma schmidti Menozzi. The following are described as new: Stenamma andersonisp. n., Stenamma atribellumsp. n., Stenamma brujitasp. n., Stenamma callipygiumsp. n., Stenamma catrachosp. n., Stenamma connectumsp. n., Stenamma crypticumsp. n., Stenamma cusucosp. n., Stenamma excisumsp. n., Stenamma expoliticosp. n., Stenamma hojarascasp. n., Stenamma ignotumsp. n., Stenamma lagunumsp. n., Stenamma llamasp. n., Stenamma leptospinumsp. n., Stenamma lobinodussp. n., Stenamma longinoisp. n., Stenamma maximonsp. n., Stenamma megamannisp. n., Stenamma monstrosumsp. n., Stenamma murallasp. n., Stenamma nanozoisp. n., Stenamma nonotchsp. n., Stenamma ochrocnemissp. n., Stenamma pelophilumsp. n., Stenamma picopicuchasp. n., Stenamma saenzaesp. n., Stenamma sandinistasp. n., Stenamma stictosomumsp. n., Stenamma tiburonsp. n., Stenamma ticosp. n., Stenamma vexatorsp. n., and Stenamma zelumsp. n. Although many of the newly defined species consist of challenging species complexes, this study establishes a robust baseline that will guide future work on the systematics of MAC Stenamma. The total global diversity of Stenamma now includes 84 extant species.