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Forests
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Functional and Phylogenetic Signals of Forest Tree Communities
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Functional and Phylogenetic Signals of Forest Tree Communities

A special issue of Forests (ISSN 1999-4907). This special issue belongs to the section "Forest Ecophysiology and Biology".

Deadline for manuscript submissions: closed (5 June 2019) | Viewed by 14995

Special Issue Editors

Dr. Andrea Coppi

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Guest Editor
Department of Biology, University of Florence, Via la Pira 4 – 50121, Florence, Italy
Interests: molecular phylogeny; community phylogenetics; population genetics; plant functional traits; ecosystem services
Special Issues, Collections and Topics in MDPI journals
Dr. Ilaria Colzi

E-Mail Website
Guest Editor
Department of Biology, University of Firenze, 50121 Firenze, Italy
Interests: plant physiology; plant responses to abiotic stress; micro and nanoplastic effects on plants
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the last 20 years, an increased amount of studies have demonstrated how reduced numbers of genes, species and functional groups of organisms in forest ecosystems, may inexorably lead to a reduction in the efficiency of species consortiums to capture and manage biologically-essential resources (nutrients, water, light, etc.). From this point of view, the phylogenetic approach is attracting growing interest in forest ecology and conservation because it can be related to processes such as extinction, resistance, resilience, and even ecosystem functioning. However, despite the large number of studies, scientific proof of the added value of phylogenetic diversity for nature conservation remains weak. In particular, only limited information has been provided regarding the relationship between phylogenetic diversity of communities and species–species interactions. This Special Issue represents a summary of high-quality scientific papers focused on the relationships among phylogenetic and functional signals, and plant interactions useful to increase the knowledge of forest systems; their functioning, management, and conservation.

Dr. Andrea Coppi
Dr. Ilaria Colzi
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Forests is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Forest diversity
  • Ecosystem services
  • Plants functional traits
  • Phylogenetic ecology
  • Plant interactions

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Published Papers (3 papers)

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Research

16 pages, 2207 KB  
Article
The Use of DNA Barcoding to Assess Phylogenetic β-Diversity in Mid-Subtropical Evergreen Broad-Leaved Forests of China
by Juan Liu, Jiajia Liu, Xuejun Ge, Guomin Huang, Zengliang Zhou and Songze Wan
Forests 2019, 10(10), 923; https://doi.org/10.3390/f10100923 - 20 Oct 2019
Cited by 3 | Viewed by 6928
Abstract
The application of quantifying phylogenetic information into measures of forest β-diversity is increasing for investigating the underlying drivers of community assembly along environmental gradients. In terms of assessing evolutionary inferences of community processes, a variety of plant DNA barcodes has been widely used [...] Read more.
The application of quantifying phylogenetic information into measures of forest β-diversity is increasing for investigating the underlying drivers of community assembly along environmental gradients. In terms of assessing evolutionary inferences of community processes, a variety of plant DNA barcodes has been widely used in phylogenetic diversity measurements. However, relatively few studies have evaluated the effectiveness of DNA barcodes with using nuclear region in estimating phylogenetic β-diversity, particularly for communities in tropical or subtropical forests. In this study, we employed DNA barcodes combing with the nuclear region to construct the community phylogeny and examined the patterns of phylogenetic β-diversity of three mid-subtropical evergreen broad-leaved forests (EBLFs) in South China. Three phylogenetic construction methods were performed, including a Phylomatic-generated tree and two ML trees based on the combination of rbcL + matK + ITS with or without a constrained tree. Our results showed that the DNA barcodes including nuclear ITS constructed a highly resolved phylogenetic tree, but the application of a constrained tree had little influence on estimation of phylogenetic diversity metrics (mean pairwise distances and mean nearest taxon distances) based on branch lengths. Using both metrics and their standardized effect size metrics, we found that the patterns of phylogenetic β-diversity in mid-subtropical forests were non-random. There was a slight decline of phylogenetic β-diversity with increasing latitudes, but no trend was found along the altitude gradient. According to the analysis of variation partition, both environmental filtering and dispersion limitation could explain the variation of phylogenetic dissimilarity between communities in mid-subtropical EBLFs of China. Our results highlight the importance of neutrality and the niche conservatism in structuring the patterns of species diversity in subtropical woody communities. Full article
(This article belongs to the Special Issue Functional and Phylogenetic Signals of Forest Tree Communities)
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15 pages, 3407 KB  
Article
Complete Chloroplast Genome of Fokienia hodginsii (Dunn) Henry et Thomas: Insights into Repeat Regions Variation and Phylogenetic Relationships in Cupressophyta
by Mingyue Zang, Qian Su, Yuhao Weng, Lu Lu, Xueyan Zheng, Daiquan Ye, Renhua Zheng, Tielong Cheng, Jisen Shi and Jinhui Chen
Forests 2019, 10(7), 528; https://doi.org/10.3390/f10070528 - 26 Jun 2019
Cited by 6 | Viewed by 3724
Abstract
Fokienia hodginsii (Dunn) Henry et Thomas is a relic gymnosperm with broad application value. It is a fit candidate when choosing species for the construction of artificial forests. We determined the complete chloroplast genome sequence of F. hodginsii, which is 129,534 bp [...] Read more.
Fokienia hodginsii (Dunn) Henry et Thomas is a relic gymnosperm with broad application value. It is a fit candidate when choosing species for the construction of artificial forests. We determined the complete chloroplast genome sequence of F. hodginsii, which is 129,534 bp in length and encodes 83 protein genes, 33 transfer RNA (tRNA) genes, as well as four ribosomal RNA genes. The GC content of the complete sequence and protein coding regions is 34.8% and 36.2%, respectively. We identified 11 tandem repeats, 11 forward repeats, and three palindromic repeats and classified them by size. Following our microsatellite analysis, a total number of 73 simple sequence repeats were detected, preferentially within the intergenic space. Being a member of Cupressophyta, F. hodginsii owns several common characters; the trnR-CCG gene has been deleted, while the trnI-CAU and trnQ-UUG genes have been duplicated. Moreover, the accD gene, which encodes acetyl-CoA carboxylase, contains 771 codons in F. hodginsii, similar to Cryptomeria japonica (L. F.) D. Don, further supporting the diversity of accD and its size expansion in Cupressophyta. Concerning the loss of inverted repeat (IR) regions, the 86-bp sequence with the duplicated trnI-CAU gene is inferred to be the footprint of IR contraction. Phylogenetically, F. hodginsii is placed as a sister taxon to Chamaecyparis hodginsii (Dunn) Rushforth. This work offers meaningful guidance as well as reference value to the breeding research and improvement of F. hodginsii. Moreover, it gives us a better understanding of the genomic structure and evolutionary history of gymnosperms, especially coniferales. Full article
(This article belongs to the Special Issue Functional and Phylogenetic Signals of Forest Tree Communities)
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16 pages, 3081 KB  
Article
Expression Patterns of MYB (V-myb Myeloblastosis Viral Oncogene Homolog) Gene Family in Resistant and Susceptible Tung Trees Responding to Fusarium Wilt Disease
by Xue Wang, Qiyan Zhang, Ming Gao, Liwen Wu, Yangdong Wang and Yicun Chen
Forests 2019, 10(2), 193; https://doi.org/10.3390/f10020193 - 21 Feb 2019
Cited by 3 | Viewed by 3610
Abstract
Vernicia fordii (tung oil tree) is famous in the world for its production of tung oil. Unfortunately, it was infected by the soil-borne fungus Fusarium oxysporum f. sp. fordii 1 (Fof-1) and suffered serious wilt disease. Conversely, its sister species V. [...] Read more.
Vernicia fordii (tung oil tree) is famous in the world for its production of tung oil. Unfortunately, it was infected by the soil-borne fungus Fusarium oxysporum f. sp. fordii 1 (Fof-1) and suffered serious wilt disease. Conversely, its sister species V. montana is highly resistant to Fof-1. The MYB (v-myb myeloblastosis viral oncogene homolog) transcription factors were activated during the pathogen Fof-1 infection according to our previous comparative transcriptomic results. Depending on whether the sequence has a complete MYB-DNA-binding domain, a total of 75 VfMYB and 77 VmMYB genes were identified in susceptible V. fordii and resistant V. montana, respectively. In addition, we detected 49 pairs of one-to-one orthologous Vf/VmMYB genes with the reciprocal-best BLAST-hits (RBH)method. In order to investigate the expression modes and the internal network of MYB transcription factors in the two species responding to Fusarium wilt disease, the expressions of Vf/VmMYBs were then investigated and we found that most orthologous Vf/VmMYB genes exhibited similar expression patterns during the Fof-1 infection. However, four pairs of Vf/VmMYB genes, annotated as unknown proteins and mediator of root architecture, demonstrated absolute opposite expression patterns in the two Vernicia species responding to Fof-1. The interaction network of VmMYB genes were further constructed using weighted gene co-expression network analysis (WGCNA) method and four hub genes showing extremely high interaction with the other 1157 genes were identified. RT-qPCR result verified the opposite expression pattern of the hub gene VmMYB011 and VmMYB041 in two Vernicia species. In summary, co-expression network of the Vf/VmMYBs and significantly opposite related pairs of genes in resistant and susceptible Vernicia species provided knowledge for understanding the molecular basis of Vernicia responding to Fusarium wilt disease. Full article
(This article belongs to the Special Issue Functional and Phylogenetic Signals of Forest Tree Communities)
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