Population differentiation in relation to conservation: nuclear microsatellite variation in the Canary Island endemic Lotus sessilifolius (Fabaceae)

Yang, Jinshui; Ojeda, Darío I.; Santos‐Guerra, Arnoldo; Molina, Ruth Jaén; Caujapé‐Castells, Juli; Cronk, Quentin

doi:10.1007/s12686-017-0778-1

Cited by 7 publications

(6 citation statements)

References 30 publications

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“…Since the article by Sosa et al (2010) was published, the knowledge of genetic diversity measured with microsatellite markers in oceanic endemics has significantly increased ( Takayama et al, 2015 ; White et al, 2016 ; Yang et al, 2017 ). Therefore, we are now able to confirm that S. palmensis presents moderate levels of genetic diversity for a rare endemic ( Sosa et al, 2011 ).…”

Section: Discussionmentioning

confidence: 99%

The restoration of the endangeredSambucus palmensisafter 30 years of conservation actions in the Garajonay National Park: genetic assessment and niche modeling

Rodríguez-Rodríguez

Castro

Sosa

2018

PeerJ

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The translocation of individuals or the reinforcement of populations are measures in the genetic rescue of endangered species. Although it can be controversial to decide which and how many individuals must be reintroduced, populations can benefit from reinforcements. Sambucus palmensis is a critically endangered endemic to the Canary Islands. During the past 30 years, the Garajonay National Park (La Gomera) has carried out an intensive program of translocations using cuttings, due to the low germination rates of seeds. To assess the effect of the restorations on the population genetics of S. palmensis in La Gomera, we collected 402 samples from all the restored sites and all known natural individuals, which were genotyped with seven microsatellite markers. In addition, we conducted a species distribution modeling approach to assess how restorations fit the ecological niche of the species. Results show that there is a high proportion of clone specimens due to the propagation method, and the natural clonal reproduction of the species. Nonetheless, the observed heterozygosity has increased with the restorations and there still are private alleles and unique genotypes in the natural populations that have not been considered in the restorations. The population of Liria constitutes a very important genetic reservoir for the species. To optimize future reintroductions, we have proposed a list of specimens that are suitable for the extraction of seeds or cuttings in a greenhouse, as well as new suitable areas obtained by the species distribution models.

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Section: Discussionmentioning

confidence: 99%

The restoration of the endangeredSambucus palmensisafter 30 years of conservation actions in the Garajonay National Park: genetic assessment and niche modeling

Rodríguez-Rodríguez

Castro

Sosa

2018

PeerJ

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“…(2010): CES (ΔBIC = −2.236); Yang et al . (2018): PES with

r_{s} = 0.5

(ΔBIC = −3.410), and Zwart et al . (2016): PES with

r_{s} = 0.25

(ΔBIC = −4.089).…”

Section: Resultsmentioning

confidence: 97%

“…We also use four empirical autotetraploid genotypic datasets to evaluate the performance of our new AMOVA framework in handling polyploids, and to compare its performance with genodive v3.04 (Meirmans 2020). Hoeltgebaum et al .’s (2017) Varronia curassavica dataset genotyped 681 individuals from 4 populations at 8 loci, Julier et al .’s (2010) Lucerne ( Medicago sativa ) dataset genotyped 463 individuals from 16 populations at 7 loci, Yang et al .’s (2018) Lotus sessilifolius dataset genotyped 48 individuals from 8 populations at 11 loci, and Zwart et al .’s (2016) Grey willow ( Salix cinereal ) dataset genotyped 139 individuals from 4 populations at 7 loci.…”

Section: Methodsmentioning

confidence: 99%

A generalized framework for AMOVA with multiple hierarchies and ploidies

et al. 2020

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The analysis of molecular variance (AMOVA) is a widely used statistical method in population genetics and molecular ecology. The classic framework of AMOVA only supports haploid and diploid data, in which the number of hierarchies ranges from two to four. In practice, natural populations can be classified into more hierarchies, and polyploidy is frequently observed in extant species. The ploidy level may even vary within the same species, and/or within the same individual. We generalized the framework of AMOVA such that it can be used for any number of hierarchies and any level of ploidy. Based on this framework, we present four methods to account for data that are multilocus genotypic and allelic phenotypic (with unknown allele dosage). We use simulated datasets and an empirical dataset to evaluate the performance of our framework. We make freely available our methods in a new software package, polygene, which is freely available at https://github.com/huangkang1987/polygene.

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“… The optimal model evaluated from BIC are: Zwart et al (): PES ( r s = 0.5) (ΔBIC = 1.95); Yang et al (): PES ( r s = 0.25) (ΔBIC = 3.41); Hoeltgebaum et al’s (): CES (ΔBIC = 1.40); Julier et al (): CES (ΔBIC = 2.24). …”

Section: Simulations and Comparisonsmentioning

confidence: 99%

polygene: Population genetics analyses for autopolyploids based on allelic phenotypes

et al. 2019

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Polyploidy has appeared in almost every ancestral plant lineage, and in extant species, occurs frequently. When present, polyploidy presents problems for genetic data analysis, which are caused by both genotypic ambiguities and double‐reduction. To address these problems, we developed a new software package, polygene, which enables the estimation of genotypic frequencies for a number of polysomic inheritance models. Specifically, polygene obtains posterior probabilities for genotypes hidden within allelic phenotypes. Comprehensive modes of genetic analyses are provided by polygene, which include genetic diversity analysis, tests for allelic phenotypic or genotypic distributions, linkage disequilibrium and genetic differentiation, genetic distance analysis, principal coordinates analysis, hierarchical clustering analysis, individual inbreeding coefficient estimation, individual heterozygosity index estimation, population assignment, pairwise relatedness estimation, parentage analysis, analysis of molecular variance and Bayesian clustering. polygene enables easy and convenient allelic phenotype‐ or genotype‐based analysis for both autopolyploids and diploids. polygene will thus facilitate molecular ecology research involving autopolyploids.

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Population differentiation in relation to conservation: nuclear microsatellite variation in the Canary Island endemic Lotus sessilifolius (Fabaceae)

Cited by 7 publications

References 30 publications

The restoration of the endangeredSambucus palmensisafter 30 years of conservation actions in the Garajonay National Park: genetic assessment and niche modeling

The restoration of the endangeredSambucus palmensisafter 30 years of conservation actions in the Garajonay National Park: genetic assessment and niche modeling

A generalized framework for AMOVA with multiple hierarchies and ploidies

polygene: Population genetics analyses for autopolyploids based on allelic phenotypes

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