Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation

Genetic diversity and its distribution, both within and between populations, may be determined by micro-evolutionary processes, such as the demographic history of populations, natural selection, and gene flow. In plants, indices of genetic diversity (e.g., k, h and π) and structure (e.g., FST) are typically inferred from sequences of chloroplast markers. Given the recent advances and popularization of molecular techniques for research in population genetics, phylogenetics, phylogeography, and ecology, we adopted a scientometric approach to compile evidence on the recent trends in the use of cpDNA sequences as markers for the analysis of genetic diversity in botanical studies, over the years. We also used phylogenetic modeling to assess the relative contribution of relatedness or ecological and reproductive characters to the genetic diversity of plants. We postulated that genetic diversity could be defined not only by microevolutionary factors and life history traits, but also by relatedness, so that species more closely related phylogenetically would have similar genetic diversities. We found a clear tendency for an increase in the number of studies over time, confirming the hypothesis that the advances in the area of molecular genetics have supported the accumulation of data on the genetic diversity of plants. However, we found that the vast majority of these data have been produced by Chinese authors, and refer specifically to populations of Chinese plants. Most of the data on genetic diversity have been obtained for species in the International Union for Conservation of Nature (IUCN) category NE (Not Evaluated), which indicates a relative lack of attention on threatened species. In general, we observed very high FST values in the groups analyzed and, as we focused primarily on species that have not been evaluated by the IUCN, the number of plant species that are threatened with extinction may be much greater than that indicated by the listing of this organization. We also found that the number of haplotypes (k) was influenced by the type of geographic distribution of the plant, while haplotype diversity (h) was affected by the type of flower, and the fixation index (FST), by the type of habitat. The plant species most closely-related phylogenetically have similar levels of genetic diversity. Overall, then, it will important to consider phylogenetic dependence in future studies that evaluate the effects of life-history traits on plant genetic diversity.

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Life-history traits controlling the survival of Tillaea aquatica: a threatened wetland plant species in intensively managed fishpond landscapes of the Czech Republic

Hydrobiologia ◽

10.1007/s10750-011-0857-3 ◽

2011 ◽

Vol 689 (1) ◽

pp. 91-110 ◽

Cited By ~ 13

Author(s):

Kateřina Šumberová ◽

Michal Ducháček ◽

Zdeňka Lososová

Keyword(s):

Life History ◽

Czech Republic ◽

Plant Species ◽

Life History Traits ◽

Wetland Plant ◽

The Czech Republic ◽

Intensively Managed

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Coalescence times, life history traits and conservation concerns: an example from four coastal shark species from the Indo-Pacific

10.22541/au.161963333.37636342/v2 ◽

2021 ◽

Author(s):

Pierre Lesturgie ◽

Serge Planes ◽

Stefano Mona

Keyword(s):

Population Structure ◽

Life History ◽

Life History Traits ◽

New Caledonia ◽

Demographic History ◽

Conservation Strategies ◽

Shark Species ◽

Effective Population ◽

Demographic Models ◽

Mobile Species

Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographic ranges and less mobile ones organized in meta-populations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (meta-population) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.

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Estructura genética de poblaciones de Eriocaulon bilobatum (Eriocaulaceae): una especie amenazada de humedades temporales

Botanical Sciences ◽

10.17129/botsci.2305 ◽

2019 ◽

Vol 85 ◽

pp. 81

Author(s):

Fabiola Magallán Hernández ◽

Mahinda Martínez ◽

Luis Hernández Sandoval ◽

Ken Oyama

Keyword(s):

Genetic Diversity ◽

Life History ◽

Genetic Structure ◽

Gel Electrophoresis ◽

Life History Traits ◽

Aquatic Environments ◽

Starch Gel Electrophoresis ◽

Temporary Wetlands ◽

Sexual And Asexual Reproduction ◽

Starch Gel

Eriocaulon bilobatum is an aquatic species that inhabits temporary wetlands in central Mexico. It is annual, herbaceous, emergent, with sexual and asexual reproduction, monoecious and insect pollinated. It is a rare and vulnerable species due to its endangered habitats. The objectives of this study were to determine the diversity and genetic structure of E. bilobatum and to know if there is a correlation with genetic diversity and its ecological and life history traits. Using horizontal starch-gel electrophoresis, we screened 160 individuals from four populations. E. bilobatum has a higher genetic diversity (A=2.32, Ae=1.31, P=69.65, Ho=0.134, He=0.197, HT=0.221) than species with similar ecological and life history traits, moderate levels of inbreeding (FIS = 0.312) and low genetic differentiation among populations (FST = 0.053 y GST = 0.048). Its diversity and genetic structure are determined by the mating system and life history traits, more than by inhabiting aquatic environments.

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One Step Away From Extinction: A Population Genomic Analysis of A Narrow Endemic, Tropical Plant Species

Frontiers in Plant Science ◽

10.3389/fpls.2021.730258 ◽

2021 ◽

Vol 12 ◽

Author(s):

Thais M. Teixeira ◽

Alison G. Nazareno

Keyword(s):

Genetic Diversity ◽

Missing Data ◽

Plant Species ◽

Threatened Species ◽

Demographic History ◽

Small Population ◽

Narrow Endemic ◽

Population Genomic ◽

Genomic Study ◽

History Of

Intraspecific genetic variation plays a fundamental role in maintaining the evolutionary potential of wild populations. Hence, the assessment of genetic diversity patterns becomes essential to guide biodiversity conservation policies, particularly for threatened species. To inform management strategies for conservation of Mimosa catharinensis – a narrow endemic, critically endangered plant species – we identified 1,497 unlinked SNP markers derived from a reduced representation sequencing method (i.e., double digest restriction site associated DNA sequencing, or ddRADseq). This set of molecular markers was employed to assess intrapopulation genetic parameters and the demographic history of one extremely small population of M. catharinensis (N=33) located in the Brazilian Atlantic Forest. Contrary to what is expected for narrow endemic and threatened species with small population sizes, we observed a moderate level of genetic diversity for M. catharinensis [uHE(0%missing data)=0.205, 95% CI (0.160, 0.250); uHE(30%missing data)=0.233, 95% CI (0.174, 0.292)]. Interestingly, M. catharinensis, which is a lianescent shrub with no indication of seed production for at least two decades, presented high levels of outcrossing [t(0%missing data)=0.883, SE±0.0483; t(30%missing data)=0.909, SE±0.011] and an apparent absence of inbreeding [F(0%missing data)=−0.145, 95% CI (−0.189, −0.101); F(30%missing data)=−0.105, 95% CI (−0.199, −0.011)]. However, the reconstruction of demographic history of M. catharinensis indicated that the population should be suffered a recent bottleneck. Our population genomic study tackles a central issue in evolution and conservation biology and we expect that it will be useful to help safeguard the remaining genetic diversity reported for this unique genetic resource.

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Evolution and seed dormancy shape plant genotypic structure through a successional cycle

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2026212118 ◽

2021 ◽

Vol 118 (34) ◽

pp. e2026212118

Author(s):

Anurag A. Agrawal ◽

Amy P. Hastings ◽

John L. Maron

Keyword(s):

Genetic Diversity ◽

Life History ◽

Environmental Change ◽

Seed Dormancy ◽

Life History Traits ◽

Rapid Evolution ◽

Insect Herbivory ◽

Oenothera Biennis ◽

The Face ◽

The Impact

Dormancy has repeatedly evolved in plants, animals, and microbes and is hypothesized to facilitate persistence in the face of environmental change. Yet previous experiments have not tracked demography and trait evolution spanning a full successional cycle to ask whether early bouts of natural selection are later reinforced or erased during periods of population dormancy. In addition, it is unclear how well short-term measures of fitness predict long-term genotypic success for species with dormancy. Here, we address these issues using experimental field populations of the plant Oenothera biennis, which evolved over five generations in plots exposed to or protected from insect herbivory. While populations existed above ground, there was rapid evolution of defensive and life-history traits, but populations lost genetic diversity and crashed as succession proceeded. After >5 y of seed dormancy, we triggered germination from the seedbank and genotyped >3,000 colonizers. Resurrected populations showed restored genetic diversity that reduced earlier responses to selection and pushed population phenotypes toward the starting conditions of a decade earlier. Nonetheless, four defense and life-history traits remained differentiated in populations with insect suppression compared with controls. These findings capture key missing elements of evolution during ecological cycles and demonstrate the impact of dormancy on future evolutionary responses to environmental change.

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Genetic differentiation among Parastichopus regalis populations from Western Mediterranean Sea: potential effects of its fishery and current connectivity.

Mediterranean Marine Science ◽

10.12681/mms.1020 ◽

2015 ◽

Vol 16 (3) ◽

pp. 489 ◽

Cited By ~ 7

Author(s):

C. MAGGI ◽

M. GONZÁLEZ-WANGÜEMERT

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Haplotype Diversity ◽

Western Mediterranean ◽

Mediterranean Coast ◽

Morphological Data ◽

Coi Gene ◽

Fixation Index ◽

Morphological Description ◽

Western Mediterranean Sea

Parastichopus regalis (Cuvier, 1817) is the most expensive seafood product on the catalonian market (NE Spain), with prices around 130 €/Kg (fresh weight). Despite its ecological and economic importance, biological and genetic information on this sea cucumber species is scarce. We provided the first insight on the genetic structure of P. regalis using sequences of cytochrome oxidase I (COI) and 16S genes, as well as a morphological description of its populations. Individuals were collected in six locations along the Spanish Mediterranean coast, including an area under fishery pressure (Catalonia). We found high haplotype diversity and low nucleotide diversity for both genes, with higher levels of genetic diversity observed on COI gene. Population pairwise fixation index (FST), AMOVA and correspondence analysis (CA) based on COI, revealed significant genetic differentiation among some locations. However, further analysis using nuclear markers (e.g. microsatellites) would be necessary to corroborate these results. Moreover, the genetic and morphological data may indicate fishery effects on the Catalonian population with decrease of the size and weight average and lower genetic diversity compared to locations without fishery pressure. For an appropriate management of this species, we suggest: 1) an accurate assessment of the stocks status along the Spanish coasts; 2) the study of the reproductive cycle of this target species and the establishment of a closed fishery season according to it; 3) the founding of protected areas (i.e. not take zones) to conserve healthy populations and favour the recruitment on the nearby areas.

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Population genetics reveals cryptic lineages and ongoing hybridization in a declining migratory fish species complex

10.1101/2021.12.04.471201 ◽

2021 ◽

Author(s):

Quentin Rougemont ◽

Charles Perrier ◽

Anne-Laure Besnard ◽

Isabelle Lebel ◽

Yann Abdallah ◽

...

Keyword(s):

Genetic Diversity ◽

Life History ◽

Demographic History ◽

Life History Strategies ◽

Secondary Contact ◽

Allis Shad ◽

Twaite Shad ◽

Genetic Diversity And Structure ◽

Demographic Processes ◽

Hybridization And Introgression

AbstractDeciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression, of two species of anadromous fish with contrasted life history strategies and which have undergone recent demographic declines, the allis shad (Alosa alosa) and the twaite shad (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species allis shad that disperse stronger distance compared to the iteroparous species, twaite shad. Individuals caught at sea were assigned at the river level for twaite shad and at the region level for allis shad. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species implicated historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence of contemporary hybridization and introgression between both species. Besides, our results support the existence of cryptic species in the Mediterranean sea. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species’ populations and their hybridization should be carefully considered while implementing conservation programs.

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Mismatches between demographic niches and geographic distributions are strongest in poorly dispersed and highly persistent plant species

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1908684117 ◽

2020 ◽

Vol 117 (7) ◽

pp. 3663-3669 ◽

Cited By ~ 6

Author(s):

Jörn Pagel ◽

Martina Treurnicht ◽

William J. Bond ◽

Tineke Kraaij ◽

Henning Nottebrock ◽

...

Keyword(s):

Life History ◽

Plant Species ◽

Ecological Niche ◽

Life History Traits ◽

Environmental Gradients ◽

Demographic Data ◽

Interspecific Variation ◽

Ecological Niches ◽

Geographic Ranges ◽

Geographic Distributions

The ecological niche of a species describes the variation in population growth rates along environmental gradients that drives geographic range dynamics. Niches are thus central for understanding and forecasting species’ geographic distributions. However, theory predicts that migration limitation, source–sink dynamics, and time-lagged local extinction can cause mismatches between niches and geographic distributions. It is still unclear how relevant these niche–distribution mismatches are for biodiversity dynamics and how they depend on species life-history traits. This is mainly due to a lack of the comprehensive, range-wide demographic data needed to directly infer ecological niches for multiple species. Here we quantify niches from extensive demographic measurements along environmental gradients across the geographic ranges of 26 plant species (Proteaceae; South Africa). We then test whether life history explains variation in species’ niches and niche–distribution mismatches. Niches are generally wider for species with high seed dispersal or persistence abilities. Life-history traits also explain the considerable interspecific variation in niche–distribution mismatches: poorer dispersers are absent from larger parts of their potential geographic ranges, whereas species with higher persistence ability more frequently occupy environments outside their ecological niche. Our study thus identifies major demographic and functional determinants of species’ niches and geographic distributions. It highlights that the inference of ecological niches from geographical distributions is most problematic for poorly dispersed and highly persistent species. We conclude that the direct quantification of ecological niches from demographic responses to environmental variation is a crucial step toward a better predictive understanding of biodiversity dynamics under environmental change.

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