When monophyly is not enough: exclusivity as the key to defining a phylogenetic species concept

A natural starting place for developing a phylogenetic species concept is to examine monophyletic groups of organisms. Proponents of “the” Phylogenetic Species Concept fall into one of two camps. The first camp denies that species even could be monophyletic and groups organisms using character traits. The second groups organisms using common ancestry and requires that species must be monophyletic. I argue that neither view is entirely correct. While monophyletic groups of organisms exist, they should not be equated with species. Instead, species must meet the more restrictive criterion of being genealogically exclusive groups where the members are more closely related to each other than to anything outside the group. I carefully spell out different versions of what this might mean and arrive at a working definition of exclusivity that forms groups that can function within phylogenetic theory. I conclude by arguing that while a phylogenetic species concept must use exclusivity as a grouping criterion, a variety of ranking criteria are consistent with the requirement that species can be placed on phylogenetic trees.

Evolution,actuality and species concept: a need for a palaeontological tool

Species concept was developed to fit neontological necessities in ordering biological variability. Transversal (horizontal, synchronic) taxonomy shows hierarchical requirements quite different from those involved in longitudinal (vertical, diachronic) classifications. Furthermore, limitations within the species concept itself make it scarcely available in many paleontological contexts. Classical species definitions are often limited by theoretic and logic constraints, that are seldom available to describe practical situations. Morphology is an uncertain source of phylogenetic information, but it is still the main ground of biological comparison for extinct populations. Therefore, efforts in species recognition should be devoted to making taxonomy a useful tool for communication. First, inferences in systematics have to be led upon the available information about characters and processes. If this information is missing or not developed, no detailed conclusions can be supported. Secondly, definitions should be sufficiently elastic and generalised to allow an adaptation to each different case-study. The final target is to synthesise actual evolutionary histories, and not biological potentialities.     

How to be a chaste species pluralist-realist: the origins of species modes and the synapomorphic species concept

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades.     

Birding and DNA: species for the new millennium

Capsule Based on the 1999 Witherby Memorial Lecture – reviews how developments in molecular and population genetics have led to a reappraisal of species limits in birds.

The taxonomy of birds of the West Palearctic has moved from the comparative stability of the ‘Voous List’ into a period of serious activity, with new data emerging in almost every issue of every evolutionary and avian journal! This activity comes from two directions. Firstly, developments in population genetics, molecular biology, acoustics, behaviour and distributional studies have opened new avenues to measuring differentiation among groups of birds. This, in turn, has led to the recognition that earlier views of what constitutes a ‘species’ are in need of modification (‘improvement’), and the emergence of the ‘lineage concept’ of species. I review some of the species concepts most relevant to avian studies, and attempt to show how and why this change has happened, and its consequences for taxonomy and species limits. Examples are given in the form of ‘case studies’, and include Carrion/Hooded Crows Corvus corone/cornix, Green-winged/Eurasian Teals Anas carolinensis/crecca and Phylloscopus warblers.     

Identifying indicator plant species of habitat quality and invasibility as a guide for peri-urban forest management

A floristic survey has been carried out in a peri-urban forest, the Sonian Forest in Brussels, to identify indicator plant species in the herbaceous layer, which could be used as an aid within the framework of a more sustainable management of the forest. Three hundred and seventy two (372) taxa have been identified, 33 of which are non-native (i.e. non-indigenous species regarding the study area, whether invasive or not). Criteria of habitat quality that have been chosen are the species richness, the commonness of the habitat, based on constitutive species, and its invasibility (vulnerability for invasion). On the basis of a comparison of the value of these criteria when each considered (potential indicator) species is present or not, 17 species have been recognised as reliable indicators of at least one of these three criteria. In particular, vegetation types containing either Anthriscus sylvestris, Galeopsis tetrahit or Senecio ovatus were found to be more susceptible to invasion than other habitats. The way to how the predictability of invasions might be effectively used as a management tool is discussed. Furthermore, we found a positive significant correlation (Bonferroni corrected probabilities) between the species richness and luminosity factor (derived from Ellenberg's indices), and the proportion of grassland and wetland species. The species richness was significantly negatively correlated with the proportion of woodland species. An increase in commonness was significantly correlated with a decrease in the proportion of geophytes. The usefulness of these results as an ecological basis for forest management is discussed.     

Methods for detecting non-randomness in species co-occurrences: a contribution

Summary Comparison of co-occurrences between species on a group of islands with those expected from a randombased null model could provide evidence on community structure. However, it is difficult to decide on the appropriate null model. Gilpin and Diamond proposed a model and a test for departure from it, but this test is shown to indicate significant structure even when applied to a matrix of random numbers. An alternative method is suggested, using the distribution of Gilpin and Diamond's deviation as test statistic, but determining the expected distribution by Monto Carlo simulation, and using many such simulations as a randomisation test of significance. The null model used accepts the observed totals of occurrences for islands and species; it therefore offers a somewhat conservative test. Applied to the Vanuatu bird data that Gilpin and Diamond used, significant departure from a null model is seen, but with an excess of extreme negative associations, the opposite result from that given by Gilpin and Diamond's method. It is not possible to tell whether the negative associations are due to autecology, biogeography, or to interactions between species.     

Variation in hostplant relations and courtship signals of weed-associated populations of the brown planthopper, Nilaparvata lugens (Stål), from Australia and Asia: a test of the recognition species concept

Populations of the morphological species, Nilaparvata lugens (Stål), were found to breed and feed on the grass, Leersia hexandra Schwartz, at six sites in Queensland, Australia. They differ from sympatric rice-feeding populations in characters of pulse repetition frequencies of male and female acoustic courtship signals. The two host-derived populations hybridize freely in the laboratory, but in mate choice experiments show very significant preferences for homogametic matings. No indication of field hybridization has been found, so that the two morphologically inseparable populations represent sympatric biological species in Australia.
Populations from L. hexandra are also reported from four localities in Sri Lanka and one in Orissa, India. These resemble previously studied populations from the Philippines. They differ significantly in courtship call characters, both from sympatric rice-associated populations and from allopatric Leersia -associated populations from Australia.
The geographical variation reported for acoustic signals is not consistent with Paterson's recognition concept of species, but may be interpreted in terms of theories of allopatric speciation involving sexual selection for mate recognition signals.     

Small-scale plant species turnover in a limestone grassland: the carousel model and some comments on the niche concept

Abstract. This study reports on small-scale changes in the distribution of plant species in a 2.5 m² plot of grazed, species-rich Veronica spicata - Avenula pratensis grassland on shallow, dry, nutrient-poor soil in the Great Alvar area (Stora Alvaret) of southern Öland, southeastern Sweden. Multivari-ate analysis of 0.001 m² and 0.25 m² quadrats within the plot showed that there is little floristic variation without any trend in the plot. Average species richness varied little throughout the study period from 1986 to 1991 with 1986 averages of 7.0 on 0.001m², 16.3 on 0.01 m², and 26.1 on 0.25 m². On 0.001 m²the highest species number found was 12, on 0.01 m², 27. However, cumulative species richness, i.e. species number in the first year plus new species appearing in later years (averaged over 40 quadrats) increased over the same period, on 0.001 m² from 7.0 in 1986 to 14.9 in 1991, and on 0.01 m² from 16.3 to 24.1. Cumulative frequency, i.e. number of quadrats out of 40 where a species occurred in the first year or/and in later years, increased as well; the number of cumulatively highly frequent (> 80%) species increased from 5 in 1986 to 18 in 1991. Species mobility on the scale of the small quadrats used implies both appearance and disappearance from these quadrats. Using six examples, species mobility is shown to vary individualistically, both in rate and degree. We postulate that in homogeneous, grazed, nutrient- and water-deficient environments many species can reach virtually all microsites within the plot, which we express through the idea of the ‘carousel model’. We also question the usefulness of the niche concept and re-interpret it by stating that all species of this plant community have the same habitat niche, while most of them are short-lived and have the same regeneration niche. The essential variation amongst the species is their individual ability to establish or re-establish by making use of favourable conditions appearing in microsites in an unknown, complex spatio-temporal pattern.     

A peculiar relationship between genetic diversity and adaptability in invasive exotic species: bluegill sunfish as a model species

A peculiar relationship exists between population genetics and invasion biology. Introduced populations often suffer a depletion of genetic variation, but they can persist and adapt to new environments. Here, we show that this relationship is observed in bluegill sunfish (Lepomis macrochirus), an invasive exotic fish in Japan. Genetic analysis using selectively neutral genetic markers reconfirmed that the bluegill introduced into Japan from the United States in 1960 had a single origin with only 15 founders. The analysis also shows that in the process of range expansion, the introduced bluegills experienced severe depletion of genetic diversity due to the founder effect and/or genetic drift. Despite such a decline in genetic diversity, the bluegill populations exhibited a divergent feeding morphology in response to the colonized environments. Such a morphological divergence can facilitate prey exploitation, thereby causing a greater negative impact on native prey resources. Further, in a trophically polymorphic bluegill population in Lake Biwa, physiological characteristics and genetic structures of the intestinal bacterial communities were associated with the difference in diet among the trophic morphs in the host bluegill population. This empirical evidence suggests that despite the severe decline in genetic diversity, the introduced bluegill populations rapidly adapted to the new environment and formed diverse functional relationships with the native bacterial community. Thus, these findings suggest that genetic variation at selectively neutral markers does not always predict adaptability and invasiveness in introduced populations.     

Reconsidering the taxomony of several Ostrinia species in the light of reproductive isolation: a tale for Ernst Mayr

We reconsider the taxonomy of a group of closely related Ostrinia spp., illustrating how useful Mayr's biological species concept remains for studying speciation patterns and processes. We review and re-analyse recent data on Ostrinia scapulalis , Ostrinia nubilalis , Ostrinia narynensis and Ostrinia orientalis , along with those obtained over > 45 years in the former Soviet Union. The ten species of the 'trilobed uncus' group in the Ostrinia genus are classified into subgroups according to male mid-tibia morphology. However, none of the characters that further discriminate between them (female sex pheromones, male genitalia and calling time) varies together with male mid-tibia morphology, and neither do molecular markers. Moreover, male mid-tibia morphology appears to depend on only two diallelic loci and seems to be unrelated to reproductive isolation between Ostrinia taxa. By contrast, reproductive isolation is strongly related to host-plant type. In accordance with Mayr's species concept, we thus propose a revision of the trilobed uncus Ostrinia spp. based primarily on host-plant type. We propose that O. narynensis Mutuura & Munroe, 1970 ( syn. nov. ) and O. orientalis Mutuura & Munroe, 1970 ( syn. nov. ) be synonymized with O. scapulalis (Walker, 1859). We further demonstrate that O. nubilalis auctt. pro parte feeding on mugwort, hop, and several other dicotyledons (previously called the ' O. nubilalis mugwort-race' in France) also belongs to O. scapulalis . Consequently, we propose that only O. nubilalis specimens feeding on maize (the former French ' O. nubilalis maize-race') belong to O. nubilalis (Hübner, 1796). The implications of this revision are discussed.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 49–72.     

Air pollution as a possible cause for the decline of some phanerogamic species in The Netherlands

In The Netherlands the decline of some phanerogamic species cannot be readily explained from obvious factors such as lowering of the groundwater table, eutrophication or land reclamation. For a number of species the hypothesis was tested that the decline is partly due to air pollution. A two-factor model was made in which decline is accounted for by (a) habitat destruction assessed from topographic maps and (b) air pollution measured as the SO₂ 95-percentile over the winter period 1978/1979. Effects of both factors were assumed to follow a sigmoid dose-effect curve. For a number of species decline proved to be significantly correlated with air pollution. These are notably species from the syntaxon Violion caninae. A comparison was made with results obtained for epiphytic lichens. It appears that for some phanerogamic species sensitivity is about the same as for moderately sensitive lichens.Nomenclature follows Heukels & van der Meijden (1983).Thanks are due to the Rijksherbarium, for providing some of their unpublished data; and to Ada Groeneveld, for technical assistance.     

Unravelling below-ground plant distributions: a real-time polymerase chain reaction method for quantifying species proportions in mixed root samples

Knowledge on below-ground plant distributions is almost lacking to date, despite the fact that such information would be very valuable in understanding below-ground competition and species-specific interactions, processes that are expected to shape community structure. Methods available so far for below-ground species determination have drawbacks that we tried to challenge. Some methods make use of differences in the chemical composition between species, but this is highly variable upon environmental factors. DNA-based techniques - far less dependent on chemical composition - such as polymerase chain reaction on internal transcribed spacer (ITS) primers can so far only determine presence-absence of a species in a mixed root sample. Here, we present a quantitative DNA-based technique that allows investigation of relative species abundances in experimental mixed root samples. We used quantitative real-time polymerase chain reaction (PCR) on species-specific markers obtained from intersimple sequence repeat (ISSR) analyses in root samples. This molecular technique is novel in the field of root ecology and its development overcame three challenges: (i) determination of species-specific DNA fragments, (ii) development and optimization of the real time PCR protocol, (iii) designing a data treatment method based on a modified delta-delta-cycle threshold (CT) analysis. The method gained robustness from using relative DNA abundances in species mixtures rather than absolute concentration readings. This requires accurate multispecies reference series as a calibration. Test samples with different known biomass ratios of all species showed proof of concept of this method. The pro's and contra's of this method are discussed in the light of its contribution to advancing ecological research on below-ground plant-plant interactions.     

Message in a bottle: Inadvertent loss of seeds of native grassland species as a result of rudimentary long‐term storage

Many practitioners are likely to have collected seeds with the intention of using that seed for conservation and/or restoration plantings, but have not got around to using the seed, sometimes for many years. Currently, it is not clear what species have short‐lived or long‐lived seed when stored under rudimentary conditions such as in paper bags or in a refrigerator. We report the germinability of 12 temperate native grassland species, comprising 16 populations, whose seeds were collected with the purpose of raising seedlings to plant into the wild, but whose seeds were subsequently stored at ~2–4°C for 25+ years. We conclude that most of the grassland species that we assessed do not have viable seed after 25 years when stored in such conditions; only two species germinated despite evidence that seed germinates well for most species when first collected. Inadvertent loss of seeds of as a result of long‐term storage is most likely in readily germinable species (e.g. members of the Asteraceae). The ways in which seeds are stored by practitioners deserves consideration given the risk of seed mortality with long‐term storage under rudimentary conditions.     

Importance of abiotic stress as a range-limit determinant for European plants: insights from species responses to climatic gradients

Aim We examined whether species occurrences are primarily limited by physiological tolerance in the abiotically more stressful end of climatic gradients (the asymmetric abiotic stress limitation (AASL) hypothesis) and the geographical predictions of this hypothesis: abiotic stress mainly determines upper‐latitudinal and upper‐altitudinal species range limits, and the importance of abiotic stress for these range limits increases the further northwards and upwards a species occurs. Location Europe and the Swiss Alps. Methods The AASL hypothesis predicts that species have skewed responses to climatic gradients, with a steep decline towards the more stressful conditions. Based on presence–absence data we examined the shape of plant species responses (measured as probability of occurrence) along three climatic gradients across latitudes in Europe (1577 species) and altitudes in the Swiss Alps (284 species) using Huisman–Olff–Fresco, generalized linear and generalized additive models. Results We found that almost half of the species from Europe and one‐third from the Swiss Alps showed responses consistent with the predictions of the AASL hypothesis. Cold temperatures and a short growing season seemed to determine the upper‐latitudinal and upper‐altitudinal range limits of up to one‐third of the species, while drought provided an important constraint at lower‐latitudinal range limits for up to one‐fifth of the species. We found a biome‐dependent influence of abiotic stress and no clear support for abiotic stress as a stronger upper range‐limit determinant for species with higher latitudinal and altitudinal distributions. However, the overall influence of climate as a range‐limit determinant increased with latitude. Main conclusions Our results support the AASL hypothesis for almost half of the studied species, and suggest that temperature‐related stress controls the upper‐latitudinal and upper‐altitudinal range limits of a large proportion of these species, while other factors including drought stress may be important at the lower range limits.     

Automata networks as preprocessing technique of artificial neural network in estimating primary production and dominating phytoplankton levels in a reservoir: An experimental work

Artificial Neural Networks (ANN) is computational architectures that can be used for estimating primary production levels and dominating phytoplankton species in reservoirs. Automata Networks (AN) were applied as a pre-processing method with subsequent ANN model development for Demirdöven Dam Reservoir. The primary purpose of using pre-processing technique was to distinguish the suitable and appropriate constituents of the input parameters' matrix, to eliminate redundancy, to enhance prediction power and calculation efficiency. The data were collected monthly over two years. The applications have yielded following results: The correlation coefficients (r values) between predicted and observed counts were as high as 0.83, 0.87, 0.83 and 0.88 for Cyclotella ocellata, Sphaerocystis schroeteri, Staurastrum longiradiatum counts, and Chlorophyll-a (Chl-a) concentrations respectively with AN. The performance of AN based pre-processing technique was compared with the performance of a well-known pre-processing technique, namely Principle Component Analysis(PCA), experimentally. r values between the predicted and observed C. ocellata, S. schroeteri and S. longiradiatum counts, and (Chl-a) were as high as 0.80, 0.86, 0.81 and 0.86 respectively with PCA.     

Anzygina, a new genus for some Australasian microleafhopper species formerly placed in the genus Zygina Fieber (Cicadellidae: Typhlocybinae: Erythroneurini)

Species of Erythroneurini (Cicadellidae: Typhlocybinae) currently placed in the genus Zygina and found in Australia, New Zealand and some neighbouring islands are transferred to the new genus Anzygina , type species Erythroneura sidnica Kirkaldy, following comparison with the type species of the genus: Typhlocyba nivea Mulsant and Rey. New combinations are Anzygina sidnica (Kirkaldy), Anzygina honiloa (Kirkaldy), Anzygina melanogaster (Kirkaldy) and Anzygina sativae (Evans) from Australia, Anzygina toetoe (Cumber), Anzygina agni (Knight), Anzygina dumbletoni (Ghauri) and Anzygina ramsayi (Knight) from New Zealand, Anzygina zealandica (Myers) from Australia and New Zealand, Anzygina jowettae (Knight) from Norfolk Island and Anzygina medioborealis (Ghauri) from Papua New Guinea. Lectotypes are designated for Erythroneura honiloa Kirkaldy and E. sidnica Kirkaldy. Anzygina billi sp.n. is described from SE Qld, and Anzygina barrattae sp.n. is described from the South Island of New Zealand. A. agni is a new record for Australia and is presumed to be Australian in origin. A. dumbletoni has a distribution which suggests that it also is introduced to New Zealand although its origins are not known. A. ramsayi, A. barrattae and A. toetoe , all of which appear to be New Zealand endemics, show affinity with each other based on aedeagal structure. A key to these species, based on males, is provided. The lack of male syntypes for Erythroneura honiala Kirkaldy and Erythroneura lubra Kirkaldy precludes establishment of their identities relative to other species of the genus, and both names are regarded as having nomen dubium status. Australian species not transferred to Anzygina are Zygina evansi (Ross) and Zygina ipoloa (Kirkaldy), both of which belong elsewhere.     

Development of PEGylated serum albumin with multiple reduced thiols as a long-circulating scavenger of reactive oxygen species for the treatment of fulminant hepatic failure in mice

Reactive oxygen species (ROS) are involved in the pathophysiology of fulminant hepatic failure. Therefore, we developed polyethylene glycol-conjugated bovine serum albumin with multiple reduced thiols (PEG-BSA-SH) for the treatment of fulminant hepatic failure. As a long-circulating ROS scavenger, PEG-BSA-SH effectively scavenged highly reactive oxygen species and hydrogen peroxide in buffer solution. PEG-BSA-SH showed a long circulation time in the plasma after intravenous injection into mice. Fulminant hepatic failure was induced by intraperitoneal injection of lipopolysaccharide and d-galactosamine (LPS/d-GalN) into mice. The LPS/d-GalN-induced elevation of plasma alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels was significantly inhibited by a bolus intravenous injection of PEG-BSA-SH. Furthermore, the changes in hepatic lipid peroxide and hepatic blood flow were effectively suppressed by PEG-BSA-SH. In contrast, l-cysteine, glutathione, and dithiothreitol, three traditional reduced thiols, had no statistically significant effects on the serum levels of ALT or AST. These findings indicate that PEG-BSA-SH is a promising ROS scavenger and useful in the treatment of fulminant hepatic failure.