Dataset Information

Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of Helianthemum (Cistaceae).

ABSTRACT: A robust phylogenetic framework, in terms of extensive geographical and taxonomic sampling, well-resolved species relationships and high certainty of tree topologies and branch length estimations, is critical in the study of macroevolutionary patterns. Whereas Sanger sequencing-based methods usually recover insufficient phylogenetic signal, especially in recently diversified lineages, reduced-representation sequencing methods tend to provide well-supported phylogenetic relationships, but usually entail remarkable bioinformatic challenges due to the inherent trade-off between the number of SNPs and the magnitude of associated error rates. The genus Helianthemum (Cistaceae) is a species-rich and taxonomically complex Palearctic group of plants that diversified mainly since the Upper Miocene. It is a challenging case study since previous attempts using Sanger sequencing were unable to resolve the intrageneric phylogenetic relationships. Aiming to obtain a robust phylogenetic reconstruction based on genotyping-by-sequencing (GBS), we established a rigorous methodological workflow in which we i) explored how variable settings during dataset assembly have an impact on error rates and on the degree of resolution under concatenation and coalescent approaches, ii) assessed the effect of two extreme parameter configurations (minimizing error rates vs. maximizing phylogenetic resolution) on tree topology and branch lengths, and iii) evaluated the effects of these two configurations on estimates of divergence times and diversification rates. Our analyses produced highly supported topologically congruent phylogenetic trees for both configurations. However, minimizing error rates did produce more reliable branch lengths, critically affecting the accuracy of downstream analyses (i.e. divergence times and diversification rates). In addition to recommending a revision of intrageneric systematics, our results enabled us to identify three highly diversified lineages in Helianthemum in contrasting geographical areas and ecological conditions, which started radiating in the Upper Miocene.

SUBMITTER: Martin-Hernanz S

PROVIDER: S-EPMC6859804 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of <i>Helianthemum</i> (Cistaceae).

Martín-Hernanz Sara S Aparicio Abelardo A Fernández-Mazuecos Mario M Rubio Encarnación E Reyes-Betancort J Alfredo JA Santos-Guerra Arnoldo A Olangua-Corral María M Albaladejo Rafael G RG

Frontiers in plant science 20191111

A robust phylogenetic framework, in terms of extensive geographical and taxonomic sampling, well-resolved species relationships and high certainty of tree topologies and branch length estimations, is critical in the study of macroevolutionary patterns. Whereas Sanger sequencing-based methods usually recover insufficient phylogenetic signal, especially in recently diversified lineages, reduced-representation sequencing methods tend to provide well-supported phylogenetic relationships, but usually ...[more]

PMID: 31781140

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Project description:Unraveling the relationships between ecological, functional traits and genetic diversity of narrow endemic plants provide opportunities for understanding how evolutionary processes operate over local spatial scales and ultimately how diversity is created and maintained. To explore these aspects in Sierra Nevada, the core of the Mediterranean Betic-Rifean hotspot, we have analyzed nuclear DNA microsatellite diversity and a set of biological and environmental factors (physicochemical soil parameters, floral traits, and community composition) in two strictly endemic taxa from dolomite outcrops of Sierra Nevada (Helianthemum pannosum and H. apenninum subsp. estevei) and two congeneric widespread taxa (H. cinereum subsp. rotundifolium and H. apenninum subsp. apenninum) that further belong to two different lineages (subgenera) of Helianthemum. We obtained rather unexpected results contrasting with the theory: (a) The narrow endemic taxa showed higher values of genetic diversity as well as higher average values of pollen production per flower and pollen-to-ovule ratio than their widespread relatives; and (b) the two taxa of subg. Helianthemum, with larger corollas, approach herkogamy and higher pollen production than the two taxa of subg. Plectolobum, displayed lower genetic diversity and higher values of inbreeding. Altogether, these results disclose how genetic diversity may be affected simultaneously by a large number of intrinsic and extrinsic factors, especially in Pleistocene glacial refugia in mountains where the spatial context harbors a great ecological heterogeneity. On the other hand, differences in mating system and the significant effect of the substrate profile, both being highly diverse in the genus Helianthemum, in the genetic variability illustrate about the importance of these two factors in the diversification and species differentiation of this paradigmatic genus in the Mediterranean and open the field to formulate and test new hypotheses of local adaptation, trait evolution, and habitat diversification.

Project description:IntroductionIn the United States, tens of thousands of inspections of tobacco retailers are conducted each year. Various sampling choices can reduce travel costs, emphasize enforcement in areas with greater noncompliance, and allow for comparability between states and over time. We sought to develop a model sampling strategy for state tobacco retailer inspections.MethodsUsing a 2014 list of 10,161 North Carolina tobacco retailers, we compared results from simple random sampling; stratified, clustered at the ZIP code sampling; and, stratified, clustered at the census tract sampling. We conducted a simulation of repeated sampling and compared approaches for their comparative level of precision, coverage, and retailer dispersion.ResultsWhile maintaining an adequate design effect and statistical precision appropriate for a public health enforcement program, both stratified, clustered ZIP- and tract-based approaches were feasible. Both ZIP and tract strategies yielded improvements over simple random sampling, with relative improvements, respectively, of average distance between retailers (reduced 5.0% and 1.9%), percent Black residents in sampled neighborhoods (increased 17.2% and 32.6%), percent Hispanic residents in sampled neighborhoods (reduced 2.2% and increased 18.3%), percentage of sampled retailers located near schools (increased 61.3% and 37.5%), and poverty rate in sampled neighborhoods (increased 14.0% and 38.2%).ConclusionsStates can make retailer inspections more efficient and targeted with stratified, clustered sampling. Use of statistically appropriate sampling strategies like these should be considered by states, researchers, and the Food and Drug Administration to improve program impact and allow for comparisons over time and across states.ImplicationsThe authors present a model tobacco retailer sampling strategy for promoting compliance and reducing costs that could be used by US states and the Food and Drug Administration (FDA). The design is feasible to implement in North Carolina. Use of the sampling design would help document the impact of FDA's compliance and enforcement program, save money, and emphasize inspections in areas where they are needed most. FDA should consider requiring probability-based sampling in their inspections contracts with states and private contractors.

Dataset Information

Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of Helianthemum (Cistaceae).

Publications

Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of <i>Helianthemum</i> (Cistaceae).

Similar Datasets

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