An autocorrelation analysis of genetic variation due to lineal fission in social groups of rhesus macaques

Cheverud, James M.; Dow, Malcolm M.

doi:10.1002/ajpa.1330670206

Cited by 87 publications

(36 citation statements)

References 33 publications

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“…Four general approaches (discussed in detail below) have been developed to address phylogenetic non-independence: analysis of phylogenetically independent contrasts (PICs, [34]), generalized least squares (GLS, [35 -37]), phylogenetic autoregression [38,39] and phylogenetic mixed models [33,40,41]. The approaches differ in attempting either to incorporate phylogenetic and other effects simultaneously (PIC, GLS, phylogenetic mixed models), or to remove phylogenetic effects and examine patterns in residual trait variation (phylogenetic autoregression).…”

Section: Coping With Phylogenetic Non-independence In Cross-species Cmentioning

confidence: 99%

“…(b) Phylogenetic autoregression Originally developed for analysis of spatial patterns [68,69], autoregression approaches have been widely used in comparative analyses to partition variance in trait values into components attributable to (i) the phylogenetic or spatial relationships among taxa, and (ii) specific, independent evolution in each taxon [38,39,48]. The central tenet of autoregression-based approaches is that only patterns in the specific phenotypic components are free of phylogenetic non-independence (box 1).…”

Section: Coping With Phylogenetic Non-independence In Cross-species Cmentioning

confidence: 99%

“…(c) Generalized least squares What we may call the Cheverud approach [38] to dealing with autocorrelation is not the only way. In the Cheverud approach, the factor causing the autocorrelation is supposedly removed, leaving a set of uncorrelated residuals for analysis.…”

Section: Coping With Phylogenetic Non-independence In Cross-species Cmentioning

confidence: 99%

“…(d) Spatial and genetic autoregression approaches to within-species analysis Early autoregression studies recognized the approach to be as applicable at the population level as it is to analyses across species [38,39]. Autocorrelationbased analyses of within-species data thus have the advantage of readily available software (e.g.…”

Section: Analysis Of Patterns Across Populations Within Speciesmentioning

confidence: 99%

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Controlling for non-independence in comparative analysis of patterns across populations within species

Stone¹,

Nee²,

Felsenstein

2011

Phil. Trans. R. Soc. B

136

127

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How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow). As a result, phenotypes measured in one population are influenced by processes acting on others, and may not be a good guide to either the strength or direction of local selection. Although many studies examine patterns across populations within species, few consider such non-independence. Here, we discuss the sources of non-independence in comparative analysis, and show why the phylogeny-based approaches widely used in cross-species analyses are unlikely to be useful in analyses across populations within species. We outline the approaches (intraspecific contrasts, generalized least squares, generalized linear mixed models and autoregression) that have been used in this context, and explain their specific assumptions. We highlight the power of 'mixed models' in many contexts where problems of non-independence arise, and show that these allow incorporation of both shared common ancestry and gene flow. We suggest what can be done when ideal solutions are inaccessible, highlight the need for incorporation of a wider range of population models in intraspecific comparative methods and call for simulation studies of the error rates associated with alternative approaches.

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Section: Coping With Phylogenetic Non-independence In Cross-species Cmentioning

confidence: 99%

Section: Coping With Phylogenetic Non-independence In Cross-species Cmentioning

confidence: 99%

Section: Coping With Phylogenetic Non-independence In Cross-species Cmentioning

confidence: 99%

Section: Analysis Of Patterns Across Populations Within Speciesmentioning

confidence: 99%

See 2 more Smart Citations

Controlling for non-independence in comparative analysis of patterns across populations within species

Stone¹,

Nee²,

Felsenstein

2011

Phil. Trans. R. Soc. B

136

127

View full text Add to dashboard Cite

show abstract

“…The magnitude of the difference between observed and predicted values was calculated using the minimum variance unbiased estimator (MVUE) of Shonkwiler (2006, 2007). Phylogenetically-predicted mass was calculated using autocorrelation (Cheverud and Dow 1985;Rohlf 2001; using the marsupial trait values and phylogeny for 61 marsupial species of Withers et al 2006) as the product of the trait (mass) and a weighting matrix (calculated from the distance matrix of phylogenetic distances between each pair of marsupial species), that was fitted as closely as possible to the actual trait values by iteration with a varying constant of proportionality (). Honey possums were also compared to the 95% prediction limits of a phylogenetically independent allometric relationship for each physiological variable, where variables were rendered independent of phylogeny by autocorrelation, again using the dataset and phylogeny of Withers et al (2006) where N is as for the conventional analysis.…”

mentioning

confidence: 99%

Metabolic, hygric and ventilatory physiology of a hypermetabolic marsupial, the honey possum (Tarsipes rostratus)

Cooper

Cruz‐Neto

2009

J Comp Physiol B

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The honey possum is the only non-volant mammal to feed exclusively on a diet of nectar and pollen. Like other mammalian and avian nectarivores, previous studies indicated that the honey possum's basal metabolic rate was higher than predicted for a marsupial of equivalent body mass. However, these early measurements have been questioned. We re-examined the basal metabolic rate (2.52 ± 0.222 ml O 2 g -1 h -1 ) of the honey possum and confirm that it is indeed higher (162%) than predicted for other marsupials both before and after accounting for phylogenetic history. This, together with its small body mass (5.4 ± 0.14 g; 1.3 % of that predicted by phylogeny) may be attributed to its nectarivorous diet and mesic distribution. Its high basal metabolic rate is associated with a high standard body temperature (36.6 ± 0.48 °C) and oxygen extraction (19.4%), but interestingly the honey possum has a high point of relative water economy (17.0°C) and its standard evaporative water loss (4.33± 0.394 mg H 2 O g -1 h -1 ) is not elevated above that of other marsupials, despite its mesic habitat and high dietary water intake.

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Species are not Uniquely Real Biological Entities

Mishler

2009

Contemporary Debates in Philosophy of Biology

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Are species uniquely real biological entities? This question is one of the most controversial topics today in such areas of biology as ecology, systematics, conservation, population genetics, and evolution. "Species" currently play a central role in both theory and practice in these areas, and have a large place in the public's perception of biological diversity as well. This question can be decomposed into two parts: (1) Are species real, and in what sense? (2) If real, is their reality the same as entities smaller or larger than themi.e., are they real in a sense that genera or subspecies are not? This paper will briefly review historical and current opinions on these questions, but will primarily advocate one particular position that appears to fit biological reality as now understood: that species properly defined are real entities, but not uniquely real. The longstanding "species problem" can be solved by realizing that there is no such thing as species after all! The so-called "species problem" is really just a special case of the taxon problem. Once a decision is made about what taxa in general are to represent, then those groups currently known as species are simply the least inclusive taxa of that type. As I favor a phylogenetic basis for taxonomy, I want to look at how to include terminal taxa in the PhyloCode, currently a controversial topic even among PhyloCode supporters. In brief, my argument is: (1) life is organized in a hierarchy of nested monophyletic groups-some of them quite fine-scale, well below the level we currently call species; (2) not all known monophyletic groups need be named, just the ones that are important to process or conservation studies and that have good support; (3) those that are named taxonomically should be given unranked (but hierarchically nested) uninomials; and (4) formal ranks, including species, should be abandoned. I will conclude with a brief discussion of the implication of my position on species for academic studies in ecology and evolution as well as for practical applications in biodiversity inventories and conservation biology.But be warned, you who thirst for knowledge, be warned about the thicket of opinions and the fight over words.

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An autocorrelation analysis of genetic variation due to lineal fission in social groups of rhesus macaques

Cited by 87 publications

References 33 publications

Controlling for non-independence in comparative analysis of patterns across populations within species

Controlling for non-independence in comparative analysis of patterns across populations within species

Metabolic, hygric and ventilatory physiology of a hypermetabolic marsupial, the honey possum (Tarsipes rostratus)

Species are not Uniquely Real Biological Entities

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