Causes,kinds and forms

Realist philosophies of science posit a dialectical relation between theoretical, explanatory knowledge and practical, including taxonomic knowledge. This paper examines the dialectic between the theory of descent and empirical, Linnaean taxonomy which is based on a logic of traditional classes. It considers the arguments of David Hull to the effect that many of the practical problems of empirical classification can be resolved by means of an ontology based upon the theory of descent in which species taxa are regarded as individuals rather than as classes or natural kinds.Contra Hull, it is argued that this view is, at best, only partially consistent with taxonomic practice and that it cannot sustain experimental practice which presupposes that species taxa be regarded as natural kinds. An outline is given of a possible alternative dialectic between a field theory of morphogenesis and a rational systematics involving a logic of relations.     

Causal and Mechanistic Explanations in Ecology

How are scientific explanations possible in ecology, given that there do not appear to be many-if any-ecological laws? To answer this question, I present and defend an account of scientific causal explanation in which ecological generalizations are explanatory if they are invariant rather than lawlike. An invariant generalization continues to hold or be valid under a special change-called an intervention-that changes the value of its variables. According to this account, causes are difference-makers that can be intervened upon to manipulate or control their effects. I apply the account to ecological generalizations to show that invariance under interventions as a criterion of explanatory relevance provides interesting interpretations for the explanatory status of many ecological generalizations. Thus, I argue that there could be causal explanations in ecology by generalizations that are not, in a strict sense, laws. I also address the issue of mechanistic explanations in ecology by arguing that invariance and modularity constitute such explanations.     

Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood

Incomplete lineage sorting can cause incongruence between the phylogenetic history of genes (the gene tree) and that of the species (the species tree), which can complicate the inference of phylogenies. In this article, I present a new coalescent-based algorithm for species tree inference with maximum likelihood. I first describe an improved method for computing the probability of a gene tree topology given a species tree, which is much faster than an existing algorithm by Degnan and Salter (2005). Based on this method, I develop a practical algorithm that takes a set of gene tree topologies and infers species trees with maximum likelihood. This algorithm searches for the best species tree by starting from initial species trees and performing heuristic search to obtain better trees with higher likelihood. This algorithm, called STELLS (which stands for Species Tree InfErence with Likelihood for Lineage Sorting), has been implemented in a program that is downloadable from the author's web page. The simulation results show that the STELLS algorithm is more accurate than an existing maximum likelihood method for many datasets, especially when there is noise in gene trees. I also show that the STELLS algorithm is efficient and can be applied to real biological datasets.     

Cellular differentiation and individuality in the ‘minor’ multicellular taxa

Biology needs a concept of individuality in order to distinguish organisms from parts of organisms and from groups of organisms, to count individuals and compare traits across taxa, and to distinguish growth from reproduction. Most of the proposed criteria for individuality were designed for ‘unitary’ or ‘paradigm’ organisms: contiguous, functionally and physiologically integrated, obligately sexually reproducing multicellular organisms with a germ line sequestered early in development. However, the vast majority of the diversity of life on Earth does not conform to all of these criteria. We consider the issue of individuality in the ‘minor’ multicellular taxa, which collectively span a large portion of the eukaryotic tree of life, reviewing their general features and focusing on a model species for each group. When the criteria designed for unitary organisms are applied to other groups, they often give conflicting answers or no answer at all to the question of whether or not a given unit is an individual. Complex life cycles, intimate bacterial symbioses, aggregative development, and strange genetic features complicate the picture. The great age of some of the groups considered shows that ‘intermediate’ forms, those with some but not all of the traits traditionally associated with individuality, cannot reasonably be considered ephemeral or assumed transitional. We discuss a handful of recent attempts to reconcile the many proposed criteria for individuality and to provide criteria that can be applied across all the domains of life. Finally, we argue that individuality should be defined without reference to any particular taxon and that understanding the emergence of new kinds of individuals requires recognizing individuality as a matter of degree.     

Benthic fauna in tropical tidal flats – a comparative perspective

Tidal flats extend seaward from mangrove forests along many tropicalcoastlines. This contribution compiles the current knowledge on tropicaltidal flats with regard to species richness, abundance, spatial distributionpatterns and ecological roles taken by major organisms. Tidal flatsencompass a variety of soft-sediment habitats which are inhabited by aspecies-rich fauna. Species numbers are generally higher than in temperatetidal flats, but vary widely between tropical sites where they have not yetbeen fully assessed due to lack of research and taxonomic problems. Theassessment of biodiversity is further complicated by a low species frequency,the small size of macroinfaunal organisms and variations in the occurrence ofspecies between sites. Mean abundance ranges from 1000–2000individuals m^-2, although figures ten times higher have beenrecorded in a mudflat in Costa Rica, and there are great variations in general.Individual densities of small-sized macrofauna are about ten times higher than for larger macrobenthos. A generalized zonation scheme for intertidaldistribution patterns of tropical tidal flat fauna is presented. The comparisonshows that the occurrence of macrofauna and especially of ecosystemengineers varies between sites, which can in turn explain the great variabilityin species abundance patterns recorded in benthic surveys of tidal flatswithin and between regions. This review revealed similarities as well asdifferences between various tropical tidal flats, which underlines the need for further comparative studies to be done, using the same methodology, before generalizations can be made.     

A new method for dealing with residual spatial autocorrelation in species distribution models

Species distribution modelling (SDM) is a widely used tool and has many applications in ecology and conservation biology. Spatial autocorrelation (SAC), a pattern in which observations are related to one another by their geographic distance, is common in georeferenced ecological data. SAC in the residuals of SDMs violates the ‘independent errors’ assumption required to justify the use of statistical models in modelling species’ distributions. The autologistic modelling approach accounts for SAC by including an additional term (the autocovariate) representing the similarity between the value of the response variable at a location and neighbouring locations. However, autologistic models have been found to introduce bias in the estimation of parameters describing the influence of explanatory variables on habitat occupancy. To address this problem we developed an extension to the autologistic approach by calculating the autocovariate on SAC in residuals (the RAC approach). Performance of the new approach was tested on simulated data with a known spatial structure and on strongly autocorrelated mangrove species’ distribution data collected in northern Australia. The RAC approach was implemented as generalized linear models (GLMs) and boosted regression tree (BRT) models. We found that the BRT models with only environmental explanatory variables can account for some SAC, but applying the standard autologistic or RAC approaches further reduced SAC in model residuals and substantially improved model predictive performance. The RAC approach showed stronger inferential performance than the standard autologistic approach, as parameter estimates were more accurate and statistically significant variables were accurately identified. The new RAC approach presented here has the potential to account for spatial autocorrelation while maintaining strong predictive and inferential performance, and can be implemented across a range of modelling approaches.     

Tree species distribution in temperate forests is more influenced by soil than by climate

Knowledge of the ecological requirements determining tree species distributions is a precondition for sustainable forest management. At present, the abiotic requirements and the relative importance of the different abiotic factors are still unclear for many temperate tree species. We therefore investigated the relative importance of climatic and edaphic factors for the abundance of 12 temperate tree species along environmental gradients. Our investigations are based on data from 1,075 forest stands across Switzerland including the cold‐induced tree line of all studied species and the drought‐induced range boundaries of several species. Four climatic and four edaphic predictors represented the important growth factors temperature, water supply, nutrient availability, and soil aeration. The climatic predictors were derived from the meteorological network of MeteoSwiss, and the edaphic predictors were available from soil profiles. Species cover abundances were recorded in field surveys. The explanatory power of the predictors was assessed by variation partitioning analyses with generalized linear models. For six of the 12 species, edaphic predictors were more important than climatic predictors in shaping species distribution. Over all species, abundances depended mainly on nutrient availability, followed by temperature, water supply, and soil aeration. The often co‐occurring species responded similar to these growth factors. Drought turned out to be a determinant of the lower range boundary for some species. We conclude that over all 12 studied tree species, soil properties were more important than climate variables in shaping tree species distribution. The inclusion of appropriate soil variables in species distribution models allowed to better explain species' ecological niches. Moreover, our study revealed that the ecological requirements of tree species assessed in local field studies and in experiments are valid at larger scales across Switzerland.     

Species as Explanatory Hypotheses: Refinements and Implications

The formal definition of species as explanatory hypotheses presented by Fitzhugh (Marine Biol 26:155–165, 2005a, b) is emended. A species is an explanatory account of the occurrences of the same character(s) among gonochoristic or cross-fertilizing hermaphroditic individuals by way of character origin and subsequent fixation during tokogeny. In addition to species, biological systematics also employs hypotheses that are ontogenetic, tokogenetic, intraspecific, and phylogenetic, each of which provides explanatory hypotheses for distinctly different classes of causal questions. It is suggested that species hypotheses can not be applied to organisms with obligate asexual, parthenogenetic, and self-fertilizing modes of reproduction. Hypotheses explaining shared characters among such organisms are, instead, strictly phylogenetic. Several implications of this emended definition are examined, especially the relations between species, intraspecific, and phylogenetic hypotheses, as well as the limitations of species names to be applied to temporally different characters within populations.     

滇中喀斯特山地半湿润常绿阔叶林的群落生态学研究

依据两个10000m2森林样地(蓑衣山和月湖)的调查,在两个样地内分别记录到植物95科142属的163种(蓑衣山)和70科110属的125种(月湖),其中,草本物种最多,乔木次之,藤本较少。两个样地的主要组成物种都为滇青冈、清香木、团花新木姜子、云南木樨榄。群落中大径级的物种和个体数相对较少,优势种主要通过较多数量的中小径级个体体现出来。按Raunkiaer生活型划分,该半湿润常绿阔叶林主要由高位芽植物(54.9%和48.8%)和地面芽植物(39.6%和41.6%)组成。按中国植被进行的生活型分类结果显示,乔木物种组成只有中、小乔木,它们在群落中仅占总物种数的1/4(25%和24%);草本植物中的多年生草本在样地总物种数中所占比例很高(42.7%和45.6%);且常绿中、小乔木与落叶中、小乔木的物种数差异不大,几乎各占一半。但如果按常绿与落叶的个体数量、或胸径总和、或重要值来判定,则落叶成分的最高比例为24·7%。鉴于此,该森林类型仍定义为混有落叶成分的半湿润常绿阔叶林。种—面积曲线结果表明,曲线在400m2点有最剧烈转折,应作为类似喀斯特山地植物群落调查的最小面积。     

Causal Regularities in the Biological World of Contingent Distributions

Former discussions of biological generalizations have focused on the question of whether there are universal laws of biology. These discussions typically analyzed generalizations out of their investigative and explanatory contexts and concluded that whatever biological generalizations are, they are not universal laws. The aim of this paper is to explain what biological generalizations are by shifting attention towards the contexts in which they are drawn. I argue that within the context of any particular biological explanation or investigation, biologists employ two types of generations. One type identifies causal regularities exhibited by particular kinds of biological entities. The other type identifies how these entities are distributed in the biological world.     

Natural Kinds in Evolution and Systematics: Metaphysical and Epistemological Considerations

Despite the traditional focus on metaphysical issues in discussions of natural kinds in biology, epistemological considerations are at least as important. By revisiting the debate as to whether taxa are kinds or individuals, I argue that both accounts are metaphysically compatible, but that one or the other approach can be pragmatically preferable depending on the epistemic context. Recent objections against construing species as homeostatic property cluster kinds are also addressed. The second part of the paper broadens the perspective by considering homologues as another example of natural kinds, comparing them with analogues as functionally defined kinds. Given that there are various types of natural kinds, I discuss the different theoretical purposes served by diverse kind concepts, suggesting that there is no clear-cut distinction between natural kinds and other kinds, such as functional kinds. Rather than attempting to offer a unique metaphysical account of 'natural' kind, a more fruitful approach consists in the epistemological study of how different natural kind concepts are employed in scientific reasoning.     

Defining Life: The Virus Viewpoint

Are viruses alive? Until very recently, answering this question was often negative and viruses were not considered in discussions on the origin and definition of life. This situation is rapidly changing, following several discoveries that have modified our vision of viruses. It has been recognized that viruses have played (and still play) a major innovative role in the evolution of cellular organisms. New definitions of viruses have been proposed and their position in the universal tree of life is actively discussed. Viruses are no more confused with their virions, but can be viewed as complex living entities that transform the infected cell into a novel organism—the virus—producing virions. I suggest here to define life (an historical process) as the mode of existence of ribosome encoding organisms (cells) and capsid encoding organisms (viruses) and their ancestors. I propose to define an organism as an ensemble of integrated organs (molecular or cellular) producing individuals evolving through natural selection. The origin of life on our planet would correspond to the establishment of the first organism corresponding to this definition.     

Assessing species density and abundance of tropical trees from remotely sensed data and geostatistics

Question: What relationships exist between remotely sensed measurements and field observations of species density and abundance of tree species? Can these relationships and spatial interpolation approaches be used to improve the accuracy of prediction of species density and abundance of tree species? Location: Quintana Roo, Yucatan peninsula, Mexico. Methods: Spatial prediction of species density and abundance of species for three functional groups was performed using regression kriging, which considers the linear relationship between dependent and explanatory variables, as well as the spatial dependence of the observations. These relationships were explored using regression analysis with species density and abundance of species of three functional groups as dependent variables, and reflectance values of spectral bands, computed NDVI (normalized difference vegetation index), standard deviation of NDVI and texture measurements of Landsat 7 Thematic Mapper (TM) imagery as explanatory variables. Akaike information criterion was employed to select a set of candidate models and calculate model‐averaged parameters. Variogram analysis was used to analyze the spatial structure of the residuals of the linear regressions. Results: Species density of trees was related to reflectance values of TM4, NDVI and spatial heterogeneity of land cover types, while the abundance of species in functional groups showed different patterns of association with remotely sensed data. Models that accounted for spatial autocorrelation improved the accuracy of estimates in all cases. Conclusions: Our approach can substantially increase the accuracy of the spatial estimates of species richness and abundance of tropical tree species and can help guide and evaluate tropical forest management and conservation.     

Survival on the ark: life history trends in captive parrots

Members of the order Psittaciformes (parrots and cockatoos) are among the most long-lived and endangered avian species. Comprehensive data on lifespan and breeding are critical to setting conservation priorities, parameterizing population viability models, and managing captive and wild populations. To meet these needs, we analyzed 83, 212 life history records of captive birds from the International Species Information System and calculated lifespan and breeding parameters for 260 species of parrots (71% of extant species). Species varied widely in lifespan, with larger species generally living longer than smaller ones. The highest maximum lifespan recorded was 92 years in Cacatua moluccensis, but only 11 other species had a maximum lifespan over 50 years. Our data indicate that while some captive individuals are capable of reaching extraordinary ages, median lifespans are generally shorter than widely assumed, albeit with some increase seen in birds presently held in zoos. Species that lived longer and bred later in life tended to be more threatened according to IUCN classifications. We documented several individuals of multiple species that were able to breed for more than two decades, but the majority of clades examined had much shorter active reproduction periods. Post-breeding periods were surprisingly long and in many cases surpassed the duration of active breeding. Our results demonstrate the value of the ISIS database to estimate life history data for an at-risk taxon that is difficult to study in the wild, and provide life history data that is crucial for predictive modeling of future species endangerment and proactively managing captive populations of parrots.     

Using a new framework of two-phase generalized additive models to incorporate prey abundance in spatial distribution models of juvenile slender lizardfish in Haizhou Bay,China

The predictive skill of species distribution models depends on the quality and quantity of input information. In addition to the physical environmental variables, prey availability is also one of the main drivers regulating spatial distribution of marine species. However, prey distribution data have rarely been considered in habitat models due to the lack of information on non-commercial prey species. This may lead to an incomplete view of species distributions and biased model predictions. In this study, we developed a new framework of two-phase generalized additive models (GAMs) based on the Tweedie distribution to incorporate the predicted prey abundance as covariates in habitat models, and applied this framework to juvenile slender lizardfish Saurida elongata in Haizhou Bay, China. This study demonstrated that the predictive skill of habitat models could be greatly improved through incorporating prey abundance as explanatory variables. The importance of prey distribution data in the habitat model confirms the essentiality of including prey data while modelling species distribution. Spatial overlap and GAM analysis demonstrated that not all dominant prey can be selected as potential explanatory variables and only those prey species showing high spatiotemporal occurrences with predators should be incorporated. The framework derived in this study could be extended to other marine organisms to improve the predictive skill of habitat models and enhance our understanding of the ecological mechanisms underlying the distribution of marine species.     

From humanized mice to human disease: guiding extrapolation from model to target

Extrapolation from a well-understood base population to a less-understood target population can fail if the base and target populations are not sufficiently similar. Differences between laboratory mice and humans, for example, can hinder extrapolation in medical research. Mice that carry a partial or complete human physiological system, known as humanized mice, are supposed to make extrapolation more reliable by simulating a variety of human diseases. But what justifies our belief that these mice are similar enough to their human counterparts to simulate human disease? I argue that, unless three requirements are met in the process of humanizing mice, very little does. My requirements are not meant to provide necessary and sufficient conditions that guarantee a particular outcome. Instead, they serve as a heuristic for guiding scientific judgments involving extrapolation. In developing each requirement, I engage with philosophical issues concerning the nature of model-based science and the mechanistic approach (and its limits) to making generalizations in the life sciences.     

A generalization of Pontryagin's maximum principle for dynamic evolutionary games among relatives

We present two theorems that generalize Pontryagin's maximum principle to the setting of dynamic evolutionary games between genetically related individuals. The two theorems correspond to two types of interactions among individuals: patch-structured populations in which individuals locally "play the field" and pairwise interactions. These generalizations can be used in the same way that Pontryagin's maximum principle is used and they are valid for diploid organisms under a single locus, diallelic genetic model. These generalizations involve an interesting, dynamic version of Hamilton's Rule from inclusive fitness theory. We illustrate how these theoretical results can be applied by modeling the evolution of lifetime resource allocation to growth and reproduction in an annual plant when there is competition for resources among related individuals.     

How to build an information gathering and processing system: lessons from naturally and artificially intelligent systems

Imagine a situation in which you had to design a physical agent that could collect information from its environment, then store and process that information to help it respond appropriately to novel situations. What kinds of information should it attend to? How should the information be represented so as to allow efficient use and re-use? What kinds of constraints and trade-offs would there be? There are no unique answers. In this paper, we discuss some of the ways in which the need to be able to address problems of varying kinds and complexity can be met by different information processing systems. We also discuss different ways in which relevant information can be obtained, and how different kinds of information can be processed and used, by both biological organisms and artificial agents. We analyse several constraints and design features, and show how they relate both to biological organisms, and to lessons that can be learned from building artificial systems. Our standpoint overlaps with Karmiloff-Smith (1992) in that we assume that a collection of mechanisms geared to learning and developing in biological environments are available in forms that constrain, but do not determine, what can or will be learnt by individuals.