Ecological selectivity and the evolution of mammalian substrate preference across the K-Pg boundary.

The Cretaceous-Paleogene (K-Pg) mass extinction 66 million years ago was characterized by a worldwide ecological catastrophe and rapid species turnover. Large-scale devastation of forested environments resulting from the Chicxulub asteroid impact likely influenced the evolutionary trajectories of multiple clades in terrestrial environments, and it has been hypothesized to have biased survivorship in favour of nonarboreal lineages across the K-Pg boundary. Here, we evaluate patterns of substrate preferences across the K-Pg boundary among crown group mammals, a group that underwent rapid diversification following the mass extinction. Using Bayesian, likelihood, and parsimony reconstructions, we identify patterns of mammalian ecological selectivity that are broadly similar to those previously hypothesized for birds. Models based on extant taxa indicate predominant K-Pg survivorship among semi- or nonarboreal taxa, followed by numerous independent transitions to arboreality in the early Cenozoic. However, contrary to the predominant signal, some or all members of total-clade Euarchonta (Primates + Dermoptera + Scandentia) appear to have maintained arboreal habits across the K-Pg boundary, suggesting ecological flexibility during an interval of global habitat instability. We further observe a pronounced shift in character state transitions away from plesiomorphic arboreality associated with the K-Pg transition. Our findings are consistent with the hypothesis that predominantly nonarboreal taxa preferentially survived the end-Cretaceous mass extinction, and emphasize the pivotal influence of the K-Pg transition in shaping the early evolutionary trajectories of extant terrestrial vertebrates.NS

Timing the extant avian radiation: The rise of modern birds, and the importance of modeling molecular rate variation

Unravelling the phylogenetic relationships among the major groups of living birds has been described as the greatest outstanding problem in dinosaur systematics. Recent work has identified portions of the avian tree of life that are particularly challenging to reconstruct, perhaps as a result of rapid cladogenesis early in crown bird evolutionary history (specifically, the interval immediately following the end-Cretaceous mass extinction). At face value this hypothesis enjoys support from the crown bird fossil record, which documents the first appearances of most major crown bird lineages in the early Cenozoic—in line with a model of rapid post-extinction niche filling among surviving avian lineages. However, molecular-clock analyses have yielded strikingly variable estimates for the age of crown birds, and conflicting inferences on the impact of the end-Cretaceous mass extinction on the extant bird radiation. This uncertainty has often been ascribed to a patchy avian fossil record, but the possibility of model misspecification in molecular divergence time analyses represents an important and relatively underexplored alternative hypothesis. Here, we highlight the necessity of further developing and using models that account for coordinated variation in rates of molecular evolution across a phylogeny (e.g. molecular early bursts) as a means of assessing support for a rapid post-Cretaceous radiation of crown birds. We discuss how relationships between life-history and substitution rates can mislead divergence time studies that do not account for directional changes in substitution rates over time, and suggest that these effects might have caused some of the variation in existing molecular date estimates for birds. We suggest multiple paths forward that could help resolve this and similar conflicts within other major eukaryotic clades.</jats:p

Genomic signature of an avian Lilliput Effect across the K-Pg Extinction

Survivorship following major mass extinctions may be associated with a decrease in body size-a phenomenon called the Lilliput Effect. Body size is a strong predictor of many life history traits (LHTs), and is known to influence demography and intrinsic biological processes. Pronounced changes in organismal size throughout Earth history are therefore likely to be associated with concomitant genome-wide changes in evolutionary rates. Here,we report pronounced heterogeneity in rates of molecular evolution (varying up to ∼20-fold) across a large-scale avian phylogenomic data set and show that nucleotide substitution rates are strongly correlated with body size and metabolic rate.We also identify potential body size reductions associated with the Cretaceous-Paleogene (K-Pg) transition, consistent with a Lilliput Effect in the wake of that mass extinction event.We posit that selection for reduced body size across theK-Pg extinction horizon may have resulted in transient increases in substitution rate along the deepest branches of the extant avian tree of life. This "hidden" rate acceleration may result in both strict and relaxed molecular clocks over-estimating the age of the avian crown group through the relationship between life history and demographic parameters that scale with molecular substitution rate. If reductions in body size (and/or selection for related demographic parameters like short generation times) are a common property of lineages surviving mass extinctions, this phenomenon may help resolve persistent divergence time debates across the tree of life. Furthermore, our results suggest that selection for certain LHTs may be associated with deterministic molecular evolutionary outcomes.</p

SUPPLEMENTAL DATA: Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

SUPPLEMENTAL DATA FOR Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes Author Affiliations: Jacob S. Berv (1,2,3), Leonardo Campagna (1,2), Teresa J. Feo (4), Ivandy Castro-Astor (5), Camila C. Ribas (6), Richard O. Prum (7), Irby J. Lovette (1,2) 1. Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA. 2. Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853, USA. 3. Department of Ecology and Evolutionary Biology, and University of Michigan Museum of Paleontology, 1105 North University Avenue, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA. 4. Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA. 5. Department of Biology, City College of New York and CUNY Graduate Center, City University of New York, New York, NY 10031, USA 6. Coordenacão de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil 7. Department of Ecology and Evolutionary Biology, and Peabody Museum of Natural History, Yale University, New Haven, Connecticut, 06520, USA. Correspondence to Jacob S. Berv ([email protected]) LAST UPDATED 28 APRIL 2021 CODE WILL ALSO BE MADE AVAILABLE AT https://github.com/jakeberv The parent directory contains many data files related to the analyses presented in this manuscript. The top level file 'Pseudopipra_code.R' contains function definitions and code used for most of the analyses in this article. This code is annotated with descriptions throughout. Note that all files referenced within various subdirectories must be unzipped for the R code to work. Download "Supplemental Data.zip" to download the entire archive, or browse individual files for download. SEE README.TXT for additional informatio

Data from: Genomic Signature of an Avian Lilliput Effect across the K-PG Extinction

Survivorship following major mass extinctions may be associated with a decrease in body size—a phenomenon called the Lilliput Effect. Body size is a strong predictor of many life history traits (LHTs), and is known to influence demography and intrinsic biological processes. Pronounced changes in organismal size throughout Earth history are therefore likely to be associated with concomitant genome-wide changes in evolutionary rates. Here, we report pronounced heterogeneity in rates of molecular evolution (varying up to ~20-fold) across a large-scale avian phylogenomic dataset, and show that nucleotide substitution rates are strongly correlated with body size and metabolic rate. We also identify potential body size reductions associated with the Cretaceous-Paleogene (K-Pg) transition, consistent with a Lilliput Effect in the wake of that mass extinction event. We posit that selection for reduced body size across the K-Pg extinction horizon may have resulted in transient increases in substitution rate along the deepest branches of the extant avian tree of life. This ‘hidden’ rate acceleration may result in both strict and relaxed molecular clocks over-estimating the age of the avian crown group through the relationship between life history and demographic parameters that scale with molecular substitution rate. If reductions in body size (and/or selection for related demographic parameters like short generation times) are a common property of lineages surviving mass extinctions, this phenomenon may help resolve persistent divergence time debates across the tree of life. Furthermore, our results suggest that selection for certain life history traits may be associated with deterministic molecular evolutionary outcomes

Genomic signature of an avian Lilliput Effect across the K-Pg Extinction

Survivorship following major mass extinctions may be associated with a decrease in body size-a phenomenon called the Lilliput Effect. Body size is a strong predictor of many life history traits (LHTs), and is known to influence demography and intrinsic biological processes. Pronounced changes in organismal size throughout Earth history are therefore likely to be associated with concomitant genome-wide changes in evolutionary rates. Here,we report pronounced heterogeneity in rates of molecular evolution (varying up to ∼20-fold) across a large-scale avian phylogenomic data set and show that nucleotide substitution rates are strongly correlated with body size and metabolic rate.We also identify potential body size reductions associated with the Cretaceous-Paleogene (K-Pg) transition, consistent with a Lilliput Effect in the wake of that mass extinction event.We posit that selection for reduced body size across theK-Pg extinction horizon may have resulted in transient increases in substitution rate along the deepest branches of the extant avian tree of life. This "hidden" rate acceleration may result in both strict and relaxed molecular clocks over-estimating the age of the avian crown group through the relationship between life history and demographic parameters that scale with molecular substitution rate. If reductions in body size (and/or selection for related demographic parameters like short generation times) are a common property of lineages surviving mass extinctions, this phenomenon may help resolve persistent divergence time debates across the tree of life. Furthermore, our results suggest that selection for certain LHTs may be associated with deterministic molecular evolutionary outcomes.</p

Divergence in morphology, calls, song, mechanical sounds, and genetics supports species status for the Inaguan hummingbird (Trochilidae: Calliphlox "evelynae" lyrura)

The Bahama Woodstar (Calliphlox evelynae), a hummingbird endemic to the Bahama Archipelago, comprises two currently recognized subspecies: Calliphlox e. evelynae, found throughout the Bahamas and in the Turks and Caicos Islands, except on Great and Little Inagua; and C. e. lyrura, named for its unique, lyre-shaped outer tail feathers and found only on the islands of Great and Little Inagua. The two were originally described as separate species, partly on the basis of their divergent tail morphology, but were subsequently lumped by Peters (1945). These taxa are members of the North American "bee" hummingbird clade, which produce mechanical sounds with their tails during courtship displays. Changes in tail shape may produce significant acoustic divergence. To determine the extent of differentiation between lyrura and evelynae, we collected field recordings of calls, songs, and courtship displays from New Providence and Great Inagua islands and surveyed morphological variation across the archipelago. We sequenced 4 nuclear loci and 2 mitochondrial genes from 9 individuals of evelynae and 6 individuals of lyrura. Both sexes of lyrura and evelynae can be diagnosed by vocal calls, and males can be diagnosed by morphology, song, and courtship display. Phylogenetic reconstructions based on the genetic data indicate that the 2 populations are reciprocally monophyletic and that they diverged ∼0.69 mya. Our data indicate that lyrura is a unique evolutionary lineage that warrants species status under both the phylogenetic and the biological species concept

Divergence in morphology, calls, song, mechanical sounds, and genetics supports species status for the Inaguan hummingbird (Trochilidae: Calliphlox "evelynae" lyrura)

The Bahama Woodstar (Calliphlox evelynae), a hummingbird endemic to the Bahama Archipelago, comprises two currently recognized subspecies: Calliphlox e. evelynae, found throughout the Bahamas and in the Turks and Caicos Islands, except on Great and Little Inagua; and C. e. lyrura, named for its unique, lyre-shaped outer tail feathers and found only on the islands of Great and Little Inagua. The two were originally described as separate species, partly on the basis of their divergent tail morphology, but were subsequently lumped by Peters (1945). These taxa are members of the North American "bee" hummingbird clade, which produce mechanical sounds with their tails during courtship displays. Changes in tail shape may produce significant acoustic divergence. To determine the extent of differentiation between lyrura and evelynae, we collected field recordings of calls, songs, and courtship displays from New Providence and Great Inagua islands and surveyed morphological variation across the archipelago. We sequenced 4 nuclear loci and 2 mitochondrial genes from 9 individuals of evelynae and 6 individuals of lyrura. Both sexes of lyrura and evelynae can be diagnosed by vocal calls, and males can be diagnosed by morphology, song, and courtship display. Phylogenetic reconstructions based on the genetic data indicate that the 2 populations are reciprocally monophyletic and that they diverged ∼0.69 mya. Our data indicate that lyrura is a unique evolutionary lineage that warrants species status under both the phylogenetic and the biological species concept