From Newsgroup: sci.bio.paleontology

Complexity of avian evolution revealed by family-level genomes

Abstract

Despite tremendous efforts in the past decades, relationships among main
avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1,2,3. Here we
address these issues by analysing the genomes of 363rCebird species4 (218rCetaxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked
degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the CretaceousrCoPalaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary
events such as ancient hybridization. Assessment of the effects of
different genomic partitions showed high heterogeneity across the
genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the CretaceousrCoPalaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of
modern birds. The resulting phylogenetic estimate offers fresh insights
into the rapid radiation of modern birds and provides a taxon-rich
backbone tree for future comparative studies.

Open access:
https://www.nature.com/articles/s41586-024-07323-1
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From Newsgroup: sci.bio.paleontology

On 5/4/24 3:09 AM, Pandora wrote:

Complexity of avian evolution revealed by family-level genomes

Abstract

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1,2,3. Here we
address these issues by analysing the genomes of 363rCebird species4 (218 rCetaxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the CretaceousrCoPalaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of
different genomic partitions showed high heterogeneity across the
genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the CretaceousrCoPalaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of
modern birds. The resulting phylogenetic estimate offers fresh insights
into the rapid radiation of modern birds and provides a taxon-rich
backbone tree for future comparative studies.

Open access:
https://www.nature.com/articles/s41586-024-07323-1

Nice that it's finally out. This is the best current single estimate of
avian phylogeny, but there are still a number of iffy nodes. Not the
final word.

I don't think there's enough attention to within-locus recombination.
They should have looked more at multiple non-recombining sections. They
do talk a bit about the Z chromosome, but oddly there's no mention at
all of the W.

Here's another pub on the potential effect of non-recombining regions:

https://www.pnas.org/doi/10.1073/pnas.2319506121

A region of suppressed recombination misleads neoavian phylogenomics

Abstract:
Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time,
recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along the genome. When examining rapid radiations such as the early diversification of Neoaves
66 Mya, typically no consistent history is observed across segments
exceeding kilobases of the genome. Here, we report an exception. We
found that a 21-Mb region in avian genomes, mapped to chicken chromosome
4, shows an extremely strong and discordance-free signal for a history different from that of the inferred species tree. Such a strong discordance-free signal, indicative of suppressed recombination across
many millions of base pairs, is not observed elsewhere in the genome for
any deep avian relationships. Although long regions with suppressed recombination have been documented in recently diverged species, our
results pertain to relationships dating circa 65 Mya. We provide
evidence that this strong signal may be due to an ancient rearrangement
that blocked recombination and remained polymorphic for several million
years prior to fixation. We show that the presence of this region has
misled previous phylogenomic efforts with lower taxon sampling, showing
the interplay between taxon and locus sampling. We predict that similar ancient rearrangements may confound phylogenetic analyses in other
clades, pointing to a need for new analytical models that incorporate
the possibility of such events.

Not much paleontology in all this, but I suppose mentions of the K/T
boundary are relevant.
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From Newsgroup: sci.bio.paleontology

On 5/4/2024 6:09 AM, Pandora wrote:

Complexity of avian evolution revealed by family-level genomes

Abstract

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1,2,3. Here we
address these issues by analysing the genomes of 363rCebird species4 (218 rCetaxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the CretaceousrCoPalaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of
different genomic partitions showed high heterogeneity across the
genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the CretaceousrCoPalaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of
modern birds. The resulting phylogenetic estimate offers fresh insights
into the rapid radiation of modern birds and provides a taxon-rich
backbone tree for future comparative studies.

Open access:
https://www.nature.com/articles/s41586-024-07323-1

I was thinking that since birds don't seem to have very much variation
from the basic bird body plan, could it be possible that exactly one
species survived the K-T event, and all modern birds are descended from
it? When would the MRCA of all birds have lived? Older protobirds seem
to have more variations not seen today. Some have teeth, some have claws
on wings, long tails and/or 4 wings/feathered legs are also wings*.

(*) I have two bantam chickens with feathers on their legs and two of
their claws on each foot. Could this be an old "4 wing" gene becoming reactivated? Or are chickens just more prehistoric? The bantams seem to
fly a little better than non-bantam chickens, but that's probably just
because they are very small. I haven't seen them try to flap their legs...
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From Newsgroup: sci.bio.paleontology

On 7/11/24 10:19 PM, Volney wrote:

On 5/4/2024 6:09 AM, Pandora wrote:

Complexity of avian evolution revealed by family-level genomes

Abstract

Despite tremendous efforts in the past decades, relationships among
main avian lineages remain heavily debated without a clear resolution.
Discrepancies have been attributed to diversity of species sampled,
phylogenetic method and the choice of genomic regions1,2,3. Here we
address these issues by analysing the genomes of 363rCebird species4
(218 rCetaxonomic families, 92% of total). Using intergenic regions and
coalescent methods, we present a well-supported tree but also a marked
degree of discordance. The tree confirms that Neoaves experienced
rapid radiation at or near the CretaceousrCoPalaeogene boundary.
Sufficient loci rather than extensive taxon sampling were more
effective in resolving difficult nodes. Remaining recalcitrant nodes
involve species that are a challenge to model due to either extreme
DNA composition, variable substitution rates, incomplete lineage
sorting or complex evolutionary events such as ancient hybridization.
Assessment of the effects of different genomic partitions showed high
heterogeneity across the genome. We discovered sharp increases in
effective population size, substitution rates and relative brain size
following the CretaceousrCoPalaeogene extinction event, supporting the
hypothesis that emerging ecological opportunities catalysed the
diversification of modern birds. The resulting phylogenetic estimate
offers fresh insights into the rapid radiation of modern birds and
provides a taxon-rich backbone tree for future comparative studies.

Open access:
https://www.nature.com/articles/s41586-024-07323-1

I was thinking that since birds don't seem to have very much variation
from the basic bird body plan, could it be possible that exactly one
species survived the K-T event, and all modern birds are descended from
it? When would the MRCA of all birds have lived? Older protobirds seem
to have more variations not seen today. Some have teeth, some have claws
on wings, long tails and/or 4 wings/feathered legs are also wings*.

Given phylogeny, there must be at some point one species ancestral to
all modern birds. When that species lived is hard to be sure of.
Molecular estimates range from around 120ma to 70ma or so. But it does
appear that more than one bird species survived the K/T extinction. Just
how many depends on how you time-calibrate the tree and on how you
interpret a few Cretaceous fossils. But I'd say it's very unlikely for
there to be a single surviving species.

A lot depends on just what Vegavis is. But it seems fairly certain that
the paleognath, galloanserine, and neoavian lineages existed in the Late Cretaceous, at least.

(*) I have two bantam chickens with feathers on their legs and two of
their claws on each foot. Could this be an old "4 wing" gene becoming reactivated? Or are chickens just more prehistoric? The bantams seem to
fly a little better than non-bantam chickens, but that's probably just because they are very small. I haven't seen them try to flap their legs...

There is no "4-wing gene", just different expression patterns of the
genes that make feathers. You're looking at some change in gene
regulation, turning on genes in a particular place and time. There are
plenty of other birds with feathers on their legs and/or toes.
Ptarmigans, for example.
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