The Species Concept as a Cognitive Tool for Biological Anthropology

Taxonomy is caught between the search for the “perfect” theory and an elusive biological variability. The lack of major advances in issues related to how “species” and other taxonomic categories are defined suggests that perhaps we should avoid excessively rigid formalism in this regard. The risk is a separation between elegant but useless theories and confusing applications of the taxonomic tools. Communication is one of the main functions of taxonomy, and stability one of the main parameters that taxonomy users should be sensitive to. An excess of stability may generate anachronistic consequences while continuous revisions may make the tool of taxonomy scarcely practical. The current tendency pushes toward more and more fragmentation of biologically valid taxa. While taxonomy specialists enjoy such challenges, many taxonomy users feel a bit nervous and discouraged when trying to use a tool that is constantly changing. Debates over taxonomy would seem particularly unrewarding for fields with limited samples and scarce biological diversity, such as palaeoanthropology. In this context, where the information available is rarely sufficient to supply consistent taxonomical evidence, there are frequently excessive efforts to create debate on species separations. The risk is that we maintain the debate on a purely theoretical level, or else we distrust a reliable use of taxonomy. A compromise (and recommended) choice between these two extremes would be to rely on shared and reasonable interpretations of homogeneous evolutionary units, without diving into fine‐grained issues that will remain, however, unresolved. Taxonomy should be a tool, not the goal, of the evolutionary biologist. Our mind needs discrete and recognizable objects to structure our perception of reality. There is no reason to expect that nature works the same way. Am. J. Primatol. 75:10‐15, 2013. © 2012 Wiley Periodicals, Inc.     

Taxonomy, slime molds, and the questions we ask

Taxonomic treatments often influence the way we both ask and attempt to answer certain biological questions. The classical taxonomy of the dictyostelid cellular slime molds (Dictyosteliales) involves a convenient set of categories that were developed independent of phylogeny. In order to test whether the characters supporting the classical taxonomy hold any phylogenetic signal, we subjected 19 described taxa belonging to two families (Acytosteliaceae and Dictyosteliaceae) and three genera (Acytostelium, Dictyostelium, and Polysphondylium) to rooted cladistic analyses using PAUP* v 4.0b4a. Neither family nor any of the three genera were found to represent monophyletic groups. These results confirm that the classical taxonomy used to delineate families and genera within these slime molds carries very little phylogenetic signal. Taxonomic character sets should be scrutinized phylogenetically in order to determine what information they provide about the relatedness of taxa within a group. Because taxonomy often drives the nature of biological inquiry, caution should be exercised when drawing conclusions regarding the evolution of developmental systems in Dictyostelium.     

Phylogenetic definitions and taxonomic philosophy

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names.     

Pheneticism reconsidered

The pheneticist philosophy holds that biological taxa are clusters of entities united by a form of all-things-considered resemblance. This view of taxonomy has come in for almost universal criticism from philosophers, and has received little praise from biologists, over the past 30 years or so. This article defends a modest pheneticism, understood as part of a pluralist view of taxonomy. First, phenetic approaches to taxonomy are alive and well in biological practice, especially in the areas of microbiology and botany. Second, the pheneticist notion of overall similarity is defensible, and is implicitly endorsed even by those (such as Quine) usually implicated in attacks on similarity. Third, there are limited biological domains within which pheneticism’s conception of species as kinds (rather than heterogeneous individuals) remains applicable.     

Essentialism, history, and biological taxa

de Queiroz (1995), Griffiths (1999) and LaPorte (2004) offer a new version of essentialism called "historical essentialism". According to this version of essentialism, relations of common ancestry are essential features of biological taxa. The main type of argument for this essentialism proposed by Griffiths (1999) and LaPorte (2004) is that the dominant school of classification, cladism, defines biological taxa in terms of common ancestry. The goal of this paper is to show that this argument for historical essentialism is unsatisfactory: cladism does not assume that relations of common ancestry are essential attributes of biological taxa. Therefore, historical essentialism is not justified by cladism.     

New proposals for naming lower-ranked taxa within the frame of the International Code of Zoological Nomenclature

The recent multiplication of cladistic hypotheses for many zoological groups poses a challenge to zoological nomenclature following the International Code of Zoological Nomenclature: in order to account for these hypotheses, we will need many more ranks than currently allowed in this system, especially in lower taxonomy (around the ranks genus and species). The current Code allows the use of as many ranks as necessary in the family-series of nomina (except above superfamily), but forbids the use of more than a few ranks in the genus and species-series. It is here argued that this limitation has no theoretical background, does not respect the freedom of taxonomic thoughts or actions, and is harmful to zoological taxonomy in two respects at least: (1) it does not allow to express in detail hypothesized cladistic relationships among taxa at lower taxonomic levels (genus and species); (2) it does not allow to point taxonomically to low-level differentiation between populations of the same species, although this would be useful in some cases for conservation biology purposes. It is here proposed to modify the rules of the Code in order to allow use by taxonomists of an indeterminate number of ranks in all nominal-series. Such an 'expanded nomenclatural system' would be highly flexible and likely to be easily adapted to any new finding or hypothesis regarding cladistic relationships between taxa, at genus and species level and below. This system could be useful for phylogeographic analysis and in conservation biology. In zoological nomenclature, whereas robustness of nomina is necessary, the same does not hold for nomenclatural ranks, as the latter are arbitrary and carry no special biological, evolutionary or other information, except concerning the mutual relationships between taxa in the taxonomic hierarchy. Compared to the Phylocode project, the new system is equally unambiguous within the frame of a given taxonomic frame, but it provides more explicit and informative nomina for non-specialist users, and is more economic in terms of number of nomina needed to account for a given hierarchy. These ideas are exemplified by a comparative study of three possible nomenclatures for the taxonomy recently proposed by Hillis and Wilcox (2005) for American frogs traditionally referred to the genus Rana.     

Fallacies and false premises—a critical assessment of the arguments for the recognition of paraphyletic taxa in botany

One of the central controversies in contemporary taxonomy and systematics revolves around whether to accept or to reject paraphyletic taxa. The present review is the result of a survey of the ongoing discussion in botany over the past ca. 15 years, and attempts to systematically and critically assess all individual arguments presented for the formal recognition of paraphyletic groups in the classification of life. Where arguments are found to be without merit, rebuttals are presented in the hope of excluding them from further discussion, which can then concentrate on those that have merit. Where arguments are found to be sound, their implications and possible solutions are discussed. The controversy around paraphyletic taxa can be broken down into three questions: whether their rejection or acceptance would lead to a classification better reflecting patterns of biological diversity and evolutionary history; whether their rejection or acceptance would lead to a more practical, useful and predictive classification; and whether their rejection is compatible with ranked and binary Linnaean taxonomy. All available arguments for paraphyletic taxa relating to the first question are demonstrated to be based on various logical fallacies or false premises, especially misunderstandings of the principles of phylogenetic systematics. The issue of usefulness is harder to resolve, as different classifications serve different needs. It is presumably unavoidable but also preferable that phylogenetic and non‐phylogenetic ways of classifying species continue to coexist, serving different needs. Finally, an insistence on monophyletic taxa is found to be incompatible with binary taxonomy under a set of very specific circumstances and assumptions whose presence and accuracy are not universally accepted. © The Willi Hennig Society 2011.     

What's in a (biological) name? The wrath of Lord Rutherford

Names in taxonomy have seven different and important properties, some due to their existence in the context of classifications. Names confer or facilitate individuation, information storage and retrieval, and set theories of relationships, explanatory power, testable predictions, conceptual power, and language. No other way of naming in science is so powerful. And this is possible because taxonomic naming is done with full consideration of the theoretical specification of empirical data (characters) and their correspondence among taxa via homology statements. Since Darwin and Hennig, sets of homologous characters distributed among taxa allow precise hypotheses of a genealogical relationship, and this relationship is reflected in the way naming results in a classification.     

A comparison of biological characteristics and distribution between Swedish threatened and non-threatened forest vascular plants

Threatened (n = 59) and non-threatened (n = 308) Swedish forest vascular plant taxa were compared with regard to a number of variables, including distribution, site factors taxonomy, morphology and flowering time A majority of the threatened taxa occur in the southern deciduous woodlands, which only constitute c 0.5% of the total forested area in Sweden There are considerably more threatened taxa in southern than in northern Sweden, a consequence of the successively higher number of forest vascular plants from the north towards the south Threatened taxa grow in forests with significantly higher soil fertility than non-threatened taxa Significant differences were also revealed regarding light conditions, soil water conditions and month of flowering Threatened taxa grow on soils with significantly higher pH and also with slightly more available nitrogen than non-threatened taxa, as measured with Ellenberg indicator values Forest stands on fertile soils are uncommon in Sweden and they are also very species-rich Soil-type rarity in combination with high species diversity in these soil types thus partly explain why taxa are included in the Swedish Red data list     

Toward a phylogenetic system of biological nomenclature

Despite the widely held belief that modem biological taxonomy is evolutionary, some of the most fundamental concepts and principles in the current system of biological nomenclature are based on a nonevolutionary convention that pre-dates widespread acceptance of an evolutionary world view by more than a century. The development of a phylogenetic system of nomenclature requires reformulating these concepts and principles so that they are no longer based on the Linnean categories but on the tenet of common descent.     

Systematics,biological knowledge and environmental conservation

Systematics and taxonomy are essential: they respectively elucidate life's history, and organize and verify biological knowledge. This knowledge is built of interrelated concepts which are ultimately accounted for by biological specimens. Such knowledge is essential to decide how much and what biodiversity survives human onslaughts. The preservation of specimens in natural history collections is the essential part of the process which builds and maintains biological knowledge. These collections and the human expertise essential to interpret specimens are the taxonomic resources which maintain accurate and verifiable concepts of biological entities. Present and future knowledge of the complexities and diversity of the biosphere depends on the integrity of taxonomic resources, vet widespread ignorance and disregard for their fundamental value has created a global crisis. Preservation of specimens in natural history collections is chronically neglected and support to study and manage collections is very insufficient. The knowledge held by experienced taxonomists is not being passed on to younger recruits. Neglect of collections has destroyed countless specimens and threatens millions more. These threats to taxonomic resources not only impinge on systematics but all biology: this tragedy jeopardizes the integrity of biological knowledge. The consequences for environmental conservation and therefore humanity are also of dire severity and the biodiversity crisis adds unprecedented weight to the barely recognized crisis in taxonomy and systematics.Where correspondence should     

A Standardised Vocabulary for Identifying Benthic Biota and Substrata from Underwater Imagery: The CATAMI Classification Scheme

Imagery collected by still and video cameras is an increasingly important tool for minimal impact, repeatable observations in the marine environment. Data generated from imagery includes identification, annotation and quantification of biological subjects and environmental features within an image. To be long-lived and useful beyond their project-specific initial purpose, and to maximize their utility across studies and disciplines, marine imagery data should use a standardised vocabulary of defined terms. This would enable the compilation of regional, national and/or global data sets from multiple sources, contributing to broad-scale management studies and development of automated annotation algorithms. The classification scheme developed under the Collaborative and Automated Tools for Analysis of Marine Imagery (CATAMI) project provides such a vocabulary. The CATAMI classification scheme introduces Australian-wide acknowledged, standardised terminology for annotating benthic substrates and biota in marine imagery. It combines coarse-level taxonomy and morphology, and is a flexible, hierarchical classification that bridges the gap between habitat/biotope characterisation and taxonomy, acknowledging limitations when describing biological taxa through imagery. It is fully described, documented, and maintained through curated online databases, and can be applied across benthic image collection methods, annotation platforms and scoring methods. Following release in 2013, the CATAMI classification scheme was taken up by a wide variety of users, including government, academia and industry. This rapid acceptance highlights the scheme’s utility and the potential to facilitate broad-scale multidisciplinary studies of marine ecosystems when applied globally. Here we present the CATAMI classification scheme, describe its conception and features, and discuss its utility and the opportunities as well as challenges arising from its use.     

Detecting cryptic species in sympatry and allopatry: analysis of hidden diversity in Polyommatus (Agrodiaetus) butterflies (Lepidoptera: Lycaenidae)

Modern multilocus molecular techniques are a powerful tool in the detection and analysis of cryptic taxa. However, its shortcoming is that with allopatric populations it reveals phylogenetic lineages, not biological species. The increasing power of coalescent multilocus analysis leads to the situation in which nearly every geographically isolated or semi‐isolated population can be identified as a lineage and therefore raised to species rank. It leads to artificial taxonomic inflation and as a consequence creates an unnecessary burden on the conservation of biodiversity. To solve this problem, we suggest combining modern lineage delimitation techniques with the biological species concept. We discuss several explicit principles on how genetic markers can be used to detect cryptic entities that have properties of biological species (i.e. of actually or potentially reproductively isolated taxa). Using these principles we rearranged the taxonomy of the butterfly species close to Polyommatus (Agrodiaetus) ripartii. The subgenus Agrodiaetus is a model system in evolutionary research, but its taxonomy is poorly elaborated because, as a rule, most of its species are morphologically poorly differentiated. The taxon P. (A.) valiabadi has been supposed to be one of the few exceptions from this rule due to its accurately distinguishable wing pattern. We discovered that in fact traditionally recognized P. valiabadi is a triplet of cryptic species, strongly differentiated by their karyotypes and mitochondrial haplotypes.     

Enhancing the performance and interpretation of freshwater biological indices: An application in arid zone streams

We assessed the performance of biological indices developed for invertebrate assemblages occurring in arid zone streams: a multimetric index (MMI) and an O/E index of taxonomic completeness. Our overall goal was to advance our understanding of the factors that affect performance and interpretation of biological indices. Our specific objectives were to (1) develop biological indices that are insensitive to natural environmental gradients, (2) develop a general method to determine if the biological potential of an assessed site is adequately represented by the population of reference sites, (3) develop a robust method to select metrics for inclusion in MMIs that ensures maximum independence of metrics, and (4) determine if a fundamental sample property (the evenness of taxa counts within a sample) affects index performance. Random Forest modeling revealed that both individual metrics and taxa composition were strongly associated with natural environmental heterogeneity, which meant both the MMI and O/E index needed to be based on site-specific expectations. We produced a precise, responsive, and ecologically robust MMI by using principal components analysis to identify 7 statistically independent metrics from a list of 31 candidate assemblage-level metrics. However, the O/E index we developed was relatively imprecise compared with O/E indices developed for other regions. This imprecision may be the consequence of low predictability in local taxa composition associated with the relatively high spatial isolation of aquatic habitats within arid regions. We were also able to assess the likelihood that the biological potential of assessed sites were adequately characterized by the population of reference sites by developing and applying a multivariate, nearest-neighbor test that determined if an assessed site occurred within the environmental space of the reference site network. This approach is robust and applicable to all biological indices. We also demonstrate that the evenness of taxa counts within a sample is positively related to estimates of sample taxa richness and thus the scores of both indices. The relationship between richness and sample evenness can potentially compromise inferences regarding biological condition, and post hoc adjustments for the effects of evenness on index scores might be desirable. Further improvements in the performance and interpretation of biological indices will require simultaneous consideration of the effects of incomplete sampling on characterization of biological assemblages and the physical and biological factors that influence community assembly.     

Pattern cladism, homology, and theory-neutrality

Pattern cladists purport to classify biological taxa in a way that is theory-neutral. The idea of a theory-neutral science is, however, philosophically problematic; and, while pattern cladists' commitment to theory-neutrality has been subject to scrutiny by both phylogenetic cladists and some philosophers, virtually no attention has been paid to the core issue of whether observation of patterns in nature is a means to theory-neutrality. This essay critically examines pattern cladists' claim to construct a theory-neutral cladistic taxonomy by relying on observation. Special attention is paid to the observations of patterns involving homologous traits.     

Least-inclusive taxonomic unit: a new taxonomic concept for biology

Phylogenetic taxonomy has been introduced as a replacement for the Linnaean system. It differs from traditional nomenclature in defining taxon names with reference to phylogenetic trees and in not employing ranks for supraspecific taxa. However, 'species' are currently kept distinct. Within a system of phylogenetic taxonomy we believe that taxon names should refer to monophyletic groups only and that species should not be recognized as taxa. To distinguish the smallest identified taxa, we here introduce the least-inclusive taxonomic unit (LITU), which are differentiated from more inclusive taxa by initial lower-case letters. LITUs imply nothing absolute about inclusiveness, only that subdivisions are not presently recognized.     

Development trends in taxonomy,with special reference to fungi

Taxonomy is a traditional subject, but it still receives attention and has become a topic of much discussion in recent years. Many of these discussions have raised concerns about the future of taxonomy, especially with regard to the workforce responsible for the discovery of new species in the context of declining biodiversity. Previous discussions were based on the taxonomic data of plants and animals, but the status of fungal taxonomy has not been mentioned. Fungi have one of the highest levels of biodiversity among all living organisms, second only to insects. The discussion of the future of taxonomy without the inclusion of fungal data is incomplete. Here, we present the results of analyses based on all new fungal taxa published since 1753. Fungal taxonomy is an ever‐growing area of study with increasing numbers of new taxa being described and growing numbers of fungal taxonomists. Compared with plants and most animal groups, there has been a much sharper increase in the rate at which new fungal taxa are being described. Furthermore, the number of taxonomists studying fungi has increased at a faster speed than those studying plants or animals. This indicates that fungal taxonomy is a prosperous subject and a dynamic area for scientific studies, and that it deserves much more attention and support. The study of fungal taxonomy will deepen our understanding of the biodiversity of our planet.     

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.