Taxa, individuals, clusters and a few other things

The recognition of species proceeds by two fairly distinct phases: (1) the sorting of individuals into groups or basic taxa (‘discovery’) (2) the checking of those taxa as candidates for species-hood (‘justification’). The target here is a rational reconstruction of phase 1, beginning with a discussion of key terms. The transmission of ‘meaning’ is regarded as bimodal: definition states the intension of the term, and diagnosis provides a disjunction of criteria for recognition of its extension. The two are connected by a spectrum, with purely theoretical definition at one pole and purely ‘operational’ diagnosis at the other, with the more operational elements explained by the more theoretical. The current plethora of species concepts provides a good example. Accepting the Ghiselin–Hull thesis, that a species is an individual, a basic taxon is therefore also an individual with organisms as its parts. In a generalised synchronic individual its parts are conceptually integrated by an integrating principle (IP), which consists of a relation applying within a plan or rule. Fully developed, such an IP ensures the maximisation of the information content of the individual. A diachronic individual is then the set of its component synchronic parts, and its IP is provided by near-identity in an appropriate space-time (not necessarily physical). The integration of parts of an individual is illuminated by Gasking's concept of a proper group (in this case a chain-group), whose members are related by the relation serially fitting together with, the IP completed by an appropriate plan or rule. Gasking also applied the term cluster to a proper group persisting over a substantial period of time, individuated by any member acting as focus. A basic taxon is therefore a cluster of individuals, integrated by the relation significantly taxonomically similar and the rule in character-space-time. The nature of those concepts is discussed and defended. A species will inherit certain of the attributes of the preceding basic taxon (taxa). In at least the synchronic version its parts (individuals) will resemble each other significantly, providing the intuitive applicability of ‘members of’ and ‘instances of’ a species. Also, the notion that a species’ name is given by pure ostension, via a name-bearer (holotype) is empirically incoherent: the name cannot be applied in practice without an appropriate set of diagnostic traits.     

Kelp flies and species concepts – the case of Coelopa frigida (Fabricius, 1805) and C. nebularum Aldrich, 1929 (Diptera: Coelopidae)

The beaches of the North Atlantic and North Pacific are home to kelp flies of the Coelopa frigida/nebularum complex, which consists of one to three different species depending on whether the two nominal species are accepted and a cryptic species proposed by Remmert is counted. The morphological differences between two populations of C. frigida ( Fabricius, 1805 ) from the North Sea and the Baltic Region and two populations of C. nebularum Aldrich, 1929 from Alaska and Japan are described and discussed for small, medium, and large specimens. Crossing experiments are used to demonstrate that, under laboratory conditions, no isolation mechanisms between either population exist. Coelopa frigida and C. nebularum are therefore regarded as a single biological species, a conclusion that is congruent with the observation that the genetic distances based on Ef 1‐α and 16S rDNA indicate lower levels of differentiation within C. frigida/nebularum than between undisputed Coelopa species. The substantial morphological, breeding and genetic information on the C. frigida/nebularum species complex is then applied to six different species concepts popular in the modern systematic literature. According to the Biological, Hennigian and Recognition Species Concepts, only a single species would be recognized. The Evolutionary Species Concept is too vague to be applicable and under two variants of the Phylogenetic Species Concept, C. frigida and C. nebularum would constitute separate species. This result confirms that Phylogenetic Species Concepts lead to a higher species number than concepts based on reproductive isolation. Practical and theoretical problems with the various species concepts are briefly discussed.     

Blackfly assemblages (Diptera,Simuliidae) of the Carpathian river: habitat characteristics,longitudinal zonation and eutrophication

Investigations were carried out in 2003–04 within a project on trend biomonitoring of macrozoobenthos in the Hron River system. They were focused on blackfly assemblages of the Hron River (Slovakia), using the distribution patterns of blackflies (18 species) from 14 sites, representing a fluent transition from epirithral to epipotamal. Two main “sister” groups were distinguished using TWINSPAN analysis. Prosimulium rufipes is an indicator species within the first group. This group typically occurs in the zone representing a part of the river upstream and its tributaries. Simulium lineatum is an indicator species within the second group that occurs in the zone representing the middle and lower part of the river. The Upstream–Downstream gradient represents, in fact, the ecological position (EP) of the studied localities of the Hron River along the River Continuum Concept. The distribution fitting analysis divides the distribution amplitude data of blackfly species into three sets of nonoverlaping intervals: (1) 0.00–0.19 stenotopic (P. rufipes in the upper course of the river, Simulium erythrocephalum in the lower course of the river), (2) 0.20–0.39 mesotopic (Simulium argyreatum, S. equinum—hyporhithral) and (3) 0.40–0.50 eurytopic (Simulium reptans, S. variegatum). According to CCA the most important variables correlated with the first axis, and were linked to the nitrate and maximal water temperature which gradually increase from the upper stretch of the river. Handling editor: K. Martens     

On the nature of species: insights from <Emphasis Type="Italic">Paramecium</Emphasis> and other ciliates

The multiple species concepts currently in use by the scientific community (e.g. Morphological, Biological, Phylogenetic) are united in that they all aim to capture the process of divergence between populations. For example, the Biological Species Concept defines a species as a natural group of organisms that is reproductively isolated from other such groups. Here we synthesize nearly a century of research on the ciliate genus Paramecium that highlights the shortcomings of our prevailing notions on the nature of species. In this lineage, there is discordance between morphology, mating behavior, and genetics, features assumed to be correlated, at least after sufficient time has passed, under all species concepts. Intriguingly, epigenetic phenomena are well documented in ciliates where they influence features such as germline/soma differentiation and mating type determination. Consequently, we hypothesize that divergence within ciliate populations is due to a dynamic interaction between genetic and epigenetic factors. The growing list of examples of epigenetic phenomena that potentially impact speciation (i.e. by influencing the dynamics of sex chromosomes, fate of hybrids, zygotic drive and genomic conflicts) suggests that interactions between genetics and epigenetics may also drive divergence in other eukaryotic lineages.     

High population density promotes the evolution of ownership

Previous studies have discussed the evolution of ownership using the Hawk–Dove–Bourgeois game. Decisive parameters are resource values (V) and contest costs (C). However, ownership may also evolve as a result of the effects of population density. To compare the effects of population density with those of resource values, I created a learning-based model of a revised Hawk–Dove–Bourgeois game. The game simulates the dynamics of agents that struggle for regions (“territories”) along a line. With appropriate sets of r (resource value) and l (reciprocal of the population density), the model showed that ownership is more likely to evolve when the resource value is small and population density is high. An area containing high-value resources is likely to accompany high population density. However, simulations showed that population density has stronger effects than resource value on the evolution of ownership.     

Useful Species Richness,Proportion of Exotic Species,and Market Orientation on Amazonian Dark Earths and Oxisols<Superscript>1</Superscript>

Useful Species Richness, Proportion of Exotic Species, and Market Orientation on Amazonian Dark Earths and Oxisols Anthropogenic soils of Amazonia, known as Amazonian Dark Earths (ADE), are environments with elevated soil fertility that can produce crops that otherwise yield poorly on the leached and highly acidic Oxisols that dominate much of the basin. While ADE sites near urban centers often attract commercial horticultural production of nutrient–demanding exotics, these soils are also considered possibly unique reservoirs of endemic agrobiodiversity because of their relationship to pre–Columbian indigenous occupation. Through botanical surveys and interviews with smallholder farmers, this study compared useful species richness, proportion of exotic species, and market orientation of farms situated on ADE and non–anthropogenic Oxisols in the municipality of Borba in Central Brazilian Amazonia. Species richness was similar on Amazonian Dark Earth and Oxisol farms (19.6 spp vs. 18.3 spp); however, ADE farms showed significantly higher proportions of exotic species (39% vs. 26%; p = 0.025). Furthermore, ADE farms in Borba demonstrated significantly higher market orientation (61.0% vs. 47.3%; p = 0.028), likely a result of the advantage of Amazonian Dark Earths for production of crops that are nutrient–demanding or pH–sensitive crops that have higher values in the nearby regional market of Manaus.     

Empirical and philosophical problems with the subspecies rank

Species‐level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species “concepts.” These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what “kind” of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology. This lack of coherence is in part responsible for the persistence of the subspecies rank, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse of incipient species. Thus, prospective events like lineages merging or diverging require information from unknowable future information. This is also conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies can seem attractive given that many lineages do not exhibit intrinsic reproductive isolation. We argue that using subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatiotemporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from evolutionary ontology and do not consider genealogy. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.     

Lower Permian Bryozoa of the Jamal Formation from Bagh-e Vang (Shotori Mountains,northeast Iran)

Lower Permian Bryozoan fauna of Jamal Formation, exposed in Bagh-e Vang (Shotori Mountains, northeast Iran) includes six species. Three species – Streblotrypa (Streblascopora) marmionensis (Etheridge 1926), Rhabdomeson bispinosum (Crockford 1944) and Alternifenestella kungurensis (Stuckenberg 1898) – indicate the Lower Permian (Artinskian to Kungurian) age of the formation. Three additional taxa – Fistulipora sp. 1, Fistulipora sp. 2 and undetermined timanodictyid bryozoan ?Timanodictya sp. could not be identified at the species level. The investigated fauna refers to Uralian and Australian palaeobiogeographic provinces.     

Butterflies and skippers (Lepidoptera,Diurna) from the Republic of Mordovia

According to the data obtained, the Mordovian fauna of diurnal lepidopterans comprises 75 species, including Hesperiidae (7 species), Papilionidae (5), Pieridae (10), Satyridae (10), Nymphalidae (27), and Lycaenidae (16). Based on the quantitative assessments, the species were characterized as rare (1–5 ind. in the collection), scarce (6–30), common (31–170), and abundant (171–940). Species with temperate (52 species or 69.3%) and subboreal (12 species or 16.0%) ranges predominated in the latitudinal distribution pattern. The total and background species diversity of the Diurna was the highest in the forests (63 species) and meadows (52), and the lowest on the steppe slopes (6). Among the species revealed, 14 were rare: Iphiclides podalirius, Zerynthia polyxena, Parnassius apollo, Driopa mnemosyne, Colias erate, Coenonympha hero, Neptis sappho, Apatura iris, Limenitis populi, Nymphalis antiopa, Fixsenia pruni, Lycaena helle, Cupido minimus, and Maculinea arion.     

Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)

Species endemic to alpine environments can evolve via steep ecological selection gradients between lowland and upland environments. Additionally, many alpine environments have faced repeated glacial episodes over the past two million years, fracturing these endemics into isolated populations. In this “glacial pulse” model of alpine diversification, cycles of allopatry and ecologically divergent glacial refugia play a role in generating biodiversity, including novel admixed (“fused”) lineages. We tested for patterns of glacial pulse lineage diversification in the Yosemite toad (Anaxyrus [Bufo] canorus), an alpine endemic tied to glacially influenced meadow environments. Using double‐digest RADseq on populations densely sampled from a portion of the species range, we identified nine distinct lineages with divergence times ranging from 18 to 724 thousand years ago (ka), coinciding with multiple Sierra Nevada glacial events. Three lineages have admixed origins, and demographic models suggest these fused lineages have persisted throughout past glacial cycles. Directionality indices supported the hypothesis that some lineages recolonized Yosemite from east of the ice sheet, whereas other lineages remained in western refugia. Finally, refugial niche reconstructions suggest that low‐ and high‐elevation lineages have convergently adapted to similar climatic niches. Our results suggest glacial cycles and refugia may be important crucibles of adaptive diversity across deep evolutionary time.     

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.     

Evolutionary relationships among photosynthetic bacteria

To understand the evolution of photosynthetic bacteria it is necessary to understand how the main groups within Bacteria have evolved from a common ancestor, a critical issue that has not been resolved in the past. Recent analysis of shared conserved inserts or deletions (indels) in protein sequences has provided a powerful means to resolve this long-standing problem in microbiology. Based on a set of 25 indels in highly conserved and widely distributed proteins, all main groups within bacteria can now be defined in clear molecular terms and their relative branching orders logically deduced. For the 82 presently completed bacterial genomes, the presence or absence of these signatures in various proteins was found to be almost exactly as predicted by the indel model, with only 11 exceptions observed in 1842 observations. The branching order of different bacterial groups as deduced using this approach is as follows: low G+C Gram-positive (Heliobacterium chlorum) ↔ high G+C Gram-positive ↔ Clostridium–Fusobacterium–Thermotoga ↔ Deinococcus–Thermus ↔ green nonsulfur bacteria (Chloroflexus aurantiacus) ↔ Cyanobacteria ↔ Spirochetes ↔ Chlamydia–Cytophaga–Flavobacteria–green sulfur bacteria (Chlorobium tepidum) ↔ Aquifex ↔ Proteobacteria (δ and ∈) ↔ Proteobacteria (α) ↔ Proteobacteria (β) and ↔ Proteobacteria (γ). The Heliobacterium species, which contain an Fe–S type of reaction center (RC 1) and represent the sole photosynthetic phylum from the Gram-positive or monoderm bacteria (i.e., bounded by only a single membrane), is indicated to be the most ancestral of the photosynthetic lineages. Among the Gram-negative or diderm bacteria (containing both inner and outer cell membranes) the green nonsulfur bacteria, which contain a pheophytin-quinone type of reaction center (RC 2), are indicated to have evolved first. The later emerging photosynthetic groups which contain either one or both of these reaction centers could have acquired such genes from the earlier branching lineages by either direct descent or by means of lateral gene transfer. This revised version was published online in August 2006 with corrections to the Cover Date.     

Microsatellite markers in the endangered Australian northern corroboree frog, Pseudophryne pengilleyi (Anura: Myobatrachidae) and amplification in other Pseudophryne species

Seven microsatellite primer pairs were isolated and characterized in the endangered Australian northern corroboree frog (Pseudophryne pengilleyi). All seven were polymorphic (2–14 alleles) and displayed high heterozygosity (0.036–0.964) in 28 sampled individuals. We also tested the microsatellites on two closely related species. Four were polymorphic in the southern corroboree frog (P. corroboree) and Bibron’s toadlet (P. bibronii). These primers will be useful in studies of conservation genetics and mating systems in Pseudophryne species.     

Phylogenetic relationships in genus <Emphasis Type="Italic">Geopora</Emphasis> (Pyronemataceae,Pezizales)

Species delimitation in the genus Geopora (Pyronemataceae) is complicated because of small number of differentiating characters, values of which tend to overlap among the species. Current classification relies mainly on size and shape of ascospores and fruit-bodies, position of the apothecia in the ground and length of excipular hairs. We measured ascospores in ca. 90 Geopora specimens. Sequences of internal transcribed spacer (ITS) rDNA gene were obtained to investigate phylogenetic relationships in the genus. Maximum parsimony (MP) and Bayesian analyses reveal that the well-supported clades detected often do not correspond to the species concepts based on morphological characters. Nine out of the ten lineages include specimens which were initially identified as belonging to different species. The dimensions of ascospores vary to great extent within the lineages. The size and shape of fruit-bodies, length of excipular hair and hymenium colour are mostly homogenous within each clade; however, these characters coincide to a great extent among the lineages and the latter can be assessed only from fresh fruit-bodies. Nuclear DNA content, and accordingly, ploidy level do not provide evidence for species distinction. Geopora arenicola, G. tenuis and G. sepulta were recognized as monophyletic species. Geopora foliacea and G. cervina could not be explicitly delimited and the G. cervina complex comprising three clades was introduced.     

Exploring the molecular diversity of Eleotridae (Gobiiformes) using mitochondrial DNA

Species with wide geographic distributions can consist of different lineages or even of different species. The present study evaluated the molecular diversity of the family Eleotridae by analyzing sequences of the COI gene from species collected in different locations in a Neotropical region as well as sequences from BOLD and GenBank. The analysis revealed the distinction and differentiation of a variety of species with high statistical support, including Gobiomorus dormitor (two lineages), Dormitator maculatus (three lineages) and Eleotris fusca (three lineages), and a number of different lineages of Microphilypnus. This indicates the existence of a number of unknown cryptic species that have not been reported previously, increasing the potential diversity of eleotrid species in the Neotropics.     

Micropropagation of 21 species of Mexican cacti by axillary proliferation

Summary We have developed micropropagation systems for 21 species of Mexican cacti using explants from seedlings germinatedin vitro or shoot segments of juvenile 2–3-yr-old greenhouse plants. The species propagated belong to the generaAstrophytum, Cephalocereus, Coryphantha, Echinocactus, Echinocereus, Echinofossulocactus, Ferocactus, Mammillaria, Nyctocereus, andStenocactus. Multiple shoot formation from areoles was achieved in Murashige and Skoog (MS) medium supplemented with either 1 or 2 mg N⁶-benzyladenine (BA) per 1 (4.44 or 8.87 μM) or BA at 1 or 2 mg/l plus naphthaleneacetic acid at 0.1 or 1 mg/l (0.54 or 5.37 μM). The requirements of growth regulators for optimal shoot proliferation, the velocity of the response, and the number of buds produced by explant were different among the genera and species studied. Rooting of the shoots generatedin vitro was achieved in MS medium supplemented with indoleacetic acid at 0.5–1 mg/l (2.85–5.71 μM) or indolebutyric acid at 0.5–1 mg/l (2.46–4.90 μM). Finally, 70–95% of the rooted plants transferred to potting medium survived.     

Interspecific variability of δ13C among trees in rainforests of French Guiana: functional groups and canopy integration

The interspecific variability of sunlit leaf carbon isotope composition (δ¹³C), an indicator of leaf intrinsic water-use efficiency (WUE, CO₂ assimilation rate/leaf conductance for water vapour), was investigated in canopy trees of three lowland rainforest stands in French Guiana, differing in floristic composition and in soil drainage characteristics, but subjected to similar climatic conditions. We sampled leaves with a rifle from 406 trees in total, representing 102 species. Eighteen species were common to the three stands. Mean species δ¹³C varied over a 6.0‰ range within each stand, corresponding to WUE varying over about a threefold range. Species occurring in at least two stands displayed remarkably stable δ¹³C values, suggesting a close genetic control of species δ¹³C. Marked differences in species δ¹³C values were found with respect to: (1) the leaf phenology pattern (average δ¹³C=–29.7‰ and –31.0‰ in deciduous-leaved and evergreen-leaved species, respectively), and (2) different types of shade tolerance defined by features reflecting the plasticity of growth dynamics with respect to contrasting light conditions. Heliophilic species exhibited more negative δ¹³C values (average δ¹³C=–30.5‰) (i.e. lower WUE) than hemitolerant species (–29.3‰). However, tolerant species (–31.4‰) displayed even more negative δ¹³C values than heliophilic ones. We could not provide a straightforward ecophysiological interpretation of this result. The negative relationship found between species δ¹³C and midday leaf water potential (Ψ_wm) suggests that low δ¹³C is associated with high whole tree leaf specific hydraulic conductance. Canopy carbon isotope discrimination (Δ _A ) calculated from the basal area-weighed integral of the species δ¹³C values was similar in the three stands (average Δ _A =23.1‰), despite differences in stand species composition and soil drainage type, reflecting the similar proportions of the three different shade-tolerance types among stands. Received: 30 November 1999 / Accepted: 23 March 2000