Phylogenetic resolution power of microsatellites and various single‐nucleotide polymorphism types assessed in 10 divergent chicken populations

Granevitze, Z.; David, Lior; Twito, T.; Weigend, Steffen; Feldman, Marcus W.; Hillel, J.

doi:10.1111/age.12088

Cited by 15 publications

(14 citation statements)

References 29 publications

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“…This result is in agreement with the conclusions of Granevitze et al (2014), who stated that microsatellite loci may perform even better than other marker types in the assignment tests applied to wild and domestic chicken populations.…”

Section: Articlesupporting

confidence: 92%

Genetic traceability of two local chicken populations, Bianca di Saluzzo and Bionda Piemontese, versus some current commercial lines

et al. 2014

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The aims of this investigation were to analyse the genetic variation of two Piemonte chicken local breeds, Bionda Piemontese and Bianca di Saluzzo, and to set them against some commercial lines. A panel of 19 microsatellite markers was used. On the overall, the results of different analyses highlight the genetic uniqueness of the two breeds; therefore they should be considered genetic resources worthy of preservation. The panel of microsatellites used in this investigation turns out to be a consistent and reliable tool for traceability. In fact, these markers are able to distinguish the two local populations from the commercial lines and they are able to confirm the existence of two genetically different clusters within the Bionda Piemontese, namely the ecotypes standard and Cuneo. Mating policies implemented to avoid inbreeding and, if necessary, a marker assisted conservation scheme would be sufficient to solve the problem of inbreeding.

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Section: Articlesupporting

confidence: 92%

Genetic traceability of two local chicken populations, Bianca di Saluzzo and Bionda Piemontese, versus some current commercial lines

et al. 2014

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“…; Granevitze et al. ; Ross et al. ), whereas ascertainment from a larger pool improved the performance of SNPs (Glover et al.…”

Section: Introductionmentioning

confidence: 99%

Challenges in analysis and interpretation of microsatellite data for population genetic studies

Putman

Carbone

2014

Ecology and Evolution

320

252

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Advancing technologies have facilitated the ever-widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (FST) statistics and Bayesian clustering algorithms and find that the former can be confusing and problematic for microsatellites and that the latter may be confounded by complex population models and lack power in certain cases. Clustering, multivariate analyses, and diversity-based statistics are increasingly being applied to infer population structure, but in some instances these methods lack formalization with microsatellites. Migration-specific methods perform well only under narrow constraints. We also examine the use of microsatellites for inferring effective population size, changes in population size, and deeper demographic history, and find that these methods are untested and/or highly context-dependent. Overall, each method possesses important weaknesses for use with microsatellites, and there are significant constraints on inferences commonly made using microsatellite markers in the areas of population structure, admixture, and effective population size. To ameliorate and better understand these constraints, researchers are encouraged to analyze simulated datasets both prior to and following data collection and analysis, the latter of which is formalized within the approximate Bayesian computation framework. We also examine trends in the literature and show that microsatellites continue to be widely used, especially in non-human subject areas. This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical limitations, and identifies lessons that could be applied toward emerging markers and high-throughput technologies in population genetics.

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“…autogamy, clonality). Guichoux et al [16] suggested that microsatellites may be better than SNP to detect mixtures of genetic clusters (see also [17, 18]. But opposite findings have also been reported and the debate on the relative performance of SNPs over SSRs remains [19].…”

Section: Introductionmentioning

confidence: 99%

Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences – a case study in the tree genus Milicia

Daïnou

Blanc-Jolivet²,

Деген³

et al. 2016

BMC Evol Biol

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BackgroundSpecies delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa. We genotyped SNP and SSR loci to identify genetic clusters, and sequenced two plastid regions (psbA-trnH, trnC-ycf6) and a nuclear gene (At103) to confirm species’ divergence and compare species delimitation methods. We also examined whether ecological niche differentiation was congruent with sampled genetic structure.ResultsWest African M. regia, West African and East African M. excelsa samples constituted three well distinct genetic clusters according to SNPs and SSRs. In Central Africa, two genetic clusters were consistently inferred by both types of markers, while a few scattered samples, sympatric with the preceding clusters but exhibiting leaf traits of M. regia, were grouped with the West African M. regia cluster based on SNPs or formed a distinct cluster based on SSRs. SSR results were confirmed by sequence data from the nuclear region At103 which revealed three distinct ‘Fields For Recombination’ corresponding to (i) West African M. regia, (ii) Central African samples with leaf traits of M. regia, and (iii) all M. excelsa samples. None of the plastid sequences provide indication of distinct clades of the three species-like units. Niche modelling techniques yielded a significant correlation between niche overlap and genetic distance.ConclusionsOur genetic data suggest that three species of Milicia could be recognized. It is surprising that the occurrence of two species in Central Africa was not reported for this well-known timber tree. Globally, our work highlights the importance of collecting samples in a systematic way and the need for combining different nuclear markers when dealing with species complexes. Recognizing cryptic species is particularly crucial for economically exploited species because some hidden taxa might actually be endangered as they are merged with more abundant species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0831-9) contains supplementary material, which is available to authorized users.

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Phylogenetic resolution power of microsatellites and various single‐nucleotide polymorphism types assessed in 10 divergent chicken populations

Cited by 15 publications

References 29 publications

Genetic traceability of two local chicken populations, Bianca di Saluzzo and Bionda Piemontese, versus some current commercial lines

Genetic traceability of two local chicken populations, Bianca di Saluzzo and Bionda Piemontese, versus some current commercial lines

Challenges in analysis and interpretation of microsatellite data for population genetic studies

Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences – a case study in the tree genus Milicia

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