Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids
Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids
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估计不完全抽样的多样化率和模式：玫瑰花的案例研究
DOI：
10.1002/ajb2.1479
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发表时间：
2020
影响因子：
3
通讯作者：
Guralnick, Robert P.
中科院分区：
文献类型：
--
作者：
Sun, Miao;Folk, Ryan A.;Gitzendanner, Matthew A.;Soltis, Pamela S.;Chen, Zhiduan;Soltis, Douglas E.;Guralnick, Robert P.
PremiseRecent进展，在产生大规模的生物多样性，使物种多样性的大规模估计。这些现在常见的方法通常的特点是（1）不完整的物种覆盖没有明确的采样方法和/或（2）稀疏的骨干代表，通常依赖于假定的系统发育位置，以说明物种没有分子数据。我们使用经验的例子来研究不完全抽样多样化估计的影响，并提供建设性的建议，生态学家和进化生物学家的基础上，这些results.MethodsWe使用超矩阵rosids和一个采样良好的亚支（葫芦科）作为实证案例研究。我们比较了结果，使用这些大的cumbergenies与那些基于先前推断的，较小的超矩阵和合成树资源与完整的分类覆盖。最后，我们模拟随机和有代表性的类群抽样，并探讨了三种常用的方法，参数（RPANDA和BAMM）和半参数（DR）的抽样的影响。ResultsWe发现，多样化估计抽样的影响是特质，往往很强。与完全经验抽样相比，代表性和随机抽样方案要么压低或膨胀的物种形成率，这取决于方法和抽样方案。没有一种方法是完全强大的穷人抽样，但BAMM是最不敏感的中等水平的缺失taxa.ConclusionsWe建议对不加批判的建模缺失的类群使用分类数据采样差的树木和使用的摘要骨干树和其他数据集具有高代表性的偏见，我们强调显式的采样方法在macroevolutionary研究的重要性。
PremiseRecent advances in generating large‐scale phylogenies enable broad‐scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results.MethodsWe used a supermatrix for rosids and one well‐sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR).ResultsWe found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa.ConclusionsWe suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.
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影响因子：
4.6
作者：
Feldberg K;Schneider H;Stadler T;Schäfer-Verwimp A;Schmidt AR;Heinrichs J
通讯作者：
Heinrichs J
影响因子：
6.6
作者：
Pascal O. Title;D. Rabosky
通讯作者：
Pascal O. Title;D. Rabosky
影响因子：
3.3
作者：
D. Rabosky
通讯作者：
D. Rabosky
影响因子：
3
作者：
Folk, Ryan A.;Sun, Miao;Guralnick, Robert P.
通讯作者：
Guralnick, Robert P.
DOI：
10.1073/pnas.1423041112
发表时间：
2015-10-13
影响因子：
11.1
作者：
Hinchliff, Cody E.;Smith, Stephen A.;Cranston, Karen A.
通讯作者：
Cranston, Karen A.