A Laurasian origin for a pantropical bird radiation is supported by genomic and fossil data (Aves: Coraciiformes)

Abstract

The evolution of pantropically distributed clades has puzzled palaeo-and neontologists for decades regarding the different hypotheses about where they originated. In this study, we explored how a pantropical distribution arose in a diverse clade with a rich fossil history: the avian order Coraciiformes. This group has played a central role in the debate of the biogeographical history of Neoaves. However, the order lacked a coherent species tree to inform study of its evolutionary dynamics. Here, we present the first complete species tree of Coraciiformes, produced with 4858 ultraconserved elements, which supports two clades: (1) Old World-restricted bee-eaters, rollers and ground-rollers; and (2) New World todies and motmots, and cosmopolitan kingfishers. Our results indicated two pulses of diversification: (1) major lineages of Coraciiformes arose in Laurasia approximately 57 Ma, followed by independent dispersals into equatorial regions, possibly due to tracking tropical habitat into the lower latitudes-the Coracii (Coraciidae + Brachypteraciidae) into the Afrotropics, bee-eaters throughout the Old World tropics, and kingfishers into the Australasian tropics; and (2) diversification of genera in the tropics during the Miocene and Pliocene. Our study supports the important role of Laurasia as the geographical origin of a major pantropical lineage and provides a new framework for comparative analyses in this charismatic bird radiation.

Extant species fail to estimate ancestral geographical ranges at older nodes in primate phylogeny

“…Recent historical biogeographic studies have yielded similar findings (e.g. [17,22]), strongly implying that ancestral range estimates based on extant taxa alone may fail to accurately capture patterns of biogeographic range evolution in the early phase of clade history owing to extinction in previously occupied areas [21]. Our results are consistent with this observation (figure 2).…”

“…Previous analyses have shown a strong influence of fossil data on ancestral range estimates at deep nodes in molecular phylogenies, particularly where extant representatives no longer occupy areas that are well represented in the fossil record (e.g. [21, 22]). To quantitatively evaluate whether mismatches were randomly distributed across shared nodes or whether there is a significant association between node depth and estimation mismatch, we also performed a logistic regression of congruence between node estimates on node age, using the glm function in the stats library [52].…”

“…Intuitively, fossil data may provide evidence of a clade’s past geographical range that cannot be obtained from extant taxa alone [13–15]. The inclusion of extinct taxa in phylogenetic biogeographic analyses, either as terminal taxa in their own right [16] or as priors on the areas occupied at nodes [17], has uncovered evidence for ancient vicariance [16] and dispersal [18,19] events and yielded ancestral range estimates that fall outside the distribution of Recent taxa [17,20–22]. However, the difficulty in obtaining comprehensive sampling of fossils in phylogenetic analyses means that most past biogeographic studies that have investigated the impact of combining extant and extinct taxa have either focused on inferring the ancestral ranges of lower-level clades, such as families or genera, or used sparse sampling of fossils to investigate the historical biogeography of larger clades.…”

Climatic refugia and reduced extinction correlate with underdispersion in mammals and birds in Africa

“…Madagascar shows some of the clearest disparities between mammals and birds within our study, perhaps due to the nature of colonization frequency and pattern by birds and mammals (Everson et al, 2016; Reddy et al, 2012) coincident with the museum‐like nature of islands for taxonomic groups that are no longer found in continental settings (Kirchman et al, 2001; McCullough et al, 2019). Notably, the insular nature of Madagascar makes it theoretically more accessible to birds than to terrestrial mammals.…”

Uneven missing data skews phylogenomic relationships within the lories and lorikeets

“…Outlier analysis using site and gene likelihood scores (Shen et al 2017;Walker et al 2018) provide a rapid means of identifying loci that have a large impact on a phylogeny reconstruction, but as we showed the resolution of this approach will depend on the trees that are available for comparison (e.g., expected relationship versus alternative phylogeny). Another, non-quantitative means of assessing the position of branches, which have high missing informative sites, is the tendency for samples to fall outside of their clade or even the ingroup, as 14 evident in previous phylogenomic studies on birds Moyle et al 2016;Andersen et al 2019;McCullough et al 2019). This was the case for seven of our excluded samples, which produced limited data and could not be accurately placed in their genus or higher-level clade.…”