Diversity

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4 pages, 200 KiB

Open AccessEditorial

Understanding Plant Diversity from Ecological and Evolutionary Perspectives

by Hong-Hu Meng and Yi-Gang Song

Diversity 2023, 15(12), 1165; https://doi.org/10.3390/d15121165 - 22 Nov 2023

Viewed by 2234

Abstract

Nowadays, we are living in a world that is benefiting from biodiversity, although environmental change is dramatic and biodiversity has been influenced by climate changes and human activities [...] Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

Research

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16 pages, 4465 KiB

Open AccessArticle

Genome-Wide Analysis of SPL Gene Families Illuminate the Evolution Patterns in Three Rubber-Producing Plants

by Renping Su, Boxuan Yuan, Yang Yang, Guoen Ao and Juanying Wang

Diversity 2023, 15(9), 983; https://doi.org/10.3390/d15090983 - 31 Aug 2023

Cited by 1 | Viewed by 1347

Abstract

Transcription factors SQUAMOSA Promoter-binding Protein-like (SPL) play a crucial role in regulating plant response to stress, root development, and flower production. However, analysis of SPL gene families in the three rubber-producing plants Taraxacum kok-saghyz, Hevea brasiliensis, and Eucommia ulmoides, renowned [...] Read more.

Transcription factors SQUAMOSA Promoter-binding Protein-like (SPL) play a crucial role in regulating plant response to stress, root development, and flower production. However, analysis of SPL gene families in the three rubber-producing plants Taraxacum kok-saghyz, Hevea brasiliensis, and Eucommia ulmoides, renowned for their natural rubber production, has not yet been conducted. In this study, we utilized reference genomes to perform genome-wide analysis, and obtained new insights on the evolution of SPL gene families in these three rubber-producing plants. Our results revealed the following: (1) T. kok-saghyz, H. brasiliensis, and E. ulmoides harbored 25, 16, and 13 SPL genes, respectively, containing conserved structural domains of SBP. (2) A phylogenetic analysis categorized 90 SPL proteins from 25 TkSPLs, 16 HbSPLs, 13 EuSPLs, 17 AtSPLs, and 19 OsSPLs into eight groups. (3) Analysis of cis-acting elements demonstrated that the promoters of EuSPLs contained a significant number of light response elements, hormone regulatory elements, and stress response elements. (4) Transcriptome data analysis revealed that the EuSPL8 gene had strong expression in bark, as well as TkSPL4 and TkSPL8 exhibit high expression levels specifically in roots and latex. This study provides valuable insights into the biological functions of the SPL gene family in the three rubber plants and might serve as a reference for identifying efficient genes. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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12 pages, 3363 KiB

Open AccessArticle

Diverse Host Spectrum and the Parasitic Process in the Pantropical Hemiparasite Cassytha filiformis L. (Lauraceae) in China

by Zhi-Fang Liu, Xiu-Qin Ci, Shi-Fang Zhang, Xiao-Yan Zhang, Xue Zhang, Li-Na Dong, John G. Conran and Jie Li

Diversity 2023, 15(4), 492; https://doi.org/10.3390/d15040492 - 27 Mar 2023

Cited by 2 | Viewed by 2607

Abstract

Many hemiparasites attach to a range of different host species, resulting in complex parasite–host interactions. Comprehensive molecular phylogenies allow the investigation of evolutionary relationships between these host plants. We surveyed the hosts of the laurel dodder (Cassytha filiformis, Lauraceae) in China, [...] Read more.

Many hemiparasites attach to a range of different host species, resulting in complex parasite–host interactions. Comprehensive molecular phylogenies allow the investigation of evolutionary relationships between these host plants. We surveyed the hosts of the laurel dodder (Cassytha filiformis, Lauraceae) in China, representing 184 species from 146 genera, 67 families, and spanning flowering plants, conifers, and ferns, using host phylogenetic relationships to investigate the susceptibility to attack by this hemiparasitic plant among the vascular plants. The process of produced well-formed haustoria by C. filiformis was also observed in detail for six different hosts. Our results show that C. filiformis grows mainly on trees and shrubs from phylogenetically divergent members of the rosid and asterid eudicot clades, often attacking multiple adjacent hosts simultaneously, and forming extensive colonies. However, whether and to what extent transitions between C. filiformis and host plants occur remain unclear. Physiological evidence for the complex parasite–host species interactions need to be studied in the future. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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14 pages, 1984 KiB

Open AccessArticle

Population Survey Combined with Genomic-Wide Genetic Variation Unravels the Endangered Status of Quercus gilva

by Yi-Gang Song, Tian-Rui Wang, Zi-Jia Lu, Bin-Jie Ge, Xin Zhong, Xiao-Chen Li, Dong-Mei Jin, Quan Yuan, Yu Li, Yi-Xin Kang, Xin Ning, Si-Si Zheng, Li-Ta Yi, Xi-Ling Dai, Jian-Guo Cao, Jung-Hyun Lee and Gregor Kozlowski

Diversity 2023, 15(2), 230; https://doi.org/10.3390/d15020230 - 6 Feb 2023

Cited by 1 | Viewed by 3065

Abstract

Since the Anthropocene, biodiversity loss owing to human activity and climate change has worsened. Quercus gilva is an evergreen oak species native to China, Japan, and South Korea and is threatened by a long history of human impact. The purpose of this study [...] Read more.

Since the Anthropocene, biodiversity loss owing to human activity and climate change has worsened. Quercus gilva is an evergreen oak species native to China, Japan, and South Korea and is threatened by a long history of human impact. The purpose of this study was to (1) reassess the threatened category of Q. gilva based on a detailed survey, and (2) identify the genetic structure and diversity of Q. gilva based on genomic data. First, we conducted a detailed survey of the populations in China. Second, we collated all the literature and information. Finally, genome-wide genetic variation was analyzed based on 65 individuals from 22 populations. We found that Q. gilva has suffered rapid population decline, and at present, most populations are very small. The evolutionary path of Q. gilva was from the southwest to east of China and then to Japan and South Korea. Quercus gilva showed no distinct genetic structure and had a relatively low genetic diversity. Among the 22 populations, most populations in southwestern China, South Korea, and Japan had high genetic diversity. The populations in Jingning (Zhejiang province; ZJN), Wuyuan (Jinaxi province; JWY), and Zherong (Fujian province; FZR) suffered a strong bottleneck. In conclusion, Q. gilva is an endangered species native to East Asia. Because of the very low genetic diversity of Q. gilva and most populations are small, we need to (1) strengthen the protection of this species, (2) conduct conservation actions with in-situ reinforcement populations, and (3) select populations with high genetic diversity as provenances for afforestation efforts. Finally, we suggest that in the future, genetic diversity should be considered as the sixth criterion for IUCN to evaluate the threatened category. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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17 pages, 5179 KiB

Open AccessArticle

Numerical Ecology and Social Network Analysis of the Forest Community in the Lienhuachih Area of Taiwan

by Tung-Yu Hsieh, Chun-Jheng Yang, Feng Li and Chyi-Rong Chiou

Diversity 2023, 15(1), 60; https://doi.org/10.3390/d15010060 - 3 Jan 2023

Cited by 1 | Viewed by 1883

Abstract

In this study, the integration of useful statistical methods from different disciplines for analyzing the forest community of the Lienhuachih area of central Taiwan was attempted. We employed a seriated heat map to confirm the presence of multiple community patterns in the area [...] Read more.

In this study, the integration of useful statistical methods from different disciplines for analyzing the forest community of the Lienhuachih area of central Taiwan was attempted. We employed a seriated heat map to confirm the presence of multiple community patterns in the area and used the gap statistics and a clustplot to confirm the number and structure of the patterns, respectively. A minimum spanning tree was used to display a succession series among the quadrats, and Renyi diversity was used to indicate the species composition of these patterns. The results confirmed the existence of six patterns with different biodiversity structures in which pattern C was the succession prototype of the local community patterns. Next, we used the patterns as nodes of a social network to perform bipartite network analysis. The results showed that a community network consisted of 108 taxa and six syntaxa. The syntaxa were highly vulnerable to extinction; therefore, the optimal conservation strategy for local species would be to first protect the syntaxa. The random forest method and bipartite modularity were used to analyze the dominant characteristic species of the six syntaxa. The results showed that these two methods are useful for detecting characteristic species of the syntaxa. Therefore, this study proposed a new nomenclature system, namely the Mathematic Code of Syntaxonomic Nomenclature, to support the results of numerical vegetation analysis. Finally, the potential for an apparently competitive network was examined, the role of an apparently competitive network in the local structuring community was explored, and six new associations in the Lienhuachih area were described. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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16 pages, 3106 KiB

Open AccessArticle

PPDP: A Data Portal of Paris polyphylla for Polyphyllin Biosynthesis and Germplasm Resource Exploration

by Qixuan Su, Xuan Zhang, Jing Li, Wenjing Yang, Qiang Ren, Xiaoyang Gao and Changning Liu

Diversity 2022, 14(12), 1057; https://doi.org/10.3390/d14121057 - 1 Dec 2022

Cited by 1 | Viewed by 1872

Abstract

Paris polyphylla Smith is a perennial medicinal herb with records from around 2000 years ago. Polyphyllins are the main bioactive compounds of this herb, which are found to have remarkable effects on bacteriostatic, antiphlogistic, sedative, and antitumor. However, the market demand for P. [...] Read more.

Paris polyphylla Smith is a perennial medicinal herb with records from around 2000 years ago. Polyphyllins are the main bioactive compounds of this herb, which are found to have remarkable effects on bacteriostatic, antiphlogistic, sedative, and antitumor. However, the market demand for P. polyphylla is sharply increasing, and the wild resources are threatened by plundering exploitation. Integrating molecular data of P. polyphylla can benefit the sustainable resource exploitation. Here, we constructed PPDP (Paris polyphylla Data Portal) to provide a data platform for polyphyllin biosynthesis and germplasm resource research. PPDP integrates related molecular data resources, functional genomics analysis, and morphological identification. The database provides abundant data (transcriptome, CDS, lncRNA, alternative splicing, gene family, SSR, and chloroplast genome) and practical analytical tools (network construction, heatmap of expression profiles, enrichment, and pathway search) with a user-friendly interface. So far, PPDP is the first biomolecular database for the genus Paris plants. In the future, we will gradually add genomic data and other necessary molecular biological information to improve the database. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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9 pages, 2398 KiB

Open AccessArticle

Geographic Patterns of the Richness and Density of Wild Orchids in Nature Reserves of Jiangxi, China

by Qinghua Zhan, Yuelong Liang, Zhong Zhang, Feihu Liu, Liyang Li, Xiaodong Tang, Zhongxuan Liang, Weixing Chen, Mingtao Hu, Shaolin Tan, Huolin Luo, Yadong Zhou and Boyun Yang

Diversity 2022, 14(10), 855; https://doi.org/10.3390/d14100855 - 9 Oct 2022

Cited by 4 | Viewed by 1875

Abstract

Orchids have attracted much attention from researchers, because of their richness of species and their great ornamental and medicinal value. Jiangxi Province, which is located in southeastern China and ringed on three sides by mountains, contains many nature reserves and harbors large number [...] Read more.

Orchids have attracted much attention from researchers, because of their richness of species and their great ornamental and medicinal value. Jiangxi Province, which is located in southeastern China and ringed on three sides by mountains, contains many nature reserves and harbors large number of orchids. Here, we conducted field surveys of orchids in 35 nature reserves in Jiangxi, using sampling lines and plots. We also analyzed the relationship between orchid richness and density with environmental variables and studied the relationship among these nature reserves. We found that the mountainous areas of southwestern, southern, and northeastern Jiangxi have a high richness and density of orchids, while the mountainous areas of central and northwestern Jiangxi have low richness and density. Jiulianshan and Jinggangshan are the two most rich-species reserves, with 58 and 55 orchids, respectively. Eight reserves (22% of those surveyed) had fewer than 10 orchids. Compared with soil, climate, and vegetation, topography was more closely related to the richness and density of orchids. Topographical variables explained 19% and 20% of the total variation in SR and SD, respectively. The result of hierarchical clustering analysis showed that the 35 nature reserves of Jiangxi obviously fall into two main clusters, which are separated by the Ganjiang River–Poyang Lake water system. In conclusion, the geographical patterns of richness and the density of orchids in Jiangxi are uneven and are affected by topography and vegetation, while their distribution is affected by the terrain of Jiangxi. Our work explains the richness and density patterns and the assembly mechanism of the orchids in Jiangxi and also provides new ideas for the protection of orchids in this region. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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15 pages, 3853 KiB

Open AccessArticle

Assessment of Climate Change and Land Use Effects on Water Lily (Nymphaea L.) Habitat Suitability in South America

by John M. Nzei, Boniface K. Ngarega, Virginia M. Mwanzia, Joseph K. Kurauka, Qing-Feng Wang, Jin-Ming Chen, Zhi-Zhong Li and Cheng Pan

Diversity 2022, 14(10), 830; https://doi.org/10.3390/d14100830 - 3 Oct 2022

Cited by 7 | Viewed by 3438

Abstract

Many aquatic species have restricted dispersal capabilities, making them the most vulnerable organisms to climate change and land use change patterns. These factors deplete Nymphaea species’ suitable habitats, threatening their populations and survival. In addition, the species are poorly documented, which may indicate [...] Read more.

Many aquatic species have restricted dispersal capabilities, making them the most vulnerable organisms to climate change and land use change patterns. These factors deplete Nymphaea species’ suitable habitats, threatening their populations and survival. In addition, the species are poorly documented, which may indicate how scarce they are or will become. Members of Nymphaea are ecologically important as well as having cultural and economic value, making them of conservation interest. Therefore, using the maximum entropy (MaxEnt) approach, climatic variables, land use, and presence points were modeled for seven Nymphaea species in South America, using three general circulation models (CCSM4, HADGEM2-AO, and MIROC5) and in two representative concentration pathways (RCPs 4.5 and 8.5) and two scenarios (2050 and 2070). Our results indicated that mean diurnal range (bio2), precipitation of the wettest month (bio13), temperature seasonality (bio15), and land use (dom_lu) were the main influencing factors. For all species, suitable areas were concentrated east of Brazil, and they were variable in northern parts of the continent. Besides, inconsistent expansion and contraction of suitable habitats were noticed among the species. For example, N. amazonum, N. rudgeana, and N. lasiophylla future habitat expansions declined and habitat contraction increased, while for N. ampla and N. jamesoniana, both future habitat expansion and contraction increased, and for N. pulchella and N. rudgeana it varied in the RCPs. Moreover, the largest projected suitable habitats were projected outside protected areas, characterized by high human impacts, despite our analysis indicating no significant change between protected and unprotected areas in suitable habitat change. Finally, understanding how climate change and land use affect species distribution is critical to developing conservation measures for aquatic species. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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17 pages, 15150 KiB

Open AccessEditor’s ChoiceArticle

Characterization of Okra (Abelmoschus esculentus L.) Accessions with Variable Drought Tolerance through Simple Sequence Repeat Markers and Phenotypic Traits

by Sonto Silindile Mkhabela, Hussein Shimelis, Abe Shegro Gerrano, Jacob Mashilo and Admire Shayanowako

Diversity 2022, 14(9), 747; https://doi.org/10.3390/d14090747 - 11 Sep 2022

Cited by 5 | Viewed by 3386

Abstract

Genetic diversity analysis of crop genetic resources is a prerequisite for parental selection with suitable and complementary profiles for breeding. The objectives of this study were to determine genetic diversity present among okra accessions using simple sequence repeat (SSR) and complementary phenotypic markers [...] Read more.

Genetic diversity analysis of crop genetic resources is a prerequisite for parental selection with suitable and complementary profiles for breeding. The objectives of this study were to determine genetic diversity present among okra accessions using simple sequence repeat (SSR) and complementary phenotypic markers and to select genetically divergent and superior parental accessions for pre-breeding. Twenty-six preliminarily selected okra accessions were assessed using nine highly polymorphic SSR markers and phenotyped under drought-stressed (DS) and non-stressed (NS) environmental conditions using a 13 × 2 alpha lattice design with two replications. Data were collected on the following eleven phenotypic traits: plant height (PH), days to 50% maturity (DTM), fresh pod length (FPL), dry pod weight (DPW), dry pod length (DPL), number of pods per plant (NPPP), pod yield per plant (PYPP), total above-ground biomass (AGB), harvest index (HI), root weight (RW), and root to shoot ratio (RSR). The SSR markers revealed an expected mean heterozygosity value of 0.54, indicating moderate genetic diversity among the tested okra accessions. Cluster analysis based on phenotypic and SSR markers differentiated the accessions into three distinct genetic groups. Wide phenotypic variation was observed for PH, FPL, NPPP, and PYPP under NS and DS conditions. PYPP was positively and significantly correlated with FPL (r = 0.81), ABG (r = 0.69), and HI (r = 0.67) under DS conditions, and FPL (r = 0.83) and AGB (r = 0.60) under NS conditions. Genetically complementary accessions such as LS04, LS05, LS06, LS07, LS08, LS10, LS11, LS15, LS18, LS23, LS24, and LS26 were identified for their high yield potential and related yield-improving traits under DS conditions. The identified accessions are recommended as parents for hybridization and selection programs to improve the yield potential of okra under drought-stressed environments. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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14 pages, 3395 KiB

Open AccessArticle

Spatial Patterns and Determinants of Endemic Taxa Richness in the Genus Viburnum (Adoxaceae) in China

by Wenjun Lyu, Shenglan Du, Jiali Ying, Veronicah Mutele Ngumbau, Sheng Huang, Shengwei Wang and Hongtao Liu

Diversity 2022, 14(9), 744; https://doi.org/10.3390/d14090744 - 10 Sep 2022

Cited by 1 | Viewed by 2266

Abstract

Understanding the distribution patterns and formation mechanisms of endemic taxa is essential for effective biodiversity conservation. China is an important distribution and endemic center for genus Viburnum in Asia. However, the distribution pattern and formation mechanism of endemic taxa of Viburnum remains unclear [...] Read more.

Understanding the distribution patterns and formation mechanisms of endemic taxa is essential for effective biodiversity conservation. China is an important distribution and endemic center for genus Viburnum in Asia. However, the distribution pattern and formation mechanism of endemic taxa of Viburnum remains unclear in China. In this study, we determined the distribution information of 61 endemic taxa of Viburnum through specimens’ review and field surveys. Species distribution models were used to clarify the distribution patterns of the endemic taxa of Viburnum. The findings shows that the hotspot for overall endemic taxa of Viburnum in China is mainly distributed in temperate and subtropical mountainous areas, and the highest richness in the mountainous regions were around the Yunnan-Guizhou Plateau and the Sichuan Basin. About one-third of the endemic taxa of Viburnum were rare species, whose distribution area was scattered and lacked protection. The distribution pattern of the endemic taxa of genus Viburnum can be well explained within the three hypotheses of environmental energy, water availability and climate seasonality. This study provides additional understanding and explanation of endemic species richness distribution and their formation mechanisms. In addition, it provides conservation measures for endemic taxa of genus Viburnum to guide conservationists and policy makers in China. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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16 pages, 1710 KiB

Open AccessArticle

Conservation Significance of the Rare and Endangered Tree Species, Trigonobalanus doichangensis (Fagaceae)

by Ling Hu, Xin-Gui Le, Shi-Shun Zhou, Can-Yu Zhang, Yun-Hong Tan, Qiang Ren, Hong-Hu Meng, Yupeng Cun and Jie Li

Diversity 2022, 14(8), 666; https://doi.org/10.3390/d14080666 - 17 Aug 2022

Cited by 8 | Viewed by 5755

Abstract

Trigonobalanus doichangensis is a rare and endangered species with important evolutionary value and extremely small populations. We investigated the genetic diversity of T. doichangensis to provide information on its effective preservation. We used genotyping-by-sequencing (GBS) technology to assess the genetic diversity, genetic structure [...] Read more.

Trigonobalanus doichangensis is a rare and endangered species with important evolutionary value and extremely small populations. We investigated the genetic diversity of T. doichangensis to provide information on its effective preservation. We used genotyping-by-sequencing (GBS) technology to assess the genetic diversity, genetic structure and gene flow of the six populations of T. doichangensis. Analysis of SNPs indicated that there was high genetic diversity in the ML and XSBN populations of T. doichangensis. F_ST values showed moderate genetic differentiation among the populations of T. doichangensis. Meanwhile, admixture, principal components and gene flow analyses indicated that the populations of T. doichangensis are not genetically separated in accordance with their geographical distributions. Habitat destruction and excessive exploitation may have led to a low gene flow, which has in turn resulted in the differences in seed and seedling morphological traits among populations. Based on these findings, we recommend that T. doichangensis be conserved through in situ approaches and artificial seedlings, including preservation of each extant population. Particularly, the ML and XSBN populations have high diversity and more ancestral information, so these two populations should be considered as conservation priorities, and seeds should be collected to obtain germplasm and increase the genetic diversity. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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16 pages, 2726 KiB

Open AccessArticle

Development of EST-SSR Markers Related to Polyphyllin Biosynthesis Reveals Genetic Diversity and Population Structure in Paris polyphylla

by Xiaoyang Gao, Qixuan Su, Baolin Yao, Wenjing Yang, Weisi Ma, Bin Yang and Changning Liu

Diversity 2022, 14(8), 589; https://doi.org/10.3390/d14080589 - 23 Jul 2022

Cited by 7 | Viewed by 2253

Abstract

Paris polyphylla is an important medicinal plant that can biosynthesize polyphyllins with multiple effective therapies, ranging from anti-inflammation to antitumor; however, the genetic diversity of Paris polyphylla is still unclear. To explore the genetic characteristics of cultivation populations in primary planting areas, we [...] Read more.

Paris polyphylla is an important medicinal plant that can biosynthesize polyphyllins with multiple effective therapies, ranging from anti-inflammation to antitumor; however, the genetic diversity of Paris polyphylla is still unclear. To explore the genetic characteristics of cultivation populations in primary planting areas, we developed 10 expressed sequence tag simple sequence repeat (EST-SSR) markers related to polyphyllin backbone biosynthesis and utilized them in 136 individuals from 10 cultivated populations of P. polyphylla var. yunnanensis. The genetic diversity index showed that ten loci had relatively high genetic polymorphism levels. Shannon information of loci suggested that more information occurred within population and less information occurred among population. In addition, the overall populations exhibited a low degree of differentiation among populations, but maintained a high degree of genetic diversity among individuals, resulting in high gene flow and general hybridization. The genetic structure analysis revealed that 10 populations possibly derived from two ancestral groups and all individuals were found with different levels of admixture. The two groups were different from the cultivation groups at population level, suggesting the cross-pollination among cultivars. These findings will provide insights into the genetic diversity of the germplasm resources and facilitate marker-assisted breeding for this medicinal herb. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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11 pages, 1657 KiB

Open AccessArticle

The Chromosome-Level Genome of Elaeagnus moorcroftii Wall., an Economically and Ecologically Important Tree Species in Drylands

by Xinxing Fu, Jingjing Wu, Xiaohui Ma, Kunpeng Li, Hui Zhang, Shengdan Wu and Kun Sun

Diversity 2022, 14(6), 468; https://doi.org/10.3390/d14060468 - 11 Jun 2022

Cited by 7 | Viewed by 3163

Abstract

Elaeagnus moorcroftii Wall. (Elaeagnaceae) is an important tree species naturally growing in arid Northwest China that has great economic and ecological values in drylands. In this study, we de novo assembled a chromosome-level genome for E. moorcroftii by using PacBio’s high-fidelity (HiFi) sequencing [...] Read more.

Elaeagnus moorcroftii Wall. (Elaeagnaceae) is an important tree species naturally growing in arid Northwest China that has great economic and ecological values in drylands. In this study, we de novo assembled a chromosome-level genome for E. moorcroftii by using PacBio’s high-fidelity (HiFi) sequencing and Hi-C-assisted assembly technology. The assembled genome size was 529.56 Mb, of which 94.56% was anchored to 14 pseudochromosomes with a contig N50 up to 28.21 Mb. In total, 29,243 protein-coding genes were annotated, and 98.5% of the Benchmarking Universal Single-Copy Orthologs (BUSCOs) were captured in the genome. Evolutionary genomic analysis showed that E. moorcroftii split with Elaeagnus mollis 9.38 million years ago (Ma), and contrasted evolutionary trajectories of gene family expansion and contraction were observed for these two closely related species. Furthermore, we identified two successive whole genome duplication (WGD) events occurred in the genome of E. moorcroftii, in addition to the ancient gamma hexaploidization event shared by core eudicots. Together, the chromosome-level genome assembly for E. moorcroftii decoded here provides valuable genomic information for the further genetic improvement and molecular breeding of this indigenous species in drylands. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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17 pages, 4020 KiB

Open AccessArticle

Phylogeography and Population History of Eleutharrhena macrocarpa (Tiliacoreae, Menispermaceae) in Southeast Asia’s Most Northerly Rainforests

by Shijie Song, Jianyong Shen, Shishun Zhou, Xianming Guo, Jinchao Zhao, Xinghui Shi, Zhiyong Yu, Qiangbang Gong, Shaohua You and Sven Landrein

Diversity 2022, 14(6), 437; https://doi.org/10.3390/d14060437 - 30 May 2022

Viewed by 2366

Abstract

The diversification of Tiliacoreae and the speciation of Eleutharrhena are closely linked to Southeast Asia’s most northerly rainforests which originate from the Himalayan uplift. Migration routes across biogeographical zones within the Asian clade, including those of Eleutharrhena, Pycnarrhena, and Macrococculus, [...] Read more.

The diversification of Tiliacoreae and the speciation of Eleutharrhena are closely linked to Southeast Asia’s most northerly rainforests which originate from the Himalayan uplift. Migration routes across biogeographical zones within the Asian clade, including those of Eleutharrhena, Pycnarrhena, and Macrococculus, and their population structures are still unexplored. We combine endocarp morphology, phylogenetic analyses, divergence time estimation, ancestral area reconstruction, as well as SCoT method to reconstruct the past diversification of Eleutharrhena macrocarpa and to understand their current distribution, rarity, and evolutionary distinctiveness. The disjunct, monospecific, and geographically restricted genera Eleutharrhena and Macrococculus both have a dry aril, a unique feature in Menispermaceae endocarps that further confirms their close relationship. Pycnarrhena and Eleutharrhena appeared during the end of the Oligocene c. 23.10 million years ago (Mya) in Indochina. Eleutharrhena speciation may be linked to climate change during this time, when humid forests became restricted to the northern range due to the Himalayan uplift. Differentiation across the Thai–Burmese range could have contributed to the isolation of the Dehong populations during the Miocene c. 15.88 Mya, when exchange between India and continental Asia ceased. Dispersal to the Lanping–Simao block and further differentiation in southeastern and southern Yunnan occurred during the Miocene, c. 6.82 Mya. The specific habitat requirements that led to the biogeographic patterns observed in E. macrocarpa contributed to a low genetic diversity overall. Population 1 from Dehong, 16 from Pu’er, and 20 from Honghe on the East of the Hua line have a higher genetic diversity and differentiation; therefore, we suggest that their conservation be prioritized. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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13 pages, 3154 KiB

Open AccessArticle

Taxonomic Uncertainty and Its Conservation Implications in Management, a Case from Pyrus hopeiensis (Rosaceae)

by Xian-Yun Mu, Jiang Wu and Jun Wu

Diversity 2022, 14(6), 417; https://doi.org/10.3390/d14060417 - 24 May 2022

Cited by 6 | Viewed by 2310

Abstract

Improved taxonomies and phylogenies are essential for understanding the evolution of organisms, the development of conservation plans, and the allocation of funds and resources, especially for threatened species with uncertain identities. Pears are an economically and nutritionally important fruit, and wild pear species [...] Read more.

Improved taxonomies and phylogenies are essential for understanding the evolution of organisms, the development of conservation plans, and the allocation of funds and resources, especially for threatened species with uncertain identities. Pears are an economically and nutritionally important fruit, and wild pear species are highly valued and protected because of their utility for the development of cultivars. Pyrus hopeiensis is an endangered species endemic to North China, which is sympatric with and difficult to distinguish from the widely distributed and morphologically similar species P. ussuriensis. To clarify its taxonomic identity, principal coordinate analysis was performed using 14 quantitative and qualitative characters from P. hopeiensis, P. ussuriensis, and P. phaeocarpa, and phylogenomic analysis was performed based on whole-genome resequencing and whole plastome data. Pyrus hopeiensis was synonymized with P. ussuriensis based on morphological and phylogenetic evidence, as well as our long-term field studies. Pyrus hopeiensis is proposed to be excluded from the list of local key protected wild plants. Given that the holotype of P. ussuriensis was not designated, a lectotype was designated in this work. Integrative evidence-based taxonomic study including museomics is suggested for organisms with uncertain identities, which will contribute to biodiversity conservation. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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13 pages, 2672 KiB

Open AccessArticle

Biogeography and Diversification of the Tropical and Subtropical Asian Genus Gastrochilus (Orchidaceae, Aeridinae)

by Yang Li, Weitao Jin, Liguo Zhang, Peng Zhou, Yan Luo, Ziwei Zhu and Xiaoguo Xiang

Diversity 2022, 14(5), 396; https://doi.org/10.3390/d14050396 - 17 May 2022

Cited by 4 | Viewed by 2991

Abstract

Tropical and subtropical Asia are major orchid diversity and endemism centers. However, the evolutionary dynamics of orchids in these areas remain poorly studied. Gastrochilus D. Don, a species-rich orchid genus from tropical and subtropical Asian forests, was employed to investigate the issue. We [...] Read more.

Tropical and subtropical Asia are major orchid diversity and endemism centers. However, the evolutionary dynamics of orchids in these areas remain poorly studied. Gastrochilus D. Don, a species-rich orchid genus from tropical and subtropical Asian forests, was employed to investigate the issue. We firstly used eight DNA regions to reconstruct the phylogeny and estimate the divergence times within Gastrochilus. We inferred the ancestral ranges and conducted a diversification analysis based on empirical and simulated data. Subsequently, we assessed the ancestral niche state and tested for phylogenetic signals in the evolution of niche conditions. Our results suggested that the most recent common ancestor of Gastrochilus occurred in the subtropical area of the East Asiatic region in the late Miocene (8.13 Ma). At least eight dispersal events and four vicariant events were inferred to explain the current distribution of Gastrochilus, associated with the global cooling from the Plio-Pleistocene. The genus experienced a slowly decreasing diversification rate since its origin, and no significant correlation between current niches and phylogenetic relatedness was observed. The diversification of Gastrochilus was attributed to accumulation through time, integrated with the intensification of the Asian Monsoon system during the Plio-Pleistocene, pollination, and epiphytism. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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17 pages, 3606 KiB

Open AccessArticle

Effects of Bamboo Forest Type and Density on the Growth of Bletilla striata and Root Endophytic Fungi

by Hao Fu, Zhilin Song, Shanmin Li, Siren Lan, Xinhua Zeng and Weichang Huang

Diversity 2022, 14(5), 391; https://doi.org/10.3390/d14050391 - 14 May 2022

Cited by 3 | Viewed by 2391

Abstract

Bletilla striata is a terrestrial orchid with high ornamental and medicinal values that is widely interplanted in bamboo forests. However, little is known about the effects of bamboo forest type and density on the growth of B. striata and its symbiotic relationship with [...] Read more.

Bletilla striata is a terrestrial orchid with high ornamental and medicinal values that is widely interplanted in bamboo forests. However, little is known about the effects of bamboo forest type and density on the growth of B. striata and its symbiotic relationship with root endophytic fungi. In this study, the growth state of B. striata, the community composition and diversity of its root endophytic fungal, and the fungal nutritional function were investigated in Phyllostachys edulis, P. iridescens and P. glauca forests with three densities. We found that the type and density of the bamboo forest had significant effects on the growth of B. striata, with the biomass, leaf width, root quantity and width being the highest in the low-density of the P. edulis forest. The community composition and abundance of root endophytic fungi in B. striata varied among different bamboo forests and densities, with P. edulis and P. iridescens forests dominated by Basidiomycota and Serendipita, while P. glauca prevailed by Ascomycota and Dactylonectria. The trophic modes of root endophytic fungi were also affected by forest types and densities. The abundance of symbiotroph fungi was the highest in P. edulis and P. iridescens forests and greatly varied with density gradient, and saprotrophic fungi comprised the highest proportion in the Ph. glauca forest. These results provide basic data for further research and the configuration between bamboo species and terrestrial orchids. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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17 pages, 2785 KiB

Open AccessArticle

Evolution of Reproductive Traits and Implications for Adaptation and Diversification in the Yam Genus Dioscorea L.

by Min Chen, Xiaoqin Sun, Jia-Yu Xue, Yifeng Zhou and Yueyu Hang

Diversity 2022, 14(5), 349; https://doi.org/10.3390/d14050349 - 29 Apr 2022

Cited by 4 | Viewed by 4766

Abstract

Dioscorea is a pantropical monocotyledonous genus encompassing several well-known tuber crops and medicinal plants. It possesses remarkable morphological diversity, especially in reproductive characteristics, which are suggested to play important roles in species adaptation and diversification. Yet there have been few studies that consider [...] Read more.

Dioscorea is a pantropical monocotyledonous genus encompassing several well-known tuber crops and medicinal plants. It possesses remarkable morphological diversity, especially in reproductive characteristics, which are suggested to play important roles in species adaptation and diversification. Yet there have been few studies that consider the evolutionary pattern followed by these characters in this genus. In this study, the phylogenetic relationships among Chinese yams were reconstructed from five chloroplast and two mitochondrial DNA sequences. The evolutionary histories of bulbil possession, inflorescence architecture, the color of the male flowers and the degree of male flower opening were reconstructed. The results suggested that yam bulbils evolved after the divergence between D. sect. Testudinaria and other species of Dioscorea except for in D. sect. Stenophora and D. sect. Apodostemon. The evolutionary trend in the degree of male flower opening ranged from fully open to nearly closed. Male flowers with dark colors and panicles were shown to be derived in Dioscorea. These characteristics were found to be closely associated with the reproductive patterns and pollinating mechanisms of the Dioscorea species. The findings also shed light on the systematic relationships within this genus. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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19 pages, 6350 KiB

Open AccessArticle

Chloroplast Genome of Salvia Sect. Drymosphace: Comparative and Phylogenetic Analysis

by Ting Su, Yan-Fei Geng, Chun-Lei Xiang, Fei Zhao, Mei Wang, Li Gu and Guo-Xiong Hu

Diversity 2022, 14(5), 324; https://doi.org/10.3390/d14050324 - 22 Apr 2022

Cited by 6 | Viewed by 2275

Abstract

Sect. Drymosphace is one of eight sections of Salvia subg. Glutinaria and includes 13 species and one dubious species that hold great economic value. Although the section is well supported, interspecific relationships remain unresolved. Moreover, most of this section’s plastome information remains unknown. [...] Read more.

Sect. Drymosphace is one of eight sections of Salvia subg. Glutinaria and includes 13 species and one dubious species that hold great economic value. Although the section is well supported, interspecific relationships remain unresolved. Moreover, most of this section’s plastome information remains unknown. In this study, we sequenced and assembled eight sect. Drymosphace plastomes and conducted comparative analyses within this section. The length of plastid genome sequences ranged from 151,330 bp to 151,614 bp, with 80 protein-coding, 30 tRNA, and four rRNA genes being annotated. The plastomes were found to be as conservative as other Lamiaceae species, showing high consistency and similarity in terms of gene content, order, and structure. Within the sect. Drymosphace, single-copy regions were more variable than IR regions, and the intergenic regions were more variable than the coding regions; nine hypervariable regions were detected, and some of them may be useful for the phylogenetic analysis of Salvia. The topologies inferred from all of the data sets indicated that sect. Drymosphace was monophyletic and that S. honania was sister to S. meiliensis. Compared to previous studies involving more sect. Drymosphace species, phylogenomic analyses can improve the phylogenetic resolution considerably. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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13 pages, 27041 KiB

Open AccessArticle

Integrative Taxonomy Supports Two New Species of Rhodiola (Crassulaceae) in Xizang, China

by Shiyong Meng, Zimeng Wang and Lv Ye

Diversity 2022, 14(4), 289; https://doi.org/10.3390/d14040289 - 12 Apr 2022

Cited by 3 | Viewed by 2457

Abstract

The Qinghai–Tibet Plateau includes the Himalayas and Hengduan Mountains and is well known for its rich biodiversity. Evolutionary radiation is one of the main ways by which plants diversify in mountains, particularly the Qinghai–Tibet Plateau. It presents a large challenge to the classification [...] Read more.

The Qinghai–Tibet Plateau includes the Himalayas and Hengduan Mountains and is well known for its rich biodiversity. Evolutionary radiation is one of the main ways by which plants diversify in mountains, particularly the Qinghai–Tibet Plateau. It presents a large challenge to the classification of taxa that radiate quickly. One way to overcome these challenges is to continue conducting detailed field studies while integrating morphological and molecular evidence to classify these taxa. The aim of this research was to provide a case for the systematic study of the complex taxa Rhodiola, which rapidly radiate. During the field study, we found two unique variants of Rhodiola in an alpine dry meadow and beds of pebbles on beaches, respectively. We utilized a morphological principal component analysis, scanning electron microscopy and molecular phylogenetic analysis to propose two new species: Rhodiola wangii S.Y. Meng and Rhodiola namlingensis S.Y. Meng. R. wangii is similar to R. stapfii (Hamet) S.H. Fu, but it differs in having an intensely broad rhombus and alternate leaves, a distinct petiole, stamens gathered together and reflexed purple scales. R. namlingensis is similar to R. prainii (Hamet) H. Ohba, but it differs in its exerted alternate leaves, the presence of more than four leaves on the stem, thick leaf blades, an obovate to inverted triangle, and short petioles. The conservation status of these two species was also assessed. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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15 pages, 2350 KiB

Open AccessArticle

Effect of Hermaphrodite–Gynomonoecious Sexual System and Pollination Mode on Fitness of Early Life History Stages of Offspring in a Cold Desert Perennial Ephemeral

by Jannathan Mamut, Junhui Cheng, Dunyan Tan, Carol C. Baskin and Jerry M. Baskin

Diversity 2022, 14(4), 268; https://doi.org/10.3390/d14040268 - 1 Apr 2022

Viewed by 3087

Abstract

Gynomonoecy, the occurrence of both pistillate (female) and perfect (hermaphroditic) flowers on the same plant, has received little attention compared to gynodioecy and other plant sexual systems. Eremurus anisopterus is a perennial ephemeral in the cold desert of northwest China with a hermaphrodite–gynomonoecious [...] Read more.

Gynomonoecy, the occurrence of both pistillate (female) and perfect (hermaphroditic) flowers on the same plant, has received little attention compared to gynodioecy and other plant sexual systems. Eremurus anisopterus is a perennial ephemeral in the cold desert of northwest China with a hermaphrodite–gynomonoecious sexual system in the same population. The primary aim of this study was to compare the early life history traits and inbreeding depression between progeny from pistillate and hermaphrodite flowers in hermaphrodites and gynomonoecious individuals. All of the traits of progeny from outcrossed pistillate flowers on gynomonoecious plants were significantly greater than for other pollination types. Selfing (vs. outcrossing) resulted in a decrease in all traits, indicating inbreeding depression (ID) during early life history stages of gynomonoecious and hermaphroditic plants. ID for seed mass, seed germination and seedling survivorship under water stress for pistillate flowers on gynomonoecious plants was significantly higher than it was for hermaphrodite flowers on both gynomonoecious and hermaphrodite plants. The advantage of the offspring of pistillate (vs. hermaphrodite) flowers may contribute to the maintenance of gynomonoecy in E. anisopterus in its cold desert sand dune habitat. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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18 pages, 5995 KiB

Open AccessArticle

Real-Time Classification of Invasive Plant Seeds Based on Improved YOLOv5 with Attention Mechanism

by Lianghai Yang, Jing Yan, Huiru Li, Xinyue Cao, Binjie Ge, Zhechen Qi and Xiaoling Yan

Diversity 2022, 14(4), 254; https://doi.org/10.3390/d14040254 - 29 Mar 2022

Cited by 13 | Viewed by 3549

Abstract

Seeds of exotic plants transported with imported goods pose a risk of alien species invasion in cross-border transportation and logistics. It is critical to develop stringent inspection and quarantine protocols with active management to control the import and export accompanied by exotic seeds. [...] Read more.

Seeds of exotic plants transported with imported goods pose a risk of alien species invasion in cross-border transportation and logistics. It is critical to develop stringent inspection and quarantine protocols with active management to control the import and export accompanied by exotic seeds. As a result, a method for promptly identifying exotic plant seeds is urgently needed. In this study, we built a database containing 3000 images of seeds of 12 invasive plants and proposed an improved YOLOv5 target detection algorithm that incorporates a channel attention mechanism. Given that certain seeds in the same family and genus are very similar in appearance and are thus difficult to differentiate, we improved the size model of the initial anchor box to converge better; moreover, we introduce three attention modules, SENet, CBAM, and ECA-Net, to enhance the extraction of globally important features while suppressing the weakening of irrelevant features, thereby effectively solving the problem of automated inspection of similar species. Experiments on an invasive alien plant seed data set reveal that the improved network model fused with ECA-Net requires only a small increase in parameters when compared to the original YOLOv5 network model and achieved greater classification and detection accuracy without affecting detection speed. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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14 pages, 5431 KiB

Open AccessFeature PaperArticle

Reproductive Ecology of Distylous Shoreside Polygonum criopolitanum Hance

by Ming-Lin Chen, Meng-Ying Qi, Bei-Bei Bai and Xue Han

Diversity 2022, 14(3), 222; https://doi.org/10.3390/d14030222 - 18 Mar 2022

Cited by 2 | Viewed by 2257

Abstract

In this study, distyly was clearly confirmed in Polygonum criopolitanum Hance, which exhibited strict self-incompatibility. Unlike other distylous species, style-morph ratios of P. criopolitanum often deviated obviously from 1:1, and many populations were solely composed of long or short stylous flowers; the 1:1 [...] Read more.

In this study, distyly was clearly confirmed in Polygonum criopolitanum Hance, which exhibited strict self-incompatibility. Unlike other distylous species, style-morph ratios of P. criopolitanum often deviated obviously from 1:1, and many populations were solely composed of long or short stylous flowers; the 1:1 style-morph ratio was occasionally found in very large populations. P. criopolitanum was dimorphic for intrinsic features such as style height and anther height and ancillary features such as pollen size and number. The L-morph flowers produced a significantly smaller and higher number of pollen grains than the S-morph flowers, and the stigma papillae of both morphs were not significantly different. We nearly found no seed sets in most wild populations and very low seed sets occasionally occurred in large populations, which was different from other species of Polygonaceae. Mating experiments showed that P. criopolitanum has a strict self-incompatibility system and clonal propagation was more common than sexual propagation, which was adaptive with the unisexual wild populations. Hygrocolous habitat, 20–60% soil water content, and height gap less than 4 m to the adjacent water were the main limiting factors for the distribution of P. criopolitanum. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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21 pages, 26163 KiB

Open AccessArticle

Effects of Landscape and Local Factors on the Diversity of Flower-Visitor Groups under an Urbanization Gradient, a Case Study in Wuhan, China

by Mengyu He, Nan Ran, Huiqian Jiang, Zemin Han, Yuanyong Dian, Xiaoxia Li, Dong Xie, Peter A. Bowler and Hui Wang

Diversity 2022, 14(3), 208; https://doi.org/10.3390/d14030208 - 11 Mar 2022

Cited by 8 | Viewed by 3525

Abstract

Urbanization is one of the primary forces driving worldwide pollinator decline. Moderate urban expansion with appropriate green space planning can help in maintaining pollinator diversity and pollination service. We investigated the relative effects of landscape and local factors on the diversity of flower-visitor [...] Read more.

Urbanization is one of the primary forces driving worldwide pollinator decline. Moderate urban expansion with appropriate green space planning can help in maintaining pollinator diversity and pollination service. We investigated the relative effects of landscape and local factors on the diversity of flower-visitor functional groups in a moderately urbanized city, Wuhan, located in central China. We found that the proportion of impervious surface had no significant effect on the number of visitations, but it was negatively associated with the diversity of flower-visitor groups. The number of visitations by Halictidae and Lepidoptera correlated positively with local flower density and flowering plant species richness, respectively. Flowering plant species richness was also positively correlated with the diversity of flower-visitor groups. The proportion of green space was negatively associated with the visitation number of Muscidae and the overall diversity of flower-visitor groups, revealing the potential influence of green space quality on pollinator assemblage. The pollination networks under three urbanization levels (with a total of 11 flower visitor groups and 43 plant species) were asymmetric, highly nested, and generalized. The suburb sites contained the highest diversity of interactions. Core flowering plants (Oenothera speciosa, Coreopsis grandiflora and Cyanus segetum) are exotic species with attractive flowers. Improving green space quality (high flower density and flowering plant species richness) and using attractive native flowering plants (Nandina domestica, Rosa chinensis, Astragalus sinicus, Cirsium arvense var. integrifolium, and Zabelia biflora) would enhance the function of urban green space to maintain pollinator diversity and ecosystem stability. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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15 pages, 1668 KiB

Open AccessArticle

Response of Phytoplankton Community Structure to Vegetation Restoration after Removal of Purse Seine in Shengjin Lake

by Xudong Zheng, Jingwen Chen, Wenli Guo, Zhongze Zhou and Xiaoxin Ye

Diversity 2022, 14(3), 178; https://doi.org/10.3390/d14030178 - 28 Feb 2022

Cited by 6 | Viewed by 2556

Abstract

Aquatic vegetation has been restored since the removal of seine nets from the lake surface of Shengjin Lake in 2018. Through four seasons of phytoplankton sampling surveys from 2019–2020, we analyzed spatial and temporal changes in phytoplankton communities, water quality, and aquatic plant [...] Read more.

Aquatic vegetation has been restored since the removal of seine nets from the lake surface of Shengjin Lake in 2018. Through four seasons of phytoplankton sampling surveys from 2019–2020, we analyzed spatial and temporal changes in phytoplankton communities, water quality, and aquatic plant recovery in conjunction with previous research literature to reveal the response mechanisms of phytoplankton community structure to rapidly recovering aquatic vegetation. The results showed that the Secchi depth increased (0.4 m to 0.7 m), the concentration of total phosphorus decreased (0.053 mg/L to 0.41 mg/L), the species of aquatic plants (5 species to 16 species), phytoplankton species (210 species to 254 species) and cell density increased after the removal of the seine. Since the removal of the seine of Shengjin Lake, the aquatic vegetation cover has exceeded 80%, the phytoplankton biodiversity has increased, and the water quality has recovered to II-III water status. Our results show that aquatic plants improve water quality through direct and indirect effects and influence phytoplankton community structure together with the water environment, which can provide guidance for the restoration situation of the middle and lower reaches of the Yangtze River through-river lake ecosystems. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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15 pages, 6778 KiB

Open AccessArticle

Bauhinia (Leguminosae) Fossils from the Paleogene of Southwestern China and Its Species Accumulation in Asia

by Lin-Bo Jia, Jin-Jin Hu, Shi-Tao Zhang, Tao Su, Robert A. Spicer, Jia Liu, Jiu-Cheng Yang, Pu Zou, Yong-Jiang Huang and Zhe-Kun Zhou

Diversity 2022, 14(3), 173; https://doi.org/10.3390/d14030173 - 27 Feb 2022

Cited by 4 | Viewed by 3533

Abstract

Extant Bauhinia (Leguminosae) is a genus of 300 species of trees, shrubs, and lianas, widely distributed in pantropical areas, but its diversification history in southeastern Asia, one of its centers of highest diversity, remains unclear. We report new fossils of three Bauhinia species [...] Read more.

Extant Bauhinia (Leguminosae) is a genus of 300 species of trees, shrubs, and lianas, widely distributed in pantropical areas, but its diversification history in southeastern Asia, one of its centers of highest diversity, remains unclear. We report new fossils of three Bauhinia species with cuticular preservation from the Paleogene of Puyang Basin, southwestern China. Our finding likely extends the emergence of Bauhinia in Asia to the late Eocene. Together with previously reported fossil records, we show that the diversification of Bauhina in Asia and the phenomenon of a small region harboring multiple Bauhinia species in southwestern China could be traced back to the Paleogene. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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16 pages, 49355 KiB

Open AccessArticle

Population Genetic Structure and Biodiversity Conservation of a Relict and Medicinal Subshrub Capparis spinosa in Arid Central Asia

by Qian Wang and Hong-Xiang Zhang

Diversity 2022, 14(2), 146; https://doi.org/10.3390/d14020146 - 17 Feb 2022

Cited by 8 | Viewed by 2850

Abstract

As a Tertiary Tethyan relict, Capparis spinosa is a typical wind-preventing and sand-fixing deciduous subshrub in arid central Asia. Due to its medicinal and energy value, this species is at risk of potential threat from human overexploitation, habitat destruction and resource depletion. In [...] Read more.

As a Tertiary Tethyan relict, Capparis spinosa is a typical wind-preventing and sand-fixing deciduous subshrub in arid central Asia. Due to its medicinal and energy value, this species is at risk of potential threat from human overexploitation, habitat destruction and resource depletion. In this study, our purpose was to evaluate the conservation strategies of C. spinosa according to its genetic structure characteristics and genetic diversity pattern among 37 natural distributional populations. Based on genomic SNP data generated from dd-RAD sequencing, genetic diversity analysis, principal component analysis, maximum likelihood phylogenetic trees and ADMIXTURE clustering, the significant population structure and differentiation were explored. The results showed the following: (1) Six distinct lineages were identified corresponding to geographic locations, and various levels of genetic diversity existed among the lineages for the natural habitat heterogeneity or human interferences; (2) The lineage divergences were influenced by isolation by distances, vicariance and restricted gene flow under complex topographic and climatic conditions. Finally, for the preservation of the genetic integrity of C. spinosa, we suggest that conservation units should be established corresponding to different geographic groups, and that attention should be paid to isolated and peripheral populations that are experiencing biodiversity loss. Simultaneously, monitoring and reducing anthropogenic disturbances in addition to rationally and sustainably utilizing wild resources would be beneficial to guarantee population resilience and evolutionary potential of this xerophyte in response to future environmental changes. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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11 pages, 4946 KiB

Open AccessArticle

Phylogenetics and Biogeography of Lilium ledebourii from the Hyrcanian Forest

by Shekoofeh Shokrollahi, Hamed Yousefzadeh, Christian Parisod, Gholamali Heshmati, Hamid Bina, Shujait Ali, Narjes Amirchakhmaghi and Yigang Song

Diversity 2022, 14(2), 137; https://doi.org/10.3390/d14020137 - 15 Feb 2022

Cited by 1 | Viewed by 3074

Abstract

Lilium ledebourii (Baker) Boiss is one of the most endangered lilies, restricted to only a few small and fragmented areas in the Hyrcanian forest. This study aimed at evaluating the taxonomy of this unique Iranian lily and reconstructing divergence time from other species [...] Read more.

Lilium ledebourii (Baker) Boiss is one of the most endangered lilies, restricted to only a few small and fragmented areas in the Hyrcanian forest. This study aimed at evaluating the taxonomy of this unique Iranian lily and reconstructing divergence time from other species of the genus Lilium to address the role of this region in its diversification. Phylogenetic trees based on nuclear ITS and chloroplastic matK strongly supported the monophyly of the genus Lilium and division into subclades hardly matching prior morphological classifications. Biogeographic analyses using S-DIVA revealed East Asia as the ancestral range from where Lilium presented a multidirectional expansion towards North America, West-Central Asia, North Asia, and Europe. Diverging from ancestral Lilium during the beginning of Eocene (50 Ma; 95% HDP: 68.8–36.8). Specific members of Lilium colonized Iran (Western Asia) separated from the Clade IV (West-Central Asia and Europe lineage), and then yielded the Iranian L.ledebourri. Accordingly, the north of Iran appears to have promoted both long-term persistence and migration of Lily species from Asia to the Europe. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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14 pages, 47948 KiB

Open AccessArticle

Genetic Diversity and Mating System of Two Mangrove Species (Rhizophora apiculata and Avicennia marina) in a Heavily Disturbed Area of China

by Wenxun Lu, Zhen Zou, Xueying Hu and Shengchang Yang

Diversity 2022, 14(2), 115; https://doi.org/10.3390/d14020115 - 6 Feb 2022

Cited by 7 | Viewed by 3469

Abstract

Mangrove forests are distributed in the intertidal zones of tropical and subtropical regions, and have been severely damaged by anthropogenic activities, climate change, and stochastic events. Although much progress has been made in the conservation and restoration of mangroves in China, studies of [...] Read more.

Mangrove forests are distributed in the intertidal zones of tropical and subtropical regions, and have been severely damaged by anthropogenic activities, climate change, and stochastic events. Although much progress has been made in the conservation and restoration of mangroves in China, studies of the genetic diversity of mangroves are lacking, especially for isolated populations, yet such studies are essential for guiding conservation and restoration efforts. Here, we evaluated the genetic diversity, spatial genetic structure, and mating system of two mangrove species, Rhizophora apiculata and Avicennia marina, in a heavily disturbed area in Tielu Harbor, Sanya City, Hainan Island, China, using 18 nuclear microsatellite markers. We found that the genetic diversity of R. apiculata, which is classified as ‘Vulnerable’ in the China Red List categories, was high and similar compared with the genetic diversity estimates of other populations reported in previous studies. In contrast, the genetic diversity of A. marina, which is classified as a species of ‘Least Concern’, was low compared with the genetic diversity estimates of other populations. We then evaluated the presence of genetic bottlenecks, spatial genetic structure, and the mating system to determine the effects that habitat destruction has had on these two species. Our findings indicate that distinct conservation and restoration approaches are needed for these two species. Generally, our results provide valuable information that will aid the development of conservation and restoration strategies for the mangroves of Tielu Harbor. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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17 pages, 2569 KiB

Open AccessArticle

Phylogeography and Genetic Structure of Sand Dune Specialist Stilpnolepis centiflora (Asteraceae) in Northwest China Revealed by Molecular Data

by Xiaojun Shi, Xiaolong Jiang, Hongxiang Zhang and Juan Qiu

Diversity 2022, 14(2), 104; https://doi.org/10.3390/d14020104 - 31 Jan 2022

Viewed by 2883

Abstract

Stilpnolepis centiflora is an endemic annual herb in the Asteraceae family found across five sand deserts in Northwest China. We aimed to investigate the genetic structure of S. centiflora and attempt to link species evolution with desert formation during the Pleistocene era. We [...] Read more.

Stilpnolepis centiflora is an endemic annual herb in the Asteraceae family found across five sand deserts in Northwest China. We aimed to investigate the genetic structure of S. centiflora and attempt to link species evolution with desert formation during the Pleistocene era. We used sequence data from nuclear and chloroplast genes to investigate genetic diversity among 28 populations. We analyzed sequence data using network analysis, spatial analysis of molecular variance (SAMOVA), and a Mantel test. We then used a molecular clock to place the genetic patterns in a temporal framework and tested for signals of expansion using neutrality tests and by determining mismatch distributions. Six distinct haplotypes and 31 ribotypes were identified. Significant chloroplast DNA population subdivision was detected (G_ST = 0.952; N_ST = 0.976), but only moderate nrDNA subdivision (G_ST = 0.360; N_ST = 0.579) was detected. SAMOVA revealed four diverging groups of related haplotypes, coinciding with the boundaries of deserts. Molecular dating suggests that the clades representing different deserts diverged from 1.2 to 0.20 Ma, concordant with the Kun-Huang Movement of Qinghai Tibet Plateau uplift and a glacial event (Naynayxungla) during the Middle–Late Pleistocene. The disjunction of S. centiflora among different deserts was correspondingly reflected in the examined genetic traits with consistent spatiotemporal evolution between species and deserts. Therefore, the evolutionary dynamics of S. centiflora appear to have been driven by geological movement and climate change. The patterns described here are potentially useful to conservation biologists and may serve as a model for other sand-obligate organisms found in the deserts of Northwest China. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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13 pages, 3313 KiB

Open AccessArticle

Species Abundance Distributions Patterns between Tiankeng Forests and Nearby Non-Tiankeng Forests in Southwest China

by Linjuan Huang, Hao Yang, Xiaofei An, Yanmei Yu, Linlan Yu, Gui Huang, Xinyu Liu, Ming Chen and Yuegui Xue

Diversity 2022, 14(2), 64; https://doi.org/10.3390/d14020064 - 19 Jan 2022

Cited by 8 | Viewed by 3111

Abstract

Identifying the species abundance distributions (SADs) in Tiankeng forests is crucial for restoring and managing degraded karst ecosystem, whereas previous studies rarely explored the differences and response of vegetation dynamics to environmental variations. The species composition and SADs of the inner and outer [...] Read more.

Identifying the species abundance distributions (SADs) in Tiankeng forests is crucial for restoring and managing degraded karst ecosystem, whereas previous studies rarely explored the differences and response of vegetation dynamics to environmental variations. The species composition and SADs of the inner and outer fringe areas of Tiankeng forest and nearby non-Tiankeng forest were compared in Southwest China. Six models were adopted to compare SADs of three habitats. Kolmogrov–Smirnov (K–S) test was selected to compare the discrepancy between the simulated and observed SAD patterns. The Akaike Information Criterion (AIC) test was adopted to compare the models, and the best model was indicated by the lowest AIC value. The results showed that (1) the species dispersal from the inside of Tiankeng forests to the nearby non-Tiankeng forests is limited, while species have unlimited dispersal from nearby non-Tiankeng forests to the inside of Tiankeng forests via the fringe of Tiankeng forests. (2) Species abundance, species rarity, richness, and species accumulation rate in the Tiankeng forests were significant in non-Tiankeng forests (p < 0.05), and most species in inner Tiankeng forests originated from nearby non-Tiankeng forests. (3) Based on the criterion of K-S values, all models have passed the K–S test (p > 0.05), which indicated that niche processes and neutral process worked together in the maintenance of community species diversity, the community in study area is a niche-neutral continuum. (4) Considered the lowest AIC value, the neutral (△_mean AIC = 1.3) models performed better than the niche (△_mean AIC = 22.7) models and statistical (△_mean AIC = 2.7) in the Tiankeng forest, while the statistical models performed better than the niche and neutral models in the non-Tiankeng forests. The results suggested that the main driving force of Tiankeng forests is the neutral process. The negative terrain in Tiankeng restricted the species dispersal due to topographic constraints. However, the species dispersal from the nearby non-Tiankeng forests could promote the species succession in the inner Tiankeng. Therefore, we propose that nearby non-Tiankeng forests should be emphasized for protecting the biodiversity of Tiankeng forests. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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18 pages, 2046 KiB

Open AccessArticle

Homogenized Phylogeographic Structure across the Indo-Burma Ranges of a Large Monoecious Fig, Ficus altissima Blume

by Jian-Feng Huang, Clive T. Darwell and Yan-Qiong Peng

Diversity 2021, 13(12), 654; https://doi.org/10.3390/d13120654 - 9 Dec 2021

Cited by 7 | Viewed by 4132

Abstract

As well as bountiful natural resources, the Indo-Burma biodiversity hotspot features high rates of habitat destruction and fragmentation due to increasing human activity; however, most of the Indo-Burma species are poorly studied. The exploration of plants closely associated with human activity will further [...] Read more.

As well as bountiful natural resources, the Indo-Burma biodiversity hotspot features high rates of habitat destruction and fragmentation due to increasing human activity; however, most of the Indo-Burma species are poorly studied. The exploration of plants closely associated with human activity will further assist us to understand our influence in the context of the ongoing extinction events in the Anthropocene. This study, based on widely and intensively sampled F. altissima across Indo-Burma and the adjacent south China ranges, using both the chloroplast psbA-trnH spacer and sixteen newly developed nuclear microsatellite markers (nSSRs), aims to explore its spatial genetic structure. The results indicated low chloroplast haplotype diversity and a moderate level of nuclear genetic diversity. Although limited seed flow was revealed by psbA-trnH, no discernible phylogeographic structure was shown due to the low resolution of cpDNA markers and dominance of an ancestral haplotype. From the nSSRs data set, phylogeographic structure was homogenized, most likely due to extensive pollen flow mediated by pollinating fig wasps. Additionally, human cultivation and human-mediated transplanting further confounded the analyses of population structure. No geographic barriers are evident across the large study range, with F. altissima constituting a single population, and extensive human cultivation is likely to have had beneficial consequences for protecting the genetic diversity of F. altissima. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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Review

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11 pages, 3492 KiB

Open AccessReview

The Molecular Phylogeny of Land Plants: Progress and Future Prospects

by Guo-Qing Liu, Lian Lian and Wei Wang

Diversity 2022, 14(10), 782; https://doi.org/10.3390/d14100782 - 21 Sep 2022

Cited by 9 | Viewed by 16807

Abstract

Phylogenetics has become a powerful tool in many areas of biology. Land plants are the most important primary producers of terrestrial ecosystems and have colonized various habitats on Earth. In the past two decades, tremendous progress has been made in our understanding of [...] Read more.

Phylogenetics has become a powerful tool in many areas of biology. Land plants are the most important primary producers of terrestrial ecosystems and have colonized various habitats on Earth. In the past two decades, tremendous progress has been made in our understanding of phylogenetic relationships at all taxonomic levels across all land plant groups by employing DNA sequence data. Here, we review the progress made in large-scale phylogenetic reconstructions of land plants and assess the current situation of phylogenetic studies of land plants. We then emphasize directions for future study. At present, the phylogenetic framework of land plants at the order and familial levels has been well built. Problematic deep-level relationships within land plants have also been well resolved by phylogenomic analyses. We pointed out five major aspects of molecular phylogenetics of land plants, which are nowadays being studied and will continue to be goals moving forward. These five aspects include: (1) constructing the genus- and species-level phylogenies for land plant groups, (2) updating the classification systems by combining morphological and molecular data, (3) integrating fossil taxa into phylogenies derived from living taxa, (4) resolving deep-level and/or rapidly divergent phylogenetic relationships using phylogenomic data, and (5) building big trees using the supermatrix method. We hope that this review paper will promote the development of plant molecular phylogenetics and other related areas. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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18 pages, 10526 KiB

Open AccessReview

Flora and Vegetation of Yunnan, Southwestern China: Diversity, Origin and Evolution

by Hua Zhu and Yunhong Tan

Diversity 2022, 14(5), 340; https://doi.org/10.3390/d14050340 - 26 Apr 2022

Cited by 19 | Viewed by 7947

Abstract

Yunnan has a complicated geological history, a particular geography, and a complex topography, which have influenced the formation of various habitats of high biodiversity: 245 families; 2140 genera; 13,253 species and varieties of seed plants; more than 12 types of vegetation; and 167 [...] Read more.

Yunnan has a complicated geological history, a particular geography, and a complex topography, which have influenced the formation of various habitats of high biodiversity: 245 families; 2140 genera; 13,253 species and varieties of seed plants; more than 12 types of vegetation; and 167 plant formations, including tropical rain forests, tropical dry forests, subtropical evergreen broad-leaved forest, cold temperate coniferous forests, and alpine bushes and meadows. An analysis of the geographic elements to the current Yunnan flora shows that the tropical distribution contributed to 51% of all families and to 57.5% of all genera, of which the genera from the tropical Asian distribution make up the highest proportion among all geographical elements. During the late evolution of Yunnan, its flora was strongly affected by the tropical Asian flora. The complicated patterns and diversity in Yunnan flora and vegetation have been shaped mainly by its particular geological histories, which include the differential uplifts in topography, the clock-wise rotation of the Simao-Lanping geoblock, and the extrusion of the Indochina geoblock by the Himalayan uplift. The flora and vegetation of Yunnan were possibly derived from tropical-subtropical Tertiary flora before later diverging. Northwestern Yunnan flora likely evolved due to rapid speciation from families and genera from cosmopolitan and northern temperate distributions during the uplift of the Himalayas and climatic oscillations after the late Tertiary. Southern Yunnan flora likely evolved into tropical Asian flora following the southeastward extrusion of the Indochina block, which brought along tropical Asian elements. Central Yunnan flora inherited most of the elements of the Tertiary flora from East Asia. The formation and strengthening of the southwest monsoon by the uplift of the Himalayas was also a direct factor in the formation of the tropical rain forests found in southern Yunnan. The flora from southern and southeastern Yunnan also diverged, with the former being more closely related to Indo-Malaysian flora and the latter being more closely related to Eastern Asian flora. This floristic divergence is well supported by the geological history of these regions: that is, the tropical flora of southeastern Yunnan derived from the South China geoblock, whereas the flora of southern and southwestern Yunnan mainly derived from the Shan-Thai geoblock. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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17 pages, 1206 KiB

Open AccessReview

Latitudinal Diversity Gradient in the Changing World: Retrospectives and Perspectives

by Yu Zhang, Yi-Gang Song, Can-Yu Zhang, Tian-Rui Wang, Tian-Hao Su, Pei-Han Huang, Hong-Hu Meng and Jie Li

Diversity 2022, 14(5), 334; https://doi.org/10.3390/d14050334 - 25 Apr 2022

Cited by 15 | Viewed by 9685

Abstract

The latitudinal diversity gradient (LDG) is one of the most extensive and important biodiversity patterns on the Earth. Various studies have established that species diversity increases with higher taxa numbers from the polar to the tropics. Studies of multicellular biotas have supported the [...] Read more.

The latitudinal diversity gradient (LDG) is one of the most extensive and important biodiversity patterns on the Earth. Various studies have established that species diversity increases with higher taxa numbers from the polar to the tropics. Studies of multicellular biotas have supported the LDG patterns from land (e.g., plants, animals, forests, wetlands, grasslands, fungi, and so forth) to oceans (e.g., marine organisms from freshwater invertebrates, continental shelve, open ocean, even to the deep sea invertebrates). So far, there are several hypotheses proposed to explore the diversity patterns and mechanisms of LDG, however, there has been no consensus on the underlying causes of LDG over the past few decades. Thus, we reviewed the progress of LDG studies in recent years. Although several explanations for the LDG have been proposed, these hypotheses are only based on species richness, evolution and the ecosystems. In this review, we summarize the effects of evolution and ecology on the LDG patterns to synthesize the formation mechanisms of the general biodiversity distribution patterns. These intertwined factors from ecology and evolution in the LDG are generally due to the wider distribution of tropical areas, which hinders efforts to distinguish their relative contributions. However, the mechanisms of LDG always engaged controversies, especially in such a context that the human activity and climate change has affected the biodiversity. With the development of molecular biology, more genetic/genomic data are available to facilitate the estimation of global biodiversity patterns with regard to climate, latitude, and other factors. Given that human activity and climate change have inevitably impacted on biodiversity loss, biodiversity conservation should focus on the change in LDG pattern. Using large-scale genetic/genomic data to disentangle the diversity mechanisms and patterns of LDG, will provide insights into biodiversity conservation and management measures. Future perspectives of LDG with integrative genetic/genomic, species, evolution, and ecosystem diversity patterns, as well as the mechanisms that apply to biodiversity conservation, are discussed. It is imperative to explore integrated approaches for recognizing the causes of LDG in the context of rapid loss of diversity in a changing world. Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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Other

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3 pages, 184 KiB

Open AccessCommentary

Tracing the Evolution of Plant Diversity in Southwestern China

by Tao Su, Robert A. Spicer and Zhe-Kun Zhou

Diversity 2022, 14(6), 434; https://doi.org/10.3390/d14060434 - 29 May 2022

Cited by 4 | Viewed by 2123

Abstract

Biodiversity hotspots are key regions for understanding the evolutionary history of biodiversity as well as the processes initiating and maintaining it [...] Full article

(This article belongs to the Special Issue Ecology, Evolution and Diversity of Plants)

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