Conservation of Forest Biodiversity: how sample size affects the estimation of genetic parameters

Costa, Leonardo Severo da; Corneleo, Nathana S.; Stefenon, Valdir Marcos

doi:10.1590/0001-3765201520140064

Cited by 7 publications

(4 citation statements)

References 15 publications

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“…Negative values indicate outbreeding [ 29 ]. Although we had a small sample size for each accession (3 individuals), small sample sizes can still provide reliable estimations if the standard deviation is acceptable [ 30 ]. The higher values of F in the set of wild accessions suggest inbreeding is much higher than in the cultivated types.…”

Section: Resultsmentioning

confidence: 99%

Genetic Diversity and Population Structure in Vicia faba L. Landraces and Wild Related Species Assessed by Nuclear SSRs

et al. 2016

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Faba bean (Vicia faba L.) is a facultative cross-pollinating legume crop with a great importance for food and feed due to its high protein content as well as the important role in soil fertility and nitrogen fixation. In this work we evaluated genetic diversity and population structure of faba bean accessions from the Western Mediterranean basin and wild related species. For that purpose we screened 53 V. faba, 2 V. johannis and 7 V. narbonensis accessions from Portugal, Spain and Morocco with 28 faba bean Single Sequence Repeats (SSR). SSR genotyping showed that the number of alleles detected per locus for the polymorphic markers ranged between 2 and 10, with Polymorphic Information Content (PIC) values between 0.662 and 0.071, and heterozygosity (HO) between 0–0.467. Heterozygosity and inbreeding coefficient levels indicate a higher level of inbreeding in wild related species than in cultivated Vicia. The analysis of molecular variance (AMOVA) showed a superior genetic diversity within accessions than between accessions even from distant regions. These results are in accordance to population structure analysis showing that individuals from the same accession can be genetically more similar to individuals from far away accessions, than from individuals from the same accession. In all three levels of analysis (whole panel of cultivated and wild accessions, cultivated faba bean accessions and Portuguese accessions) no population structure was observed based on geography or climatic factors. Differences between V. narbonensis and V. johannis are undetectable although these wild taxa are clearly distinct from V. faba accessions. Thus, a limited gene flow occurred between cultivated accessions and wild relatives. Contrastingly, the lack of population structure seems to indicate a high degree of gene flow between V. faba accessions, possibly explained by the partially allogamous habit in association with frequent seed exchange/introduction.

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Section: Resultsmentioning

confidence: 99%

Genetic Diversity and Population Structure in Vicia faba L. Landraces and Wild Related Species Assessed by Nuclear SSRs

et al. 2016

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“…According to Lindblom (2009), well-developed sampling designs within the field of molecular biodiversity science should be formulated around three basic areas: research study questions, research study aims and taxonomic focus. In addition to these three areas, Costa, Corneleo, and Stefenon (2015) point to further considerations: planning the number and geographic distribution of specimens to be sampled, the category and number of genetic loci to be examined, and the spatial distribution and number of individuals to be sampled within each species' population. While there is a lack of clear sampling guidelines currently in place for optimal spatio-temporal assessment of species populations, Pante et al (2015) argue that such schemes should be guided by adequate coverage of both the putative geographic/ecologic range of the species under study, and potentially closely related species over its entire range.…”

Section: Introductionmentioning

confidence: 99%

Incomplete estimates of genetic diversity within species: Implications for DNA barcoding

Phillips

Gillis

Hanner

2019

Ecology and Evolution

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DNA barcoding has greatly accelerated the pace of specimen identification to the species level, as well as species delineation. Whereas the application of DNA barcoding to the matching of unknown specimens to known species is straightforward, its use for species delimitation is more controversial, as species discovery hinges critically on present levels of haplotype diversity, as well as patterning of standing genetic variation that exists within and between species. Typical sample sizes for molecular biodiversity assessment using DNA barcodes range from 5 to 10 individuals per species. However, required levels that are necessary to fully gauge haplotype variation at the species level are presumed to be strongly taxon‐specific. Importantly, little attention has been paid to determining appropriate specimen sample sizes that are necessary to reveal the majority of intraspecific haplotype variation within any one species. In this paper, we present a brief outline of the current literature and methods on intraspecific sample size estimation for the assessment of COI DNA barcode haplotype sampling completeness. The importance of adequate sample sizes for studies of molecular biodiversity is stressed, with application to a variety of metazoan taxa, through reviewing foundational statistical and population genetic models, with specific application to ray‐finned fishes (Chordata: Actinopterygii). Finally, promising avenues for further research in this area are highlighted.

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“…Given the inconsistencies among the available data on A. radiata life history, population genetics, and population status, management of the species in the North Atlantic remains a conundrum. It may be that genomic and spatial sampling has so far been insufficient to capture subtle signals of biologically relevant variation that explain observed patterns (Costa et al, 2015) because most previous genetic analyses have not included samples from the species' full geographic range, particularly US waters of the Gulf of Maine and Georges Bank (Chevolot et al, 2007;Lynghammar et al, 2014Lynghammar et al, , 2016. The most comprehensively sampled locus in A. radiata analyses to date-the mitochondrion-also exhibits a heterogeneous process history, where different pressures have been exerted in different regions, resulting in a variety of signatures (Rubinoff et al, 2006).…”

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confidence: 99%

Mitogenomic evidence of population differentiation of thorny skate, Amblyraja radiata, in the North Atlantic

Denton,

Kneebone,

Yang

et al. 2024

Journal of Fish Biology

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Management of thorny skate (Amblyraja radiata) in the Northwest Atlantic has posed a conservation dilemma for several decades due to the species' lack of response to strong conservation efforts in the US Gulf of Maine and the Canadian Scotian Shelf, confusion over the relationship between two reproductive size morphs of differing life histories that are sympatric in the Northwest Atlantic, and conflicting data on regional population connectivity throughout the species' broader range. To better assess potential A. radiata regional population differentiation and genetic links to life‐history variation, we analysed complete mitochondrial genome sequences from 527 specimens collected across the species' North Atlantic geographic range, with particular emphasis on the Northwest Atlantic region. A high level of genetic diversity was evident across the North Atlantic, but significant genetic differentiation was identified between specimens inhabiting the Northwest (Gulf of Maine and Newfoundland) and Northeast (Greenland, Iceland, North Sea, and Arctic Circle) Atlantic. In the Northwest Atlantic, significant differentiation between the Gulf of Maine and Newfoundland regions was revealed; however, the overall level of differentiation was very low. No genetic difference was identified between the large and small reproductive morphs. The results of this study advance our understanding of A. radiata population structure in the North Atlantic but do not resolve all the questions confounding our understanding of the species' biology and evolutionary history.

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Conservation of Forest Biodiversity: how sample size affects the estimation of genetic parameters

Cited by 7 publications

References 15 publications

Genetic Diversity and Population Structure in Vicia faba L. Landraces and Wild Related Species Assessed by Nuclear SSRs

Genetic Diversity and Population Structure in Vicia faba L. Landraces and Wild Related Species Assessed by Nuclear SSRs

Incomplete estimates of genetic diversity within species: Implications for DNA barcoding

Mitogenomic evidence of population differentiation of thorny skate, Amblyraja radiata, in the North Atlantic

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