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Table of Content
25 July 2024, Volume 46 Issue 04
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Progress in systematics and biogeography of Orchidaceae
Yajun Wang, Hanchen Wang, Chao Ye, Zhiping Wang, Chongbo Ma, Dongliang Lin, Xiaohua Jin
2024, 46(04): 425-434. doi:
10.1016/j.pld.2024.05.002
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Orchidaceae are one of the largest families of angiosperms in terms of species richness. In the last decade, numerous studies have delved into reconstructing the phylogenetic framework of Orchidaceae, leveraging data from plastid, mitochondrial and nuclear sources. These studies have provided new insights into the systematics, diversification and biogeography of Orchidaceae, establishing a robust foundation for future research. Nevertheless, pronounced controversies persist regarding the precise placement of certain lineages within these phylogenetic frameworks. To address these discrepancies and deepen our understanding of the phylogenetic structure of Orchidaceae, we provide a comprehensive overview and analysis of phylogenetic studies focusing on contentious groups within Orchidaceae since 2015, delving into discussions on the underlying reasons for observed topological conflicts. We also provide a novel phylogenetic framework at the subtribal level. Furthermore, we examine the tempo and mode underlying orchid species diversity from the perspective of historical biogeography, highlighting factors contributing to extensive speciation. Ultimately, we delineate avenues for future research aimed at enhancing our understanding of Orchidaceae phylogeny and diversity.
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A new infrageneric classification of
Gastrochilus
(Orchidaceae: Epidendroideae) based on molecular and morphological data
Jun-Yi Zhang, Yue-Hong Cheng, Min Liao, Yu Feng, Sen-Long Jin, Ting-Mei He, Hai He, Bo Xu
2024, 46(04): 435-447. doi:
10.1016/j.pld.2023.08.001
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Gastrochilus
is an orchid genus containing 73 species of mainly epiphytic on trees or rocks in mountain forests of tropical and subtropical Asia. Previous phylogenetic analyses and morphological assessments have failed to produce a well-resolved phylogeny at the infrageneric level. In the present study, a new infrageneric classification of
Gastrochilus
is proposed based on thoroughly morphological and phylogenetic analyses based on 52 species. Our phylogenetic analysis divided the genus into six sections including three new sections,
G.
sect.
Pseudodistichi
,
G.
sect.
Brachycaules
and
G.
sect.
Acinacifolii
. We also reinstate
G
.
suavis
to the specific rank. Furthermore, two new species,
G
.
armeniacus
Jun Y. Zhang, B. Xu & Yue H. Cheng and
G. minjiangensis
Jun Y. Zhang, B. Xu & Yue H. Cheng, are described and illustrated. A key to six sections of the genus is presented.
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Plastid phylogenomics provides new insights into the systematics, diversification, and biogeography of
Cymbidium
(Orchidaceae)
Hai-Yao Chen, Zhi-Rong Zhang, Xin Yao, Ji-Dong Ya, Xiao-Hua Jin, Lin Wang, Lu Lu, De-Zhu Li, Jun-Bo Yang, Wen-Bin Yu
2024, 46(04): 448-461. doi:
10.1016/j.pld.2024.03.001
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Cymbidium
(Orchidaceae: Epidendroideae), with around 60 species, is widely-distributed across Southeast Asia, providing a nice system for studying the processes that underlie patterns of biodiversity in the region. However, phylogenetic relationships of
Cymbidium
have not been well resolved, hampering investigations of species diversification and the biogeographical history of this genus. In this study, we construct a plastome phylogeny of 56
Cymbidium
species, with four well-resolved major clades, which provides a framework for biogeographical and diversification rate analyses. Molecular dating and biogeographical analyses show that
Cymbidium
likely originated in the region spanning northern Indo-Burma to the eastern Himalayas during the early Miocene (~21.10 Ma). It then rapidly diversified into four major clades in East Asia within approximately a million years during the middle Miocene.
Cymbidium
spp. migration to the adjacent regions (Borneo, Philippines, and Sulawesi) primarily occurred during the Pliocene-Pleistocene period. Our analyses indicate that the net diversification rate of
Cymbidium
has decreased since its origin, and is positively associated with changes in temperature and monsoon intensity. Favorable hydrothermal conditions brought by monsoon intensification in the early Miocene possibly contributed to the initial rapid diversification, after which the net diversification rate was reduced with the cooling climate after the middle Miocene. The transition from epiphytic to terrestrial habits may have enabled adaptation to cooler environments and colonization of northern niches, yet without a significant effect on diversification rates. This study provides new insights into how monsoon activity and temperature changes affected the diversification dynamics of plants in Southeast Asia.
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Molecular phylogeny and taxonomy of
Phlomoides
(Lamiaceae subfamily Lamioideae) in China: Insights from molecular and morphological data
Yue Zhao, Ya-Ping Chen, Bryan T. Drew, Fei Zhao, Maryam Almasi, Orzimat T. Turginov, Jin-Fei Xiao, Abdul G. Karimi, Yasaman Salmaki, Xiang-Qin Yu, Chun-Lei Xiang
2024, 46(04): 462-475. doi:
10.1016/j.pld.2024.04.011
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27
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Phlomoides
, with 150–170 species, is the second largest and perhaps most taxonomically challenging genus within the subfamily Lamioideae (Lamiaceae). With about 60 species, China is one of three major biodiversity centers of
Phlomoides
. Although some
Phlomoides
species from China have been included in previous molecular phylogenetic studies, a robust and broad phylogeny of this lineage has yet to be completed. Moreover, given the myriad new additions to the genus, the existing infrageneric classification needs to be evaluated and revised. Here, we combine molecular and morphological data to investigate relationships within
Phlomoides
, with a focus on Chinese species. We observed that plastid DNA sequences can resolve relationships within
Phlomoides
better than nuclear ribosomal internal and external transcribed spacer regions (nrITS and nrETS). Molecular phylogenetic analyses confirm the monophyly of
Phlomoides
, but most previously defined infrageneric groups are not monophyletic. In addition, morphological analysis demonstrates the significant taxonomic value of eight characters to the genus. Based on our molecular phylogenetic analyses and morphological data, we establish a novel section
Notochaete
within
Phlomoides
, and propose three new combinations as well as three new synonyms. This study presents the first molecular phylogenetic analyses of
Phlomoides
in which taxa representative of the entire genus are included, and highlights the phylogenetic and taxonomic value of several morphological characters from species of
Phlomoides
from China. Our study suggests that a taxonomic revision and reclassification for the entire genus is necessary in the future.
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Origin and evolution of a new tetraploid mangrove species in an intertidal zone
Hui Feng, Achyut Kumar Banerjee, Wuxia Guo, Yang Yuan, Fuyuan Duan, Wei Lun Ng, Xuming Zhao, Yuting Liu, Chunmei Li, Ying Liu, Linfeng Li, Yelin Huang
2024, 46(04): 476-490. doi:
10.1016/j.pld.2024.04.007
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Polyploidy is a major factor in the evolution of plants, yet we know little about the origin and evolution of polyploidy in intertidal species. This study aimed to identify the evolutionary transitions in three true-mangrove species of the genus
Acanthus
distributed in the Indo–West Pacific region. For this purpose, we took an integrative approach that combined data on morphology, cytology, climatic niche, phylogeny, and biogeography of 493 samples from 42 geographic sites. Our results show that the
Acanthus ilicifolius
lineage distributed east of the Thai–Malay Peninsula possesses a tetraploid karyotype, which is morphologically distinct from that of the lineage on the west side. The haplotype networks and phylogenetic trees for the chloroplast genome and eight nuclear genes reveal that the tetraploid species has two sub-genomes, one each from
A. ilicifolius
and
A
.
ebracteatus
, the paternal and maternal parents, respectively. Population structure analysis also supports the hybrid speciation history of the new tetraploid species. The two sub-genomes of the tetraploid species diverged from their diploid progenitors during the Pleistocene. Environmental niche models revealed that the tetraploid species not only occupied the near-entire niche space of the diploids, but also expanded into novel environments. Our findings suggest that
A. ilicifolius
species distributed on the east side of the Thai–Malay Peninsula should be regarded as a new species,
A
.
tetraploideus
, which originated from hybridization between
A. ilicifolius
and
A. ebracteatus
, followed by chromosome doubling. This is the first report of a true-mangrove allopolyploid species that can reproduce sexually and clonally reproduction, which explains the long-term adaptive potential of the species.
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Woody plant taxonomic, functional, and phylogenetic diversity decrease along elevational gradients in Andean tropical montane forests: Environmental filtering and arrival of temperate taxa
Guillermo Bañares-de-Dios, Manuel J. Macía, Gabriel Arellano, Íñigo Granzow-de la Cerda, Julia Vega-Álvarez, Itziar Arnelas, Carlos I. Espinosa, Norma Salinas, Luis Cayuela
2024, 46(04): 491-501. doi:
10.1016/j.pld.2024.03.005
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Mountains are paramount for exploring biodiversity patterns due to the mosaic of topographies and climates encompassed over short distances. Biodiversity research has traditionally focused on taxonomic diversity when investigating changes along elevational gradients, but other facets should be considered. For first time, we simultaneously assessed elevational trends in taxonomic, functional, and phylogenetic diversity of woody plants in Andean tropical montane forests and explored their underlying ecological and evolutionary causes. This investigation covered four transects (traversing
ca
. 2200 m a.s.l.) encompassing 114 plots of 0.1 ha across a broad latitudinal range (
ca
. 10°). Using Hill numbers to quantify abundance-based diversity among 37,869 individuals we observed a consistent decrease in taxonomic, functional, and phylogenetic diversity as elevation increased, although the decrease was less pronounced for higher Hill orders. The exception was a slight increase in phylogenetic diversity when dominant species were over-weighted. The decrease in taxonomic and functional diversity might be attributed to an environmental filtering process towards highlands, where the increasingly harsher conditions exclude species and functional strategies. Besides, the differences in steepness decrease between Hill orders suggest that rare species disproportionately contribute to functional diversity. For phylogenetic diversity the shifting elevational trend between Hill orders indicates a greater than previously considered influence in central Andean highlands of tropical lowlands originated species with strong niche conservatism relative to distantly related temperate lineages. This could be explained by a decreasing presence and abundance of temperate, extratropical taxa towards the central Andes relative to northern or southern Andes, where they are more prevalent.
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The mid-domain effect in flowering phenology
Yanjun Du, Rongchen Zhang, Xinran Tang, Xinyang Wang, Lingfeng Mao, Guoke Chen, Jiangshan Lai, Keping Ma
2024, 46(04): 502-509. doi:
10.1016/j.pld.2024.05.005
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The timing of flowering is an important driver of species distribution and community assembly patterns. However, we still have much to learn about the factors that shape flowering diversity (i.e., number of species flowering per period) in plant communities. One potential explanation of flowering diversity is the mid-domain effect, which states that geometric constraints on species ranges within a bounded domain (space or time) will yield a mid-domain peak in diversity regardless of ecological factors. Here, we determine whether the mid-domain effect explains peak flowering time (i.e., when most species of communities are flowering) across China. We used phenological data of 16,267 herbaceous and woody species from the provincial
Flora
in China and species distribution data from the Chinese Vascular Plant Distribution Database to determine relationships between the observed number of species flowering and the number of species flowering as predicted by the mid-domain effect model, as well as between three climatic variables (mean minimum monthly temperature, mean monthly precipitation, and mean monthly sunshine duration). We found that the mid-domain effect explained a significant proportion of the temporal variation in flowering diversity across all species in China. Further, the mid-domain effect explained a greater proportion of variance in flowering diversity at higher latitudes than at lower latitudes. The patterns of flowering diversity for both herbaceous and woody species were related to both the mid-domain effect and environmental variables. Our findings indicate that including geometric constraints in conjunction with abiotic and biotic predictors will improve predictions of flowering diversity patterns.
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Increased dependence on nitrogen-fixation of a native legume in competition with an invasive plant
Meixu Han, Haiyang Zhang, Mingchao Liu, Jinqi Tang, Xiaocheng Guo, Weizheng Ren, Yong Zhao, Qingpei Yang, Binglin Guo, Qinwen Han, Yulong Feng, Zhipei Feng, Honghui Wu, Xitian Yang, Deliang Kong
2024, 46(04): 510-518. doi:
10.1016/j.pld.2024.04.003
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Suppression of roots and/or their symbiotic microorganisms, such as mycorrhizal fungi and rhizobia, is an effective way for alien plants to outcompete native plants. However, little is known about how invasive and native plants interact with the
quantity
and
activity
of nutrient-acquisition agents. Here a pot experiment was conducted with monoculture and mixed plantings of an invasive plant,
Xanthium strumarium
, and a common native legume,
Glycine max
. We measured traits related to root and nodule quantity and activity and mycorrhizal colonization. Compared to the monoculture, fine root
quantity
(biomass, surface area) and
activity
(root nitrogen (N) concentration, acid phosphatase activity) of
G. max
decreased in mixed plantings; nodule
quantity
(biomass) decreased by 45%, while nodule
activity
in N-fixing via rhizobium increased by 106%; mycorrhizal colonization was unaffected. Contribution of N fixation to leaf N content in
G. max
increased in the mixed plantings, and this increase was attributed to a decrease in the rhizosphere soil N of
G. max
in the mixed plantings. Increased root
quantity
and
activity
, along with a higher mycorrhizal association was observed in
X. strumarium
in the mixed compared to monoculture. Together, the invasive plant did not directly scavenge N from nodule-fixed N, but rather depleted the rhizosphere soil N of the legume, thereby stimulating the
activity
of N-fixation and increasing the dependence of the native legume on this N source. The
quantity
–
activity
framework holds promise for future studies on how native legumes respond to alien plant invasions.
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Salicylic acid positively regulates maize defenses against lepidopteran insects
Yohannes Besufekad Setotaw, Jing Li, Jinfeng Qi, Canrong Ma, Mou Zhang, Cuilian Huang, Lei Wang, Jianqiang Wu
2024, 46(04): 519-529. doi:
10.1016/j.pld.2024.03.004
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In response to insect attack, plants use intricate signaling pathways, including phytohormones, such as jasmonate (JA), ethylene (ET), and salicylic acid (SA), to activate defenses. Maize (
Zea mays
) is one of the most important staple food crops around the world. Previous studies have shown that the JA and ET signaling play important roles in maize defense against insects, but little is known about whether and how SA regulates maize resistance to insect herbivores. In this study, we ectopically expressed the
NahG
(
salicylate hydroxylase
) gene in maize plants (
NahG
maize) to block the accumulation of SA. It was found that compared with the wild-type (WT) maize, the
NahG
maize exhibited decreased resistance to the generalist insects
S
podoptera
litura
and
Spodoptera frugiperda
and the specialist
Mythimna separata
, and the compromised resistance in the
NahG
maize was associated with decreased levels of defensive metabolites benzoxazinoids (Bxs) and chlorogenic acid (CA). Quantification of simulated
S. litura
feeding-induced JA, JA-isoleucine conjugate (JA-Ile), and ET in the WT and
NahG
maize indicated that SA does not regulate JA or JA-Ile, but positively controls ET. We provide evidence suggesting that the SA pathway does not crosstalk with the JA or the ET signaling in regulating the accumulation of Bxs and CA. Transcriptome analysis revealed that the bHLH, ERF, and WRKY transcription factors might be involved in SA-regulated defenses. This study uncovers a novel and important phytohormone pathway in maize defense against lepidopterous larvae.
Short communications
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Aboveground biomass stocks of species-rich natural forests in southern China are influenced by stand structural attributes, species richness and precipitation
Wen-Hao Zeng, Shi-Dan Zhu, Ying-Hua Luo, Wei Shi, Yong-Qiang Wang, Kun-Fang Cao
2024, 46(04): 530-536. doi:
10.1016/j.pld.2024.04.012
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Forests, the largest terrestrial carbon sinks, play an important role in carbon sequestration and climate change mitigation. Although forest attributes and environmental factors have been shown to impact aboveground biomass, their influence on biomass stocks in species-rich forests in southern China, a biodiversity hotspot, has rarely been investigated. In this study, we characterized the effects of environmental factors, forest structure, and species diversity on aboveground biomass stocks of 30 plots (1 ha each) in natural forests located within seven nature reserves distributed across subtropical and marginal tropical zones in Guangxi, China. Our results indicate that forest aboveground biomass stocks in this region are lower than those in mature tropical and subtropical forests in other regions. Furthermore, we found that aboveground biomass was positively correlated with stand age, mean annual precipitation, elevation, structural attributes and species richness, although not with species evenness. When we compared stands with the same basal area, we found that aboveground biomass stock was higher in communities with a higher coefficient of variation of diameter at breast height. These findings highlight the importance of maintaining forest structural diversity and species richness to promote aboveground biomass accumulation and reveal the potential impacts of precipitation changes resulting from climate warming on the ecosystem services of subtropical and northern tropical forests in China. Notably, many natural forests in southern China are not fully stocked. Therefore, their continued growth will increase their carbon storage over time.
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Strong evidence for latitudinal diversity gradient in mosses across the world
Hong Qian, Zun Dai, Jian Wang
2024, 46(04): 537-541. doi:
10.1016/j.pld.2024.05.004
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Species richness generally decreases with increasing latitude, a biodiversity gradient that has long been considered as one of the few laws in ecology. This latitudinal diversity gradient has been observed in many major groups of organisms. In plants, the latitudinal diversity gradient has been observed in vascular plants, angiosperms, ferns, and liverworts. However, a conspicuous latitudinal diversity gradient in mosses at a global or continental scale has not been observed until now. Here, we analyze a comprehensive data set including moss species in each band of 20° in latitude worldwide. Our results show that moss species richness decreases strongly with increasing latitude, regardless of whether the globe is considered as a whole or different longitudinal segments (e.g., Old World versus New World) are considered separately. This result holds when variation in area size among latitudinal bands is taken into account. Pearson's correlation coefficient between latitude and species richness is -0.99 for both the Northern and Southern Hemispheres. Because bryophytes are an extant lineage of early land plants and because mosses not only include most of extant species of bryophytes but also are important constituents of most terrestrial ecosystems, understanding geographic patterns of mosses is particularly important. The finding of our study fills a critical knowledge gap.
Software Article
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Evaluating the relative importance of predictors in Generalized Additive Models using the
gam.hp
R package
Jiangshan Lai, Jing Tang, Tingyuan Li, Aiying Zhang, Lingfeng Mao
2024, 46(04): 542-546. doi:
10.1016/j.pld.2024.06.002
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Generalized Additive Models (GAMs) are widely employed in ecological research, serving as a powerful tool for ecologists to explore complex nonlinear relationships between a response variable and predictors. Nevertheless, evaluating the relative importance of predictors with concurvity (analogous to collinearity) on response variables in GAMs remains a challenge. To address this challenge, we developed an R package named
gam.hp
.
gam.hp
calculates individual
R
2
values for predictors, based on the concept of ‘average shared variance’, a method previously introduced for multiple regression and canonical analyses. Through these individual
R
2
s, which add up to the overall
R
2
, researchers can evaluate the relative importance of each predictor within GAMs. We illustrate the utility of the
gam.hp
package by evaluating the relative importance of emission sources and meteorological factors in explaining ozone concentration variability in air quality data from London, UK. We believe that the
gam.hp
package will improve the interpretation of results obtained from GAMs.
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Comparative analysis shows high level of lineage sorting in genomic regions with low recombination in the extended
Picea likiangensis
species complex
Hui Zhu, Weixiao Lei, Qing Lai, Yongshuai Sun, Dafu Ru
2024, 46(04): 547-550. doi:
10.1016/j.pld.2024.04.004
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