Supplementary Figures-Caribbean Plate

Molecular phylogenies and Ancestral area estimates of Poeciliidae and Cichlida

molecular data matrix

Aligned molecular data set of five concatenated genes including two mitochondrial and three nuclea

Shift from slow- to fast-water habitats accelerates lineage and phenotype evolution in a clade of Neotropical suckermouth catfishes (Loricariidae: Hypoptopomatinae)

<div><p>Identifying habitat characteristics that accelerate organismal evolution is essential to understanding both the origins of life on Earth and the ecosystem properties that are most critical to maintaining life into the future. Searching for these characteristics on a large scale has only recently become possible via advances in phylogenetic reconstruction, time-calibration, and comparative analyses. In this study, we combine these tools with habitat and phenotype data for 105 species in a clade of Neotropical suckermouth catfishes commonly known as cascudinhos. Our goal was to determine whether riverine mesohabitats defined by different flow rates (i.e., pools vs. rapids) and substrates (plants vs. rocks) have affected rates of cascudinho cladogenesis and morphological diversification. In contrast to predictions based on general theory related to life in fast-flowing, rocky riverine habitats, Neoplecostomini lineages associated with these habitats exhibited increased body size, head shape diversity, and lineage and phenotype diversification rates. These findings are consistent with a growing understanding of river rapids as incubators of biological diversification and specialization. They also highlight the urgent need to conserve rapids habitats throughout the major rivers of the world.</p></div

Phylorate plots showing speciation rates for the subfamily Hypoptopomatinae.

<p>Branch colors denote instantaneous rates (cool colors = slow, warm = fast). The large cladogram at top depicts mean Phylorate, with colors indicating the mean evolutionary rate across all shift configurations sampled during simulation. Smaller cladograms at bottom show the five distinct shift configurations having the highest posterior probabilities. For each distinct shift configuration, the locations of rate increases are shown as red circles. Text labels denote the posterior probability of each shift configuration. The small Rate-Through-Time plots at left display the cumulative speciation rate from the root of the tree to the present computed from the joint posterior density in BAMM for the entire subfamily (red) and for each tribe (black = Hypoptopomatini; blue = Neoplecostomini; green = Otothyrini). The order of terminal taxa follows that in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178240#pone.0178240.g001" target="_blank">Fig 1</a>.</p

Phylomorphospace plot for the subfamily Hypoptopomatinae in which terminal colors correspond to habitat and the shaded convex hull encloses all examined species of the tribe Neoplecostomini.

<p>The y-axis is the first principal component (PC) from a PC analysis of log-normalized linear distances between 14 external landmarks on the head (following head landmarks originally proposed by Armbruster [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178240#pone.0178240.ref054" target="_blank">54</a>]) and the x-axis is log maximum body size (MBS).</p

Phylorate plots showing rates of maximum body size (MBS) evolution throughout the subfamily Hypoptopomatinae.

<p>Branch colors denote instantaneous rates (cool colors = slow, warm = fast). The large cladogram at top depicts mean Phylorate, with red circles indicating the most frequent rate increases along all sampled trees of the Bayesian analysis. Smaller cladograms at bottom show the seven distinct shift configurations having the highest posterior probabilities. For each distinct shift configuration, the locations of rate increases are shown as red circles. Text labels denote the posterior probability of each shift configuration. The small Rate-Through-Time plots at left display cumulative MBS rates from the root to the present computed from the joint posterior density in BAMM for the subfamily Hypoptopomatinae (red) and each tribe (black = Hypoptopomatini; blue = Neoplecostomini; green = Otothyrini). The order of terminal taxa follows that in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178240#pone.0178240.g001" target="_blank">Fig 1</a>.</p

Phylorate plots showing head-shape diversification rates for the subfamily Hypoptopomatinae.

<p>Branch colors denote instantaneous rates (cool colors = slow, warm = fast). The large cladogram at top depicts the mean Phylorate with the red circle indicating the most frequent rate increase along all sampled trees of the Bayesian analysis. Smaller cladograms at bottom show the three distinct shift configurations having the highest posterior probabilities for head shape evolutionary rate. For each distinct shift configuration, the locations of rate increases are shown as red circles. Text labels denote the posterior probability of each shift configuration. The small Rate-Through-Time plots at left display the cumulative head-shape diversification rate from the root of the tree to the present computed from the joint posterior density in BAMM for the subfamily Hypoptopomatinae (red plot) and each tribe (black = Hypoptopomatini; blue = Neoplecostomini; green = Otothyrini). The order of terminal taxa follows that in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178240#pone.0178240.g001" target="_blank">Fig 1</a>.</p