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Lanfear R.,Australian National University | Lanfear R.,National Evolutionary Synthesis Center | Kokko H.,Australian National University | Eyre-Walker A.,University of Sussex
Trends in Ecology and Evolution | Year: 2014

Does evolution proceed faster in larger or smaller populations? The relationship between effective population size (Ne) and the rate of evolution has consequences for our ability to understand and interpret genomic variation, and is central to many aspects of evolution and ecology. Many factors affect the relationship between Ne and the rate of evolution, and recent theoretical and empirical studies have shown some surprising and sometimes counterintuitive results. Some mechanisms tend to make the relationship positive, others negative, and they can act simultaneously. The relationship also depends on whether one is interested in the rate of neutral, adaptive, or deleterious evolution. Here, we synthesize theoretical and empirical approaches to understanding the relationship and highlight areas that remain poorly understood. © 2013.

Slater G.J.,University of California at Los Angeles | Slater G.J.,Smithsonian Institution | Pennell M.W.,University of Idaho | Pennell M.W.,National Evolutionary Synthesis Center
Systematic Biology | Year: 2014

A central prediction of much theory on adaptive radiations is that traits should evolve rapidly during the early stages of a clade's history and subsequently slowdown in rate as niches become saturated - a so-called "Early Burst." Although a common pattern in the fossil record, evidence for early bursts of trait evolution in phylogenetic comparative data has been equivocal at best. We show here that this may not necessarily be due to the absence of this pattern in nature. Rather, commonly used methods to infer its presence perform poorly when when the strength of the burst - the rate at which phenotypic evolution declines - is small, and when some morphological convergence is present within the clade. We present two modifications to existing comparative methods that allow greater power to detect early bursts in simulated datasets. First, we develop posterior predictive simulation approaches and show that they outperform maximum likelihood approaches at identifying early bursts at moderate strength. Second, we use a robust regression procedure that allows for the identification and down-weighting of convergent taxa, leading to moderate increases in method performance. We demonstrate the utility and power of these approach by investigating the evolution of body size in cetaceans. Model fitting using maximum likelihood is equivocal with regards the mode of cetacean body size evolution. However, posterior predictive simulation combined with a robust node height test return low support for Brownian motion or rate shift models, but not the early burst model. While the jury is still out on whether early bursts are actually common in nature, our approach will hopefully facilitate more robust testing of this hypothesis. We advocate the adoption of similar posterior predictive approaches to improve the fit and to assess the adequacy of macroevolutionary models in general. [Adaptive Radiations, Early Burst, Posterior Predictive Simulations, Quantitative Characters] © The Author(s) 2013.

Santos J.C.,University of Texas at Austin | Santos J.C.,National Evolutionary Synthesis Center
Molecular Biology and Evolution | Year: 2012

Molecular evolution is simultaneously paced by mutation rate, genetic drift, and natural selection. Life history traits also affect the speed of accumulation of nucleotide changes. For instance, small body size, rapid generation time, production of reactive oxygen species (ROS), and high resting metabolic rate (RMR) are suggested to be associated with faster rates of molecular evolution. However, phylogenetic correlation analyses failed to support a relationship between RMR and molecular evolution in ectotherms. In addition, RMR might underestimate the metabolic budget (e.g., digestion, reproduction, or escaping predation). An alternative is to test other metabolic rates, such as active metabolic rate (AMR), and their association with molecular evolution. Here, I present comparative analyses of the associations between life history traits (i.e., AMR, RMR, body mass, and fecundity) with rates of molecular evolution of and mitochondrial loci from a large ectotherm clade, the poison frogs (Dendrobatidae). My results support a strong positive association between mass-specific AMR and rates of molecular evolution for both mitochondrial and nuclear loci. In addition, I found weaker and genome-specific covariates such as body mass and fecundity for mitochondrial and nuclear loci, respectively. No direct association was found between mass-specific RMR and rates of molecular evolution. Thus, I provide a mechanistic hypothesis of the link between AMRs and the rate of molecular evolution based on an increase in ROS within germ line cells during periodic bouts of hypoxia/hyperoxia related to aerobic exercise. Finally, I propose a multifactorial model that includes AMR as a predictor of the rate of molecular evolution in ectothermic lineages. © The Author 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.

McClain C.R.,National Evolutionary Synthesis Center | Hardy S.M.,University of Alaska Fairbanks
Proceedings of the Royal Society B: Biological Sciences | Year: 2010

Anthropogenic disturbances such as fishing, mining, oil drilling, bioprospecting, warming, and acidification in the deep sea are increasing, yet generalities about deep-sea biogeography remain elusive. Owing to the lack of perceived environmental variability and geographical barriers, ranges of deep-sea species were traditionally assumed to be exceedingly large. In contrast, seamount and chemosynthetic habitats with reported high endemicity challenge the broad applicability of a single biogeographic paradigm for the deep sea. New research benefiting from higher resolution sampling, molecular methods and public databases can now more rigorously examine dispersal distances and species ranges on the vast ocean floor. Here, we explore the major outstanding questions in deep-sea biogeography. Based on current evidence, many taxa appear broadly distributed across the deep sea, a pattern replicated in both the abyssal plains and specialized environments such as hydrothermal vents. Cold waters may slow larval metabolism and development augmenting the great intrinsic ability for dispersal among many deep-sea species. Currents, environmental shifts, and topography can prove to be dispersal barriers but are often semipermeable. Evidence of historical events such as points of faunal origin and climatic fluctuations are also evident in contemporary biogeographic ranges. Continued synthetic analysis, database construction, theoretical advancement and field sampling will be required to further refine hypotheses regarding deep-sea biogeography. © 2010 The Royal Society.

Govindaraju D.R.,National Evolutionary Synthesis Center
Advances in Genetics | Year: 2014

Natural selection defined by differential survival and reproduction of individuals in populations is influenced by genetic, developmental, and environmental factors operating at every age and stage in human life history: generation of gametes, conception, birth, maturation, reproduction, senescence, and death. Biological systems are built upon a hierarchical organization nesting subcellular organelles, cells, tissues, and organs within individuals, individuals within families, and families within populations, and the latter among other populations. Natural selection often acts simultaneously at more than one level of biological organization and on specific traits, which we define as multilevel selection. Under this model, the individual is a fundamental unit of biological organization and also of selection, imbedded in a larger evolutionary context, just as it is a unit of medical intervention imbedded in larger biological, cultural, and environmental contexts. Here, we view human health and life span as necessary consequences of natural selection, operating at all levels and phases of biological hierarchy in human life history as well as in sociological and environmental milieu. An understanding of the spectrum of opportunities for natural selection will help us develop novel approaches to improving healthy life span through specific and global interventions that simultaneously focus on multiple levels of biological organization. Indeed, many opportunities exist to apply multilevel selection models employed in evolutionary biology and biodemography to improving human health at all hierarchical levels. Multilevel selection perspective provides a rational theoretical foundation for a synthesis of medicine and evolution that could lead to discovering effective predictive, preventive, palliative, potentially curative, and individualized approaches in medicine and in global health programs. © 2014 Elsevier Inc.

Deans A.R.,North Carolina State University | Yoder M.J.,North Carolina State University | Balhoff J.P.,National Evolutionary Synthesis Center | Balhoff J.P.,University of North Carolina at Chapel Hill
Trends in Ecology and Evolution | Year: 2012

Taxonomists are arguably the most active annotators of the natural world, collecting and publishing millions of phenotype data annually through descriptions of new taxa. By formalizing these data, preferably as they are collected, taxonomists stand to contribute a data set with research potential that rivals or even surpasses genomics. Over a decade of electronic innovation and debate has initiated a revolution in the way that the biodiversity is described. Here, we opine that a new generation of semantically based digital scaffolding, presently in various stages of completeness, and a commitment by taxonomists and their colleagues to undertake this transformation, are required to complete the taxonomic revolution and critically broaden the relevance of its products. © 2011 Elsevier Ltd.

The research field of comparative genomics is moving from a focus on genes to a more holistic view including the repetitive complement. This study aimed to characterize relative proportions of the repetitive fraction of large, complex genomes in a nonmodel system. The monocotyledonous plant order Asparagales (onion, asparagus, agave) comprises some of the largest angiosperm genomes and represents variation in both genome size and structure (karyotype). Anonymous, low coverage, single-end Illumina data from 11 exemplar Asparagales taxa were assembled using a de novo method. Resulting contigs were annotated using a reference library of available monocot repetitive sequences. Mapping reads to contigs provided rough estimates of relative proportions of each type of transposon in the nuclear genome. The results were parsed into general repeat types and synthesized with genome size estimates and a phylogenetic context to describe the pattern of transposable element evolution among these lineages. The major finding is that although some lineages in Asparagales exhibit conservation in repeat proportions, there is generally wide variation in types and frequency of repeats. This approach is an appropriate first step in characterizing repeats in evolutionary lineages with a paucity of genomic resources. © 2013 Published by NRC Research Press.

Meachen-Samuels J.A.,National Evolutionary Synthesis Center
Paleobiology | Year: 2012

Sabertooth members of the Felidae, Nimravidae, and Barbourofelidae are well-known for their elongated saber-shaped canines. However, within these groups, there is a wide range of independently derived tooth shapes and lengths, including dirk-tooth and scimitar-tooth morphs. In conjunction with the saberteeth, forelimbs were also used to subdue prey. Thus, there may be a functional link between canine shape and forelimb morphology. Because there are no living sabertooth forms for comparison, extant felids make a good proxy for examining the morphology of these extinct organisms. Here, I examine the forelimb morphology of different sabertooth groups from across North America; I address whether forelimb morphologies are associated with tooth morphologies, and whether these associated tooth and forelimb morphologies are convergent among different families. To answer these questions, I analyzed six functional indices of the forelimbs and two canine characters for 13 species of sabertooth predators and 15 extant felid species. Results indicate that sabertooth morphs with longer, thinner canines show more robust limb proportions. These patterns were convergent among sabertooth felids, nimravids, and barbourofelids, and indicate a positive functional relationship between saber elongation and increased forelimb robustness. This suggests that sabertooth carnivorans demonstrated niche partitioning of predation strategies according to canine shape and corresponding forelimb morphology. © 2012 The Paleontological Society.

Smith N.A.,National Evolutionary Synthesis Center
Journal of Systematic Palaeontology | Year: 2014

The auklets Aethia and Ptychoramphus comprise the smallest known Alcidae (Aves, Charadriiformes) and have a fossil record that extends into the Miocene. The evolution of auklets is poorly understood because systematic hypotheses of relationships among extant auklets are largely incongruent, the morphology of auklet fossils has not been evaluated in detail, and extinct species of auklets have not been previously included in a phylogenetic analysis. Previously described auklet fossil remains are reviewed and two new species of auklet, Aethia barnesi sp. nov. and Aethia storeri sp. nov., are described from the Miocene and Pliocene of southern California, USA. Previously described auklet fossil remains, the two newly described extinct species of auklet, and extant species of auklets and other alcids are included in combined phylogenetic analyses of morphological and molecular sequence data. Based on the results of the phylogenetic analyses, the taxonomy of fossils referred to Aethiini is revised and the evolution of the clade is evaluated in a phylogenetic context. The osteological morphology of extinct auklets appears to be little changed from their extant relatives, suggesting that the ecological attributes of these small wing-propelled divers may also be relatively unchanged since the Miocene. © 2013 The Trustees of the Natural History Museum, London.

Lajeunesse M.J.,University of South Florida | Lajeunesse M.J.,National Evolutionary Synthesis Center
Bioinformatics | Year: 2011

Summary: phyloMeta is an easy to use console program for integrating phylogenetic information into meta-analysis. It is designed to help ecologists, evolutionary biologists and conservation biologists analyze effect size data extracted from published studies in a comparative phylogenetic context. This software estimates phylogenetic versions of all the traditional meta-analytical statistics used for: pooling effect sizes with weighted regressions; evaluating the homogeneity of these effect sizes; performing moderator tests akin to ANOVA style analyses; and analyzing data with fixed- and random-effects models. phyloMeta is developed in C/C++ and can be used via command line in MS Windows environments. © The Author 2011. Published by Oxford University Press. All rights reserved.

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