Estimating repertoire size in a songbird: a comparison of three techniques

Many animals produce multiple types of breeding vocalizations that, together, constitute a vocal repertoire. In some species, the size of an individual’s repertoire is important because it correlates with brain size, territory size or social behaviour. Quantifying repertoire size is challenging because the long recordings needed to sample a repertoire comprehensively are difficult to obtain and analyse. The most basic quantification technique is simple enumeration, where one counts unique vocalization types until no new types are detected. Alternative techniques estimate repertoire size from subsamples, but these techniques are useful only if they are accurate. Using 12 years of acoustic data from a population of rufous-and-white wrens in Costa Rica, we used simple enumeration to measure the repertoire size for 40 males. We then compared these to the estimates generated by three estimation techniques: curve fitting, capture–recapture and a new technique based on the coupon collector’s problem. To understand how sampling effort affects the accuracy and precision of estimates, we applied each technique to six different-sized subsets of data per male. When averaged across subset sizes, the capture–recapture and coupon collector techniques showed the highest accuracy, whereas the curve fitting technique underestimated repertoire size. Precision (the average absolute difference between the estimated and true repertoire size) was significantly better for the capture–recapture technique than the coupon collector and curve fitting techniques. Both accuracy and precision improved as subset size increased. We conclude that capture–recapture is the best technique for estimating the sizes of small repertoires.     

Ig V kappa family repertoire of plasma cells derived from autoimmune MRL mice.

V kappa gene family usage was determined in the resident in vivo-activated plasma cells of individual diseased MRL mice by using in situ hybridization. In this way, the entire autoimmune repertoire could be analyzed. Autoantibody levels and extent of glomerulonephritis were also measured, so that the severity of disease could be assessed. It was found that V kappa expression was highly variable from mouse to mouse. Some animals displayed a V kappa family repertoire similar to mitogen-stimulated cells and consistent with the size of the families. These animals tended to have lower disease indices. Other animals, which had higher disease indices, displayed considerable over- or underutilization of individual V kappa families. However, no particular V kappa families were repeatedly biased in their expression, as was found at the VH level with J558. Importantly, in the 10% of animals that expressed VH J558 exclusively, four or more V kappa families were expressed and multiple antiself specificities were produced. The data are most consistent with a number of J558 genes being expanded in a variety of self-specificities. However, because only VH J558 is expressed in these sicker animals, nonspecific polyclonal activation is highly unlikely. These results underscore the continuing evolution of the autoimmune repertoire, with considerable diversity at early stages followed by a highly selected repertoire in which a potential role for nonspecific polyclonal activation is virtually excluded.     

Leaf Processing by Wild Chimpanzees: Physically Defended Leaves Reveal Complex Manual Skills

The manual processing of eight species of leaf was investigated in the M‐group chimpanzees of Mahale Mountains National Park, Tanzania. Leaf species varied in the extent to which physical defences made consumption difficult. In all, 96 distinct techniques for leaf processing were identified, but two species with defended leaves (Ficus asperifolia and F. exasperata) required 2.5 as many techniques as did any of the six undefended species. Moreover, chimpanzees made more multiple leaf detachments, and made more subsequent modifications of the leaves, when dealing with the leaves of these two Ficus species, compared with the undefended leaf species. This greater complexity was associated with evidence of flexible, hierarchical organization of the process: iteration of modules consisting of several processing elements, facultative omission of modules, or substitutions of alternative modules. Comparison with data from mountain gorillas is made, and is consistent with similar cognitive architecture in the two species. We consider that, not only is hierarchical organization currently associated with mechanical difficulty in food processing, but that over evolutionary time‐scales difficulties in food processing may have selected for cognitive advance.     

Element repertoire: change and development with age in Whitethroat Sylvia communis song

Song repertoires are often important determining factors in sexual selection. In several species, older males have larger repertoires than 1-year-old males. The development of large song repertoires by an individual is, however, poorly understood. We studied song element repertoire changes in five individual male Whitethroats Sylvia communis sampled as 1- and 2-year olds. These males increased the size of their element repertoire between their first and second year, but song length and number of different elements per song did not change. On average, 44.3% of the song elements in the first-year repertoire were also found in the second-year repertoire. Elements shared between years were found earlier in the songs and tended to occur in sequences. Sequences of shared elements also seemed to be conserved between years. The study suggests that the song element repertoire of the second year is partly based on the first-year repertoire, which may explain why large song repertoires are mainly expressed by males at least 2 years of age. It would appear, therefore, that song element repertoire size could be a reliable signal of male age.     

茶树CsCCD基因家族全基因组鉴定及乌龙茶LED补光晾青下表达分析

类胡萝卜素裂解双加氧酶(carotenoid cleavage dioxygenase, CCD)家族成员能催化类胡萝卜素裂解生成挥发性芳香物质并参与植物激素的合成。为探究茶树CsCCD基因家族成员生物学功能及基因表达模式,采用生物信息学手段进行了茶树全基因组CsCCD基因家族成员的鉴定,预测分析了其基因结构、保守基序、染色体定位、蛋白的理化性质、进化特性、互作网络、启动子顺式作用元件,并通过RT-qPCR测定了茶树不同叶位、乌龙茶加工过程中光照处理下CsCCD的相对表达量。共鉴定出11个茶树CsCCD基因家族成员,含有1–11个外显子、0–10个内含子不等;平均氨基酸个数为519 aa,平均分子质量为57 643.35 Da;聚类分析显示,CCD1、CCD4、CCD7、CCD8和NCED5个亚族各自聚成一类。茶树CsCCD基因家族主要含有胁迫响应元件、激素响应元件、光响应元件与多因素响应元件,且以光响应元件最多(142个)。进一步对茶树CsCCD基因在茶树不同叶位及乌龙茶加工过程中LED补光晾青过程的表达模式分析发现,CsCCD1、CsCCD4在成熟叶中表达量高于嫩叶及嫩茎,且随做青...     

Elemental variation in the termite fishing of wild chimpanzees (Pan troglodytes)

Chimpanzee tool behaviours vary dramatically in their complexity and extent of geographical distribution. The use of tool sets with specific design features to gather termites extends across a large portion of central Africa. Detailed examination of the composition and uniformity of such complex tool tasks has the potential to advance our understanding of the cognitive capabilities of tool users and processes underlying the maintenance of technological skills. In this study, we examined variation in chimpanzee tool use in termite gathering from video-recorded sequences that were scored to the level of functionally distinct behavioural elements. Overall, we found a high degree of similarity in tool-using techniques exhibited by individuals in this population. The number of elements in each individual's repertoire often exceeded that necessary to accomplish the task, with consistent differences in repertoire sizes between age classes. Adults and subadults had the largest repertoires and more consistently exhibited element strings than younger individuals. Larger repertoires were typically associated with incorporation of rare variants, some of which indicate flexibility and intelligence. These tool using apes aid us in understanding the evolution of technology, including that of our human ancestors, which showed a high degree of uniformity over large spatial scales.     

Vertebral pathology in the afar australopithecines

Ten vertebral elements from the AL-288 partial hominid skeleton and 11 elements from the AL-333 collection are described. The AL-288 column presents a marked kyphosis at the level of thoracic vertebrae 6 through 10, with pronounced new bone formation on the ventral surfaces of these vertebrae. These features, associated with narrowed disc space and minor osteophytosis, resemble Scheuermann disease in the human. Even though this diagnosis is consistent with a basically human, bipedal locomotor repertoire, the presence of Scheuermann disease suggests that lifting, climbing, or acrobatic activities may have been important in early hominids.     

Thermal biology and mate acquisition in ectotherms

Many elements of the behavioural repertoire of ectothermic animals depend on body temperature. Under differing thermal conditions, behaviours in insects, reptiles and other terrestrial ectotherms may therefore vary widely, and in any given thermal regime there may be simple physical and physiological character differences between individuals that lead to a predictable variation of behaviour. Where mating behaviour patterns are involved, digferential fitness may result. Recent studies show that the interactions of physiology with behavioural ecology should be a fruitful area for future research.     

Rearing infant monkeys (Macaca nemestrina) in pairs produces deficient social development compared with rearing in single cages

Many scientists and colony managers assume that social housing is a beneficial living condition for all captive primates. Several older studies of primate development question the generality of this assumption. We recently tested this assumption by comparing the social development of pigtailed macaque infants raised in pairs and those that were raised in individual cages. All animals received 30 min of daily socialization in a playroom. Infants paired from postnatal week 3 through month 4 developed a playroom behavioral repertoire consisting largely of mutual clinging, fear, and social withdrawal. This was especially true of females. Unlike the singly caged infants, pair-reared monkeys did not successfully adapt to living in a large social group at 8–10 months of age. In this situation, pair-reared infants were subordinate and spent almost all of their time huddling on the pen floor. It was concluded that rearing macaque infants in pairs produces a behavioral repertoire that is maladaptive with respect to social development.     

Relationships between xylem sap constituents and leaf conductance of well-watered and water-stressed maize across three xylem sap sampling techniques

Many different techniques have been used for xylem sap collection, but few direct comparisons of techniques have been conducted and few comparisons have been based on comprehensive analyses of xylem sap. Moreover, the suitability of extraction techniques for use on plants grown under water-stress conditions has not been addressed. Xylem sap was extracted from both well-watered and water-stressed Zea mays plants using three different techniques. The main aim was to determine how the extraction method altered the correlations between sap constituents and stomatal conductance in order to determine which relationships change with extraction technique. A 'root pressure' technique was the simplest method of extracting large volumes of sap, but the low sap delivery rates altered the composition of sap. Two pressurization techniques that varied in the position from which sap was collected were tested. The pressurization techniques allowed for the control of delivery rates that influence sap constituent concentrations. The position from which xylem sap was collected on the plant was also found to be important. All three techniques produced consistent correlations between ABA and chloride delivery rates and changes in stomatal conductance, suggesting that each technique could be applied to identify certain putative xylem-borne signals.     

The composition of the T cell receptor repertoire in nude mice

Previous results from several laboratories have demonstrated the presence of functional T lymphocytes in congenitally athymic (nude) mice. The present study represents an analysis of the T cell receptor repertoire exhibited by such cells. Clones of H-2Kb-specific cytotoxic T lymphocytes (CTL) were generated under primary limiting dilution conditions by using spleen cells from nude mice. These clones were analyzed on a panel of Kb mutant target cells to assess the receptor specificity of each clone. Unlike thymic bearing mice the CTL repertoires of which are exceedingly diverse, it was found that in most cases the vast majority of clones from each individual exhibited the same reactivity pattern. The particular pattern varied from individual to individual. Clones from three animals that exhibited this phenomenon were additionally analyzed by using a monoclonal antibody that can detect the utilization of the gene products of the V beta 8 family. In one animal all clones were V beta 8 positive, whereas in the others, all clones were negative. We conclude that the T cell receptor repertoire in nude mice is extremely limited and represents in vivo expansion of a relatively small number of functional precursors.     

The evolution of courtship display repertoire size in the dabbling ducks (Anatini)

Many animals possess multiple ornaments or behaviours that seem to have evolved via sexual selection. A complete understanding of sexual selection requires an explanation for such multiple traits. The dabbling ducks (Tribe: Anatini) exhibit considerable variation among species in the number of displays in the male courtship repertoire. I tested five hypotheses concerning the evolution of the variation in display repertoire size of dabbling ducks: (1) species recognition, (2) courtship habitat, (3) sexual selection intensity, (4) display media tradeoff and (5) time constraints on pair formation. I tested these hypotheses, using an explicit phylogenetic hypothesis developed from DNA sequences for the dabbling ducks, with two types of statistical comparative methods (discrete and continuous character). The variation observed in male courtship display repertoire size in dabbling ducks was consistent with the courtship habitat and sexual selection intensity hypotheses. Specifically, the size of the display repertoire was larger in species that exhibit courtship exclusively on water and larger in species with dimorphic plumage. These results suggest that ecological (habitat) as well as social (sexual selection) factors may be important in driving the evolution of displays in the dabbling ducks.     

An automated program to find animals and crop photographs for individual recognition

Detailed data on individual animals are critical to ecological and evolutionary studies, but attaching identifying marks can alter individual fates and behavior leading to biases in parameter estimates and ethical issues. Individual-recognition software has been developed to assist in identifying many species from non-invasive photographic data. These programs utilize algorithms to find unique individual characteristics and compare images to a catalogue of known individuals. Currently, all applications for individual identification require manual processing to crop images so only the area of interest remains, or the area of interest must be manually delineated in each image. Thus, one of the main bottlenecks in processing data from photographic capture-recapture surveys is in cropping to an area of interest so that matching algorithms can identify the individual. Here, we describe the development and testing of an automated cropping program. The methods and techniques we describe are broadly applicable to any system where raw photos must be cropped down to a specific area of interest before pattern recognition software can be used for individual identification. We developed and tested the program for use with identification photos of wild giraffes.     

Density dependence is not very prevalent in a heterogeneous subtropical forest

There is a growing body of evidence demonstrating that tree survival is influenced by negative density‐dependence, but it is still controversial how the effect may vary with life‐stage, and to what extent it plays a role in regulating tree survival in heterogeneous subtropical forests. In this study, we investigated density‐dependent effects on tree survival of six tree species in a 5‐ha subtropical forest in eastern China. The roughly 45 000 individuals in the forest were fully censused in 2003 and 2008. For each of these species, we used an inhomogeneous pair‐correlation function to quantify the change in spatial distribution for different size classes, and a case‐control design to study seedling–adult associations in 2003. Autologistic regression was used to determine the influence of neighborhood factors on individual survival from 2003 to 2008. We found that seedlings of five species were repulsed by distance to nearest conspecific adults in terms of their survival, consistent with predictions of the Janzen–Connell mechanism. By contrast, only the least shade‐tolerant Schima superba had a negative relationship with individual survival and conspecific distance‐weighted basal area. This suggests that the Janzen–Connell effect is only prevalent at the early seedling stage or seed‐to‐seedling phase. The strength of clustering significantly declined at sapling–pole and pole–adult transitions for Sycopsis sinensis and at seedling–sapling transition for Cleyera pachyphylla. Correlations between individual survival and conspecific abundance for these species were consistent with trends in the strength of clustering. These results suggest that density dependence plays a limited role in individual survival and species spatial structure beyond the early seedling stage (i.e. after true leaves growing) in this forest. In addition, this study indicates that including individuals from early life‐stages and factoring out potential confounding factors such as habitat preference are important in studies that seek evidence for density dependence in forest trees.     

The modularity of biological regulatory networks

A useful approach to complex regulatory networks consists of modeling their elements and interactions by Boolean equations. In this context, feedback circuits (i.e. circular sequences of interactions) have been shown to play key dynamical roles: whereas positive circuits are able to generate multistationarity, negative circuits may generate oscillatory behavior. In this paper, we principally focus on the case of gene networks. These are represented by fully connected Boolean networks where each element interacts with all elements including itself. Flexibility in network design is introduced by the use of Boolean parameters, one associated with each interaction or group of interactions affecting a given element. Within this formalism, a feedback circuit will generate its typical dynamical behavior (i.e. multistationarity or oscillations) only for appropriate values of some of the logical parameters. Whenever it does, we say that the circuit is 'functional'. More interestingly, this formalism allows the computation of the constraints on the logical parameters to have any feedback circuit functional in a network. Using this methodology, we found that the fraction of the total number of consistent combinations of parameter values that make a circuit functional decreases geometrically with the circuit length. From a biological point of view, this suggests that regulatory networks could be decomposed into small and relatively independent feedback circuits or 'regulatory modules'.     

Ion competition effects on the selective absorption of radionuclides by komatsuna (Brassica rapa var. perviridis)

The selective absorption coefficient, which is a parameter of an uptake model of radionuclides by plants, was determined for various radionuclides by a multitracer technique. Komatsuna, Brassica rapa var. perviridis, was hydroponically cultivated in a nutrient solution containing a multitracer for 1 day. Nutrient concentration dependence of the selective absorption coefficient of various elements from Be to Re was obtained separately for leaves and roots. The selective absorption coefficients of these elements were, in general, found to decrease with an increase in the concentration of nutrient solutions. Regression equations of the power function for the selective absorption coefficients and the concentration of nutrient solutions were obtained for the leaves and roots. The effects of photon flux and growth stage of plants on the selective absorption coefficients were also studied. It was found that the photon flux influenced the accumulation of radionuclides in the roots but had no significant effect on the selective absorption coefficients for the leaves in 1-day cultivation with the multitracer. The selective absorption coefficients of Mn and Zn in the leaves of the plants at the development stage were higher than those at the maturation stage. For the other elements, no significant effects of the growth stage on the selective absorption coefficients were observed.     

Development of the macronuclear anlage in the ciliate Chilodonella uncinata

The development of the macronuclear anlage in C. uncinata occurs in three steps. During stage I, distinct Feulgen-positive elements are visible in the anlage. Along with the increase in the volume of the anlage, the DNA content of the latter increases from 2 C to about 32 C, indicating four cycles of replication. Simultaneously, the number of Feulgen-positive elements also increases, suggesting that these bodies represent the individual chromosomes and that after each duplication cycle, the daughter chromosomes fall apart. During stage II, the anlage increases greatly in volume and shows a diffused Feulgen stain, in which no structured elements are discernible. During stage III, small Feulgen-positive granules reappear inside the anlage, and gradually become bigger as well as more numerous; at the same time the anlage as a whole starts condensing and becomes more and more densely staining, until it attains the appearance of a vegetative macronucleus about to divide. During stages II and III, the DNA content of the macronuclear anlage goes on increasing, until it nearly reaches the G₂ value of the vegetative macronucleus, which is about 128 C. The problem as to whether there is an elimination of some DNA in between stages I and II has however not yet been resolved and needs further study.