Recent developments in the analysis of comparative data

A phylogenetic approach to understand the evolution of reproduction in coleoid cephalopods

A central question in the evolution of life-histories is whether organisms reproduce once or repeatedly. For cephalopods, the main differences between semelparous and iteroparous are based on ovulation pattern and spawning type. The different reproductive strategies in coleoid cephalopods could be related to the habitat in which the species dwell (coastal vs. oceanic) and/or to environmental forces, thus, both aspects should be quantitatively evaluated under an evolutionary perspective to reconstruct: (a) the ancestral ovulation type of coleoid cephalopods, and (b) the potential of correlated evolution between ovulation type versus habitat and environment. Ancestral states of ovulation type were estimated using stochastic mapping based on literature data (i.e. synchronous or asynchronous), and this information was combined with a new molecular phylogeny including 165 species. The evolutionary correlation between ovulation type, habitat, and environment was estimated by means of the Markov model comparing the rates of gain and loss. The estimates of ancestral states of ovulation type for coleoid cephalopods resulted in a high probability that Octopodiformes evolved from synchronous ovulation type, and Decapodiformes from asynchronous ovulation type. The three traits evaluated presented phylogenetic signal, although no correlation was found between habitat and ovulation type. Overall, species in stable environments showed a tendency towards synchronous ovulation type, while the asynchronous ovulation pattern was found more frequently in species that live in unstable environments, being this last trait also responsible for triggering the change of ovulation type in some species throughout evolution.

A Bayesian extension of phylogenetic generalized least squares: Incorporating uncertainty in the comparative study of trait relationships and evolutionary rates

Phylogenetic comparative methods use tree topology, branch lengths, and models of phenotypic change to take into account nonindependence in statistical analysis. However, these methods normally assume that trees and models are known without error. Approaches relying on evolutionary regimes also assume specific distributions of character states across a tree, which often result from ancestral state reconstructions that are subject to uncertainty. Several methods have been proposed to deal with some of these sources of uncertainty, but approaches accounting for all of them are less common. Here, we show how Bayesian statistics facilitates this task while relaxing the homogeneous rate assumption of the well-known phylogenetic generalized least squares (PGLS) framework. This Bayesian formulation allows uncertainty about phylogeny, evolutionary regimes, or other statistical parameters to be taken into account for studies as simple as testing for coevolution in two traits or as complex as testing whether bursts of phenotypic change are associated with evolutionary shifts in intertrait correlations. A mixture of validation approaches indicates that the approach has good inferential properties and predictive performance. We provide suggestions for implementation and show its usefulness by exploring the coevolution of ankle posture and forefoot proportions in Carnivora.

Ecological filtering in scrub fragments restructures the taxonomic and functional composition of native bee assemblages

Predicting the long-term consequences of habitat alteration for the preservation of biodiversity and ecosystem function requires an understanding of how ecological filters drive taxonomic and functional biodiversity loss. Here, we test a set of predictions concerning the role of ecological filters in restructuring native bee assemblages inhabiting fragmented coastal sage scrub ecosystems in southern California, USA. In 2011 and 2012, we collected native bees in scrub habitat belonging to two treatment categories: large natural reserves and small habitat fragments embedded in an urban landscape. We compared bee assemblages in reserve and fragment sites with respect to their taxonomic and functional alpha diversity, beta diversity, assemblage composition, and mean geographical range size estimated via distribution maps compiled for this study from digitized specimen records. We found multiple lines of evidence that ecological filtering drove bee diversity loss in fragments: a disproportionate loss of functional diversity relative to taxonomic diversity, shifts in assemblage composition driven largely by the preferential extirpation of reserve-associated indicator species, and disproportionate loss of range-restricted species. However, we found no evidence of taxonomic or functional homogenization across fragment bee assemblages, suggesting that filtering was not sufficiently strong to cause a subset of functional traits (and their associated species) to dominate assemblages in fragments. Our results suggest that ecological filtering altered bee assemblages in habitat fragments, even when such fragments contained well-preserved native plant assemblages, underscoring the importance of preserving large areas of natural habitat for the conservation of bees (especially range-restricted taxa) and their associated ecological functions.

HOW MAMMALS PRODUCE LARGE-BRAINED OFFSPRING

Two explanations for species differences in neonatal brain size in eutherian mammals relate the size of the brain at birth to maternal metabolic rate. Martin (1981, 1983) argued that maternal basal metabolic rate puts an upper bound on the mother's ability to supply energy to the fetus, thereby limiting neonatal brain size. Hofman (1983) proposed that gestation length in mammals is constrained by maternal metabolic rate, implying an indirect constraint on neonatal brain size. Since individuals of precocial species have much larger neonatal brain sizes and are gestated longer for a given maternal body size than individuals of altricial species, Martin's and Hofman's ideas also require that mothers of precocial offspring have higher metabolic rates for their body sizes than mothers of altricial offspring. Data on 116 mammal species from 13 orders show that neither neonatal brain size nor gestation length is correlated with maternal metabolic rate when maternal body-size effects are removed. For a given maternal size, there is no difference in metabolic rates between precocial and altricial species, despite a two-fold difference between them in average neonatal brain size. However, neonatal brain size is strongly correlated with gestation length and litter size, independently of maternal size and metabolic rate. Analyses conducted within orders replicated the findings for gestation length and suggested that neonatal brain size may be at best only weakly related to metabolic rate. Differences in neonatal brain size appear to have evolved primarily with species differences in gestation length and litter size but not with differences in metabolic rate; large-brained offspring are typically produced from litters of one that have been gestated for a long time relative to maternal size. We conclude that species differences in relative neonatal brain size reflect different life-history tactics rather than constraints imposed by metabolic rate.

FISHER'S SEX RATIO THEORY MAY EXPLAIN HATCHING PATTERNS IN BIRDS

I present the hypothesis that asynchronous hatching is a means of ensuring an equal degree of parental investment in the progeny of each sex in altricial species of birds that are sexually dimorphic in size. In a comparative analysis of bird species of Africa and the Western Palearctic, I find a positive relationship between hatching asynchrony and sexual size dimorphism, in support of the hypothesis. The relation is significant for species in which males are larger than females, and in species in which females are larger than males. In addition, it holds even if allometric effects of body size are controlled for. No such relationship is found in species with self-feeding young. Alternative hypotheses to explain asynchronous hatching in altricial birds are discussed. The results of the comparative study are also consistent with some of these hypotheses. For instance, asynchronous hatching may be a mechanism used by parents of dimorphic species to deal with unpredictable primary sex ratios; it may be a way of avoiding simultaneous peak food demands by the young; or it may be a way of advancing the time of hatching so that the division of labor between the parents is optimized.

NUCLEOTYPIC EFFECT IN HOMEOTHERMS: BODY-MASS INDEPENDENT RESTING METABOLIC RATE OF PASSERINE BIRDS IS RELATED TO GENOME SIZE

The resting metabolic rate of passerines is shown to be negatively correlated with genome size when body mass is held constant (r = -0.75, P < 0.01). This finding extends previous conclusion for mammals to this bird order. The result holds when higher taxonomic levels are used instead of the species (for genera, r = -0.76, P < 0.03; for families, r = -0.991, P < 0.01) as well as when the independent contrasts derived from the resolved phylogeny are used instead of the taxa (r = -0.73, P < 0.02), with the evolutionarily older contrasts being more strongly correlated (for the contrasts older than 30 million yr, r = -0.998, P < 0.002). The concept of evolutionary characters consolidation (ECC), previously formulated for mammals, is tested with special reference to the error fraction in the total character variance. In this test, the ECC for the nucleotypic effect cannot be proven for mammals as a whole class, but it holds for the two separate orders tested, rodents and passerine birds. An upper taxonomic limit for the ECC is suggested.

HISTORICAL EXAMINATION OF DELAYED PLUMAGE MATURATION IN THE SHOREBIRDS (AVES: CHARADRIIFORMES)

Delayed plumage maturation refers to the presence of nonadultlike immature plumages (juvenal plumage excluded). It is usually considered the result of selection for distinctive first-winter or first-summer appearance. In the present study, evolution of delayed plumage maturation is examined in the shorebirds: the sandpipers, plovers, gulls, and their allies. Nine plumage-maturation characters were identified, and their states were superimposed onto topologies generated during two recent investigations of shorebird relationships (Sibley and Ahlquist; revised Strauch). The characters were then optimized so as to assign character states to interior nodes of the trees in the most parsimonious way. Reconstructions of character evolution on six of the shortest revised Strauch trees were ambiguous with respect to delayed plumage maturation in the hypothetical ancestral shorebird. If plumage maturation was not delayed in the shorebird ancestor, optimization indicated that delay appeared when nonadultlike juvenal feathers were acquired. In contrast, on the single Sibley and Ahlquist tree, absence of delayed plumage maturation in the shorebird ancestor was indicated unambiguously, with three evolutionary novelties (nonadultlike juvenal feathers, seasonal plumage change, and a reduced first-spring molt) implicated in its acquisition. Optimization indicated that delayed plumage maturation in shorebirds can be explained plausibly without invoking selection for distinctive first-winter or first-summer appearance. Two of the novel conditions generating delayed plumage maturation (modified juvenal feathers and seasonal plumage change) did so only because they were acquired in a taxon possessing restricted first-year molts, which are primitive. Given these observations, it seems simplest to explain the delay in plumage maturation as an incidental consequence of the phylogenetic inertia of shorebird molts. The third novelty that generates delayed plumage maturation, a reduced first-spring molt, may have been acquired to reduce molt-associated energetic demands in young birds.

PHYLOGENETIC ANALYSES OF THE CORRELATED EVOLUTION OF CONTINUOUS CHARACTERS: A SIMULATION STUDY

We use computer simulation to compare the statistical properties of several methods that have been proposed for estimating the evolutionary correlation between two continuous traits, and define alternative evolutionary correlations that may be of interest. We focus on Felsenstein's (1985) method and some variations of it and on several "minimum evolution" methods (of which the procedure of Huey and Bennett [1987] is a special case), as compared with a nonphylogenetic correlation. The last, a simple correlation of trait values across the tips of a phylogeny, virtually always yields inflated Type I error rates, relatively low power, and relatively poor estimates of evolutionary correlations. We therefore cannot recommend its use. In contrast, Felsenstein's (1985) method yields acceptable significance tests, high power, and good estimates of what we term the input correlation and the standardized realized evolutionary correlation, given complete phylogenetic information and knowledge of the rate and mode of character change (e.g., gradual and proportional to time ["Brownian motion"] or punctuational, with change only at speciation events). Inaccurate branch length information may affect any method adversely, but only rarely does it cause Felsenstein's (1985) method to perform worse than do the others tested. Other proposed methods generally yield inflated Type I error rates and have lower power. However, certain minimum evolution methods (although not the specific procedure used by Huey and Bennett [1987]) often provide more accurate estimates of what we term the unstandardized realized evolutionary correlation, and their use is recommended when estimation of this correlation is desired. We also demonstrate how correct Type I error rates can be obtained for any method by reference to an empirical null distribution derived from computer simulations, and provide practical suggestions on choosing an analytical method, based both on the evolutionary correlation of interest and on the availability of branch lengths and knowledge of the model of evolutionary change appropriate for the characters being analyzed. Computer programs that implement the various methods and that will simulate (correlated) character evolution along a known phylogeny are available from the authors on request. These programs can be used to test the effectiveness of any new methods that might be proposed, and to check the generality of our conclusions with regard to other phylogenies.

The Chiropteran Brain Database: Volumetric Survey of the Hypophysis in 165 Species

For nearly two decades, a database of brain structures from a large sample (272 species) of chiropterans has been widely accessible and used for socioecological analyses of mammals. However, this database remains incomplete since the hypophysis has not been measured. Since this glandular/neural structure has reproductive significance to chiropterans as for other mammals, this investigation was carried out using serial coronal sections of bat brains comprising the Heinz Stephan collection, Düsseldorf, Germany. Complete serially sectioned brains were examined in 313 individuals (165 species, 15 families). Using a well-documented method, hypophyseal volumes were determined from every fourth or sixth section in each individual. The strongest correlation was between body weight and the hypophysis (R(2) = 0.887) and its various components as well as between body weight and adenohypophysis (R(2) = 0.830) and neurohypophysis (R(2) = 0.925). Correlations were also strong for brain weight-adenohypophysis (R(2) = 0.817) and brain weight- neurohypophysis (R(2) = 0.911). Results indicated that: (1) in regression analyses, hipposiderids stand apart as having relatively large adenohypophysis; (2) analysis of residuals generated using least-squares regression of hypophyseal components suggests a trend among microchiropterans where females have a relatively larger adenohypophysis than males. However, this difference is only statistically significant in the largest samples: Phyllostomidae and Vespertilionidae. Pteropodids do not appear to follow this trend. Our findings suggest both phylogenetic and sexual differences in the adenohypophysis in particular, and indicate the need for investigation of larger samples by species, especially those best understood in reproductive and social biology.

The habits of highly effective phages: population dynamics as a framework for identifying therapeutic phages

The use of bacteriophages as antibacterial agents is being actively researched on a global scale. Typically, the phages used are isolated from the wild by plating on the bacteria of interest, and a far larger set of candidate phages is often available than can be used in any application. When an excess of phages is available, how should the best phages be identified? Here we consider phage-bacterial population dynamics as a basis for evaluating and predicting phage success. A central question is whether the innate dynamical properties of phages are the determinants of success, or instead, whether extrinsic, indirect effects can be responsible. We address the dynamical perspective, motivated in part by the absence of dynamics in previously suggested principles of phage therapy. Current mathematical models of bacterial-phage dynamics do not capture the realities of in vivo dynamics, nor is this likely to change, but they do give insight to qualitative properties that may be generalizable. In particular, phage adsorption rate may be critical to treatment success, so understanding the effects of the in vivo environment on host availability may allow prediction of useful phages prior to in vivo experimentation. Principles for predicting efficacy may be derived by developing a greater understanding of the in vivo system, or such principles could be determined empirically by comparing phages with known differences in their dynamic properties. The comparative approach promises to be a powerful method of discovering the key to phage success. We offer five recommendations for future study: (i) compare phages differing in treatment efficacy to identify the phage properties associated with success, (ii) assay dynamics in vivo, (iii) understand mechanisms of bacterial escape from phages, (iv) test phages in model infections that are relevant to the intended clinical applications, and (v) develop new classes of models for phage growth in spatially heterogeneous environments.

Prevalent structural disorder carries signature of prokaryotic adaptation to oxic atmosphere

Microbes have adopted efficient mechanisms to contend with environmental changes. The emergence of oxygen was a major event that led to an abrupt change in Earth's atmosphere. To adjust with this shift in environmental condition ancient microbes must have undergone several modifications. Although some proteomic and genomic attributes were proposed to facilitate survival of microorganisms in the presence of oxygen, the process of adaptation still remains elusive. Recent studies have focused that intrinsically disordered proteins play crucial roles in adaptation to a wide range of ecological conditions. Therefore, it is likely that disordered proteins could also play indispensable roles in microbial adaptation to the aerobic environment. To test this hypothesis we measured the disorder content of 679 prokaryotes from four oxygen requirement groups. Our result revealed that aerobic proteomes are endowed with the highest protein disorder followed by facultative microbes. Minimal disorder was observed in anaerobic and microaerophilic microbes with no significant difference in their disorder content. Considering all the potential confounding factors that can modulate protein disorder, here we established that the high protein disorder in aerobic microbe is not a by-product of adaptation to any other selective pressure. On the functional level, we found that the high disorder in aerobic proteomes has been utilized for processes that are important for their aerobic lifestyle. Moreover, aerobic proteomes were found to be enriched with disordered binding sites and to contain transcription factors with high disorder propensity. Based on our results, here we proposed that the high protein disorder is an adaptive opportunity for aerobic microbes to fit with the genomic and functional complexities of the aerobic lifestyle.

Patterns of genome size diversity in bats (order Chiroptera)

Despite being a group of particular interest in considering relationships between genome size and metabolic parameters, bats have not been well studied from this perspective. This study presents new estimates for 121 "microbat" species from 12 families and complements a previous study on members of the family Pteropodidae ("megabats"). The results confirm that diversity in genome size in bats is very limited even compared with other mammals, varying approximately 2-fold from 1.63 pg in Lophostoma carrikeri to 3.17 pg in Rhinopoma hardwickii and averaging only 2.35 pg ± 0.02 SE (versus 3.5 pg overall for mammals). However, contrary to some other vertebrate groups, and perhaps owing to the narrow range observed, genome size correlations were not apparent with any chromosomal, physiological, flight-related, developmental, or ecological characteristics within the order Chiroptera. Genome size is positively correlated with measures of body size in bats, though the strength of the relationships differs between pteropodids ("megabats") and nonpteropodids ("microbats").

A novel population of cholinergic neurons in the macaque spinal dorsal horn of potential clinical relevance for pain therapy

Endogenous acetylcholine (ACh) is a well-known modulator of nociceptive transmission in the spinal cord of rodents. It arises mainly from a sparse population of cholinergic interneurons located in the dorsal horn of the spinal cord. This population was thought to be absent from the spinal cord of monkey, what might suggest that spinal ACh would not be a relevant clinical target for pain therapy. In humans, however, pain responses can be modulated by spinal ACh, as evidenced by the increasingly used analgesic procedure (for postoperative and labor patients) consisting of the epidural injection of the acetylcholinesterase inhibitor neostigmine. The source and target of this ACh remain yet to be elucidated. In this study, we used an immunolabeling for choline acetyltransferase to demonstrate, for the first time, the presence of a plexus of cholinergic fibers in laminae II-III of the dorsal horn of the macaque monkey. Moreover, we show the presence of numerous cholinergic cell bodies within the same laminae and compared their density and morphological properties with those previously described in rodents. An electron microscopy analysis demonstrates that cholinergic boutons are presynaptic to dorsal horn neurons as well as to the terminals of sensory primary afferents, suggesting that they are likely to modulate incoming somatosensory information. Our data suggest that this newly identified dorsal horn cholinergic system in monkeys is the source of the ACh involved in the analgesic effects of epidural neostigmine and could be more specifically targeted for novel therapeutic strategies for pain management in humans.

Cost of reproduction and covariation of life history traits in birds

Evolution of life history traits can be studied at two different levels: (1) current selection processes, including trade-offs in life history traits in natural populations as revealed by observations or, preferably, exieriments; and (2) patterns of variation in life history traits with each other and with ecology among extant species. Selection is not evolution, but selection pressures must have caused evolutionary change and led to current patterns of life history traits. These problems are exemplified by recent research on clutch size in birds.

Low birth weight does not predict the ontogeny of relative leg length of infants and children: an allometric analysis of the NHANES III sample

Previous research links both low birth weight (LBW) and relative leg length (RLL) to a similar set of adult pathologies, including type II diabetes, coronary vascular disease, and some cancers. Historically, LBW has been frequently used as a broad indicator of the quality of the intrauterine environment, while RLL has been considered a sensitive measure of childhood environmental quality. While these observations have been taken to suggest that these measures reflect independent exposures at different life-stages, their mutual association with a similar set of later pathologies makes this assumption less certain than it may have previously seemed. Nationally representative data from the Third National Health and Nutrition Examination Survey (NHANES III) are used to test the hypothesis that LBW predicts reductions in the development of leg length relative to stature. After controls for important socioeconomic exposures that might confound measurement of such a relationship, we find statistical and biological evidence that variation in birth weight and variation in the development of leg length relative to stature (RLL) are independent. The results suggest that these two measures may represent independent information on prenatal and postnatal environmental quality.

Expensive Brains: "Brainy" Rodents have Higher Metabolic Rate

Brains are the centers of the nervous system of animals, controlling the organ systems of the body and coordinating responses to changes in the ecological and social environment. The evolution of traits that correlate with cognitive ability, such as relative brain size is thus of broad interest. Brain mass relative to body mass (BM) varies among mammals, and diverse factors have been proposed to explain this variation. A recent study provided evidence that energetics play an important role in brain evolution (Isler and van Schaik, 2006). Using composite phylogenies and data drawn from multiple sources, these authors showed that basal metabolic rate (BMR) correlates with brain mass across mammals. However, no such relationship was found within rodents. Here we re-examined the relationship between BMR and brain mass within Rodentia using a novel species-level phylogeny. Our results are sensitive to parameter evaluation; in particular how species mass is estimated. We detect no pattern when applying an approach used by previous studies, where each species BM is represented by two different numbers, one being the individual that happened to be used for BMR estimates of that species. However, this approach may compromise the analysis. When using a single value of BM for each species, whether representing a single individual, or available species mean, our findings provide evidence that brain mass (independent of BM) and BMR are correlated. These findings are thus consistent with the hypothesis that large brains evolve when the payoff for increased brain mass is greater than the energetic cost they incur.

An evolutionary analysis of rules regulating human inbreeding and marriage

Evolutionary theory predicts that humans should avoid incest because of the negative effects incest has on individual reproduction: production of defective offspring. Selection for the avoidance of close-kin mating has apparently resulted in a psychological mechanism that promotes voluntary incest avoidance. Most human societies are thought to have rules regulating incest. If incest is avoided, why are social rules constructed to regulate it? This target article suggests that incest rules do not exist primarily to regulate close-kin mating but to regulate inbreeding between more distant kin (especially cousin categories) and sexual relations between affinal relatives (often nonkin). Three evolutionary hypotheses about cousin marriage and affinal kin mating follow from this suggestion: (1) Rules regulating mating between affinal kin are means of paternity protection. Cousin marriage (inbreeding) is regulated because, if it occurs, it can concentrate wealth and power within families to the detriment of (2) the powerful positions of rulers in stratified societies and (3) the relatively equal social statuses of most men in egalitarian societies. Tests using the comparative method on a worldwide sample of 129 societies supported the three hypotheses. Two alternative anthropological hypotheses (derived from Freudian theory and alliance theory) failed to be supported.

Setting conservation priorities for the Moroccan herpetofauna: the utility of regional red lists

We assess the national conservation status of the amphibians and reptiles of Morocco by applying the IUCN Red List Criteria at the national level and assess its utility as a planning tool to establish regional priorities for conservation. We rely on the accessory data accompanying regional red lists, mainly distribution range and habitats used by, and threats affecting, species of conservation concern. We also correlated some natural history traits to examine the nature and causes of the risk of extinction. With 13 species of amphibians (31% regionally threatened) and 99 species of reptiles (14% regionally threatened), Morocco is one of the Mediterranean countries with the highest diversity of herpetofauna, mainly because of the high percentage of endemism (amphibians 31%, reptiles 24%). The relative frequencies of threatened species were found to be contingent on both taxonomic group and habitat. The overwhelming importance of the threats of small range and number of habitats used by species is different from the threats to the same species at the global level; this demonstrates the usefulness of national or regional analyses of conservation status for setting conservation priorities. The importance of regional assessment derives from the fact that the boundaries set for conservation management are mainly political rather than biogeographical.