The up to date household tree, detailed in two complementary papers revealed in the present day within the journal Nature and the Proceedings of the National Academy of Sciences, reveals patterns within the evolutionary historical past of birds following the cataclysmic mass extinction occasion that worn out the dinosaurs 66 million years in the past. The authors noticed sharp will increase in efficient inhabitants dimension, substitution charges and relative mind dimension in early birds, shedding new mild on the adaptive mechanisms that drove avian diversification within the aftermath of this pivotal occasion. The researchers additionally intently examined one of many branches of the brand new household tree and located that flamingos and doves are extra distantly associated than earlier genome-wide analyses had proven.
The up to date hen household tree delineating 93 million years of evolutionary relationships between 363 hen species. Image credit score: Jon Fjeldså / Josefin Stiller.
“Our goal is to reconstruct the entire evolutionary history of all birds,” mentioned Professor Siavash Mirarab, a researcher on the University of California, San Diego.
The work is a part of the Bird 10,000 Genomes (B10K) Project, a multi-institutional effort led by the University of Copenhagen, Zhejiang University and the University of California, San Diego that goals to generate draft genome sequences for about 10,500 extant hen species.
At the center of those research lies a collection of algorithms referred to as ASTRAL, which Professor Mirarab and colleagues developed to deduce evolutionary relationships with unprecedented scalability, accuracy and pace.
By harnessing the ability of those algorithms, they built-in genomic knowledge from over 60,000 genomic areas, offering a sturdy statistical basis for his or her analyses.
The researchers then examined the evolutionary historical past of individual segments throughout the genome.
From there, they pieced collectively a mosaic of gene timber, which have been then compiled right into a complete species tree.
This meticulous method enabled the researchers to assemble a brand new and improved hen household tree that delineates advanced branching occasions with exceptional precision and element, even in instances of historic uncertainty.
“We found that our method of adding tens of thousands of genes to our analysis was actually necessary to resolve evolutionary relationships between bird species,” Professor Mirarab mentioned.
“You really need all that genomic data to recover what happened in this certain period of time 65-67 million years ago with high confidence.”
The scientists additionally seemed on the results of various genome sampling strategies on the accuracy of the tree.
They confirmed that two methods — sequencing many genes from every species, in addition to sequencing many species — mixed collectively are necessary for reconstructing this evolutionary historical past.
“Because we used a mixture of both strategies, we could test which approach has stronger impacts on phylogenetic reconstruction,” mentioned University of Copenhagen’s Professor Josefin Stiller.
We discovered that it was extra necessary to pattern many genetic sequences from every organism than it was to pattern from a broader vary of species, though the latter methodology helped us thus far when totally different teams advanced.”
Mirarab et al. intently examined one of many branches of the up to date hen household tree and located that teams together with flamingos and doves are extra distantly associated than earlier genome-wide analyses had proven and attributed the consequence to an uncommon area of chromosome 4. Image credit score: Ed Braun / Daniel J. Field / Siavash Miarab.
With assistance from their superior computational strategies, the researchers have been additionally in a position to make clear one thing uncommon that that they had found in certainly one of their earlier research: a specific part of 1 chromosome within the hen genome had remained unchanged for thousands and thousands of years, void of the anticipated patterns of genetic recombination.
“Ten years ago, we pieced together a family tree for the Neoaves, a group that includes the vast majority of bird species,” mentioned University of Florida’s Professor Edward Braun.
“Based on the genomes of 48 species, we split the Neoaves into two big categories: doves and flamingos in one group, all the rest in the other.”
“When repeating a similar analysis this year using 363 species, a different family tree emerged that split up doves and flamingos into two distinct groups.”
“With two mutually exclusive family trees in hand, we went hunting for explanations that could tell them which tree was correct.”
“When we looked at the individual genes and what tree they supported, all of a sudden it popped out that all the genes that support the older tree, they’re all in one spot. That’s what started the whole thing,” he defined.
“Investigating this spot, we noticed it was not as mixed together as it should have been over millions of years of sexual reproduction.”
“Like humans, birds combine genes from a father and a mother into the next generation.”
“But birds and humans alike first mix the genes they inherited from their parents when creating sperm and eggs.”
“This process is called recombination, and it maximizes a species’ genetic diversity by making sure no two siblings are quite the same.”
The authors discovered proof that one part of 1 hen chromosome had suppressed this recombination course of for a number of million years across the time the dinosaurs disappeared.
Whether the extinction occasion and the genomic anomalies are associated is unclear.
The consequence was that the flamingos and doves seemed just like each other on this chunk of frozen DNA.
But considering the total genome, it turned clear that the 2 teams are extra distantly associated.
“What’s surprising is that this period of suppressed recombination could mislead the analysis,” Professor Braun mentioned.
“And because it could mislead the analysis, it was actually detectable more than 60 million years in the future. That’s the cool part.”
“Such a mystery could be lurking in the genomes of other organisms as well.”
“We discovered this misleading region in birds because we put a lot of energy into sequencing birds’ genomes.”
“I think there are cases like this out there for other species that are just not known right now.”
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J. Stiller et al. 2024. Complexity of avian evolution revealed by family-level genomes. Nature, in press;
Siavash Mirarab et al. 2024. A area of suppressed recombination misleads neoavian phylogenomics. PNAS 121: e2319506121; doi: 10.1073/pnas.2319506121
