The Northern Flicker, Colaptes auratus, is a member of the bird group Coraciimorphae. Berv and co-authors identify this group of birds and others as having close ties to the end-Cretaceous mass extinction that occurred in the wake of the Chicxulub asteroid impact approximately 66 million years ago.
Image credit: Daniel Field, University of Cambridge
Another major milestone in the history of life on Earth happened, like almost everything else, in that long pre-Creation Week history that creationists need to ignore. It was the mass extinction about 66 million years ago that killed the non-avian dinosaurs and most megafauna, leaving vacant niches that could be exploited by the descendants of survivors. It's no surprise to anyone who understands how evolution works, that this led to a proliferation of new species as existing species diversified to fill those niches.
That much was known already from the fossil record, but now a University of Michigan study has found how this maps onto changes in the genome of the major bird families, as a kind of DNA fossil, just as the TOE predicts.
The major difference between the different taxons is how developed the chicks are on hatching and how dependent they are on their parents. In ducks, geese, the ratites and ground-nesting birds such as the plovers, chickens and turkeys, the chicks are mobile and able to feed themselves (precocial) almost as soon as they've hatched. At the other end of the scale, many passerines are helpless on hatching and are entirely dependent on their parents for food and shelter (altricial) for several weeks.
As the birds evolved and diversified, they tended to become smaller and also more altricial. This reduction in body size and increased altriciality are reflected in the genomes. It was these transitional changed that the researchers detected.
These major changes were occurring within 3-5 million years after the mass extinction.
Can you supply an evolutionary family tree for the main bird families since the mass extinction about 66 million years ago? Certainly! Here's an overview of the evolutionary family tree of birds, highlighting the major bird families since the mass extinction event about 66 million years ago (the Cretaceous-Paleogene extinction event). This tree is simplified to focus on the primary branches and notable families.
Evolutionary Family Tree of Birds
This tree represents a broad overview, capturing the main evolutionary lineages and prominent bird families that emerged after the mass extinction event 66 million years ago. Each of these orders contains numerous families and species, reflecting the vast diversity and adaptability of birds through their evolutionary history.
- Paleognathae (ancient jaw)
- Struthioniformes: Ostriches
- Rheiformes: Rheas
- Casuariiformes: Emus, Cassowaries
- Apterygiformes: Kiwis
- Tinamiformes: Tinamous
- Neognathae (new jaw)
b. Neoaves (new birds)
a. Galloanserae (fowl)
- Anseriformes: Ducks, Geese, Swans
- Galliformes: Chickens, Turkeys, Quails, Pheasants
- Columbaves: Pigeons, Doves, Sandgrouse
- Columbiformes: Pigeons, Doves
- Pterocliformes: Sandgrouse
- Mirandornithes: Flamingos, Grebes
- Phoenicopteriformes: Flamingos
- Podicipediformes: Grebes
- Gruiformes: Cranes, Rails
- Otidimorphae: Bustards, Turacos, Cuckoos
- Otidiformes: Bustards
- Musophagiformes: Turacos
- Cuculiformes: Cuckoos
- Strisores: Nightjars, Swifts, Hummingbirds
- Caprimulgiformes: Nightjars, Frogmouths
- Apodiformes: Swifts, Hummingbirds
- Aequornithes: Water birds
- Gaviiformes: Loons
- Procellariiformes: Albatrosses, Petrels
- Sphenisciformes: Penguins
- Ciconiiformes: Storks
- Pelecaniformes: Pelicans, Herons, Ibises
- Suliformes: Cormorants, Boobies
- Inopinaves: Diverse land birds
- Accipitriformes: Hawks, Eagles
- Cathartiformes: New World Vultures
- Strigiformes: Owls
- Coraciimorphae: Kingfishers, Rollers
- Coraciiformes: Kingfishers, Bee-eaters
- Piciformes: Woodpeckers, Toucans
- Trogoniformes: Trogons
- Coliiformes: Mousebirds
- Leptosomiformes: Cuckoo-roller
- Australaves: Austral birds
- Cariamiformes: Seriemas
- Falconiformes: Falcons
- Psittaciformes: Parrots
- Passeriformes: Perching birds (largest order, includes sparrows, crows, and many others)
Mass extinction 66 million years ago triggered rapid evolution of bird genomes
Shortly after an asteroid slammed into Earth 66 million years ago, life for non-avian dinosaurs ended, but the evolutionary story for the early ancestors of birds began.
The fossil record tells us that the early ancestors of living birds began their evolutionary journey just after the mass extinction event caused by the asteroid, but researchers weren’t sure how they would see that story reflected in bird genomes. Now, a University of Michigan study has identified important changes in birds’ genomes sparked by the mass extinction, called the end-Cretaceous mass extinction event, ultimately contributing to the incredible diversity of living birds.
The study examined the evolutionary trajectory of all major bird groups and found evidence of “genomic fossils” in birds’ DNA that mark critical evolutionary steps as birds evolved into more than 10,000 living species. The research is published as an open-access article in the journal Science Advances.
By studying the DNA of living birds, we can try to detect patterns of genetic sequences that changed just after one of the most important events in Earth’s history. The signature of those events seems to have imprinted into the genomes of the survivors in a way that we can detect tens of millions of years later.
Jacob S. Berv, lead author
Department of Ecology and Evolutionary Biology
University of Michigan, Ann Arbor, MI, USA.
The Speckled Mousebird, Colius striatus, is a member of the bird group Coraciimorphae. Berv and co-authors identify this group of birds and others as having close ties to the end-Cretaceous mass extinction that occurred in the wake of the Chicxulub asteroid impact approximately 66 million years ago.Image credit: Daniel Field, University of Cambridge
A living organism’s genome comprises four nucleotide molecules, referred to by the letters A, T, G and C. The order of these nucleotides in a genome defines the “blueprint” of life. The DNA code can sometimes evolve in a way that shifts the overall composition of DNA nucleotides across the whole genome. These compositional changes are crucial in determining what kind of genetic variation is possible, contributing to an organism’s evolutionary potential, or its ability to evolve.
The researchers found that the mass extinction event sparked shifts in nucleotide composition. They also found that these shifts seem to be connected to the way birds develop as babies, their adult size and their metabolism.
For example, within approximately 3 million to 5 million years of the mass extinction, surviving bird lineages tended to develop smaller body sizes. They also changed how they developed as hatchlings, with more species becoming “altricial.” This means they are still very embryonic when they hatch, need their parents to feed them, and can take weeks to fledge, Berv says. Birds that hatch ready to fend for themselves, like chickens and turkeys, are called “precocial.”
We found that adult body size and patterns of pre-hatching development are two important features of bird biology we can link to the genetic changes we’re detecting.
Jacob S. Berv
Berv says one of the most significant challenges in evolutionary biology and ornithology is teasing out the relationships between major bird groups—it’s difficult to determine the structure of the tree of life for living birds. Over the past 15 years, researchers have been applying increasingly large genomic data sets to try to solve the problem.
Previously, researchers used genomic data to study the evolution of birds’ genomes using statistical models that make strong assumptions. These “traditional” models allow researchers to reconstruct the history of genetic changes, but they typically assume that the composition of DNA, its proportion of A, T, G and C nucleotides, does not change across evolutionary history.
In late 2019, Berv began working with Stephen Smith, U-M professor of ecology and evolutionary biology, who was developing a software tool to more closely track DNA composition over time and across different branches of the tree of life. With this tool, the researchers were able to relax the assumption that the composition of DNA remains constant. Smith said that this allowed the “model” of DNA evolution to vary across the evolutionary tree and identify places where there was likely a shift in DNA composition.
The Malachite Kingfisher, Alcedo cristata, is a member of the bird group Coraciimorphae. Berv and co-authors identify this group of birds and others as having close ties to the end-Cretaceous mass extinction that occurred in the wake of the Chicxulub asteroid impact approximately 66 million years ago.
Image credit: Daniel Field, University of Cambridge
For this new research, these shifts were concentrated in time, within about 5 million years of the end-Cretaceous mass extinction, Berv says. Their approach also allowed them to estimate which bird traits were most closely associated with these shifts in DNA composition.
This is an important type of genetic change that we think we can link to the mass extinction event. As far as we know, changes in DNA composition have not been previously associated with the end-Cretaceous mass extinction in such a clear way.
Jacob S. Berv
Daniel Field, professor of vertebrate paleontology at the University of Cambridge and co-author of the study, has been interested in understanding how the end-Cretaceous mass extinction affected the evolution of birds. He provided guidance related to early bird evolution following the mass extinction.
The Lilac-breasted Roller, Coracias caudatus, is a member of the bird group Coraciimorphae. Berv and co-authors identify this group of birds and others as having close ties to the end-Cretaceous mass extinction that occurred in the wake of the Chicxulub asteroid impact approximately 66 million years ago.Image credit: Daniel Field, University of CambridgeWe know that mass extinction events can dramatically affect biodiversity, ecology and organismal form. Our study emphasizes that these extinction events can actually influence organismal biology even more profoundly—by altering important aspects of how genomes evolve. This work furthers our understanding of the dramatic biological impacts of mass extinction events and highlights that the mass extinction that wiped out the giant dinosaurs was one of the most biologically impactful events in the entire history of our planet.
Daniel J. Field, co-author
Department of Earth Sciences
University of Cambridge, Cambridge, UK.
The researchers say that by relaxing the typical assumptions used in evolutionary biology, they are building more nuanced insight into the sequence of events that occurred in the early history of birds.
We have typically not looked at the change in DNA composition and model across the tree of life as a change that something interesting has happened at a particular point of time and place. This study illustrates that we have probably been missing something.
Stephen A. Smith, co-author.
Department of Ecology and Evolutionary Biology
University of Michigan, Ann Arbor, MI, USA.
U-M co-authors include Benjamin Winger, assistant professor of ecology and evolutionary biology and curator of birds at the U-M Museum of Zoology, and Matt Friedman, professor of earth and environmental sciences and director of the U-M Museum of Paleontology.
Other study co-authors include Sonal Singhal, California State University; Nathanael Walker-Hale, University of Cambridge; Sean McHugh, Washington University; J. Ryan Shipley, Swiss Federal Institute for Forest, Snow and Landscape Research; Eliot Miller, Cornell Lab of Ornithology; Rebecca Kimball and Edward Braun, University of Florida; Alex Dornburg, University of North Carolina; C. Tomomi Parins-Fukuchi, University of Toronto; and Richard Prum, Yale University.
AbstractSo triple trouble for creationists in this casual and incidental refutation of creationism.
Complex patterns of genome evolution associated with the end-Cretaceous [Cretaceous-Paleogene (K–Pg)] mass extinction limit our understanding of the early evolutionary history of modern birds. Here, we analyzed patterns of avian molecular evolution and identified distinct macroevolutionary regimes across exons, introns, untranslated regions, and mitochondrial genomes. Bird clades originating near the K–Pg boundary exhibited numerous shifts in the mode of molecular evolution, suggesting a burst of genomic heterogeneity at this point in Earth’s history. These inferred shifts in substitution patterns were closely related to evolutionary shifts in developmental mode, adult body mass, and patterns of metabolic scaling. Our results suggest that the end-Cretaceous mass extinction triggered integrated patterns of evolution across avian genomes, physiology, and life history near the dawn of the modern bird radiation.
INTRODUCTION
Over 40 ago, Alvarez et al. (1) provided chemical evidence indicating that the Cretaceous-Paleogene (K–Pg) mass extinction was associated with an extraterrestrial impact. Subsequent research has refined our understanding of how this cataclysmic event influenced biodiversity [e.g., (2, 3)]. Mounting evidence suggests that the K–Pg extinction event triggered convergent patterns of life-history evolution. For example, some lineages may have experienced a transient “Lilliput effect” in which average body sizes became smaller, likely through faunal sorting, dwarfing, or miniaturization (4, 5). While great effort has been devoted to investigating extinction patterns among various groups across the K–Pg boundary [e.g., (6–8)], the impact of the end-Cretaceous mass extinction on the genomes of surviving lineages has received less attention.
Given that life-history traits such as body mass, generation length, and metabolic rates are linked to different aspects of molecular evolution (9), it is plausible that convergent patterns of life-history evolution across extinction boundaries impart distinct signatures in the genomes of surviving lineages (10–12). For example, in plants, repeated evolution of polyploidy may be associated with the K–Pg transition (13). Similarly, increased avian substitution rates may reflect extinction-related size-selectivity (11, 12). Still, only a few studies have attempted to investigate how the aftermath of the K–Pg mass extinction shaped genome evolution [e.g., (11, 13–16)]. We generally expect life-history evolution to influence phylogenetic patterns [e.g., (17)] because factors like effective population size (Ne) and body mass are linked through environmental carrying capacity (18, 19). The phenomenon of GC-biased gene conversion also appears to have an important role in driving patterns of avian base composition (20, 21), but this has never been directly linked to the K–Pg transition. Such a link might be expected, however, because of the relationships among life history, Ne, recombination, and the efficacy of gene conversion (21, 22).
Many studies attempting to connect events in Earth’s history to patterns of genome evolution rely on inferences from molecular clock analyses [e.g., (11, 13)]. These approaches can reveal heterogeneous patterns in the tempo of molecular evolution [e.g., (10, 23)] but typically assume that the underlying sequence data evolved according to the expectations of a homogeneous nucleotide substitution model. If this assumption is violated, time-homogeneous models may obscure important evolutionary patterns [e.g., (17)]. Nevertheless, techniques that enable substitution models to vary across a clade’s evolutionary history have not yet seen widespread adoption in the macroevolution literature [e.g., (24–26)]. Detecting where one model has shifted to another on a phylogeny may provide evidence of evolutionary transitions in the “mode” or process that generated the observed data (23, 27–29). Thus, investigating patterns of model shifts across both genome and life-history traits may reveal unknown links among Earth’s history and evolutionary processes.
Here, we combine approaches from molecular systematics and phylogenetic comparative methods to investigate molecular model heterogeneity across the avian tree of life. We apply a novel stepwise approach to estimating the phylogenetic position of shifts in molecular substitution model parameters, implemented in Janus (Materials and Methods) (30). Our approach relaxes the assumption that the sequence data–generating process has remained constant through evolutionary time, enabling us to test the hypothesis that the radiation of birds near the end-Cretaceous extinction was accompanied by concurrent diversification in the mode of molecular evolution. Specifically, our phylogenomic analysis focused on evolutionary shifts in base composition, a well-established proxy of avian genome architecture (21, 30–32). After inferring molecular shifts, we applied a random forest machine learning classifier to survey the organismal traits associated with inferred shifts. We also applied multivariate Ornstein-Uhlenbeck (OU) models (27–29) to investigate the hypothesis that molecular shifts co-occur with changes in the adaptive landscape or evolutionary allometries of key traits. We assessed aspects of breeding ecology, development, senescence, and metabolism that may have undergone intense selection or relaxation of evolutionary constraints during the K–Pg transition [e.g., (10, 11, 33–35)]. Model shifts across many dimensions of biodiversity were constrained to clade originations temporally associated with the K–Pg transition, linking patterns of genomic variation to life history, physiology, and macroevolutionary patterns detected from the fossil record.
Fig. 1. Inferred model shifts across phylogenomic and life-history data.
Thirteen phylogenetic regimes encompassing 17 molecular model shifts were required to explain heterogeneity in equilibrium base frequencies across genetic data types (branches with distinct colors). Fifteen shifts were inferred at nodes with stem ages within ~5 Ma of the K–Pg boundary (39). (Top) The aggregate signal of molecular model shifts across nuclear and mitochondrial data types identified by Janus, mapped onto the MRL3 supertree, with the ancestral regime “0” in black [*Otidae = Otidimorphae + Strisores, (150)]. Patterns of molecular model shifts across phylogenetic edges are summarized as 2 × 2 grids (see legend above; figs. S3 and S7). Numeric labels at each grid position correspond to a molecular shift in a specific data type. Pie charts summarize the detection rate (“P”) for shifts in trait optima θ(t) across eight life-history traits relative to a simulated null false-positive (“FP”) rate {e.g., ℓ1ou detection rate / [ℓ1ou detection rate + false-positive rate] (statistical precision), under AICc; see fig. S4A}. (Below) Estimated magnitude of shifts in equilibrium base frequencies relative to the empirical base frequencies for a given taxon partition for each data type, ordered by dataset size (Discussion and fig. S7, A to D). Edges with well-supported shifts in metabolic allometry are labeled with an asterisk, with the most substantial support observed for Coraciimorphae (pp = 98%, Fig. 3).
Jacob S. Berv et al.
Genome and life-history evolution link bird diversification to the end-Cretaceous mass extinction.
Sci. Adv.10,eadp0114(2024).DOI:10.1126/sciadv.adp0114
Copyright: © 2024 The authors.
Published by American Association for the Advancement of Science. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
Firstly, there is the fact that this all happened so long before their supposed 'Creation Week' when they believe the Universe was magicked out of nothing by a magic man made of nothing.
Secondly, there is the evidence of transitional fossils in the genomes of modern birds
And thirdly there is the dependence of the scientists on the Theory of Evolution to explain what they see with still no hint of the impending abandonment of it in favour of the magical creationists superstition with its unproven magic entity and non-falsifiability, that their cult leaders assure them is going to happen any day now, real soon!
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