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      Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics

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          Abstract

          Vertebrates have evolved to gigantic sizes repeatedly over the past 250 Myr, reaching their extreme in today's baleen whales (Mysticeti). Hypotheses for the evolution of exceptionally large size in mysticetes range from niche partitioning to predator avoidance, but there has been no quantitative examination of body size evolutionary dynamics in this clade and it remains unclear when, why or how gigantism evolved. By fitting phylogenetic macroevolutionary models to a dataset consisting of living and extinct species, we show that mysticetes underwent a clade-wide shift in their mode of body size evolution during the Plio-Pleistocene. This transition, from Brownian motion-like dynamics to a trended random walk towards larger size, is temporally linked to the onset of seasonally intensified upwelling along coastal ecosystems. High prey densities resulting from wind-driven upwelling, rather than abundant resources alone, are the primary determinant of efficient foraging in extant mysticetes and Late Pliocene changes in ocean dynamics may have provided an ecological pathway to gigantism in multiple independent lineages.

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          Testing for phylogenetic signal in comparative data: behavioral traits are more labile.

          Simon Blomberg, Anthony Ives, Theodore Garland (2003)
          The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal alpha = 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformations, one based on the Ornstein-Uhlenbeck (OU) model of stabilizing selection, the other based on a new model in which character evolution can accelerate or decelerate (ACDC) in rate (e.g., as may occur during or after an adaptive radiation). Maximum likelihood estimation of the OU (d) and ACDC (g) parameters can serve as tests for phylogenetic signal because an estimate of d or g near zero implies that a phylogeny with little hierarchical structure (a star) offers a good fit to the data. Transformations that improve the fit of a tree to comparative data will increase power to detect phylogenetic signal and may also be preferable for further comparative analyses, such as of correlated character evolution. Application of the methods to data from the literature revealed that, for trees with 20 or more species, 92% of traits exhibited significant phylogenetic signal (randomization test), including behavioral and ecological ones that are thought to be relatively evolutionarily malleable (e.g., highly adaptive) and/or subject to relatively strong environmental (nongenetic) effects or high levels of measurement error. Irrespective of sample size, most traits (but not body size, on average) showed less signal than expected given the topology, branch lengths, and a Brownian motion model of evolution (i.e., K was less than one), which may be attributed to adaptation and/or measurement error in the broad sense (including errors in estimates of phenotypes, branch lengths, and topology). Analysis of variance of log K for all 121 traits (from 35 trees) indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits. In addition, physiological traits (corrected for body size) showed less signal than did body size itself. For trees with 20 or more species, the estimated OU (25% of traits) and/or ACDC (40%) transformation parameter differed significantly from both zero and unity, indicating that a hierarchical tree with less (or occasionally more) structure than the original better fit the data and so could be preferred for comparative analyses.
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            geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees.

            Matthew Pennell, Jonathan M Eastman, Graham Slater … (2014)
            Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased dramatically in the past few years. Many existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger v2.0, a complete overhaul of the popular R package geiger. We have reimplemented existing methods with more efficient algorithms and have developed several new approaches for accomodating heterogeneous models and data types.
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              The fossilized birth-death process for coherent calibration of divergence-time estimates.

              Tracy A. Heath, John P. Huelsenbeck, Tanja Stadler (2014)
              Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because molecular sequence data are not informative on absolute time, external data--most commonly, fossil age estimates--are required to calibrate estimates of species divergence dates. For Bayesian divergence time methods, the common practice for calibration using fossil information involves placing arbitrarily chosen parametric distributions on internal nodes, often disregarding most of the information in the fossil record. We introduce the "fossilized birth-death" (FBD) process--a model for calibrating divergence time estimates in a Bayesian framework, explicitly acknowledging that extant species and fossils are part of the same macroevolutionary process. Under this model, absolute node age estimates are calibrated by a single diversification model and arbitrary calibration densities are not necessary. Moreover, the FBD model allows for inclusion of all available fossils. We performed analyses of simulated data and show that node age estimation under the FBD model results in robust and accurate estimates of species divergence times with realistic measures of statistical uncertainty, overcoming major limitations of standard divergence time estimation methods. We used this model to estimate the speciation times for a dataset composed of all living bears, indicating that the genus Ursus diversified in the Late Miocene to Middle Pliocene.
              Article 0 comments Cited 295 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Proc Biol Sci
                Journal ID (iso-abbrev): Proc. Biol. Sci
                Journal ID (publisher-id): RSPB
                Journal ID (hwp): royprsb
                Title: Proceedings of the Royal Society B: Biological Sciences
                Publisher: The Royal Society
                ISSN (Print): 0962-8452
                ISSN (Electronic): 1471-2954
                Publication date (Print): 31 May 2017
                Publication date (Electronic): 24 May 2017
                Publication date PMC-release: 24 May 2017
                Volume: 284
                Issue: 1855
                Electronic Location Identifier: 20170546
                Affiliations
                [1 ]Department of the Geophysical Sciences, University of Chicago , Chicago, IL, USA
                [2 ]Department of Biology, Hopkins Marine Station, Stanford University , Pacific Grove, CA, USA
                [3 ]Department of Paleobiology, National Museum of Natural History, Washington, DC, USA
                Author notes

                Electronic supplementary material is available online at https://dx.doi.org/10.6084/m9.figshare.c.3768689.

                Author information
                http://orcid.org/0000-0002-6306-0911
                http://orcid.org/0000-0003-4678-5782
                Article
                Publisher ID: rspb20170546
                DOI: 10.1098/rspb.2017.0546
                PMC ID: 5454272
                PubMed ID: 28539520
                SO-VID: bf624c3d-8152-4242-9d30-2099cac0a509
                Copyright © © 2017 The Author(s).
                License:

                Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

                History
                Date received : 14 March 2017
                Date accepted : 13 April 2017
                Funding
                Funded by: Smithsonian Institution, its Remington Kellogg Fund;
                Categories
                Subject: 1001
                Subject: 70
                Subject: 144
                Subject: Palaeobiology
                Subject: Research Article
                Custom metadata
                cover-date May 31, 2017

                ScienceOpen disciplines: Life sciences
                Keywords: macroevolution,tempo and mode,phylogeny,fossil,body size,trend
                Data availability:
                ScienceOpen disciplines: Life sciences
                Keywords: macroevolution, tempo and mode, phylogeny, fossil, body size, trend

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