title: Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal.
abstract: Low-copy nuclear genes (LCNGs) have complex genetic architectures and evolutionary dynamics. However, unlike multicopy nuclear genes, LCNGs are rarely subject to gene conversion or concerted evolution, and they have higher mutation rates than organellar or nuclear ribosomal DNA markers, so they have great potential for improving the robustness of phylogenetic reconstructions at all taxonomic levels. In this study, our first objective is to evaluate the evolutionary dynamics of the LCNG β-amylase by testing for potential pseudogenization, paralogy, homeology, recombination, and phylogenetic incongruence within a broad representation of the main Pooideae lineages. Our second objective is to determine whether β-amylase shows sufficient phylogenetic signal to reconstruct the evolutionary history of the Pooid grasses. A multigenic (ITS, matK, ndhF, trnTL, and trnLF) tree of the study group provided a framework for assessing the β-amylase phylogeny. Eight accessions showed complete absence of selection, suggesting putative pseudogenic copies or other relaxed selection pressures; resolution of Vulpia alopecuros 2x clones indicated its potential (semi) paralogy; and homeologous copies of allopolyploid species Festuca simensis, F. fenas, and F. arundinacea tracked their Mediterranean origin. Two recombination events were found within early-diverged Pooideae lineages, and five within the PACCMAD clade. The unexpected phylogenetic relationships of 37 grass species (26% of the sampled species) highlight the frequent occurrence of non-treelike evolutionary events, so this LCNG should be used with caution as a phylogenetic marker. However, once the pitfalls are identified and removed, the phylogenetic reconstruction of the grasses based on the β-amylase exon+intron positions is optimal at all taxonomic levels.
authors.affiliation: Departamento de Ciencias Agrarias y del Medio Natural (Botánica), Escuela Politécnica Superior-Huesca, Universidad de Zaragoza, Ctra Cuarte km 1, 22071 Huesca, Spain. Electronic address: miguel.minay@gmail.com.
authors.forename: Miguel
authors.initials: M
authors.lastname: Minaya
authors.affiliation: Departamento de Ciencias Agrarias y del Medio Natural (Botánica), Escuela Politécnica Superior-Huesca, Universidad de Zaragoza, Ctra Cuarte km 1, 22071 Huesca, Spain; Instituto de Genética y Centro de Investigaciones en Biotecnología Agrícola (CIBA), Facultad de Agronomía, Universidad Central de Venezuela, 2101 Maracay, Aragua, Venezuela. Electronic address: antonio.dz.pz@gmail.com.
authors.forename: Antonio
authors.initials: A
authors.lastname: Díaz-Pérez
authors.affiliation: Department of Biological Sciences, University of Illinois at Chicago, USA. Electronic address: robie@uic.edu.
authors.forename: Roberta
authors.initials: R
authors.lastname: Mason-Gamer
authors.affiliation: Grupo de Investigación en Bioloxía Evolutiva (GIBE), Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira sn., 15071 A Coruña, Spain. Electronic address: mpimentel@udc.es.
authors.forename: Manuel
authors.initials: M
authors.lastname: Pimentel
authors.affiliation: Departamento de Ciencias Agrarias y del Medio Natural (Botánica), Escuela Politécnica Superior-Huesca, Universidad de Zaragoza, Ctra Cuarte km 1, 22071 Huesca, Spain; Department of Botany, Institute of Biology, Tomsk State University, Lenin Av. 36, Tomsk 634050, Russia. Electronic address: pcatalan@unizar.es.
authors.forename: Pilar
authors.initials: P
authors.lastname: Catalán
mesh_terms: D019143:Evolution, Molecular; D017343:Genes, Plant; D005819:Genetic Markers; D007438:Introns; D010802:Phylogeny; D006109:Poaceae / Q000145:classification* / Q000235:genetics*; D011544:Pseudogenes; D011995:Recombination, Genetic; D012641:Selection, Genetic; D001614:beta-Amylase / Q000145:classification / Q000235:genetics*
chemical_list: D005819:Genetic Markers; D001614:beta-Amylase
keywords: Low copy nuclear genes; Phylogenetic incongruence; Pooideae; Pseudogenization; Purifying and diversifying selection; β-amylase phylogeny