Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families
Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families
复制标题
在双壳类的一个密集采样的单世代中，假设分叉或出芽来校准单世代改变推断的宏观进化动力学
DOI：
10.1098/rspb.2021.2178
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发表时间：
2021-12-08
影响因子：
4.7
通讯作者：
Jablonski, David
中科院分区：
文献类型：
--
作者：
Crouch, Nicholas M. A.;Edie, Stewart M.;Jablonski, David
进化动力学的分析取决于系统发育数据的时间尺度。对现存分类群的大多数分析都假设了一个纯粹的分叉模型，其中节点是用化石记录中较老的第一次出现的子代谱系来校准的。这与萌芽阶段不同，在萌芽阶段，节点是使用较年轻的第一个出现的节点进行校准的。在这里，我们使用广泛的双壳类软体动物化石记录来大规模评估分支模型如何影响宏观进化分析。在97个现存的双壳类家族的系统发育中，我们对91%的节点进行了时间校准，年龄范围从2.59 Ma到485 Ma。允许基于萌芽的校准将树和观察到的化石记录之间的冲突降至最低，并将推断的“幽灵谱系”的总和持续时间从67.6亿年(Gyr；分叉模型)减少到1.00 Gyr(萌芽)。加上31个已灭绝的副血统家族，幽灵谱系总数将增加到7.86Gyr(分叉)和1.92Gyr(萌芽)，但纳入了更多关于不同谱系之间的日期差异的信息。分叉模型下的宏观演化分析与古生代末期灭绝程度的其他古生物证据相冲突，并大大减少了新生代的多样性。在节点校准系统发育时，考虑不同的分支模型是必不可少的，对于有可靠化石记录的主要分支，萌芽模型似乎更合适。
Analyses of evolutionary dynamics depend on how phylogenetic data are time-scaled. Most analyses of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. This contrasts with budding, where nodes are calibrated using the younger first occurrence. Here, we use the extensive fossil record of bivalve molluscs for a large-scale evaluation of how branching models affect macroevolutionary analyses. We time-calibrated 91% of nodes, ranging in age from 2.59 to 485 Ma, in a phylogeny of 97 extant bivalve families. Allowing budding-based calibrations minimizes conflict between the tree and observed fossil record, and reduces the summed duration of inferred 'ghost lineages' from 6.76 billion years (Gyr; bifurcating model) to 1.00 Gyr (budding). Adding 31 extinct paraphyletic families raises ghost lineage totals to 7.86 Gyr (bifurcating) and 1.92 Gyr (budding), but incorporates more information to date divergences between lineages. Macroevolutionary analyses under a bifurcating model conflict with other palaeontological evidence on the magnitude of the end-Palaeozoic extinction, and strongly reduce Cenozoic diversification. Consideration of different branching models is essential when node-calibrating phylogenies, and for a major clade with a robust fossil record, a budding model appears more appropriate.