Earth history and the passerine superradiation

Abstract

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.

Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault

“…The ability to incorporate museum specimens into modern molecular systematics offers plenty of research possibilities, as evidenced by the plethora of studies published in recent years. One obvious benefit in systematics is the inclusion of rare, difficult to collect, endangered or extinct taxa in phylogenomic analyses (Hedin et al, ; Hedin, Derkarabetian, Blair, et al, ; Hedin, Derkarabetian, Ramírez, et al, ; Oliveros et al, ; Tsai et al, ; Wood et al, ), or even datasets consisting entirely of museum specimens (Tsai et al, ). One important consideration will be the proportion of specimens in the final dataset that are historical museum specimens.…”

“…In this regard, museum specimens can be considered genomic resources (McCormack, Rodríguez-Gómez, Tsai, & Faircloth, 2017) and can be used for diverse types of studies. Examples of such studies are fine-scale population genomics and genotyping (Bi et al, 2013;Lim & Braun, 2016), genome sequencing (Staats et al, 2013), metagenomics (Der Sarkissian et al, 2017), epigenomics (Rubi, Knowles, & Dantzer, 2019), barcoding (Miller, Beentjes, van Helsdingen, & IJland, 2013); Prosser, deWaard, Miller, & Hebert, 2016), species delimitation (Hedin, Derkarabetian, Blair, & Paquin, 2018;Kehlmaier et al, 2019), and phylogenomics (Blaimer, Lloyd, Guillory, & Brady, 2016;Hedin, Derkarabetian, Ramírez, Vink, & Bond, 2018;Ruane & Austin, 2017;Sproul & Maddison, 2017;Starrett et al, 2017;Wood, González, Lloyd, Coddington, & Scharff, 2018), including phylogenomic studies that incorporate genetic data from rare, endangered and/or extinct taxa held in historical collections (Hedin, Derkarabetian, Blair, et al, 2018;Oliveros et al, 2019;Tsai et al, 2019). This was not the case just a few years ago, when historical museum samples were not routinely used for molecular work.…”

Reliable confidence intervals for RelTime estimates of evolutionary divergence times

“…We obtained six empirical datasets that employed different calibration strategies from five published studies (Table 1) (Bond et al 2014;Tong et al 2015;Barba-Montoya et al 2017;Nauheimer et al 2018;Oliveros et al 2019). Molecular data were obtained from supplementary files of original studies.…”

“…RelTime analyses were conducted in MEGA X . For Oliveros et al (2019)'s data, the published Bayesian timetree was summarized from 10 timetrees inferred using 10 different random subsets of the full dataset, because BEAST was computationally infeasible to analyze the full dataset. Since the original study has shown that 10 subsets provided similar results, we only conducted RelTime analysis using one subset.…”

Genome of an iconic Australian bird: High‐quality assembly and linkage map of the superb fairy‐wren (Malurus cyaneus)

“…Among the oscine passerines, by far the largest radiation of birds, these resources are limited to five species from the Passerides clade. Yet the early evolution of the Oscines involved multiple branching in the Australo‐Papuan region in the Oligocene before the emergence of the Corvides and Passerides, the two groups that ultimately gave the oscines their numerical and ecological dominance (Marki et al, ; Oliveros et al, ). The superb fairy‐wren is an exemplar of the largest clade of that early radiation, the Meliphagides, which has almost 300 species.…”