Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.
School of Earth, Environmental and Biological Sciences, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.
Genome Biol Evol. 2018 Jan 1;10(1):33-44. doi: 10.1093/gbe/evx245.
The iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary relationship within the two genera, Macropus and Wallabia, is controversial: mitochondrial and nuclear genes, and morphological data have produced conflicting scenarios regarding the phylogenetic relationships, which in turn impact the classification and taxonomy. We sequenced and analyzed the genomes of 11 kangaroos to investigate the evolutionary cause of the observed phylogenetic conflict. A multilocus coalescent analysis using ∼14,900 genome fragments, each 10 kb long, significantly resolved the species relationships between and among the sister-genera Macropus and Wallabia. The phylogenomic approach reconstructed the swamp wallaby (Wallabia) as nested inside Macropus, making this genus paraphyletic. However, the phylogenomic analyses indicate multiple conflicting phylogenetic signals in the swamp wallaby genome. This is interpreted as at least one introgression event between the ancestor of the genus Wallabia and a now extinct ghost lineage outside the genus Macropus. Additional phylogenetic signals must therefore be caused by incomplete lineage sorting and/or introgression, but available statistical methods cannot convincingly disentangle the two processes. In addition, the relationships inside the Macropus subgenus M. (Notamacropus) represent a hard polytomy. Thus, the relationships between tammar, red-necked, agile, and parma wallabies remain unresolvable even with whole-genome data. Even if most methods resolve bifurcating trees from genomic data, hard polytomies, incomplete lineage sorting, and introgression complicate the interpretation of the phylogeny and thus taxonomy.
标志性的澳大拉西亚袋鼠和沙袋鼠代表了有袋类动物的成功辐射。然而，两个属——大袋鼠属（Macropus）和沙袋鼠属（Wallabia）之间的进化关系存在争议：线粒体和核基因以及形态学数据对系统发育关系产生了相互矛盾的情景，这反过来又影响了分类和分类学。我们对 11 只袋鼠进行了测序和分析，以研究观察到的系统发育冲突的进化原因。使用约 14900 个基因组片段（每个片段长 10kb）进行的多基因聚合并分析，显著解决了姐妹属大袋鼠属和沙袋鼠属之间和内部的物种关系。基因组系统发育分析将沼泽沙袋鼠（Wallabia）重建为嵌套在大袋鼠属内，使这个属成为并系群。然而，基因组系统发育分析表明，沼泽沙袋鼠基因组中存在多个相互冲突的系统发育信号。这被解释为至少有一个属沙袋鼠的祖先与现在已经灭绝的属 Macropus 以外的幽灵谱系之间的基因渗入事件。因此，必须有其他的系统发育信号是由不完全谱系分选和/或基因渗入引起的，但现有的统计方法无法令人信服地将这两个过程区分开来。此外，Macropus 亚属 M.（Notamacropus）内部的关系代表了一个硬聚点。因此，即使有全基因组数据，塔马尔袋鼠、红颈袋鼠、敏捷袋鼠和帕玛袋鼠之间的关系仍然无法解决。即使大多数方法从基因组数据中解析出分支树，硬聚点、不完全谱系分选和基因渗入也会使系统发育的解释变得复杂，从而影响分类学。
