干旱区生态环境知识资源中心(Arid): 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

Arid

DOI	10.1093/gbe/evab260
	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
	Finger, Nicholas; Farleigh, Keaka; Bracken, Jason T.; Leache, Adam D.; Francois, Olivier; Yang, Ziheng; Flouri, Tomas; Charran, Tristan; Jezkova, Tereza; Williams, Dean A.; Blair, Christopher
通讯作者	Blair, C (corresponding author)，CUNY, Dept Biol Sci, New York City Coll Technol, Brooklyn, NY 11210 USA. ; Blair, C (corresponding author)，CUNY, Grad Ctr, Biol PhD Program, New York, NY 10016 USA.
来源期刊	GENOME BIOLOGY AND EVOLUTION
ISSN	1759-6653
出版年	2022
卷号	14 期号:1
英文摘要	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.
英文关键词	demography introgression lizards phylogeography speciation
类型	Article
语种	英语
开放获取类型	Green Published, gold
收录类别	SCI-E
WOS记录号	WOS:000747583400006
WOS关键词	MULTISPECIES COALESCENT MODEL ; SPECIES TREE ESTIMATION ; LAST GLACIAL MAXIMUM ; DNA-SEQUENCE DATA ; GENE FLOW ; SECONDARY CONTACT ; R PACKAGE ; NICHE CONSERVATISM ; CLIMATE SURFACES ; DIVERSIFICATION
WOS类目	Evolutionary Biology ; Genetics & Heredity
WOS研究方向	Evolutionary Biology ; Genetics & Heredity
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/376751
作者单位	[Finger, Nicholas; Charran, Tristan; Blair, Christopher] CUNY, Dept Biol Sci, New York City Coll Technol, Brooklyn, NY 11210 USA; [Farleigh, Keaka; Bracken, Jason T.; Jezkova, Tereza] Miami Univ, Dept Biol, Oxford, OH 45056 USA; [Leache, Adam D.] Univ Washington, Dept Biol, Seattle, WA 98195 USA; [Leache, Adam D.] Univ Washington, Burke Museum Nat Hist & Culture, Seattle, WA 98195 USA; [Francois, Olivier] Univ Grenoble Alpes, Fac Med, Grenoble, France; [Yang, Ziheng; Flouri, Tomas] UCL, Dept Genet Evolut & Environm, London, England; [Williams, Dean A.] Texas Christian Univ, Dept Biol, Ft Worth, TX 76129 USA; [Blair, Christopher] CUNY, Grad Ctr, Biol PhD Program, New York, NY 10016 USA
推荐引用方式 GB/T 7714	Finger, Nicholas,Farleigh, Keaka,Bracken, Jason T.,et al. 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[J],2022,14(1).
APA	Finger, Nicholas.,Farleigh, Keaka.,Bracken, Jason T..,Leache, Adam D..,Francois, Olivier.,...&Blair, Christopher.(2022).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 BIOLOGY AND EVOLUTION,14(1).
MLA	Finger, Nicholas,et al."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 BIOLOGY AND EVOLUTION 14.1(2022).