Phylogeny of the bee genus Halictus (Hymenoptera: halictidae) based on parsimony and likelihood analyses of nuclear EF-1alpha sequence data

The new annotated checklist of the wild bees of Europe (Hymenoptera: Anthophila)

At a time when nature conservation has become essential to ensure the long-term sustainability of our environment, it is widely acknowledged that conservation actions must be implemented within a solid taxonomic framework. In preparation for the upcoming update of the IUCN Red List, we here update the European checklist of the wild bees (sensu the IUCN geographical framework). The original checklist, published in 2014, was revised for the first time in 2017. In the present revision, we add one genus, four subgenera and 67 species recently described, 40 species newly recorded since the latest revision (including two species that are not native to Europe), 26 species overlooked in the previous European checklists and 63 published synonymies. We provide original records for eight species previously unknown to the continent and, as original taxonomic acts, we provide three new synonyms, we consider two names as nomina nuda, ten names as nomina dubia, three as species inquirenda, synonymize three species and exclude 40 species from the previous checklist. Around a hundred other taxonomic changes and clarifications are also included and discussed. The present work revises the total number of genera for IUCN Europe to 77 and the total number of species to 2,138. In addition to specifying the taxonomic changes necessary to update the forthcoming Red List of European bees, we discuss the sampling and taxonomic biases that characterise research on the European bee fauna and highlight the growing importance of range expansions and species invasions.

Testing the systematic status of Homalictus and Rostrohalictus with weakened cross-vein groups within Halictini (Hymenoptera: Halictidae) using low-coverage whole-genome sequencing

The halictid genus Lasioglossum, as one of the most species-rich bee groups with persistently contentious subgeneric boundaries, is one of the most challenging bee groups from a systematic standpoint. An enduring question is the relationship of Lasioglossum and Homalictus, whether all halictine bees with weakened distal wing venation comprise one or multiple genera. Here, we analyzed the phylogenetic relationships among the subgroups within Lasioglossum s.l. based on thousands of single-copy orthologs and ultraconserved elements, which were extracted from 23 newly sequenced low-coverage whole genomes alongside a published genome (22 ingroups plus 2 outgroups). Both marker sets provided consistent results across maximum likelihood and coalescent-based species tree approaches. The phylogenetic and topology test results show that the Lasioglossum and Hemihalictus series are reciprocally monophyletic and Homalictus and Rostrohalictus are valid subgenera of Lasioglossum. Consequently, we lower Homalictus to subgenus status within Lasioglossum again, and we also raise Rostrohalictus to subgenus status from its prior synonymy with subgenus Hemihalictus. Lasioglossum przewalskyi is also transferred to the subgenus Hemihalictus. Ultimately, we redefine Lasioglossum to include all halictine bees with weakened distal wing venation.

The Loss of Sociality Is Accompanied by Reduced Neural Investment in Mushroom Body Volume in the Sweat Bee Augochlora Pura (Hymenoptera: Halictidae)

Social behavior has been predicted to select for increased neural investment (the social brain hypothesis) and also to select for decreased neural investment (the distributed cognition hypothesis). Here, we use two related bees, the social Augochlorella aurata (Smith) (Hymenoptera: Halictidae) and the related Augochlora pura (Say), which has lost social behavior, to test the contrasting predictions of these two hypotheses in these taxa. We measured the volumes of the mushroom body (MB) calyces, a brain area shown to be important for cognition in previous studies, as well as the optic lobes and antennal lobes. We compared females at the nest foundress stage when both species are solitary so that brain development would not be influenced by social interactions. We show that the loss of sociality was accompanied by a loss in relative neural investment in the MB calyces. This is consistent with the predictions of the social brain hypothesis. Ovary size did not correlate with MB calyx volume. This is the first study to demonstrate changes in mosaic brain evolution in response to the loss of sociality.

Chemical Variation among Castes, Female Life Stages and Populations of the Facultative Eusocial Sweat Bee Halictus rubicundus (Hymenoptera: Halictidae)

In eusocial insects, chemical communication is crucial for mediating many aspects of social activities, especially the regulation of reproduction. Though queen signals are known to decrease ovarian activation of workers in highly eusocial species, little is known about their evolution. In contrast, some primitively eusocial species are thought to control worker reproduction through physical aggression by the queen rather than via pheromones, suggesting the evolutionary establishment of chemical signals with more derived sociality. However, studies supporting this hypothesis are largely missing. Socially polymorphic halictid bees, such as Halictus rubicundus, with social and solitary populations in both Europe and North America, offer excellent opportunities to illuminate the evolution of caste-specific signals. Here we compared the chemical profiles of social and solitary populations from both continents and tested whether (i) population or social level affect chemical dissimilarity and whether (ii) caste-specific patterns reflect a conserved queen signal. Our results demonstrate unique odor profiles of European and North American populations, mainly due to different isomers of n-alkenes and macrocyclic lactones; chemical differences may be indicative of phylogeographic drift in odor profiles. We also found common compounds overproduced in queens compared to workers in both populations, indicating a potential conserved queen signal. However, North American populations have a lower caste-specific chemical dissimilarity than European populations which raises the question if both use different mechanisms of regulating reproductive division of labor. Therefore, our study gives new insights into the evolution of eusocial behavior and the role of chemical communication in the inhibition of reproduction.

Feeding specialization and longer generation time are associated with relatively larger brains in bees

Despite their miniature brains, insects exhibit substantial variation in brain size. Although the functional significance of this variation is increasingly recognized, research on whether differences in insect brain sizes are mainly the result of constraints or selective pressures has hardly been performed. Here, we address this gap by combining prospective and retrospective phylogenetic-based analyses of brain size for a major insect group, bees (superfamily Apoidea). Using a brain dataset of 93 species from North America and Europe, we found that body size was the single best predictor of brain size in bees. However, the analyses also revealed that substantial variation in brain size remained even when adjusting for body size. We consequently asked whether such variation in relative brain size might be explained by adaptive hypotheses. We found that ecologically specialized species with single generations have larger brains-relative to their body size-than generalist or multi-generation species, but we did not find an effect of sociality on relative brain size. Phylogenetic reconstruction further supported the existence of different adaptive optima for relative brain size in lineages differing in feeding specialization and reproductive strategy. Our findings shed new light on the evolution of the insect brain, highlighting the importance of ecological pressures over social factors and suggesting that these pressures are different from those previously found to influence brain evolution in other taxa.

The evolutionary history of the cellophane bee genus Colletes Latreille (Hymenoptera: Colletidae): Molecular phylogeny, biogeography and implications for a global infrageneric classification

Colletes Latreille (Hymenoptera: Colletidae) is a diverse genus with 518 valid species distributed in all biogeographic realms, except Australasia and Antarctica. Here we provide a comprehensive dated phylogeny for Colletes based on Bayesian and maximum likelihood-based analyses of DNA sequence data of six loci: 28S rDNA, cytochrome c oxidase subunit 1, elongation factor-1α copy F2, long-wavelength rhodopsin, RNA polymerase II and wingless. In total, our multilocus matrix consists of 4824 aligned base pairs for 143 species, including 112 Colletes species plus 31 outgroups (one stenotritid and a diverse array of colletids representing all subfamilies). Overall, analyses of each of the six single-locus datasets resulted in poorly resolved consensus trees with conflicting phylogenetic signal. However, our analyses of the multilocus matrix provided strong support for the monophyly of Colletes and show that it can be subdivided into five major clades. The implications of our phylogenetic results for future attempts at infrageneric classification for the Colletes of the world are discussed. We propose species groups for the Neotropical species of Colletes, the only major biogeographic realm for which no species groups have been proposed to date. Our dating analysis indicated that Colletes diverged from its sister taxon, Hemicotelles Toro and Cabezas, in the early Oligocene and that its extant lineages began diversifying only in the late Oligocene. According to our biogeographic reconstruction, Colletes originated in the Neotropics (most likely within South America) and then spread to the Nearctic very early in its evolutionary history. Geodispersal to the Old World occurred soon after colonization of the Northern Hemisphere. Lastly, the historical biogeography of Colletes is analyzed in light of available geological and palaeoenvironmental data.

Phylogeny and biogeography of the cleptoparasitic bee genus Epeolus (Hymenoptera: Apidae) and cophylogenetic analysis with its host bee genus Colletes (Hymenoptera: Colletidae)

The bee genus Epeolus Latreille (Hymenoptera: Apidae) consists of 109 species, which are known to be exclusively cleptoparasites of polyester (or cellophane) bees of the genus Colletes Latreille (Hymenoptera: Colletidae). Both genera have a nearly cosmopolitan distribution and are represented on all continents except Antarctica and Australia. We present the most comprehensive phylogeny for Epeolus to date, based on combined molecular and morphological data. In total, 59 ingroup taxa (species of Epeolus) and 7 outgroup taxa (other Epeolini) were scored for 99 morphological characters, and sequence data were obtained for seven genes (one mitochondrial and six nuclear, 5399 bp in total). Epeolus was found to be monophyletic, with a crown age estimated to be 25.0-13.4 Ma (95% HPD) and its origins traced to the Nearctic region. Epeolus was found to contain six major clades, five of which were well supported. The evolutionary history of Epeolus is explored in the context of earth history events and the evolutionary history of its host genus Colletes, for which a molecular phylogeny was constructed based on the same seven genes. A comparison of Epeolus and Colletes phylogenies limited to taxa for which there is evidence of an association suggests there was some cospeciation. However, more cladogenetic events in Epeolus were linked to instances of dispersal/vicariance. It is not yet clear the extent to which allopatric speciation contributed to diversification in Colletes, but the genus' success in having colonized and diversified across much of the globe made it possible for Epeolus to do the same.

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.

DNA barcoding a nightmare taxon: assessing barcode index numbers and barcode gaps for sweat bees

There is an ongoing campaign to DNA barcode the world’s >20 000 bee species. Recent revisions of Lasioglossum (Dialictus) (Hymenoptera: Halictidae) for Canada and the eastern United States were completed using integrative taxonomy. DNA barcode data from 110 species of L. (Dialictus) are examined for their value in identification and discovering additional taxonomic diversity. Specimen identification success was estimated using the best close match method. Error rates were 20% relative to current taxonomic understanding. Barcode Index Numbers (BINs) assigned using Refined Single Linkage Analysis (RESL) and barcode gaps using the Automatic Barcode Gap Discovery (ABGD) method were also assessed. RESL was incongruent for 44.5% of species, although some cryptic diversity may exist. Forty-three of 110 species were part of merged BINs with multiple species. The barcode gap is non-existent for the data set as a whole and ABGD showed levels of discordance similar to the RESL. The viridatum species-group is particularly problematic, so that DNA barcodes alone would be misleading for species delimitation and specimen identification. Character-based methods using fixed nucleotide substitutions could improve specimen identification success in some cases. The use of DNA barcoding for species discovery for standard taxonomic practice in the absence of a well-defined barcode gap is discussed.

Playing with extremes: Origins and evolution of exaggerated female forelegs in South African Rediviva bees

Despite close ecological interactions between plants and their pollinators, only some highly specialised pollinators adapt to a specific host plant trait by evolving a bizarre morphology. Here we investigated the evolution of extremely elongated forelegs in females of the South African bee genus Rediviva (Hymenoptera: Melittidae), in which long forelegs are hypothesised to be an adaptation for collecting oils from the extended spurs of their Diascia host flowers. We first reconstructed the phylogeny of the genus Rediviva using seven genes and inferred an origin of Rediviva at around 29MYA (95% HPD=19.2-40.5), concurrent with the origin and radiation of the Succulent Karoo flora. The common ancestor of Rediviva was inferred to be a short-legged species that did not visit Diascia. Interestingly, all our analyses strongly supported at least two independent origins of long legs within Rediviva. Leg length was not correlated with any variable we tested (ecological specialisation, Diascia visitation, geographic distribution, pilosity type) but seems to have evolved very rapidly. Overall, our results indicate that foreleg length is an evolutionary highly labile, rapidly evolving trait that might enable Rediviva bees to respond quickly to changing floral resource availability.

Phylogenetic systematics and a revised generic classification of anthidiine bees (Hymenoptera: Megachilidae)

The bee tribe Anthidiini (Hymenoptera: Megachilidae) is a large, cosmopolitan group of solitary bees that exhibit intriguing nesting behavior. We present the first molecular-based phylogenetic analysis of relationships within Anthidiini using model-based methods and a large, multi-locus dataset (five nuclear genes, 5081 base pairs), as well as a combined analysis using our molecular dataset in conjunction with a previously published morphological matrix. We discuss the evolution of nesting behavior in Anthidiini and the relationship between nesting material and female mandibular morphology. Following an examination of the morphological characters historically used to recognize anthidiine genera, we recommend the use of a molecular-based phylogenetic backbone to define taxonomic groups prior to the assignment of diagnostic morphological characters for these groups. Finally, our results reveal the paraphyly of numerous genera and have significant consequences for anthidiine classification. In order to promote a classification system based on stable, monophyletic clades, we hereby make the following changes to Michener's (2007) classification: The subgenera Afranthidium (Zosteranthidium) Michener and Griswold, 1994, Afranthidium (Branthidium) Pasteels, 1969 and Afranthidium (Immanthidium) Pasteels, 1969 are moved into the genus Pseudoanthidium, thus forming the new combinations Pseudoanthidium (Zosteranthidium), Pseudoanthidium (Branthidium), and Pseudoanthidium (Immanthidium). The genus Neanthidium Pasteels, 1969 is also moved into the genus Pseudoanthidium, thus forming the new combination Pseudoanthidium (Neanthidium). Based on morphological characters shared with our new definition of the genus Pseudoanthidium, the subgenus Afranthidium (Mesanthidiellum) Pasteels, 1969 and the genus Gnathanthidium Pasteels, 1969 are also moved into the genus Pseudoanthidium, thus forming the new combinations Pseudoanthidium (Mesanthidiellum) and Pseudoanthidium (Gnathanthidium).

Phylogenetic relationships of yellowjackets inferred from nine loci (Hymenoptera: Vespidae, Vespinae, Vespula and Dolichovespula)

Eusociality has arisen repeatedly and independently in the history of insects, often leading to evolutionary success and ecological dominance. Eusocial wasps of the genera Vespula and Dolichovespula, or yellowjackets, have developed advanced social traits in a relatively small number of species. The origin of traits such as effective paternity and colony size has been interpreted with reference to an established phylogenetic hypothesis that is based on phenotypic data, while the application of molecular evidence to phylogenetic analysis within yellowjackets has been limited. Here, we investigate the evolutionary history of yellowjackets on the basis of mitochondrial and nuclear markers (nuclear: 28S, EF1α, Pol II, and wg; mitochondrial: 12S, 16S, COI, COII, and Cytb). We use these data to test the monophyly of yellowjackets and species groups, and resolve species-level relationships within each genus using parsimony and Bayesian inference. Our results indicate that a yellowjacket clade is either weakly supported (parsimony) or rejected (Bayesian inference). However, the monophyly of each yellowjacket genus as well as species groups are strongly supported and concordant between methods. Our results agree with previous studies regarding the monophyly of the Vespula vulgaris group and the sister relationship between the V. rufa and V. squamosa groups. This suggests convergence of large colony size and high effective paternity in the vulgaris group and V. squamosa, or a single origin of both traits in the most recent common ancestor of all Vespula species and their evolutionary reversal in the rufa group.

Origins, evolution, and diversification of cleptoparasitic lineages in long-tongued bees

The evolution of parasitic behavior may catalyze the exploitation of new ecological niches yet also binds the fate of a parasite to that of its host. It is thus not clear whether evolutionary transitions from free-living organism to parasite lead to increased or decreased rates of diversification. We explore the evolution of brood parasitism in long-tongued bees and find decreased rates of diversification in eight of 10 brood parasitic clades. We propose a pathway for the evolution of brood parasitic strategy and find that a strategy in which a closed host nest cell is parasitized and the host offspring is killed by the adult parasite represents an obligate first step in the appearance of a brood parasitic lineage; this ultimately evolves into a strategy in which an open host cell is parasitized and the host offspring is killed by a specialized larval instar. The transition to parasitizing open nest cells expanded the range of potential hosts for brood parasitic bees and played a fundamental role in the patterns of diversification seen in brood parasitic clades. We address the prevalence of brood parasitic lineages in certain families of bees and examine the evolution of brood parasitism in other groups of organisms.

Seladonia (Pachyceble) henanensis sp. n. (Hymenoptera, Halictidae) from China

Seladonia (Pachyceble) henanensissp. n., is described from Henan Province, the eastern-central part of China. This species is separated from its allied species by a combination of the following morphological characters: head broad in female, inner hind tibial spur of female with 7–8 slender teeth, T1 basolaterally with appressed hair tuft in both sexes, and genitalia with long and large lower gonostylus in male. Important taxonomic characters are illustrated with photographs, scanning electron micrographs, and line drawings.

Flexible host choice and common host switches in the evolution of generalist and specialist cuckoo bees (Anthophila: Sphecodes)

Specialization makes resource use more efficient and should therefore be a common process in animal evolution. However, this process is not as universal in nature as one might expect. Our study shows that Sphecodes (Halictidae) cuckoo bees frequently change their host over the course of their evolution. To test the evolutionary scenario of host specialization in cuckoo bees, we constructed well-supported phylogenetic trees based on partial sequences of five genes for subtribe Sphecodina (Halictini). We detected up to 17 host switches during Sphecodes evolution based on 37 ingroup species subject to mapping analysis of the hosts associated with the cuckoo bee species. We also examine the direction of evolution of host specialization in Sphecodes using the likelihood ratio test and obtain results to support the bidirectional evolutionary scenario in which specialists can arise from generalists, and vice versa. We explain the existence of generalist species in Sphecodes based on their specialization at the individual level, which is recently known in two species. Our findings suggest flexible host choice and frequent host switches in the evolution of Sphecodes cuckoo bees. This scenario leads us to propose an individual choice constancy hypothesis based on the individual specialization strategy in cuckoo bees. Choice constancy has a close relationship to flower constancy in bees and might be an extension of the latter. Our analysis also shows relationships among the genera Microsphecodes, Eupetersia, Sphecodes and Austrosphecodes, a formerly proposed Sphecodes subgenus. Austrosphecodes species form a basal lineage of the subtribe, and Microsphecodes makes it paraphyletic.

Evolutionary history of nematodes associated with sweat bees

Organisms that live in close association with other organisms make up a large part of the world's diversity. One driver of this diversity is the evolution of host-species specificity, which can occur via reproductive isolation following a host-switch or, given the correct circumstances, via cospeciation. In this study, we explored the diversity and evolutionary history of Acrostichus nematodes that are associated with halictid bees in North America. First, we conducted surveys of bees in Virginia, and found six halictid species that host Acrostichus. To test the hypothesis of cospeciation, we constructed phylogenetic hypotheses of Acrostichus based on three genes. We found Acrostichus puri and Acrostichus halicti to be species complexes comprising cryptic, host-specific species. Although several nodes in the host and symbiont phylogenies were congruent and tests for cospeciation were significant, the host's biogeography, the apparent patchiness of the association across the host's phylogeny, and the amount of evolution in the nematode sequence suggested a mixture of cospeciation, host switching, and extinction events instead of strict cospeciation. Cospeciation can explain the relationships between Ac. puri and its augochlorine hosts, but colonization of Halictus hosts is more likely than cospeciation. The nematodes are vertically transmitted, but sexual transmission is also likely. Both of these transmission modes may explain host-species specificity and congruent bee and nematode phylogenies. Additionally, all halictid hosts come from eusocial or socially polymorphic lineages, suggesting that sociality may be a factor in the suitability of hosts for Acrostichus.

The impact of molecular data on our understanding of bee phylogeny and evolution

Our understanding of bee phylogeny has improved over the past fifteen years as a result of new data, primarily nucleotide sequence data, and new methods, primarily model-based methods of phylogeny reconstruction. Phylogenetic studies based on single or, more commonly, multilocus data sets have helped resolve the placement of bees within the superfamily Apoidea; the relationships among the seven families of bees; and the relationships among bee subfamilies, tribes, genera, and species. In addition, molecular phylogenies have played an important role in inferring evolutionary patterns and processes in bees. Phylogenies have provided the comparative framework for understanding the evolution of host-plant associations and pollen specialization, the evolution of social behavior, and the evolution of parasitism. In this paper, we present an overview of significant discoveries in bee phylogeny based primarily on the application of molecular data. We review the phylogenetic hypotheses family-by-family and then describe how the new phylogenetic insights have altered our understanding of bee biology.

Why do leafcutter bees cut leaves? New insights into the early evolution of bees

Stark contrasts in clade species diversity are reported across the tree of life and are especially conspicuous when observed in closely related lineages. The explanation for such disparity has often been attributed to the evolution of key innovations that facilitate colonization of new ecological niches. The factors underlying diversification in bees remain poorly explored. Bees are thought to have originated from apoid wasps during the Mid-Cretaceous, a period that coincides with the appearance of angiosperm eudicot pollen grains in the fossil record. The reliance of bees on angiosperm pollen and their fundamental role as angiosperm pollinators have contributed to the idea that both groups may have undergone simultaneous radiations. We demonstrate that one key innovation--the inclusion of foreign material in nest construction--underlies both a massive range expansion and a significant increase in the rate of diversification within the second largest bee family, Megachilidae. Basal clades within the family are restricted to deserts and exhibit plesiomorphic features rarely observed among modern bees, but prevalent among apoid wasps. Our results suggest that early bees inherited a suite of behavioural traits that acted as powerful evolutionary constraints. While the transition to pollen as a larval food source opened an enormous ecological niche for the early bees, the exploitation of this niche and the subsequent diversification of bees only became possible after bees had evolved adaptations to overcome these constraints.

Comprehensive phylogeny of apid bees reveals the evolutionary origins and antiquity of cleptoparasitism

Apidae is the most speciose and behaviorally diverse family of bees. It includes solitary, eusocial, socially parasitic, and an exceptionally high proportion of cleptoparasitic species. Cleptoparasitic bees, which are brood parasites in the nests of other bees, have long caused problems in resolving the phylogenetic relationships within Apidae based on morphological data because of the tendency for parasites to converge on a suite of traits, making it difficult to differentiate similarity caused by common ancestry from convergence. Here, we resolve the evolutionary history of apid cleptoparasitism by conducting a detailed, comprehensive molecular phylogenetic analysis of all 33 apid tribes (based on 190 species), including representatives from every hypothesized origin of cleptoparasitism. Based on Bayesian ancestral state reconstruction, we show that cleptoparasitism has arisen just four times in Apidae, which is fewer times than previously estimated. Our results indicate that 99% of cleptoparasitic apid bees form a monophyletic group. Divergence time estimates reveal that cleptoparasitism is an ancient behavior in bees that first evolved in the late Cretaceous 95 Mya [95% highest posterior density (HPD) = 87-103]. Our phylogenetic analysis of the Apidae sheds light on the macroevolution of a bee family that is of evolutionary, ecological, and economic importance.

Ancestral state reconstruction reveals multiple independent evolution of diagnostic morphological characters in the "Higher Oribatida" (Acari), conflicting with current classification schemes

BACKGROUND

The use of molecular genetic data in phylogenetic systematics has revolutionized this field of research in that several taxonomic groupings defined by traditional taxonomic approaches have been rejected by molecular data. The taxonomic classification of the oribatid mite group Circumdehiscentiae ("Higher Oribatida") is largely based on morphological characters and several different classification schemes, all based upon the validity of diagnostic morphological characters, have been proposed by various authors. The aims of this study were to test the appropriateness of the current taxonomic classification schemes for the Circumdehiscentiae and to trace the evolution of the main diagnostic traits (the four nymphal traits scalps, centrodorsal setae, sclerits and wrinkled cuticle plus octotaxic system and pteromorphs both in adults) on the basis of a molecular phylogenetic hypothesis by means of parsimony, likelihood and Bayesian approaches.

RESULTS

The molecular phylogeny based on three nuclear markers (28S rDNA, ef-1alpha, hsp82) revealed considerable discrepancies to the traditional classification of the five "circumdehiscent" subdivisions, suggesting paraphyly of the three families Scutoverticidae, Ameronothridae, Cymbaeremaeidae and also of the genus Achipteria. Ancestral state reconstructions of six common diagnostic characters and statistical evaluation of alternative phylogenetic hypotheses also partially rejected the current morphology-based classification and suggested multiple convergent evolution (both gain and loss) of some traits, after a period of rapid cladogenesis, rendering several subgroups paraphyletic.

CONCLUSIONS

Phylogenetic studies revealed non-monophyly of three families and one genus as a result of a lack of adequate synapomorphic morphological characters, calling for further detailed investigations in a framework of integrative taxonomy. Character histories of six morphological traits indicate that their evolution followed a rather complex pattern of multiple independent gains (and losses). Thus, the observed pattern largely conflicts with current morphological classifications of the Circumdehiscentiae, suggesting that the current taxonomic classification schemes are not appropriate, apart from a recently proposed subdivision into 24 superfamilies.

Molecular phylogeny of the small carpenter bees (Hymenoptera: Apidae: Ceratinini) indicates early and rapid global dispersal

The small carpenter bees (tribe Ceratinini, family Apidae) are recorded from all continents except Antarctica. The Ceratinini have a near-global distribution which contrasts strongly with their sister tribe, the Allodapini which has a largely southern Old World distribution. The Ceratinini therefore provides an excellent group to understand the factors that help determine the biogeography and radiation of the bees. This is the first molecular study of ceratinine bees covering representatives from both northern and southern hemisphere Old and New World regions. We use two mitochondrial and one nuclear marker (totalling 2807 nucleotides) to examine the age, cladogenesis and historical biogeography of this tribe. Tree topology and molecular dating support an African origin at about 47 Mya with subsequent dispersal into Eurasia 44 Mya, and followed by an American invasion 32 Mya. Concentrated African and Malagasy sampling revealed there were two or three dispersals events into Madagascar ranging from 25 to 9 Mya. Lineage through time analyses suggest higher rates of cladogenesis close to the origin of the tribe, and this corresponds to both major dispersal events and divergences of lineages leading to extant subgenera. Ceratinini have potentially great importance for future studies to understand the relative roles of dispersal ability and time of origin in determining bee biogeography.

Comparison of methods for species-tree inference in the sawfly genus Neodiprion (Hymenoptera: Diprionidae)

Conifer-feeding sawflies in the genus Neodiprion provide an excellent opportunity to investigate the origin and maintenance of barriers to reproduction, but obtaining a phylogenetic estimate for comparative studies of Neodiprion speciation has proved difficult. Specifically, nonmonophyly within and discordance between individual gene trees, both of which are common in groups that diverged recently and/or rapidly, make it impossible to infer a species tree using methods that are designed to estimate gene trees. Therefore, in this study, we estimate relationships between members of the lecontei species group using four approaches that are intended to estimate species, not gene, trees: (1) minimize deep coalescences (MDC), (2) shallowest divergences (SD), (3) Bayesian estimation of species trees (BEST), and (4) a novel approach that combines concatenation with monophyly constraints (CMC). Multiple populations are sampled for most species and all four methods incorporate this intraspecific variation into estimates of interspecific relationships. We investigate the sensitivity of each method to taxonomic sampling, and, for the BEST method, we assess the impact of prior choice on species-tree inference. We also compare species-tree estimates to one another and to a morphologically based hypothesis to identify clades that are supported by multiple analyses and lines of evidence. We find that both taxonomic sampling and method choice impact species-tree estimates and that, for these data, the BEST method is strongly influenced by Theta and branch-length priors. We also find that the CMC method is the least sensitive to taxonomic sampling. Finally, although interspecific genetic variation is low due to the recent divergence of the lecontei group, our results to date suggest that incomplete lineage sorting and interspecific gene flow are the main factors complicating species-tree inference in Neodiprion. Based on these analyses, we propose a phylogenetic hypothesis for the lecontei group. Finally, our results suggest that, even for very challenging groups like Neodiprion, an underlying species-tree signal can be extracted from multi-locus data as long as intraspecific variation is adequately sampled and methods that focus on the estimation of species trees are used.

Phylogeny of colletid bees (Hymenoptera: Colletidae) inferred from four nuclear genes

Colletidae comprise approximately 2500 species of bees primarily distributed in the southern continents (only two colletid genera are widely distributed: Colletes and Hylaeus). Previously published studies have failed to resolve phylogenetic relationships on a worldwide basis and this has been a major barrier to the progress of research regarding systematics and evolution of colletid bees. For this study, data from four nuclear gene loci: elongation factor-1alpha (F2 copy), opsin, wingless, and 28S rRNA were analyzed for 122 species of colletid bees, representing all subfamilies and tribes currently recognized; 22 species belonging to three other bee families were used as outgroups. Bayesian, maximum likelihood, and parsimony methods were employed to investigate the phylogenetic relationships within Colletidae and resulted in highly congruent and well-resolved trees. The phylogenetic results show that Colletidae are monophyletic and that all traditionally recognized subfamilies (except Paracolletinae) are also strongly supported as monophyletic. Our phylogenetic hypothesis provides a framework within which broad questions related to the taxonomy, biogeography, morphology, evolution, and ecology of colletid bees can be addressed.

Phylogeny and biogeography of bees of the tribe Osmiini (Hymenoptera: Megachilidae)

The Osmiini (Megachilidae) constitute a taxonomically and biologically diverse tribe of bees. To resolve their generic and suprageneric relationships, we inferred a phylogeny based on three nuclear genes (Elongation factor 1-alpha, LW-rhodopsin and CAD) applying both parsimony and Bayesian methods. Our phylogeny, which includes 95 osmiine species representing 18 of the 19 currently recognized genera, is well resolved with high support for most basal nodes. The core osmiine genera were found to form a well-supported monophyletic group, but four small genera, Noteriades, Afroheriades,Pseudoheriades and possibly Ochreriades, formerly included in the Osmiini, do not appear to belong within this tribe. Our phylogeny results in the following taxonomic changes: Stenosmia and Hoplosmia are reduced to subgeneric rank in Hoplitis and Osmia, respectively, Micreriades is recognized as a subgenus in Hoplitis and the subgenus Nasutosmia is transferred from Hoplitis to Osmia. We inferred a biogeographic scenario for the Osmiini applying maximum likelihood inference and models of character evolution. We provide evidence that the Osmiini originated in the Palearctic, and that extensive exchanges occurred between the Palearctic and the Nearctic. The latter finding may relate to the fact that many osmiine species nest in wood or in stems, facilitating dispersal by overseas transport of the nests.

MITONUCLEAR DISCORDANCE IS CAUSED BY RAMPANT MITOCHONDRIAL INTROGRESSION IN NEODIPRION (HYMENOPTERA: DIPRIONIDAE) SAWFLIES

We investigate the pervasiveness of hybridization and mitochondrial introgression in Neodiprion Rohwer (Hymenoptera; Diprionidae), a Holarctic genus of conifer-feeding sawflies. A phylogenetic analysis of the lecontei species group revealed extensive discordance between a contiguous mitochondrial region spanning three genes (COI, tRNA-leucine, and COII) and three nuclear loci (EF1alpha, CAD, and an anonymous nuclear locus). Bayesian tests of monophyly and Shimodaira-Hasegawa (SH) tests of topological congruence were consistent with mitochondrial introgression; however, these patterns could also be explained by lineage sorting (i.e., deep coalescence). Therefore, to explicitly test the mitochondrial introgression hypothesis, we used a novel application of coalescent-based isolation with migration (IM) models to measure interspecific gene flow at each locus. In support of our hypothesis, mitochondrial gene flow was consistently higher than nuclear gene flow across 120 pairwise species comparisons (P < 1 x 10(-12)). We combine phylogenetic and coalescent evidence to identify likely cases of recent and ancient introgression in Neodiprion, and based on these observations, we hypothesize that shared hosts and/or pheromones facilitate hybridization, whereas disparate abundances between hybridizing species promote mitochondrial introgression. Our results carry implications for phylogenetic analysis, and we advocate the separation of high and low gene flow regions to inform analyses of hybridization and speciational history, respectively.

Low nuclear DNA variation supports a recent origin of Hawaiian Hylaeus bees (Hymenoptera: Colletidae)

Previous phylogenetic work on the Hawaiian bees of the genus Hylaeus, based on mitochondrial DNA and morphology, appeared to support a recent origin for the group, but support for the resulting tree was weak. Four nuclear genes with varying evolutionary rates -- arginine kinase, EF-1alpha, opsin, and wingless -- were sequenced for a reduced taxon set in an attempt to find one or more data set that would provide better support. All showed very low variation (<2%) in the ingroup. Comparison among genes revealed a much higher than expected rate of evolution in mtDNA, especially at first and second positions. While the data from the nuclear genes showed insufficient variation for phylogenetic analysis, the strong sequence similarity among the Hawaiian species supports the previous hypothesis of a recent origin for the group.

Changing paradigms in insect social evolution: insights from halictine and allodapine bees

Until the 1980s theories of social insect evolution drew strongly on halictine and allodapine bees. However, that early work suffered from a lack of sound phylogenetic inference and detailed information on social behavior in many critical taxa. Recent studies have changed our understanding of these bee groups in profound ways. It has become apparent that forms of social organization, caste determination, and sex allocation are more labile and complex than previously thought, although the terminologies for describing them are still inadequate. Furthermore, the unexpected complexity means that many key parameters in kin selection and reproductive skew models remain unquantified, and addressing this lack of information will be formidable. At the same time, phylogenetic questions have become more tractable, and DNA sequence-based studies have resolved questions that earlier studies could not resolve, radically changing our understanding of the number of origins and losses of sociality in these bees.

The phylogenetic relationship between Astigmata and Oribatida (Acari) as indicated by molecular markers

Astigmata comprise a diverse group of acariform mite species with a remarkable range of life histories, most of which involve parasitic or commensal relationships with other organisms. Several authors have suggested that Astigmata evolved as a paedomorphic clade from within Oribatida, and both morphology and gland-chemistry strongly suggest that their sister-clade is within the oribatid subgroup Desmonomata. The biologies of these groups contrast greatly, since oribatid mites are mostly soil-living detritivores and fungivores, and have life cycles that are much longer than those in Astigmata. We tested the hypothesis that Astigmata evolved from within Desmonomata using two molecular markers, the ribosomal 18S region (18S) and the nuclear elongation factor 1 alpha (ef1alpha) gene. Representative acariform mites included 28 species of Oribatida, eight of Astigmata, two of Prostigmata and two of Endeostigmata; outgroups included members of Opilioacariformes, Parasitiformes and Ricinulei. To minimize the possibility of long-branch attraction artifacts, we limited highly variable sites by removing gaps (18S) and third codon positions (ef1alpha) from the sequences. Maximum parsimony, neighbor-joining and Bayesian algorithms formed trees that consistently placed Astigmata outside monophyletic Oribatida, usually as sister-group of the endeostigmatid mite Alicorhagia sp. Analyses with and without outgroups resulted in similar topologies, showing no evidence for long-branch artifacts and leaving the conflict with morphological and biochemical data unexplained.

The history of early bee diversification based on five genes plus morphology

Bees, the largest (>16,000 species) and most important radiation of pollinating insects, originated in early to mid-Cretaceous, roughly in synchrony with the angiosperms (flowering plants). Understanding the diversification of the bees and the coevolutionary history of bees and angiosperms requires a well supported phylogeny of bees (as well as angiosperms). We reconstructed a robust phylogeny of bees at the family and subfamily levels using a data set of five genes (4,299 nucleotide sites) plus morphology (109 characters). The molecular data set included protein coding (elongation factor-1alpha, RNA polymerase II, and LW rhodopsin), as well as ribosomal (28S and 18S) nuclear gene data. Analyses of both the DNA data set and the DNA+morphology data set by parsimony and Bayesian methods yielded a single well supported family-level tree topology that places Melittidae as a paraphyletic group at the base of the phylogeny of bees. This topology ("Melittidae-LT basal") is significantly better than a previously proposed alternative topology ("Colletidae basal") based both on likelihood and Bayesian methods. Our results have important implications for understanding the early diversification, historical biogeography, host-plant evolution, and fossil record of bees. The earliest branches of bee phylogeny include lineages that are predominantly host-plant specialists, suggesting that host-plant specificity is an ancestral trait in bees. Our results suggest an African origin for bees, because the earliest branches of the tree include predominantly African lineages. These results also help explain the predominance of Melittidae, Apidae, and Megachilidae among the earliest fossil bees.

Recent and simultaneous origins of eusociality in halictid bees

Eusocial organisms are characterized by cooperative brood care, generation overlap and reproductive division of labour. Traits associated with eusociality are most developed in ants, termites, paper wasps and corbiculate bees; the fossil record indicates that each of these advanced eusocial taxa evolved in the Late Cretaceous or earlier (greater than 65 Myr ago). Halictid bees also include a large and diverse number of eusocial members, but, in contrast to advanced eusocial taxa, they are characterized by substantial intra- and inter-specific variation in social behaviour, which may be indicative of more recent eusocial evolution. To test this hypothesis, we used over 2400 bp of DNA sequence data gathered from three protein-coding nuclear genes (opsin, wingless and EF-1a) to infer the phylogeny of eusocial halictid lineages and their relatives. Results from relaxed molecular clock dating techniques that utilize a combination of molecular and fossil data indicate that the three independent origins of eusociality in halictid bees occurred within a narrow time frame between approximately 20 and 22 Myr ago. This relatively recent evolution helps to explain the pronounced levels of social variation observed within these bees. The three origins of eusociality appear to be temporally correlated with a period of global warming, suggesting that climate may have had an important role in the evolution and maintenance of eusociality in these bees.

Analysis of family-level relationships in bees (Hymenoptera: Apiformes) using 28S and two previously unexplored nuclear genes: CAD and RNA polymerase II

We analyzed a combined data set of two protein-coding nuclear genes (CAD and RNA polymerase II) and a nuclear ribosomal gene (28S D2-D4 region) for 68 bee species and 11 wasp outgroups. Our taxon sampling included all seven extant bee families, 17 of 20 subfamilies, and diverse tribes. Wasp outgroups included the two families most closely related to bees: Crabronidae and Sphecidae. We analyzed the combined and single gene data sets using parsimony and Bayesian methods, which yielded largely congruent results. Our results provide reasonably strong support for family and subfamily-level relationships among bees. Our data set strongly supports the sister-group relationship of the Colletidae and Stenotritidae, and places Halictidae as sister to this clade combined. Our analyses place the Melittidae and the long-tongued (LT) bee clade (Apidae+Megachilidae) near the base of the tree with Colletidae (and Stenotritidae) in a fairly highly derived position. This topology ("Melittidae-LT basal") was obtained in previous morphological studies under certain methods of character coding. A more widely accepted tree topology that places Colletidae (and/or Stenotritidae) as sister to all other bees ("Colletidae basal") is not supported by our data. The "Melittidae-LT basal" hypothesis may better explain patterns in the bee fossil record as well as historical biogeography of certain bee groups. Our results provide new insights into higher-level bee phylogeny and indicate that CAD, RNA polymerase II, and 28S are useful data sets for resolving Cretaceous-age divergences in bees and other Hymenoptera.

Phylogeny of the Callandrena subgenus of Andrena (Hymenoptera: Andrenidae) based on mitochondrial and nuclear DNA data: Polyphyly and convergent evolution

We propose a phylogenetic hypothesis of relationships within Callandrena, a North American subgenus of the bee genus Andrena, based on both mitochondrial and nuclear DNA sequences. Our data included 695 aligned base pairs comprising parts of the mitochondrial genes cytochrome oxidase subunits I and II and the intervening tRNA-leucine and 767 aligned base pairs of the F2 copy of the nuclear gene elongation factor-1alpha. We also suggest a preliminary hypothesis of relationships of the North American subgenera in the genus. Our analyses included 54 species of Callandrena, 42 species of Andrena representing 24 additional subgenera, and 11 outgroup species in the family Andrenidae. Parsimony analyses of each marker separately suggested that Callandrena was polyphyletic, with a combined analysis suggesting that there were at least two phylogenetically independent clades of bees with similar morphological features. Maximum likelihood and Bayesian analyses supported this conclusion, as did the non-parametric bootstrapping SOWH test. Convergence in morphological characters was likely due to their common use of members of Asteraceae as pollen hosts.

Molecular phylogeny of the bumble bee subgenus Pyrobombus (Hymenoptera:Apidae:Bombus) with insights into gene utility for lower-level analysis

Comprising nearly 20% of all bumble bees, the subgenus Pyrobombus is distributed across diverse habitats in the Northern Hemisphere and exhibits considerable morphological and behavioural variation relative to other subgenera. Its size and variation have led to questions concerning its monophyly and intrasubgeneric relationships, but too few known morphological synapomorphies and insufficient taxon sampling have precluded robust answers to these questions. To obtain a robust phylogeny of the group, we obtained DNA sequences for 36 of the 43 species from four genes (mitochondrial 16S rRNA and three nuclear genes: elongation factor – 1α (EF-1α), long wavelength rhodopsin (LW Rh or opsin) and arginine kinase (ArgK)). Both Bayesian and parsimony phylogenies are well resolved and indicate a monophyletic Pyrobombus when assessed against representatives of 20 additional subgenera. The more conserved nuclear genes, especially EF-1α and ArgK, provided good support across all of the taxonomic levels examined, whereas support of the more rapidly evolving mt16S was restricted mostly to close relationships at the tips of the tree. The exon regions of ArgK were the most conserved and may be promising for higher-level phylogenetics. We discuss species relationships within Pyrobombus and its sister-group, Bombus s.s. + Alpinobombus, in relation to previous taxonomic studies.

Single-copy nuclear genes recover cretaceous-age divergences in bees

We analyzed the higher level phylogeny of the bee family Halictidae based on the coding regions of three single-copy nuclear genes (long-wavelength [LW] opsin, wingless, and elongation factor 1-alpha [EF-1 alpha]). Our combined data set consisted of 2,234 aligned nucleotide sites (702 base pairs [bp] for LW opsin, 405 bp for wingless, and 1,127 bp for EF-1 alpha) and 779 parsimony-informative sites. We included 58 species of halictid bees from 33 genera, representing all subfamilies and tribes, and rooted the trees using seven outgroups from other bee families: Colletidae, Andrenidae, Melittidae, and Apidae. We analyzed the separate and combined data sets by a variety of methods, including equal weights parsimony, maximum likelihood, and Bayesian methods. Analysis of the combined data set produced a strong phylogenetic signal with high bootstrap and Bremer support and high posterior probability well into the base of the tree. The phylogeny recovered the monophyly of the Halictidae and of all four subfamilies and both tribes, recovered relationships among the subfamilies and tribes congruent with morphology, and provided robust support for the relationships among the numerous genera in the tribe Halictini, sensu Michener (2000). Using our combined nucleotide data set, several recently described halictid fossils from the Oligocene and Eocene, and recently developed Bayesian methods, we estimated the antiquity of major clades within the family. Our results indicate that each of the four subfamilies arose well before the Cretaceous-Tertiary boundary and suggest that the early radiation of halictid bees involved substantial African-South American interchange roughly coincident with the separation of these two continents in the late Cretaceous. This combination of single-copy nuclear genes is capable of recovering Cretaceous-age divergences in bees with high levels of support. We propose that LW opsin, wingless, and EF-1 alpha(F2 copy) may be useful in resolving relationships among bee families and other Cretaceous-age insect lineages.

Phylogeny of the orchid bees (Hymenoptera: Apinae: Euglossini): DNA and morphology yield equivalent patterns

Orchid bees (Euglossini) are spectacular long-tongued Neotropical bees important in the pollination of Neotropical long-corolla flowers, particularly some orchids. Besides remarkably long tongues, males in particular exhibit other flower-related adaptations, including setal brushes on the foretarsi used for rasping the petals of orchids while collecting aromatic compounds. These compounds are stored in large swollen tibiae and are thought to play an important role in courtship behavior. Euglossini are also unusual in lacking sociality; they are the only tribe among the corbiculate bees that are not eusocial, and two of the genera are cleptoparasitic. Each genus exhibits distinct behavioral traits including nest architecture and host-parasite interactions, yet their evolution is unknown. Despite previous phylogenetic studies of on morphological characters, the relationships among the five euglossine genera remain under debate. We investigate euglossine generic relationships using DNA sequence data from four genes and new morphological characters. The morphological and molecular data yield congruent evolutionary patterns, and combining the data gives a fully resolved and well supported phylogeny of Euglossini.

How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets

We analyzed 12 combined mitochondrial and nuclear gene datasets in seven orders of insects using both equal weights parsimony (to evaluate phylogenetic utility) and Bayesian methods (to investigate substitution patterns). For the Bayesian analyses we used relatively complex models (e.g., general time reversible models with rate variation) that allowed us to quantitatively compare relative rates among genes and codon positions, patterns of rate variation among genes, and substitution patterns within genes. Our analyses indicate that nuclear and mitochondrial genes differ in a number of important ways, some of which are correlated with phylogenetic utility. First and most obviously, nuclear genes generally evolve more slowly than mitochondrial genes (except in one case), making them better markers for deep divergences. Second, nuclear genes showed universally high values of CI and (generally) contribute more to overall tree resolution than mitochondrial genes (as measured by partitioned Bremer support). Third, nuclear genes show more homogeneous patterns of among-site rate variation (higher values of alpha than mitochondrial genes). Finally, nuclear genes show more symmetrical transformation rate matrices than mitochondrial genes. The combination of low values of alpha and highly asymmetrical transformation rate matrices may explain the overall poor performance of mitochondrial genes when compared to nuclear genes in the same analysis. Our analyses indicate that some parameters are highly correlated. For example, A/T bias was positively and significantly associated with relative rate and CI was positively and significantly associated with alpha (the shape of the gamma distribution). These results provide important insights into the substitution patterns that might characterized high quality genes for phylogenetic analysis: high values of alpha, unbiased base composition, and symmetrical transformation rate matrices. We argue that insect molecular systematists should increasingly focus on nuclear rather than mitochondrial gene datasets because nuclear genes do not suffer from the same substitutional biases that characterize mitochondrial genes.

A novel social polymorphism in a primitively eusocial bee

Halictine sweat bees (Hymenoptera, Halictidae) are model organisms for the evolution of altruism, reproductive castes, and eusocial colony organization. Halictine social behavior is not only extremely variable, but also ecologically and evolutionarily labile. Among social species, colony social organization ranges from communal societies of egalitarian females to eusocial and semisocial ones with reproductive queens and more or less sterile workers. A striking aspect of halictine social variation is the mutual exclusivity of communal and eusocial types of colony social organization within the same species, these two types of social behavior being characteristic of different genera and subgenera. We report a recently discovered exception to this rule in a population of Halictus sexcinctus (Fabricius) at Daimonia-Pyla in southern Greece, that contained both communal and eusocial colonies. Moreover, communal and eusocial females exhibit morphological differences that imply a preimaginal developmental switch, which could also underlie the two types of social behavior. That the communal and eusocial forms are not merely cryptic sister species with different social behavior is indicated by the comparison of mitochondrial DNA sequences of two sections of cytochrome oxidase I, which indicate that Greek specimens of both social types are more similar than they are to conspecifics from elsewhere in Europe. The phylogenetic position of Halictus sexcinctus suggests that this unusual communal/eusocial polymorphism may represent an unstable intermediate step in an evolutionary reversal from eusocial to solitary behavior.

Complex sociogenetic organization and reproductive skew in a primitively eusocial sweat bee, Lasioglossum malachurum, as revealed by microsatellites

The sweat bees (Family Halictidae) are a socially diverse taxon in which eusociality has arisen independently numerous times. The obligate, primitively eusocial Lasioglossum malachurum, distributed widely throughout Europe, has been considered the zenith of sociality within halictids. A single queen heads a colony of smaller daughter workers which, by mid-summer, produce new sexuals (males and gynes), of which only the mated gynes overwinter to found new colonies the following spring. We excavated successfully 18 nests during the worker- and gyne-producing phases of the colony cycle and analysed each nest's queen and either all workers or all gynes using highly variable microsatellite loci developed specifically for this species. Three important points arise from our analyses. First, queens are facultatively polyandrous (queen effective mating frequency: range 1-3, harmonic mean 1.13). Second, queens may head colonies containing unrelated individuals (n = 6 of 18 nests), most probably a consequence of colony usurpation during the early phase of the colony cycle before worker emergence. Third, nonqueen's workers may, but the queen's own workers do not, lay fertilized eggs in the presence of the queen that successfully develop into gynes, in agreement with so-called 'concession' models of reproductive skew.