干旱区生态环境知识资源中心(Arid): Species boundaries in the messy middle-A genome-scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi

Arid

DOI	10.1002/ece3.8467
	Species boundaries in the messy middle-A genome-scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi
	Jorna, Jesse; Linde, Jackson B.; Searle, Peter C.; Jackson, Abigail C.; Nielsen, Mary-Elise; Nate, Madeleine S.; Saxton, Natalie A.; Grewe, Felix; Herrera-Campos, Maria de los Angeles; Spjut, Richard W.; Wu, Huini; Ho, Brian; Lumbsch, H. Thorsten; Leavitt, Steven D.
通讯作者	Leavitt, SD (corresponding author), Brigham Young Univ, Dept Biol, Provo, UT 84602 USA.
来源期刊	ECOLOGY AND EVOLUTION
ISSN	2045-7758
出版年	2021
英文摘要	Species delimitation among closely related species is challenging because traditional phenotype-based approaches, for example, using morphology, ecological, or chemical characteristics, may not coincide with natural groupings. With the advent of high-throughput sequencing, it has become increasingly cost-effective to acquire genome-scale data which can resolve previously ambiguous species boundaries. As the availability of genome-scale data has increased, numerous species delimitation analyses, such as BPP and SNAPP+Bayes factor delimitation (BFD*), have been developed to delimit species boundaries. However, even empirical molecular species delimitation approaches can be biased by confounding evolutionary factors, for example, hybridization/introgression and incomplete lineage sorting, and computational limitations. Here, we investigate species boundaries and the potential for micro-endemism in a lineage of lichen-forming fungi, Niebla Rundel & Bowler, in the family Ramalinaceae by analyzing single-locus and genome-scale data consisting of (a) single-locus species delimitation analysis using ASAP, (b) maximum likelihood-based phylogenetic tree inference, (c) genome-scale species delimitation models, e.g., BPP and SNAPP+BFD, and (d) species validation using the genealogical divergence index (gdi). We specifically use these methods to cross-validate results between genome-scale and single-locus datasets, differently sampled subsets of genomic data and to control for population-level genetic divergence. Our species delimitation models tend to support more speciose groupings that were inconsistent with traditional taxonomy, supporting a hypothesis of micro-endemism, which may include morphologically cryptic species. However, the models did not converge on robust, consistent species delimitations. While the results of our analysis are somewhat ambiguous in terms of species boundaries, they provide a valuable perspective on how to use these empirical species delimitation methods in a nonmodel system. This study thus highlights the challenges inherent in delimiting species, particularly in groups such as Niebla, with complex, relatively recent phylogeographic histories.
英文关键词	Baja California Bayes factor delimitation (BFD*) genealogical divergence index (gdi) RADseq species delimitation
类型	Article
语种	英语
开放获取类型	gold
收录类别	SCI-E
WOS记录号	WOS:000733394300001
WOS关键词	SEQUENCE DATA ; HYBRIDIZATION ; SYSTEMATICS ; ASCOMYCOTA ; INFERENCE ; ALIGNMENT ; FULL ; TREE
WOS类目	Ecology ; Evolutionary Biology
WOS研究方向	Environmental Sciences & Ecology ; Evolutionary Biology
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/374732
作者单位	[Jorna, Jesse; Linde, Jackson B.; Searle, Peter C.; Jackson, Abigail C.; Nielsen, Mary-Elise; Nate, Madeleine S.; Saxton, Natalie A.; Leavitt, Steven D.] Brigham Young Univ, Dept Biol, Provo, UT 84602 USA; [Grewe, Felix; Wu, Huini; Ho, Brian; Lumbsch, H. Thorsten] Grainger Bioinformat Ctr, Sci & Educ, Field Museum, Chicago, IL USA; [Herrera-Campos, Maria de los Angeles] Univ Nacl Autonoma Mexico, Inst Biol, Dept Bot, Mexico City, DF, Mexico; [Spjut, Richard W.] World Bot Associates, Bakersfield, CA USA; [Leavitt, Steven D.] Brigham Young Univ, Monte L Bean Life Sci Museum, Provo, UT 84602 USA
推荐引用方式 GB/T 7714	Jorna, Jesse,Linde, Jackson B.,Searle, Peter C.,et al. Species boundaries in the messy middle-A genome-scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi[J],2021.
APA	Jorna, Jesse.,Linde, Jackson B..,Searle, Peter C..,Jackson, Abigail C..,Nielsen, Mary-Elise.,...&Leavitt, Steven D..(2021).Species boundaries in the messy middle-A genome-scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi.ECOLOGY AND EVOLUTION.
MLA	Jorna, Jesse,et al."Species boundaries in the messy middle-A genome-scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi".ECOLOGY AND EVOLUTION (2021).