The Effect of Intraspecific Sample Size on Type I and Type Ii Error Rates in Comparative Studies

Harmon, Luke J.; Losos, Jonathan B.

doi:10.1111/j.0014-3820.2005.tb00981.x

Cited by 95 publications

(57 citation statements)

References 24 publications

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“…Controlling for within-species variation had little effect on the relationship between group size and neocortex ratio given this moderate repeatability. This finding is consistent with the results of a simulation study that found within-species variation has weak effects on the results of comparative analyses when at least 60% of the total variation in traits is explained by variation between species (Harmon and Losos, 2005). …”

Section: Discussionsupporting

confidence: 90%

“…For example, simulations revealed that failure to account for intraspecific variation can lead to a high Type I error rate (Harmon and Losos, 2005; Felsenstein, 2008; Silvestro et al, 2015). In cases where within-species variation exceeds between-species variation, it may be inappropriate to use mean values to represent an entire species in interspecific comparisons.…”

Section: Introductionmentioning

confidence: 99%

“…The default procedure assumes that no within-species variation exists. The effect of ignoring intraspecific variation in comparative analyses has been studied for only a few systems, predominantly relying on simulated rather than actual data (Harmon and Losos, 2005; Ives et al, 2007; Felsenstein, 2008; Hansen and Bartoszek, 2012). Researchers have only recently begun to assess intraspecific variation in a comparative context (e.g., Kamilar and Baden, 2014; Pap et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…In contrast, when repeatability is low, considerable variation exists within species. When between-species repeatability is low, controlling for intraspecific variation becomes particularly important for comparative studies (Harmon and Losos, 2005). …”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Assessing sources of error in comparative analyses of primate behavior: Intraspecific variation in group size and the social brain hypothesis

Sandel

Miller

Mitani

et al. 2016

Journal of Human Evolution

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Phylogenetic comparative methods have become standard for investigating evolutionary hypotheses, including in studies of human evolution. While these methods account for the non-independence of trait data due to phylogeny, they often fail to consider intraspecific variation, which may lead to biased or erroneous results. We assessed the degree to which intraspecific variation impacts the results of comparative analyses by investigating the “social brain” hypothesis, which has provided a framework for explaining complex cognition and large brains in humans. This hypothesis suggests that group life imposes a cognitive challenge, with species living in larger social groups having comparably larger neocortex ratios than those living in smaller groups. Primates, however, vary considerably in group size within species, a fact that has been ignored in previous analyses. When within-species variation in group size is high, the common practice of using a mean value to represent the species may be inappropriate. We conducted regression and resampling analyses to ascertain whether the relationship between neocortex ratio and group size across primate species persists after controlling for within-species variation in group size. We found that in a sample of 23 primates, 70% of the variation in group size was due to between-species variation. Controlling for within-species variation in group size did not affect the results of phylogenetic analyses, which continued to show a positive relationship between neocortex ratio and group size. Analyses restricted to non-monogamous primates revealed considerable intraspecific variation in group size, but the positive association between neocortex ratio and group size remained even after controlling for within-species variation in group size. Our findings suggest that the relationship between neocortex size and group size in primates is robust. In addition, our methods and associated computer code provide a way to assess and account for intraspecific variation in other comparative analyses of primate evolution.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Assessing sources of error in comparative analyses of primate behavior: Intraspecific variation in group size and the social brain hypothesis

Sandel

Miller

Mitani

et al. 2016

Journal of Human Evolution

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“…Intraspecific variation is abundant in all types of systematic characters which could cause bias in the phylogenetic analyses [43]. Systematists use different ways to deal with intraspecific variation [26].…”

Section: Discussionmentioning

confidence: 99%

Distinct Origin of the Y and St Genome in Elymus Species: Evidence from the Analysis of a Large Sample of St Genome Species Using Two Nuclear Genes

Yan

Sun

2011

PLoS ONE

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BackgroundPrevious cytological and single copy nuclear genes data suggested the St and Y genome in the StY-genomic Elymus species originated from different donors: the St from a diploid species in Pseudoroegneria and the Y from an unknown diploid species, which are now extinct or undiscovered. However, ITS data suggested that the Y and St genome shared the same progenitor although rather few St genome species were studied. In a recent analysis of many samples of St genome species Pseudoroegneria spicata (Pursh) À. Löve suggested that one accession of P. spicata species was the most likely donor of the Y genome. The present study tested whether intraspecific variation during sampling could affect the outcome of analyses to determining the origin of Y genome in allotetraploid StY species. We also explored the evolutionary dynamics of these species.Methodology/Principal FindingsTwo single copy nuclear genes, the second largest subunit of RNA polymerase II (RPB2) and the translation elongation factor G (EF-G) sequences from 58 accessions of Pseudoroegneria and Elymus species, together with those from Hordeum (H), Agropyron (P), Australopyrum (W), Lophopyrum (Ee), Thinopyrum (Ea), Thinopyrum (Eb), and Dasypyrum (V) were analyzed using maximum parsimony, maximum likelihood and Bayesian methods. Sequence comparisons among all these genomes revealed that the St and Y genomes are relatively dissimilar. Extensive sequence variations have been detected not only between the sequences from St and Y genome, but also among the sequences from diploid St genome species. Phylogenetic analyses separated the Y sequences from the St sequences.Conclusions/SignificanceOur results confirmed that St and Y genome in Elymus species have originated from different donors, and demonstrated that intraspecific variation does not affect the identification of genome origin in polyploids. Moreover, sequence data showed evidence to support the suggestion of the genome convergent evolution in allopolyploid StY genome species.

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Phylogenetic Analyses: Comparing Species to Infer Adaptations and Physiological Mechanisms

Rezende

Diniz‐Filho

2012

Comprehensive Physiology

103

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Comparisons among species have been a standard tool in animal physiology to understand how organisms function and adapt to their surrounding environment. During the last two decades, conceptual and methodological advances from different fields, including evolutionary biology and systematics, have revolutionized the way comparative analyses are performed, resulting in the advent of modern phylogenetic statistical methods. This development stems from the realization that conventional analytical methods assume that observations are statistically independent, which is not the case for comparative data because species often resemble each other due to shared ancestry. By taking evolutionary history explicitly into consideration, phylogenetic statistical methods can account for the confounding effects of shared ancestry in interspecific comparisons, improving the reliability of standard approaches such as regressions or correlations in comparative analyses. Importantly, these methods have also enabled researchers to address entirely new evolutionary questions, such as the historical sequence of events that resulted in current patterns of form and function, which can only be studied with a phylogenetic perspective. Here, we provide an overview of phylogenetic approaches and their importance for studying the evolution of physiological processes and mechanisms. We discuss the conceptual framework underlying these methods, and explain when and how phylogenetic information should be employed. We then outline the difficulties and limitations inherent to comparative approaches and discuss potential problems researchers may encounter when designing a comparative study. These issues are illustrated with examples from the literature in which the incorporation of phylogenetic information has been useful, or even crucial, for inferences on how species evolve and adapt to their surrounding environment.

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The Effect of Intraspecific Sample Size on Type I and Type Ii Error Rates in Comparative Studies

Cited by 95 publications

References 24 publications

Assessing sources of error in comparative analyses of primate behavior: Intraspecific variation in group size and the social brain hypothesis

Assessing sources of error in comparative analyses of primate behavior: Intraspecific variation in group size and the social brain hypothesis

Distinct Origin of the Y and St Genome in Elymus Species: Evidence from the Analysis of a Large Sample of St Genome Species Using Two Nuclear Genes

Phylogenetic Analyses: Comparing Species to Infer Adaptations and Physiological Mechanisms

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