A population genetics perspective on the evolutionary histories of three clonal, endemic, and dominant grass species of the Qinghai–Tibet Plateau: Orinus (Poaceae)

Abstract

We performed analyses of amplified fragment length polymorphism (AFLP) in order to characterize the evolutionary history of Orinus according to its population genetic structure, as well as to investigate putative hybrid origins of O. intermedius and to provide additional insights into relationships among species. The genus Orinus comprises three clonal grasses that are dominant species within xeric alpine grasslands of the Qinghai–Tibet Plateau (QTP). Here, we used eight selectively obtained primer pairs of EcoRI/MseI to perform amplifications in 231 individuals of Orinus representing 48 populations and all three species. We compared our resulting data to genetic models of hybridization using a Bayesian algorithm within NewHybrids software. We determined that genetic variation in Orinus was 56.65% within populations while the among‐species component was 30.04% using standard population genetics statistics. Nevertheless, we detected that species of Orinus were clustered into three highly distinct genetic groups corresponding to classic species identities. Our results suggest that there is some introgression among species. Thus, we tested explicit models of hybridization using a Bayesian approach within NewHybrids software. However, O. intermedius likely derives from a common ancestor with O. kokonoricus and is probably not the result of hybrid speciation between O. kokonoricus and O. thoroldii. We suspect that recent isolation of species of Orinus in allopatry via vicariance may explain the patterns in diversity that we observed, and this is corroborated by a Mantel test that showed significant positive correlation between geographic and genetic distance (r = 0.05, p < 0.05). Recent isolation may explain why Orinus differs from many other clonal species by exhibiting the highest diversity within populations rather than among them.

Hybrid Speciation and Introgression Both Underlie the Genetic Structures and Evolutionary Relationships of Three Morphologically Distinct Species of Lilium (Liliaceae) Forming a Hybrid Zone Along an Elevational Gradient

“…Therefore, we tested 25 alternative hypotheses for parental contribution, ranging from none, to the existence of F1 hybrids, to very small contributions from potential donors involving only 5% of loci ( Supplementary File 1 ). Within an analysis, hybridization can be evaluated between only two lineages or species (see also Liu et al, 2019 ). Thus, we performed the tests of the 25 hypotheses on three datasets: a dataset of all sampled accessions of the three species of Lilium , a dataset comprising only LG and LS (in total 49 individuals with population codes LGXn, LGm, LSs, including the putative hybrid LSn) (Hypothesis 1, hereafter), and a third consisting of LG and LM (in total 64 individuals with population codes LMXn, LMXs, LMn, LGs, LGXs) (Hypothesis 2, hereafter).…”

Population genetic structure and evolutionary history of Psammochloa villosa (Trin.) Bor (Poaceae) revealed by AFLP marker

“…The selective amplification was conducted in 25 μl volume of reaction mixture containing of 1.0 μl EcoR I/Mse I primer combinations (AAC/CAA, AAG/CAC, ACA/CAG, ACT/CAT, ACC/CTA, ACG/CTC, AGC/CTG, AGG/CTT; Table 1). Subsequently, we separated the fluorescently-labeled fragments on an ABI PRISM 377 DNA Calibrator (Applied Biosystems) using GeneScan ROX-500 with an internal size standard, allowing visual inspection of all individual sites (Liu, Harris, Gao, Su, & Ren, 2019). We recorded the presence or absence of AFLP amplification bands (Figure S2) in a binary matrix as 1 or 0, respectively, based on interpretations from GeneScan 3.1 (Applied Biosystems).…”

“…We used AFLPs because they remain extremely efficient for investigating genetic diversity, genetic structure, and population demography due to their high levels of polymorphism (Wang, Wang, Liu, Yang, & Chen, 2008), their reproducible, reliable re-sults that are unaffected by the developmental stage of plant materials, and their universality among plant species. In addition, they have been used to resolve genetic structures and population demography in many diverse grass species such as Oryza sativa , Leymus racemosus , Orinus thoroldii and O. kokonoricus (Zhang & Jia, 2002;Sim, 2005;Li, 2015;Cai, 2017;Liu, Harris, Gao, Su, & Ren, 2019). Our main objectives were to (1) analyze the genetic structure from 43 populations of P. villosa from Inner Mongolian Plateau using an AFLP dataset, (2) test whether historical genetic divergence occurred among populations in response to Quaternary climate oscillations, and (3) evaluate the abiotic factors that are most influential in driving the distributions of P. villosa .…”

Population genetic structure and evolutionary history of Psammochloa villosa (Trin.) Bor (Poaceae) revealed by AFLP marker

“…In addition, they have been used to resolve genetic structures and population demography in many diverse grass species such as Oryza sativa, Leymus racemosus, Orinus thoroldii, and O. kokonoricus (Cai et al, 2017;Liu et al, 2019;Zhang & Jia, 2002). Our main objectives were to (1) analyze the genetic structure of P. villosa from the Inner Mongolian Plateau using an AFLP dataset representing 43 populations, (2) test whether historical genetic divergence occurred among populations in response to Quaternary climate oscillations, and (3) evaluate the abiotic factors that are most influential in driving the distributions of P. villosa through time.…”