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Yang X, Yan H, Hao C, Hu J, Yang G, An S, Wang L, Ouyang F, Zhang M, Wang J. Climate of origin shapes variations in wood anatomical properties of 17 Picea species. BMC PLANT BIOLOGY 2024; 24:414. [PMID: 38760680 PMCID: PMC11100223 DOI: 10.1186/s12870-024-05103-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 05/05/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Variations in hydraulic conductivity may arise from species-specific differences in the anatomical structure and function of the xylem, reflecting a spectrum of plant strategies along a slow-fast resource economy continuum. Spruce (Picea spp.), a widely distributed and highly adaptable tree species, is crucial in preventing soil erosion and enabling climate regulation. However, a comprehensive understanding of the variability in anatomical traits of stems and their underlying drivers in the Picea genus is currently lacking especially in a common garden. RESULTS We assessed 19 stem economic properties and hydraulic characteristics of 17 Picea species grown in a common garden in Tianshui, Gansu Province, China. Significant interspecific differences in growth and anatomical characteristics were observed among the species. Specifically, xylem hydraulic conductivity (Ks) and hydraulic diameter exhibited a significant negative correlation with the thickness to span ratio (TSR), cell wall ratio, and tracheid density and a significant positive correlation with fiber length, and size of the radial tracheid. PCA revealed that the first two axes accounted for 64.40% of the variance, with PC1 reflecting the trade-off between hydraulic efficiency and mechanical support and PC2 representing the trade-off between high embolism resistance and strong pit flexibility. Regression analysis and structural equation modelling further confirmed that tracheid size positively influenced Ks, whereas the traits DWT, D_r, and TSR have influenced Ks indirectly. All traits failed to show significant phylogenetic associations. Pearson's correlation analysis demonstrated strong correlations between most traits and longitude, with the notable influence of the mean temperature during the driest quarter, annual precipitation, precipitation during the wettest quarter, and aridity index. CONCLUSIONS Our results showed that xylem anatomical traits demonstrated considerable variability across phylogenies, consistent with the pattern of parallel sympatric radiation evolution and global diversity in spruce. By integrating the anatomical structure of the stem xylem as well as environmental factors of origin and evolutionary relationships, our findings provide novel insights into the ecological adaptations of the Picea genus.
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Affiliation(s)
- Xiaowei Yang
- State Key Laboratory of Forest Cultivation, Central South University of Forestry and Technology, Changsha, 410000, People's Republic of China
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Huiling Yan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Chunhui Hao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Jiwen Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Guijuan Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Sanping An
- Gansu Provincial Key Laboratory of Secondary Forest Cultivation, Research Institute of Forestry of Xiaolong Mountain, Tianshui, 741022, People's Republic of China
| | - Lifang Wang
- Gansu Provincial Key Laboratory of Secondary Forest Cultivation, Research Institute of Forestry of Xiaolong Mountain, Tianshui, 741022, People's Republic of China
| | - Fangqun Ouyang
- Beijing Floriculture Engineering Technology Research Centre, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Botanical Garden, Beijing, 100093, China
| | - Miaomiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.
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Blanchard F, Bruneau A, Laliberté E. Foliar spectra accurately distinguish most temperate tree species and show strong phylogenetic signal. AMERICAN JOURNAL OF BOTANY 2024:e16314. [PMID: 38641918 DOI: 10.1002/ajb2.16314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 01/17/2024] [Accepted: 02/02/2024] [Indexed: 04/21/2024]
Abstract
PREMISE Spectroscopy is a powerful remote sensing tool for monitoring plant biodiversity over broad geographic areas. Increasing evidence suggests that foliar spectral reflectance can be used to identify trees at the species level. However, most studies have focused on only a limited number of species at a time, and few studies have explored the underlying phylogenetic structure of leaf spectra. Accurate species identifications are important for reliable estimations of biodiversity from spectral data. METHODS Using over 3500 leaf-level spectral measurements, we evaluated whether foliar reflectance spectra (400-2400 nm) can accurately differentiate most tree species from a regional species pool in eastern North America. We explored relationships between spectral, phylogenetic, and leaf functional trait variation as well as their influence on species classification using a hurdle regression model. RESULTS Spectral reflectance accurately differentiated tree species (κ = 0.736, ±0.005). Foliar spectra showed strong phylogenetic signal, and classification errors from foliar spectra, although present at higher taxonomic levels, were found predominantly between closely related species, often of the same genus. In addition, we find functional and phylogenetic distance broadly control the occurrence and frequency of spectral classification mistakes among species. CONCLUSIONS Our results further support the link between leaf spectral diversity, taxonomic hierarchy, and phylogenetic and functional diversity, and highlight the potential of spectroscopy to remotely sense plant biodiversity and vegetation response to global change.
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Affiliation(s)
- Florence Blanchard
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Anne Bruneau
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Etienne Laliberté
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
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Venette RC, Ambourn A, Aukema BH, Jetton RM, Petrice TR. Hosts and impacts of elongate hemlock scale (Hemiptera: Diaspididae): A critical review. FRONTIERS IN INSECT SCIENCE 2024; 4:1356036. [PMID: 38469337 PMCID: PMC10926514 DOI: 10.3389/finsc.2024.1356036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/22/2024] [Indexed: 03/13/2024]
Abstract
Fiorinia externa Ferris, elongate hemlock scale, was inadvertently introduced to North America from Japan. This insect is particularly problematic on hemlock, Tsuga spp., though it has been reported in association with several other conifers. The evidence that other conifers might be hosts, capable of supporting growing populations of the insect, has not been previously reviewed. Our review confirms that F. externa is an oligophagous pest of members of Pinaceae. Although species of Cupressaceae and Taxaceae have been reported as hosts of F. externa, they seem unable to support population growth of this pest. Evidence of the tree-killing potential of the insect, even on suitable hosts, is remarkably scant. The degree of pest risk posed by F. externa with respect to tree mortality in areas beyond the geographic range of hemlock seems modest, but uncertain.
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Affiliation(s)
- Robert C. Venette
- Northern Research Station, U.S. Department of Agriculture (USDA) Forest Service, St. Paul, MN, United States
| | - Angie Ambourn
- Plant Protection Division, Minnesota Department of Agriculture, St. Paul, MN, United States
| | - Brian H. Aukema
- Department of Entomology, University of Minnesota, St. Paul, MN, United States
| | - Robert M. Jetton
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Toby R. Petrice
- Northern Research Station, U.S. Department of Agriculture (USDA) Forest Service, East Lansing, MI, United States
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4
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Feng M, Zhang A, Nguyen V, Bisht A, Almqvist C, De Veylder L, Carlsbecker A, Melnyk CW. A conserved graft formation process in Norway spruce and Arabidopsis identifies the PAT gene family as central regulators of wound healing. NATURE PLANTS 2024; 10:53-65. [PMID: 38168607 PMCID: PMC10808061 DOI: 10.1038/s41477-023-01568-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 10/23/2023] [Indexed: 01/05/2024]
Abstract
The widespread use of plant grafting enables eudicots and gymnosperms to join with closely related species and grow as one. Gymnosperms have dominated forests for over 200 million years, and despite their economic and ecological relevance, we know little about how they graft. Here we developed a micrografting method in conifers using young tissues that allowed efficient grafting with closely related species and between distantly related genera. Conifer graft junctions rapidly connected vasculature and differentially expressed thousands of genes including auxin and cell-wall-related genes. By comparing these genes to those induced during Arabidopsis thaliana graft formation, we found a common activation of cambium, cell division, phloem and xylem-related genes. A gene regulatory network analysis in Norway spruce (Picea abies) predicted that PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) acted as a core regulator of graft healing. This gene was strongly up-regulated during both spruce and Arabidopsis grafting, and Arabidopsis mutants lacking PAT genes failed to attach tissues or successfully graft. Complementing Arabidopsis PAT mutants with the spruce PAT1 homolog rescued tissue attachment and enhanced callus formation. Together, our data show an ability for young tissues to graft with distantly related species and identifies the PAT gene family as conserved regulators of graft healing and tissue regeneration.
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Affiliation(s)
- Ming Feng
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ai Zhang
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Van Nguyen
- Department of Organismal Biology, Physiological Botany, Evolutionary Biology Centre and Linnean Centre for Plant Biology, Uppsala University, Uppsala, Sweden
| | - Anchal Bisht
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Curt Almqvist
- Skogforsk (The Forestry Research Institute of Sweden), Uppsala Science Park, Uppsala, Sweden
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Annelie Carlsbecker
- Department of Organismal Biology, Physiological Botany, Evolutionary Biology Centre and Linnean Centre for Plant Biology, Uppsala University, Uppsala, Sweden
| | - Charles W Melnyk
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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5
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Barba-Montoya J, Sharma S, Kumar S. Molecular timetrees using relaxed clocks and uncertain phylogenies. FRONTIERS IN BIOINFORMATICS 2023; 3:1225807. [PMID: 37600967 PMCID: PMC10435864 DOI: 10.3389/fbinf.2023.1225807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
A common practice in molecular systematics is to infer phylogeny and then scale it to time by using a relaxed clock method and calibrations. This sequential analysis practice ignores the effect of phylogenetic uncertainty on divergence time estimates and their confidence/credibility intervals. An alternative is to infer phylogeny and times jointly to incorporate phylogenetic errors into molecular dating. We compared the performance of these two alternatives in reconstructing evolutionary timetrees using computer-simulated and empirical datasets. We found sequential and joint analyses to produce similar divergence times and phylogenetic relationships, except for some nodes in particular cases. The joint inference performed better when the phylogeny was not well resolved, situations in which the joint inference should be preferred. However, joint inference can be infeasible for large datasets because available Bayesian methods are computationally burdensome. We present an alternative approach for joint inference that combines the bag of little bootstraps, maximum likelihood, and RelTime approaches for simultaneously inferring evolutionary relationships, divergence times, and confidence intervals, incorporating phylogeny uncertainty. The new method alleviates the high computational burden imposed by Bayesian methods while achieving a similar result.
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Affiliation(s)
- Jose Barba-Montoya
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Sudip Sharma
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
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6
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Kinneberg VB, Lü DS, Peris D, Ravinet M, Skrede I. Introgression between highly divergent fungal sister species. J Evol Biol 2023; 36:1133-1149. [PMID: 37363874 DOI: 10.1111/jeb.14190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Abstract
To understand how species evolve and adapt to changing environments, it is important to study gene flow and introgression due to their influence on speciation and radiation events. Here, we apply a novel experimental system for investigating these mechanisms using natural populations. The system is based on two fungal sister species with morphological and ecological similarities occurring in overlapping habitats. We examined introgression between these species by conducting whole genome sequencing of individuals from populations in North America and Europe. We assessed genome-wide nucleotide divergence and performed crossing experiments to study reproductive barriers. We further used ABBA-BABA statistics together with a network analysis to investigate introgression, and conducted demographic modelling to gain insight into divergence times and introgression events. The results revealed that the species are highly divergent and incompatible in vitro. Despite this, small regions of introgression were scattered throughout the genomes and one introgression event likely involves a ghost population (extant or extinct). This study demonstrates that introgression can be found among divergent species and that population histories can be studied without collections of all the populations involved. Moreover, the experimental system is shown to be a useful tool for research on reproductive isolation in natural populations.
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Affiliation(s)
- Vilde Bruhn Kinneberg
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Evolution and Paleobiology, Natural History Museum, University of Oslo, Oslo, Norway
| | - Dabao Sun Lü
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David Peris
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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7
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Zhao ZY, Tong YP, Jiang W, Zang Y, Xiong J, Li J, Hu JF. Structurally Diverse Triterpene-26-oic Acids as Potential Dual ACL and ACC1 Inhibitors from the Vulnerable Conifer Keteleeria fortunei. JOURNAL OF NATURAL PRODUCTS 2023; 86:1487-1499. [PMID: 37291059 DOI: 10.1021/acs.jnatprod.3c00181] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A preliminary phytochemical investigation on the 90% MeOH extract from the twigs and needles of the vulnerable conifer Keteleeria fortunei led to the isolation and characterization of 17 structurally diverse triterpen-26-oic acids, including nine previously undescribed ones (fortunefuroic acids A-I, 1-9) featuring a rare furoic acid moiety in the lateral chain. Among them, 1-5 are uncommon 9βH-lanostane-type triterpenoic acids. Friedo-rearranged triterpenoids 6 and 7 feature a unique 17,14-friedo-lanostane skeleton, whereas 9 possesses a rare 17,13-friedo-cycloartane-type framework. Their structures and absolute configurations were elucidated by extensive spectroscopic (e.g., detailed 2D NMR) and computational (NMR/ECD) calculations and the modified Mosher's method. In addition, the absolute structure of compound 1 was ascertained by single-crystal X-ray diffraction analyses. Fortunefuroic acids B (2), G (7), and I (9), along with isomangiferolic acid (12) and 3α,27-dihydroxycycloart-24E-en-26-oic acid (14), exhibited dual inhibitory effects against the adenosine triphosphate (ATP)-citrate lyase (ACL, IC50s: 5.7-11.4 μM) and acetyl-CoA carboxylase 1 (ACC1, IC50s: 7.5-10.5 μM), both of which are key enzymes for glycolipid metabolism. The interactions of the bioactive triterpenoids with both enzymes were examined by molecular docking studies. The above findings reveal the important role of protecting plant species diversity in support of chemical diversity and potential sources of new therapeutics for ACL-/ACC1-associated diseases.
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Affiliation(s)
- Ze-Yu Zhao
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang 318000, People's Republic of China
| | - Ying-Peng Tong
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang 318000, People's Republic of China
| | - Wei Jiang
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
- School of Life Science and Technology, Wuhan Polytechnic University, Hubei 430023, People's Republic of China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai 201203, People's Republic of China
| | - Juan Xiong
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai 201203, People's Republic of China
| | - Jin-Feng Hu
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang 318000, People's Republic of China
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Jiang K, Du C, Huang L, Luo J, Liu T, Huang S. Phylotranscriptomics and evolution of key genes for terpene biosynthesis in Pinaceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1114579. [PMID: 36875589 PMCID: PMC9982022 DOI: 10.3389/fpls.2023.1114579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Pinaceae is the largest family of conifers, dominating forest ecosystems and serving as the backbone of northern, temperate and mountain forests. The terpenoid metabolism of conifers is responsive to pests, diseases, and environmental stress. Determining the phylogeny and evolution of terpene synthase genes in Pinaceae may shed light on early adaptive evolution. We used different inference methods and datasets to reconstruct the Pinaceae phylogeny based on our assembled transcriptomes. We identified the final species tree of Pinaceae by comparing and summarizing different phylogenetic trees. The genes encoding terpene synthase (TPS) and cytochrome P450 proteins in Pinaceae showed a trend of expansion compared with those in Cycas. Gene family analysis revealed that the number of TPS genes decreased while the number of P450 genes increased in loblolly pine. Expression profiles showed that TPSs and P450s were mainly expressed in leaf buds and needles, which may be the result of long-term evolution to protect these two vulnerable tissues. Our research provides insights into the phylogeny and evolution of terpene synthase genes in Pinaceae and offers some useful references for the investigation of terpenoids in conifers.
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Affiliation(s)
- Kaibin Jiang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Chengju Du
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Linwang Huang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Jiexian Luo
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Tianyi Liu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Shaowei Huang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
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9
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History cooling events contributed to the endangered status of Pseudotsuga brevifolia endemic to limestone habitats. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
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10
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Costa FP, Schrago CG, Mello B. Assessing the relative performance of fast molecular dating methods for phylogenomic data. BMC Genomics 2022; 23:798. [PMID: 36460948 PMCID: PMC9719170 DOI: 10.1186/s12864-022-09030-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
Abstract
Advances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a computational challenge for molecular dating with Bayesian approaches. Rapid molecular dating methods have been proposed over the last few decades to overcome these issues. However, a comparative evaluation of their relative performance on empirical data sets is lacking. We analyzed 23 empirical phylogenomic datasets to investigate the performance of two commonly employed fast dating methodologies: penalized likelihood (PL), implemented in treePL, and the relative rate framework (RRF), implemented in RelTime. They were compared to Bayesian analyses using the closest possible substitution models and calibration settings. We found that RRF was computationally faster and generally provided node age estimates statistically equivalent to Bayesian divergence times. PL time estimates consistently exhibited low levels of uncertainty. Overall, to approximate Bayesian approaches, RelTime is an efficient method with significantly lower computational demand, being more than 100 times faster than treePL. Thus, to alleviate the computational burden of Bayesian divergence time inference in the era of massive genomic data, molecular dating can be facilitated using the RRF, allowing evolutionary hypotheses to be tested more quickly and efficiently.
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Affiliation(s)
- Fernanda P. Costa
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
| | - Carlos G. Schrago
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
| | - Beatriz Mello
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
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Liu L, Liu Q, Gao T. Genome-wide survey reveals the phylogenomic relationships of Chirolophisjaponicus Herzenstein, 1890 (Stichaeidae, Perciformes). Zookeys 2022; 1129:55-72. [PMID: 36761850 PMCID: PMC9836534 DOI: 10.3897/zookeys.1129.91543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
Fish are the largest vertebrate group, consisting of more than 30 000 species with important ecological and economical value, while less than 3% of fish genomes have been published. Herein, a fish, Chirolophisjaponicus, was sequenced using the next-generation sequencing. Approximately 595.7 megabase pair of the C.japonicus genome was assembled (49 901 contigs with 42.61% GC contents), leading to a prediction of 46 729 protein-coding gene models. A total of 554 136 simple sequence repeats was identified in the whole genome of C.japonicus, and dinucleotide microsatellite motifs were the most abundant, accounting for 59.49%. Phylogenomic analysis of 16 genomes based on the 694 single-copy genes suggests that C.japonicus is closely related with Anarrhichthysocellatus, Cebidichthysviolaceus, and Pholisgunnellus. The results provide more thorough genetic information of C.japonicus and a theoretical basis and reference for further genome-wide analysis.
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Affiliation(s)
- Lu Liu
- Naval Architecture and Port Engineering College, Shandong Jiaotong University, Weihai, ChinaShandong Jiaotong UniversityWeihaiChina
| | - Qi Liu
- Wuhan Onemore-tech Co., Ltd. Wuhan, Hubei, ChinaWuhan Onemore-tech Co., LtdWuhanChina
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, ChinaZhejiang Ocean UniversityZhoushanChina,Zhejiang Provincial Key Laboratory of Mariculture and Enhancement, Zhejiang Marine Fisheries Research Institute, Zhoushan, ChinaZhejiang Marine Fisheries Research InstituteZhoushanChina
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12
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Early Cretaceous Keteleerioxylon Wood in the Songliao Basin, Northeast China, and Its Geographic and Environmental Implications. BIOLOGY 2022; 11:biology11111624. [DOI: 10.3390/biology11111624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
The extant Keteleeria is endemic to east and southeast Asia, while Keteleeria-like trees were widely distributed in the northern hemisphere in Earth’s history. In this paper, we reported a novel wood fossil of Keteleerioxylon changchunense Shi, Sun, Meng et Yu sp. nov., collected from the middle part of the Yingcheng Formation, Yingcheng Coal Mine, Changchun City, Jilin Province, northeast China. The quantitative growth-ring analyses of K. changchunense indicate that it was evergreen with a leaf longevity of 1–3 years, which is consistent with the foliar retention of extant Keteleeria. Its high ring-markedness index (RMI) indicates that the climate seasonality was pronounced during the Early Albian period in the Songliao Basin, northeast China. The fossil records of Keteleeria and closely related taxa indicate that this group might have originated from high latitudes in the northern hemisphere, then spread and migrated southward during the Late Jurassic and Cretaceous periods, gradually decreased in the Cenozoic period, and so far only survives in east and southeast Asia.
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Huang KY, Kan SL, Shen TT, Gong P, Feng YY, Du H, Zhao YP, Wan T, Wang XQ, Ran JH. A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms. Int J Mol Sci 2022; 23:ijms231810844. [PMID: 36142757 PMCID: PMC9505161 DOI: 10.3390/ijms231810844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 12/05/2022] Open
Abstract
Although more than 9100 plant plastomes have been sequenced, RNA editing sites of the whole plastome have been experimentally verified in only approximately 21 species, which seriously hampers the comprehensive evolutionary study of chloroplast RNA editing. We investigated the evolutionary pattern of chloroplast RNA editing sites in 19 species from all 13 families of gymnosperms based on a combination of genomic and transcriptomic data. We found that the chloroplast C-to-U RNA editing sites of gymnosperms shared many common characteristics with those of other land plants, but also exhibited many unique characteristics. In contrast to that noted in angiosperms, the density of RNA editing sites in ndh genes was not the highest in the sampled gymnosperms, and both loss and gain events at editing sites occurred frequently during the evolution of gymnosperms. In addition, GC content and plastomic size were positively correlated with the number of chloroplast RNA editing sites in gymnosperms, suggesting that the increase in GC content could provide more materials for RNA editing and facilitate the evolution of RNA editing in land plants or vice versa. Interestingly, novel G-to-A RNA editing events were commonly found in all sampled gymnosperm species, and G-to-A RNA editing exhibits many different characteristics from C-to-U RNA editing in gymnosperms. This study revealed a comprehensive evolutionary scenario for chloroplast RNA editing sites in gymnosperms, and reported that a novel type of G-to-A RNA editing is prevalent in gymnosperms.
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Affiliation(s)
- Kai-Yuan Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sheng-Long Kan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ting-Ting Shen
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
| | - Pin Gong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuan-Yuan Feng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yun-Peng Zhao
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tao Wan
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
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14
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Phylogeny and evolution of Cupressaceae: Updates on intergeneric relationships and new insights on ancient intergeneric hybridization. Mol Phylogenet Evol 2022; 177:107606. [PMID: 35952837 DOI: 10.1016/j.ympev.2022.107606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/24/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022]
Abstract
After the merger of the former Taxodiaceae and Cupressaceae s.s., currently the conifer family Cupressaceae (sensu lato) comprises seven subfamilies and 32 genera, most of which are important components of temperate and mountainous forests. With the exception of a recently published genus-level phylogeny of gymnosperms inferred from sequence analysis of 790 orthologs, previous phylogenetic studies of Cupressaceae were based mainly on morphological characters or a few molecular markers, and did not completely resolve the intergeneric relationships. In this study, we reconstructed a robust and well-resolved phylogeny of Cupressaceae represented by all 32 genera, using 1944 genes (Orthogroups) generated from transcriptome sequencing. Reticulate evolution analyses detected a possible ancient hybridization that occurred between ancestors of two subclades of Cupressoideae, including Microbiota-Platycladus-Tetraclinis (MPT) and Juniperus-Cupressus-Hesperocyparis-Callitropsis-Xanthocyparis (JCHCX), although both concatenation and coalescent trees are highly supported. Moreover, divergence time estimation and ancestral area reconstruction indicate that Cupressaceae very likely originated in Asia in the Triassic, and geographic isolation caused by continental separation drove the vicariant evolution of the two subfamilies Cupressoideae and Callitroideae in the northern and southern hemispheres, respectively. Evolutionary analyses of some morphological characters suggest that helically arranged linear-acicular leaves and imbricate bract-scale complexes represent ancestral states, and the shift from linear-acicular leaves to scale-like leaves was associated with the shift from helical to decussate arrangement. Our study sheds new light on phylogeny and evolutionary history of Cupressaceae, and strongly suggests that both dichotomous phylogenetic and reticulate evolution analyses be conducted in phylogenomic studies.
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15
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Zhao H, Zhou M, Liu XY, Wu F, Dai YC. Phylogeny, Divergence Time Estimation and Biogeography of the Genus Onnia (Basidiomycota, Hymenochaetaceae). Front Microbiol 2022; 13:907961. [PMID: 35875515 PMCID: PMC9301299 DOI: 10.3389/fmicb.2022.907961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
Species of Onnia are important tree pathogens and play a crucial role in forest ecosystems. The species diversity and distribution of Onnia have been studied, however, its evolutionary history is poorly understood. In this study, we reconstructed the phylogeny of Onnia using internal transcribed spacers (ITS) and large subunit (LSU) rDNA sequence data. Molecular clock analyses developed the divergence times of Onnia based on a dataset (ITS + LSU rDNA + rpb1 + rpb2 + tef1α). Reconstruct Ancestral State in Phylogenies (RASP) was used to reconstruct the historical biogeography for the genus Onnia with a Dispersal Extinction Cladogenesis (DEC) model. Here, we provide a robust phylogeny of Onnia, with a description of a new species, Onnia himalayana from Yunnan Province, China. Molecular clock analyses suggested that the common ancestor of Onnia and Porodaedalea emerged in the Paleogene period with full support and a mean stem age of 56.9 Mya (95% highest posterior density of 35.9–81.6 Mya), and most species occurred in the Neogene period. Biogeographic studies suggest that Asia, especially in the Hengduan-Himalayan region, is probably the ancestral area. Five dispersals and two vicariances indicate that species of Onnia were rapidly diversified. Speciation occurred in the Old World and New World due to geographic separation. This study is the first inference of the divergence times, biogeography, and speciation of the genus Onnia.
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Affiliation(s)
- Heng Zhao
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Meng Zhou
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Fang Wu
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
- *Correspondence: Fang Wu,
| | - Yu-Cheng Dai
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
- Yu-Cheng Dai,
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16
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Yang Y, Ferguson DK, Liu B, Mao KS, Gao LM, Zhang SZ, Wan T, Rushforth K, Zhang ZX. Recent advances on phylogenomics of gymnosperms and a new classification. PLANT DIVERSITY 2022; 44:340-350. [PMID: 35967253 PMCID: PMC9363647 DOI: 10.1016/j.pld.2022.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 05/30/2023]
Abstract
Living gymnosperms comprise four major groups: cycads, Ginkgo, conifers, and gnetophytes. Relationships among/within these lineages have not been fully resolved. Next generation sequencing has made available a large number of sequences, including both plastomes and single-copy nuclear genes, for reconstruction of solid phylogenetic trees. Recent advances in gymnosperm phylogenomic studies have updated our knowledge of gymnosperm systematics. Here, we review major advances of gymnosperm phylogeny over the past 10 years and propose an updated classification of extant gymnosperms. This new classification includes three classes (Cycadopsida, Ginkgoopsida, and Pinopsida), five subclasses (Cycadidae, Ginkgoidae, Cupressidae, Pinidae, and Gnetidae), eight orders (Cycadales, Ginkgoales, Araucariales, Cupressales, Pinales, Ephedrales, Gnetales, and Welwitschiales), 13 families, and 86 genera. We also described six new tribes including Acmopyleae Y. Yang, Austrocedreae Y. Yang, Chamaecyparideae Y. Yang, Microcachrydeae Y. Yang, Papuacedreae Y. Yang, and Prumnopityeae Y. Yang, and made 27 new combinations in the genus Sabina.
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Affiliation(s)
- Yong Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, 159 Longpan Road, Nanjing Forestry University, Nanjing 210037, China
| | | | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Kang-Shan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, China
| | - Shou-Zhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, FairyLake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Tao Wan
- Key Laboratory of Southern Subtropical Plant Diversity, FairyLake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | | | - Zhi-Xiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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17
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Klymiuk AA, Rothwell GW, Stockey RA. A novel cupulate seed plant, Xadzigacalix quatsinoensis gen. et sp. nov., provides new insight into the Mesozoic radiation of gymnosperms. AMERICAN JOURNAL OF BOTANY 2022; 109:966-985. [PMID: 35435244 PMCID: PMC9328379 DOI: 10.1002/ajb2.1853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
PREMISE Anatomically preserved evidence for a novel clade of gymnosperms emphasizes diversity of seed plants immediately prior to the appearance of angiosperm fossils in the paleontological record. METHODS Cupulate seeds from the Early Cretaceous Apple Bay locality (Vancouver Island) are described from serial cellulose acetate peels and three-dimensional reconstruction. Phylogenetic context is assessed through the comparative analysis of gymnosperm seed producing fructifications and maximum parsimony analysis of a revised morphological data set for seed plant phylogeny. RESULTS Xadzigacalix quatsinoensis gen. et sp. nov. is characterized by an orthotropous ovule with an elongated micropyle and complex integument, enclosed within a radial cupule. The micropylar canal is elongated; and the nucellus extends into the micropyle to seal the post pollination ovule. Except at the apex of the micropyle, the seed is completely enclosed by a parenchymatous cupule with ca. 20 axially elongated secretory ducts. The cupulate seed is produced upon a triangular woody stele, consisting of a parenchymatous pith surrounded by radially aligned tracheids. The stele produces three short terete traces that terminate within the base of the cupule as transfusion tissue at the seed chalaza. CONCLUSIONS Organography, vascularization, nature of the integument and nucellus, and configuration of the micropylar canal distinguish Xadzigacalix quatsinoensis from all other gymnosperm clades. Cladistic analyses suggest the new plant may have affinities with gnetophytes or angiosperms. These results are complemented with a critical re-evaluation of ovulate structures for Mesozoic gymnosperms, providing new insight into plant diversity immediately antecedent to the explosive diversification of flowering plants.
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Affiliation(s)
- Ashley A. Klymiuk
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaR3T 2N2Canada
- Gantz Family Collections Center, Field Museum, 1400 S Lake Shore DriveChicagoIL60605USA
| | - Gar W. Rothwell
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331−2902USA
- Department of Environmental and Plant Biology317 Porter Hall, Ohio UniversityAthensOH45701USA
| | - Ruth A. Stockey
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331−2902USA
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18
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Zhang R, Shi XF, Liu PG, Wilson AW, Mueller GM. Host Shift Speciation of the Ectomycorrhizal Genus Suillus (Suillineae, Boletales) and Biogeographic Comparison With Its Host Pinaceae. Front Microbiol 2022; 13:831450. [PMID: 35432238 PMCID: PMC9009389 DOI: 10.3389/fmicb.2022.831450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Suillus is a genus of ectomycorrhizal fungi associated almost exclusively with Pinaceae. Lack of sample collections in East Asia and unresolved basal phylogenetic relationships of the genus are the major obstacles for better understanding the Suillus evolution. A resolved phylogeny of Suillus representing global diversity was achieved by sequencing multiple nuclear ribosomal and protein coding genes and extensive samples collected in East Asia. Fungal fossils are extremely rare, and the Eocene ectomycorrhizal symbiosis (ECM) fossil of Pinus root has been widely used for calibration. This study explored an alternative calibration scenario of the ECM fossil for controversy. Ancestral host associations of Suillus were estimated by maximum likelihood and Bayesian Markov chain Monte Carlo (MCMC) analyses, inferred from current host information from root tips and field observation. Host shift speciation explains the diversification of Suillus major clades. The three basal subgenera of Suillus were inferred to be associated with Larix, and diverged in early Eocene or Upper Cretaceous. In the early Oligocene or Paleocene, subgenus Suillus diverged and switched host to Pinus subgenus Strobus, and then switched to subgenus Pinus four times. Suillus subgenus Douglasii switched host from Larix to Pseudotsuga in Oligocene or Eocene. Increased species diversity occurred in subgenus Suillus after it switched host to Pinus but no associated speciation rate shifts were detected. Ancestral biogeographic distributions of Suillus and Pinaceae were estimated under the Dispersal Extinction Cladogenesis (DEC) model. Ancestral distribution patterns of Suillus and Pinaceae are related but generally discordant. Dispersals between Eurasia and North America explain the prevalence of disjunct Suillus taxa.
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Affiliation(s)
- Rui Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Plant Conservation Science, Chicago Botanic Garden, Glencoe, IL, United States
| | - Xiao-fei Shi
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Plant Conservation Science, Chicago Botanic Garden, Glencoe, IL, United States
| | - Pei-gui Liu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Plant Conservation Science, Chicago Botanic Garden, Glencoe, IL, United States
| | - Andrew W. Wilson
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Sam Mitchel Herbarium of Fungi, Denver Botanic Garden, Denver, CO, United States
| | - Gregory M. Mueller
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
- Plant Conservation Science, Chicago Botanic Garden, Glencoe, IL, United States
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19
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Zhang Q, Zhao L, Folk RA, Zhao JL, Zamora NA, Yang SX, Soltis DE, Soltis PS, Gao LM, Peng H, Yu XQ. Phylotranscriptomics of Theaceae: generic-level relationships, reticulation and whole-genome duplication. ANNALS OF BOTANY 2022; 129:457-471. [PMID: 35037017 PMCID: PMC8944729 DOI: 10.1093/aob/mcac007] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/16/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Theaceae, with three tribes, nine genera and more than 200 species, are of great economic and ecological importance. Recent phylogenetic analyses based on plastomic data resolved the relationships among the three tribes and the intergeneric relationships within two of those tribes. However, generic-level relationships within the largest tribe, Theeae, were not fully resolved. The role of putative whole-genome duplication (WGD) events in the family and possible hybridization events among genera within Theeae also remain to be tested further. METHODS Transcriptomes or low-depth whole-genome sequencing of 57 species of Theaceae, as well as additional plastome sequence data, were generated. Using a dataset of low-copy nuclear genes, we reconstructed phylogenetic relationships using concatenated, species tree and phylogenetic network approaches. We further conducted molecular dating analyses and inferred possible WGD events by examining the distribution of the number of synonymous substitutions per synonymous site (Ks) for paralogues in each species. For plastid protein-coding sequences , phylogenies were reconstructed for comparison with the results obtained from analysis of the nuclear dataset. RESULTS Based on the 610 low-copy nuclear genes (858 606 bp in length) investigated, Stewartieae was resolved as sister to the other two tribes. Within Theeae, the Apterosperma-Laplacea clade grouped with Pyrenaria, leaving Camellia and Polyspora as sister. The estimated ages within Theaceae were largely consistent with previous studies based mainly on plastome data. Two reticulation events within Camellia and one between the common ancestor of Gordonia and Schima were found. All members of the tea family shared two WGD events, an older At-γ and a recent Ad-β; both events were also shared with the outgroups (Diapensiaceae, Pentaphylacaceae, Styracaceae and Symplocaceae). CONCLUSIONS Our analyses using low-copy nuclear genes improved understanding of phylogenetic relationships at the tribal and generic levels previously proposed based on plastome data, but the phylogenetic position of the Apterosperma-Laplacea clade needs more attention. There is no evidence for extensive intergeneric hybridization within Theeae or for a Theaceae-specific WGD event. Land bridges (e.g. the Bering land bridge) during the Late Oligocene may have permitted the intercontinental plant movements that facilitated the putative ancient introgression between the common ancestor of Gordonia and Schima.
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Affiliation(s)
- Qiong Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, MS, USA
| | - Jian-Li Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
| | - Nelson A Zamora
- National Herbarium of Costa Rica (CR), Natural History Department of National Museum of Costa Rica, San José, Costa Rica
| | - Shi-Xiong Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan Lijiang Forest Ecosystem National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, China
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20
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Craig JM, Kumar S, Hedges SB. Limitations of phylogenomic data can drive inferred speciation rate shifts. Mol Biol Evol 2022; 39:6528856. [PMID: 35166841 PMCID: PMC8896619 DOI: 10.1093/molbev/msac038] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Biodiversity analyses of phylogenomic timetrees have produced many high-profile examples of shifts in the rate of speciation across the tree of life. Temporally correlated events in ecology, climate, and biogeography are frequently invoked to explain these rate shifts. In a re-examination of 15 genomic timetrees and 25 major published studies of the pattern of speciation through time, we observed an unexpected correlation between the timing of reported rate shifts and the information content of sequence alignments. Here, we show that the paucity of sequence variation and insufficient species sampling in phylogenomic datasets are the likely drivers of many inferred speciation rate shifts, rather than the proposed biological explanations. Therefore, data limitations can produce predictable but spurious signals of rate shifts even when speciation rates may be similar across taxa and time. Our results suggest that the reliable detection of speciation rate shifts requires the acquisition and assembly of long phylogenomic alignments with near-complete species sampling and accurate estimates of species richness for the clades of study.
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Affiliation(s)
- Jack M Craig
- Center for Biodiversity, Temple University, Philadelphia, United States.,Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, United States.,Department of Biology, Temple University, Philadelphia, United States
| | - Sudhir Kumar
- Center for Biodiversity, Temple University, Philadelphia, United States.,Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, United States.,Department of Biology, Temple University, Philadelphia, United States.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - S Blair Hedges
- Center for Biodiversity, Temple University, Philadelphia, United States.,Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, United States.,Department of Biology, Temple University, Philadelphia, United States
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21
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Wang XW, Jiang JH, Liu SL, Gafforov Y, Zhou LW. Species Diversification of the Coniferous Pathogenic Fungal Genus Coniferiporia (Hymenochaetales, Basidiomycota) in Association with Its Biogeography and Host Plants. PHYTOPATHOLOGY 2022; 112:404-413. [PMID: 34170760 DOI: 10.1094/phyto-05-21-0181-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Coniferiporia, belonging to Hymenochaetaceae and now segregated from Phellinidium, is a wood-inhabiting fungal genus with three species, each having a specific geographic distribution and a strong host specificity as a forest pathogen of coniferous trees. In this study, the species diversity of Coniferiporia is further clarified with the aid of a wider sampling and multilocus-based phylogenetic analysis, which reveals a new species Coniferiporia uzbekistanensis. The molecular clock and ancestral geographic origin analyses indicate that the ancestor of Coniferiporia emerged in one of the Pinaceae and Cupressaceae, then jumped to the other plant family originated in eastern Eurasia 17.01 million years ago (Mya; 95% highest posterior density: 9.46 to 25.86 Mya), and later extended its distribution to western North America, Central Asia, and eastern Europe. Coniferiporia sulphurascens speciated on Pinaceae in eastern Eurasia 8.78 Mya (9.46 to 25.86 Mya) and then extended its distribution to western North America and eastern Europe. Coniferiporia qilianensis and C. uzbekistanensis speciated on Juniperus przewalskii in eastern Eurasia 3.67 Mya (0.36 to 8.02 Mya) and on Juniperus polycarpos in Central Asia 4.35 Mya (0.94 to 8.37 Mya), respectively. The speciation event of Coniferiporia weirii occurred 4.45 Mya (0.77 to 9.33 Mya) right after the emergence of its host, the endemic Cupressaceae species Thuja plicata, and soon after, this fungus evolved to also inhabit another endemic Cupressaceae species Calocedrus decurrens. In summary, this study for the first time unambiguously clarified and timed the adaptive evolutionary event of Coniferiporia in association with its biogeography and host plants.
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Affiliation(s)
- Xue-Wei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji-Hang Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shi-Liang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yusufjon Gafforov
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Laboratory of Mycology, Institute of Botany, Academy of Sciences of the Republic of Uzbekistan, Tashkent 100125, Uzbekistan
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
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22
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Hajhashemi V, Zolfaghari B, Amin P. Anti-nociceptive and anti-inflammatory effects of hydroalcoholic extract and essential oil of Pinus eldarica in animal models. AVICENNA JOURNAL OF PHYTOMEDICINE 2021; 11:494-504. [PMID: 34745921 PMCID: PMC8554284 DOI: 10.22038/ajp.2021.18038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/22/2021] [Accepted: 04/04/2021] [Indexed: 11/06/2022]
Abstract
Objective: Several species of Pinus have shown anti-nociceptive and anti-inflammatory properties. This study was aimed to evaluate anti-nociceptive and anti-inflammatory effects of hydroalcoholic extract of bark and essential oil of leaves of P. eldarica in animal models. Materials and Methods: Hydroalcoholic extract of bark and essential oil of leaves of P. eldarica were prepared and phenolic content and essential oil composition were analyzed using Folin-Ciocalteu method and GC/MS, respectively. Anti-nociceptive effect was assessed using acetic acid, formalin and hot plate tests in male Swiss mice (25-30 g) and for evaluation of anti-inflammatory activity, carrageenan test in male Wistar rats (180-200 g) and croton oil-induced ear edema in male mice, were used. Involvement of opioid, α2-adrenergic, 5-HT3 receptors and adenosine triphosphate (ATP)-dependent K+ channels in pain relief was tested using naloxone, ondansetron, yohimbine and glibenclamide. Results: The total phenolic content of the extract in terms of gallic acid equivalent was 404.9±7.7 mg/g of the extract powder. P. eldarica hydroalcoholic extract (200 and 400 mg/kg) and essential oil (100 and 200 µl/kg) significantly (all, p<0.001) decreased pain behavior in acetic acid and formalin tests but not in hot plate test. The extract and essential oil suppressed edema in carrageenan and croton tests. Glibenclamide partially reversed the anti-nociceptive effect of hydroalcoholic extract while the other antagonists were ineffective. Conclusion: Hydroalcoholic extract of bark and essential oil of leaves of P. eldarica significantly decreased acute and chronic pain as well as inflammation. ATP-dependent K+ channels mediate a part of the observed anti-nociceptive effect.
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Affiliation(s)
- Valiollah Hajhashemi
- Department of Pharmacology and Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Behzad Zolfaghari
- Department of Pharmacognosy, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Pooya Amin
- Department of Pharmacology and Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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Sharma S, Kumar S. Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps. NATURE COMPUTATIONAL SCIENCE 2021; 1:573-577. [PMID: 34734192 PMCID: PMC8560003 DOI: 10.1038/s43588-021-00129-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/13/2021] [Indexed: 12/30/2022]
Abstract
Felsenstein's bootstrap approach is widely used to assess confidence in species relationships inferred from multiple sequence alignments. It resamples sites randomly with replacement to build alignment replicates of the same size as the original alignment and infers a phylogeny from each replicate dataset. The proportion of phylogenies recovering the same grouping of species is its bootstrap confidence limit. But, standard bootstrap imposes a high computational burden in applications involving long sequence alignments. Here, we introduce the bag of little bootstraps approach to phylogenetics, bootstrapping only a few little samples, each containing a small subset of sites. We report that the median bagging of bootstrap confidence limits from little samples produces confidence in inferred species relationships similar to standard bootstrap but in a fraction of computational time and memory. Therefore, the little bootstraps approach can potentially enhance the rigor, efficiency, and parallelization of big data phylogenomic analyses.
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Affiliation(s)
- Sudip Sharma
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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24
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Kong H, Condamine FL, Yang L, Harris AJ, Feng C, Wen F, Kang M. Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene. Syst Biol 2021; 71:589-609. [PMID: 34396416 PMCID: PMC9016594 DOI: 10.1093/sysbio/syab068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 12/02/2022] Open
Abstract
Mountain systems harbor a substantial fraction of global biodiversity and, thus, provide excellent opportunities to study rapid diversification and to understand the historical processes underlying the assembly of biodiversity hotspots. The rich biodiversity in mountains is widely regarded as having arisen under the influence of geological and climatic processes as well as the complex interactions among them. However, the relative contribution of geology and climate in driving species radiation is seldom explored. Here, we studied the evolutionary radiation of Oreocharis (Gesneriaceae), which has diversified extensively throughout East Asia, especially within the Hengduan Mountains (HDM), using transcriptomic data and a time calibrated phylogeny for 88% (111/126) of all species of the genus. In particular, we applied phylogenetic reconstructions to evaluate the extent of incomplete lineage sorting accompanying the early and rapid radiation in the genus. We then fit macroevolutionary models to explore its spatial and diversification dynamics in Oreocharis and applied explicit birth–death models to investigate the effects of past environmental changes on its diversification. Evidence from 574 orthologous loci suggest that Oreocharis underwent an impressive early burst of speciation starting ca. 12 Ma in the Miocene, followed by a drastic decline in speciation toward the present. Although we found no evidence for a shift in diversification rate across the phylogeny of Oreocharis, we showed a difference in diversification dynamics between the HDM and non-HDM lineages, with higher diversification rates in the HDM. The diversification dynamic of Oreocharis is most likely positively associated with temperature-dependent speciation and dependency on the Asian monsoons. We suggest that the warm and humid climate of the mid-Miocene was probably the primary driver of the rapid diversification in Oreocharis, while mountain building of the HDM might have indirectly affected species diversification of the HDM lineage. This study highlights the importance of past climatic changes, combined with mountain building, in creating strong environmental heterogeneity and driving diversification of mountain plants, and suggests that the biodiversity in the HDM cannot directly be attributed to mountain uplift, contrary to many recent speculations.[East Asian monsoons; environmental heterogeneity; Hengduan Mountains; incomplete lineage sorting; Oreocharis; past climate change; rapid diversification; transcriptome.]
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Affiliation(s)
- Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
| | - Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
| | - Fang Wen
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, 541006 Guilin, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, 510650 Guangzhou, China
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Herrera F, Shi G, Bickner MA, Ichinnorov N, Leslie AB, Crane PR, Herendeen PS. Early Cretaceous abietoid Pinaceae from Mongolia and the history of seed scale shedding. AMERICAN JOURNAL OF BOTANY 2021; 108:1483-1499. [PMID: 34458982 DOI: 10.1002/ajb2.1713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/10/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Seed cones of extant Pinaceae exhibit two mechanisms of seed release. In "flexers" the cone scales remain attached to the central axis, while flexing and separating from each other to release the seeds. In "shedders" scales are shed from the axis, with the seeds either remaining attached to the scale or becoming detached. The early fossil history of Pinaceae from the Jurassic to Early Cretaceous is dominated by flexing seed cones, while the systematic information provided by shedding fossil cones has been overlooked and rarely integrated with data based on compression and permineralized specimens. We describe the earliest and best-documented evidence of a "shedder" seed cone from the Aptian-Albian of Mongolia. METHODS Lignite samples from Tevshiin Govi locality were disaggregated in water, washed, and dried in air. Fossils were compared to material of extant Pinaceae using LM and CT scans. RESULTS Lepidocasus mellonae gen. et sp. nov. is characterized by a seed cone that disarticulated at maturity and shed obovate bract-scale complexes that have a distinctive ribbed surface and an abaxial surface covered with abundant trichomes. The ovuliferous scale has ca. 30-40 resin canals, but only scarce xylem near the attachment to the cone axis. Resin vesicles are present in the seed integument. Phylogenetic analysis places Lepidocasus as sister to extant Cedrus within the abietoid grade. CONCLUSIONS The exquisite preservation of the trichomes in L. mellonae raises questions about their potential ecological function in the cones of fossil and living Pinaceae. Lepidocasus mellonae also shows that a shedding dispersal syndrome, a feature that has often been overlooked, evolved early in the history of Pinaceae during the Early Cretaceous.
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Affiliation(s)
| | - Gongle Shi
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, 210008, China
| | | | - Niiden Ichinnorov
- Institute of Paleontology, Mongolian Academy of Sciences, Ulaanbaatar-15160, Mongolia
| | - Andrew B Leslie
- Department of Geological Sciences, Stanford University, California, 94305, USA
| | - Peter R Crane
- Oak Spring Garden Foundation, Oak Spring, Upperville, Virginia, 20184, USA
- Yale School of the Environment, Yale University, New Haven, Connecticut, 06511, USA
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Kan SL, Shen TT, Ran JH, Wang XQ. Both Conifer II and Gnetales are characterized by a high frequency of ancient mitochondrial gene transfer to the nuclear genome. BMC Biol 2021; 19:146. [PMID: 34320951 PMCID: PMC8317393 DOI: 10.1186/s12915-021-01096-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial gene transfer/loss is common in land plants, and therefore the fate of missing mitochondrial genes has attracted more and more attention. The gene content of gymnosperm mitochondria varies greatly, supplying a system for studying the evolutionary fate of missing mitochondrial genes. RESULTS Here, we studied the tempo and pattern of mitochondrial gene transfer/loss in gymnosperms represented by all 13 families, using high-throughput sequencing of both DNA and cDNA. All 41 mitochondrial protein-coding genes were found in cycads, Ginkgo and Pinaceae, whereas multiple mitochondrial genes were absent in Conifer II and Gnetales. In Conifer II, gene transfer from mitochondria to the nucleus followed by loss of the mitochondrial copy was common, but complete loss of a gene in both mitochondrial and nuclear genomes was rare. In contrast, both gene transfer and loss were commonly found in Gnetales. Notably, in Conifer II and Gnetales, the same five mitochondrial genes were transferred to the nuclear genome, and these gene transfer events occurred, respectively, in ancestors of the two lineages. A two-step transfer mechanism (retroprocessing and subsequent DNA-mediated gene transfer) may be responsible for mitochondrial gene transfer in Conifer II and Gnetales. Moreover, the mitochondrial gene content variation is correlated with gene length, GC content, hydrophobicity, and nucleotide substitution rates in land plants. CONCLUSIONS This study reveals a complete evolutionary scenario for variations of mitochondrial gene transferring in gymnosperms, and the factors responsible for mitochondrial gene content variation in land plants.
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Affiliation(s)
- Sheng-Long Kan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ting-Ting Shen
- School of Earth Sciences, East China University of Technology, Nanchang, 330013, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines. Proc Natl Acad Sci U S A 2021; 118:2022302118. [PMID: 33941644 PMCID: PMC8157994 DOI: 10.1073/pnas.2022302118] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
How coniferous forests evolved in the Northern Hemisphere remains largely unknown. Unlike most groups of organisms that generally follow a latitudinal diversity gradient, most conifer species in the Northern Hemisphere are distributed in mountainous areas at middle latitudes. It is of great interest to know whether the midlatitude region has been an evolutionary cradle or museum for conifers and how evolutionary and ecological factors have driven their spatiotemporal evolution. Here, we investigated the macroevolution of Pinus, the largest conifer genus and characteristic of northern temperate coniferous forests, based on nearly complete species sampling. Using 1,662 genes from transcriptome sequences, we reconstructed a robust species phylogeny and reestimated divergence times of global pines. We found that ∼90% of extant pine species originated in the Miocene in sharp contrast to the ancient origin of Pinus, indicating a Neogene rediversification. Surprisingly, species at middle latitudes are much older than those at other latitudes. This finding, coupled with net diversification rate analysis, indicates that the midlatitude region has provided an evolutionary museum for global pines. Analyses of 31 environmental variables, together with a comparison of evolutionary rates of niche and phenotypic traits with a net diversification rate, found that topography played a primary role in pine diversification, and the aridity index was decisive for the niche rate shift. Moreover, fire has forced diversification and adaptive evolution of Pinus Our study highlights the importance of integrating phylogenomic and ecological approaches to address evolution of biological groups at the global scale.
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Liquid and Vapor Phase of Four Conifer-Derived Essential Oils: Comparison of Chemical Compositions and Antimicrobial and Antioxidant Properties. Pharmaceuticals (Basel) 2021; 14:ph14020134. [PMID: 33567501 PMCID: PMC7914598 DOI: 10.3390/ph14020134] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 01/07/2023] Open
Abstract
In this study, the chemical composition of the vapor and liquid phase of Pinus cembra L., Pinus mugo Turra, Picea abies L., and Abies Alba M. needles essential oils (EOs) was investigated by Headspace-Gas Chromatography/Mass Spectrometry (HS-GC/MS). In the examined EOs, a total of twenty-eight components were identified, most of which belong to the monoterpenes family. α-Pinene (16.6-44.0%), β-pinene (7.5-44.7%), limonene (9.5-32.5%), and γ-terpinene (0.3-19.7%) were the most abundant components of the liquid phase. Such major compounds were also detected in the vapor phase of all EOs, and α-pinene reached higher relative percentages than in the liquid phase. Then, both the liquid and vapor phases were evaluated in terms of antibacterial activity against three Gram-negative bacteria (Escherichia coli, Pseudomonas fluorescens, and Acinetobacter bohemicus) and two Gram-positive bacteria (Kocuria marina and Bacillus cereus) using a microwell dilution assay, disc diffusion assay, and vapor phase test. The lowest Minimum Inhibitory Concentration (MIC) (13.28 mg/mL) and Minimal Bactericidal Concentration (MBC) (26.56 mg/mL) values, which correspond to the highest antibacterial activities, were reported for P. abies EO against A. bohemicus and for A. alba EO against A. bohemicus and B. cereus. The vapor phase of all the tested EOs was more active than liquid phase, showing the inhibition halos from 41.00 ± 10.15 mm to 80.00 ± 0.00 mm for three bacterial strains (A. bohemicus, K. marina, and B. cereus). Furthermore, antioxidant activities were also investigated by 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azinobis (3- ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) assays, and a concentration-dependent antioxidant capacity for all EOs was found. P. mugo EO showed the best antioxidant activity than the other Pinaceae EOs. The four Pinaceae EOs could be further investigated for their promising antibacterial and antioxidant properties, and, in particular, α-pinene seems to have interesting possibilities for use as a novel natural antibacterial agent.
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Meng R, Luo LY, Zhang JY, Zhang DG, Nie ZL, Meng Y. The Deep Evolutionary Relationships of the Morphologically Heterogeneous Nolinoideae (Asparagaceae) Revealed by Transcriptome Data. FRONTIERS IN PLANT SCIENCE 2021; 11:584981. [PMID: 33519845 PMCID: PMC7840527 DOI: 10.3389/fpls.2020.584981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
The subfamily Nolinoideae of Asparagaceae is an extremely morphologically heterogeneous group, which is comprised of seven lineages, formerly known as Eriospermaceae, Polygonateae, Ophiopogoneae, Convallarieae, Ruscaceae s.s., Dracaenaceae, and Nolinaceae from different families or even orders. Their drastically divergent morphologies and low level of molecular resolution have hindered our understanding on their evolutionary history. To resolve reliable and clear phylogenetic relationships of the Nolinoideae, a phylogenetic study was conducted based on transcriptomic sequencing of 15 species representing all the seven lineages. A dataset containing up to 2,850,331 sites across 2,126 genes was analyzed using both concatenated and coalescent methods. Except for Eriospermum as outgroup, the transcriptomic data strongly resolved the remaining six lineages into two groups, one is a paraphyletic grade including the woody lineages of dracaenoids, ruscoids, and nolinoids and a monophyletic herbaceous clade. Within the herbaceous group, the Ophiopogoneae + Theropogon is sister to a clade that is composed of Convallarieae and the monophyletic Polygonateae. Our work provides a first robust deep relationship of the highly heterogeneous Nolinoideae and paves the way for further investigations of its complex evolution.
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Feng YY, Shen TT, Shao CC, Du H, Ran JH, Wang XQ. Phylotranscriptomics reveals the complex evolutionary and biogeographic history of the genus Tsuga with an East Asian-North American disjunct distribution. Mol Phylogenet Evol 2020; 157:107066. [PMID: 33387645 DOI: 10.1016/j.ympev.2020.107066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/26/2020] [Accepted: 12/24/2020] [Indexed: 12/27/2022]
Abstract
The disjunct distribution between East Asia and North America is one of the best established biogeographic patterns. A robust phylogeny is fundamental for understanding the biogeographic histories of taxa with this distribution pattern. Tsuga (hemlock) is a genus of Pinaceae with a typical intercontinental disjunct distribution in East Asia and eastern and western North America, and its phylogeny has not been completely reconstructed in previous studies. In this study, we reconstructed a highly resolved phylogeny of Tsuga using 881 nuclear genes, 60 chloroplast genes and 23 mitochondrial genes and explored its biogeographic and reticulate evolutionary history. The results of phylogenetic analysis, molecular dating and ancestral area reconstruction indicate that Tsuga very likely originated from North America in the late Oligocene and dispersed from America to East Asia via the Bering Land Bridge during the middle Miocene. In particular, we found complex reticulate evolutionary pattern among the East Asian hemlock species. T. sieboldii possibly originated from hybridization with the ancestor of T. chinensis from mainland China and T. forrestii as the paternal donor and the ancestor of T. diversifolia and T. ulleungensis as the maternal donor. T. chinensis (Taiwan) could have originated by hybridization together with T. sieboldii and then evolved independently after dispersal to the Taiwan Island, subsequently experiencing mitochondrial DNA introgression with T. chinensis from mainland China. Moreover, our study found that T. chinensis from western China is more closely related to T. forrestii than to T. chinensis from eastern China. The nonmonophyletic T. chinensis needs taxonomic reconsideration.
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Affiliation(s)
- Yuan-Yuan Feng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting-Ting Shen
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
| | - Cheng-Cheng Shao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hong Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Wu H, Yu Q, Ran JH, Wang XQ. Unbiased Subgenome Evolution in Allotetraploid Species of Ephedra and Its Implications for the Evolution of Large Genomes in Gymnosperms. Genome Biol Evol 2020; 13:5983329. [PMID: 33196777 PMCID: PMC7900875 DOI: 10.1093/gbe/evaa236] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2020] [Indexed: 12/22/2022] Open
Abstract
The evolutionary dynamics of polyploid genomes and consequences of polyploidy have been studied extensively in angiosperms but very rarely in gymnosperms. The gymnospermous genus Ephedra is characterized by a high frequency of polyploidy, and thus provides an ideal system to investigate the evolutionary mode of allopolyploid genomes and test whether subgenome dominance has occurred in gymnosperms. Here, we sequenced transcriptomes of two allotetraploid species of Ephedra and their putative diploid progenitors, identified expressed homeologs, and analyzed alternative splicing and homeolog expression based on PacBio Iso-Seq and Illumina RNA-seq data. We found that the two subgenomes of the allotetraploids had similar numbers of expressed homeologs, similar percentages of homeologs with dominant expression, and approximately equal numbers of isoforms with alternative splicing, showing an unbiased subgenome evolution as in a few polyploid angiosperms, with a divergence of the two subgenomes at ∼8 Ma. In addition, the nuclear DNA content of the allotetraploid species is almost equal to the sum of two putative progenitors, suggesting limited genome restructuring after allotetraploid speciation. The allopolyploid species of Ephedra might have undergone slow diploidization, and the unbiased subgenome evolution implies that the formation of large genomes in gymnosperms could be attributed to even and slow fractionation following polyploidization.
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Affiliation(s)
- Hui Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Qiong Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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Fan D, Wang X, Zhang W, Zhang X, Zhang S, Xie Z. Does Cathaya argyrophylla, an ancient and threatened Pinaceae species endemic to China, show eco-physiological outliers to its Pinaceae relatives? CONSERVATION PHYSIOLOGY 2020; 8:coaa094. [PMID: 33093958 PMCID: PMC7566968 DOI: 10.1093/conphys/coaa094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 09/08/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
Cathaya argyrophylla is an ancient and threatened Pinaceae species endemic to China, but its eco-physiological traits are rarely reported. We hypothesized that Cathaya showed eco-physiological outliers to its Pinaceae relatives, which lead to its current endangered status. Here we collected the photosynthetic capacity (P n, maximum photosynthesis rate) and branchlet hydraulic safety (P 50, the water potential at which a 50% loss in conductivity occurs) of Pinaceae species globally, including our measurements on Cathaya. We applied the phylogenetic comparative methods to investigate: (i) the phylogenetic signal of the two key traits across Pinaceae species, and (ii) the trait-climate relationships and the photosynthesis-cavitation resistance relationship across Pinaceae species. We applied the polygenetic quantile regression (PQR) method to assess whether Cathaya showed eco-physiological outliers to its Pinaceae relatives in terms of cavitation resistance and photosynthetic capacity. It was found that P 50, and to a less extent, P n, had a strong phylogenetic signal consistent with niche conservation among Pinaceae species. Hydraulic safety largely determined non-threatened Pinaceae species' distribution across moisture gradients at the global scale. There was also an adaptive trade-off relationship between P n and P 50. Cathaya is a high cavitation resistant, low photosynthetic capacity species. It showed eco-physiological outliers to its Pinaceae relatives because it had lower P 50 and P n below the 10% quantile boundaries along moisture and/or temperature gradients; also, it was above the 90% quantile boundary of the P n and P 50 relationship across non-endangered Pinaceae species. The PQR output demonstrated that in the subtropical area of China characterized by abundant rainfall, Cathaya has extra high hydraulic safety, suggesting inefficiency of carbon economy associated with either competition or other life history strategies, which lead to its current endangered status.
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Affiliation(s)
- Dayong Fan
- College of Forestry, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Xiangping Wang
- College of Forestry, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Wangfeng Zhang
- The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Corps, Shihezi University, No. 221, Beisi Road, Shihezi 832000, China
| | - Xiangying Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, No. 20, Xiangshan Nanxin Cun, Haidian District, Beijing 100093, China
| | - Shouren Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, No. 20, Xiangshan Nanxin Cun, Haidian District, Beijing 100093, China
| | - Zongqiang Xie
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, No. 20, Xiangshan Nanxin Cun, Haidian District, Beijing 100093, China
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Du H, Ran JH, Feng YY, Wang XQ. The flattened and needlelike leaves of the pine family (Pinaceae) share a conserved genetic network for adaxial-abaxial polarity but have diverged for photosynthetic adaptation. BMC Evol Biol 2020; 20:131. [PMID: 33028198 PMCID: PMC7542717 DOI: 10.1186/s12862-020-01694-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/21/2020] [Indexed: 11/10/2022] Open
Abstract
Background Leaves have highly diverse morphologies. However, with an evolutionary history of approximately 200 million years, leaves of the pine family are relatively monotonous and often collectively called “needles”, although they vary in length, width and cross-section shapes. It would be of great interest to determine whether Pinaceae leaves share similar morpho-physiological features and even consistent developmental and adaptive mechanisms. Results Based on a detailed morpho-anatomical study of leaves from all 11 Pinaceae genera, we particularly investigated the expression patterns of adaxial-abaxial polarity genes in two types of leaves (needlelike and flattened) and compared their photosynthetic capacities. We found that the two types of leaves share conserved spatial patterning of vasculatures and genetic networks for adaxial-abaxial polarity, although they display different anatomical structures in the mesophyll tissue differentiation and distribution direction. In addition, the species with needlelike leaves exhibited better photosynthetic capacity than the species with flattened leaves. Conclusions Our study provides the first evidence for the existence of a conserved genetic module controlling adaxial-abaxial polarity in the development of different Pinaceae leaves.
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Affiliation(s)
- Hong Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan-Yuan Feng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Phylogeny and highland adaptation of Chinese species in Allium section Daghestanica (Amaryllidaceae) revealed by transcriptome sequencing. Mol Phylogenet Evol 2020; 146:106737. [PMID: 31982455 DOI: 10.1016/j.ympev.2020.106737] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 01/27/2023]
Abstract
Allium L. is one of the largest monocotyledonous genera with extensive distribution in the Northern Hemisphere. The fundamental phylogenies of Allium have been investigated using many morphological and molecular characters. However, the morphological characters may not agree with the molecular results in some Allium groups or sections (such as the Chinese Allium section Daghestanica), which may result in ambiguous species relationships and hinder further evolutionary and adaptive researches. Here, transcriptome sequences of the six Chinese endemics from Allium section Daghestanica were collected, with their single-copy genes (SCGs) were extracted. The interspecies relationships were analyzed using concatenation and coalescent methods. The branch-site model (BSM) was conducted to detect the positively selected genes (PSGs) in five highland species of this section. Based on 1644, 1281 and 1580 SCGs in flowers, leaves, and flowers-leaves combination respectively, a robust consistent and well-resolved phylogeny was generated from the concatenation method. Strong conflicts among individual gene trees were detected in the coalescent method, and morphological characters were incongruent with molecular relationships to some degree. Many PSGs were involved in responses of various stresses and stimuli (e.g. hypoxia, low temperature, aridity), DNA repair, metabolism, nutrient or energy intake, photosynthesis, and signal transduction. Our study revealed a clear interspecies relationship of Chinese endemics in Allium section Daghestanica and suggested that the discordance between morphological characters and molecular relationships might result from that the former are more susceptible to convergence compared with the latter. PSGs detected in our study may provide some insights into highland adaptation in Allium species.
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Herrera F, Shi G, Mays C, Ichinnorov N, Takahashi M, Bevitt JJ, Herendeen PS, Crane PR. Reconstructing Krassilovia mongolica supports recognition of a new and unusual group of Mesozoic conifers. PLoS One 2020; 15:e0226779. [PMID: 31940374 PMCID: PMC6961850 DOI: 10.1371/journal.pone.0226779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/03/2019] [Indexed: 11/19/2022] Open
Abstract
Previously unrecognized anatomical features of the cone scales of the enigmatic Early Cretaceous conifer Krassilovia mongolica include the presence of transversely oriented paracytic stomata, which is unusual for all other extinct and extant conifers. Identical stomata are present on co-occurring broad, linear, multiveined leaves assigned to Podozamites harrisii, providing evidence that K. mongolica and P. harrisii are the seed cones and leaves of the same extinct plant. Phylogenetic analyses of the relationships of the reconstructed Krassilovia plant place it in an informal clade that we name the Krassilovia Clade, which also includes Swedenborgia cryptomerioides-Podozamites schenkii, and Cycadocarpidium erdmanni-Podozamites schenkii. All three of these plants have linear leaves that are relatively broad compared to most living conifers, and that are also multiveined with transversely oriented paracytic stomata. We propose that these may be general features of the Krassilovia Clade. Paracytic stomata, and other features of this new group, recall features of extant and fossil Gnetales, raising questions about the phylogenetic homogeneity of the conifer clade similar to those raised by phylogenetic analyses of molecular data.
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Affiliation(s)
- Fabiany Herrera
- Chicago Botanic Garden, Glencoe, Illinois, United States of America
| | - Gongle Shi
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, People’s Republic of China
| | - Chris Mays
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
- School of Earth, Atmosphere and Environment, Monash University, Clayton, Victoria, Australia
| | - Niiden Ichinnorov
- Institute of Paleontology and Geology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Masamichi Takahashi
- Department of Environmental Sciences, Faculty of Science, Niigata University, Nishi-ku, Niigata, Japan
| | - Joseph J. Bevitt
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, New South Wales, Australia
| | | | - Peter R. Crane
- Oak Spring Garden Foundation, Upperville, Virginia, United States of America
- School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut, United States of America
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Shen TT, Ran JH, Wang XQ. Phylogenomics disentangles the evolutionary history of spruces (Picea) in the Qinghai-Tibetan Plateau: Implications for the design of population genetic studies and species delimitation of conifers. Mol Phylogenet Evol 2019; 141:106612. [DOI: 10.1016/j.ympev.2019.106612] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 12/13/2022]
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Shao CC, Shen TT, Jin WT, Mao HJ, Ran JH, Wang XQ. Phylotranscriptomics resolves interspecific relationships and indicates multiple historical out-of-North America dispersals through the Bering Land Bridge for the genus Picea (Pinaceae). Mol Phylogenet Evol 2019; 141:106610. [DOI: 10.1016/j.ympev.2019.106610] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/30/2019] [Accepted: 09/05/2019] [Indexed: 01/21/2023]
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Li Y, Zhang C, Zhang M, Li Y, Wang X, Duan Y. The complete chloroplast genome sequence of Keteleeria fortunei (Pinaceae). Mitochondrial DNA B Resour 2019; 4:3157-3158. [PMID: 33365897 PMCID: PMC7706782 DOI: 10.1080/23802359.2019.1667896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/16/2019] [Indexed: 10/26/2022] Open
Abstract
Here, the complete chloroplast genome of Keteleeria fortunei, a vulnerable species in China, was sequenced by next-generation sequencing platform. Its circular genome was 117,183 bp in length and the GC content was 38.5%. A total of 101 genes were annotated, including 4 rRNA genes, 20 tRNA genes, and 71 protein coding genes. This study would further our understanding of the genomics and the conservation and utilization of K. fortunei.
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Affiliation(s)
- Yuanyuan Li
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Cheng Zhang
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Min Zhang
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yongfu Li
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xianrong Wang
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yifan Duan
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
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Discovery of Rhizopogon associated with Larix from northeastern Siberia: Insights into host shift of ectomycorrhizal fungi. MYCOSCIENCE 2019. [DOI: 10.1016/j.myc.2019.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Lu M, Hodgins KA, Degner JC, Yeaman S. Purifying selection does not drive signatures of convergent local adaptation of lodgepole pine and interior spruce. BMC Evol Biol 2019; 19:110. [PMID: 31138118 PMCID: PMC6537219 DOI: 10.1186/s12862-019-1438-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lodgepole pine (Pinus contorta) and interior spruce (Picea glauca, Picea engelmannii, and their hybrids) are distantly related conifer species. Previous studies identified 47 genes containing variants associated with environmental variables in both species, providing evidence of convergent local adaptation. However, if the intensity of purifying selection varies with the environment, clines in nucleotide diversity could evolve through linked (background) selection that would yield allele frequency-environment signatures resembling local adaptation. If similar geographic patterns in the strength of purifying selection occur in these species, this could result in the convergent signatures of local adaptation, especially if the landscape of recombination is conserved. In the present study, we investigated whether spatially/environmentally varying purifying selection could give rise to the convergent signatures of local adaptation that had previously reported. RESULTS We analyzed 86 lodgepole pine and 50 interior spruce natural populations spanning heterogeneous environments in western Canada where previous analyses had found signatures of convergent local adaptation. We estimated nucleotide diversity and Tajima's D for each gene within each population and calculated the strength of correlations between nucleotide diversity and environmental variables. Overall, these estimates in the genes with previously identified convergent local adaptation signatures had no similar pattern between pine and spruce. Clines in nucleotide diversity along environmental variables were found for interior spruce, but not for lodgepole pine. In spruce, genes with convergent adaption signatures showed a higher strength of correlations than genes without convergent adaption signatures, but there was no such disparity in pine, which suggests the pattern in spruce may have arisen due to a combination of selection and hybridization. CONCLUSIONS The results rule out purifying/background selection as a driver of convergent local adaption signatures in lodgepole pine and interior spruce.
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Affiliation(s)
- Mengmeng Lu
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, T2N 4S8, Canada.
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University - Clayton Campus, Building 17, Wellington Road, Melbourne, 3800, Australia
| | - Jon C Degner
- Department of Forest and Conservation Sciences, Forest Sciences Centre 3041, University of British Columbia, 2424 Main Mall, Vancouver, V6T 1Z4, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, T2N 4S8, Canada
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Wang XH, Halling RE, Hofstetter V, Lebel T, Buyck B. Phylogeny, biogeography and taxonomic re-assessment of Multifurca (Russulaceae, Russulales) using three-locus data. PLoS One 2018; 13:e0205840. [PMID: 30403698 PMCID: PMC6221288 DOI: 10.1371/journal.pone.0205840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 10/01/2018] [Indexed: 11/19/2022] Open
Abstract
Multifurca is a small genus newly established to accommodate lactarioid and russuloid species with some characters reminiscent of corticoid members of Russulaceae. It shows an amphi-pacific distribution with strong preference for the tropical zone of the Northern Hemisphere and thus has particular significance for biogeographical study. Using worldwide samples and three loci (ITS, 28S rDNA and rpb2), we demonstrated that Multifurca is split into two highly supported major clades that are here recognized at the subgeneric level: subg. Furcata subg. nov. exclusively includes lactarioid species, while subg. Multifurca includes species with a russuloid habit. Using phylogenetic species recognition and comparison of genetic distances we recognize five new and six previously described species, almost double the known number of species before this study. Molecular dating using a Bayesian method suggested that Multifurca originated in early Paleocene and diversified in the Eocene. The most recent interspecific divergences occurred both in Asia and America, roughly at the same time around the Pliocene. Ancestral area reconstruction and comparisons of genetic distances and morphology suggested an early divergence within Australasia or tropical Asia. From the early Miocene to Pliocene, multiple dispersals/migrations to Australasia and North America by island hopping or land bridge likely happened. Vicariance at the late Tertiary might be the most likely mechanism accounting for the eastern Asia-southeastern North America and Australasia-tropical Asia disjunct distributions. The shared polymorphisms in the ITS alignment, numerous degenerated base pairs in the rpb2 sequences and weak conflict between the ITS and LSU genealogies of M. subg. Furcata suggest recent speciation. Host specificity of Multifurca species or species pairs is relatively low. Host shifts are believed to have aided establishment in new territories during the dispersals and migrations.
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Affiliation(s)
- Xiang-Hua Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, P. R. China
| | - Roy E. Halling
- New York Botanical Garden, Institute of Systematic Botany, Bronx, New York, United States of America
| | - Valérie Hofstetter
- Agroscope, Plant Protection, Mycology and Biotechnology Lab, Nyon, Switzerland
| | - Teresa Lebel
- National Herbarium of Victoria, Royal Botanic Gardens Victoria, Melbourne, Australia
| | - Bart Buyck
- Institut de Systématique, Ecologie, Biodiversité (ISYEB), Muséum national D’histoire naturelle, CNRS, Sorbonne Université, Paris, France
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