当前位置: X-MOL 学术Syst. Biol. › 论文详情
Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)
Evaluating Species Delimitation Methods in Radiations: The Land Snail Albinaria cretensis Complex on Crete
Systematic Biology ( IF 6.5 ) Pub Date : 2021-06-27 , DOI: 10.1093/sysbio/syab050
Sonja Bamberger 1 , Jie Xu 1 , Bernhard Hausdorf 1
Affiliation  

Delimiting species in radiations is notoriously difficult because of the small differences between the incipient species, the star-like tree with short branches between species, incomplete lineage sorting, and the possibility of introgression between several of the incipient species. Next-generation sequencing data may help to overcome some of these problems. We evaluated methods for species delimitation based on genome-wide markers in a land snail radiation on Crete. Species delimitation in the Albinaria cretensis group was based exclusively on shell characters until now and resulted in classifications distinguishing 3–9 species. We generated sequences of 4270 loci for 140 specimens of the A. cretensis group from 48 populations by double-digest restriction site-associated DNA sequencing. We evaluated three methods for species discovery. The multispecies coalescent approach implemented in the program Bayesian Phylogenetics and Phylogeography resulted in a drastic overestimating of the number of species, whereas Gaussian clustering resulted in an overlumping. Primary species hypotheses based on the maximum percentage of the genome of the individuals derived from ancestral populations as estimated with the program ADMIXTURE moderately overestimated the number of species, but this was the only approach that provided information about gene flow between groups. Two of the methods for species validation that we applied, BFD* and delimitR, resulted in an acceptance of almost all primary species hypotheses, even such based on arbitrary subdivisions of hypotheses based on ADMIXTURE. In contrast, secondary species hypotheses, resulting from an evaluation of primary species hypotheses based on ADMIXTURE with isolation by distance tests, approached the morphological classification, but also uncovered two cryptic species and indicated that some of the previously delimited units should be combined. Thus, we recommend this combination of approaches that provided more detailed insights in the distinctness of barriers between the taxa of a species complex and the spatial distribution of admixture between them than the other methods. The recognition and delimitation of undersampled species remained a major challenge. [ADMIXTURE; Clausiliidae; delimitR, Gaussian clustering; isolation-by-distance; land snails; multispecies coalescent; species delimitation.]

中文翻译:

评估辐射中的物种划分方法:克里特岛上的陆地蜗牛 Albinaria cretensis 复合体

众所周知,在辐射中划定物种是很困难的,因为早期物种之间的差异很小,物种之间的分支短的星状树,不完整的谱系分类,以及几个早期物种之间渗入的可能性。下一代测序数据可能有助于克服其中一些问题。我们评估了基于克里特岛蜗牛辐射中的全基因组标记的物种划界方法。迄今为止,Albinaria cretensis 组的物种划分仅基于壳特征,并导致区分 3-9 个物种的分类。我们通过双酶切限制性位点相关 DNA 测序,为来自 48 个种群的 A. cretensis 组的 140 个样本生成了 4270 个基因座的序列。我们评估了三种物种发现方法。贝叶斯系统发育学和系统地理学计划中实施的多物种合并方法导致物种数量被严重高估,而高斯聚类导致过度集结。根据 ADMIXTURE 程序估计的源自祖先群体的个体基因组的最大百分比的主要物种假设适度高估了物种的数量,但这是提供有关群体之间基因流动信息的唯一方法。我们应用的两种物种验证方法,BFD* 和 delimitR,导致接受几乎所有主要物种假设,即使是基于 ADMIXTURE 的假设的任意细分。相比之下,次生种假设,通过对基于 ADMIXTURE 和距离测试隔离的主要物种假设的评估得出,接近了形态分类,但也发现了两个神秘的物种,并表明应该组合一些先前划定的单位。因此,我们推荐这种方法组合,与其他方法相比,这些方法在物种复合体的分类群之间的障碍的独特性和它们之间的混合物的空间分布方面提供了更详细的见解。对采样不足的物种的识别和划界仍然是一项重大挑战。[混合物; 克劳斯科; delimitR,高斯聚类;距离隔离;蜗牛; 多物种聚结;物种划分。] 但也发现了两个神秘的物种,并表示应该合并一些以前划定的单元。因此,我们推荐这种方法组合,与其他方法相比,这些方法在物种复合体的分类群之间的障碍的独特性和它们之间的混合物的空间分布方面提供了更详细的见解。对采样不足的物种的识别和划界仍然是一项重大挑战。[混合物; 克劳斯科; delimitR,高斯聚类;距离隔离;蜗牛; 多物种聚结;物种划分。] 但也发现了两个神秘的物种,并表示应该合并一些以前划定的单元。因此,我们推荐这种方法组合,与其他方法相比,这些方法在物种复合体的分类群之间的障碍的独特性和它们之间的混合物的空间分布方面提供了更详细的见解。对采样不足的物种的识别和划界仍然是一项重大挑战。[混合物; 克劳斯科; delimitR,高斯聚类;距离隔离;蜗牛; 多物种聚结;物种划分。] 我们推荐这种方法的组合,与其他方法相比,这些方法在物种复合体的分类群之间的障碍的独特性以及它们之间的混合物的空间分布方面提供了更详细的见解。对采样不足的物种的识别和划界仍然是一项重大挑战。[混合物; 克劳斯科; delimitR,高斯聚类;距离隔离;蜗牛; 多物种聚结;物种划分。] 我们推荐这种方法的组合,与其他方法相比,这些方法在物种复合体的分类群之间的障碍的独特性以及它们之间的混合物的空间分布方面提供了更详细的见解。对采样不足的物种的识别和划界仍然是一项重大挑战。[混合物; 克劳斯科; delimitR,高斯聚类;距离隔离;蜗牛; 多物种聚结;物种划分。]
更新日期:2021-06-27
down
wechat
bug