Diversification and dispersal in the Americas revealed by new phylogenies of the wrens and allies (Passeriformes: Certhioidea)

The passerine superfamily Certhioidea lacks a complete phylogeny despite decades of recognition as a clade and extensive systematic work within all its constituent families. Here, we inferred a near-complete species level phylogeny of Certhioidea from a molecular supermatrix, including the first comprehensive sampling of the wrens (Troglodytidae), and used this phylogeny to infer its biogeographic and diversification histories. We also inferred an expanded phylogeny including nearly 100 putative phylospecies previously documented in the literature, and we found that including this diversity had notable impacts on the inferred evolutionary history of Certhioidea. This phylospecies-level tree documented a few instances of species paraphyly, some previously described in the literature and some novel. We found that Certhioidea originated largely in Eurasia and dispersed into North America five times in the last 20 million years, including at the origin of the “New World certhioids”, wrens a..., , , # Diversification and dispersal in the Americas revealed by new phylogenies of the wrens and allies (Passeriformes: Certhioidea)

Tyler S. Imfeld, F. Keith Barker, Hernán Vázquez-Miranda, Jaime A. Chaves, Patricia Escalante, Garth M. Spellman, and John Klicka

SEQUENCE DATA AND XML FILES:

1. Certh_spp_UCE.xml
A .xml file used to run the species-level phylogenetic analysis in BEAST with UCE node constraints.

2. Certh_spp_Unconstrained.xml
A .xml file used to run the species-level phylogenetic analysis in BEAST without any node constraints.

3. Certhioidea_Charsets_v4.txt
A .txt file that includes the locus-specific character sets used in the species-level RAxML analyses.

4. Certhioidea_concatenated_v4.nex
A NEXUS-formatted sequence data file of the concatenated sequence matrix used in species-level analyses.

5. Certhioidea_concatenated_v4.phylogeny
A phylip-formatted sequence data file of the concatenated sequence matrix used in species-level analyses.

6. C...

尽管旋木雀总科（Certhioidea）作为演化支被学界认可已有数十年，且其所有下属类群均已开展过广泛的系统学研究，但目前仍缺乏完整的系统发育树。本研究通过分子超级矩阵构建了旋木雀总科近乎完整的物种级系统发育树，首次实现了对鹪鹩科（Troglodytidae）类群的全面采样，并基于该系统发育树推断了其生物地理演化与物种分化历史。此外，我们还构建了包含近100个文献中已报道的推定系统种的扩展系统发育树，结果显示纳入此类多样性对旋木雀总科的推断演化历史产生了显著影响。该系统种级系统发育树揭示了数例物种并系现象，其中部分此前已在文献中被报道，其余则为新发现。研究发现，旋木雀总科主要起源于欧亚大陆，并在过去2000万年中五次扩散至北美洲，包括“新大陆旋木雀类群”的起源——鹪鹩类群及……
# 基于鹪鹩类群及其近缘类群全新系统发育树揭示美洲的物种分化与扩散（雀形目：旋木雀总科）
作者：Tyler S. Imfeld、F. Keith Barker、Hernán Vázquez-Miranda、Jaime A. Chaves、Patricia Escalante、Garth M. Spellman、John Klicka

## 序列数据与XML文件
1. "Certh_spp_UCE.xml"：用于在BEAST软件中开展物种级系统发育分析的XML格式文件，附带超保守元件（Ultra-Conserved Elements, UCE）节点约束。
2. "Certh_spp_Unconstrained.xml"：用于在BEAST软件中开展物种级系统发育分析的XML格式文件，无任何节点约束。
3. "Certhioidea_Charsets_v4.txt"：包含物种级RAxML分析所用位点特异性字符集的文本文件。
4. "Certhioidea_concatenated_v4.nex"：用于物种级分析的串联序列矩阵的NEXUS格式序列数据文件。
5. "Certhioidea_concatenated_v4.phylogeny"：用于物种级分析的串联序列矩阵的phylip格式序列数据文件。
6. C...