Playing for keeps

The hypothesis that play behavior is more prevalent in larger-brained animals has recently been challenged. It may be, for example, that only certain brain structures are related to play. Here, we analyze social play behavior with regards to the cerebellum: a structure strongly implicated in motor-development, and possibly also in cognitive skills. We present an evolutionary analysis of social play and the cerebellum, using a phylogenetic comparative method. Social play frequency and relative cerebellum size are positively correlated. Hence, there appears to be a link between the evolutionary elaboration of social play and the cerebellum. Kerrie Lewis recently received her Ph.D. from the University of Durham, U.K., under the supervision of Robert Barton. She is currently working in a postdoctoral position at Duke University, conducting research into primate numerical cognition. Robert Barton is a Reader in Evolutionary Anthropology at the University of Durham. His interests comprise primate behavior and brain evolution. Both authors are keen advocates for the use of the comparative method in evolutionary studies.     

Putting phylogeny into the analysis of biological traits: A methodological approach

Phylogenetic comparative methods have long considered phylogenetic signal as a source of statistical bias in the correlative analysis of biological traits. However, the main life-history strategies existing in a set of taxa are often combinations of life history traits that are inherently phylogenetically structured. In this paper, we present a method for identifying evolutionary strategies from large sets of biological traits, using phylogeny as a source of meaningful historical and ecological information. Our methodology extends a multivariate method developed for the analysis of spatial patterns, and relies on finding combinations of traits that are phylogenetically autocorrelated. Using extensive simulations, we show that our method efficiently uncovers phylogenetic structures with respect to various tree topologies, and remains powerful in cases where a large majority of traits are not phylogenetically structured. Our methodology is illustrated using empirical data, and implemented in the adephylo package for the free software R.     

A Comparison of Predictive Methods in Extinction Risk Studies: Contrasts and Decision Trees

Over the last two decades an increasing emphasis has been placed on the importance of controlling for phylogeny when examining cross-species data; so-called comparative methods. These methods are appropriate for testing hypotheses about correlations between evolutionary events in the history of a clade and adaptive responses to those changes. When this approach is applied to extinction risk, possible correlations between evolutionary changes in, for example, body size or habitat specialisation and some measure(s) of current threat status are examined. However, there may be a mismatch here between the results of such studies, and the real, pragmatic needs of species conservation. This kind of approach certainly adds to our knowledge of some fundamental processes, but it is more difficult to see how this can be applied to conservation decision-making. For more practical purposes a decision-tree approach can be extremely useful. This paper illustrates the use of a contrasts based analysis of extinction risk compared with a decision-tree analysis for Galliformes (Aves). While the contrasts analyses concur with some general macroecological trends found in other studies, the decision-tree models provide lists of species predicted to be more at risk than current assessments would suggest. We argue that in practical terms, decision tree models might be more useful than a macroecological linear model-based approach.     

Phylogenetic systematics and biomecha cs in ecomorphology

Synopsis Research in all fields of biology increasingly uses phylogenetic systematics to interpret biological data in an evolutionary context. It is becoming widely accepted that comparative studies of the correlation of biological features, such as ecomorphological studies, must frame their analyses within the context of a phylogenetic hierarchy rather than treating each taxonomic unit as an independent replicate. Recent methods for the interpretation of ecological and functional data in the framework of a phylogeny can reveal the degree to which ecomorphological characters are correlated with one another, and are congruent with hierarchical cladistic groups. An example of the ecomorphology of labrid fishes is used here to illustrate the application of several of these methods. The structural design and mechanics of the jaws of labrids are tested for ecomorphological associations with the natural diets of these fishes. Methods for analysis of the correlated evolution of both discrete and continuous quantitative characters within a phylogeny are practiced on a single ecomorphological data set. Techniques used include character coding, character mapping, phylogenetic autocorrelation, independent contrasts, and squared change parsimony. These approaches to diverse biological data allow the study of ecomorphology to account for patterns of phylogenetic ancestry. Biomechanics or functional morphology also plays a vital role in the determination of ecomorphological relationships by clarifying the mechanisms by which morphologies can perform behaviors important to the organism's ecology. The synthesis of systematics with biomechanics is an example of interdisciplinary study in which information exchange can elucidate patterns of evolution in ecomorphology.     

Phylogenetic comparative analysis of life-history variation among populations of the lizard Sceloporus undulatus: an example and prognosis

Over the past 15 years, phylogenetic comparative methods (PCMs) have become standard in the study of life-history evolution. To date, most studies have focused on variation among species or higher taxonomic levels, generally revealing the presence of significant phylogenetic effects as well as residual variation potentially attributable to adaptive evolution. Recently, population-level phylogenetic hypotheses have become available for many species, making it possible to apply PCMs directly to the level at which experiments are typically used to test adaptive hypotheses. In this study, we present the results of PCMs applied to life-history variation among populations of the widespread and well-studied lizard Sceloporus undulatus. Using S. undulatus (which may represent four closely related species) as an example, we explore the benefits of using PCMs at the population level, as well as consider the importance of several thorny methodological problems including but not limited to nonindependence of populations, lack of sufficient variation in traits, and the typically small sample sizes dictated by the difficulty of collecting detailed demographic data. We show that phylogenetic effects on life-history variation among populations of S. undulatus appear to be unimportant, and that several classic trade-offs expected by theory and revealed by many interspecific comparisons are absent. Our results suggest that PCMs applied to variation in life-history traits below the species level may be of limited value, but more studies like ours are needed to draw a general conclusion. Finally, we discuss several outstanding problems that face studies seeking to apply PCMs below the species level.     

The effect of intraspecific sample size on type I and type II error rates in comparative studies

Comparative studies have increased greatly in number in recent years due to advances in statistical and phylogenetic methodologies. For these studies, a trade-off often exists between the number of species that can be included in any given study and the number of individuals examined per species. Here, we describe a simple simulation study examining the effect of intraspecific sample size on statistical error in comparative studies. We find that ignoring measurement error has no effect on type I error of nonphylogenetic analyses, but can lead to increased type I error under some circumstances when using independent contrasts. We suggest using ANOVA to evaluate the relative amounts of within- and between-species variation when considering a phylogenetic comparative study. If within-species variance is particularly large and intraspecific sample sizes small, then either larger sample sizes or comparative methods that account for measurement error are necessary.     

Power and metabolic scope of bird flight: a phylogenetic analysis of biomechanical predictions

For flying animals aerodynamic theory predicts that mechanical power required to fly scales as P proportional, variant m (7/6) in a series of isometric birds, and that the flight metabolic scope (P/BMR; BMR is basal metabolic rate) scales as P (scope) proportional, variant m (5/12). I tested these predictions by using phylogenetic independent contrasts from a set of 20 bird species, where flight metabolic rate was measured during laboratory conditions (mainly in wind tunnels). The body mass scaling exponent for P was 0.90, significantly lower than the predicted 7/6. This is partially due to the fact that real birds show an allometric scaling of wing span, which reduces flight cost. P (scope) was estimated using direct measurements of BMR in combination with allometric equations. The body mass scaling of P (scope) ranged between 0.31 and 0.51 for three data sets, respectively, and none differed significantly from the prediction of 5/12. Body mass scaling exponents of P (scope) differed significantly from 0 in all cases, and so P (scope) showed a positive body mass scaling in birds in accordance with the prediction.     

The characterization of complete mitochondrial genome and phylogenetic relationship within Rattus genus (Rodentia: Muridae)

The genus Rattus is one of the main pest genus of rodent. Most species of the genus carry all kinds of pathogenic bacteria to human being. They are traditionally considered to be a least understood group. The complete mitochondrial genome of the White-Footed Indochinese Rat, Rattus nitidus was determined in this study. The characterization of mitochondrial genomes of Rattus genus was also analyzed based on comprehensive comparison. The result of evolutionary patterns of protein-coding genes (PCGs) suggested purifying selection was the predominant evolutionary forces in the mitochondrial genomes of Rattus genus. The NADH dehydrogenase 4 gene (ND4) showed a highly elevated Ka/Ks ratio compared to the other protein-coding genes, which indicated ND4 was most likely under relaxed selection pressure. Phylogenetic analysis provided a well-supported outline of Rattus genus, and revealed two groups in the genus. R. nitidus had a sister relationship with R. norvegicus.     

THE EVOLUTION OF FEMALE-BIASED SEXUAL SIZE DIMORPHISM: A POPULATION-LEVEL COMPARATIVE STUDY IN HORNED LIZARDS (PHRYNOSOMA)

Female-biased sexual size dimorphism is uncommon among vertebrates and traditionally has been attributed to asymmetric selective pressures favoring large fecund females (the fecundity-advantage hypothesis) and/or small mobile males (the small-male advantage hypothesis). I use a phylogenetically based comparative method to address these hypotheses for the evolution and maintenance of sexual size dimorphism among populations of three closely related lizard species (Phrynosoma douglasi, P. ditmarsi, and P. hernandezi). With independent contrasts I estimate evolutionary correlations among female body size, male body size, and sexual size dimorphism (SSD) to determine whether males have become small, females have become large, or both sexes have diverged concurrently in body size during the evolutionary Xhistory of this group. Population differences in degree of SSD are inversely correlated with average male body size, but are not correlated with average female body size. Thus, variation in SSD among populations has occurred predominantly through changes in male size, suggesting that selective pressures on small males may affect degree of SSD in this group. I explore three possible evolutionary mechanisms by which the mean male body size in a population could evolve: changes in size at maturity, changes in the variance of male body sizes, and changes in skewness of male body size distributions. Comparative analyses indicate that population differentiation in male body size is achieved by changes in male size at maturity, without changes in the variance or skewness of male and female size distributions. This study demonstrates the potential of comparative methods at lower taxonomic levels (among populations and closely related species) for studying microevolutionary processes that underlie population differentiation.     

A phylogenetic analysis of basal metabolism,total evaporative water loss,and life-history among foxes from desert and mesic regions

We measured basal metabolic rate (BMR) and total evaporative water loss (TEWL) of species of foxes that exist on the Arabian Peninsula, Blanfords fox (Vulpes cana) and two subspecies of Red fox (Vulpes vulpes). Combining these data with that on other canids from the literature, we searched for specialization of physiological traits among desert foxes using both conventional least squares regression and regressions based on phylogenetic independent contrasts. Further, we explored the consequences of reduced body size of foxes on life history parameters such as litter size and neonate mass. For Blanfords foxes, Red foxes from the central desert of Arabia, and Red foxes from the more mesic Asir mountains, body mass averaged 1,285±52 g, 1,967±289 g, and 3,060±482 g, respectively, whereas mean BMR, during summer, was 304.5±32.3 kJ/day, 418.0±32.4 kJ/day, and 724.1±120.2 kJ/day (±SD). An analysis of covariance with body mass as a covariate showed no statistical differences in BMR among foxes. Analysis of covariance indicated that Red fox from the Asir mountains had a higher TEWL than Red foxes from central Arabia or than Blanfords foxes also from the mountains. Comparisons of all species of desert and mesic foxes showed no significant differences in BMR, nor did desert foxes have a significantly lower BMR than other carnivores. TEWL of desert foxes was lower than other more mesic carnivores; deviations in TEWL ranged from –17.7% for the Fennec fox (Fennecus zerda) to –57.4% for the Kit fox (Vulpes velox). Although desert foxes have a BMR comparable to other more mesic species, it appears that desert foxes do have a smaller body mass, lowering overall energy requirements. We attribute this reduction in body size to the resource limitation hypothesis whereby natural selection favors smaller individuals in a resource-limited environment, especially during periods of severe food shortage. However, until common garden experiments are performed, developmental plasticity and acclimation cannot be ruled out as contributors to this pattern.Abbreviations BMR basal metabolic rate - CLSR conventional least squares regression - MYA million years ago - PIC phylogenetic independent contrasts - T _a ambient temperature - TEWL total evaporative water loss - TNZ thermoneutral zone - O ₂ oxygen consumption Communicated by G. Heldmaier     

A simulation test of Smith's “degrees of freedom” correction for comparative studies

Computer simulation was used to test Smith's (1994) correction for phylogenetic nonindependence in comparative studies. Smith's method finds effective N, which is computed using nested analysis of variance, and uses this value in place of observed N as the baseline degrees of freedom (df) for calculating statistical significance levels. If Smith's formula finds the correct df, distributions of computer-generated statistics from simulations with observed N nonindependent species should match theoretical distributions (from statistical tables) with the df based on effective N. The computer program developed to test Smith's method simulates character evolution down user-specified phylogenies. Parameters were systematically varied to discover their effects on Smith's method. In simulations in which the phylogeny and taxonomy were identical (tests of narrow-sense validity), Smith's method always gave conservative statistical results when the taxonomy had fewer than five levels. This conservative departure gave way to a liberal deviation in type I error rates in simulations using more than five taxonomic levels, except when species values were nearly independent. Reducing the number of taxonomic levels used in the analysis, and thereby eliminating available information regarding evolutionary relationships, also increased type I error rates (broad-sense validity), indicating that this may be inappropriate under conditions shown to have high type I error rates. However, the use of taxonomic categories over more accurate phylogenies did not create a liberal bias in all cases in the analysis performed here. The effect of correlated trait evolution was ambiguous but, relative to other parameters, negligible. © 1995 Wiley-Liss, Inc.     

A Comparative Test of Adaptive Explanations for Hypsodonty in Ungulates and Rodents

Hypsodonty has long been recognized as an adaptation for grazing: grazing is suggested to increase tooth wear due to endogenous (e.g., fiber, silica) and/or exogenous (e.g., dust, grit) properties of ingested food. However, it is unknown whether tooth crown height is correlated with the mastication of high fiber or silica in grasses, the ingestion of external abrasives, or both. Furthermore, comparative studies of hypsodonty have not explicitly taken into account phylogenetic biases due to shared ancestry in tooth morphology and/or feeding behavior. This study highlights the relationship between molar crown height and feeding habits in African ungulates and South American rodents when phylogenetic effects are controlled. Among ungulates, high hypsodonty indices are significantly associated with specific plant and foraging height preferences, while habitat and climate show no correlation with tooth crown height. For rodents, grass-eating species are significantly more hypsodont than frugivorous or folivorous species, and arboreal rodents are less hypsodont than terrestrial species. These results as well as those of a posteriori analyses controlling for aspects of the behavioral ecology (e.g., grass-eating, substrate preference) of the sample species confirm the role of both diet and grit in shaping the evolution of cheek tooth crown height in herbivorous mammals.     

利用全测序基因组数据对被子植物纤维素合成酶基因的进化分析

利用已经分离的植物纤维素合成酶基因的Cellulose_synt结构域为检索序列,从NCBI和其他数据库中调取已完成测序的物种的纤维素合成酶的氨基酸序列,共涉及10个物种的171个基因,基于以上氨基酸序列,应用MEGA4.0生成系统进化树。结果表明:CesA基因和Csl基因直向的相似度远大于平行的相似度,且它们的分化可能在单子叶和真双子叶植物分化之前,单子叶和真双子叶植物的最近共同祖先中至少存在7个CesA基因,综合已知的模式植物CesA基因的功能(初生壁或次生壁形成特异性),可为推测其他物种中该基因的功能提供帮助。     

Parental care: a freshwater phenomenon?

Synopsis Attempts have been made to explain the over-representation of parental care in teleost fish families in freshwater habitats by selection due to environmental conditions typical of freshwater. I argue that alternative hypotheses, such as selection for pelagic spawning in marine habitats, can account for the pattern. The fact that parental care is less common among primary freshwater fishes contradicts the view that there is strong selection for parental care in fresh waters, and suggests that phylogenetic relationships must be taken into account.     

Testing the genetic constraint hypothesis in a phylogenetic context: a simulation study

Quantitative genetic theory predicts that when populations diverge by drift the interspecific divergence (D matrix), calculated from species means, will be proportional to the average value of the additive genetic variance-covariance matrix, or G matrix. Most empirical studies in which this hypothesis has been investigated have ignored phylogenetic nonindependence among included taxa. Baker and Wilkinson (2003; also Revell et al. 2007) used a test for constraint in which the D matrix is calculated from phylogenetically independent contrasts (Felsenstein 1985) instead of directly from the species means. I use computer simulations to show that, on average, when the process of evolution is genetic drift, the divergence matrix calculated from independent contrasts (D(IC)) is more highly correlated with G than is the divergence matrix calculated ignoring phylogenetic nonindependence (D). This effect is more pronounced when speciation is initially slow but increases over time than when speciation decreases over time. Finally, when evolution is primarily by drift but phenotype space is bounded (as if by functional constraint) the average correlation is decreased between both G and D or D(IC), however the correlation between G and D(IC) is much larger than between G and D. Although limited in scope, to my knowledge this is the first study to use individual-based quantitative genetic simulations in a phylogenetic context.     

四种胃蛋白酶原检测试剂的性能比较

目的:比较四种胃蛋白酶原检测试剂的性能。方法:使用Beckman Coulter AU5800全自动生化分析仪,采用免疫比浊法,对两种国产和两种进口蛋白酶原检测试剂的校准和质控、精密度、线性范围、检测灵敏度、前带反应影响和抗干扰能力进行比较。结果:四家公司的校准和质控指标均达到合格标准,两家进口试剂变异系数较小,在线性、准确性、灵敏度、前带反应等指标全面领先。结论:综合各项指标判断,目前使用的胃蛋白酶原检测试剂以两种进口产品性能为佳,国产品尚有一定差距。     

欧亚大陆分布的大花菟丝子叶绿体基因组插入缺失分析

运用鸟枪法在Illumina测序仪上对亚洲分布的大花菟丝子(Cuscuta reflexa叶绿体基因组核苷酸全序列进行测定,并与已经发表的分布于欧洲的大花菟丝子进行了比较分析.研究结果表明亚洲分布的大花菟丝子叶绿体基因组总长度为120 972 bp,由79 499 bp的长单拷贝区,8 369 bp的短单拷贝区,以及两个16 552 bp的反向重复区组成,其长度比欧洲分布的大花菟丝子小了549 bp;基因组总GC含量为38.3％,稍高于欧洲分布的大花菟丝子.两地区的大花菟丝子叶绿体全基因组编码的功能基因完全相同,且基因排列顺序也完全一致.另外,经过进一步序列比对后发现亚洲分布的大花菟丝子与欧洲分布的存在251个插入和210个缺失现象,总插入缺失及碱基替换长度分别为7 649 bp和3 720 bp,最大的插入和缺失长度分别为426 bp和435 bp.很多插入缺失都是单碱基,但仍然存在四个长度超过200 bp的大突变,两个大的缺失发生在ycf2基因中,两个大的插入分别发生在trn F-psbE和matK-trnQ间隔区,详细的对比后发现大量的插入缺失都发生在大单拷贝区的基因间隔区,且插入缺失在反向重复区的发生频率较低.本研究首次报道不同大洲分布的同种异养植物的叶绿体全基因组比较分析,为研究这两个区域的居群多样性提供了基础资料.