Resolving the phylogenetic position of Hygrobiidae (Coleoptera: Adephaga) requires objective statistical tests and exhaustive phylogenetic methodology: a response to Cai et al. (2020)

Morphology and distribution of sensilla on head appendages in the water beetle Hygrobia hermanni (Coleoptera: Adephaga: Hygrobiidae)

Sensilla on head appendages were studied in detail for the first time in a member of the relict family Hygrobiidae (squeak beetles), closely related to Dytiscidae (diving beetles). Adult and third instar larval stage specimens of Hygrobia hermanni (Fabricius, 1775) were examined using scanning electron microscopy, focusing on antennae, palps and larval mandibles. In total, 37 sensilla subtypes are described, including 22 observed in the adult (basiconica: 3; Böhm's bristles: 2; circumvallate sensilla: 2; coeloconica: 10; ovoid placodea: 3; digitiform placodea: 2) and 16 in the larva (basiconica: 4; campaniformia: 1; chaetica: 4; coeloconica: 5; trichodea: 1; unnamed: 1). Only one subtype (of sensilla coeloconica) was shared between the adult and the larva. Autapomorphies of Hygrobiidae and Dytiscidae, and putatively shared derived characters (synapomorphies) of Hygrobiidae + Dytiscidae are discussed. Among the latter, the most remarkable is the acquisition of a special sensory field, located on the apical segment of the adult maxillary palp, subapically and postero-dorsally. This sensory field is made up of ovoid multiporous sensilla placodea otherwise present on the anterior (internal) surface of antennal segments, suggesting that in a common ancestor of Hygrobiidae and Dytiscidae, maxillary palps might have taken over enhanced capacities of longe-range molecule detection.

Genome-scale approach to reconstructing the phylogenetic tree of psyllids (superfamily Psylloidea) with account of systematic bias

Psyllids (class Insecta: order Hemiptera: superfamily Psylloidea) are a taxonomically and phylogenetically challenging clade. Recent studies have largely advanced the phylogeny of this group, yet the family-level relationships among Aphalaridae, Carsidaridae, and others remain unresolved. Genome-scale phylogenetic analysis is known to provide a finer resolution for problems like that. However, such phylogenomics also introduces new problems: incorrect trees with high confidence yielded due to systematic error (bias). Here we addressed these issues using hundreds of single-copy orthologous (SCO) genes in psyllid transcriptomes and genomes. Our analyses revealed conflicts between the nucleotide-based and amino-acid-based phylogenetic trees. While the nucleotide-based phylogeny strongly supported the (Aphalaridae + Carsidaridae) + Others relationship, the amino-acid-based one recovered Aphalaridae + (Carsidaridae + Others) with 100% support. Further inspection revealed significant compositional heterogeneity in nucleotide sequences for 67% of SCO genes, but not in the corresponding translated amino acid sequences. We then used different strategies to combat this compositional bias, and found that using the RY-coding strategy (coding the standard nucleotides as purines and pyrimidines) the nucleotide-based phylogeny became consistent with the amino-acid-based one. We further applied RY-coding to a published concatenated nucleotide dataset and recovered the Aphalaridae monophyly (which is refuted by the original literature on non-recoded sequences) at the base of psyllid tree. Moreover, it was found that variations in evolutionary rate could lead to errors in nucleotide-based phylogeny. The fast-evolving Heteropsylla cubana (Psyllidae: Ciriacreminae) was incorrectly placed within the subfamily Psyllinae. This bias can be avoided by using data removal or RY-coding strategies. Together, our results strongly support the family relationship of Aphalaridae + (Carsidaridae + Others), and show that the amino-acid-based concatenation analysis is more robust than nucleotide-based one. Future phylogenomic analysis of psyllid nucleotide sequences should take into account methods such as the RY-coding scheme to address potential systematic biases arising from composition and rate heterogeneities.

Data Types and the Phylogeny of Neoaves

The phylogeny of Neoaves, the largest clade of extant birds, has remained unclear despite intense study. The difficulty associated with resolving the early branches in Neoaves is likely driven by the rapid radiation of this group. However, conflicts among studies may be exacerbated by the data type analyzed. For example, analyses of coding exons typically yield trees that place Strisores (nightjars and allies) sister to the remaining Neoaves, while analyses of non-coding data typically yield trees where Mirandornites (flamingos and grebes) is the sister of the remaining Neoaves. Our understanding of data type effects is hampered by the fact that previous analyses have used different taxa, loci, and types of non-coding data. Herein, we provide strong corroboration of the data type effects hypothesis for Neoaves by comparing trees based on coding and non-coding data derived from the same taxa and gene regions. A simple analytical method known to minimize biases due to base composition (coding nucleotides as purines and pyrimidines) resulted in coding exon data with increased congruence to the non-coding topology using concatenated analyses. These results improve our understanding of the resolution of neoavian phylogeny and point to a challenge—data type effects—that is likely to be an important factor in phylogenetic analyses of birds (and many other taxonomic groups). Using our results, we provide a summary phylogeny that identifies well-corroborated relationships and highlights specific nodes where future efforts should focus.