Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: Phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences

Abstract

The Cracidae (curassows, guans, and chachalacas) include some of the most spectacular and endangered Neotropical bird species. They lack a comprehensive phylogenetic hypothesis, hence their geographic origin and the history of their diversification remain unclear. We present a species-level phylogeny of Cracidae inferred from a matrix of 430 ultraconserved elements (UCEs; at least one species sampled per genus) and eight more variable loci (introns and mtDNA; all available species). We use this phylogeny along with probabilistic biogeographic modeling to test whether Gondwanan vicariance, ancient dispersal to South America, ancient dispersal from South America, or massive global cooling isolated cracids in the Neotropics. Contrary to previous estimates that extant cracids diversified in the Cretaceous, our fossil-calibrated divergence time estimates instead support that crown Cracidae originated in the late Miocene. Species-rich genera Crax, Penelope, and Ortalis began diversifying as recently as 3Mya. Biogeographic reconstructions indicate that modern cracids originated in Mesoamerica and were isolated from a widespread Laurasian ancestor, consistent with the massive global cooling hypothesis. Current South American diversity is the result of multiple colonization events following uplift of the Panamanian Isthmus, coupled with rapid diversification and evolution of secondary sympatry. Of the four major cracid lineages (curassows, chachalacas, typical guans, horned guan), the only lineage that has failed to colonize and diversify South America is the unique horned guan (Oreophasis derbianus), which is sister to curassows and chachalacas rather than typical guans.

How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)

“…We selected the optimal partitioning scheme using the Bayesian information criterion and the rclusterf algorithm [43] in PARTITIONFINDER 2.0-pre11 [44], and quantified support with 100 thorough bootstrap replicates. We implemented MCMCtree (PAML 4.8 [45]) using a relaxed clock and six galliform fossil calibrations [30,46] to calibrate minimum node ages (electronic supplementary material, table S2) and infer an ultrametric, timecalibrated phylogeny. We restricted analysis to the largest single DNA sequence partition identified by PARTITIONFINDER to reduce among-site rate heterogeneity and computation time.…”

“…Continental vicariance of Madagascar and Australasia far preceded diversification of phasianoids [30] and modern birds in general [31][32][33], meaning Margaroperdix and Anurophasis ancestors must have crossed permanent marine barriers. How did these 'non-vagile' phasianoids come to inhabit their present insular distributions?…”

FrogCap: A modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales

“…protein-coding exons, non-coding regions, ultra-conserved elements [UCEs], or single nucleotide polymorphisms [SNPS]) is an increasingly important issue when dealing with the challenges of analyzing large phylogenomic datasets. Each phylogenomic marker type may be useful at various timescales and may present different biases for analyses (Lemmon & Lemmon 2013;McCormack et al 2013;Hosner et al 2016). For example, there is debate over whether protein-coding or non-coding markers are more appropriate for phylogenetic analyses, because selection on protein-coding exons may mask homology and bias phylogenetic signal Chen et al 2017;Reddy et al 2017).…”

“…Both AHE and UCEs are now widely used in inferring phylogenies across broad and shallow phylogenetic scales Smith et al 2014;Brandley et al 2015;Prum et al 2015;Streicher et al 2018). For population genetics, UCEs have been used with some success (Hosner et al 2016;Zarza et al 2016;Andermann et al 2019). In contrast, AHE produces a smaller number of markers (less than 400 exons) and generally results in fewer independent variants as required by many types of analyses in comparison to these other sets of markers (Lanier & Knowles 2012;Hedge & Wilson 2014;Springer & Gatesy 2018).…”

Morphology of the copulatory organ in Ortalis canicollis (Aves: Cracidae) and early evolution of the phallus in birds

“…Some studies considered Cracidae and Megapodiidae as a monophyletic group, and it was considered as a sister group of the rest of the Galliformes (Feduccia, 1999). However, the morphological and molecular studies suggest that cracids are a sister taxon of the clade (Numididae (Phasianidae Odontophoridae)) and the Megapodiidae is a sister group of other families (Dyke, Gulas, & Growe, 2003;Hosner, Braun, & Kimball, 2016;Stein, Brown, & Mooers, 2015).…”