Evaluating the Impact of Anatomical Partitioning on Summary Topologies Obtained with Bayesian Phylogenetic Analyses of Morphological Data.

Morphological data are a fundamental source of evidence to reconstruct the Tree of Life, and Bayesian phylogenetic methods are increasingly being used for this task. Bayesian phylogenetic analyses require the use of evolutionary models, which have been intensively studied in the past few years, with significant improvements to our knowledge. Notwithstanding, a systematic evaluation of the performance of partitioned models for morphological data has never been performed. Here we evaluate the influence of partitioned models, defined by anatomical criteria, on the precision and accuracy of summary tree topologies considering the effects of model misspecification. We simulated datasets using partitioning schemes, trees, and other properties obtained from two empirical datasets, and conducted Bayesian phylogenetic analyses. Additionally, we reanalyzed 32 empirical datasets for different groups of vertebrates, applying unpartitioned and partitioned models, and, as a focused study case, we reanalyzed a dataset including living and fossil armadillos, testing alternative partitioning hypotheses based on functional and ontogenetic modules. We found that, in general, partitioning by anatomy has little influence on summary topologies analyzed under alternative partitioning schemes with a varying number of partitions. Nevertheless, models with unlinked branch lengths, which account for heterotachy across partitions, improve topological precision at the cost of reducing accuracy. In some instances, more complex partitioning schemes led to topological changes, as tested for armadillos, mostly associated with models with unlinked branch lengths. We compare our results with other empirical evaluations of morphological data and those from empirical and simulation studies of the partitioning of molecular data, considering the adequacy of anatomical partitioning relative to alternative methods of partitioning morphological datasets. [Evolutionary rates; heterogeneity; morphology; Mk model; partition; topology.].

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.

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.

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.

New genus and subgenus of South American long-horned bees (Apidae, Eucerini).

As part of a broader treatment of Eucerini systematics, a new genus and a new subgenus are described to accommodate previously described species. Savannychapis gen. n. is described to accommodate Gaesischia interrupta Urban 1989, originally described as a species of Gaesischia (Gaesischiana) Michener et al. 1955, and Gaesischia (Gaesischioides) subgen. n. to accommodate Gaesischia hyptidis (Ducke 1910), previously included in Gaesischia s. str. Michener et al. 1955 and G. (Agaesischia) Moure & Michener 1955. These new taxa are only known in the South American dry diagonal, a set of open vegetation biomes of central-eastern South America.

Synopsis of the bee genus Thygater Holmberg 1884 (Hymenoptera, Apidae) in the Brazilian state of Minas Gerais, with the description of a new species and a key to all Brazilian species.

Thygater Holmberg 1884, a Neotropical bee genus distributed from Argentina to Mexico, was last revised almost 50 years ago. Considering the species recognized then, and a few others described subsequently, 30 species are currently included in the genus. The Brazilian state of Minas Gerais is a large, environmentally heterogeneous territory, including areas in the phytogeographic domains of the Atlantic Tropical Rain Forest, the semiarid Caatinga and the highly seasonal Cerrado. The state insect fauna has been poorly sampled and studied. As part of a taxonomic and phylogenetic study of the genus, a synopsis of Thygater occurring in the state of Minas Gerais was produced, including the description of a new species (Thygater danunciae Freitas & Silveira, sp. n.), the recognition of two new synonymies, and an identification key for all 15 species of Thygater recorded for Brazil.

Morphology of male reproductive system of two solitary bee species (Hymenoptera: Apidae).

Bees can form all levels of social organization, from solitary to advanced eusocial societies. Although 80% of the species exist as solitary species, most researches emphasize social species. This study focuses on the description of the male reproductive system of the solitary beesThygater analis (Lepeletier) and Melitoma segmentaria (Fabricius) and searches for traits that support behavioral and phylogenetic studies. The reproductive system of males were dissected, fixed in 2.5% glutaraldehyde in 0.1 M sodium cacodylate buffer pH 7.2 and post-fixed with 1% osmium tetroxide. The tissue was dissected and included for light microscopy. The species presented similar anatomical traits, including paired testicles, seminal vesicles, deferent ducts, accessory glands and an ejaculatory duct. Each testicle was composed of four follicles. In both species, a testicle and a seminal vesicle were surrounded by a joint capsule, forming a seminal vesicle-testicle complex. The two species presented accessory glands with very distinct morphological traits. The anatomic pattern and the histological traits of the reproductive system of the species studied were similar to those described for other bees. In addition, these traits can be used to differentiate species and allow inferences concerning their reproductive biology.

Morphology of male reproductive system of two solitary bee species (Hymenoptera: Apidae)

Bees can form all levels of social organization, from solitary to advanced eusocial societies. Although 80 percent of the species exist as solitary species, most researches emphasize social species. This study focuses on the description of the male reproductive system of the solitary beesThygater analis (Lepeletier) and Melitoma segmentaria (Fabricius) and searches for traits that support behavioral and phylogenetic studies. The reproductive system of males were dissected, fixed in 2.5 percent glutaraldehyde in 0.1 M sodium cacodylate buffer pH 7.2 and post-fixed with 1 percent osmium tetroxide. The tissue was dissected and included for light microscopy. The species presented similar anatomical traits, including paired testicles, seminal vesicles, deferent ducts, accessory glands and an ejaculatory duct. Each testicle was composed of four follicles. In both species, a testicle and a seminal vesicle were surrounded by a joint capsule, forming a seminal vesicle-testicle complex. The two species presented accessory glands with very distinct morphological traits. The anatomic pattern and the histological traits of the reproductive system of the species studied were similar to those described for other bees. In addition, these traits can be used to differentiate species and allow inferences concerning their reproductive biology.