Efficacy or convenience? Model‐based approaches to phylogeny estimation using morphological data

Model‐based approaches (e.g. maximum likelihood, Bayesian inference) are widely used with molecular data, where they might be more appropriate than maximum parsimony for estimating phylogenies under various models of molecular evolution. Recently, there has been an increase in the application of model‐based approaches with morphological (mainly fossil) data; however, there is some doubt as to the effectiveness of the model of morphological evolution. The input parameters (prior probabilities) for the model are unclear, particularly when concerned with unobserved character states. Despite this, some systematists are suggesting superiority of these model‐based methods over maximum parsimony based on, for example, increased resolution or, in the current study, the preferred phylogenetic placement of an iconic taxon. Here, we revisit a recently published analysis implying such superiority and document the discrepancies between parsimony‐based and model‐based approaches to phylogeny estimation. We find that although some taxa are shifted back to their “traditional” phylogenetic placement, other clades are disturbed. The model‐based phylogenies are better resolved; however, due to the lack of an appropriate model of morphological evolution, the increase in resolving power is probably not meaningful. Similarly, some of the preferred phylogenetic positions of taxa, particularly of labile taxa such as Archaeopteryx, are based solely on analyses employing maximum parsimony as the optimality criterion. Poor resolution and labile taxa indicate a need for further examination of the morphology and not a change in method.     

Are behavioral differences among wild chimpanzee communities genetic or cultural? An assessment using tool‐use data and phylogenetic methods

Over the last 30 years it has become increasingly apparent that there are many behavioral differences among wild communities of Pan troglodytes. Some researchers argue these differences are a consequence of the behaviors being socially learned, and thus may be considered cultural. Others contend that the available evidence is too weak to discount the alternative possibility that the behaviors are genetically determined. Previous phylogenetic analyses of chimpanzee behavior have not supported the predictions of the genetic hypothesis. However, the results of these studies are potentially problematic because the behavioral sample employed did not include communities from central Africa. Here, we present the results of a study designed to address this shortcoming. We carried out cladistic analyses of presence/absence data pertaining to 19 tool‐use behaviors in 10 different P. troglodytes communities plus an outgroup (P. paniscus). Genetic data indicate that chimpanzee communities in West Africa are well differentiated from those in eastern and central Africa, while the latter are not reciprocally monophyletic. Thus, we predicted that if the genetic hypothesis is correct, the tool‐use data should mirror the genetic data in terms of structure. The three measures of phylogenetic structure we employed (the Retention Index, the bootstrap, and the Permutation Tail Probability Test) did not support the genetic hypothesis. They were all lower when all 10 communities were included than when the three western African communities are excluded. Hence, our study refutes the genetic hypothesis and provides further evidence that patterns of behavior in chimpanzees are the product of social learning and therefore meet the main condition for culture. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Is Niagara Falls a barrier to gene flow in riverine fishes? A test using genome‐wide SNP data from seven native species

Since the early Holocene, fish population genetics in the Laurentian Great Lakes have been shaped by the dual influences of habitat structure and post‐glacial dispersal. Riverscape genetics theory predicts that longitudinal habitat corridors and unidirectional downstream water‐flow drive the downstream accumulation of genetic diversity, whereas post‐glacial dispersal theory predicts that fish genetic diversity should decrease with increasing distance from glacial refugia. This study examines populations of seven native fish species codistributed above and below the 58 m high Niagara Falls – a hypothesized barrier to gene flow in aquatic species. A better understanding of Niagara Falls’ role as a barrier to gene flow and dispersal is needed to identify drivers of Great Lakes genetic diversity and guide strategies to limit exotic species invasions. We used genome‐wide SNPs and coalescent models to test whether populations are: (a) genetically distinct, consistent with the Niagara Falls barrier hypothesis; (b) more genetically diverse upstream, consistent with post‐glacial expansion theory, or downstream, consistent with the riverscape habitat theory; and (c) have migrated either upstream or downstream past Niagara Falls. We found that genetic diversity is consistently greater below Niagara Falls and the falls are an effective barrier to migration, but two species have probably dispersed upstream past the falls after glacial retreat yet before opening of the Welland Canal. Models restricting migration to after opening of the Welland Canal were generally rejected. These results help explain how river habitat features affect aquatic species’ genetic diversity and highlight the need to better understand post‐glacial dispersal pathways.     

Is the tiger shark Galeocerdo cuvier a coastal species? Expanding its distribution range in the Atlantic Ocean using at‐sea observer data

The occurrence of tiger shark Galeocerdo cuvier in the Atlantic Ocean was assessed using at‐sea observer data from multiple pelagic longline fisheries. Geographic positions of 2764 G. cuvier recorded between 1992 and 2013 and covering a wide area of the Atlantic Ocean were compared with the currently accepted distribution ranges of the species. Most records fell outside those ranges in both the Southern and Northern Hemispheres, which strongly suggests that the distribution range of G. cuvier in the open ocean is considerably larger than previously described     

What stabilizes the 314‐helix in β3‐peptides? A conformational analysis using molecular simulation

β‐Peptides are analogs of natural α‐peptides and form a variety of remarkably stable structures. Having an additional carbon atom in the backbone of each residue, their folded conformation is not only influenced by the side‐chain sequence but also and foremost by their substitution pattern. The precise mechanism by which the side chains interact with the backbone is, however, hitherto not completely known. To unravel the various effects by which the side chains influence the backbone conformation, we quantify to which extent the dihedral angles of a β³‐substited peptide with an additional methyl group on the central C_α‐atom can be regarded as independent degrees of freedom and analyze the distributions of these dihedral angles. We also selectively capture the steric effect of substituents on the C_α‐ and C_β‐atoms of the central residue by alchemically changing them into dummy atoms, which have no nonbonded interactions. We find that the folded state of the β³‐peptide is primarily stabilized by a steric exclusion of large parts of the unfolded state (entropic effect) and only subsequently by mutual dependence of the ψ‐dihedral angles (enthalpic effect). The folded state of β‐peptides is stabilized by a different mechanism than that of α‐peptides. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Does climate variability influence the demography of wild primates? Evidence from long‐term life‐history data in seven species

Earth's rapidly changing climate creates a growing need to understand how demographic processes in natural populations are affected by climate variability, particularly among organisms threatened by extinction. Long‐term, large‐scale, and cross‐taxon studies of vital rate variation in relation to climate variability can be particularly valuable because they can reveal environmental drivers that affect multiple species over extensive regions. Few such data exist for animals with slow life histories, particularly in the tropics, where climate variation over large‐scale space is asynchronous. As our closest relatives, nonhuman primates are especially valuable as a resource to understand the roles of climate variability and climate change in human evolutionary history. Here, we provide the first comprehensive investigation of vital rate variation in relation to climate variability among wild primates. We ask whether primates are sensitive to global changes that are universal (e.g., higher temperature, large‐scale climate oscillations) or whether they are more sensitive to global change effects that are local (e.g., more rain in some places), which would complicate predictions of how primates in general will respond to climate change. To address these questions, we use a database of long‐term life‐history data for natural populations of seven primate species that have been studied for 29–52 years to investigate associations between vital rate variation, local climate variability, and global climate oscillations. Associations between vital rates and climate variability varied among species and depended on the time windows considered, highlighting the importance of temporal scale in detection of such effects. We found strong climate signals in the fertility rates of three species. However, survival, which has a greater impact on population growth, was little affected by climate variability. Thus, we found evidence for demographic buffering of life histories, but also evidence of mechanisms by which climate change could affect the fates of wild primates.     

How reliable are harvesting data for analyses of spatio‐temporal population dynamics?

Harvest data are commonly used as proxy for count data, especially in studies of long‐term temporal and spatial patterns of population fluctuations. However, usually the concurrence of the conclusions based on different types of data is impossible to verify due to the lack of count data. Here, we use annual (1964–2004) harvest and population census data for capercaillie, black grouse and hazel grouse from 14 game management districts covering Finland, and demonstrate some mismatch in the information that these data sets provide. Overall, linear regressions of annual harvest against population count give a reasonable fit, but the slopes are less than 1 in every species. Harvest bags have been proportionally larger in north and eastern Finland than in southwestern Finland, with marked species‐specific differences. Considering population variation, the CV% in the census data (30–50%) is consistently smaller than it is in the harvest data (60–70%). Most importantly, conclusions on the spatio‐temporal patterns of the population dynamics are different if based on harvest rather than count data. In capercaillie, synchrony decreases faster with distance according to the harvest data, while in black grouse and hazel grouse the census data show the steeper decline. In addition, the autocorrelation coefficients in the census time series are higher in capercaillie and black grouse than in harvest data, but in hazel grouse the opposite is true. Finally, the parameter estimates for a second order autoregressive model using different data sets differ, and these differences are species‐specific. Despite the fact that annual harvest is a positive and linear function of annual grouse population density, the pattern of population dynamics derived from the bag data is different from that shown by the census data. This result urges caution in using wildlife bag data as reliable indices of population dynamics. deceased August 2008.     

Do virus‐resistant plants pose a threat to non‐target ecosystems? II. Risk assessment of an Australian pathosystem using multi‐scale field experiments

It has been widely argued that the acquisition of novel disease resistance genes by wild host populations following the release of novel pathogen‐resistant plants into agricultural systems could pose a significant threat to non‐target plant communities. However, predicting the magnitude of ecological release in wild plant populations following the removal of disease remains a major challenge. In this paper we report on the second phase of a tiered risk assessment designed to investigate the role of disease on host growth, survival, fecundity and fitness in a model pathosystem (the pasture species Trifolium repens infected with Clover yellow vein virus, ClYVV) and to assess the level of risk posed to at‐risk native plant communities in southeast Australia by newly developed genetically modified and conventionally bred virus‐resistant T. repens genotypes. Multi‐year field experiments conducted in woodland and grassland environments using host‐pathogen arrays derived from 14 ClYVV isolates and 21 T. repens genotypes indicate that viral infection reduces fecundity, growth and survival of wild T. repens plants but that the severity of these effects depends on host tolerance to infection, isolate aggressiveness and specific spatial and temporal environmental conditions. Demographic modelling showed that by reducing host survival and growth, ClYVV also limits the intrinsic population growth rate and niche size of wild T. repens populations. Given the significant fitness cost associated with viral infection we conclude that virus‐resistant T. repens genotypes may pose a threat to some high conservation‐value non‐target ecosystems in SE Australia. We also argue that long‐term, multi‐tiered experiments conducted in a range of controlled and non‐controlled environments are necessary to detect and accurately quantify risks associated with the release of disease‐resistant plants in general.     

Early Cambrian food webs on a trophic knife‐edge? A hypothesis and preliminary data from a modern stromatolite‐based ecosystem

Here we use the theory of ecological stoichiometry to propose and provide a preliminary test of a novel hypothesis that the Cambrian 'explosion' may have been triggered by changes in circulating P availability in the biosphere. We exposed living stromatolites from a spring-fed stream in Mexico to a gradient of P enrichment to examine subsequent effects on stromatolite C : P ratio and on the primary grazer, an endemic snail. Consistent with a previously hypothesized stoichiometric 'knife-edge', snail performance was maximal at intermediate P-enrichment, indicating in situ stoichiometric constraints because of high stromatolite C : P ratio along with high sensitivity to excessive P intake. These results are consistent with the idea that stoichiometric constraints may have delayed the evolutionary proliferation of animals in ancient stromatolite-dominated ecosystems and also suggest that high food P content can significantly impair consumers. We propose that ecosystem P availability may have impacted both the expansion and decline of animal taxa in the history of life.     

Sex‐biased migration in humans: what should we expect from genetic data?

Different patterns of mitochondrial and Y-chromosome diversity have been cited as evidence of long-term patrilocality in human populations. However, what patterns are expected depends on the nature of the sampling scheme. Samples from a local region reveal only the recent demographic history of that region, whereas sampling over larger geographic scales accesses older demographic processes. A historical change in migration becomes evident first at local geographic scales, and alters global patterns of genetic diversity only after sufficient time has passed. Analysis of forager populations in the ethnographic record suggests that patrilocality may not have predominated among pre-agricultural humans. The higher female migration rate inferred by some genetic studies may reflect a shift to patrilocality in association with the emergence of agriculture. A recent global survey does not show the expected effects of higher female migration, possibly because the sampling scheme used for this study is accessing pre-agricultural human migration patterns. In this paper, we show how the demographic shift associated with agriculture might affect genetic diversity over different spatial scales. We also consider the prospects for studying sex-biased migration using the X-linked and autosomal markers. These multi-locus comparisons have the potential of providing more robust estimates of sex differences than Y-linked and mitochondrial data, but only if a very large number of loci are included in the analysis.     

What can and can't we say about indirect land‐use change in Brazil using an integrated economic – land‐use change model?

It is commonly recognized that large uncertainties exist in modelled biofuel‐induced indirect land‐use change, but until now, spatially explicit quantification of such uncertainties by means of error propagation modelling has never been performed. In this study, we demonstrate a general methodology to stochastically calculate direct and indirect land‐use change (dLUC and iLUC) caused by an increasing demand for biofuels, with an integrated economic – land‐use change model. We use the global Computable General Equilibrium model MAGNET, connected to the spatially explicit land‐use change model PLUC. We quantify important uncertainties in the modelling chain. Next, dLUC and iLUC projections for Brazil up to 2030 at different spatial scales and the uncertainty herein are assessed. Our results show that cell‐based (5 × 5 km²) probabilities of dLUC range from 0 to 0.77, and of iLUC from 0 to 0.43, indicating that it is difficult to project exactly where dLUC and iLUC will occur, with more difficulties for iLUC than for dLUC. At country level, dLUC area can be projected with high certainty, having a coefficient of variation (cv) of only 0.02, while iLUC area is still uncertain, having a cv of 0.72. The latter means that, considering the 95% confidence interval, the iLUC area in Brazil might be 2.4 times as high or as low as the projected mean. Because this confidence interval is so wide that it is likely to straddle any legislation threshold, our opinion is that threshold evaluation for iLUC indicators should not be implemented in legislation. For future studies, we emphasize the need for provision of quantitative uncertainty estimates together with the calculated LUC indicators, to allow users to evaluate the reliability of these indicators and the effects of their uncertainty on the impacts of land‐use change, such as greenhouse gas emissions.     

Estimating individual fitness in the wild using capture–recapture data

The concept of Darwinian fitness is central in evolutionary ecology, and its estimation has motivated the development of several approaches. However, measuring individual fitness remains challenging in empirical case studies in the wild. Measuring fitness requires a continuous monitoring of individuals from birth to death, which is very difficult to get in part because individuals may or may not be controlled at each reproductive event and recovered at death. Imperfect detection hampers keeping track of mortality and reproductive events over the whole lifetime of individuals. We propose a new statistical approach to estimate individual fitness while accounting for imperfect detection. Based on hidden process modelling of longitudinal data on marked animals, we show that standard metrics to quantify fitness, namely lifetime reproductive success, individual growth rate and lifetime individual contribution to population growth, can be extended to cope with imperfect detection inherent to most monitoring programs in the wild. We illustrate our approach using data collected on individual roe deer in an intensively monitored population.     

Opt‐in or opt‐out to increase organ donation in South Africa? Appraising proposed strategies using an empirical ethics analysis

Utilising empirical ethics analysis, we evaluate the merits of systems proposed to increase deceased organ donation in South Africa (SA). We conclude that SA should maintain its soft opt‐in policy, and enhance it with ‘required transplant referral’ in order to maximise donor numbers within an ethically and legally acceptable framework. In SA, as is the case worldwide, the demand for donor organs far exceeds the supply thereof. Currently utilising a soft opt‐in system, SA faces the challenge of how to increase donor numbers in a context which is imbued with inequalities in access to healthcare, multiplicitous personal beliefs and practices, distrust of organ transplant and varying levels of education and health literacy. We argue that a hard opt‐in, opt‐out or mandated consent system would be problematic, and we present empirical data from Gauteng Province illustrating barriers to ethically sound practice in soft consent systems. Ultimately, we argue that in spite of some limitations, a soft opt‐in system is most realistic for SA because its implementation does not require extensive public education campaigns at national level, and it does not threaten to further erode trust at a clinical level. However, to circumvent some of the clinical‐level barriers identified in our empirical study, we propose a contextually sensitive option for “enabling” soft opt‐in through “required transplant referral”. We argue that this system is legally defensible, enhances ethical practice and could also increase donor numbers as it has in many other countries.     

Are Normal‐Weight Americans Over‐Fat?

Data from National Health and Nutrition Examination Surveys (NHANES) 1999-2004 have recently shown the percent body fat of American adults. Average American men and women have ~28 and 40% body fat. When categorized by BMI and age, the data also show high percent body fat values, particularly in lower BMI categories. These data should make one reflect on the health status of Americans in all BMI categories and the use of these data for public health recommendations.     

Do model‐based phylogenetic analyses perform better than parsimony? A test with empirical data

The use of model‐based methods to infer a phylogenetic tree from a given data set is frequently motivated by the truism that under certain circumstances the parsimony approach (MP) may produce incorrect topologies, while explicit model‐based approaches are believed to avoid this problem. In the realm of empirical data from actual taxa, it is not known (or knowable) how commonly MP, maximum‐likelihood or Bayesian inference are inaccurate. To test the perceived need for “sophisticated” model‐based approaches, we assessed the degree of congruence between empirical phylogenetic hypotheses generated by alternative methods applied to DNA sequence data in a sample of 1000 recently published articles. Of 504 articles that employed multiple methods, only two exhibited strongly supported incongruence among alternative methods. This result suggests that the MP approach does not produce deviant hypotheses of relationship due to convergent evolution in long branches. Our finding therefore indicates that the use of multiple analytical methods is largely superfluous. We encourage the use of analytical approaches unencumbered by ad hoc assumptions that sap the explanatory power of the evidence. © The Willi Hennig Society 2010.     

Are long‐term widespread avian body size changes related to food availability? A test using contemporaneous changes in carotenoid‐based color

Recent changes in global climate have been linked with changes in animal body size. While declines in body size are commonly explained as an adaptive thermoregulatory response to climate warming, many species do not decline in size, and alternative explanations for size change exist. One possibility is that temporal changes in animal body size are driven by changes in environmental productivity and food availability. This hypothesis is difficult to test due to the lack of suitable estimates that go back in time. Here, we use an alternative, indirect, approach and assess whether continent‐wide changes over the previous 100 years in body size in 15 species of Australian birds are associated with changes in their yellow carotenoid‐based plumage coloration. This type of coloration is strongly affected by food availability because birds cannot synthesize carotenoids and need to ingest them, and because color expression depends on general body condition. We found significant continent‐wide intraspecific temporal changes in body size (wing length) and yellow carotenoid‐based color (plumage reflectance) for half the species. Direction and magnitude of changes were highly variable among species. Meta‐analysis indicated that neither body size nor yellow plumage color showed a consistent temporal trend and that changes in color were not correlated with changes in size over the past 100 years. We conclude that our data provide no evidence that broad‐scale variation in food availability is a general explanation for continent‐wide changes in body size in this group of species. The interspecific variability in temporal changes in size as well as color suggests that it might be unlikely that a single factor drives these changes, and more detailed studies of museum specimens and long‐term field studies are required to disentangle the processes involved.     

Unconstrained evolution in short introns? – An analysis of genome‐wide polymorphism and divergence data from Drosophila

An unconstrained reference sequence facilitates the detection of selection. In Drosophila, sequence variation in short introns seems to be least influenced by selection and dominated by mutation and drift. Here, we test this with genome‐wide sequences using an African population (Malawi) of D. melanogaster and data from the related outgroup species D. simulans, D. sechellia, D. erecta and D. yakuba. The distribution of mutations deviates from equilibrium, and the content of A and T (AT) nucleotides shows an excess of variance among introns. We explain this by a complex mutational pattern: a shift in mutational bias towards AT, leading to a slight nonequilibrium in base composition and context‐dependent mutation rates, with G or C (GC) sites mutating most frequently in AT‐rich introns. By comparing the corresponding allele frequency spectra of AT‐rich vs. GC‐rich introns, we can rule out the influence of directional selection or biased gene conversion on the mutational pattern. Compared with neutral equilibrium expectations, polymorphism spectra show an excess of low frequency and a paucity of intermediate frequency variants, irrespective of the direction of mutation. Combining the information from different outgroups with the polymorphism data and using a generalized linear model, we find evidence for shared ancestral polymorphism between D. melanogaster and D. simulans, D. sechellia, arguing against a bottleneck in D. melanogaster. Generally, we find that short introns can be used as a neutral reference on a genome‐wide level, if the spatially and temporally varying mutational pattern is accounted for.     

Profile or group discriminative techniques? Generating reliable species distribution models using pseudo‐absences and target‐group absences from natural history collections

Aim The presence‐only data stored in natural history collections is the most important source of information available regarding the distribution of organisms. These data and profile techniques can be used to generate species distribution models (SDMs), but pseudo‐absences must be generated to use group discriminative techniques. In this study, we evaluated whether the SDMs generated with pseudo‐absences are reliable and also if there are differences in the results obtained with profile and group discriminative techniques. Location Ecuador, South America. Methods The SDMs were generated with a training data set for each of the five species of Anthurium and six different methods: two profile techniques (BIOCLIM and Gower’s distance index), three group discriminative techniques [logistic multiple regression (LMR), multivariate adaptative regression splines (MARS) and Maxent ] and a mixed modelling approach genetic algorithm for rule‐set production (GARP), which employs a combination of profile and group discriminative techniques and generates its own pseudo‐absences. For LMR, MARS and Maxent , three types of absences were generated: (1) random pseudo‐absences in equal number to presences and excluding a buffer area around presences (except for Maxent , which assumes that this background sample includes presences), (2) a large number (10,000) of random pseudo‐absences, also excluding a buffer area around each presence and (3) ‘target‐group absences’ (TGA), consisting of sites where other species of the group have been collected by the specialist, but not the species being modelled. To compare the predictive performance of the SDMs, the area under the curve statistic was calculated using an independent testing data set for each species. Results MARS, Maxent and LMR produce better results than the profile techniques. The models created with TGA are generally more accurate than those generated with pseudo‐absences. Main conclusions The advantages and disadvantages of different options for using pseudo‐absences and TGA with profile and group discriminative modelling techniques are explained and recommendations are made for the future.