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Forests
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Genetic Variation and Adaptation of Forest Trees to Environmental Changes
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Genetic Variation and Adaptation of Forest Trees to Environmental Changes

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

Deadline for manuscript submissions: closed (23 August 2024) | Viewed by 17541

Special Issue Editors

Prof. Dr. Ronan Xavier Corrêa

E-Mail Website
Guest Editor
Department of Biological Sciences, State University of Santa Cruz (UESC), Ilhéus, BA, Brazil
Interests: molecular genetics, conservation of biodiversity and plant improvement, genetic diversity, plant breeding
Prof. Dr. Andrei Caíque Pires Nunes

E-Mail Website
Guest Editor
Training Center in Agroforestry Sciences (CFCAf) of the Federal University of Southern Bahia (UFSB), Itabuna, BA, Brazil
Interests: forest genetic improvement, quantitative genetics, quantitative genomics, statistics, mixed models, grafting of forest species, silviculture

Special Issue Information

Dear Colleagues,

Background: Forests are essential in providing many ecosystem services and timber and non-timber products for human use; they guarantee a habitat for the conservation of biodiversity. In this way, many studies have been carried out to understand forests from multiple areas of knowledge.

Aim and scope: This Special Issue aims to disseminate knowledge about the genetic variation and adaptation of forest species to the environment in the context of ancient, historical, and contemporary changes in climate, soil, nutrition, and water.

History: Genetic studies are based on multiple methodological strategies, ranging from the analysis of endogenous plants (physiology, molecular polymorphism, and genomics) to external phenotypic evaluations (morphology, growth, development, and phenology). All of these aspects reveal the influence of the environment, either by natural phenomena from ancient times or by recent human actions, actions which cause accelerated environmental and climate changes. We expect that the greater the genetic variability in a tree population in the forest, the greater the chances of its adaptation to changes in the climate and environment. Thus, different studies have sought to understand the effects of these changes on the diversity and genetic structure of different forest species and their adaptation to the environment.

Cutting-edge research: In the current context of accelerated environmental changes, genetic studies help conservation strategies for tree species and their sustainable use. Currently, the use of multiple research strategies has accelerated research on tree species. Thus, both classical (molecular markers, phenology, biostatistics, etc.) and recent methodologies (phenomics, genomics, artificial intelligence, etc.) are becoming combined. These different research strategies integrate multiple areas of knowledge (bioinformatics, ecology, forest engineering, physiology, genetics, etc.) to better understand the variability and adaptation of trees.

The kind of papers we are soliciting: We are looking to receive research papers and systematic or integrative reviews. The potential topics include, but are not limited to:

  1. The diversity and genetic structure of a species of tree: case studies.
  2. Agroforestry systems and the conservation of species and habitats.
  3. The methods and strategies for assessing tree variation and adaptation.
  4. The variation and adaptation of tree species in the context of environmental changes.
  5. Timber and non-timber products as allies of genetic conservation.
  6. The training of researchers in the area of genetics and evolution of tree species.

Prof. Dr. Ronan Xavier Corrêa
Prof. Dr. Andrei Caíque Pires Nunes
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

  • agroforest systems
  • climate, soil, and water changes
  • conservation genetics
  • genetic diversity
  • native trees
  • non-native trees
  • evolution
  • genomics
  • ecology
  • sustainable developing goals

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (9 papers)

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Research

14 pages, 4349 KiB  
Article
Alien Species Introduction and Demographic Changes Contributed to the Population Genetic Structure of the Nut-Yielding Conifer Torreya grandis (Taxaceae)
by Yuming Tan, Qian Ou, Xin Huang, Yujin Wang and Yixuan Kou
Forests 2024, 15(8), 1451; https://doi.org/10.3390/f15081451 - 17 Aug 2024
Cited by 1 | Viewed by 1331
Abstract
Understanding population genetic structure and its possible causal factors is critical for utilizing genetic resources and genetic breeding of economically important plants. Although Torreya grandis is an important conifer producing nuts in China, little is known about its population structure, let alone the [...] Read more.
Understanding population genetic structure and its possible causal factors is critical for utilizing genetic resources and genetic breeding of economically important plants. Although Torreya grandis is an important conifer producing nuts in China, little is known about its population structure, let alone the causal factors that shaped its genetic variation pattern and population structure. In this work, we intended to characterize the genetic variation pattern and population structure of the nut-yielding conifer T. grandis throughout its whole geographical distribution and further explore the potentially causal factors for the population structure using multiple approaches. A moderate level of genetic diversity and a novel population structure were revealed in T. grandis based on eleven robust EST-SSR loci and three chloroplast fragments. Alien genetic composition derived from the closely related species T. nucifera endemic to Japan was detected in the Kuaiji Mountain area, where the seed quality of T. grandis is considered the best in China. Demography history and niche modeling were inferred and performed, and the contribution of geographic isolation to its population structure was compared with that of environmental isolation. Significant demographic changes occurred, including a dramatic population contraction during the Quaternary, and population divergence was significantly correlated with geographic distance. These results suggested that early breeding activities and demographic changes significantly contributed to the population structure of T. grandis. In turn, the population structure was potentially associated with the excellent variants and adaptation of cultivars of T. grandis. The findings provide important information for utilizing genetic resources and genetic breeding of T. grandis in the future. Full article
(This article belongs to the Special Issue Genetic Variation and Adaptation of Forest Trees to Environmental Changes)
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16 pages, 3187 KiB  
Article
Genetic Divergence and Evolutionary Adaption of Four Wild Almond Species (Prunus spp. L.)
by Hong-Xiang Zhang, Xiao-Fang Zhang and Jian Zhang
Forests 2024, 15(5), 834; https://doi.org/10.3390/f15050834 - 10 May 2024
Cited by 1 | Viewed by 1290
Abstract
Parallel evolution usually occurs among related species with similar morphological characters in adaptation to particular environments. Four wild almond species (Prunus) sharing the character of dry mesocarp splitting are distributed in China, most of which occur in arid Northwestern China. In [...] Read more.
Parallel evolution usually occurs among related species with similar morphological characters in adaptation to particular environments. Four wild almond species (Prunus) sharing the character of dry mesocarp splitting are distributed in China, most of which occur in arid Northwestern China. In the present study, we aimed to clarify the phylogenetic relationship, evolutionary history, and environmental adaptation of these wild almond species based on genome-wide SNP data and chloroplast genomes. Chloroplast phylogeny showed P. pedunculata and P. tenella were clustered with wild cherry species (Prunus), while P. mongolica and P. tangutica were clustered with wild peach species (Prunus). Genomic phylogeny suggested P. tenella formed an independent clade. An ABC-RF approach showed P. pedunculata was merged with P. tenella and, then, diverged from the ancestor of P. mongolica and P. tangutica. P. tenella was split from other wild almond species at ca. 7.81 to 17.77 Ma. Genetic environment association analysis showed precipitation variables contributed the most to genetic variations between P. mongolica from an arid environment and P. tangutica from a humid environment. Finally, a total of 29 adaptive loci were successfully annotated, which were related to physiological processes in response to abiotic stresses. Inconsistent genomic and chloroplast phylogenetic positions of P. tenella suggested this species could have originated from historical hybridization among different clades of Prunus. Physiological mechanisms promoted P. mongolica in adapting to the arid environment in Northwestern China. Full article
(This article belongs to the Special Issue Genetic Variation and Adaptation of Forest Trees to Environmental Changes)
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20 pages, 54553 KiB  
Article
Climate Change Responses of High-Elevation Polylepis Forests
by Larry E. Bedoya-Canas, Felipe López-Hernández and Andrés J. Cortés
Forests 2024, 15(5), 811; https://doi.org/10.3390/f15050811 - 4 May 2024
Cited by 5 | Viewed by 2260
Abstract
The high mountain forests on Earth are characterized by sharp environmental heterogeneity, high species endemism, and unique phenotypic adaptations. Yet, global warming is jeopardizing this ecosystem as no other as some forests may have nowhere to go beyond the mountain’s summits. One of [...] Read more.
The high mountain forests on Earth are characterized by sharp environmental heterogeneity, high species endemism, and unique phenotypic adaptations. Yet, global warming is jeopardizing this ecosystem as no other as some forests may have nowhere to go beyond the mountain’s summits. One of the most human-endangered high-elevation ecosystems is the Polylepis forest. Despite its vulnerability, forecasting climate reactions in this distinctive high mountain forest type remains a formidable challenge. Therefore, in this study, we modeled climate change responses of high-elevation allopatric Polylepis sericea and P. quadrijuga (Rosaceae) in the northern Andes. The analysis took into account VIF-prioritized bioclimatic variables for near-to-present and future (2081–2100 MPI-ESM1-2-HR) conditions. Model selection was carried out following the AUC scores of 12 MaxEnt and six machine learning algorithms. Predictive power reached 0.97 for MaxEnt’s model fc.H_rm.1 (H-1). Results indicate a moderate vulnerability of P. sericea, with a 29% loss of area in the trailing edge, due to climate change for the period 2081–2100. On the other hand, P. quadrijuga is likely to experience even larger distribution losses, up to 99%, for the same period. The findings of this study suggest that P. quadrijuga, as compared to P. sericea, exhibits a restricted ability to maintain the corresponding habitat requirements in the face of climatic change. Higher niche specialization of P. quadrijuga in the environmentally heterogeneous Eastern Cordillera contrasts with the more generalist nature of P. sericea in the topographically less complex Central Cordillera. In addition to climate change, this trend may be exacerbated by the detrimental effects of agriculture, mining, and an expanding rural population, which represent significant human-driven pressures yet to be modeled in the northern Andean highlands. Yet, based on previous studies, the historical population dynamics during the past glacial cycles suggests that range shifts could play a more significant role at deeper time scales than previously forecasted in the species’ reaction to climate change. Additionally, Polylepis forests may be able to endure at the current locations via local adaptation and plasticity, major drivers of the phenotypic variation in long-lived trees, counteracting the vulnerability scenario under a niche conservatism hypothesis. Ultimately, the modeling procedure employed in this study provides insights into the potential effects of climate change on Polylepis forests 70 years from now. Oncoming studies may consider alternative responses inherent to the gene pool of the species and the interaction with edaphic and biotic agents. We advocate for the application of comparable estimations in other high-elevation tree communities found at the tree line. Full article
(This article belongs to the Special Issue Genetic Variation and Adaptation of Forest Trees to Environmental Changes)
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13 pages, 3496 KiB  
Article
Analysis of the Genetic Diversity and Mating System of the Endangered Plant Keteleeria davidiana var. calcarea
by Xinfeng Pan, Huizhen Qin, Haidu Jiang, Lihui Peng, Yishan Yang, Jianmin Tang, Rong Zou, Zongyou Chen, Xiao Wei and Shengfeng Chai
Forests 2024, 15(5), 793; https://doi.org/10.3390/f15050793 - 30 Apr 2024
Cited by 1 | Viewed by 2482
Abstract
Keteleeria davidiana var. calcarea is an endangered plant endemic to China. It is mainly distributed in the karst areas of the Guangxi and Guizhou Provinces. It is characterized by small populations and intermittent distribution. This study aimed to explore the genetic diversity and [...] Read more.
Keteleeria davidiana var. calcarea is an endangered plant endemic to China. It is mainly distributed in the karst areas of the Guangxi and Guizhou Provinces. It is characterized by small populations and intermittent distribution. This study aimed to explore the genetic diversity and mating system of wild populations of Keteleeria davidiana var. calcarea in fragmented habitats. To achieve this, we genotyped 46 maternal trees and 214 progenies from four fragmented populations of Keteleeria davidiana var. calcarea using nine pairs of microsatellite primers. The genetic diversity of Keteleeria davidiana var. calcarea (Ho = 0.68, He = 0.63) was lower than that of the species overall but higher than that of other Keteleeria plants. The incidence of unbiased expected heterozygosity (uHe) and allelic richness (Ar) was higher in the maternal generation than in the progeny. This suggests that the genetic diversity of the progeny was lower than that of the maternal generation. Keteleeria davidiana var. calcarea is divided into four populations, but there is significant genetic exchange between the populations according to STRUCTURE and gene flow analyses. The multilocus mating system analysis (MLTR) results indicate that the multilocus outcrossing rate (tm) was 0.902, the single-locus outcrossing rate (ts) was 0.606, the bimaternal inbreeding coefficient (tm-ts) was 0.295, and the coefficient of inbreeding depression(δ) was 0.904. These results suggest a certain degree of selfing and inbreeding in Keteleeria davidiana var. calcarea. To prevent problems associated with inbreeding and conserve the genetic diversity of Keteleeria davidiana var. calcarea, we recommend establishing seed gardens, using artificial pollination, and employing asexual propagation techniques for conservation intervention. Full article
(This article belongs to the Special Issue Genetic Variation and Adaptation of Forest Trees to Environmental Changes)
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19 pages, 2344 KiB  
Article
Development of SSR Markers for and Fingerprinting of Walnut Genetic Resources
by Suilin Zhang, Yang Li, Yan Li, Yunqi Zhang, Yanbin Hao, Zhixia Hou and Jianxun Qi
Forests 2024, 15(3), 405; https://doi.org/10.3390/f15030405 - 20 Feb 2024
Cited by 5 | Viewed by 2011
Abstract
Walnut is one of four major nuts in the world. China has abundant walnut germplasm resources, but there are still shortcomings in the identification of germplasm resources. This study used different walnut varieties as materials and developed 14 high-quality SSR molecular markers from [...] Read more.
Walnut is one of four major nuts in the world. China has abundant walnut germplasm resources, but there are still shortcomings in the identification of germplasm resources. This study used different walnut varieties as materials and developed 14 high-quality SSR molecular markers from 60 pairs of primers based on genome re-sequencing results. This study analyzed the genetic diversity of Chinese walnut genetic resources using 14 selected SSR markers. A total of 64 alleles were detected in 47 walnut resources, with an average of 4.571 alleles per locus. The variation range of polymorphism information content was 0.096~0.711, with an average value of 0.422. Cluster analysis, population genetic structure, and principal coordinate analysis divided 47 walnut resources into ordinary walnuts, Juglans hopeiensis, and Liaoyi 1. In addition, core SSR markers (Jr45, Jr40, Jr29, Jr35, and Jr11) were selected from 14 SSR markers, which were sufficient to distinguish 47 walnut resources. At the same time, 47 unique molecular fingerprints of walnuts were constructed using these core SSR markers. This study provides strong scientific support for rapid and efficient identification, germplasm innovation, and a variety of property protection of walnut germplasm. Full article
(This article belongs to the Special Issue Genetic Variation and Adaptation of Forest Trees to Environmental Changes)
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13 pages, 3250 KiB  
Article
Transcriptome Analysis Provides Insights into Korean Pine Tree Aging and Response to Shading
by Zha-Long Ye, Jin-Yi Liu, Jian Feng and Wan-Feng Li
Forests 2024, 15(2), 291; https://doi.org/10.3390/f15020291 - 3 Feb 2024
Cited by 2 | Viewed by 1701
Abstract
Age controls a tree’s responses to environmental cues and shading influences tree growth and physiology. These are basic principles of “Afforestation under canopy”, an approach that is widely used in the regeneration of Korean pine forests. Studying the underlying mechanism helps us to [...] Read more.
Age controls a tree’s responses to environmental cues and shading influences tree growth and physiology. These are basic principles of “Afforestation under canopy”, an approach that is widely used in the regeneration of Korean pine forests. Studying the underlying mechanism helps us to understand tree adaptation and utilize it in forest management. In this study, we investigated the transcriptomic changes in the uppermost main stems of the Korean pine tree (Pinus koraiensis, Sieb. et Zucc.) at different ages (5, 7, 10, 14, and 17 years) and in different growth conditions (open-grown and shade-grown trees) using RNA-Seq. In total, 434,005,837 reads were produced and assembled into 111,786 unigenes. After pairwise comparisons, 568 differentially expressed unigenes (DEUs) were identified. The greatest number of DEUs was identified in the comparison between 5-year-old open-grown trees and 17-year-old shade-grown trees, while no DEUs were identified in 15 pairwise comparisons. Among these 568 DEUs, 45 were assigned to gene ontology (GO) terms associated with response to environmental changes, including “response to stress” (26) and “response to light and temperature” (19); 12 were assigned to GO terms associated with sexual reproduction, such as “sexual reproduction”, “specification of floral organ identity”, “pollen tube guidance”, and “fruit ripening”; 15 were heat shock protein genes and showed decreased expression patterns with age; and one, annotated as Pinus tabuliformis DEFICIENS-AGAMOUS-LIKE 1, showed an increased expression pattern with age, independent of the reproductive state or growth conditions of Korean pine trees. Altogether, these findings not only demonstrate the molecular aspects of the developmental and physiological effects of age and shading on Korean pine trees, but also improve our understanding of the basic principles of “Afforestation under canopy”. Full article
(This article belongs to the Special Issue Genetic Variation and Adaptation of Forest Trees to Environmental Changes)
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25 pages, 4208 KiB  
Article
A Study on the Genetic Variations and Germination Characteristics of Rhododendron sohayakiense to Prepare for Climate Change Threat
by Eun-hye Kim, Sle-gee Lee, Sung-won Son, So-yeon Lee and Hayan Lee
Forests 2024, 15(2), 224; https://doi.org/10.3390/f15020224 - 23 Jan 2024
Viewed by 1724
Abstract
Rhododendron sobayakiense is an endemic and near-threatened species (Korean Red List, NT) found in the alpine regions of South Korea that requires conservation. This study investigated the species’ genetic variations and seed germination characteristics and predicted its potential habitat change according to climate [...] Read more.
Rhododendron sobayakiense is an endemic and near-threatened species (Korean Red List, NT) found in the alpine regions of South Korea that requires conservation. This study investigated the species’ genetic variations and seed germination characteristics and predicted its potential habitat change according to climate change scenarios. The genetic diversity of R. sobayakiense at the species level (P = 88.6%; S.I. = 0.435; h = 0.282) was somewhat similar to that observed for the same genus. The inter-population genetic differentiation was 19% and revealed a relatively stable level of gene exchange at 1.22 in each population. The main cause of gene flow and genetic differentiation was presumed to be the Apis mellifera pollinator. Seed germination characteristics indicated non-deep physiological dormancy, with germination at ≥10 °C and the highest percent germination (PG) of ≥60% at 15–25 °C, while the PG was ≥50% at 30 °C. The PG increased at constant temperature than at variable temperatures; the mean germination time decreased as temperature increased. The climate scenarios SSP3 and SSP5 were analyzed to predict future R. sobayakiense habitat changes. The variables of the main effects were Identified as follows: elevation > temperature seasonality > mean diurnal range. Full article
(This article belongs to the Special Issue Genetic Variation and Adaptation of Forest Trees to Environmental Changes)
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12 pages, 2414 KiB  
Article
Genetic Structure and Diversity of Dalbergia nigra from Brazilian Atlantic Forest Fragments
by Mariana A. Barreto, Jonathan J. Mucherino-Muñoz, Ivandilson P. P. Menezes, Roberto Tarazi, Janisete G. Silva, Fernanda A. Gaiotto and Ronan X. Corrêa
Forests 2023, 14(11), 2165; https://doi.org/10.3390/f14112165 - 30 Oct 2023
Cited by 2 | Viewed by 1912
Abstract
Dalbergia nigra is a long-living tree endemic to the Atlantic Rain Forest. Due to its high commercial value, this species has been widely exploited for timber production and is now endangered. It is widely known that understanding patterns of genetic structure is paramount [...] Read more.
Dalbergia nigra is a long-living tree endemic to the Atlantic Rain Forest. Due to its high commercial value, this species has been widely exploited for timber production and is now endangered. It is widely known that understanding patterns of genetic structure is paramount for conserving threatened species. We analyzed the genetic diversity of 140 individuals from four different forest fragments in the southern region of Bahia, Brazil, to verify the possible effects of fragmentation on these populations and provide information for conservation initiatives. High polymorphism levels were detected from the genotyping of nine microsatellite loci (mean HE = 0.733). All populations showed high genetic diversity; however, a reduction of genetic diversity was detected in each population (HO < HE). The average fixation index was high and significant (f = 0.167), which could be due to the occurrence of inbreeding, the Wahlund effect, reproductive system, or from null alleles. Genetic differentiation among populations was high (mean θP = 0.118), suggesting strong isolation, a pattern consistent with historically low gene flow. The Bayesian analysis revealed five different genetic groups, among which three groups correspond to three different forest fragments, and two groups showed the genetic subdivision of individuals from the other forest fragment. Based on our results, the suggested conservation strategy for D. nigra populations in the southern region of Bahia, Brazil, involves high environmental investments to protect all sampled forest fragments and individuals. Another strategy would be to collect seeds from all individuals from the sampled fragments and start a new population with human interference in its evolutive history inside a protection unit. Full article
(This article belongs to the Special Issue Genetic Variation and Adaptation of Forest Trees to Environmental Changes)
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16 pages, 5040 KiB  
Article
Comparative Chloroplast Genomics Reveals a Unique Gene Inversion in Two Cordia Trees (Cordiaceae)
by Mohammad S. Alawfi and Enas J. Albokhari
Forests 2023, 14(9), 1778; https://doi.org/10.3390/f14091778 - 31 Aug 2023
Cited by 3 | Viewed by 1581
Abstract
Cordiaceae is a family comprising more than 400 species in the order Boraginales. The classification of this family has undergone changes over time, transitioning between family and subfamily status. In the present study, the complete chloroplast (cp) genomes of Cordia monoica and Cordia [...] Read more.
Cordiaceae is a family comprising more than 400 species in the order Boraginales. The classification of this family has undergone changes over time, transitioning between family and subfamily status. In the present study, the complete chloroplast (cp) genomes of Cordia monoica and Cordia sinensis were sequenced, and their cp genomes were then characterized, analyzed, and compared to those of closely related taxa. The lengths of the cp genomes of C. monoica and C. sinensis were 151,813 bp and 152,050 bp, respectively. Both genomes consisted of 114 genes, divided into 4 ribosomal RNA genes, 30 transfer RNA genes, and 80 protein-coding genes. We observed a unique gene inversion in the trnM-rbcL region of both Cordia species. The long repeats analysis revealed that both species’ chloroplast genomes contained forward and palindromic repeats. The simple sequence repeats (SSRs) analysis detected 155 microsatellites in each genome, with the majority being mononucleotide repeats (A/T). Phylogenetic analysis based on maximum likelihood and Bayesian analyses confirmed two major clades in the order Boraginales: clade I comprised Boraginaceae, while clade II included Cordiaceae, Ehretiaceae, and Heliotropiaceae. This study expands our knowledge of the evolutionary relationships across the order Boraginales and offers useful genetic resources. Full article
(This article belongs to the Special Issue Genetic Variation and Adaptation of Forest Trees to Environmental Changes)
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