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Turtles group with crocodiles and birds (NOT squamates) based on genome size

From: Ben Creisler

The following paper may be of interest--it appears to support a common
ancestor for birds, crocodiles, and turtles that is separate from the
squamate clade. A paper in Biology Letters back in July 2011 cited the
identification of similar microRNAs as evidence that turtles and
lizards (squamates) group together.  Clearly a full sequencing of
multiple turtle genomes is in order to straighten this out.

Fumio Kasai, Patricia C. M. O'Brien and Malcolm A. Ferguson-Smith (2012)
Reassessment of genome size in turtle and crocodile based on
chromosome measurement by flow karyotyping: close similarity to
Biology Letters (advance online publication)
doi: 10.1098/rsbl.2012.0141

The genome size in turtles and crocodiles is thought to be much larger
than the 1.2 Gb of the chicken (Gallus gallus domesticus, GGA),
according to the animal genome size database. However, GGA
macrochromosomes show extensive homology in the karyotypes of the red
eared slider (Trachemys scripta elegans, TSC) and the Nile crocodile
(Crocodylus niloticus, CNI), and bird and reptile genomes have been
highly conserved during evolution. In this study, size and GC content
of all chromosomes are measured from the flow karyotypes of GGA, TSC
and CNI. Genome sizes estimated from the total chromosome size
demonstrate that TSC and CNI are 1.21 Gb and 1.29 Gb, respectively.
This refines previous overestimations and reveals similar genome sizes
in chicken, turtle and crocodile. Analysis of chromosome GC content in
each of these three species shows a higher GC content in smaller
chromosomes than in larger chromosomes. This contrasts with mammals
and squamates in which GC content does not correlate with chromosome
size. These data suggest that a common ancestor of birds, turtles and
crocodiles had a small genome size and a chromosomal size-dependent GC
bias, distinct from the squamate lineage.

Compare to:

T. R. Lyson, E. A. Sperling, A. M. Heimberg, J. A. Gauthier, B. L.
King, K. J. Peterson (2012).
MicroRNAs support a turtle + lizard clade.
Biology Letters,(advance in 2011); published in Biology Letters 8(1):104-107
DOI: 10.1098/rsbl.2011.0477

Despite much interest in amniote systematics, the origin of turtles
remains elusive. Traditional morphological phylogenetic analyses place
turtles outside Diapsida—amniotes whose ancestor had two fenestrae in
the temporal region of the skull (among the living forms the tuatara,
lizards, birds and crocodilians)—and allied with some
unfenestrate-skulled (anapsid) taxa. Nonetheless, some morphological
analyses place turtles within Diapsida, allied with Lepidosauria
(tuatara and lizards). Most molecular studies agree that turtles are
diapsids, but rather than allying them with lepidosaurs, instead place
turtles near or within Archosauria (crocodilians and birds). Thus,
three basic phylogenetic positions for turtles with respect to extant
Diapsida are currently debated: (i) sister to Diapsida, (ii) sister to
Lepidosauria, or (iii) sister to, or within, Archosauria.
Interestingly, although these three alternatives are consistent with a
single unrooted four-taxon tree for extant reptiles, they differ with
respect to the position of the root. Here, we apply a novel molecular
dataset, the presence versus absence of specific microRNAs, to the
problem of the phylogenetic position of turtles and the root of the
reptilian tree, and find that this dataset unambiguously supports a
turtle + lepidosaur group. We find that turtles and lizards share four
unique miRNA gene families that are not found in any other organisms'
genome or small RNA library, and no miRNAs are found in all diapsids
but not turtles, or in turtles and archosaurs but not in lizards. The
concordance between our result and some morphological analyses
suggests that there have been numerous morphological convergences and
reversals in reptile phylogeny, including the loss of temporal