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

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.España, MINECO grants CGL2014- 52459-P and CGL2017-82465-PEspaña, Ministerio de Economía, Industria y Competitividad, reference IJCI-2015-2345

Uma abordagem holística à conservação de duas espécies endémicas costeiras, Azorina vidalii e Lotus azoricus

A secção UAciência é coordenada pelo Professor Universitário Armindo Rodrigues.A flora vascular dos Açores é composta por cerca de 1000 espécies de plantas, das quais, estima-se que 74 sejam endémicas. Apesar da baixa diversidade e taxa de endemismos, comparativamente com os arquipélagos vizinhos (Madeira e Canárias), novas descobertas feitas em estudos de biologia molecular, associadas ao facto de se encontrarem várias espécies e habitats únicos nos Açores, fazem da sua conservação uma prioridade. As espécies endémicas típicas de zonas costeiras estão naturalmente sujeitas a diversas ameaças, não só de foro ambiental (salinidade, seca, espécies invasoras, erosão, alterações ao uso do solo, alterações climáticas, etc.), mas também de origem humana, que contribuem para a redução drástica das populações ou mesmo para o seu desaparecimento. […].info:eu-repo/semantics/publishedVersio

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

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.This research was funded by grants CGL2014-52459-P and CGL2017-82465-P from the Spanish Ministerio de Economía y Competitividad to AA. SM-H is currently funded by the Spanish Secretaría de Estado de Investigación, Desarrollo e Innovación (FPI fellowship, 2015). MF-M was supported by a Juan de la Cierva fellowship (Spanish Ministerio de Economía, Industria y Competitividad, reference IJCI-2015-2345