Genome-Scale Data Reveal Deep Lineage Divergence and a Complex Demographic History in the Texas Horned Lizard (Phrynosoma cornutum) throughout the Southwestern and Central United States.
Genome-Scale Data Reveal Deep Lineage Divergence and a Complex Demographic History in the Texas Horned Lizard (Phrynosoma cornutum) throughout the Southwestern and Central United States.
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基因组规模的数据揭示了整个美国西南部和中部的得克萨斯州角蜥蜴（Phrynosoma cornutum）中的深层差异和复杂的人口统计历史。
DOI：
10.1093/gbe/evab260
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发表时间：
2022-01-04
影响因子：
3.3
通讯作者：
Blair C
中科院分区：
文献类型：
--
作者：
Finger N;Farleigh K;Bracken JT;Leaché AD;François O;Yang Z;Flouri T;Charran T;Jezkova T;Williams DA;Blair C
美国西南部和中部是测试生物多样性替代假设的理想地区。基因组数据现在可以与复杂的计算模型相结合，以量化古气候变化，地理特征和栖息地异质性对遗传多样性空间格局的影响。在这项研究中，我们结合联合收割机成千上万的基因分型测序（GBS）位点与线粒体DNA序列（ND1）从得克萨斯州角蜥（Phrynosoma cornutum），以量化不同的催化剂的多样化的相对支持。GBS数据的系统发育和聚类分析表明支持至少三个主要人群。种群的空间分布与生境类型一致，在AZ和NM的沙漠种群显示出最大的遗传分化，从其余的人口。mtDNA数据也支持一个分歧的沙漠人口，但其他关系不同，并建议mtDNA渐渗。与生物气候变量的基因型环境关联支持分歧沿着降水梯度比沿着温度梯度。人口分析支持一个复杂的历史，与渐渗和基因流动发挥了重要作用，在多样化。贝叶斯多物种结合分析与渐渗（MSCI）分析也表明，种群之间发生的基因流。古物种分布模型支持两个南部避难所，地理上对应于当代血统。我们发现，分歧的时间被低估，人口规模被高估时，渗入发生，并被忽略在结合分析，此外，推断古代渗入事件和人口历史是敏感的，包括一个单一的最近混合的样品。我们的分析不能反驳河流屏障或冰川避难所假说。结果还表明，人口继续分化沿着生境梯度。最后，强有力的证据混合，基因流，和种群之间的mtDNA渐渗表明，P. cornutum应该被认为是一个单一的广泛分布的物种下的一般谱系物种的概念。
The southwestern and central United States serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models to quantify the impacts of paleoclimate change, geographic features, and habitat heterogeneity on spatial patterns of genetic diversity. In this study, we combine thousands of genotyping-by-sequencing (GBS) loci with mtDNA sequences (ND1) from the Texas horned lizard (Phrynosoma cornutum) to quantify relative support for different catalysts of diversification. Phylogenetic and clustering analyses of the GBS data indicate support for at least three primary populations. The spatial distribution of populations appears concordant with habitat type, with desert populations in AZ and NM showing the largest genetic divergence from the remaining populations. The mtDNA data also support a divergent desert population, but other relationships differ and suggest mtDNA introgression. Genotype–environment association with bioclimatic variables supports divergence along precipitation gradients more than along temperature gradients. Demographic analyses support a complex history, with introgression and gene flow playing an important role during diversification. Bayesian multispecies coalescent analyses with introgression (MSci) analyses also suggest that gene flow occurred between populations. Paleo-species distribution models support two southern refugia that geographically correspond to contemporary lineages. We find that divergence times are underestimated and population sizes are overestimated when introgression occurred and is ignored in coalescent analyses, and furthermore, inference of ancient introgression events and demographic history is sensitive to inclusion of a single recently admixed sample. Our analyses cannot refute the riverine barrier or glacial refugia hypotheses. Results also suggest that populations are continuing to diverge along habitat gradients. Finally, the strong evidence of admixture, gene flow, and mtDNA introgression among populations suggests that P. cornutum should be considered a single widespread species under the General Lineage Species Concept.
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影响因子：
3.4
作者：
Bouckaert RR;Drummond AJ
通讯作者：
Drummond AJ
DOI：
10.1198/108571102320
发表时间：
2002-09-01
影响因子：
1.4
作者：
Clarke, RT;Rothery, P;Raybould, AF
通讯作者：
Raybould, AF
影响因子：
10.7
作者：
Coffman, Alec J.;Hsieh, Ping Hsun;Gutenkunst, Ryan N.
通讯作者：
Gutenkunst, Ryan N.
影响因子：
4.6
作者：
Castro-Insua A;Gómez-Rodríguez C;Wiens JJ;Baselga A
通讯作者：
Baselga A
影响因子：
5.8
作者：
Bacon, Christine D.;Molnar, Peter;Camila Vallejo-Pareja, Maria
通讯作者：
Camila Vallejo-Pareja, Maria