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Diversity
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Conservation Genetics and Biogeography of Seed Plant Species
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Conservation Genetics and Biogeography of Seed Plant Species

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Plant Diversity".

Deadline for manuscript submissions: closed (15 August 2021) | Viewed by 27526

Special Issue Editors

Dr. Jordi López-Pujol

E-Mail Website
Guest Editor
CSIC-ICUB—Instituto Botanico de Barcelona, 08038 Barcelona, Spain
Interests: biogeography; conservation genetics; East Asia; ecological niche modeling; invasive alien species; Mediterranean Basin; phylogeography; rare and endangered species
Special Issues, Collections and Topics in MDPI journals
Dr. Roser Vilatersana

E-Mail Website
Guest Editor
CSIC-ICUB - Instituto Botanico de Barcelona, 08038 Barcelona, Spain
Interests: biogeography; evolution; invasive species; Mediterranean Basin; molecular dating; phylogeography; polyploidy; rare and endangered species; speciation; systematics
Special Issues, Collections and Topics in MDPI journals
Dr. Núria Garcia-Jacas

E-Mail Website
Guest Editor
CSIC-ICUB - Instituto Botanico de Barcelona, 08038 Barcelona, Spain
Interests: biogeography; conservation genetics; evolution; hybridization; phylogeny; polyploidy; speciation; systematics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Spermatophytes or seed plants are the largest and most diverse group among land plants, with over 300,000 described and accepted species. Having appeared on Earth at the end of the Devonian (ca. 370 mya), the extraordinary geological and climatic changes that have occurred since then have interplayed with genetic diversity (the raw material on which evolution acts), creating and transforming, but also extinguishing plant species.

Maintaining sufficient levels of genetic variability in populations of seed plant species is the basis for their adaptation to novel, changing environments (and, thus, for molecular/phenotypic evolution and lineage diversification), but also it may help in preventing processes such as genetic drift and inbreeding and, ultimately, their extinction. The development of neutral molecular markers such as allozymes, microsatellites, AFLPs, or ISSRs has allowed the evaluation of genetic diversity within and between populations, at local, regional, and global levels. These studies can also be very useful to select populations worthy of conservation measures (both in situ and ex situ), to define management units, and even to design population reinforcements or reintroductions. Genetic diversity studies can also provide new insights into the biological and evolutionary aspects of species (e.g., detection of hybridization events, bottlenecks and founder effects, and characterization of polyploidy). With the advent of phylogeographic markers (cpDNA and mtDNA and more recently SNPs and NGS-based markers), we have improved our understanding of the effect of time and space on genetic variation, allowing inferences about the location of Pleistocene refugia, but also reconstructing recolonization routes and estimating lineage age and identifying evolutionarily significant units. This information, in turn, is of utmost importance for the design of adequate conservation measures if the species under study is rare or threatened.

This Special Issue provides a platform to highlight new research from both empirical and theoretical perspectives. There are still many questions to be explored on biogeography, evolution, speciation and population genetics, and this research topic welcomes articles, opinions and reviews addressing any of these issues.

Dr. Jordi López-Pujol
Dr. Roser Vilatersana
Dr. Núria Garcia-Jacas
Guest Editors

Manuscript Submission Information

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

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

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2100 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Conservation genetics
  • Genetic diversity
  • Molecular markers
  • Phylogeography
  • Seed plants

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Published Papers (8 papers)

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Research

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15 pages, 1913 KiB  
Article
Subtle East–West Phylogeographic Break of Asteropyrum (Ranunculaceae) in Subtropical China and Adjacent Areas
by Shanmei Cheng, Weidong Zeng, Dengmei Fan, Hua Liang, Yi Yang, Yixuan Kou and Zhiyong Zhang
Diversity 2021, 13(12), 627; https://doi.org/10.3390/d13120627 - 29 Nov 2021
Cited by 4 | Viewed by 2076
Abstract
East–west phylogeographic break is common among plant species in subtropical China. However, the estimation time of east–west phylogeographic break has always relied on inferences of calibrated phylogenies, and the contribution of environmental heterogeneity to population differentiation has largely been ignored. In this study, [...] Read more.
East–west phylogeographic break is common among plant species in subtropical China. However, the estimation time of east–west phylogeographic break has always relied on inferences of calibrated phylogenies, and the contribution of environmental heterogeneity to population differentiation has largely been ignored. In this study, we estimated the divergence time of Asteropyrum populations through coalescent-based approaches based on DNA sequences of ten nuclear loci and evaluated the contribution of environmental heterogeneity to population differentiation. The results showed that there were two chloroplast clades and nuclear groups within Asteropyrum, displaying a subtle pattern of east–west differentiation. The divergence time of the two nuclear groups was dated to ~1.2 Ma, which is associated with climate changes during the Mid-Pleistocene transition. A genetic admixture event between the two genetic groups happened at ~0.46 Ma, resulting in several admixed populations. Isolation by environmental distance (IBE) explained the majority (46.32%) of population differentiation, but that isolation by geographic distance (IBD) only contributed 4.66%. The results of this study suggest that climate changes during the Pleistocene may be a major cause for the east–west phylogeographic break in subtropical China. However, the complex terrain and high environmental heterogeneity in the west of subtropical China (and adjacent regions such as the Hengduan Mountains and the Himalayan Moutains) caused by strong geological uplift may have profoundly shaped the population structure of plant species in subtropical China. Full article
(This article belongs to the Special Issue Conservation Genetics and Biogeography of Seed Plant Species)
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17 pages, 2469 KiB  
Article
Genetic Divergence between Two Sympatric Ecotypes of Phalaenopsis pulcherrima on Hainan Island
by Xiangyu Hu, Siren Lan, Xiqiang Song, Fusun Yang, Zhe Zhang, Donghui Peng and Mingxun Ren
Diversity 2021, 13(9), 446; https://doi.org/10.3390/d13090446 - 17 Sep 2021
Cited by 4 | Viewed by 2604
Abstract
Ecotypes are the result of ecological differentiation at the early stages of speciation. Adaptation to soil conditions offers arguably the best examples of local adaptation in plants. Two sympatric ecotypes, with either a red or green abaxial leaf surface, were found without clear [...] Read more.
Ecotypes are the result of ecological differentiation at the early stages of speciation. Adaptation to soil conditions offers arguably the best examples of local adaptation in plants. Two sympatric ecotypes, with either a red or green abaxial leaf surface, were found without clear geographical isolation in Phalaenopsis pulcherrima, a Southeast Asia endemic and endangered orchid. The soil of the red leaf ecotype has a higher water content and nutrient content than the green ecotype. What is the genetic structure of the two ecotypes? Is there complete or partial reproductive isolation between the two ecotypes? In this work, leaf reflection of the two ecotypes in P. pulcherrima were compared, to illustrate their difference in leaf color. The genetic differentiation between two ecotypes was examined, using ISSR and SRAP markers to determine the genetic structure of the populations. Our results showed that the green ecotype had reflectance spectrum peaks at 530 nm and 620 nm, while in the red ecotype, the peak at 530 nm was absent. A total of 165 ISSR and SRAP loci showed a high level of genetic diversity within the green ecotype, and analyses of the population structure revealed two genetic clusters that corresponded to the red and green ecotypes. The percentage of variation between the two ecotypes (24.55%) was greater than the percentage of variation among the populations (16.54%)—indicating partial reproductive isolation, high genetic differentiation, and that ecological differentiation has been more important than geographical barriers among populations within ecotypes. Most pairwise FST values between the populations within either ecotype on Hainan Island were less than 0.15; however, the FST between both the Thai and Malaysian populations and the Hainan Island population was greater than 0.25, due to South China sea isolation. Ecotypic differentiation is an important part of speciation; therefore, we must take into account the axes along which lineages sort, when formulating protection strategies. Full article
(This article belongs to the Special Issue Conservation Genetics and Biogeography of Seed Plant Species)
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12 pages, 3231 KiB  
Article
Spatial Genetic Structure of Prunus mongolica in Arid Northwestern China Based on RAD Sequencing Data
by Hong-Xiang Zhang, Qian Wang and Zhi-Bin Wen
Diversity 2021, 13(8), 397; https://doi.org/10.3390/d13080397 - 23 Aug 2021
Cited by 5 | Viewed by 2499
Abstract
The extensive range of sand deserts, gravel deserts, and recent human activities have shaped habitat fragmentation of relict and endangered plants in arid northwestern China. Prunus mongolica is a relict and endangered shrub that is mainly distributed in the study area. In the [...] Read more.
The extensive range of sand deserts, gravel deserts, and recent human activities have shaped habitat fragmentation of relict and endangered plants in arid northwestern China. Prunus mongolica is a relict and endangered shrub that is mainly distributed in the study area. In the present study, population genomics was integrated with a species distribution model (SDM) to investigate the spatial genetic diversity and structure of P. mongolica populations in response to habitat fragmentation and create a proposal for the conservation of this endangered species. The results showed that the northern marginal populations were the first isolated from other populations. The SDM suggested that these marginal populations had low levels of habitat suitability during the glacial period. They could not obtain migration corridors, and thus possessed low levels of gene flow connection with other populations. Additionally, several populations underwent secondarily geographical isolation from other central populations, which preserved particular genetic lineages. Genetic diversity was higher in southern populations than in northern ones. It was concluded that long-term geographical isolation after historical habitat fragmentation promoted the divergence of marginal populations and refugial populations along mountains from other populations. The southern populations could have persisted in their distribution ranges and harbored higher levels of genetic diversity than the northern populations, whose distribution ranges fluctuated in response to paleoclimatic changes. We propose that the marginal populations of P. mongolica should be well considered in conservation management. Full article
(This article belongs to the Special Issue Conservation Genetics and Biogeography of Seed Plant Species)
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17 pages, 2960 KiB  
Article
Geographic Patterns of Genetic Variation among Cacao (Theobroma cacao L.) Populations Based on Chloroplast Markers
by Helmuth Edisson Nieves-Orduña, Markus Müller, Konstantin V. Krutovsky and Oliver Gailing
Diversity 2021, 13(6), 249; https://doi.org/10.3390/d13060249 - 5 Jun 2021
Cited by 6 | Viewed by 5457
Abstract
The cacao tree (Theobroma cacao L.) is native to the Amazon basin and widely cultivated in the tropics to produce seeds, the valuable raw material for the chocolate industry. Conservation of cacao genetic resources and their availability for breeding and production programs [...] Read more.
The cacao tree (Theobroma cacao L.) is native to the Amazon basin and widely cultivated in the tropics to produce seeds, the valuable raw material for the chocolate industry. Conservation of cacao genetic resources and their availability for breeding and production programs are vital for securing cacao supply. However, relatively little is still known about the phylogeographic structure of natural cacao populations. We studied the geographic distribution of cpDNA variation in different populations representing natural cacao stands, cacao farms in Ecuador, and breeding populations. We used six earlier published cacao chloroplast microsatellite markers to genotype 233 cacao samples. In total, 23 chloroplast haplotypes were identified. The highest variation of haplotypes was observed in western Amazonia including geographically restricted haplotypes. Two observed haplotypes were widespread across the Amazon basin suggesting long distance seed dispersal from west to east in Amazonia. Most cacao genetic groups identified earlier using nuclear SSRs are associated with specific chloroplast haplotypes. A single haplotype was common in selections representing cacao plantations in west Ecuador and reference Trinitario accessions. Our results can be used to determine the chloroplast diversity of accessions and in combination with phenotypic assessments can help to select geographically distinctive varieties for cacao breeding programs. Full article
(This article belongs to the Special Issue Conservation Genetics and Biogeography of Seed Plant Species)
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14 pages, 4509 KiB  
Article
Reusing Old and Producing New Data Is Useful for Species Delimitation in the Taxonomically Controversial Iberian Endemic Pair Petrocoptis montsicciana/P. pardoi (Caryophyllaceae)
by Neus Nualart, Sonia Herrando-Moraira, Eduardo Cires, Moisès Guardiola, Emilio Laguna, David Pérez-Prieto, Llorenç Sáez and Jordi López-Pujol
Diversity 2021, 13(5), 205; https://doi.org/10.3390/d13050205 - 12 May 2021
Cited by 2 | Viewed by 2809
Abstract
Petrocoptis montsicciana and P. pardoi are two Iberian endemic taxa of Caryophyllaceae family with an unclear taxonomic delimitation, being variously treated as independent species, subspecies or even synonyms. In the present study, allozyme raw data obtained in the early 2000s have been reused [...] Read more.
Petrocoptis montsicciana and P. pardoi are two Iberian endemic taxa of Caryophyllaceae family with an unclear taxonomic delimitation, being variously treated as independent species, subspecies or even synonyms. In the present study, allozyme raw data obtained in the early 2000s have been reused with improved tools to survey genetic structure, and complemented with modeling and niche comparative analyses to shed light on species delimitation. Genetic structure was investigated using four approaches: Bayesian clustering, Monmonier’s algorithm, Principal Coordinate Analysis (PCoA), and Analysis of Molecular Variance (AMOVA). Ecological niche differences have been assessed through Ecological Niche Modeling (ENM) using MaxEnt, and Principal Component Analysis using both occurrence records and background climate (PCA-env). Genetic analysis confirms the distinction between both taxa, and the scenario of a progenitor–derivative (P–D) is suggested. In agreement with genetic data, niche analysis shows clear differences between their climate regarding species occurrences and background spaces. Climate divergence could be explained, at least partially, by the abundance of rocks where species live although differences at the microclimate instead of the regional climate should be explored in future research. Given the genetic distinction between P. montsicciana and P. pardoi, both taxa should be regarded as separate ‘Management Units’ (MUs). Full article
(This article belongs to the Special Issue Conservation Genetics and Biogeography of Seed Plant Species)
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24 pages, 4376 KiB  
Article
Conservation Genetics of Four Critically Endangered Greek Endemic Plants: A Preliminary Assessment
by Konstantinos Kougioumoutzis, Panayiota Kotsakiozi, Efthalia Stathi, Panayiotis Trigas and Aristeidis Parmakelis
Diversity 2021, 13(4), 152; https://doi.org/10.3390/d13040152 - 31 Mar 2021
Cited by 9 | Viewed by 4511
Abstract
The Mediterranean basin constitutes one of the largest global biodiversity hotspots, hosting more than 11,000 endemic plants, and it is recognised as an area with a high proportion of threatened taxa. Nevertheless, only a tiny fraction of the threatened Mediterranean endemics have their [...] Read more.
The Mediterranean basin constitutes one of the largest global biodiversity hotspots, hosting more than 11,000 endemic plants, and it is recognised as an area with a high proportion of threatened taxa. Nevertheless, only a tiny fraction of the threatened Mediterranean endemics have their genetic diversity assessed, and we are unaware if and how climate change might impact their conservation status. This is even more pronounced in Eastern Mediterranean countries with a rich endemic flora, such as Greece, which hosts a large portion of the plant taxa assessed at the European level under the IUCN criteria. Using inter simple sequence repeats (ISSR) markers and species distribution models, we analysed the genetic diversity and investigated the impacts of climate change on four critically endangered and extremely narrow and rare Greek island endemic plants, namely Aethionema retsina, Allium iatrouinum, Convolvulus argyrothamnos, and Saponaria jagelii. All four species are facing intense anthropogenic threats and display moderate genetic diversity (uHe: 0.254–0.322), while climate change is expected to have a profound impact on their range size during the coming decades. A combination of in- and ex-situ measures, such as population reinforcement and seed bank conservation, are urgently needed in order to preserve these highly threatened and rare Greek endemics. Full article
(This article belongs to the Special Issue Conservation Genetics and Biogeography of Seed Plant Species)
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19 pages, 6211 KiB  
Article
Genesis, Evolution, and Genetic Diversity of the Hexaploid, Narrow Endemic Centaurea tentudaica
by Lucía D. Moreyra, Francisco Márquez, Alfonso Susanna, Núria Garcia-Jacas, Francisco María Vázquez and Jordi López-Pujol
Diversity 2021, 13(2), 72; https://doi.org/10.3390/d13020072 - 9 Feb 2021
Cited by 5 | Viewed by 3701
Abstract
Within the genus Centaurea L., polyploidy is very common, and it is believed that, as to all angiosperms, it was key in the history of its diversification and evolution. Centaurea tentudaica is a hexaploid from subsect. Chamaecyanus of unknown origin. In this study, [...] Read more.
Within the genus Centaurea L., polyploidy is very common, and it is believed that, as to all angiosperms, it was key in the history of its diversification and evolution. Centaurea tentudaica is a hexaploid from subsect. Chamaecyanus of unknown origin. In this study, we examined the possible autopolyploid or allopolyploid origin using allozymes and sequences of three molecular markers: nuclear-ribosomic region ETS, and low-copy genes AGT1 and PgiC. We also included three species geographically and morphologically close to C. tentudaica: C. amblensis, C. galianoi, and C. ornata. Neighbor-Net and Bayesian analyses show a close relationship between C. amblensis and C. tentudaica and no relationship to any of the other species, which suggest that C. tentudaica is an autopolyploid of C. amblensis. Allozyme banding pattern also supports the autopolyploidy hypothesis and shows high levels of genetic diversity in the polyploid, which could suggest multiple origins by recurrent crosses of tetraploid and diploid cytotypes of C. amblensis. Environmental niche modeling was used to analyze the distribution of the possible parental species during the present, Last Glacial Maximum (LGM), Last Interglacial Period (LIG), and Penultimate Glacial Maximum (PGM) environmental conditions. Supporting the molecular suggestions that C. tentudaica originated from C. amblensis, environmental niche modeling confirms that past distribution of C. amblensis overlapped with the distribution of C. tentudaica. Full article
(This article belongs to the Special Issue Conservation Genetics and Biogeography of Seed Plant Species)
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Review

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11 pages, 474 KiB  
Review
Plant Conservation Practitioners Can Benefit from Neutral Genetic Diversity
by Mi Yoon Chung, Sungwon Son, Jordi López-Pujol, Kangshan Mao and Myong Gi Chung
Diversity 2021, 13(11), 552; https://doi.org/10.3390/d13110552 - 30 Oct 2021
Cited by 2 | Viewed by 2313
Abstract
Several papers deal with a conservation genetics gap in which plant conservation and restoration managers or practitioners do not soundly integrate population genetics information into conservation management. Authors concerned about this issue point out that practitioners perceive genetic research results to be impractical [...] Read more.
Several papers deal with a conservation genetics gap in which plant conservation and restoration managers or practitioners do not soundly integrate population genetics information into conservation management. Authors concerned about this issue point out that practitioners perceive genetic research results to be impractical or unnecessary in the short term due to time and financial constraints. In addition, researchers often fail to translate research findings into comprehensive, jargon-free recommendations effectively. If possible, conservation-related or conservation-oriented articles should be easily written to bridge the research–implementation gap. Finally, based on a previously published prioritization framework for conservation genetics scenarios, we introduce four simple genetic categories by exemplifying each case. We hope that conservation practitioners could employ these suggested guidelines for the prioritization of population- and species-level management. Full article
(This article belongs to the Special Issue Conservation Genetics and Biogeography of Seed Plant Species)
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