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The complete mitochondrial genomes of the Galápagos iguanas, Amblyrhynchus cristatus and Conolophus subcristatus

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The complete mitochondrial genomes of the Galápagos iguanas, Amblyrhynchus cristatus and Conolophus subcristatus

Abstract and Figures

The Galápagos iguanas are among the oldest vertebrate lineages on the Galápagos archipelago, and the evolutionary history of this clade is of great interest to biologists. We describe here the complete mitochondrial genomes of the marine iguana, Amblyrhynchus cristatus (Genbank accession number: KT277937) and the land iguana Conolophus subcristatus (Genbank accession number: KT277936). The genomes contain 13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs genes, as well as a control region (CR). Both species have an identical gene order, which matches that of Iguana iguana. The CR of both Galápagos iguanas features similar tandem repeats units, which are absent in I. iguana. We present a phylogeny of the Iguanidae based on complete mitochondrial genomes, which confirms the sister-group relationship of Galápagos iguanas. These new mitochondrial genomes constitute an important data source for future exploration of the phylogenetic relationships and evolutionary history of the Galápagos iguanas.
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ISSN: 1940-1736 (print), 1940-1744 (electronic)
Mitochondrial DNA, Early Online: 1–2
!2015 Taylor & Francis. DOI: 10.3109/19401736.2015.1079863
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genomes of the Gala
´pagos iguanas,
Amblyrhynchus cristatus and Conolophus subcristatus
Amy MacLeod
1
, Iker Irisarri
2
, Miguel Vences
1
, and Sebastian Steinfartz
1
1
Department of Evolutionary Biology, Zoological Institute, Technische Universita
¨t Braunschweig, Braunschweig, Germany and
2
Laboratory for
Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
Abstract
The Gala
´pagos iguanas are among the oldest vertebrate lineages on the Gala
´pagos
archipelago, and the evolutionary history of this clade is of great interest to biologists. We
describe here the complete mitochondrial genomes of the marine iguana, Amblyrhynchus
cristatus (Genbank accession number: KT277937) and the land iguana Conolophus subcristatus
(Genbank accession number: KT277936). The genomes contain 13 protein-coding genes, 22
transfer RNAs, and two ribosomal RNAs genes, as well as a control region (CR). Both species
have an identical gene order, which matches that of Iguana iguana. The CR of both Gala
´pagos
iguanas features similar tandem repeats units, which are absent in I. iguana. We present a
phylogeny of the Iguanidae based on complete mitochondrial genomes, which confirms the
sister-group relationship of Gala
´pagos iguanas. These new mitochondrial genomes constitute
an important data source for future exploration of the phylogenetic relationships and
evolutionary history of the Gala
´pagos iguanas.
Keywords
Evolutionary relationships, Gala
´pagos
archipelago, Iguanidae, Islands,
phylogenetics
History
Received 15 July 2015
Revised 20 July 2015
Accepted 29 July 2015
Published online 3 September 2015
The Gala
´pagos iguanas are sister taxa that diverged from a
common ancestor on the Gala
´pagos archipelago some 4.5 million
years ago (MacLeod et al., 2015). This clade, including one
species of marine iguana (genus Amblyrynchus) and three species
of land iguana (genus Conolophus), represents one of the most
ancient endemic clades of the Gala
´pagos, and molecular studies
of them have produced important insights into evolutionary
processes (e.g. MacLeod et al., 2015; Rassmann et al., 1997;
Steinfartz et al., 2009). We describe here the first complete
mitochondrial genome sequences of Amblyrhynchus cristatus and
Conolophus subcristatus. In addition, we present a mitogenomic
phylogeny of the Iguanidae, which illustrates the position of the
Gala
´pagos iguanas in relation to other species for which complete
mitochondrial genomes are available.
Genomic DNA was isolated from blood samples collected with
permission of the Gala
´pagos National Park service. A. cristatus
was sampled on San Cristo
´bal Island, and C. subcristatus on
Fernandina Island. Mitochondrial genomes were amplified and
sequenced using a primer-walking approach. PCR involved
primers available from the literature, as well as new primers
developed for the study (details available upon request).
Sequences were assembled in CodonCode (V4.2.5; CodonCode
Corporation, Dedham, MA) and full length mitogenomes
were annotated with the MITOS pipeline (Bernt et al., 2013)
and manually checked by comparison to Iguana iguana
(Genbank accession number: NC002793). Nucleotide gene
alignments were performed with TranslatorX (Abascal et al.,
2010) and MAFFT (Katoh & Standley, 2013) for protein-coding
and ribosomal RNA genes respectively, and concatenated into a
single matrix for phylogenetic analysis. Maximum likelihood
phylogenetic reconstruction was performed with RAxML v.8.1.16
(Stamatakis, 2014) using independent gene partitions under
GTR + G and 100 independent maximum likelihood searches.
Branch support was assessed with 1000 replicates of non-
parametric bootstrapping. A Bayesian analysis was performed
with PhyloBayes MPI v.1.5 (Lartillot et al., 2013) under the CAT-
GTR model and by running two MCMC chains until convergence.
The mitogenomes of A. cristatus and C. subcristatus are,
respectively, 16 897 bp and 16 892 bp long. Gene order was
identical in both species and matches exactly with that of I.
iguana, corresponding to the ancestral vertebrate mitochondrial
gene order. Our findings confirm the repetitive elements found in
the control region in previous studies (Hanley & Caccone, 2005),
with both Gala
´pagos iguanas displaying four repetitive regions of
73 and 74 bp for Conolophus and Amblyrynchus, respectively.
These repetitive sequences have a high sequence identity (uncor-
rected p-distance: 0.35), implying that they have probably evolved
from a common ancestor. However, such repetitive elements are
absent in the CR of both I. iguana (Janke et al., 2001) and Cyclura
pinguis (Genbank accession number: NC027089), and may prove
interesting for future phylogenetic applications. Our phylogenetic
reconstruction confirms the sister-group relationship between the
Gala
´pagos iguanas with strong support, and indicates a relatively
close relationship with Iguana and Cyclura (Figure 1), confirming
earlier work (Pyron et al., 2013). The mitogenomes presented here
will enhance further study into the evolutionary relationships of
the Gala
´pagos iguanas as mitogenomes of additional species and
lineages of these lizards become available.
Correspondence: Amy MacLeod, Department of Evolutionary Biology,
Zoological Institute, Technische Universita
¨t Braunschweig,
Mendelssohnstr. 4, 38106 Braunschweig, Germany. E-mail:
ms.amymacleod@gmail.com
Downloaded by [208.167.254.208] at 08:12 11 September 2015
Acknowledgements
The authors thank K. Rassmann and F. Trillmich for sample collection,
M. Kondermann, J. Juras and L. M. Ko
¨pping for assistance with the
laboratory work, and A. Meyer for logistic assistance. This publication is
contribution number 2119 of the Charles Darwin Foundation for the
Galapagos Islands.
Declaration of interest
This study was supported by grants from the Swiss Friends of the
Gala
´pagos Islands. I. Irisarri was supported by postdoc fellowships of the
Alexander von Humboldt Foundation and EMBO. The authors declare
that they have no conflicting interests.
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Figure 1. Maximum likelihood (RAxML) tree
from full mitogenome data including a
selection of iguanid species and two out-
groups (Chamaeleo and Brookesia), which
are not shown in the figure for the sake of
clarity. Numbers at nodes are support values
from non-parametric bootstrap, and posterior
probabilities from the Bayesian analysis
(PhyloBayes), both transformed into percent.
Both trees agree on the close sister-relation-
ship of the Galapagos iguanas,
Amblyrhynchus cristatus and Conolophus
subcristatus. Genbank accession numbers:
Cyclura pinguis NC027089, Urosaurus
nigricaudus NC026308, Uta stansburiana
NC027261, Anolis carolinensis NC010972,
Polychrus marmoratus NC012839,
Chalarodon madagascariensis NC012836,
Leiocephalus personatus NC012834,
Gambelia wislizenii NC012831, Basiliscus
vittatus NC012829, Oplurus grandidieri
NC012827, Sceloporus occidentalis
NC005960, Iguana iguana NC002793, and
Anolis carolinensis EU747728.2.
2A. MacLeod et al. Mitochondrial DNA, Early Online: 1–2
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