Comparative analyses in aquatic microbial ecology: how far do they go?

Methodological developments in recent years have led to an increase in empirical databases on the abundance and functions of aquatic microbes, now allowing synthesis studies. Most of these studies have adopted a comparative approach, such that comparative analyses are now available for most aspects of aquatic microbial food webs (more than 50 papers published in the last 15 years). Some of these analyses apparently yield conflicting results, introducing confusion and unnecessary disputes in the field. We briefly review the comparative analyses so far produced and we highlight generalities, show that some of the perceived discrepancies largely derive from partial analyses of a general underlying trend and formulate predictions based on these general trends that provide new avenues for research.     

Temporal shifts on tree species niches: how do they affect species dynamics and community diversity?

Plant Ecology - Species–habitat associations can be used as a proxy for species niches. Previous research has shown that niche plasticity may increase diversity in plant communities, and that...     

The influence of “Homage to Santa Rosalia” on aquatic ecology: a scientometric approach

In 1959, G.E. Hutchinson provided a general explanation for the diversity of species in his paper “Homage to Santa Rosalia or why are there so many kinds of animals?” To assess the contribution of the ideas Hutchinson introduced in “The Homage” to aquatic ecology research, we performed a bibliometric evaluation of all the articles that cited this paper between 1960 and 2009. The articles were retrieved using the database from Thomson Reuters (ISI Web of Knowledge) in March 2009. For each paper, we first identified the studied environment (terrestrial, marine or freshwater) and whether the study was theoretical or empirical. For marine and freshwater studies, we recorded the journal where the article was published, the year of publication, the number of citations, the taxonomic group (e.g. fish, phytoplankton, zooplankton, macroinvertebrates or macrophytes), the habitat (e.g. wetlands, lakes, rivers, streams or ocean) and the main ideas addressed. A total of 1345 articles cited “The Homage”, and the number of citations increased significantly with time. Most of the articles that cited “The Homage” described research carried out in a terrestrial environment or were theoretical, and a lesser number of citations came from freshwater and marine papers, which used mainly fish and invertebrates as model organisms. In the aquatic sciences, most of the papers discussed the influences of competition and energy (productivity) on diversity. Our results indicate that “The Homage” can still be considered a “citation classic” and a breakthrough contribution, and that it is still having a great impact on different fields of ecology, including limnology and marine ecology.     

Microsporidian species known to infect humans are present in aquatic birds: implications for transmission via water?

Human microsporidiosis, a serious disease of immunocompetent and immunosuppressed people, can be due to zoonotic and environmental transmission of microsporidian spores. A survey utilizing conventional and molecular techniques for examining feces from 570 free-ranging, captive, and livestock birds demonstrated that 21 animals shed microsporidian spores of species known to infect humans, including Encephalitozoon hellem (20 birds; 3.5%) and Encephalitozoon intestinalis (1 bird; 0.2%). Of 11 avian species that shed E. hellem and E. intestinalis, 8 were aquatic birds (i.e., common waterfowl). The prevalence of microsporidian infections in waterfowl (8.6%) was significantly higher than the prevalence of microsporidian infections in other birds (1.1%) (P < 0.03); waterfowl fecal droppings contained significantly more spores (mean, 3.6 x 10(5) spores/g) than nonaquatic bird droppings contained (mean, 4.4 x 10(4) spores/g) (P < 0.003); and the presence of microsporidian spores of species known to infect humans in fecal samples was statistically associated with the aquatic status of the avian host (P < 0.001). We demonstrated that a single visit of a waterfowl flock can introduce into the surface water approximately 9.1 x 10(8) microsporidian spores of species known to infect humans. Our findings demonstrate that waterborne microsporidian spores of species that infect people can originate from common waterfowl, which usually occur in large numbers and have unlimited access to surface waters, including waters used for production of drinking water.     

On the use of climate covariates in aquatic species distribution models: are we at risk of throwing out the baby with the bath water?

Species distribution models (SDMs) in river ecosystems can incorporate climate information by using air temperature and precipitation as surrogate measures of instream conditions or by using independent models of water temperature and hydrology to link climate to instream habitat. The latter approach is preferable but constrained by the logistical burden of developing water temperature and hydrology models. We therefore assessed whether regional scale, freshwater SDM predictions are fundamentally different when climate data versus instream temperature and hydrology are used as covariates. Maximum entropy (MaxEnt) SDMs were built for 15 freshwater fishes using one of two covariate sets: 1) air temperature and precipitation (climate variables) in combination with physical habitat variables; or 2) water temperature, hydrology (instream variables) and physical habitat. Three procedures were then used to compare results from climate vs instream models. First, equivalence tests assessed average pairwise differences (site‐specific comparisons throughout each species’ range) among climate and instream models. Second, ‘congruence’ tests determined how often the same stream segments were assigned high habitat suitability by climate and instream models. Third, Schoener's D and Warren's I niche overlap statistics quantified range‐wide similarity in predicted habitat suitability from climate vs instream models. Equivalence tests revealed small, pairwise differences in habitat suitability between climate and instream models (mean pairwise differences in MaxEnt raw scores for all species < 3 × 10^–4). Congruence tests showed a strong tendency for climate and instream models to predict high habitat suitability at the same stream segments (median congruence = 68%). D and I statistics reflected a high margin of overlap among climate and instream models (median D = 0.78, median I = 0.96). Overall, we found little support for the hypothesis that SDM predictions are fundamentally different when climate versus instream covariates are used to model fish species’ distributions at the scale of the Columbia Basin.     

From evergreen to deciduous tropical forests: how energy–water balance,temperature, and space influence the tree species composition in a high diversity region

Background: Understanding floristic and geographic patterns in one of the most biodiverse regions in the world – the Atlantic forest of eastern Bahia, Brazil – can identify the drivers of diversity in tropical forests and provide useful information for biological conservation.

Aims: To understand the role of both climate and geographical location on variation in tree species composition in a region characterised by an abrupt transition from wet forests to semi-arid thorn-woodlands. To test whether a regional classification of forests according to elevation belts and leaf flush pattern is consistent with floristic composition.

Methods: We submitted 14,094 tree species occurrence records and 31 geo-climatic variables prepared for 57 sites in eastern Bahia, Brazil, to multivariate and regression analyses and variance partitioning.

Results: Climate and space were both significantly (P ≤ 0.05) contributing to explaining floristic variations. Actual evapotranspiration, duration of water deficit, and minimum temperature of coldest month were the main predictors. Floristic differences were significant except when comparing evergreen lower plains and upper plains forests.

Conclusions: Although distance among sites may play an important role, species composition is chiefly influenced by environmental gradients. This highlights environmental heterogeneity as a key factor in the planning of biodiversity conservation in tropical forests.     

Overwintering waterfowl on Swiss lakes: how are abundance and species richness influenced by trophic status and lake morphology?

During the period 1980–1990 long-term physical, chemical and ecological studies were carried out, to study the changes induced by the building of a storm-surge barrier in the mouth of the Oosterschelde estuary and two large auxiliary compartment dams in the rear ends of the estuary. The storm-surge barrier was constructed in the mouth of Oosterschelde estuary (SW Netherlands) during the period 1979–1986. The barrier allows the tides to enter the estuary freely, and, on the other hand, the barrier guarantees safety for the human population and their properties when a stormflood threatens the area.Oosterschelde estuary is isolated from the river input, the rear ends of the ecosystem were separated from the estuary by sea-walls and the strongly decreased tidal exchange with the North Sea induced sheltered circumstances. The Oosterschelde changed from a turbid estuary into a tidal bay, and yet primary production responses appear to be robust and resilient, and the biological communities showed only quantitative shifts from the dominance of specific species assemblages to other assemblages. In many cases predicted changes in the structure of the biological communities could not be verified owing to the large natural variability mainly caused by physical factors (e.g. temperature).     

Molecules,ecology, morphology,and songs in concert: how many species is Arremon torquatus (Aves: Emberizidae)?

The acceptance of the generalized or unified concept of species (i.e. that species are segments of population lineages) implies that an important task for systematists is to focus on identifying lineages and on testing hypotheses about the acquisition of properties such as phenotypic diagnosability, reciprocal monophyly, or mechanisms of reproductive isolation. However, delimiting species objectively remains one of the most challenging problems faced by biologists. In the present study, we begin to tackle the thorny issue of species delimitation in a complicated group of Neotropical passerine birds (the Arremon torquatus complex, Emberizidae) in which sets of characters vary substantially across space, but do not obviously vary in a concerted fashion. To earlier discussions of species limits in the group, we add a historical perspective offered by a recent molecular phylogeny, present quantitative analyses of morphological and vocal variation, and incorporate ecological niche models as a new tool that aids species delimitation by highlighting cases of ecological distinctiveness and cases where populations appear to be in independent evolutionary trajectories, despite being connected by environments unlikely to represent barriers to gene flow. We demonstrate that at least one pair of taxa (and likely another) currently treated as conspecific are, in fact, distinct lineages that merit species status under essentially any species criterion. However, other pairwise comparisons are not as straightforward owing to nonconcordant patterns of variation in different traits and to the impossibility of distinguishing which characters are causes and which are consequences of reproductive (and evolutionary) isolation. After considering several alternatives, we propose a provisional classification of the complex recognizing eight tentative species‐level taxa. Although this classification is likely to change as more detailed work is conducted, it provides a better foundation for studying the biology of these birds and helps to better describe their diversity, which is obscured when all taxa are subsumed into a single species name. The present study highlights several outstanding challenges, both practical and conceptual, for future studies. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 152–176.     

“Forms” of water mites (Acari: Hydrachnidia): intraspecific variation or valid species?

In many groups of organisms, especially in the older literature, it has been common practice to recognize sympatrically occurring phenotypic variants of a species as “forms”. However, what these forms really represent often remains unclear, especially in poorly studied groups. With new algorithms for DNA‐based species delimitation, the status of forms can be explicitly tested with molecular data. In this study, we test a number of what is now recognized as valid species of water mites (Hydrachnidia), but have in the past been treated as forms sympatrically occurring with their nominate species. We also test a form without prior taxonomical status, using DNA and morphometrics. The barcoding fragment of COI, nuclear 28S and quantitative analyses of morphological data were used to test whether these taxa merit species status, as suggested by several taxonomists. Our results confirm valid species. Genetic distances between the form and nominate species (Piona dispersa and Piona variabilis, COI 11%), as well as likelihood ratio tests under the general mixed‐Yule coalescent model, supported that these are separately evolving lineages as defined by the unified species concept. In addition, they can be diagnosed with morphological characters. The study also reveals that some taxa genetically represent more than one species. We propose that P. dispersa are recognized as valid taxa at the species level. Unionicola minor (which may consist of several species), Piona stjordalensis, P. imminuta s. lat., and P. rotundoides are confirmed as species using this model. The results also imply that future studies of other water mite species complexes are likely to reveal many more genetically and morphologically distinct species.     

Geographical distribution and genetic diversity of Gymnogobius sp. “Chokai-endemic species” (Perciformes: Gobiidae)

Ichthyological Research - The geographical distribution and intraspecific genetic diversity of an endangered freshwater goby, Gymnogobius sp. “Chokai-endemic species”, was surveyed...     

Towards minimizing transport of aquatic nuisance species in ballast water: Do organisms in different size classes respond uniformly to biocidal treatment?

To reduce the transport and delivery of aquatic nuisance species in ships’ ballast water and comply with standards for the number of living organisms that may be discharged, biocidal agents and processes, such as chemical dosing, have been repurposed to treat ballast water. We evaluated whether marine planktonic organisms—the typical targets of these biocides—respond in unison to simulated treatment. Organisms were concentrated from seawater, which was amended with dissolved and particulate matter and cultured microalgae, and then treated by chlorination, ultraviolet radiation, or deoxygenation. Living organisms in three size classes (≥50, ≥10 and <50, and <10 µm [represented by culturable, heterotrophic bacteria]) were counted prior to and periodically after treatment. Regardless of whether the differences in concentrations between the control and treatments were significant or insignificant, in general, organisms across the size classes reacted comparably to treatments, with some exceptions in the <10 µm size class. The parallel responses of organisms to treatment—if shown to generalize to other water conditions, assemblages of organisms, and scales of treatment—may justify using a single size class to predict the responses of organisms across the broad size spectra. Notably, because most ballast water management systems employ a filtration step to remove organisms ≥50 µm, if organisms in the ≥10 and <50 µm size class were assessed to determine a vessel’s compliance with the discharge standard, it would be imperative that any filters would be evaluated to ensure they were functioning properly and removed organisms as designed.     

Tracing Si–N–P ecosystem-pathways: is relative uptake in riparian vegetation influenced by soil waterlogging,mowing management and species diversity?

Despite the growing concern about the importance of silicon (Si) in controlling ecological processes in aquatic ecosystems, little is known about its processing in riparian vegetation, especially compared to nitrogen (N) and phosphorus (P). We present experimental evidence that relative plant uptake of N and P compared to Si in riparian vegetation is dependent on mowing practices, water-logging and species composition. Results are obtained from a controlled and replicated mesocosm experiment, with a full-factorial design of soil water logging and mowing management. In our experiments, the Si excluding species Plantago lanceolata was dominant in the mown and non-waterlogged treatments, while Si accumulating meadow grasses and Phalaris arundinacea dominated the waterlogged treatments. Although species composition, management and soil moisture interacted strongly in their effect on relative Si:N and Si:P uptake ratios, the uptake of N to P remained virtually unchanged over the different treatments. Our study sheds new light on the impact of riparian wetland ecosystems on nutrient transport to rivers. It indicates that it is essential to include Si in future studies of the impact of riparian vegetation on nutrient transport, as these are often implemented as a measure to moderate excessive N and P inputs.     

“Australopithecus afarensis”: A composite species

In response to a critique byFerguson (1989),Leonard (1991) reiterates most of his original arguments for supporting “Australopithecus afarensis”Johanson, White, andCoppens, 1978 as a single species. He disregards the principle of morphological equivalence by comparing the dental metrics and morphology of a hominid with those of species of the Pongidae, which do not correspond with the degree of variation in hominids, instead of with those of species of the Hominidae. He fails to refute clear evidence that the range of variation of dental metrics and morphology in “A. afarensis” exceeds that seen in species of the Hominidae. On the basis of extreme variation, “A. afarensis” is, therefore, interpreted as representing a composite species.     

Beyond taxonomic diversity patterns: how do α, β and γ components of bird functional and phylogenetic diversity respond to environmental gradients across France?

Aim To test how far can macroecological hypotheses relating diversity to environmental factors be extrapolated to functional and phylogenetic diversities, i.e. to the extent to which functional traits and evolutionary backgrounds vary among species in a community or region. We use a spatial partitioning of diversity where regional or γ‐diversity is calculated by aggregating information on local communities, local or α‐diversity corresponds to diversity in one locality, and turnover or β‐diversity corresponds to the average turnover between localities and the region. Location France. Methods We used the Rao quadratic entropy decomposition of diversity to calculate local, regional and turnover diversity for each of three diversity facets (taxonomic, phylogenetic and functional) in breeding bird communities of France. Spatial autoregressive models and partial regression analyses were used to analyse the relationships between each diversity facet and environmental gradients (climate and land use). Results Changes in γ‐diversity are driven by changes in both α‐ and β‐diversity. Low levels of human impact generally favour all three facets of regional diversity and heterogeneous landscapes usually harbour higher β‐diversity in the three facets of diversity, although functional and phylogenetic turnover show some relationships in the opposite direction. Spatial and environmental factors explain a large percentage of the variation in the three diversity facets (>60%), and this is especially true for phylogenetic diversity. In all cases, spatial structure plays a preponderant role in explaining diversity gradients, suggesting an important role for dispersal limitations in structuring diversity at different spatial scales. Main conclusions Our results generally support the idea that hypotheses that have previously been applied to taxonomic diversity, both at local and regional scales, can be extended to phylogenetic and functional diversity. Specifically, changes in regional diversity are the result of changes in both local and turnover diversity, some environmental conditions such as human development have a great impact on diversity levels, and heterogeneous landscapes tend to have higher diversity levels. Interestingly, differences between diversity facets could potentially provide further insights into how large‐ and small‐scale ecological processes interact at the onset of macroecological patterns.     

What prevents phenological adjustment to climate change in migrant bird species? Evidence against the “arrival constraint” hypothesis

Phenological studies have demonstrated changes in the timing of seasonal events across multiple taxonomic groups as the climate warms. Some northern European migrant bird populations, however, show little or no significant change in breeding phenology, resulting in synchrony with key food sources becoming mismatched. This phenological inertia has often been ascribed to migration constraints (i.e. arrival date at breeding grounds preventing earlier laying). This has been based primarily on research in The Netherlands and Germany where time between arrival and breeding is short (often as few as 9 days). Here, we test the arrival constraint hypothesis over a 15-year period for a U.K. pied flycatcher (Ficedula hypoleuca) population where laying date is not constrained by arrival as the period between arrival and breeding is substantial and consistent (average 27 ± 4.57 days SD). Despite increasing spring temperatures and quantifiably stronger selection for early laying on the basis of number of offspring to fledge, we found no significant change in breeding phenology, in contrast with co-occurring resident blue tits (Cyanistes caeruleus). We discuss possible non-migratory constraints on phenological adjustment, including limitations on plasticity, genetic constraints and competition, as well as the possibility of counter-selection pressures relating to adult survival, longevity or future reproductive success. We propose that such factors need to be considered in conjunction with the arrival constraint hypothesis.     

Species and “strange species” in zoology: Do we need a “unified concept of species”?

Eidonomy is the field of taxonomy, which addresses the “species problem”. The latter has several dimensions. The first is the confusions frequently made between species as an evolutionary unit, a taxon, a taxonomic category and a nomenclatural rank. The second is the reductionist temptation to recognize in nature only one kind of “basic entities” of biodiversity. From a practical viewpoint and for all non-systematist users of specific nomina, any animal organism should be referred to a taxon of nomenclatural rank species, designated by a Latin binomen. These nomina are indispensable for administrative and legal documents, for management and conservation of biodiversity, as well as for all biological research. But this does not imply that all these taxa should be referred to a single taxonomic category, a “unified concept of species”. In nature, several kinds of entities correspond to different “species concepts” or specions that are irreducible one to another. These categories can be defined according to the modalities of their reproduction, i.e., of their gametopoiesis (mode of formation of gametes), of their kinetogenesis (mode of initiation of the development of the ovum) and of the gene flow between individuals. The best known of these categories is that of mayron or “mixiological species concept”, which points to an independent bisexual panmictic entity, constituting a protected gene pool, but others do exist. In order to better understand their differences, it is useful to consider the various patterns of speciation. These can be referred to three main categories: monogeny (change within a single lineage), diplogeny (birth of two specions from a single one) and mixogeny (hybridization between two specions). The splitting in two of a single initial gene pool is a rather long process, which often shows different stages. The latter can be expressed taxonomically through the use of particular eidonomic categories. Speciation can be considered completed only when it has become irreversible in case of new contact between the two stocks after a period of separation. In allopatry, it is difficult or impossible to know if this stage has been reached. This is not a reason for abandoning the mixiological criterion for identifying sympatric or parapatric specions. In allopatry, the method of inference can be used and, in the absence of sufficient information, it is fully possible to use “by default” the “phylogenetic concept of species” or simpson. The situation is further complicated by the fact that some of the basic entities of biodiversity of hybrid origin, the kyons, are not mayrons, as they have particular reproductive modes. Contrary to isolated and “normal” hybrids, such entities may persist in the long term in nature. Their gametopoiesis implies either an ameiosis (mitoses) or a metameiosis (modified meiosis), and their kinetogenesis implies zygogenesis (fertilization), gynogenesis or parthenogenesis. Kyons are of two main categories. The klonons are unisexual female entities in which genetic transmission is clonal, reproduction being often through parthenogenesis, or following other mechanisms with similar results in genetic terms. The kleptons are unisexual or bisexual entities, which depend for their reproduction, at each generation, on a mayron or another klepton. Their metameiosis produces particular gametes, which start their development either by zygogenesis (zygokleptons), by gynogenesis (gynokleptons) or by a combination of both systems (tychokleptons). All these particular cases do not constitute, as it has long been believed, “evolutionary dead ends”. On the contrary, some of these forms are advantaged in some conditions, and may also, in some cases, be at the origin of allopolyploid specions. The latter include both “normal mayrons” or eumayrons (allotetraploid bisexual entities) and heteromayrons (allotriploid bisexual entities with metameiosis). Mayron, klepton, klonon and simpson, and their subcategories, are different taxonomic categories which correspond to a single nomenclatural rank, that of species. The existence of interspecific hybridization in nature is a very common phenomenon in animals, the importance of which has long been underestimated. Reticulous relationships between specions have played a major role in the scenario of evolution. This should be acknowledged by the rejection of the “universal tree of life” model for organic evolution and its replacement by a “network of life” model.