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1.
Ecol Lett ; 21(8): 1200-1210, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-29797760

RESUMO

The analysis of functional diversity (FD) has gained increasing importance due to its generality and utility in ecology. In particular, patterns in the spatial distribution and temporal change of FD are being used to predict locations and functional groups that are immediately vulnerable to global changes. A major impediment to the accurate measurement of FD is the pervasiveness of missing data in trait datasets. While such prevalent data gaps can engender misleading inferences in FD analyses, we currently lack any practical guide to handle missing data in trait datasets. Here, we identify significant mismatches between true FD and values derived from datasets that contain missing data. We demonstrate that imputing missing data with a phylogeny-informed approach reduces the risk of misinterpretation of FD patterns, and provides baseline information against which central questions in ecology can be evaluated.


Assuntos
Ecologia , Fenótipo , Filogenia
2.
Phytochemistry ; 144: 197-207, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28957714

RESUMO

Many studies quantify total phenolics or total tannins, but understanding the ecological role of polyphenolic secondary metabolites requires at least an understanding of the diversity of phenolic groups present. We used UPLC-MS/MS to measure concentrations of different polyphenol groups - including the four most common tannin groups, the three most common flavonoid groups, and quinic acid derivatives - in foliage from 628 eucalypts from the genera Eucalyptus, Angophora and Corymbia. We also tested for phylogenetic signal in each of the phenolic groups. Many eucalypts contained high concentrations of polyphenols, particularly ellagitannins, which have been relatively poorly studied, but may possess strong oxidative activity. Because the biosynthetic pathways of many phenolic compounds share either precursors or enzymes, we found negative correlations between the concentrations of several of the constituents that we measured, including proanthocyanidins (PAs) and hydrolysable tannins (HTs), HTs and flavonol derivatives, and HTs and quinic acid derivatives. We observed moderate phylogenetic signal in all polyphenol constituents, apart from the concentration of the prodelphinidin subunit of PAs and the mean degree of polymerisation of PAs. These two traits, which have previously been shown to be important in determining plants' protein precipitation capacity, may have evolved under selection, perhaps in response to climate or herbivore pressure. Hence, the signature of evolutionary history appears to have been erased for these traits. This study is an important step in moving away from analysing "totals" to a better understanding of how phylogenetic effects influence phenolic composition, and how this in turn influences ecological processes.


Assuntos
Eucalyptus/química , Polifenóis/análise , Estrutura Molecular , Filogenia , Taninos/análise
3.
PLoS One ; 12(4): e0175385, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28388681

RESUMO

Animal social behaviour can have important effects on the long-term dynamics of diseases. In particular, preferential spatial relationships between individuals can lead to differences in the rates of disease spread within a population. We examined the concurrent influence of genetic relatedness, sex, age, home range overlap, time of year, and prion disease status on proximal associations of adult Rocky Mountain mule deer (Odocoileus hemionus hemionus) in a chronic wasting disease endemic area. We also quantified the temporal stability of these associations across different sex, age, and disease status classes. We used three years of high frequency telemetry data from 74 individuals to record encounters within 25 m of each other, and to calculate seasonal home range overlap measured by volume of intersection (VI). The strength of pairwise spatial association between adult mule deer was independent of genetic relatedness, age and disease status. Seasonal variation in association strength was not consistent across years, perhaps due to annual changes in weather conditions. The influence of home range overlap on association strength varied seasonally, whereby associations were stronger in pre-rut and fawning than in the rest of the seasons. The sexes of individuals also interacted with both VI and season. At increasing levels of VI, associations were stronger between females than between males and between females and males. The strongest associations in pre-rut were between males, while the strongest in rut were between females and males. The temporal stability of associations was markedly dependant on the sex and the diagnosis of the associating pair. Our findings highlight the importance of considering concurrent effects of biological and environmental factors when seeking to understand the role of social preference in behavioural ecology and disease spread. Applying this knowledge in epidemiological modelling will shed light on the dynamics of disease transmission among mule deer.


Assuntos
Cervos , Doenças Priônicas/transmissão , Zoonoses/transmissão , Animais , Clima , Feminino , Masculino , Doenças Priônicas/epidemiologia , Estações do Ano
4.
Glob Chang Biol ; 23(2): 621-634, 2017 02.
Artigo em Inglês | MEDLINE | ID: mdl-27396586

RESUMO

Each year, two or three species that had been considered to be extinct are rediscovered. Uncertainty about whether or not a species is extinct is common, because rare and highly threatened species are difficult to detect. Biological traits such as body size and range size are expected to be associated with extinction. However, these traits, together with the intensity of search effort, might influence the probability of detection and extinction differently. This makes statistical analysis of extinction and rediscovery challenging. Here, we use a variant of survival analysis known as cure rate modelling to differentiate factors that influence rediscovery from those that influence extinction. We analyse a global data set of 99 mammals that have been categorized as extinct or possibly extinct. We estimate the probability that each of these mammals is still extant and thus estimate the proportion of missing (presumed extinct) mammals that are incorrectly assigned extinction. We find that body mass and population density are predictors of extinction, and body mass and search effort predict rediscovery. In mammals, extinction rate increases with body mass and population density, and these traits act synergistically to greatly elevate extinction rate in large species that also occurred in formerly dense populations. However, when they remain extant, larger-bodied missing species are rediscovered sooner than smaller species. Greater search effort increases the probability of rediscovery in larger species of missing mammals, but has a minimal effect on small species, which take longer to be rediscovered, if extant. By separating the effects of species characteristics on extinction and detection, and using models with the assumption that a proportion of missing species will never be rediscovered, our new approach provides estimates of extinction probability in species with few observation records and scant ecological information.


Assuntos
Espécies em Perigo de Extinção , Extinção Biológica , Mamíferos , Animais , Tamanho Corporal , Probabilidade
5.
Proc Natl Acad Sci U S A ; 113(1): 230-5, 2016 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-26699477

RESUMO

The identification of patterns in life-history strategies across the tree of life is essential to our prediction of population persistence, extinction, and diversification. Plants exhibit a wide range of patterns of longevity, growth, and reproduction, but the general determinants of this enormous variation in life history are poorly understood. We use demographic data from 418 plant species in the wild, from annual herbs to supercentennial trees, to examine how growth form, habitat, and phylogenetic relationships structure plant life histories and to develop a framework to predict population performance. We show that 55% of the variation in plant life-history strategies is adequately characterized using two independent axes: the fast-slow continuum, including fast-growing, short-lived plant species at one end and slow-growing, long-lived species at the other, and a reproductive strategy axis, with highly reproductive, iteroparous species at one extreme and poorly reproductive, semelparous plants with frequent shrinkage at the other. Our findings remain consistent across major habitats and are minimally affected by plant growth form and phylogenetic ancestry, suggesting that the relative independence of the fast-slow and reproduction strategy axes is general in the plant kingdom. Our findings have similarities with how life-history strategies are structured in mammals, birds, and reptiles. The position of plant species populations in the 2D space produced by both axes predicts their rate of recovery from disturbances and population growth rate. This life-history framework may complement trait-based frameworks on leaf and wood economics; together these frameworks may allow prediction of responses of plants to anthropogenic disturbances and changing environments.


Assuntos
Desenvolvimento Vegetal , Plantas/classificação , Reprodução , Ecossistema , Meio Ambiente , Filogenia , Folhas de Planta/crescimento & desenvolvimento , Dinâmica Populacional , Crescimento Demográfico , Madeira/crescimento & desenvolvimento
6.
PLoS One ; 10(9): e0136275, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26375711

RESUMO

Genetic diversity within species may promote resilience to environmental change, yet little is known about how such variation is distributed at broad geographic scales. Here we develop a novel Bayesian methodology to analyse multi-species genetic diversity data in order to identify regions of high or low genetic diversity. We apply this method to co-distributed taxa from Australian marine waters. We extracted published summary statistics of population genetic diversity from 118 studies of 101 species and > 1000 populations from the Australian marine economic zone. We analysed these data using two approaches: a linear mixed model for standardised data, and a mixed beta-regression for unstandardised data, within a Bayesian framework. Our beta-regression approach performed better than models using standardised data, based on posterior predictive tests. The best model included region (Integrated Marine and Coastal Regionalisation of Australia (IMCRA) bioregions), latitude and latitude squared. Removing region as an explanatory variable greatly reduced model performance (delta DIC 23.4). Several bioregions were identified as possessing notably high genetic diversity. Genetic diversity increased towards the equator with a 'hump' in diversity across the range studied (-9.4 to -43.7°S). Our results suggest that factors correlated with both region and latitude play a role in shaping intra-specific genetic diversity, and that bioregion can be a useful management unit for intra-specific as well as species biodiversity. Our novel statistical model should prove useful for future analyses of within species genetic diversity at broad taxonomic and geographic scales.


Assuntos
Organismos Aquáticos/genética , Variação Genética , Austrália , Teorema de Bayes , Geografia , Modelos Estatísticos
7.
PLoS One ; 10(6): e0130626, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26111037

RESUMO

Australia has experienced dramatic declines and extinctions of its native rodent species over the last 200 years, particularly in southern Australia. In the tropical savanna of northern Australia significant declines have occurred only in recent decades. The later onset of these declines suggests that the causes may differ from earlier declines in the south. We examine potential regional effects (northern versus southern Australia) on biological and ecological correlates of range decline in Australian rodents. We demonstrate that rodent declines have been greater in the south than in the tropical north, are strongly influenced by phylogeny, and are consistently greater for species inhabiting relatively open or sparsely vegetated habitat. Unlike in marsupials, where some species have much larger body size than rodents, body mass was not an important predictor of decline in rodents. All Australian rodent species are within the prey-size range of cats (throughout the continent) and red foxes (in the south). Contrary to the hypothesis that mammal declines are related directly to ecosystem productivity (annual rainfall), our results are consistent with the hypothesis that disturbances such as fire and grazing, which occur in non-rainforest habitats and remove cover used by rodents for shelter, nesting and foraging, increase predation risk. We agree with calls to introduce conservation management that limits the size and intensity of fires, increases fire patchiness and reduces grazing impacts at ecological scales appropriate for rodents. Controlling feral predators, even creating predator-free reserves in relatively sparsely-vegetated habitats, is urgently required to ensure the survival of rodent species, particularly in northern Australia where declines are not yet as severe as those in the south.


Assuntos
Conservação dos Recursos Naturais/métodos , Ecossistema , Cadeia Alimentar , Animais , Austrália , Raposas , Marsupiais , Dinâmica Populacional , Comportamento Predatório , Roedores , Austrália do Sul
8.
Am Nat ; 184(1): 52-64, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24921600

RESUMO

Dispersal is a fundamental species characteristic that should directly affect both rates of gene flow among spatially distributed populations and opportunities for speciation. Yet no single trait associated with dispersal has been demonstrated to affect both micro- and macroevolutionary patterns of diversity across a diverse biological assemblage. Here, we examine patterns of genetic differentiation and species richness in reef fishes, an assemblage of over 7,000 species comprising approximately one-third of the extant bony fishes and over one-tenth of living vertebrates. In reef fishes, dispersal occurs primarily during a planktonic larval stage. There are two major reproductive and parental investment syndromes among reef fishes, and the differences between them have implications for dispersal: (1) benthic guarding fishes lay negatively buoyant eggs, typically guarded by the male parent, and from these eggs hatch large, strongly swimming larvae; in contrast, (2) pelagic spawning fishes release small floating eggs directly into the water column, which drift unprotected before small weakly swimming larvae hatch. Using phylogenetic comparative methods, we show that benthic guarders have significantly greater population structure than pelagic spawners and additionally that taxonomic families of benthic guarders are more species rich than families of pelagic spawners. Our findings provide a compelling case for the continuity between micro- and macroevolutionary processes of biological diversification and underscore the importance of dispersal-related traits in influencing the mode and tempo of evolution.


Assuntos
Distribuição Animal , Recifes de Corais , Peixes/genética , Genética Populacional , Animais , Evolução Biológica , Larva/genética , Filogenia , Reprodução
9.
Proc Natl Acad Sci U S A ; 110(44): 17910-4, 2013 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-24101455

RESUMO

Suicidal reproduction (semelparity) has evolved in only four genera of mammals. In these insectivorous marsupials, all males die after mating, when failure of the corticosteroid feedback mechanism elevates stress hormone levels during the mating season and causes lethal immune system collapse (die-off). We quantitatively test and resolve the evolutionary causes of this surprising and extreme life history strategy. We show that as marsupial predators in Australia, South America, and Papua New Guinea diversified into higher latitudes, seasonal predictability in abundance of their arthropod prey increased in multiple habitats. More-predictable prey peaks were associated with shorter annual breeding seasons, consistent with the suggestion that females accrue fitness benefits by timing peak energy demands of reproduction to coincide with maximum food abundance. We demonstrate that short mating seasons intensified reproductive competition between males, increasing male energy investment in copulations and reducing male postmating survival. However, predictability of annual prey cycles alone does not explain suicidal reproduction, because unlike insect abundance, peak ovulation dates in semelparous species are often synchronized to the day among years, triggered by a species-specific rate of change of photoperiod. Among species with low postmating male survival, we show that those with suicidal reproduction have shorter mating seasons and larger testes relative to body size. This indicates that lethal effort is adaptive in males because females escalate sperm competition by further shortening and synchronizing the annual mating period and mating promiscuously. We conclude that precopulatory sexual selection by females favored the evolution of suicidal reproduction in mammals.


Assuntos
Evolução Biológica , Marsupiais/fisiologia , Preferência de Acasalamento Animal/fisiologia , Reprodução/fisiologia , Comportamento Sexual Animal/fisiologia , Espermatozoides/fisiologia , Animais , Austrália , Teorema de Bayes , Feminino , Cadeia Alimentar , Masculino , Papua Nova Guiné , Dinâmica Populacional , Análise de Regressão , Estações do Ano , América do Sul , Análise de Sobrevida , Testículo/anatomia & histologia
10.
Proc Biol Sci ; 280(1765): 20131092, 2013 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-23825210

RESUMO

Phylogenetic information is becoming a recognized basis for evaluating conservation priorities, but associations between extinction risk and properties of a phylogeny such as diversification rates and phylogenetic lineage ages remain unclear. Limited taxon-specific analyses suggest that species in older lineages are at greater risk. We calculate quantitative properties of the mammalian phylogeny and model extinction risk as an ordinal index based on International Union for Conservation of Nature Red List categories. We test for associations between lineage age, clade size, evolutionary distinctiveness and extinction risk for 3308 species of terrestrial mammals. We show no significant global or regional associations, and three significant relationships within taxonomic groups. Extinction risk increases for evolutionarily distinctive primates and decreases with lineage age when lemurs are excluded. Lagomorph species (rabbits, hares and pikas) that have more close relatives are less threatened. We examine the relationship between net diversification rates and extinction risk for 173 genera and find no pattern. We conclude that despite being under-represented in the frequency distribution of lineage ages, species in older, slower evolving and distinct lineages are not more threatened or extinction-prone. Their extinction, however, would represent a disproportionate loss of unique evolutionary history.


Assuntos
Extinção Biológica , Mamíferos/genética , Filogenia , Animais , Conservação dos Recursos Naturais , Mamíferos/classificação , Modelos Biológicos , Risco , Especificidade da Espécie
11.
BMC Evol Biol ; 12: 102, 2012 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-22741602

RESUMO

BACKGROUND: Uncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow) and inflated significance in hypothesis testing (e.g. p-values will be too small). Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable. METHODS: We developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses. RESULTS: We demonstrate applications in linear regression, quantification of phylogenetic signal, and measurement error models. Phylogenetic uncertainty was incorporated by applying a prior distribution for the phylogeny, where this distribution consisted of the posterior tree sets from Bayesian phylogenetic tree estimation programs. The models were analysed using simulated data sets, and applied to a real data set on plant traits, from rainforest plant species in Northern Australia. Analyses were performed using the free and open source software OpenBUGS and JAGS. CONCLUSIONS: Incorporating phylogenetic uncertainty through an empirical prior distribution of trees leads to more precise estimation of regression model parameters than using a single consensus tree and enables a more realistic estimation of confidence intervals. In addition, models incorporating measurement errors and/or individual variation, in one or both variables, are easily formulated in the Bayesian framework. We show that BUGS is a useful, flexible general purpose tool for phylogenetic comparative analyses, particularly for modelling in the face of phylogenetic uncertainty and accounting for measurement error or individual variation in explanatory variables. Code for all models is provided in the BUGS model description language.


Assuntos
Teorema de Bayes , Modelos Genéticos , Filogenia , Incerteza , Austrália , Simulação por Computador , Modelos Lineares , Cadeias de Markov , Método de Monte Carlo , Software , Árvores/genética
12.
Syst Biol ; 61(3): 382-91, 2012 May.
Artigo em Inglês | MEDLINE | ID: mdl-22215720

RESUMO

We prove that the slope parameter of the ordinary least squares regression of phylogenetically independent contrasts (PICs) conducted through the origin is identical to the slope parameter of the method of generalized least squares (GLSs) regression under a Brownian motion model of evolution. This equivalence has several implications: 1. Understanding the structure of the linear model for GLS regression provides insight into when and why phylogeny is important in comparative studies. 2. The limitations of the PIC regression analysis are the same as the limitations of the GLS model. In particular, phylogenetic covariance applies only to the response variable in the regression and the explanatory variable should be regarded as fixed. Calculation of PICs for explanatory variables should be treated as a mathematical idiosyncrasy of the PIC regression algorithm. 3. Since the GLS estimator is the best linear unbiased estimator (BLUE), the slope parameter estimated using PICs is also BLUE. 4. If the slope is estimated using different branch lengths for the explanatory and response variables in the PIC algorithm, the estimator is no longer the BLUE, so this is not recommended. Finally, we discuss whether or not and how to accommodate phylogenetic covariance in regression analyses, particularly in relation to the problem of phylogenetic uncertainty. This discussion is from both frequentist and Bayesian perspectives.


Assuntos
Classificação/métodos , Interpretação Estatística de Dados , Análise dos Mínimos Quadrados , Algoritmos , Teorema de Bayes , Simulação por Computador , Filogenia
13.
Conserv Biol ; 26(1): 57-67, 2012 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-22136403

RESUMO

For species with five or more sightings, quantitative techniques exist to test whether a species is extinct on the basis of distribution of sightings. However, 70% of purportedly extinct mammals are known from fewer than five sightings, and such models do not include some important indicators of the likelihood of extinction such as threats, biological traits, search effort, and demography. Previously, we developed a quantitative method that we based on species' traits in which we used Cox proportional hazards regression to calculate the probability of rediscovery of species regarded as extinct. Here, we used two versions of the Cox regression model to determine the probability of extinction in purportedly extinct mammals and compared the results of these two models with those of stationary Poisson, nonparametric, and Weibull sighting-distribution models. For mammals with five or more sightings, the stationary Poisson model categorized all but two critically endangered (flagged as possibly extinct) species in our data set as extinct, and results with this model were consistent with current categories of the International Union for the Conservation of Nature. The scores of probability of rediscovery for individual species in one version of our Cox regression model were correlated with scores assigned by the stationary Poisson model. Thus, we used this Cox regression model to determine the probability of extinction of mammals with sparse records. On the basis of the Cox regression model, the most likely mammals to be rediscovered were the Montane monkey-faced bat (Pteralopex pulchra), Armenian myotis (Myotis hajastanicus), Alcorn's pocket gopher (Pappogeomys alcorni), and Wimmer's shrew (Crocidura wimmeri). The Cox model categorized two species that have recently disappeared as extinct: the baiji (Lipotes vexillifer) and the Christmas Island pipistrelle (Pipistrellus murrayi). Our new method can be used to test whether species with few records or recent last-sighting dates are likely to be extinct.


Assuntos
Conservação dos Recursos Naturais/métodos , Extinção Biológica , Mamíferos , Modelos Estatísticos , Animais , Distribuição de Poisson
14.
PLoS One ; 6(6): e21201, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21731670

RESUMO

Cleaning behaviour is deemed a mutualism, however the benefit of cleaning interactions to client individuals is unknown. Furthermore, mechanisms that may shift fish community structure in the presence of cleaning organisms are unclear. Here we show that on patch reefs (61-285 m²) which had all cleaner wrasse Labroides dimidiatus (Labridae) experimentally removed (1-5 adults reef⁻¹) and which were then maintained cleaner-fish free over 8.5 years, individuals of two site-attached (resident) client damselfishes (Pomacentridae) were smaller compared to those on control reefs. Furthermore, resident fishes were 37% less abundant and 23% less species rich per reef, compared to control reefs. Such changes in site-attached fish may reflect lower fish growth rates and/or survivorship. Additionally, juveniles of visitors (fish likely to move between reefs) were 65% less abundant on removal reefs suggesting cleaners may also affect recruitment. This may, in part, explain the 23% lower abundance and 33% lower species richness of visitor fishes, and 66% lower abundance of visitor herbivores (Acanthuridae) on removal reefs that we also observed. This is the first study to demonstrate a benefit of cleaning behaviour to client individuals, in the form of increased size, and to elucidate potential mechanisms leading to community-wide effects on the fish population. Many of the fish groups affected may also indirectly affect other reef organisms, thus further impacting the reef community. The large-scale effect of the presence of the relatively small and uncommon fish, Labroides dimidiadus, on other fishes is unparalleled on coral reefs.


Assuntos
Biota , Recifes de Corais , Peixes/fisiologia , Animais , Peixes/crescimento & desenvolvimento , Dinâmica Populacional , Especificidade da Espécie , Fatores de Tempo
15.
PLoS One ; 6(1): e15226, 2011 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-21249185

RESUMO

Evolutionary explanations for life history diversity are based on the idea of costs of reproduction, particularly on the concept of a trade-off between age-specific reproduction and parental survival, and between expenditure on current and future offspring. Such trade-offs are often difficult to detect in population studies of wild mammals. Terminal investment theory predicts that reproductive effort by older parents should increase, because individual offspring become more valuable to parents as the conflict between current versus potential future offspring declines with age. In order to demonstrate this phenomenon in females, there must be an increase in maternal expenditure on offspring with age, imposing a fitness cost on the mother. Clear evidence of both the expenditure and fitness cost components has rarely been found. In this study, we quantify costs of reproduction throughout the lifespan of female antechinuses. Antechinuses are nocturnal, insectivorous, forest-dwelling small (20-40 g) marsupials, which nest in tree hollows. They have a single synchronized mating season of around three weeks, which occurs on predictable dates each year in a population. Females produce only one litter per year. Unlike almost all other mammals, all males, and in the smaller species, most females are semelparous. We show that increased allocation to current reproduction reduces maternal survival, and that offspring growth and survival in the first breeding season is traded-off with performance of the second litter in iteroparous females. In iteroparous females, increased allocation to second litters is associated with severe weight loss in late lactation and post-lactation death of mothers, but increased offspring growth in late lactation and survival to weaning. These findings are consistent with terminal investment. Iteroparity did not increase lifetime reproductive success, indicating that terminal investment in the first breeding season at the expense of maternal survival (i.e. semelparity) is likely to be advantageous for females.


Assuntos
Marsupiais/fisiologia , Reprodução/fisiologia , Fatores Etários , Envelhecimento , Animais , Feminino , Lactação , Longevidade , Sobrevida
16.
Proc Biol Sci ; 278(1708): 1090-7, 2011 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-20880890

RESUMO

Extinction is difficult to detect, even in well-known taxa such as mammals. Species with long gaps in their sighting records, which might be considered possibly extinct, are often rediscovered. We used data on rediscovery rates of missing mammals to test whether extinction from different causes is equally detectable and to find which traits affect the probability of rediscovery. We find that species affected by habitat loss were much more likely to be misclassified as extinct or to remain missing than those affected by introduced predators and diseases, or overkill, unless they had very restricted distributions. We conclude that extinctions owing to habitat loss are most difficult to detect; hence, impacts of habitat loss on extinction have probably been overestimated, especially relative to introduced species. It is most likely that the highest rates of rediscovery will come from searching for species that have gone missing during the 20th century and have relatively large ranges threatened by habitat loss, rather than from additional effort focused on charismatic missing species.


Assuntos
Biodiversidade , Extinção Biológica , Mamíferos/fisiologia , Probabilidade , Animais , Conservação dos Recursos Naturais/métodos , Conservação dos Recursos Naturais/estatística & dados numéricos , Ecossistema , Atividades Humanas , Humanos , Espécies Introduzidas , Mamíferos/classificação , Medição de Risco/métodos
17.
Ecol Lett ; 13(9): 1182-97, 2010 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-20561015

RESUMO

Explaining variation in population growth rates is fundamental to predicting population dynamics and population responses to environmental change. In this study, we used matrix population models, which link birth, growth and survival to population growth rate, to examine how and why population growth rates vary within and among 50 terrestrial plant species. Population growth rates were more similar within species than among species; with phylogeny having a minimal influence on among-species variation. Most population growth rates decreased over the observation period and were negatively autocorrelated between years; that is, higher than average population growth rates tended to be followed by lower than average population growth rates. Population growth rates varied more through time than space; this temporal variation was due mostly to variation in post-seedling survival and for a subset of species was partly explained by response to environmental factors, such as fire and herbivory. Stochastic population growth rates departed from mean matrix population growth rate for temporally autocorrelated environments. Our findings indicate that demographic data and models of closely related plant species cannot necessarily be used to make recommendations for conservation or control, and that post-seedling survival and the sequence of environmental conditions are critical for determining plant population growth rate.


Assuntos
Desenvolvimento Vegetal , Ecossistema , Modelos Biológicos , Filogenia , Plantas/classificação , Plantas/genética , Densidade Demográfica , Dinâmica Populacional , Especificidade da Espécie , Processos Estocásticos
18.
Bioinformatics ; 26(11): 1463-4, 2010 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-20395285

RESUMO

SUMMARY: Picante is a software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities. The package calculates phylogenetic diversity metrics, performs trait comparative analyses, manipulates phenotypic and phylogenetic data, and performs tests for phylogenetic signal in trait distributions, community structure and species interactions. AVAILABILITY: Picante is a package for the R statistical language and environment written in R and C, released under a GPL v2 open-source license, and freely available on the web (http://picante.r-forge.r-project.org) and from CRAN (http://cran.r-project.org).


Assuntos
Biodiversidade , Filogenia , Software , Ecologia , Fenótipo
19.
PLoS One ; 4(11): e7851, 2009 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-19924245

RESUMO

BACKGROUND: Protein crystallisation screening involves the parallel testing of large numbers of candidate conditions with the aim of identifying conditions suitable as a starting point for the production of diffraction quality crystals. Generally, condition screening is performed in 96-well plates. While previous studies have examined the effects of protein construct, protein purity, or crystallisation condition ingredients on protein crystallisation, few have examined the effect of the crystallisation plate. METHODOLOGY/PRINCIPAL FINDINGS: We performed a statistically rigorous examination of protein crystallisation, and evaluated interactions between crystallisation success and plate row/column, different plates of same make, different plate makes and different proteins. From our analysis of protein crystallisation, we found a significant interaction between plate make and the specific protein being crystallised. CONCLUSIONS/SIGNIFICANCE: Protein crystal structure determination is the principal method for determining protein structure but is limited by the need to produce crystals of the protein under study. Many important proteins are difficult to crystallize, so that identification of factors that assist crystallisation could open up the structure determination of these more challenging targets. Our findings suggest that protein crystallisation success may be improved by matching a protein with its optimal plate make.


Assuntos
Cristalização/métodos , Proteínas/química , Animais , Antígenos/química , Catalase/química , Bovinos , Galinhas , Cristalografia por Raios X/instrumentação , Cristalografia por Raios X/métodos , Clara de Ovo/química , Escherichia coli/metabolismo , Humanos , Concentração de Íons de Hidrogênio , Fígado/enzimologia , Camundongos , Muramidase/química , Projetos Piloto , Streptomyces/metabolismo
20.
Curr Biol ; 19(15): 1283-7, 2009 Aug 11.
Artigo em Inglês | MEDLINE | ID: mdl-19592250

RESUMO

Marine cleaning symbioses are classic examples of mutualism: cleaners remove and consume ectoparasites from "client" fish, while clients benefit from a reduction in ectoparasites. However, how clients recognize cleaners and decide not to eat them is unclear. Color and body pattern are thought to be important in signaling cleaning services to coral reef fish; in this study, we tested the long-held belief that cleaner fish display a blue "guild" coloration. Via color analytical techniques and phylogenetic comparisons, we show that cleaner fish are more likely to display a blue coloration, in addition to a yellow coloration, compared to noncleaner fish. Via theoretical vision models, we show that, from the perspective of potential signal receivers, blue is the most spectrally contrasting color against coral reef backgrounds, whereas yellow is most contrasting against blue water backgrounds or against black lateral stripes. Finally, behavioral experiments confirm that blue within the cleaner fish pattern attracts more client reef fish to cleaning stations. Cleaner fish have evolved some of the most conspicuous combinations of colors and patterns in the marine environment, and this is likely to underpin the success of the cleaner-client relationship on the reef.


Assuntos
Comunicação Animal , Visão de Cores/fisiologia , Asseio Animal/fisiologia , Perciformes/fisiologia , Pigmentação/fisiologia , Animais , Cor , Filogenia , Especificidade da Espécie
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