title: Rapid cladogenesis in marine fishes revisited.
abstract: Lineages that underwent rapid cladogenesis are attractive systems for the study of mechanisms underlying taxonomic, ecological, morphological, and behavioral diversification. Recently developed statistical methods provide insights into historical patterns of diversity and allow distinguishing bursts of cladogenesis from stochastic background rates in the presence of confounding factors such as extinction and incomplete taxon sampling. Here, we compare the dynamics of speciation in several marine fish lineages some of which were previously proposed to have undergone significant changes of cladogenesis through time. We tested for evidence of episodes of rapid cladogenesis using the constant rate and Monte Carlo constant rate tests that are robust to incomplete taxon sampling. These tests employ the statistic gamma to measure the relative position of internal node in a chronogram. For the first time, we conducted a comparative analysis to address the behavior of the statistic under different chronogram-constructing methods (Langley-Fitch, nonparametric rate smoothing, and penalized likelihood). Although estimates of gamma sometimes differ widely among methods, acceptance or rejection of the constant rate model within a particular clade appears to be robust to the choice of method. Bursts of cladogenesis were detected in 14 of 34 studied datasets. Some of these were previously proposed to represent marine fish "radiations," whereas others are identified anew. Our results indicate that the wider application of tree shape methods that are able to detect significantly elevated rates of speciation is useful to more precisely define clades that underwent episodes of rapid cladogenesis in marine fish clades. Contrasting the patterns of phylogenetic diversification in marine fish lineages may facilitate the identification of common evolutionary trajectories versus idiosyncrasies, and ultimately help towards a better understanding of the factors and processes underlying speciation in the marine realm.
authors.affiliation: Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal 2, 28006 Madrid, Spain. ruber@mncn.csic.es
authors.forename: Lukas
authors.initials: L
authors.lastname: Rüber
authors.forename: Rafael
authors.initials: R
authors.lastname: Zardoya
mesh_terms: D000818:Animals; D004275:DNA, Ribosomal / Q000235:genetics; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D005399:Fishes / Q000235:genetics*; D016013:Likelihood Functions; D008386:Marine Biology; D008962:Models, Theoretical; D009010:Monte Carlo Method; D010802:Phylogeny; D011506:Proteins / Q000235:genetics; D016415:Sequence Alignment; D013045:Species Specificity; D013997:Time Factors
chemical_list: D004275:DNA, Ribosomal; D011506:Proteins