Data from: Phylogenomics and historical biogeography of West Indian Rock Iguanas (genus Cyclura)

The genus Cyclura includes nine extant species and six subspecies of West
Indian Rock Iguanas and is one of the most imperiled genera of squamate
reptiles globally. An understanding of species diversity, evolutionary
relationships, diversification, and historical biogeography in this group
is crucial for implementing sound long-term conservation strategies. We
collected DNA samples from 1–10 individuals per taxon from all Cyclura
taxa (n = 70 ingroup individuals), focusing where possible on
incorporating individuals from different populations of each species. We
also collected 1–2 individuals from each of seven outgroup species of
iguanas (Iguana delicatissima; five Ctenosaura species) and Anolis sagrei
(n = 12 outgroup individuals). We used targeted genomic sequence capture
to isolate and to sequence 1,872 loci comprising of 687,308 base pairs
(bp) from each of the 82 individuals from across the nuclear genome. We
extracted mitochondrial reads and assembled and annotated mitogenomes for
all Cyclura taxa plus outgroup species. We present well-supported
phylogenomic gene tree/species tree analyses for all extant species of
Cyclura using ASTRAL-III, SVDQuartets, and starBEAST methods, and discuss
the taxonomic, biogeographic, and conservation implications of these data.
We find a most recent common ancestor of the genus 9.91 million years ago.
The earliest divergence within Cyclura separates C. pinguis from a clade
comprising all Cyclura except C. pinguis. Within the latter group, a clade
comprising C. carinata from the southern Lucayan Islands and C. ricordii
from Hispaniola is the sister taxon to a clade comprising the other
Cyclura. Among the other Cyclura, the species C. cornuta and C. stejnegeri
(from Hispaniola and Isla Mona) form the sister taxon to a clade of
species from Jamaica (C. collei), Cuba and Cayman Islands (C. nubila), and
the eastern (C. rileyi) and western (C. cychlura) Lucayan Islands. Cyclura
cychlura and C. rileyi form a clade whose sister taxon is C. nubila.
Cyclura collei is the sister taxon to these three species combined.

Cyclura属包含9个现存物种及6个西印度岩鬣蜥（West Indian Rock Iguanas）亚种，是全球受威胁程度最高的有鳞爬行动物（squamate reptiles）类群之一。明晰该类群的物种多样性、演化关系、分化模式与历史生物地理学特征，对于制定科学合理的长期保护策略至关重要。
本研究采集了Cyclura属所有类群的DNA样本（共70个内类群（ingroup）个体），每个类群采样1~10个个体，并尽可能涵盖每个物种的不同种群个体。同时采集了7个外类群（outgroup）鬣蜥物种的1~2个个体，包括细鳞鬣蜥（Iguana delicatissima）、5种栉尾蜥属（Ctenosaura）物种，以及安乐蜥（Anolis sagrei），外类群个体总计12个。
我们采用靶向基因组序列捕获（targeted genomic sequence capture）技术，对来自核基因组的1872个位点（总计687308个碱基对（base pairs，缩写bp））进行分离与测序，样本覆盖全部82个个体。此外，我们提取了线粒体测序读段，组装并注释了所有Cyclura属类群及外类群物种的线粒体基因组（mitogenomes）。
本研究利用ASTRAL-III、SVDQuartets与starBEAST三种方法，对Cyclura属所有现存物种开展了高支持度的系统发育基因组学基因树/物种树（phylogenomic gene tree/species tree）分析，并探讨了这些数据在分类学、生物地理学与保护生物学层面的研究意义。研究发现，Cyclura属的最近共同祖先可追溯至991万年前。
Cyclura属内最早的分化事件将圆尾鬣蜥（C. pinguis）与其余所有Cyclura属物种组成的演化支分离开来。在后者类群中，来自南部卢卡亚群岛的卡林塔岩鬣蜥（C. carinata）与来自伊斯帕尼奥拉岛（Hispaniola）的雷科德岩鬣蜥（C. ricordii）组成的演化支，是其余Cyclura属物种组成演化支的姊妹群。
在其余Cyclura属物种中，来自伊斯帕尼奥拉岛与莫纳岛（Isla Mona）的犀牛鬣蜥（C. cornuta）与斯泰因杰鬣蜥（C. stejnegeri）组成的演化支，是来自牙买加的科利岩鬣蜥（C. collei）、古巴与开曼群岛的古巴岩鬣蜥（C. nubila），以及东部卢卡亚群岛的莱利岩鬣蜥（C. rileyi）与西部卢卡亚群岛的奇克拉鬣蜥（C. cychlura）组成的演化支的姊妹群。奇克拉鬣蜥（C. cychlura）与莱利岩鬣蜥（C. rileyi）组成一个演化支，其姊妹群为古巴岩鬣蜥（C. nubila）；而科利岩鬣蜥（C. collei）是这三个物种组成类群的姊妹群。