Comparing phylogenetic signal in intraspecific and interspecific body size datasets

Phylogenetic comparative methods have become a standard statistical approach for analysing interspecific data, under the assumption that traits of species are more similar than expected by chance (i.e. phylogenetic signal is present). Here I test for phylogenetic signal in intraspecific body size datasets to evaluate whether intraspecific datasets may require phylogenetic analysis. I also compare amounts of phylogenetic signal in intraspecific and interspecific body size datasets. Some intraspecific body size datasets contain significant phylogenetic signal. Detection of significant phylogenetic signal was dependant upon the number of populations (n) and the amount of phylogenetic signal (K) for a given dataset. Amounts of phylogenetic signal do not differ between intraspecific and interspecific datasets. Further, relationships between significance of phylogenetic signal and sample size and amount of phylogenetic signal are similar for intraspecific and interspecific datasets. Thus, intraspecific body size datasets are similar to interspecific body size datasets with respect to phylogenetic signal. Whether these results are general for all characters requires further study.     

The best of both worlds: Phylogenetic eigenvector regression and mapping

Eigenfunction analyses have been widely used to model patterns of autocorrelation in time, space and phylogeny. In a phylogenetic context, Diniz-Filho et al. (1998) proposed what they called Phylogenetic Eigenvector Regression (PVR), in which pairwise phylogenetic distances among species are submitted to a Principal Coordinate Analysis, and eigenvectors are then used as explanatory variables in regression, correlation or ANOVAs. More recently, a new approach called Phylogenetic Eigenvector Mapping (PEM) was proposed, with the main advantage of explicitly incorporating a model-based warping in phylogenetic distance in which an Ornstein-Uhlenbeck (O-U) process is fitted to data before eigenvector extraction. Here we compared PVR and PEM in respect to estimated phylogenetic signal, correlated evolution under alternative evolutionary models and phylogenetic imputation, using simulated data. Despite similarity between the two approaches, PEM has a slightly higher prediction ability and is more general than the original PVR. Even so, in a conceptual sense, PEM may provide a technique in the best of both worlds, combining the flexibility of data-driven and empirical eigenfunction analyses and the sounding insights provided by evolutionary models well known in comparative analyses.     

The effect of body size and habitat on the evolution of alarm vocalizations in rodents

When confronted with a predator, many mammalian species emit vocalizations known as alarm calls. Vocal structure variation results from the interactive effects of different selective pressures and constraints affecting their production, transmission, and detection. Body size is an important morphological constraint influencing the lowest frequencies that an organism can produce. The acoustic environment influences signal degradation; low frequencies should be favoured in dense forests compared to more open habitats (i.e. the ‘acoustic adaptation hypothesis’). Such hypotheses have been mainly examined in birds, whereas the proximate and ultimate factors affecting vocalizations in nonprimate mammals have received less attention. In the present study, we investigated the relationships between the frequency of alarm calls, body mass, and habitat in 65 species of rodents. Although we found the expected negative relationship between call frequency and body mass, we found no significant differences in acoustic characteristics between closed and open‐habitat species. The results of the present study show that the acoustic frequencies of alarm calls can provide reliable information about the size of a sender in this taxonomic group, although they generally do not support the acoustic adaptation hypothesis.     

Comparative bioacoustics: a roadmap for quantifying and comparing animal sounds across diverse taxa

Animals produce a wide array of sounds with highly variable acoustic structures. It is possible to understand the causes and consequences of this variation across taxa with phylogenetic comparative analyses. Acoustic and evolutionary analyses are rapidly increasing in sophistication such that choosing appropriate acoustic and evolutionary approaches is increasingly difficult. However, the correct choice of analysis can have profound effects on output and evolutionary inferences. Here, we identify and address some of the challenges for this growing field by providing a roadmap for quantifying and comparing sound in a phylogenetic context for researchers with a broad range of scientific backgrounds. Sound, as a continuous, multidimensional trait can be particularly challenging to measure because it can be hard to identify variables that can be compared across taxa and it is also no small feat to process and analyse the resulting high-dimensional acoustic data using approaches that are appropriate for subsequent evolutionary analysis. Additionally, terminological inconsistencies and the role of learning in the development of acoustic traits need to be considered. Phylogenetic comparative analyses also have their own sets of caveats to consider. We provide a set of recommendations for delimiting acoustic signals into discrete, comparable acoustic units. We also present a three-stage workflow for extracting relevant acoustic data, including options for multivariate analyses and dimensionality reduction that is compatible with phylogenetic comparative analysis. We then summarize available phylogenetic comparative approaches and how they have been used in comparative bioacoustics, and address the limitations of comparative analyses with behavioural data. Lastly, we recommend how to apply these methods to acoustic data across a range of study systems. In this way, we provide an integrated framework to aid in quantitative analysis of cross-taxa variation in animal sounds for comparative phylogenetic analysis. In addition, we advocate the standardization of acoustic terminology across disciplines and taxa, adoption of automated methods for acoustic feature extraction, and establishment of strong data archival practices for acoustic recordings and data analyses. Combining such practices with our proposed workflow will greatly advance the reproducibility, biological interpretation, and longevity of comparative bioacoustic studies.     

Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species

Ecologists are increasingly adopting an evolutionary perspective, and in recent years, the idea that closely related species are ecologically similar has become widespread. In this regard, phylogenetic signal must be distinguished from phylogenetic niche conservatism. Phylogenetic niche conservatism results when closely related species are more ecologically similar that would be expected based on their phylogenetic relationships; its occurrence suggests that some process is constraining divergence among closely related species. In contrast, phylogenetic signal refers to the situation in which ecological similarity between species is related to phylogenetic relatedness; this is the expected outcome of Brownian motion divergence and thus is necessary, but not sufficient, evidence for the existence of phylogenetic niche conservatism. Although many workers consider phylogenetic niche conservatism to be common, a review of case studies indicates that ecological and phylogenetic similarities often are not related. Consequently, ecologists should not assume that phylogenetic niche conservatism exists, but rather should empirically examine the extent to which it occurs.     

Phylogenetic analysis of interspecific variation in nectar of hummingbird-visited plants

We tested whether phylogeny, flower size and/or altitude were significant predictors of interspecific variation in nectar production of hummingbird-visited plants in an assembled database (289 species, in 22 orders, 56 families and 131 genera). Although the study is focused on hummingbird-pollinated plants (241 plant species), plants with different pollinator syndromes (48 species) are also included in the analyses. Nectar volume secreted in a given time period (usually 24 h) by a given flower, its sugar concentration and corolla length were compiled mainly from the literature. Altitude was also obtained from the original references. Sugar production was computed basically as the product of nectar secretion and sugar concentration, and expressed on a per 24-h basis. All nectar traits and corolla length (all log transformed), as well as altitude, showed statistically significant phylogenetic signal. Both nonphylogenetic and phylogenetically informed (independent contrasts) analyses indicated a highly significant positive correlation between corolla length and both nectar volume and sugar production. In addition, altitude (which is partially a surrogate for temperature) was significantly negatively correlated with both sugar concentration and production. Possible reasons for coadaptation of nectar production and sugar production with corolla length are discussed.     

Phylogenetic Correlation Between Male Nuptial Color and Behavioral Responses to Color Across a Diverse and Colorful Genus of Freshwater Fish (Etheostoma spp., Teleostei: Percidae)

Sexual selection theory predicts that preferences in both sexes select for the elaboration of male nuptial coloration, with empirical evidence supporting these predictions. Empirical studies are often limited in their taxonomic inclusiveness, however, and typically do not examine how male and female preferences contribute to macroevolutionary patterns of male color variation across multiple lineages in a clade. This study examined color preferences in a group of dichromatic freshwater fishes known as darters (genus Etheostoma) that vary in the presence of male coloration. The strengths of attraction to black, blue, gray, and red models were tested in females of 18 species, in addition to males of five species. We found a positive association between the presence of red or orange on the body and the amount of time associating with red models, suggesting color variation is at least in part due to variation in female preferences between species. Males also spent more time associating with colors that most closely resembled conspecifics, suggesting that preferential responses to color in males also can contribute to the diversity of nuptial coloration in darters.     

农作物钾离子通道基因的生物信息学分析

以AtAKT1所编码的氨基酸序列为检索序列,通过对GenBank NR数据库以及EMBL、DDBJ、PDB数据库进行检索,发现水稻、小麦、大麦、玉米、烟草等作物中具有cds全长的34个疑似K~+通道基因.其中:水稻7个,玉米6个,烟草4个,马铃薯、胡萝卜、大麦各3个,葡萄、番茄各2个,蚕豆、小麦、油菜、甜瓜等各1个;有25个基因经过功能验证确定为K~+通道基因.利用比较基因组学,将剩余的9个基因确定为K~+通道基因.对34个K~+基因进化关系的分析表明,与AtAKT1的同源性较高的K~+通道基因为马铃薯的SKT1(相似性71%)、番茄的LKT1(相似性71%)、胡萝卜的DKT1(相似性69%)、烟草的NKT1(相似性62%).     

A comparison of individual distinctiveness in three vocalizations of the dwarf mongoose (Helogale parvula)

Individual specificity can be found in the vocalizations of many avian and mammalian species. However, it is often difficult to determine whether these vocal cues to identity rise from “unselected” individual differences in vocal morphology or whether they have been accentuated by selection for the purposes of advertising caller identity. By comparing the level of acoustic individuality of different vocalizations within the repertoire of a single species, it is possible to ascertain whether selection for individual recognition has modified the vocal cues to identity in particular contexts. We used discriminant function analyses to determine the level of accuracy with which calls could be classified to the correct individual caller, for three dwarf mongoose (Helogale parvula) vocalizations: contact, snake, and isolation calls. These calls were similar in acoustic structure but divergent in context and function. We found that all three call types showed individual specificity but levels varied with call type (increasing from snake to contact to isolation call). The individual distinctiveness of each call type appeared to be directly related to the degree of benefit that signalers were likely to accrue from advertising their identity within that call context. We conclude that dwarf mongoose signalers have undergone selection to facilitate vocal individual recognition, particularly in relation to the species’ isolation call.     

The evolutionary convergence of avian lifestyles and their constrained coevolution with species' ecological niche

The fit between life histories and ecological niche is a paradigm of phenotypic evolution, also widely used to explain patterns of species co-occurrence. By analysing the lifestyles of a sympatric avian assemblage, we show that species'' solutions to environmental problems are not unbound. We identify a life-history continuum structured on the cost of reproduction along a temperature gradient, as well as habitat-driven parental behaviour. However, environmental fit and trait convergence are limited by niche filling and by within-species variability of niche traits, which is greater than variability of life histories. Phylogeny, allometry and trade-offs are other important constraints: lifetime reproductive investment is tightly bound to body size, and the optimal allocation to reproduction for a given size is not established by niche characteristics but by trade-offs with survival. Life histories thus keep pace with habitat and climate, but under the limitations imposed by metabolism, trade-offs among traits and species'' realized niche.     

Reduced geographic variation in roars in different habitats rejects the acoustic adaptation hypothesis in the black-and-gold howler monkey (Alouatta caraya)

Vocalizations used for long-range communication must disperse without significant structural changes to be decoded by receivers. The acoustic adaptation hypothesis (AAH) holds that, since acoustic signals are influenced by the habitat in which they disperse, sounds will possess specific structural characteristics to diminish sound degradation. Additionally, vocalizations can also be influenced by genetics, anatomy, and/or cultural aspects. Here, we tested the AAH through quantitative comparisons of roars in four allopatric populations of the black-and-gold howler monkey (Alouatta caraya) across an environmental gradient from open to closed, in northeastern Argentina. At each site, we obtained good-quality recordings from three adult males, also between July and November 2013, conducted vegetation surveys (measuring tree density, canopy closure, and vertical structure), evaluated potential masking of roars by gathering environmental sound samples, and assessed sound attenuation of a synthetic tone at three different distances: 10 m (landmark reference distance), 50, and 100 m. We also tested the alternative hypothesis that acoustic properties of roars could be explained by population genetic divergence. Our results did not support the AAH. Although our four study sites were significantly different in vegetation structure, conforming to an open-to-closed gradient, roars of A. caraya were not different among populations. Likewise, although environmental sound differed between sites, we found no evidence of environmental sound affecting the acoustic properties of roars. The attenuation of the synthetic tone was only near significant at 100 m distance between both extreme sites from the environmental gradient. The four A. caraya study populations grouped into three genetically differentiated clusters. Since roar features were independent from population genetic clustering, we reject the genetic hypothesis too. The combination of high amplitude and low peak frequency of roars, coupled to small home range size and extensive overlap between neighboring groups, allows roars to keep their communication value across habitats without need of specific environmental tuning.     

Temporal variation and characterization of grunt sounds produced by Atlantic cod Gadus morhua and pollack Pollachius pollachius during the spawning season

Fine‐scale temporal patterning in grunt production and variation in grunt attributes in Atlantic cod Gadus morhua and pollack Pollachius pollachius was examined. Pollachius pollachius produced only a single sound type, the grunt, similar to that previously described for G. morhua. Sound production and egg production were correlated in P. pollachius but not in G. morhua. Only G. morhua displayed a strongly cyclical pattern, producing more grunts at night. Finer‐scale temporal patterning in grunt production was observed in both species which produced significantly fewer grunts following a period of high grunt production. These quieter periods lasted up to 45 min for P. pollachius and up to 1 h in G. morhua. Grunts were not always produced in isolation but organized into bouts in both species. Longer bouts were more frequent during periods of increased sound activity and were linked with changes in grunt characteristics including increased grunt duration, pulse duration and repetition period of each pulse combined with decreased dominant frequency. This study provides the first evidence of acoustic signalling being used by spawning P. pollachius and presents the most detailed analysis of the complexity of gadoid sound production.     

Exploring patterns of interspecific variation in quantitative traits using sequential phylogenetic eigenvector regressions

A number of metrics have been developed for estimating phylogenetic signal in data and to evaluate correlated evolution, inferring broad-scale evolutionary and ecological processes. Here, we proposed an approach called phylogenetic signal-representation (PSR) curve, built upon phylogenetic eigenvector regression (PVR). In PVR, selected eigenvectors extracted from a phylogenetic distance matrix are used to model interspecific variation. In the PSR curve, sequential PVR models are fitted after successively increasing the number of eigenvectors and plotting their R(2) against the accumulated eigenvalues. We used simulations to show that a linear PSR curve is expected under Brownian motion and that its shape changes under alternative evolutionary models. The PSR area, expressing deviations from Brownian motion, is strongly correlated (r= 0.873; P < 0.01) with Blomberg's K-statistics, so nonlinear PSR curves reveal if traits are evolving at a slower or higher rate than expected by Brownian motion. The PSR area is also correlated with phylogenetic half-life under an Ornstein-Uhlenbeck process, suggesting how both methods describe the shape of the relationship between interspecific variation and time since divergence among species. The PSR curve provides an elegant exploratory method to understand deviations from Brownian motion, in terms of acceleration or deceleration of evolutionary rates occurring at large or small phylogenetic distances.     

Phylogenetic analysis and in-depth characterization of functionally and structurally diverse CE5 cutinases

Cutinases are esterases that release fatty acids from the apoplastic layer in plants. As they accept bulky and hydrophobic substrates, cutinases could be used in many applications, ranging from valorization of bark-rich side streams to plastic recycling. Advancement of these applications, however, requires deeper knowledge of cutinases’ biodiversity and structure–function relationships. Here, we mined over 3000 members from carbohydrate esterase family 5 for putative cutinases and condensed it to 151 genes from known or putative lignocellulose-targeting organisms. The 151 genes were subjected to a phylogenetic analysis, which showed that cutinases with available crystal structures were phylogenetically closely related. We then selected nine phylogenic diverse cutinases for recombinant production and characterized their kinetic activity against para-nitrophenol substrates esterified with consecutively longer alkyl chains (pNP-C₂ to C₁₆). Each investigated cutinase had a unique activity fingerprint against the tested pNP substrates. The five enzymes with the highest activity on pNP-C₁₂ and C₁₆, indicative of activity on bulky hydrophobic compounds, were selected for in-depth kinetic and structure–function analysis. All five enzymes showed a decrease in k_cat values with increasing substrate chain length, whereas K_M values and binding energies (calculated from in silico docking analysis) improved. Two cutinases from Fusarium solani and Cryptococcus sp. exhibited outstandingly low K_M values, resulting in high catalytic efficiencies toward pNP-C₁₆. Docking analysis suggested that different clades of the phylogenetic tree may harbor enzymes with different modes of substrate interaction, involving a solvent-exposed catalytic triad, a lipase-like lid, or a clamshell-like active site possibly formed by flexible loops.     

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.     

Living fast and dying of infection: host life history drives interspecific variation in infection and disease risk

Parasite infections often lead to dramatically different outcomes among host species. Although an emerging body of ecoimmunological research proposes that hosts experience a fundamental trade-off between pathogen defences and life-history activities, this line of inquiry has rarely been extended to the most essential outcomes of host-pathogen interactions: namely, infection and disease pathology. Using a comparative experimental approach involving 13 amphibian host species and a virulent parasite, we test the hypothesis that 'pace-of-life' predicts parasite infection and host pathology. Trematode exposure increased mortality and malformations in nine host species. After accounting for evolutionary history, species that developed quickly and metamorphosed smaller ('fast-species') were particularly prone to infection and pathology. This pattern likely resulted from both weaker host defences and greater adaptation by parasites to infect common hosts. Broader integration between life history theory and disease ecology can aid in identifying both reservoir hosts and species at risk of disease-driven declines.     

Geographic variation in the vocalizations of Australian palm cockatoos (Probosciger aterrimus)*

Vocal dialects have been well studied in songbirds, but there have been fewer examples from parrots. The Australian population of palm cockatoos (Probosciger aterrimus aterrimus) from Cape York Peninsula in far north Queensland has an unusually large vocal repertoire for a parrot. Most calls are made during their unique display ritual, which also includes a variety of postures, gestures and the use of a manufactured sound tool. Here, we quantify the geographic structural variation of contact calls within and between six major populations of palm cockatoos in Australia, as well as the extent to which frequently given call types are shared. We found that palm cockatoos from the east coast (Iron Range National Park) possess unique contact calls and have fewer call types in common with other locations. This may have resulted from their long-term isolation in rainforest habitat refugia. Such variety in vocal traits presents a rare opportunity to investigate the evolutionary forces creating behavioural diversity in wild parrots. This is also a step towards assessing links between behavioural variation and population connectivity, which is important information for determining the conservation status of palm cockatoos.