Insertion events of CR1 retrotransposable elements elucidate the phylogenetic branching order in galliform birds
Insertion events of CR1 retrotransposable elements elucidate the phylogenetic branching order in galliform birds
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DOI：
10.1093/molbev/msl164
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发表时间：
2007-01-01
影响因子：
10.7
通讯作者：
Ellegren, Hans
中科院分区：
文献类型：
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作者：
Kaiser, Vera B.;van Tuinen, Marcel;Ellegren, Hans
使用标准的系统发生学方法，很难分辨出在遥远的过去和很短的时间内进化出新的谱系时，物种形成事件发生的顺序。例如，鸡形鸟（包括鸡、火鸡和鹌鹑等著名物种）的遗传多样性通常在短的内部分支处显示出较低的自举支持值，反映了这些鸟类在始新世的快速多样化。然而，鉴于鸡和相关家禽物种在农业，进化，一般生物学和疾病研究中的关键作用，了解它们的内部关系非常重要。最近，转座元件的插入模式（例如长和短散布的核元件标记）已被证明在揭示困难的系统发育的分支顺序方面具有强大的作用。在这里，我们根据鸡重复序列1（CR 1）转座元件的插入事件来破译一组27个鸡形物种的物种形成事件的顺序。从鸡基因组的草图序列和火鸡BAC克隆序列中鉴定了44个CR 1标记位点，并通过扩增产物的电泳大小分离和随后的DNA测序确认研究了跨物种标记的存在或不存在。有30个标记可用于电泳分型，其中20个标记可提供遗传学信息。这些重复元件的分布支持一个单一的无同源性的分支图，这证实了，megapodes，cracids，新世界鹌鹑，珍珠鸡形成外类群雉科和鹌鹑，野鸡，鹧鸪是每一个多系群。重要的是，我们表明，鸡是一个外群火鸡和鹌鹑，观察没有显着的支持，从以前的DNA序列和DNA-DNA杂交为基础的树，并具有重要的意义，从鸡的序列或核型数据的基础上进行进化研究。我们讨论的潜力和局限性，使用基因组为基础的逆转录转座子的方法，在解决鸟类之间有问题的遗传。
Using standard phylogenetic methods, it can be hard to resolve the order in which speciation events took place when new lineages evolved in the distant past and within a short time frame. As an example, phylogenies of galliform birds (including well-known species such as chicken, turkey, and quail) usually show low bootstrap support values at short internal branches, reflecting the rapid diversification of these birds in the Eocene. However, given the key role of chicken and related poultry species in agricultural, evolutionary, general biological and disease studies, it is important to know their internal relationships. Recently, insertion patterns of transposable elements such as long and short interspersed nuclear element markers have proved powerful in revealing branching orders of difficult phylogenies.Here we decipher the order of speciation events in a group of 27 galliform species based on insertion events of chicken repeat 1 (CR1) transposable elements. Forty-four CR1 marker loci were identified from the draft sequence of the chicken genome, and from turkey BAC clone sequence, and the presence or absence of markers across species was investigated via electrophoretic size separation of amplification products and subsequent confirmation by DNA sequencing. Thirty markers proved possible to type with electrophoresis of which 20 were phylogenetically informative. The distribution of these repeat elements supported a single homoplasy-free cladogram, which confirmed that megapodes, cracids, New World quail, and guinea fowl form outgroups to Phasianidae and that quails, pheasants, and partridges are each polyphyletic groups. Importantly, we show that chicken is an outgroup to turkey and quail, an observation which does not have significant support from previous DNA sequence- and DNA-DNA hybridization-based trees and has important implications for evolutionary studies based on sequence or karyotype data from galliforms. We discuss the potential and limitations of using a genome-based retrotransposon approach in resolving problematic phylogenies among birds.