Brain reorganization,not relative brain size,primarily characterizes anthropoid brain evolution

Comparative analyses of primate brain evolution have highlighted changes in size and internal organization as key factors underlying species diversity. It remains, however, unclear (i) how much variation in mosaic brain reorganization versus variation in relative brain size contributes to explaining the structural neural diversity observed across species, (ii) which mosaic changes contribute most to explaining diversity, and (iii) what the temporal origin, rates and processes are that underlie evolutionary shifts in mosaic reorganization for individual branches of the primate tree of life. We address these questions by combining novel comparative methods that allow assessing the temporal origin, rate and process of evolutionary changes on individual branches of the tree of life, with newly available data on volumes of key brain structures (prefrontal cortex, frontal motor areas and cerebrocerebellum) for a sample of 17 species (including humans). We identify patterns of mosaic change in brain evolution that mirror brain systems previously identified by electrophysiological and anatomical tract-tracing studies in non-human primates and functional connectivity MRI studies in humans. Across more than 40 Myr of anthropoid primate evolution, mosaic changes contribute more to explaining neural diversity than changes in relative brain size, and different mosaic patterns are differentially selected for when brains increase or decrease in size. We identify lineage-specific evolutionary specializations for all branches of the tree of life covered by our sample and demonstrate deep evolutionary roots for mosaic patterns associated with motor control and learning.     

Feeding ecology and dietary differences between blue monkey (Cercopithecus mitis stuhlmanni Matschie) groups in logged and unlogged forest, Budongo Forest Reserve, Uganda

Several studies have investigated the effects of logging on primate population density, and attempted to relate density differences to changes in vegetation composition. As population density in some forest primates may be considerably influenced by dietary quality, it is important to understand how the effects of vegetation changes commonly associated with logging influence primate feeding ecology. Results are presented from a study carried out in the Budongo Forest Reserve in Uganda to investigate differences in blue monkey (Cercopithecus mitis stuhlmanni) feeding ecology in forest blocks with different logging history. Dietary composition differed between logged and unlogged forest, with a higher proportion of unripe fruit consumed in logged forest. By contrast, the proportion of young leaves, invertebrates and seeds in the diet was higher in unlogged forest. Variations in the intake of fruit was also higher in unlogged forest, but feeding patterns on other dietary items were more selective. These differences in diet reflect differences in availability of different categories of food items, as determined by tree species composition, abundance and plant phenological patterns. The observed differences between feeding ecology in logged and unlogged forest are discussed in relation to primate feeding ecology and habitat composition in Budongo.     

Classification of vegetation sequences in Toohey Forest,Queensland

In this paper we consider one method of mapping larger units identified from the spatial pattern of sequences of vegetation types. The basic data were presence/absence data for 6450 stands arranged in 90 transects. A second set of data was derived by averaging the species occurrences in non-overlapping groups of 5 stands. A divisive numerical classification was used to determine the primary vegetation units. In all, 5 different sets of primary types were derived, using different species suites, different sample sizes and different numerical methods. We briefly discuss the types identified and their spatial patterns in the area.Each of these types was then used to define a string of type-codes for every transect so that each transect represents a sample from the landscape containing information on the frequency and spatial distribution of the primary vegetation types. The transects may be classified using a Levenshtein dissimilarity measure and agglomerative hierarchical classification, giving 5 analyses of transects, one for each of the primary types discussed above. We then examine these transect classifications to investigate the stability of the vegetation landspace patterns under changes in species used for the primary classification, in size of sample unit and in method of primary classifications. There is a considerable degree of stability in the results. However it seems with this vegetation that the tree species and non-tree species have considerable independence. We also indicate some problems with this approach and some possible extensions.     

Feeding Ecology of Cross River Gorillas (Gorilla gorilla diehli) at Mawambi Hills: The Influence of Resource Seasonality

Determining the composition of primate diet and identifying factors that affect food choice are important in understanding habitat requirements of primates and designing conservation plans. We studied the diet of Cross River gorillas (Gorilla gorilla diehli) in relation to availability of food resources, in a semideciduous lowland forest site (Mawambi Hills) in Cameroon, from November 2009 to September 2011. Based on 109 d of feeding trail data, 203 fecal samples, and 22 mo of phenological monitoring, we determined that gorillas consumed a total of 242 food items, including 240 plant items from 186 species and 55 taxonomic families. Mawambi gorillas diversified fruit consumption when fruit availability increased, and consumed more fibrous foods (pith, leaf, bark) during times of fruit scarcity, consistent with results of other gorilla studies. However, fruit availability was not related to rainfall, and the period of fruit scarcity was more pronounced at Mawambi than at other gorilla study sites, due to a single long dry season and extreme rainfall at the end of the rainy season that delayed fruit production and ripening. We found no relationship between the daily path length of the gorillas and fruit consumption. We found feeding habits of Mawambi gorillas to be notably similar to those of a population of Cross River gorillas at Afi Mountain, Nigeria, although subtle differences existed, possibly due to site-specific differences in forest composition and altitude. At both sites the liana Landolphia spp. was the single most important food species: the leaves are a staple and the fruits are consumed during periods of fruit scarcity. Snails and maggots were consumed but we observed no further faunivory. We suggest that tree leaves and lianas are important fallback food sources in the gorilla diet in seasonally dry forests.     

Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets

Nonparamtric bootstrapping methods may be useful for assessing confidence in a supertree inference. We examined the performance of two supertree bootstrapping methods on four published data sets that each include sequence data from more than 100 genes. In "input tree bootstrapping," input gene trees are sampled with replacement and then combined in replicate supertree analyses; in "stratified bootstrapping," trees from each gene's separate (conventional) bootstrap tree set are sampled randomly with replacement and then combined. Generally, support values from both supertree bootstrap methods were similar or slightly lower than corresponding bootstrap values from a total evidence, or supermatrix, analysis. Yet, supertree bootstrap support also exceeded supermatrix bootstrap support for a number of clades. There was little overall difference in support scores between the input tree and stratified bootstrapping methods. Results from supertree bootstrapping methods, when compared to results from corresponding supermatrix bootstrapping, may provide insights into patterns of variation among genes in genome-scale data sets.     

Searching for a Needle in a Haystack: Evaluating Survey Methods for Non-indigenous Plant Species

The control and management of non-indigenous plant species (NIS) can be conceptually divided into three phases: inventory/survey, monitoring and management. Here we focus on phase one, determining which species are present and where they are located within the environment. Sampling for NIS is inherently time-consuming and thus costly. Many management areas are large and therefore can only be surveyed (partial observation of the total area by sampling) and not inventoried (total observation of area). Survey data should reflect the spatial distribution of the target species populations over the landscape. Such data can then be used in combination with environmental data, to create probability maps of target species occurrence for the entire area of interest. We used a GIS model to evaluate seven different survey methods for consistency and reliability of intersecting NIS species’ patches and producing samples which reflect the spatial distribution of the population, and which can be performed in a cost and time-efficient manner. The GIS model was developed to create NIS populations which were then sampled using the different survey methods, and the results recorded. To improve the applicability of the model, four patch sizes and levels of occurrence were used, along with random and weighted distribution patterns in relation to patch proximity to roads and trails. Grid and random points, and targeted (stratified continuous) transects (starting on a road or trail (rights of way (RoW)) and finishing 2 km from any RoW) methods provided the most consistent samples of the population. Logistically, point methods required an unrealistic distance and time commitment in comparison with transect methods. The importance of collecting information on the size of NIS patches was demonstrated as more small patches were intersected than larger ones when the area infested was held constant. Thus, if frequency of patches is used to explain the results of a survey then comparisons between species and methods are difficult to interpret thus leading to erroneous conclusions. However, use of percentage of area infested estimates provides for easier comparison between species and sample methods. The targeted transect method provided the most reliable, efficient and consistent sample with the expected spatial distribution.     

Estimating sexual dimorphism and size differences in the fossil record: A test of methods

Investigations of size variation in fossil and archaeological skeletal assemblages may be complicated by incomplete skeletons, biased representation of sexes, and the lack of morphological features that identify sex. In order to refine our ability to evaluate size variation, we test the accuracy of three methods that are currently used to estimate size differences in unsexed (pooled) samples: the means method, the median method, and a newly applied technique, the method of moments. Using body mass data from 42 primate species, we calculated actual levels of sexual dimorphism for each species and compared these values to estimates produced by each method. Multivariate regression was used to examine the effects of sample distribution characteristics, including sample size, kurtosis, skewness, sample variance, sex ratio, and intrasexual variance on the performance of the methods. None of the methods appears to be especially accurate. However, one of the simplest methods, the means method, performs relatively well. Factors that lead to inaccuracies in estimation are not readily evident based on multiple regression analysis. We urge caution in the utilization of these techniques, and advocate further analysis of simulated data. Am J Phys Anthropol 110: 95–104, 1999. © 1999 Wiley-Liss, Inc.     

Fruit availability, chimpanzee diet, and grouping patterns on Rubondo Island, Tanzania

We examined seasonal patterns of fruit availability, dietary quality, and group size in the descendants of an introduced chimpanzee population on Rubondo Island, Tanzania. The site has supported a free-ranging population without provisioning for 40 years. Our goals were to determine whether Rubondo chimpanzees experience periods of fruit shortage, and whether they respond to changes in fruit availability similarly to chimpanzees at endemic sites. We indexed the fruit availability of tree and liana species on transects stratified across three chimpanzee ranging areas. We used fecal analyses to evaluate seasonal changes in diet, and used data on party size and nesting group size to examine seasonal patterns of grouping. Tree fruit availability was positively correlated with rainfall, with a period of relative tree fruit scarcity corresponding with the long dry season. Liana fruit availability was not related to rainfall, and lianas exhibited less variable fruiting patterns across seasons. Fruits made up the majority of the chimpanzee diet, with lianas accounting for 35% of dietary fruit species. Fruits of the liana Saba comorensis were available during all months of phenological monitoring, but they were consumed more when tree fruit was scarce, suggesting that Saba comorensis fruits may be a fallback food for Rubondo chimpanzees. There were no increases in consumption of lower-quality plant parts between seasons, and there were no changes in group size between seasons. These results contrast with evidence from several endemic chimpanzee study sites, and indicate that Rubondo chimpanzees may have access to abundant and high-quality foods year round.     

Vegetative and reproductive phenology of some multipurpose tree species in the homegardens of Barak Valley, northeast India

Traditional homegardens are an important component of the farming systems in many rural communities and have been highlighted considerably due to their sustainability and role in the conservation of biodiversity. However, the functional aspect of the homegardens, which includes the phenological behavior of the dominant tree species in such agroforestry systems, has been undermined till date, and there is a lack of adequate data on this aspect of the traditional homegardens. As a step in this direction the present study was carried out to determine the phenological behavior of important multipurpose trees in the homegardens of the village of Dargakona, Assam, northeast India. The study revealed the dominance of periodic growth deciduous species from a total of 25 tree species selected for phenological observation. The diversity of multipurpose trees in the homegardens is represented by different plant functional types with different phenological behavior which showed significant changes in their responses to inter-annual climatic variations. The diversity of tree species with different phenological behavior has implications for the temporal partitioning of resources, especially during periods of scarcity, thereby resulting in efficient utilization of resources such as water. Also the diverse phenological behavior plays an important role in regulating the food supply for the herbivore population and the year-round availability of products, and such information can be useful in the selection of species for integration into other agroforestry systems which can be sustainable in the long run.     

Abundance of Diurnal Primates in Mwanihana Forest, Udzungwa Mountains, Tanzania

Many individual researchers have used line transect counts to estimate forest primate abundance. They have devoted less attention to the interpretation of line transect data obtained by several observers, as is often the case in long-term monitoring programs. We present primate relative abundance data that 5 observers collected over 6 yr (not continuous) along 4 different transects each 4 km long in the Mwanihana Forest, Udzungwa Mountains National Park, Tanzania. Total distance walked during transect repetitions is ca. 700 km. The species we saw most frequently was the endemic Udzungwa red colobus Procolobus gordonorum (mean 0.59 groups/km walked), followed by the Angolan black-and-white colobus Colobus angolensis (0.43 groups/km) and Sykes’s monkey Cercopithecus mitis (0.35 groups/km). We sighted the endemic Sanje mangabey Cercocebus galeritus sanjei and the yellow baboon Papio cynocephalus infrequently, the latter being confined to the deciduous forest parts of the transects. We analyzed sighting frequency by gross habitat type, transect, season, and observer. Interobserver differences in the relative abundance of each species were moderate and the few cases of significant variations were due to discordance of only 1 observer from the others. Estimated distances of primate group sightings differ significantly among observers, thus preventing us from deriving estimates of absolute density. Frequency distributions of distance-class intervals are not significantly different among observers, which may indicate gross interobserver consistency in the width of the area sampled. We conclude that unless consistency in data collection is checked, as we did for 2 observers who collected data simultaneously, potential interobserver differences remain an underlying source of variance in the results that cannot be separated from other sources of variance.     

Composition and structure of a species rich Amazonian rain forest obtained by two different sample methods

Inventory data for trees ≥ 10 cm DBH from a hectare plot are compared to data obtained by the Point-Centered Quarter Method along a line transect from the same locality in Anangu, Amazonian Ecuador. The one-hectare quadrat plot of 100 × 100 m had 734 individuals, 153 species, 46 families, a total basal area of 22.2 m², and an estimated above ground tree volume of 240.5 m³. The line transect had a calculated density of 728 individuals per hectare, which included 239 species, 51 families, a total basal area of 34.1 m², and an estimated above ground tree volume of 409.6 m³. Of the 20 species with the highest IVI, only four were shared by the two samples. The most important species were Quararibea ochrocalyx on the hectare plot and Iriartea deltoidea on the line transect, constituting 26.6 and 13.3% of the individuals, respectively. The five families with the highest FIV on the hectare plot (Bombacaceae, Arecaceae, Moraceae, Caesalpinaceae, and Lauraceae) and on the line transect (Arecaceae, Moraceae, Meliaceae, Mimosaceae and Caesalpinaceae) constitute 40.4% and 35.4% of the Family Importance Values of the samples, respectively. The Point-Centered Quarter Method used along a line transect reflects maximum diversity and provides average values of density and tree size in the area. The quadrat plot reflects the local structure and composition of the forest within the plot.     

Diurnal primate densities and biomass in the Kakamega Forest: an evaluation of census methods and a comparison with other forests

Line-transect surveys were conducted at the Isecheno study site in the Kakamega Forest, western Kenya to estimate diurnal primate densities. The estimates from several different methods of analysis of census data were compared to "true" density values based on home range size and overlap for two species. The Whitesides method [Whitesides et al., 1988], which incorporates species-specific mean group spread into its formula for estimating transect width, provided the most accurate density estimates. The importance of including as many groups as possible when calculating density from home range size and overlap is demonstrated with long-term data from Colobus guereza and Cercopithecus mitis. Colobus guereza group density at Isecheno was much lower than that published from a recent brief study [von Hippel, 1996]. Cercopithecus mitis group density has fallen while overall population biomass appears to have remained stable over 20 years of study. Isecheno has the second highest diurnal primate biomass of the ten Guineo-Congolian rainforest sites for which biomass data are available, despite having the lowest primate species richness. Within the Guineo-Congolian rainforest system, primate biomass appears to vary to some extent between ecogeographic regions: two of three mid-elevation East African sites have high biomasses, two of two lowland West African sites have intermediate biomasses, and four of five lowland Central African sites have low biomasses. There is a strong positive correlation between total colobine biomass and total primate biomass at the ten Guineo-Congolian rainforest sites.     

Summation and quantity judgments of sequentially presented sets by capuchin monkeys (Cebus apella)

Capuchin monkeys (Cebus apella) were presented with two sets of food items, identical in food type but differing in number. Animals selected one set and were permitted to consume their choice. Set sizes ranged from 1 to 6 items. In experiment 1, each set was uncovered and recovered before a response was made, and the monkeys selected the larger set at high levels. Experiment 2 presented sets that had both visible and nonvisible food items in them at the time of the response, thus requiring the monkeys to sum the total amount of food that was available. The monkeys again selected the larger set with no decrement in performance. Overall, the data indicate that capuchins, like other more extensively studied primate species in this area of research, are responsive to quantitative differences between sets. Capuchins succeed in making these quantity judgments when sets are nonvisible at choice time and when summation of items must be performed, thus demonstrating coordination of quantification skills and memory. Capuchins also inhibit responses to visible food items when those items are only part of an overall smaller quantity of food compared with a completely nonvisible set.     

Densités de primates en forêt guyanaise. Test d'une méthode d'estimation par transect

The results of a classical transect method designed to evaluate primate density are compared with estimates obtained from long-term studies on three species within a community inhabiting an undisturbed rain forest (French Guiana). Combining results of both methods, the total density of the primate community, which includes six species, is about 70 individuals per square kilometre. The concordance of data noted in Alouatta seniculus, Cebus apella and Saguinus midas, makes the transect method a reliable approach to low primate densities overall. However, it requires that long cumulative distances are walked and does not guarantee that rare species will not be missed. The predominance of Alouatta within the community, as observed in numerous Amazonian communities, is interpreted in relation to the nutritional quality of its environment and weak feeding competition between primate species.     

The Value of Measuring Food Availability on the Ground for a Semiterrestrial Frugivore, the Tana River Mangabey (Cercocebus galeritus) of Kenya

Collecting phenological data, seasonal availability of plant resources that primates feed on, allows us to understand feeding ecology better. A number of primates are terrestrial or semiterrestrial frugivores, yet phenology is generally measured only in the canopy. I hypothesized that combining measurements of food availability on the ground with canopy measurements would more strongly correlate with diet than canopy measurements alone for a semiterrestrial frugivore, the Tana River mangabey (Cercocebus galeritus). From July 2005 until June 2006, I conducted monthly follows on a mangabey group. Phenology was measured in 105 individuals of their top seven food tree species. I measured canopy phenology on a 0–5 scale and counted fruits in three 1 m³ areas of the canopy, and measured ground phenology by counting fruits and seeds in four 1 m² quadrats under the canopy. I calculated each tree’s canopy volume and canopy shadow, and each species’ mean fruit weight, mean seed weight, and density. Monthly biomasses were calculated as kilograms per hectare. Spearman correlations were performed between diet contribution and canopy biomass, ground biomass, and total biomass. The hypothesis was not supported for seven species individually or combined. The hypothesis was supported for 3 of 12 diet items, although canopy biomass was also significant for 2 of those items. Two diet items correlated only with ground biomass. Studies of the Tana River mangabey may benefit from measuring ground phenology only for those items eaten exclusively on the ground. Primatologists studying terrestrial or semiterrestrial frugivores should consider feeding height when deciding on phenology methods.     

The effects of preservation on fish tissue stable isotope signatures

The effects of formalin and ethanol preservation on the δ¹³C and δ¹⁵N isotope signatures of Arctic charr Salvelinus alpinus muscle tissue were examined. The lipid content of the tissue samples studied ranged from 3·6 to 6·1% and was not correlated with the magnitude of observed isotopic shifts in preserved samples. Ethanol and formalin significantly depleted and enriched, respectively, the δ¹³C isotope signatures of preserved tissues when compared to control samples. Ethanol did not significantly enrich δ¹⁵N signatures in comparison to controls, whereas formalin did. A meta-analysis of multiple species effects further demonstrated significant preservation effects in fish tissue. Statistical analysis of data obtained by correcting preserved tissue isotope signatures with literature, bootstrapped or meta-analysis derived correction factors demonstrated significant differences between corrected and control sample isotope signatures or failure to produce a unity slope when the data sets were regressed against one another. Species-specific, bootstrapped linear correction models resulted in no such errors. Results suggest that species-specific correction methods should be used for fishes because of the known wide variation in fish tissue lipid content and composition. Accordingly, the use of pilot studies will be required to develop correction factors that properly adjust for preservation effects when interpreting temporal patterns in historic analyses of food webs.     

Measuring fruit patch size for three sympatric indonesian primate species

Food availability is one of the basic factors affecting primate density and socioecology, but food availability is difficult to assess. Two different ways to obtain accurate estimates of food availability have been proposed: using phenology data or using the behaviour of animals. Phenology data can be refined by only including trees that are large enough to be used; including (potential) tree species in which by the concerned primate species forage; or including (fruiting) trees of these species that actually produce fruit. Alternatively, the sizes of the actually visited trees (foraging trees) give an estimate of fruit availability. These measures are compared for three sympatric primate species at the Ketambe Research Station, Sumatra, Indonesia: the Thomas langur, the long-tailed macaque and the orangutan. The sizes of fruiting trees and the foraging trees are larger than the potential trees. The sizes of the potential trees and of the fruiting trees are similar for the three primate species. This, however, is not reflected in the use of trees: the langurs forage on average in trees of similar size to those producing fruit, whereas the macaques and orangutans forage in trees larger than those producing fruit. The use of trees does not necessitate a different cut off point of included dbhs for the three compared primate species. The use of trees of different sizes, however, may be regulated by food competition. This indicates that sympatric primates make different foraging decisions and that behavioural measures of food availability will be less reliable.     

Evaluating δ15N–body size relationships across taxonomic levels using hierarchical models

Ecologists routinely set out to estimate the trophic position of individuals, populations, and species composing food webs, and nitrogen stable isotopes (δ¹⁵N) are a widely used proxy for trophic position. Although δ¹⁵N values are often sampled at the level of individuals, estimates and confidence intervals are frequently sought for aggregations of individuals. If individual δ¹⁵N values are correlated as an artifact of sampling design (e.g., clustering of samples in space or time) or due to intrinsic groupings (e.g., life history stages, social groups, taxonomy), such estimates may be biased and exhibit overly optimistic confidence intervals. However, these issues can be accommodated using hierarchical modeling methods. Here, we demonstrate how hierarchical models offer an additional quantitative tool for investigating δ¹⁵N variability and we explicitly evaluate how δ¹⁵N varies with body size at successively higher levels of taxonomic aggregation in a diverse fish assemblage. The models take advantage of all available data, better account for uncertainty in parameters estimates, may improve inferences on coefficients corresponding to groups with small to moderate sample sizes, and partition variation across model levels, which provides convenient summaries of the ‘importance’ of each level in terms of unexplained heterogeneity in the data. These methods can easily be applied to diet-based studies of trophic position. Although hierarchical models are well-understood and established tools, their benefits have yet to be fully reaped by stable isotope and food web ecologists. We suggest that hierarchical models can provide a robust framework for conceptualizing and statistically modeling trophic position at multiple levels of aggregation.     

Models and estimators linking individual-based and sample-based rarefaction,extrapolation and comparison of assemblages

Aims In ecology and conservation biology, the number of species counted in a biodiversity study is a key metric but is usually a biased underestimate of total species richness because many rare species are not detected. Moreover, comparing species richness among sites or samples is a statistical challenge because the observed number of species is sensitive to the number of individuals counted or the area sampled. For individual-based data, we treat a single, empirical sample of species abundances from an investigator-defined species assemblage or community as a reference point for two estimation objectives under two sampling models: estimating the expected number of species (and its unconditional variance) in a random sample of (i) a smaller number of individuals (multinomial model) or a smaller area sampled (Poisson model) and (ii) a larger number of individuals or a larger area sampled. For sample-based incidence (presence–absence) data, under a Bernoulli product model, we treat a single set of species incidence frequencies as the reference point to estimate richness for smaller and larger numbers of sampling units.Methods The first objective is a problem in interpolation that we address with classical rarefaction (multinomial model) and Coleman rarefaction (Poisson model) for individual-based data and with sample-based rarefaction (Bernoulli product model) for incidence frequencies. The second is a problem in extrapolation that we address with sampling-theoretic predictors for the number of species in a larger sample (multinomial model), a larger area (Poisson model) or a larger number of sampling units (Bernoulli product model), based on an estimate of asymptotic species richness. Although published methods exist for many of these objectives, we bring them together here with some new estimators under a unified statistical and notational framework. This novel integration of mathematically distinct approaches allowed us to link interpolated (rarefaction) curves and extrapolated curves to plot a unified species accumulation curve for empirical examples. We provide new, unconditional variance estimators for classical, individual-based rarefaction and for Coleman rarefaction, long missing from the toolkit of biodiversity measurement. We illustrate these methods with datasets for tropical beetles, tropical trees and tropical ants.Important findings Surprisingly, for all datasets we examined, the interpolation (rarefaction) curve and the extrapolation curve meet smoothly at the reference sample, yielding a single curve. Moreover, curves representing 95% confidence intervals for interpolated and extrapolated richness estimates also meet smoothly, allowing rigorous statistical comparison of samples not only for rarefaction but also for extrapolated richness values. The confidence intervals widen as the extrapolation moves further beyond the reference sample, but the method gives reasonable results for extrapolations up to about double or triple the original abundance or area of the reference sample. We found that the multinomial and Poisson models produced indistinguishable results, in units of estimated species, for all estimators and datasets. For sample-based abundance data, which allows the comparison of all three models, the Bernoulli product model generally yields lower richness estimates for rarefied data than either the multinomial or the Poisson models because of the ubiquity of non-random spatial distributions in nature.     

The Use (and Misuse) of Phylogenetic Trees in Comparative Behavioral Analyses

Phylogenetic comparative methods play a critical role in our understanding of the adaptive origin of primate behaviors. To incorporate evolutionary history directly into comparative behavioral research, behavioral ecologists rely on strong, well-resolved phylogenetic trees. Phylogenies provide the framework on which behaviors can be compared and homologies can be distinguished from similarities due to convergent or parallel evolution. Phylogenetic reconstructions are also of critical importance when inferring the ancestral state of behavioral patterns and when suggesting the evolutionary changes that behavior has undergone. Improvements in genome sequencing technologies have increased the amount of data available to researchers. Recently, several primate phylogenetic studies have used multiple loci to produce robust phylogenetic trees that include hundreds of primate species. These trees are now commonly used in comparative analyses and there is a perception that we have a complete picture of the primate tree. But how confident can we be in those phylogenies? And how reliable are comparative analyses based on such trees? Herein, we argue that even recent molecular phylogenies should be treated cautiously because they rely on many assumptions and have many shortcomings. Most phylogenetic studies do not model gene tree diversity and can produce misleading results, such as strong support for an incorrect species tree, especially in the case of rapid and recent radiations. We discuss implications that incorrect phylogenies can have for reconstructing the evolution of primate behaviors and we urge primatologists to be aware of the current limitations of phylogenetic reconstructions when applying phylogenetic comparative methods.