Uneven missing data skews phylogenomic relationships within the lories and lorikeets

Abstract

Resolution of the Tree of Life has accelerated with advances in DNA sequencing technology. To achieve dense sampling, it is often necessary to obtain DNA from historical museum specimens to supplement modern genetic samples. However, DNA from historical material is generally degraded and fragmented, which presents various challenges. In this study, we evaluated how the read depth at variant sites and missing data among historical and modern sample types impacts phylogenomic inference. We explored these patterns in the brush-tongued parrots (lories and lorikeets) of Australasia by sampling ultraconserved elements in 105 taxa. Trees estimated with low coverage sites had several clades where historical or modern samples clustered together, which were not observed in trees with more stringent filtering. To assess if the aberrant relationships were affected by missing data, we performed an outlier analysis of sites and genes for trees built with and without low coverage sites, and with and without missing data. Outlier analyses showed that 6.6% of total sites were driving the topological differences, and at these sites, historical samples had 7.5x more missing data. An examination of subclades found loci biased by missing data, and the exclusion of these loci shifted phylogenetic relationships. Predictive modeling found that outlier analysis scores were not correlated with summary statistics of locus alignments, indicating that outlier loci do not have characteristics differing from other loci. After accounting for biased loci and understanding the stability of relationships, we inferred a more robust phylogenetic hypothesis for lories and lorikeets.

A Phylogenomic Supertree of Birds

“…Faircloth et al [55] NEORNITHES 9 2.5K UCE probe set McCormack et al [36] NEOAVES 33 YES 2.5K UCE probe set Baker et al [56] PALAEOGNATHAE 7 Subset of Faircloth et al [55] loci Jarvis et al [37] NEORNITHES 48 YES Whole genomes Sun et al [40] Phasianidae (peafowl) 15 5k UCE probe set Prum et al [38] NEORNITHES 197 YES AHE probe set Bryson et al [57] Passerellidae 30 YES 5k UCE probe set Hosner et al [58] Cracidae 23 5k UCE probe set Hosner et al [21] Phasianidae 90 5k UCE probe set Manthey et al [59] Piranga 11 YES 5k UCE probe set McCormack et al [22] Aphelocoma 1 (3) 5k UCE probe set Meiklejohn et al [60] Phasianidae (gallopheasants) 18 5k UCE probe set Ottenburghs et al [61] Anatidae-Anserini 19 YES Whole genomes Persons et al [62] Phasianidae (grouse) 11 5k UCE probe set Zarza et al [63] Aphelocoma 3 YES 5k UCE probe set Burga et al [64] Phalacrocorax 7 YES Whole genomes Hosner et al [42] Phasianidae 115 YES 5k UCE probe set Reddy et al [39] NEORNITHES 235 YES legacy with data mining Wang et al [65] Phasianidae 20 YES 5k UCE probe set White et al [66] Nyctibiidae 12 YES 5k UCE probe set Yonezawa et al [67] PALAEOGNATHAE YES legacy with data mining Andersen et al [68] Alcedinidae 21 YES 5k UCE probe set Bruxaux et al [69] Goura 6 YES Subset of UCE and AHE loci Campillo et al [70] Arachnothera 17 YES 5k UCE probe set Chen et al [71] Phasianidae 27 YES 5k UCE probe set Musher & Cracraft [72] Pachyramphus 18 YES 2.5K/5k UCE probe set Smith et al 2018 [73] Psittaculidae-Loriini 54 YES 5k UCE probe set Younger et al [74] Newtonia 4 YES 5k UCE probe set Sackton et al [75] PALAEOGNATHAE 15 YES Whole genomes 1 Redundant trees were omitted. 2 UCE (Ultraconserved Element) probe sets are described at https://www.…”

Macroevolutionary bursts and constraints generate a rainbow in a clade of tropical birds

“…To quantify color, we photographed the lateral, ventral, and dorsal sides of one male museum skin for 98 taxa deposited at the American Museum of Natural History (Additional file 5: Table S3). This sampling represents 92% of the described diversity in Loriini, all described genera, and all taxa for which phylogenomic data exists [19,20]. Because the majority of lorikeets do not exhibit sexual dichromatism, we chose only males to standardize our sampling scheme [14].…”

“…Phylogenetic relationships among major groups of parrots are reasonably well known [18], yet few subclades have the dense taxon-sampling necessary for detailed comparative analysis. The one exception is the the brush-tongued parrots, or lories and lorikeets (Tribe: Loriini; hereafter lorikeets) [19]. Lorikeets have radiated into over 100 taxa across the Australasian region [12] since their origin in the mid-Miocene [20].…”

Macroevolutionary bursts and constraints generate a rainbow in a clade of tropical birds

“…(figure 1a) We inputted the red, blue, and green values of the tetrahedral colour space (figure 1b) into the RGB method in the R package 160 grDevices version 3.4.3 to generate hex colours for each of the 35 patches [28,30]. Images were plotted as tip labels on a published phylogeny representing 92% of described taxa in Loriini ( [23], figure 1c) using ggtree v. 1.10.4 in R [29,31]. To convert the branch lengths of the tree to absolute time, we used a secondary calibration from [24] and specified the age for the node separating the Loriini from their sister taxon, Melopsittacus undulatus, to 11-17 million years 165 ago (Mya) using the program reePL [32].…”

“…Psittacofulvin concentration in feathers is linked to antibacterial resistance, and parrot colour can provide anti-predator defense [20,21]. Phylogenetic relationships among all parrots are reasonably well known [22], and some 105 subclades have the dense taxon-sampling [23] necessary for detailed comparative analysis, such as the the brush-tongued parrots or lories and lorikeets (Tribe: Loriini; hereafter lorikeets). In comparison to other parrots, lorikeets are species-rich given their age [24], which may be linked to the evolution of their specialized nectarivorous diet [25].…”