A natural species concept for prokaryotes

Direct molecular analyses of natural microbial populations reveal patterns that should compel microbiologists to adopt a more natural species concept that has been known to biologists for decades. The species debate can be exploited to address a larger issue - microbiologists need, in general, to take a more natural view of the organisms they study.     

What is a species? Essences and generation

Arguments against essentialism in biology rely strongly on a claim that modern biology abandoned Aristotle’s notion of a species as a class of necessary and sufficient properties. However, neither his theory of essentialism, nor his logical definition of species and genus (eidos and genos) play much of a role in biological research and taxonomy, including his own. The objections to natural kinds thinking by early twentieth century biologists wrestling with the new genetics overlooked the fact that species have typical developmental cycles and most have a large shared genetic component. These are the “what-it-is-to-be” members of that species. An intrinsic biological essentialism does not commit us to Aristotelian notions, nor even modern notions, of essence. There is a long-standing definition of “species” and its precursor notions that goes back to the Greeks, and which Darwin and pretty well all biologists since him share, that I call the Generative Conception of Species. It relies on there being a shared generative power that makes progeny resemble parents. The “what-it-is-to-be” a member of that species is that developmental type, mistakes in development notwithstanding. Moreover, such “essences” have always been understood to include deviations from the type. Finally, I shall examine some implications of the collapse of the narrative about essences in biology.     

Digest: Disentangled bank: Less diverse urban environments modify the shape and magnitude of natural selection*

Urbanization provides a natural experiment for biologists to test how anthropogenic environmental change affects evolution in real time and frames predictions for anticipated evolutionary outcomes worldwide. Start et al. ( 2018 ) found that changes in species interactions (herbivore abundance and avian predation) along urbanization gradients predictably alter the shape and magnitude of natural selection on gall size (a defensive trait), suggesting that rapid global environmental change can alter species interactions, which may have foreseeable evolutionary consequences.     

The role of taxonomy in species conservation

Taxonomy and species conservation are often assumed to be completely interdependent activities. However, a shortage of taxonomic information and skills, and confusion over where the limits to 'species' should be set, both cause problems for conservationists. There is no simple solution because species lists used for conservation planning (e.g. threatened species, species richness estimates, species covered by legislation) are often also used to determine which units should be the focus of conservation actions; this despite the fact that the two processes have such different goals and information needs. Species conservation needs two kinds of taxonomic solution: (i) a set of practical rules to standardize the species units included on lists; and (ii) an approach to the units chosen for conservation recovery planning which recognizes the dynamic nature of natural systems and the differences from the units in listing processes that result. These solutions are well within our grasp but require a new kind of collaboration among conservation biologists, taxonomists and legislators, as well as an increased resource of taxonomists with relevant and high-quality skills.     

Generalizations and kinds in natural science: the case of species

Species in biology are traditionally perceived as kinds of organisms about which explanatory and predictive generalizations can be made, and biologists commonly use species in this manner. This perception of species is, however, in stark contrast with the currently accepted view that species are not kinds or classes at all, but individuals. In this paper I investigate the conditions under which the two views of species might be held simultaneously. Specifically, I ask whether upon acceptance of an ontology of species as diachronic segments of the tree of life (this is one version of the species as individuals ontology) species can perform the epistemic role of kinds of organisms to which explanatory and predictive generalizations apply. I show that, for species-level segments of the tree of life, several requirements have to be met before the performance of this epistemic role is possible, and I argue that these requirements can be met by defining species according to the Composite Species Concept proposed by Kornet and McAllister in the 1990s.     

Modeling the evolution of interconnected processes: It is the song and the singers

Recently, Doolittle and Inkpen formulated a thought provoking theory, asserting that evolution by natural selection was responsible for the sideways evolution of two radically different kinds of selective units (also called Domains). The former entities, termed singers, correspond to the usual objects studied by evolutionary biologists (gene, genomes, individuals, species, etc.), whereas the later, termed songs, correspond to re‐produced biological and ecosystemic functions, processes, information, and memes. Singers perform songs through selected patterns of interactions, meaning that a wealth of critical phenomena might receive novel evolutionary explanations. However, this theory did not provide an empirical approach to study evolution in such a broadened context. Here, we show that analyzing songs and singers, using patterns of interaction networks as a common ontology for both, offers a novel, actionable, inclusive and mathematical way to analyze not only the re‐production but also the evolution and fitness of biological and ecosystemic interconnected processes.     

Testing the accuracy of non-experts in biodiversity monitoring exercises using fern species richness in the Ecuadorian Amazon

Assessing environmental change is often constrained by time, money and expertise. Community-based monitoring schemes attempt to address these limitations by providing local communities with the skills to measure changes in natural resources and contribute locally relevant information for local and regional management decisions. Despite the increasing popularity of community-based monitoring schemes, there is little information about the accuracy of the data they produce. In this study we use visual guides and hands-on training to teach groups of leaders from local communities in the Ecuadorian Amazon to measure the species richness of ferns. We compare their results to data obtained by experienced field biologists and show strong positive correlations in species richness estimates between the results obtained by groups receiving visual guides, groups receiving hands-on training and biologists. Our results show that, even with relatively little training, communities can use simple and cost-effective methodologies to yield data that accurately reflect levels of species richness.     

Reconciling evolutionary theory and taxonomic practice

The notion of evolution is a notion of change; yet, biologists customarily define each species as if it were a static class. One approach to this supposed disconnect between evolutionary theories and taxonomic practices would be to change those practices. Instead, the author claims this alleged disparity is a misreading. For the most part, it disappears under a proposed modified essentialist species concept involving unique species‐specific developmental suites. Each suite specific to a natural species is envisioned as a number of dispositional alternatives expressed distributively among the organisms in that species. There is support for this species concept in recent work in comparative genomics and developmental genetics. The concept is compatible with intraspecific variation and gradual evolution, and unifies practice and theory. It leads to an extended model of speciation and to an observational protocol for testing the concept and model.     

Conspecific Attraction is a Missing Component in Wildlife Habitat Modeling

Abstract Wildlife biologists use knowledge about wildlife-habitat relationships to create habitat models to predict species occurrence across a landscape. Researchers attribute limitations in predictive ability of a habitat model to data deficiencies, missing parameters, error introduced by specifications of the statistical model, and natural variation. Few wildlife biologists, however, have incorporated intra- and interspecific interactions (e.g., conspecific attraction, competition, predator-prey relationships) to increase predictive accuracy of habitat models. Based on our literature review and preliminary data analysis, conspecific attraction can be a primary factor influencing habitat selection in wildlife. Conspecific attraction can lead to clustered distributions of wildlife within available habitat, reducing the predictive ability of habitat models based on vegetative and geographic parameters alone. We suggest wildlife biologists consider incorporating a parameter in habitat models for the clustered distribution of individuals within available habitat and investigate the mechanisms leading to clustered distributions of species, especially conspecific attraction.     

Habitat preferences of an endangered insect species,Cepero’s ground-hopper (<Emphasis Type="Italic">Tetrix ceperoi</Emphasis>)

Preventing the global decline in biodiversity is a major task for conservation biologists. Although habitat loss has been identified as a key factor driving extinction processes, our knowledge on the habitat requirements of many endangered species, particularly invertebrates, is still sparse. We present a feasible method to study the microhabitat preferences of insect species. In Central Europe, the endangered Cepero’s ground-hopper, Tetrix ceperoi, is believed to have its only remaining natural habitats in dune slacks of the Wadden Sea Islands. Our results suggest that this species performs an active habitat choice of damp, bare patches with high temperatures. While ponds and fens in dune slacks provide large areas of damp bare ground and algal mats, grasslands, degraded dune slacks and the transitional zone between salt marsh and dunes are less suited as habitats. The major threat for T. ceperoi is found in the succession of its pioneer habitats due to the reduced natural dynamics. In industrialized countries, pioneer habitats and species are threatened substantially by coastal protection and floodplain regulation. This is only compensated in part by anthropogenic creation of secondary habitats, such as different kinds of pits or coal heaps. Nevertheless, there is a strong need for restoration of dynamic habitats by floodplain revitalization and dune slack restoration.     

Influenza Hemagglutinin and Neuraminidase Membrane Glycoproteins

Considerable progress has been made toward understanding the structural basis of the interaction of the two major surface glycoproteins of influenza A virus with their common ligand/substrate: carbohydrate chains terminating in sialic acid. The specificity of virus attachment to target cells is mediated by hemagglutinin, which acquires characteristic changes in its receptor-binding site to switch its host from avian species to humans. Anti-influenza drugs mimic the natural sialic acid substrate of the virus neuraminidase enzyme but utilize the much tighter binding of the drugs for efficacy. Resistance to one of the two main antiviral drugs is differentially acquired by the two distinct subsets of neuraminidase as a consequence of structural differences in the enzyme active site between the two phylogenetic groups.     

Biology and law

The terms “biology” and “biological” are widely used in ways that confuse and denigrate possible contributions of biologists to human self-understanding. As with social scientists, biologists deal with learning, developmental plasticity, and strategizing in virtually all species they study. It is from theories about how human strategizing is molded by selection that biologists can contribute to understanding topics like law.     

Biodiversity,biological uncertainty,and setting conservation priorities

In a world of massive extinctions where not all taxa can be saved, how ought biologists to decide their preservation priorities? When biologists make recommendations regarding conservation, should their analyses be based on scientific criteria, on public or lay criteria, on economic or some other criteria? As a first step in answering this question, we examine the issue of whether biologists ought to try to save the endangered Florida panther, a well known “glamour” taxon. To evaluate the merits of panther preservation, we examine three important arguments of biologists who are skeptical about the desirability of panther preservation. These arguments are (1) that conservation dollars ought to be spent in more efficient ways than panther preservation; (2) that biologists and conservationists ought to work to preserve species before subspecies; and (3) that biologists and conservationists ought to work to save habitats before species or subspecies. We conclude that, although all three arguments are persuasive, none of them provides convincing grounds for foregoing panther preservation in favor of other, more scientifically significant conservation efforts. Our conclusion is based, in part, on the argument that biologists ought to employ ethical, as well as scientific, rationality in setting conservation priorities and that ethical rationality may provide persuasive grounds for preserving taxa that often are not viewed by biologists as of great importance.     

生态位分化与森林群落物种多样性维持研究展望

一直以来,生态学家和进化生物学家对森林群落物种多样格局及其形成机制持有不同的观点。虽然Robert Ricklefs将进化和生态过程整合的观点已经被群落生态学家广泛接受,但是区域物种进化历史以及局域群落微进化过程是否能够影响群落生态学过程以及这些过程如何影响群落结构和动态还有待商榷。经典的生态位理论同时强调了种间和种内生态位分化对群落多样性维持的影响。但是生态学家普遍认为种间差异足以代表群落内个体间的相互作用关系,并且由于进化过程导致的种内分化往往涉及较长的时间尺度,因此,虽然种内差异是自然选择的重要材料,物种对环境的适应性进化过程所导致的种内分化对群落构建的影响往往被生态学家所忽视。为此,通过回顾种间和个体生态位分化的研究历史,对两类研究分别进行简要阐述,强调在今后的群落生态学研究中需要考虑个体分化对局域群落构建的影响。     

Logic in systematics

Systematic biologists attempt to infer the taxonomic relationship of one species to another based on the available evidence. Phylogenetic systematists demand that these species relationships reflect evolutionary history (they expect their taxa to be monophyletic). Just exactly how this is to be achieved remains a subject of debate. There are many different kinds of evidence, and many different ways of inferring taxonomic relationships (plus evolutionary history) from them. In this paper, we argue that one such way of inferring species relationships, the hypothetico‐deductive method, proves a bad fit with phylogenetic systematics because it requires an excessively strong assumption of the relationship that obtains between hypotheses of descent and the available evidence.     

Extra-pair paternity in birds: explaining variation between species and populations

Molecular techniques used to assign paternity have revealed previously unknown incidences of extra-pair paternity in socially monogamous bird species. DNA fingerprinting has now been used sufficiently often for mating-system biologists to appreciate the natural variation in the frequency of broods showing extra-pair young. The variation between species and between populations of the same species is surprisingly marked. Explaining this variation may help us to understand the factors promoting sexual selection. Recent comparative studies and detailed behavioural studies suggest that factors such as breeding density, genetic variation in the population and the intensity of sexual conflicts determine the costs and benefits to males and females of engaging in extra-pair copulations, and therefore contribute to the variation among populations.     

Explanation and Falsification in Phylogenetic Inference: Exercises in Popperian Philosophy

Deduction leads to causal explanation in phylogenetic inference when the evidence, the systematic character, is conceptualized as a transformation series. Also, the deductive entailment of modus tollens is satisfied when those kinds of events are operationalized as patristic difference. Arguments to the contrary are based largely on the premise that character-states are defined intensionally as objects, in terms of similarity relations. However, such relations leave biologists without epistemological access to the causal explanation and explanatory power of historical statements. Moreover, the prediction-making to which those kinds of relations are limited in practice can lead to a category error—the mental conversion of an abstraction (the classes defined in terms of similarity relations) into a thing (such as an historical individual). The latter practices and problems characterize pattern cladistics, taxa being interpreted as homeostatic property cluster natural kinds, and other instrumentalist research programs.     

Combined effects of parasites and contaminants on animal health: parasites do matter

The cumulative effects of multiple stressors are becoming a priority concern for ecotoxicologists, ecologists and conservation biologists working to understand threats to ecosystems and species. In that context, parasites and pathogens are increasingly a focus of attention. Parasites interact with natural and anthropogenic stressors to increase mortality and reduce animal health in myriad ways in a wide spectrum of host and parasite taxa. The combined effects of parasites and other stressors can reduce either resistance or tolerance to infection. Recommendations are provided to guide further research.