Phylogenetic species delimitation unravels a new species in the genus Sclerorhachis (Rech.f.) Rech.f. (Compositae, Anthemideae)

Hassanpour, Hajar; Zare‐Maivan, Hassan; Sonboli, Ali; Osaloo, Shahrokh Kazempour; Wagner, Florian; Tomasello, Salvatore; Oberprieler, Christoph

doi:10.1007/s00606-017-1461-4

Cited by 9 publications

(7 citation statements)

References 64 publications

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“…Species boundaries in Scrophulariaceae were determined following Hassanpour’s methods [ 64 ] using the coalescence-based species delimitation methods implemented in bGMYC [ 65 ] and bPTP [ 66 ]. For the bGMYC analysis, 10,000 random ultrametric trees of the whole chloroplast dataset obtained from the posterior distribution of the BEAST analysis outputs were sampled as an input to integrate over the uncertainty of tree topology.…”

Section: Methodsmentioning

confidence: 99%

Characterization of the Complete Chloroplast Genomes of Buddleja colvilei and B. sessilifolia: Implications for the Taxonomy of Buddleja L.

Cai

et al. 2018

Molecules

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Buddleja colvilei Hook.f. & Thomson (Scrophulariaceae) is a threatened alpine plant with a distribution throughout the Himalayas, also used as an ornamental plant. The name Buddleja sessilifolia B.S. Sun ex S.Y. Pao was assigned in 1983 to a plant distributed throughout the Gaoligong Mountains, but the name was later placed in synonymy with B. colvilei in the Flora of China. In this study we sequenced the complete chloroplast (cp) genomes of two individuals of B. colvilei and three individuals of B. sessilifolia from across the range. Both molecular and morphological analysis support the revision of B. sessilifolia. The phylogenetic analysis constructed with the whole cp genomes, the large single-copy regions (LSC), small single-copy regions (SSC), inverted repeat (IR) and the nuclear genes 18S/ITS1/5.8S/ITS2/28S all supported B. sessilifolia as a distinct species. Additionally, coalescence-based species delimitation methods (bGMYC, bPTP) using the whole chloroplast datasets also supported B. sessilifolia as a distinct species. The results suggest that the B. sessilifolia lineage was early diverging among the Asian Buddleja species. Overall gene contents were similar and gene arrangements were found to be highly conserved in the two species, however, fixed differences were found between the two species. A total of 474 single nucleotide polymorphisms (SNPs) were identified between the two species. The Principal Coordinate Analysis of the morphological characters resolved two groups and supported B. sessilifolia as a distinct species. Discrimination of B. colvilei and B. sessilifolia using morphological characters and the redescription of B. sessilifolia are detailed here.

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Section: Methodsmentioning

confidence: 99%

Characterization of the Complete Chloroplast Genomes of Buddleja colvilei and B. sessilifolia: Implications for the Taxonomy of Buddleja L.

Cai

et al. 2018

Molecules

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“…Different methods capable to infer species delimitation under the coalescent model have been proposed in the last years (Pons & al., 2006; Leliaert & al., 2009; Zhang & al., 2013; Yang & Rannala, 2014; Jones & al., 2015). Although for more than a decade they have been applied to animal, fungal, and algal species complexes, only in the last years these methods have been increasingly employed on plant systems (Hu & al., 2015; Ruiz‐Sanchez, 2015; Toprak & al., 2016; Naciri & al., 2017; Wagner & al., 2017; Hassanpour & al., 2018; Tomasello, 2018).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics supported by geometric morphometrics reveals delimitation of sexual species within the polyploid apomictic Ranunculus auricomus complex (Ranunculaceae)

Karbstein

Tomasello

Hodač

et al. 2020

TAXON

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Species are the basic units of biodiversity and evolution. Nowadays, they are widely considered as ancestor-descendant lineages. Their definition remains a persistent challenge for taxonomists due to lineage evolutionary role and circumscription, i.e., persistence in time and space, ecological niche, or a shared phenotype. Recognizing and delimiting species is particularly methodically challenging in fast-evolving, evolutionary young species complexes often characterized by low genetic divergence, hybrid origin, introgression, and incomplete lineage sorting. Ranunculus auricomus is a large Eurasian apomictic polyploid complex that probably has arisen from the hybridization of a few sexual progenitor species. However, even delimitation of and relationships among diploid sexual progenitors are unclear, ranging from 2 to 12 species. Here, we present an innovative workflow combining phylogenomic methods based on 86,782 parameter-optimized RADseq loci and target enrichment of 663 nuclear genes accompanied by geometric morphometrics to delimit sexual species in this evolutionary young complex (<1 Mya). For the first time, we revealed a fully resolved and well-supported maximum likelihood tree phylogeny congruent to neighbor-net network and STRUCTURE results based on RADseq data. In a few clades, we found evidence of discordant patterns indicated by quartet sampling, and reticulation events in the neighbor-net network probably caused by introgression and incomplete lineage sorting. Together with coalescent-based species delimitation approaches based on target enrichment data, we found five main genetic lineages, with an allopatric distribution in central and southern Europe. A concatenated geometric morphometric dataset including data from basal and stem leaves, as well as receptacles, revealed the same five main clusters. We accept those five morphologically differentiated, geographically isolated, genetic main lineages as species: R.

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“…Different methods capable to infer species delimitation under the coalescent have been proposed in the last years (Pons & al., 2006; Leliaert & al., 2009; Zhang & al., 2013; Yang & Rannala, 2014; Jones & al., 2015). Although for more than a decade they have been applied to animal, fungi and algal species complexes, only in the last years they have been increasingly employed on plant systems (Hu & al., 2015; Ruiz-Sanchez, 2015; Toprak & al., 2016; Naciri & al., 2017; Wagner & al., 2017; Hassanpour & al., 2018; Tomasello, 2018).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics supported by geometric morphometrics reveals delimitation of sexual species within the polyploid apomicticRanunculus auricomuscomplex (Ranunculaceae)

Karbstein

Tomasello

Hodač

et al. 2020

Preprint

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Phylogenetic species delimitation unravels a new species in the genus Sclerorhachis (Rech.f.) Rech.f. (Compositae, Anthemideae)

Cited by 9 publications

References 64 publications

Characterization of the Complete Chloroplast Genomes of Buddleja colvilei and B. sessilifolia: Implications for the Taxonomy of Buddleja L.

Characterization of the Complete Chloroplast Genomes of Buddleja colvilei and B. sessilifolia: Implications for the Taxonomy of Buddleja L.

Phylogenomics supported by geometric morphometrics reveals delimitation of sexual species within the polyploid apomictic Ranunculus auricomus complex (Ranunculaceae)

Phylogenomics supported by geometric morphometrics reveals delimitation of sexual species within the polyploid apomicticRanunculus auricomuscomplex (Ranunculaceae)

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