Ecology, Evolution and Organismal Biology

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Phylogenetic ANOVA: Group-clade aggregation, biological challenges, and a refined permutation procedure

2018-06 , Adams, Dean , Ecology, Evolution and Organismal Biology

Phylogenetic regression is frequently utilized in macroevolutionary studies, and its statistical properties have been thoroughly investigated. By contrast, phylogenetic ANOVA has received relatively less attention, and the conditions leading to incorrect statistical and biological inferences when comparing multivariate phenotypes among groups remains underexplored. Here we propose a refined method of randomizing residuals in a permutation procedure (RRPP) for evaluating phenotypic differences among groups while conditioning the data on the phylogeny. We show that RRPP displays appropriate statistical properties for both phylogenetic ANOVA and regression models, and for univariate and multivariate datasets. For ANOVA, we find that RRPP exhibits higher statistical power than methods utilizing phylogenetic simulation. Additionally, we investigate how group dispersion across the phylogeny affects inferences, and reveal that highly aggregated groups generate strong and significant correlations with the phylogeny, which reduce statistical power and subsequently affect biological interpretations. We discuss the broader implications of this phylogenetic group aggregation, and its relation to challenges encountered with other comparative methods where one or a few transitions in discrete traits are observed on the phylogeny. Finally, we recommend that phylogenetic comparative studies of continuous trait data utilize RRPP for assessing the significance of indicator variables as sources of trait variation.

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Technological advances in maize breeding: past, present and future

2019-01-01 , Andorf, Carson , Beavis, William , Hufford, Matthew , Lubberstedt, Thomas , Smith, Stephen , Suza, Walter , Wang, Kan , Woodhouse, Margaret , Yu, Jianming , Lubberstedt, Thomas , Agronomy , Ecology, Evolution and Organismal Biology

Maize has for many decades been both one of the most important crops worldwide and one of the primary genetic model organisms. More recently, maize breeding has been impacted by rapid technological advances in sequencing and genotyping technology, transformation including genome editing, doubled haploid technology, parallelled by progress in data sciences and the development of novel breeding approaches utilizing genomic information. Herein, we report on past, current and future developments relevant for maize breeding with regard to (1) genome analysis, (2) germplasm diversity characterization and utilization, (3) manipulation of genetic diversity by transformation and genome editing, (4) inbred line development and hybrid seed production, (5) understanding and prediction of hybrid performance, (6) breeding methodology and (7) synthesis of opportunities and challenges for future maize breeding.

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Defining Reference Information for Restoring Ecologically Rare Tallgrass Oak Savannas in the Midwestern United States

2005-10-01 , Asbjornsen, H. , Brudvig, L. A. , Mabry McMullen, Catherine , Evans, C. W. , Karnitz, H. M. , Natural Resource Ecology and Management , Ecology, Evolution and Organismal Biology

Reference information is commonly used in ecological restorations to guide management decisions and assess progress toward achieving goals. However, for extremely rare or degraded ecosystems, obtaining reliable reference information may be a daunting task. This article explores the limitations and potentials for identifying reference information for ecologically rare tallgrass oak savanna ecosystems, using a case study from central Iowa. Preliminary results suggest that restoration goals related to certain ecosystem parameters, such as vegetation structure, may be achieved relatively quickly, whereas other parameters, such as species composition, require longer timescales. The importance of developing additional reference information through experimental and adaptive management approaches is emphasized.

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Book Review of Serendipity: An Ecologist’s Quest to Understand Nature

2017-10-03 , Ball, E. E. , Adams, D. M. , Dupuie, J. N. , Jones, M. M. , Klaver, Robert , McGovern, P. G. , Ruden, R. M. , Schmidt, S. R. , Vaziri, G. J. , Eeling, J. S. , Kirk, B. D. , McCombs, A. L. , Rabinowitz, A. B. , Thompson, K. M. , Hudson, Z. J. , Klaver, Robert , Natural Resource Ecology and Management , Ecology, Evolution and Organismal Biology , Horticulture

A common thought among graduate students is: “how do established scientists get where they are today?” In Serendipity: An Ecologist’s Quest to Understand Nature, James Estes offers a personal reflection on research experiences spanning his 50-year career, beginning as a Ph.D. student in 1970 and concluding with recognition as a member of the National Academy of Sciences in 2014. Estes chronologically outlines the foundational trophic cascade ecology research that he and colleagues conducted in the Aleutian Islands, examining key relationships among kelp forests, sea otters, sea urchins, and killer whales through anecdotal stories of achievement and challenge. Estes’ 3 main goals in writing this book are to: (1) recount what he had learned from 50 years of research; (2) provide a larger story of how predators and prey interact with one another; and (3) explain how science “really happens.”

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Comparing the strength of modular signal, and evaluating alternative modular hypotheses, using covariance ratio effect sizes with morphometric data

2019-12 , Adams, Dean , Ecology, Evolution and Organismal Biology

The study of modularity is paramount for understanding trends of phenotypic evolution, and for determining the extent to which covariation patterns are conserved across taxa and levels of biological organization. However, biologists currently lack quantitative methods for statistically comparing the strength of modular signal across datasets, and a robust approach for evaluating alternative modular hypotheses for the same dataset. As a solution to these challenges, we propose an effect size measure ( ) derived from the covariance ratio, and develop hypothesis-testing procedures for their comparison. Computer simulations demonstrate that displays appropriate statistical properties and low levels of mis-specification, implying that it correctly identifies modular signal, when present. By contrast, alternative methods based on likelihood (EMMLi) and goodness of fit (MINT) suffer from high false positive rates and high model mis-specification rates. An empirical example in sigmodontine rodent mandibles is provided to illustrate the utility of for comparing modular hypotheses. Overall, we find that covariance ratio effect sizes are useful for comparing patterns of modular signal across datasets or for evaluating alternative modular hypotheses for the same dataset. Finally, the statistical philosophy for pairwise model comparisons using effect sizes should accommodate any future analytical developments for characterizing modular signal.

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Bill size correlates with telomere length in male American Redstarts

2015-04-01 , Angelier, Frederic , Vleck, Carol , Vleck, Carol , Holberton, Rebecca , Marra, Peter , Ecology, Evolution and Organismal Biology

Telomere length (TL) has been shown to be a potential predictor of survival in wild vertebrates, and, as a consequence, there is growing interest in understanding the causes of inter-individual variability in TL. In that context, developmental conditions deserve a specific attention because they are thought to be a major driver of telomere shortening. Because poor developmental conditions can accelerate telomere shortening and impair growth (resulting in a small adult size), a positive correlation between TL and body size is expected. However, and surprisingly, the relationship between body size and telomere length has rarely been described in wild vertebrates. Here, we specifically examined this question in hatch-year (HY) and after hatch-year (AHY) male wintering American Redstarts (Setophaga ruticilla). Although tarsus size was not related to TL, we found a significant positive correlation between bill size and TL in HY male Redstarts, therefore supporting the idea that determinants of some components of individual size are also important determinants of TL in young birds. Moreover, this positive relationship between bill size and TL was also found for AHY birds, suggesting that adult TL may be, at least partly, explained by the telomere dynamics that occurred during the developmental phase.

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Variation in eye abundance among scallops reveals ontogenetic and evolutionary convergence associated with life habits

2022 , Audino, Jorge A. , Adams, Dean , Serb, Jeanne , Ecology, Evolution and Organismal Biology

Eyes are remarkable systems to investigate the complex interaction between ecological drivers and phenotypic outcomes. Some animals, such as scallops, have many eyes for visual perception, but to date, the evolution of multiple-eye systems remains obscure. For instance, it is unclear whether eye number changes over a lifetime or varies among species. Scallops are a suitable model group to investigate these questions considering the interspecific variation of adult size and ecological diversity. We tested whether eye abundance scales with body size among individuals and species and whether it varies with life habits. We performed comparative analyses, including a phylogenetic ANCOVA and evolutionary model comparisons, based on eye count and shell height (as a proxy of body size) across 31 scallop species. Our analyses reveal that patterns of increasing relationship with body size are not concordant among taxa and suggest ontogenetic convergence caused by similar ecologies. Accordingly, selective optima in eye numbers are associated with shifts in life habits. For instance, species with increased mobility have significantly more eyes than less mobile species. The convergent evolution of greater eye abundance in more mobile scallops likely indicates a visual improvement based on increased levels of oversampling the surrounding environment.

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Consilience of methods for phylogenetic analysis of variance

2022-05-06 , Adams, Dean , Ecology, Evolution and Organismal Biology

Simulation-based and permutation-based inferential methods are commonplace in phylogenetic comparative methods, especially as evolutionary data have become more complex and parametric methods more limited for their analysis. Both approaches simulate many random outcomes from a null model to empirically generate sampling distributions of statistics. Although simulation-based and permutation-based methods seem commensurate in purpose, results from analysis of variance (ANOVA) based on the distributions of random -statistics produced by these methods can be quite different in practice. Differences could be from either the null model process that generates variation across many simulations or random permutations of the data, or different estimation methods for linear model coefficients and statistics. Unfortunately, because null model process and coefficient estimation are intrinsically linked in phylogenetic ANOVA methods, the precise reason for methodological differences has not been fully considered. Here we show that the null model processes of phylogenetic simulation and randomization of residuals in a permutation procedure (RRPP) are indeed commensurate, and that both also produce results consistent with parametric ANOVA, for cases where parametric ANOVA is possible. We also provide results that caution against using ordinary least-squares estimation along with phylogenetic simulation; a typical phylogenetic ANOVA implementation.

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Telomere length, non-breeding habitat and return rate in male American redstarts

2013-01-01 , Angelier, Frederic , Vleck, Carol , Vleck, Carol , Holberton, Rebecca , Marra, Peter , Ecology, Evolution and Organismal Biology

  1. Telomeres are long repetitive noncoding sequences of DNA located at the ends of chromosomes. Recently, the study of telomere dynamics has been increasingly used to investigate ecological questions. However, little is currently known about the relationships that link environmental conditions, telomere dynamics and fitness in wild vertebrates.
  2. Using a small migratory bird (American redstart, Setophaga ruticilla), we investigated how telomere dynamics can be affected by non-breeding habitat quality and to what extent telomere length can predict the return rate of males.
  3. We show that telomeres shorten in most individuals over a 1-year period and, importantly, that telomeres of individuals wintering in a low-quality habitat shorten more than those of individuals wintering in a high-quality habitat.
  4. In addition, we found that longer telomeres are associated with a higher return rate than shorter telomeres, although the relationship between return rate and telomere length did not depend on habitat quality.
  5. Our study suggests that telomere dynamics are affected by environmental conditions and are related to indices of fitness in a migratory bird species.

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Is salamander arboreality limited by broad-scale climatic conditions?

2021-08-18 , Baken, Erica K. , Mellenthin, Lauren E. , Adams, Dean , Ecology, Evolution and Organismal Biology

Identifying the historical processes that drive microhabitat transitions across deep time is of great interest to evolutionary biologists. Morphological variation can often reveal such mechanisms, but in clades with high microhabitat diversity and no concomitant morphological specialization, the factors influencing animal transitions across microhabitats are more difficult to identify. Lungless salamanders (family: Plethodontidae) have transitioned into and out of the arboreal microhabitat many times throughout their evolutionary history without substantial morphological specialization. In this study, we explore the relationship between microhabitat use and broad-scale climatic patterns across species’ ranges to test the role of climate in determining the availability of the arboreal microhabitat. Using phylogenetic comparative methods, we reveal that arboreal species live in warmer, lower elevation regions than terrestrial species. We also employ ecological niche modeling as a complementary approach, quantifying species-level pairwise comparisons of niche overlap. The results of this approach demonstrate that arboreal species on average display more niche overlap with other arboreal species than with terrestrial species after accounting for non-independence of niche model pairs caused by geographic and phylogenetic distances. Our results suggest that occupation of the arboreal microhabitat by salamanders may only be possible in sufficiently warm, low elevation conditions. More broadly, this study indicates that the impact of micro-environmental conditions on temporary microhabitat use, as demonstrated by small-scale ecological studies, may scale up dramatically to shape macroevolutionary patterns.