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.     

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.     

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.     

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 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.     

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.     

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.     

Comparative genomic analysis of CIPK gene family in <Emphasis Type="Italic">Arabidopsis</Emphasis> and <Emphasis Type="Italic">Populus</Emphasis>

Calcium serves as a second messenger in various signal transduction pathways in plants. CBL-interacting protein kinases (CIPKs), which have a variety of functions, are involved in calcium signal transduction. Previous, the studies on CIPK family members focused on Arabidopsis and rice. Here, we present a comparative genomic analysis of the CIPK gene family in Arabidopsis and poplar, a model tree species. Twenty-seven potential CIPKs were identified from poplar using genome-wide analysis. Like the CIPK gene family from Arabidopsis, CIPK genes from poplar were also divided into intron-free and intron-harboring groups. In the intron-harboring group, the intron distribution of CIPKs is rather conserved during the genome evolutionary process. Many homologous gene pairs were found in the CIPK gene family, indicating duplication events might contribute to the amplification of this gene family. The phylogenetic comparison of CIPKs in combination with intron distribution analysis revealed that CIPK genes from both Arabidopsis and poplar might have an ancient origin, which formed earlier than the separation of these two eudicot species. Our genomic and bioinformatic analysis will provide an important foundation for further functional dissection of the CBL-CIPK signaling network in poplars. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Comparative protein analysis of the chitin metabolic pathway in extant organisms: A complex network approach

Chitin is a structural endogenous carbohydrate, which is a major component of fungal cell walls and arthropod exoskeletons. A renewable resource and the second most abundant polysaccharide in nature after cellulose, chitin is currently used for waste water clearing, cosmetics, medical, and veterinary applications. This work comprises data mining of protein sequences related to the chitin metabolic pathway of completely sequenced genomes of extant organisms pertaining to the three life domains, followed by meta-analysis using traditional sequence similarity comparison and complex network approaches. Complex networks involving proteins of the chitin metabolic pathway in extant organisms were constructed based on protein sequence similarity. Several usual network indices were estimated in order to obtain information on the topology of these networks, including those related to higher order neighborhood properties. Due to the assumed evolutionary character of the system, we also discuss issues related to modularity properties, with the concept of edge betweenness playing a particularly important role in our analysis. Complex network approach correctly identifies clusters of organisms that belong to phylogenetic groups without any a priori knowledge about the biological features of the investigated protein sequences. We envisage the prospect of using such a complex network approach as a high-throughput phylogenetic method.     

Relaxed Neighbor Joining: A Fast Distance-Based Phylogenetic Tree Construction Method

Our ability to construct very large phylogenetic trees is becoming more important as vast amounts of sequence data are becoming readily available. Neighbor joining (NJ) is a widely used distance-based phylogenetic tree construction method that has historically been considered fast, but it is prohibitively slow for building trees from increasingly large datasets. We developed a fast variant of NJ called relaxed neighbor joining (RNJ) and performed experiments to measure the speed improvement over NJ. Since repeated runs of the RNJ algorithm generate a superset of the trees that repeated NJ runs generate, we also assessed tree quality. RNJ is dramatically faster than NJ, and the quality of resulting trees is very similar for the two algorithms. The results indicate that RNJ is a reasonable alternative to NJ and that it is especially well suited for uses that involve large numbers of taxa or highly repetitive procedures such as bootstrapping. [Reviewing Editor: Dr. James Bull]     

A new method for calculating Risk Tolerance in the assessment of threatened flora

This paper reports on a proposed method for evaluating threat categories for regional flora, based mainly on phytogeographical data. The method involves the creation of current distribution maps, analysis of threat factors and use of the RAMAS Red List software to facilitate rapid and objective classification of taxa in accordance with 2001 IUCN criteria. In order to ensure a more objective approach by the assessor and reduce the range of uncertainty, an index was created for calculating Risk Tolerance (RT) that enabled adjustment of the results obtained and thus supplemented the software used. For trial purposes, the proposed model was applied to Spanish gypsophilous flora currently protected under Spanish regional legislation. When classified using the new model, the taxa in question were placed in very different categories, ranging from least concern (LC) to endangered (EN), indicating the need to redefine both their current legal status and recommended management measures. Use of this method will enable scientists to optimise available information on the geographical distribution of endangered taxa, and help governments both to optimise their financial investment in conservation and to define their priorities. The authors endorse the use of IUCN categories in legal protection texts, and advocate as essential a greater degree of coordination between scientists and governments.     

哺乳动物NMDA受体NR3亚基的比较基因组学研究

目的：通过比较基因组学方法对哺乳动物NR3亚基进行分析,探讨其种间功能及结构差异,并预测其功能。方法：应用人类NR3A和NR3B所编码氨基酸序列作为检索探针,通过TBLASTN检索数据库,并应用生物软件进行进化分析及序列对比。结果：共检索到30个哺乳动物NR3A及NR3B基因,其中28个具有完整CDS。进化树显示相同种属均形成独立分支,与人类相似度越高的物种进化距离越近,氨基酸种间比较显示邻接半胱氨酸序列及loopl结构保守性较好,而富含脯氨酸序列在灵长类和啮齿类存在差异。结论：NR3A亚基在人类和啮齿类可能存在功能差异,应用动物模型进行实验应考虑差异可能带来的影响,此外,可推断哺乳动物间NR3亚基富含半胱氨酸序列及loopl结构产生的生理过程及功能相似。     

Phylogenetic and Comparative Sequence Analysis of Thermostable Alpha Amylases of kingdom Archea,Prokaryotes and Eukaryotes

Alpha amylase family is generally defined as a group of enzymes that can hydrolyse and transglycosylase α-(1, 4) or α-(1, 6) glycosidic bonds along with the preservation of anomeric configuration. For the comparative analysis of alpha amylase family, nucleotide sequences of seven thermo stable organisms of Kingdom Archea i.e. Pyrococcus furiosus (100-105°C), Kingdom Prokaryotes i.e. Bacillus licheniformis (90-95°C), Geobacillus stearothermophilus (75°C), Bacillus amyloliquefaciens (72°C), Bacillus subtilis (70°C) and Bacillus KSM K38 (55°C) and Eukaryotes i.e. Aspergillus oryzae (60°C) were selected from NCBI. Primary structure composition analysis and Conserved sequence analysis were conducted through Bio Edit tools. Results from BioEdit shown only three conserved regions of base pairs and least similarity in MSA of the above mentioned alpha amylases. In Mega 5.1 Phylogeny of thermo stable alpha amylases of Kingdom Archea, Prokaryotes and Eukaryote was handled by Neighbor-Joining (NJ) algorithm. Mega 5.1 phylogenetic results suggested that alpha amylases of thermo stable organisms i.e. Pyrococcus furiosus (100-105°C), Bacillus licheniformis (90-95°C), Geobacillus stearothermophilus (75°C) and Bacillus amyloliquefaciens (72°C) are more distantly related as compared to less thermo stable organisms. By keeping in mind the characteristics of most thermo stable alpha amylases novel and improved features can be introduced in less thermo stable alpha amylases so that they become more thermo tolerant and productive for industry.     

Dead Shrimp Blues: A Global Assessment of Extinction Risk in Freshwater Shrimps (Crustacea: Decapoda: Caridea)

We present the first global assessment of extinction risk for a major group of freshwater invertebrates, caridean shrimps. The risk of extinction for all 763 species was assessed using the IUCN Red List criteria that include geographic ranges, habitats, ecology and past and present threats. The Indo-Malayan region holds over half of global species diversity, with a peak in Indo-China and southern China. Shrimps primarily inhabit flowing water; however, a significant subterranean component is present, which is more threatened than the surface fauna. Two species are extinct with a further 10 possibly extinct, and almost one third of species are either threatened or Near Threatened (NT). Threats to freshwater shrimps include agricultural and urban pollution impact over two-thirds of threatened and NT species. Invasive species and climate change have the greatest overall impact of all threats (based on combined timing, scope and severity of threats).