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DATE 2019-09-01

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MESSAGE
DATE 2019-09-25
FROM Ruben Safir
SUBJECT Subject: [Hangout - NYLXS] Fwd: [dinosaur] Genomic-scale data for
From hangout-bounces-at-nylxs.com Wed Sep 25 01:12:32 2019
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Subject: [Hangout - NYLXS] Fwd: [dinosaur] Genomic-scale data for
Squamata--no support for traditional morphological relationships
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Ben Creisler
bcreisler-at-gmail.com


A new paper:

Frank T. Burbrink, Felipe G. Grazziotin, R. Alexander Pyron, David Cundall,
Steve Donnellan, Frances Irish, J. Scott Keogh, Fred Kraus, Robert W.
Murphy, Brice Noonan, Christopher J. Raxworthy, Sara Ruane, Alan R. Lemmon,
Emily Moriarty Lemmon & Hussam Zaher (2019)
Interrogating genomic-scale data for Squamata (lizards, snakes, and
amphisbaenians) shows no support for key traditional morphological
relationships.
Systematic Biology, syz062 (advance online publication)
doi:
https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1093_sysbio_syz062&d=DwIBaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=2gtV1e0G2Uf5HG7aqbCI6R2iJN778ONjAh09K-bduGU&s=ccSXzA6MmSajo2xORr5De5TIGJkrJgHPSx85HYacBZY&e=
https://urldefense.proofpoint.com/v2/url?u=https-3A__academic.oup.com_sysbio_advance-2Darticle-2Dabstract_doi_10.1093_sysbio_syz062_5573126&d=DwIBaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=2gtV1e0G2Uf5HG7aqbCI6R2iJN778ONjAh09K-bduGU&s=lm64JS5m1wolO4loP86_yuszsPvBwO_9mqdeL6FrqKM&e=



Genomics is narrowing uncertainty in the phylogenetic structure for many
amniote groups. For one of the most diverse and species-rich groups, the
squamate reptiles (lizards and snakes, amphisbaenians), an inverse
correlation between the number of taxa and loci sampled still persists
across all publications using DNA sequence data and reaching a consensus on
the relationships among them has been highly problematic. Here, we use
high-throughput sequence data from 289 samples covering 75 families of
squamates to address phylogenetic affinities, estimate divergence times,
and characterize residual topological uncertainty in the presence of genome
scale data. Importantly, we address genomic support for the traditional
taxonomic groupings Scleroglossa and Macrostomata using novel
machine-learning techniques. We interrogate genes using various metrics
inherent to these loci, including parsimony-informative sites, phylogenetic
informativeness, length, gaps, number of substitutions, and site
concordance to understand why certain loci fail to find previously
well-supported molecular clades and how they fail to support species-tree
estimates. We show that both incomplete lineage sorting and poor gene-tree
estimation (due to a few undesirable gene properties, such as an
insufficient number of parsimony informative sites), may account for most
gene and species-tree discordance. We find overwhelming signal for
Toxicofera, and also show that none of the loci included in this study
supports Scleroglossa or Macrostomata. We comment on the origins and
diversification of Squamata throughout the Mesozoic and underscore
remaining uncertainties that persist in both deeper parts of the tree
(e.g., relationships between Dibamia, Gekkota, and remaining squamates; and
between the three toxiferan clades Iguania, Serpentes, and Anguiformes) and
within specific clades (e.g., affinities among gekkotan, pleurodont
iguanians, and colubroid families).

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