New World Monkey Nightmares: Science,Art, Use,and Abuse (?) in Platyrrhine Taxonomic Nomenclature

The taxonomy and nomenclature of New World monkeys is becoming precariously unstable and impractical, plagued by revisions aimed at conforming to approaches that reject the Biological Species Concept for narrowly construed reasons and resulting in a hyperinflated taxonomy at species (often) and genus (sometimes) levels. This undermines a major goal of classification at the most basic taxonomic levels to ease communication and facilitate research. Since it is difficult to justify extensive changes in terminology without a deeply justified theoretical purpose or without showing what scientific benefits these alterations can bring, working primatologists need not accept this doctrinaire trend. Knowing as little as we do about what a species actually is, does not justify contorting the value of a species nomenclature so that it reflects nothing more than coat color, a node, or endpoint of a dendrogram. Am. J. Primatol. 74:692‐695, 2012. © 2012 Wiley Periodicals, Inc.     

Why the Phylogenetic Species Concept?—Elementary

Although species play a number of unique and necessary roles in biology, none are more important than as the elements of phylogeny, nomenclature, and biodiversity study. Species are not divisible into any smaller units among which shared derived characters can be recognized with fidelity. Biodiversity inventory, assessment, and conservation are dependent upon a uniformly applicable species concept. Species are the fundamental units in formal Linnaean classification and zoological nomenclature. The Biological Species Concept, long given nominal support by most zoologists, forced an essentialy taxonomic problem (what are species?) into a population genetics framework (why are there species?). Early efforts at a phylogenetic species concept focused on correcting problems in the Biological Species Concept associated with ancestral populations, then applying phylogenetic logic to species themselves. Subsequently, Eldredge and Cracraft, and Nelson and Platnick, each proposed essentially identical and truly phylogenetic species concepts that permitted the rigorous recognition of species prior to and for the purposes of phylogenetic analysis, yet maintained the integrity of the Phylogenetic Species Concept outside of cladistic analysis. Such phylogenetic elements have many benefits, including giving to biology a unit species concept applicable across all kinds of living things including sexual and asexual forms. This is possible because the Phylogenetic Species Concept is based on patterns of character distributions and is therefore consistent with the full range of possible evolutionary processes that contribute to species formation, including both biotic and abiotic (even random) factors.     

Mammals and meaningful taxonomic units: the debate about species concepts and conservation

Mammalian taxonomy based on the diagnosability version of the Phylogenetic Species Concept has recently been declared the only sound approach to mammalian classification. In this article, based on the underlying evolutionary ontology of species taxa, I explain the fallacy of these arguments and hold that in a ‘grey area’ after lineage sundering, completely objective species delimitation is impossible, making both lumping and splitting equally correct or incorrect. As a consequence, we may have to get used to the idea that described species are often a poor guide to the delineation of meaningful taxonomic units for conservation.     

A genetic approach to the species problem in wild potato

Wild potatoes are native to the Americas, where they present very wide geographical and ecological distribution. Most are diploid, obligate out-crossers due to a multiallelic gametophytic self-incompatibility (S) locus that prevents self-fertilisation and crossing between individuals carrying identical S-alleles. They have two alternative modes of reproduction: sexual (by seeds) and asexual (by stolons and tubers), which provide, respectively, for genetic flexibility in changing environments and high fitness of adapted genotypes under stable conditions. Since the early twentieth century, their taxonomic classification has been mostly based on morphological phenotypes (Taxonomic Species Concept). More recently, attempts have been made to establish phylogenetic relationships, applying molecular tools in samples of populations (accessions) with a previously assigned specific category. However, neither the reproductive biology and breeding relations among spontaneous populations nor the morphological and genetic variability expected in obligate allogamous populations are considered when the taxonomic species concept is applied. In nature, wild potato populations are isolated through external and internal hybridisation barriers; the latter, which are genetically determined, can be either pre-zygotic (pollen-pistil incompatibility) or post-zygotic (abortion of embryo, endosperm or both tissues, sterility, and hybrid weakness and breakdown in segregating generations). The internal barriers, however, can be incomplete, providing opportunities for hybridisation and introgression within and between populations and ploidy levels in areas of overlap. The widespread occurrence of spontaneous hybrids in nature was recognised in the mid-twentieth century. Using genetic approaches, results have been obtained that provide strong support to the assertion that populations are at different stages of genetic divergence and are not at the end of the evolutionary process, as presupposed by the Taxonomic Species Concept. Furthermore, since wild potatoes have uniparental and biparental overlapping generations, the Biological Species Concept - developed for sexually reproducing biparental organisms - cannot be applied to them. In this paper, morphological, genetic, molecular and taxonomic studies in wild potato are reviewed, considering the genetic consequences of their reproductive biology, in an attempt to shed light on the species problem, because of its relevance in germplasm conservation and breeding.     

Thinking about Possible People: A Comment on Tooley and Rachels

Most people believe it would be wrong to bring a child into the world if in all likelihood its life would be miserable. But if pain and suffering count against bringing someone into existence, why do pleasure and happiness not count in favour of bringing them into existence? Recently in this journal Michael Tooley has re‐affirmed his rights‐based explanation for this asymmetry. In a nutshell: to create an individual whose life is not worth living would be to wrong that individual – to create an obligation that cannot be fulfilled – but it is not possible to wrong an individual who is not brought into existence. In the same issue of this journal, in an article covering a range of arguments for and against the claim that it would be good for additional people to exist, Stuart Rachels objects to Tooley’s account on the ground that it has counterintuitive implications. His most interesting argument involves a Parfit‐style counterexample: a woman is about to take a fertility pill that will result in twins, one of whom will be healthy and the other of whom will not. Does it make a difference, morally speaking, if the woman knows which of the twins will be healthy and which will not? In this paper I argue that both Rachels’ criticism of Tooley’s rights‐based account, and Tooley’s own defence of it, are unsuccessful due to their failure to come to grips with the semantics of names for possible individuals. Both of them implicitly assume that it is possible to have a potential person in mind, in a way that misleads them about the fairness of actions that involve possible people. The significance of this extends to other areas such as abortion, population policy, and embryo experimentation, where examples involving possible people are common.     

Wildlife conservation planning under the United States Forest Service's 2012 planning rule

In 2012, the United States Forest Service (USFS) promulgated new planning regulations in accordance with the National Forest Management Act (NFMA). These regulations represent the most significant change in federal forest policy in decades and have sweeping implications for wildlife populations. We provide a brief overview of the history of the NFMA planning regulations and their wildlife provisions and review the current science on planning for effective wildlife conservation at the landscape scale. We then discuss the approach to wildlife conservation planning in the 2012 rule and compare it to alternatives that were not selected and previous iterations of the planning rule. The new planning rule is of concern because of its highly discretionary nature and the inconsistency between its intent on the one hand and operational requirements on the other. Therefore, we recommend that the USFS include in the Directives for implementing the rule commitments to directly monitor populations of selected species of conservation concern and focal species and to maintain the viability of both categories of species. Additional guidance must be included to ensure the effective selection of species of conservation concern and focal species, and these categories should overlap when possible. If the USFS determines that the planning unit is not inherently capable of maintaining viable populations of a species, this finding should be made available for scientific review and public comment, and in such cases the USFS should commit to doing nothing that would further impair the viability of such species. In cases where extrinsic factors decrease the viability of species, the USFS has an increased, not lessened, responsibility to protect those species. Monitoring plans must include trigger points that will initiate a review of management actions, and plans must include provisions to ensure monitoring takes place as planned. If wildlife provisions in forest plans are implemented so that they are enforceable and ensure consistency between intent and operational requirements, this will help to prevent the need for additional listings under the Endangered Species Act and facilitate delisting. Although the discretionary nature of the wildlife provisions in the planning rule gives cause for concern, forward-thinking USFS officials have the opportunity under the 2012 rule to create a robust and effective framework for wildlife conservation planning. © 2013 The Wildlife Society.     

Quantitative criteria for species delimitation

Species are the fundamental units of biology, ecology and conservation, and progress in these fields is therefore hampered by widespread taxonomic bias and uncertainty. Numerous operational techniques based on molecular or phenotypic data have been designed to overcome this problem, yet existing procedures remain subjective or inconsistent, particularly when applying the biological species concept. We address this issue by developing quantitative methods for a classic technique in systematic zoology, namely the use of divergence between undisputed sympatric species as a yardstick for assessing the taxonomic status of allopatric forms. We calculated mean levels of differentiation in multiple phenotypic characters – including biometrics, plumage and voice – for 58 sympatric or parapatric species‐pairs from 29 avian families. We then used estimates of mean divergence to develop criteria for species delimitation based on data‐driven thresholds. Preliminary tests show that these criteria result in relatively few changes to avian taxonomy in Europe, yet are capable of extensive reassignment of species limits in poorly known tropical regions. While we recognize that species limits are in many cases inherently arbitrary, we argue that our system can be applied to the global avifauna to deliver taxonomic decisions with a high level of objectivity, consistency and transparency.     

Species extinction in finite replicator systems

Species extinction in finite random replicator systems is investigated as a function of within‐species interaction pressure. Extinctions are shown to increase with increased symmetry of among‐species interactions. The proportion of extinct species increases with increased system size. The effect of system connectance is reduced to a variability effect: connectivity geometry appears unimportant as long as closed subspaces are not formed. A small system can be interpreted as a closed subsystem of a larger system, which allows size‐scaling of the interaction pressure. At large interaction pressure, the scaling unifies the proportion of extinct species. At the limit of small within‐species interaction pressure, a small number of species survive, and the proportion of extinct species shows a system size effect. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 689–697.     

Phytochemical fingerprinting to thwart black cohosh adulteration: a 15 Actaea species analysis

Introduction – The popular use of black cohosh products (Actaea racemosa L., syn. Cimicifuga racemosa L.) is growing as the demand for alternatives to estrogen therapy has increased. Critical to safe use is the assurance of unadulterated, high‐quality products. Questions have been raised about the safety of black cohosh due to cases of liver toxicity in patients who reported taking it; subsequent evaluation found some products to be adulterated with other related herbal species. Correct plant species identification is a key first step for good manufacturing practices of safe black cohosh products. Objectives – To develop analytical methods which distinguish black cohosh from other species (American and Asian) of Actaea increasingly found as adulterants in commercially available black cohosh products. Material and methods – Fifteen species of Actaea were collected from North America and Asia, and the phytochemical fingerprints of these samples were established using HPLC‐PDA and LC‐MS techniques. Results – The HPLC and LC‐MS fingerprints for polyphenols and triterpene glycosides revealed distinct patterns that make black cohosh clearly distinguishable from most other species of Actaea. Two marker compounds, cimifugin and cimiracemoside F, were found to be important to distinguish black cohosh from most Asian species of Actaea. Formononetin was not found from either Asian or American species of Actaea. Conclusions – Phytochemical fingerprinting is a practical, reliable method for authenticating black cohosh and distinguishing it from other species of Actaea increasingly found as adulterants in commercially available black cohosh products. This should facilitate the continued development of high‐quality, unadulterated black cohosh products. Copyright © 2011 John Wiley & Sons, Ltd.     

Benthic species of the Kerguelen Plateau show contrasting distribution shifts in response to environmental changes

Marine life of the Southern Ocean has been facing environmental changes and the direct impact of human activities during the past decades. Benthic communities have particularly been affected by such changes although we only slowly understand the effect of environmental changes on species physiology, biogeography, and distribution. Species distribution models (SDM) can help explore species geographic responses to main environmental changes. In this work, we modeled the distribution of four echinoid species with contrasting ecological niches. Models developed for [2005–2012] were projected to different time periods, and the magnitude of distribution range shifts was assessed for recent‐past conditions [1955–1974] and for the future, under scenario RCP 8.5 for [2050–2099]. Our results suggest that species distribution shifts are expected to be more important in a near future compared to the past. The geographic response of species may vary between poleward shift, latitudinal reduction, and local extinction. Species with broad ecological niches and not limited by biogeographic barriers would be the least affected by environmental changes, in contrast to endemic species, restricted to coastal areas, which are predicted to be more sensitive.     

Forecasting species range dynamics with process‐explicit models: matching methods to applications

Knowing where species occur is fundamental to many ecological and environmental applications. Species distribution models (SDMs) are typically based on correlations between species occurrence data and environmental predictors, with ecological processes captured only implicitly. However, there is a growing interest in approaches that explicitly model processes such as physiology, dispersal, demography and biotic interactions. These models are believed to offer more robust predictions, particularly when extrapolating to novel conditions. Many process–explicit approaches are now available, but it is not clear how we can best draw on this expanded modelling toolbox to address ecological problems and inform management decisions. Here, we review a range of process–explicit models to determine their strengths and limitations, as well as their current use. Focusing on four common applications of SDMs – regulatory planning, extinction risk, climate refugia and invasive species – we then explore which models best meet management needs. We identify barriers to more widespread and effective use of process‐explicit models and outline how these might be overcome. As well as technical and data challenges, there is a pressing need for more thorough evaluation of model predictions to guide investment in method development and ensure the promise of these new approaches is fully realised.     

Species richness estimations of the megadiverse scuttle fly genus Megaselia (Diptera: Phoridae) in a wildfire‐affected hemiboreal forest

Abstract The species richness of the scuttle fly (Diptera: Phoridae) genus Megaselia was estimated by various non‐parametric estimators from EstimateS, Species Prediction And Diversity Estimation (SPADE) and Ws2m, based on material from a Swedish hemiboreal forest area recently affected by major wildfires, Tyresta National Park and Nature Reserve (TNPNR), south of Stockholm. A total of 21 249 individuals were collected in Malaise traps, of which males constituted 16 976 and females 4 273. The analysed dataset represents 37 samples containing 18 549 specimens sorted into 330 species (184 described, 146 are either undescribed or of unsettled taxonomic status). It was not possible to estimate the total species richness using all samples due to heterogeneity caused by inclusion of different communities and temporal incoherencies between samples within and between years. Even with material obtained from a sampling program that was not designed for species richness estimates, it was possible to obtain reliable results when sample heterogeneity was minimized. By dividing the data into community‐specific datasets – for bog, forest and wildfire – it was possible to obtain asymptotic curves for the smaller of the two wildfire datasets. A total estimate of 357–439 (95% CI) was attained by using the smaller wildfire dataset and adding the 85 unique species from the samples not included in the estimation analysis. TNPNR has one of the richest known scuttle fly communities in Europe, consisting of almost 50% of the currently named Megaselia species; 48 of these species are reported as new records for Sweden in this study.     

With eyes wide open: a revision of species within and closely related to the Pocillopora damicornis species complex (Scleractinia; Pocilloporidae) using morphology and genetics

Molecular studies have been instrumental for refining species boundaries in the coral genus Pocillopora and revealing hidden species diversity within the extensively studied global species Pocillopora damicornis. Here we formally revise the taxonomic status of species closely related to and within the P. damicornis species complex, taking into account both genetic evidence and new data on morphometrics, including fine‐scale corallite and coenosteum structure. We found that mitochondrial molecular phylogenies are congruent with groups based on gross‐morphology, therefore reflecting species‐level differentiation. However, high levels of gross morphological plasticity and shared morphological characteristics mask clear separation for some groups. Fine‐scale morphological variation, particularly the shape and type of columella, was useful for differentiating between clades and provides an excellent signature of the evolutionary relationships among genetic lineages. As introgressive hybridization and incomplete lineage sorting complicate the delineation of species within the genus on the basis of a single species concept, the Unified Species Concept may represent a suitable approach in revising Pocillopora taxonomy. Eight species are herein described (P. damicornis, P. acuta, P. aliciae, P. verrucosa, P. meandrina, P. eydouxi, P. cf. brevicornis), including a novel taxon – P ocillopora bairdi sp. nov. (Schmidt‐Roach, this study). Citation synonyms and type materials are presented. © 2014 The Linnean Society of London     

Reconciling topographic and climatic effects on widespread and range-restricted species richness

Aim To identify the reasons behind differing geographical species richness patterns of range‐restricted and widespread species. Location The Western Hemisphere. Methods We used regression to determine the strongest environmental predictors of richness for widespread and range‐restricted mammal species in 10,000 km² quadrats in the continental Americas. We then used range‐placement models to predict the expected correlation between range‐restricted and widespread species richness were they to be determined by identical, random, or contrasting environmental factors. Finally, to determine the reasons underlying deviations from these predictions, we divided the Americas into 5% quantiles based on temperature and topographic heterogeneity and correlated richness of these two assemblages across quantiles – an approach that avoids constraints on statistical testing imposed by low potential for range overlap among range‐restricted species. Results Minimum annual temperature was the strongest predictor of widespread species richness while topographic heterogeneity was the best, although weak, predictor of range‐restricted species richness in conventional regression analysis. Our models revealed that the observed correlation between range‐restricted and widespread species richness was similar to what would be observed if both range‐restricted and widespread species richness were determined by temperature. Patterns of range‐restricted and widespread species richness were highly correlated across temperature quantiles, but range‐restricted species uniquely showed an increasing pattern across heterogeneity quantiles. Main conclusions Species richness gradients among range‐restricted species differ from those of widespread species, but not as extensively or for the reasons reported previously. Instead, these assemblages appear to share some but not all underlying environmental determinants of species richness. Our new approach to examining species richness patterns reveals that range‐restricted and widespread species richnesses share a common response to temperature that conventional analyses have not previously revealed. However, topographic heterogeneity has assemblage‐specific effects on range‐restricted species.     

Integration, individuality and species concepts

Integration (interaction among parts of an entity) is suggested to be necessary for individuality (contra, Metaphysics and the Origin of Species). A synchronic species is an integrated individual that can evolve as a unified whole; a diachronic lineage is a non-integrated historical entity that cannot evolve. Synchronic species and diachronic lineages are consequently suggested to be ontologically distinct entities, rather than alternative perspectives of the same underlying entity (contra Baum (1998), Syst. Biol. 47, 641–653; de Queiroz (1995), Endless Forms: Species and Speciation, pp. 57–75; Genes, Categories and Species). Species concepts usually refer to either one or the other entity; for instance, the Biological Species Concept refers to synchronic species, whereas the Cladistic Species Concept refers to diachronic lineages. The debate over species concepts has often failed to recognise this distinction, resulting in invalid comparisons between definitions that attempt to delineate fundamentally different entities. This revised version was published online in July 2006 with corrections to the Cover Date.     

The nature of species: A rejoinder to Zachos et al.

I argue strongly that the Phylogenetic Species Concept offers the only way of defining species that makes them testable, as any scientific hypothesis should be. The criticisms made by Zachos et al. (in press) are not cogent, and do not offer a means of testing species proposals. Nonetheless, their comments on species concepts in conservation do provide support to the value of the Phylogenetic Species Concept.     

Signals of range expansions and contractions of vascular plants in the high Alps: observations (1994–2004) at the GLORIA* master site Schrankogel,Tyrol, Austria

High mountain ecosystems are defined by low temperatures and are therefore considered to react sensitively to climate warming. Responding to observed changes in plant species richness on high peaks of the European Alps, an extensive setup of 1 m × 1 m permanent plots was established at the alpine‐nival ecotone (between 2900 and 3450 m) on Mount Schrankogel, a GLORIA master site in the central Tyrolean Alps, Austria, in 1994. Recording was repeated in a representative selection of 362 quadrats in 2004. Ten years after the first recording, we observed an average change in vascular plant species richness from 11.4 to 12.7 species per plot, an increase of 11.8% (or of at least 10.6% at a 95% confidence level). The increase in species richness involved 23 species (about 43% of all taxa found at the ecotone), comprising both alpine and nival species and was pronouncedly higher in plots with subnival/nival vegetation than in plots with alpine grassland vegetation. Only three species showed a decrease in plot occupancy: one was an annual species, one was rare, and one a common nival plant that decreased in one part of the area but increased in the uppermost part. Species cover changed in relation to altitudinal preferences of species, showing significant declines of all subnival to nival plants, whereas alpine pioneer species increased in cover. Recent climate warming in the Alps, which has been twice as high as the global average, is considered to be the primary driver of the observed differential changes in species cover. Our results indicate an ongoing range contraction of subnival to nival species at their rear (i.e. lower) edge and a concurrent expansion of alpine pioneer species at their leading edge. Although this was expected from predictive distribution models and different temperature‐related habitat preferences of alpine and nival species, we provide first evidence on – most likely – warming‐induced species declines in the high European Alps. The projected acceleration of climate warming raises concerns that this phenomenon could become the major threat to biodiversity in high mountains.     

Butterfly populations in two forest fragments at the Kenya coast

Species richness, diversity and composition of butterflies in two Kenya coastal forest remnants, Muhaka and Mrima hill, were investigated. Sixty‐three species were recorded from each forest remnant from a total of 1329 individuals. Species accumulation curves for both forests did not reach an asymptote. High species similarity was recorded between the forest interior and the surrounding matrix, primarily due to invasion of the forest interior clearings by the savanna species. Despite their small sizes, these forest remnants were found to maintain viable populations of true forest butterflies. However, the number of species was less than half that recorded from the larger forest reserve of Arabuko‐Sokoke, located in the same geographical area. Records from Muhaka forest show species unique to it, not found in the larger forest reserves, underscoring the importance of small remnants in the preservation of forest biodiversity. The high species similarity between the forest remnants implied that if habitat corridors were created, gene flow between these remnants and other larger forest reserves would be possible. This would reduce the isolation of true forest butterfly populations within the remnants and potential local extinction.