Ultraconserved elements put the final nail in the coffin of traditional use of the genus Meliphaga (Aves: Meliphagidae)

Abstract

Molecular systematics is bringing taxonomy into the 21st Century by updating our nomenclature to reflect phylogenetic relationships of taxa. This transformation is evidenced by massive changes in avian taxonomy, ranging from ordinal to subspecies changes. In this study, we employ target capture of ultraconserved elements to resolve genus‐level systematics of a problematic group of honeyeaters (Aves: Meliphagidae). With near complete species‐level taxon sampling of the Australo‐Papuan species within the traditionally recognized Meliphaga and Oreornis, we investigate generic limits using a genomic dataset. Likelihood and species tree methods confirm two clades within this group and found the New Guinea endemic Oreornis chrysogenys embedded within one of these clades. Our study supports earlier recommendations that Meliphaga Lewin, 1808 should be restricted to three species, M. aruensis, M. lewinii and M. notata. We make a case for recognizing three genera in the remaining species, Oreornis van Oort, 1910, Microptilotis Mathews, 1912 and Territornis Mathews, 1924.

Geographic range size and speciation in honeyeaters

“…2 ). The topology of genera within the tree is concordant with Andersen et al [ 59 ] and relationships within the genus Meliphaga follow McCullough et al [ 60 ]. In general, relationships between species within genera broadly follow previous reconstructions ([ 53 ]; see Additional file 1 : Fig.…”

“…For the phylogenomic data we used information from two recent phylogenomic studies based on ultraconserved elements (UCE); one resolved genus-level relationships of honeyeaters [ 59 ] and the second resolved some species-level relationships within the genus Meliphaga [ 60 ]. Unfortunately, sequence data for ultraconserved elements were not publicly available from the genus-level study [ 59 ].…”

“…3 by Andersen et al [ 59 ] to use as a constraint tree. UCEs were downloaded for 12 species of honeyeater ([ 60 ]; BioProject PRJNA509981; see Additional file 2 : Table S12 for UCE accession numbers and the species included in the constraint tree). Ultraconserved elements were clustered based on locus, aligned using MAFFT [ 85 ], and trees for each locus were generated with IQ-TREE [ 83 ] using a mixed GTR model.…”

Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds

“…This is because DNA from museum study skins tend to be fragmented (McCormack et al, 2016; Mundy et al, 1997; Tsai et al, 2019). For toepads, we followed protocols we have used previously (Andersen et al, 2019; McCullough et al, 2019). Toepad‐derived libraries were pooled with samples from other projects and sequenced at OMRF using the same sequencing parameters as the tissue‐derived libraries.…”

Additional notes on the life history of the Tagula Honeyeater Microptilotis vicina in Papua New Guinea

“…The genus Microptilotis exemplifies this lack of knowledge. There are nine species in this complicated group (sensu McCullough et al 2019) and, apart from the Australian Cryptic and Graceful Honeyeater forms [Microptilotis gracilis imitatrix (Cryptic Honeyeater) and M. g. gracilis (Graceful Honeyeater): see Nielsen 2018;Gill et al 2020], the clade is dominated by New Guinean species (McCullough et al 2019). The clutch-sizes of four of the nine species have not been recorded and aspects on life history such as developmental periods remain unknown for nearly all New Guinean representatives (Coates 1990;Higgins et al 2020).…”