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.

Description of the immature stages of the endangered Japanese endemic Oreodytes kanoi (Kamiya, 1938) (Coleoptera: Dytiscidae: Hydroporinae) and comparison with the known larvae of Oreodytes Seidlitz, 1887.

The larvae and pupa of the Japanese endemic Oreodytes kanoi (Kamiya, 1938) are described and compared with those known of other species of Oreodytes Seidlitz, 1887. Larvae of O. kanoi and other species of the alpinus species-group share the presence of dorsal secondary setae on tarsi, a unique feature amongst Oreodytes. The morphology of the pupa of O. kanoi is briefly discussed with some information on the ecology of this species.

Data curation and modeling of compositional heterogeneity in insect phylogenomics: A case study of the phylogeny of Dytiscoidea (Coleoptera: Adephaga).

Diving beetles and their allies are an almost ubiquitous group of freshwater predators. Knowledge of the phylogeny of the adephagan superfamily Dytiscoidea has significantly improved since the advent of molecular phylogenetics. However, despite recent comprehensive phylogenomic studies, some phylogenetic relationships among the constituent families remain elusive. In particular, the position of the family Hygrobiidae remains uncertain. We address these issues by re-analyzing recently published phylogenomic datasets for Dytiscoidea, using approaches to reduce compositional heterogeneity and adopting a site-heterogeneous mixture model. We obtained a consistent, well-resolved, and strongly supported tree. Consistent with previous studies, our analyses support Aspidytidae as the monophyletic sister group of Amphizoidae, and more importantly, Hygrobiidae as the sister of the diverse Dytiscidae, in agreement with morphology-based phylogenies. Our analyses provide a backbone phylogeny of Dytiscoidea, which lays the foundation for better understanding the evolution of morphological characters, life habits, and feeding behaviors of dytiscoid beetles.

The Hydradephaga (Coleoptera, Haliplidae, Gyrinidae, and Dytiscidae) fauna of Cape Breton Island, Nova Scotia, Canada: new records, distributions, and faunal composition.

The Haliplidae, Gyrinidae, and Dytiscidae (Coleoptera) of Cape Breton Island, Nova Scotia, Canada were surveyed during the years 2006-2007. A total of 2027 individuals from 85 species was collected from 94 different localities, which brings to 87 the number of species recorded for this locality. Among these, Heterosternuta allegheniana (Matta & Wolfe), H. wickhami (Zaitzev), Hydroporus appalachius Sherman, H. gossei Larson & Roughley, H. nigellus Mannerheim, H. puberulus LeConte, Ilybius picipes (Kirby), and I. wasastjernae (C.R. Sahlberg) are reported for the first time in Nova Scotia. The Nearctic component of the fauna is made up of 71 species (81.6%), the Holarctic component of 16 species (18.4%). Most species are characteristic of both the Boreal and Atlantic Maritime Ecozones and have a transcontinental distribution but 19 species (21.8%), which are generally recognized as species with eastern affinities. In an examination of the Hydradephaga of insular portions of Atlantic Canada, it was shown that the island faunas of Cape Breton Island and Prince Edward Island are very similar (87 and 84 species, respectively) despite differences in composition suggesting that more Hydradephaga species have yet to be found on Cape Breton Island.

Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error.

The beetle superfamily Dytiscoidea, placed within the suborder Adephaga, comprises six families. The phylogenetic relationships of these families, whose species are aquatic, remain highly contentious. In particular the monophyly of the geographically disjunct Aspidytidae (China and South Africa) remains unclear. Here we use a phylogenomic approach to demonstrate that Aspidytidae are indeed monophyletic, as we inferred this phylogenetic relationship from analyzing nucleotide sequence data filtered for compositional heterogeneity and from analyzing amino-acid sequence data. Our analyses suggest that Aspidytidae are the sister group of Amphizoidae, although the support for this relationship is not unequivocal. A sister group relationship of Hygrobiidae to a clade comprising Amphizoidae, Aspidytidae, and Dytiscidae is supported by analyses in which model assumptions are violated the least. In general, we find that both concatenation and the applied coalescent method are sensitive to the effect of among-species compositional heterogeneity. Four-cluster likelihood-mapping suggests that despite the substantial size of the dataset and the use of advanced analytical methods, statistical support is weak for the inferred phylogenetic placement of Hygrobiidae. These results indicate that other kinds of data (e.g. genomic meta-characters) are possibly required to resolve the above-specified persisting phylogenetic uncertainties. Our study illustrates various data-driven confounding effects in phylogenetic reconstructions and highlights the need for careful monitoring of model violations prior to phylogenomic analysis.

The mitogenome phylogeny of Adephaga (Coleoptera).

The beetle suborder Adephaga consists of several aquatic ('Hydradephaga') and terrestrial ('Geadephaga') families whose relationships remain poorly known. In particular, the position of Cicindelidae (tiger beetles) appears problematic, as recent studies have found them either within the Hydradephaga based on mitogenomes, or together with several unlikely relatives in Geadephaga based on 18S rRNA genes. We newly sequenced nine mitogenomes of representatives of Cicindelidae and three ground beetles (Carabidae), and conducted phylogenetic analyses together with 29 existing mitogenomes of Adephaga. Our results support a basal split of Geadephaga and Hydradephaga, and reveal Cicindelidae, together with Trachypachidae, as sister to all other Geadephaga, supporting their status as Family. We show that alternative arrangements of basal adephagan relationships coincide with increased rates of evolutionary change and with nucleotide compositional bias, but these confounding factors were overcome by the CAT-Poisson model of PhyloBayes. The mitogenome + 18S rRNA combined matrix supports the same topology only after removal of the hypervariable expansion segments. Densely sampled mitogenomes, analyzed with site heterogeneous mixture models, support a plausible hypothesis of basal relationships in the Adephaga.

Further contributions to the Hydradephaga (Coleoptera, Haliplidae, Gyrinidae and Dytiscidae) fauna of Prince Edward Island, Canada: new records, distributions and faunal composition.

The Haliplidae, Gyrinidae and Dytiscidae (Coleoptera) of Prince Edward Island, Canada were surveyed during the years 2004-2005. A total of 2450 individuals from 79 species were collected from 98 different localities, among which 30 species are newly recorded from that region. Among these, Acilius sylvanus Hilsenhoff, Rhantus consimilis Motschulsky and Neoporus sulcipennis (Fall) stand out as representing the easternmost reports of these species in Canada. Once removed, Gyrinus aquiris LeConte (Gyrinidae) is reinstated in the faunal list of Prince Edward Island. According to this study and literature 84 species of Hydradephaga are currently known from Prince Edward Island. The Nearctic component of the fauna is made up of 68 species (80.9%) and the Holarctic component of 16 species (19.1%). Most species are characteristic of the Boreal and Atlantic Maritime Ecozones and have a transcontinental distribution. In an examination of the Hydradephaga of insular portions of Atlantic Canada, we found that despite significantly different land areas and different distances to the neighbouring continental mainland the island faunas of Prince Edward Island and insular Newfoundland are very similar in the number of species (84 and 94 species respectively) despite differences in composition. With a land area significantly larger than that of Prince Edward Island, however, the fauna of Cape Breton Island was 39% smaller consisting of 53 species. This difference could be due to the comparative lack of collecting efforts on Cape Breton Island.