Integrating coalescent‐based species delimitation with ecological niche modeling delimited two species within theStewartia sinensiscomplex (Theaceae)

Abstract

Accurate species delimitation is the key to precise estimation of species diversity and is fundamental to most branches of biology. Unclear species boundaries within species complexes could lead to the underestimation of species diversity. However, species delimitation of species complexes remains challenging due to the continuum of phenotypic variations. To robustly examine species boundaries within a species complex, integrative approaches in phylogeny, ecology, and morphology were applied to the Stewartia sinensis complex (Theaceae) endemic to China. Multispecies coalescent‐based species delimitation using 572 nuclear ortholog sequences (anchored enrichment) supported reciprocal phylogenetic monophyly of the northern lineage (NL) and southern lineage (SL), which were not sister clades. Niche equivalency and similarity tests demonstrated significant climatic niche differentiation between NL and SL with observed Warren et al.'s I = 0.0073 and Schoener's D = 0.0021. Species distribution modeling also separated their potential distribution. Morphometric analyses suggested significant interlineage differentiation of multiple traits including the ratio of length and width, leaf width, and pedicel length, although overall similarity did not differ. Based on the integrative species concept, two distinct species were proposed with legitimate names of Stewartia gemmata for SL and S. sinensis for NL. Our empirical study of the S. sinensis complex highlights the importance of applying multiple species criteria, in particular the underappreciated niche differentiation, to species delimitation in species complexes pervasive in plants.

Nested singletons in molecular trees: Utility of adding morphological and geographical data from digitized herbarium specimens to test taxon concepts at species level in the case of Casearia (Salicaceae)

“…Moreover, they allow to include the wealth of existing specimens in herbaria. We further observe that phylogenomic analyses increase the resolution within shallow clades, encompassing one to several putative species (Prata et al, 2018 ; Lin et al, 2021 ; Smith et al, 2022 ). However, the delimitation of species, and the subsequent circumscription and naming of taxa, from the background of the molecular topology is usually being done by matching morphological character states to parts of the topology, underscoring the relevance of an integrated taxonomic approach.…”

“…Moreover, they allow to include the wealth of existing specimens in herbaria. We further observe that phylogenomic analyses increase the resolution within shallow clades, encompassing one to several putative species (Prata et al, 2018;Lin et al, 2021;Smith et al, 2022). However, the delimitation of species, and the subse-…”

“…Whereas morphological evidence has been very frequently matched with phylogenetic or phylogeographic trees and networks to illuminate species limits and support species classification (Huang et al, 2016 ; Šmíd et al, 2017 ; Perkins, 2019 ; Yang et al, 2021 ; Andriamihaja et al, 2022 ), the inclusion of ecological data to achieve this goal is more recent (Boucher et al, 2016 ; Duan et al, 2019 ). Recently, various studies have successfully focused on solving species limits with the combined use of molecular analysis, morphometric with PCA or multidimensional scaling analysis (MSA), and ecological niche modeling or niche equivalency or niche similarity tests (Prata et al, 2018 ; Frajman et al, 2019 ; Lin et al, 2021 ). Such investigations typically employ a dedicated study design, including field collection of representative material, to ensure that all specimens can be consistently examined for all kinds of data.…”

The Warps and Wefts of a Polyploidy Complex: Integrative Species Delimitation of the Diploid Leucanthemum (Compositae, Anthemideae) Representatives

“…Both climatological and edaphic variables were incorporated into our analyses on the abiotic ecological niches of the morpho-species of the two Leucanthemum species groups and followed traditional ecological niche modeling (ENM) as proposed by Raxworthy et al [ 40 ]. For niche comparisons, we adopted the niche equivalency tests of Warren et al [ 41 ], whose efficacy for SD has been demonstrated in recent studies (e.g., [ 42 , 43 ]). Our analyses show that the abiotic ecological niches are significantly different for all pairwise comparisons, except for the pair L. vulgare – L. pyrenaicum .…”

Genomics and ecological modelling clarify species integrity in a confusing group of butterflies

“…Species delimitation can be both challenging and inconsistent, particularly when evolutionary lineages are not easily distinguished by morphology and are superficially similar in their ecological associations (Bagley et al, 2015; Chambers & Hillis, 2020; Lin et al, 2021). In light of these challenges, many modern delimitation frameworks have relied on genetic or genomic data to identify discrete evolutionary units and assign species identities to individuals, resulting in phylogenies that are consistent with a variety of species criteria (e.g., genomic integrity, genotypic cluster, or phylogenetic species concepts; Sperling, 2003, and reviews in de Queiroz, 2007; Hausdorf, 2011).…”