The evolution of the diatoms (Bacillariophyta). I. Origin of the group and assessment of the monophyly of its major divisions

The diatoms are one of the best characterised algal groups. Despite this, little is known of the evolution of the group from the earliest cell to the myriad of taxa known today. Relationships among taxa at the family or generic level have been recognised in some diatoms. However, relationships at higher taxonomic levels are poorly understood and have often been strongly influenced by the first appearances of key taxa in the fossil record. An independent assessment of relationships among the diatoms at these higher taxonomic levels has been made using rRNA sequence data to infer phylogenetic relationships. In this paper we present an analysis of 18S rRNA data from several chosen centric, araphid and raphid pennate taxa. The phylogenetic inferences from these 18S rRNA sequences are supported by evidence from the fossil record and evidence from ontogenetic data. Ribosomal RNA data indicate that both the centric and araphid pennate lineages may not be monophyletic.     

Infraspecific variation in Cerastium alpinum s. lat. (Caryophyllaceae) in Central Norway

Within Cerastium alpinum s. lat., several taxa have been circumscribed. Three infraspecific taxa are currently recognized in Nordic literature, but the opinions have varied about their taxonomic levels and relations to each other. Populations of these three taxa — alpinum, glabratum and lanatum — were investigated in Central Norway to elucidate taxonomic relationships on a regional scale. Morphometric analyses (PCA ordination) based on two data sets; one with 61 characters, and one without the 35 indumentum characters, gave different results. The former partly support the use of a higher rank for glabratum , but this analysis may put too much weight on indumentum characters. The reduced data set gave a more continuous transition between the three taxa, with no special status for glabratum. Crossing experiments between the taxa indicated full cross compatibility as far as relative seed set was concerned. Finally, vegetation analysis (DCA ordination) indicated that the three taxa have somewhat different ecological demands. This suggests that they, in spite of hybridization abilities, normally are maintained as separate entities due to habitat differences. A delimitation of three infraspecific taxa at the same level within C. alpinum s. lat. is thus supported by this study. Whether these taxa should be treated as subspecies or varieties strongly depends upon the definitions of these categories. Viewed in a wide geographical context, however, the arguments for subspecific rank are strengthened.     

Logic in systematics

Systematic biologists attempt to infer the taxonomic relationship of one species to another based on the available evidence. Phylogenetic systematists demand that these species relationships reflect evolutionary history (they expect their taxa to be monophyletic). Just exactly how this is to be achieved remains a subject of debate. There are many different kinds of evidence, and many different ways of inferring taxonomic relationships (plus evolutionary history) from them. In this paper, we argue that one such way of inferring species relationships, the hypothetico‐deductive method, proves a bad fit with phylogenetic systematics because it requires an excessively strong assumption of the relationship that obtains between hypotheses of descent and the available evidence.     

Terrestrial invertebrate surveys and rapid biodiversity assessment in New Zealand: lessons from Australia

Although invertebrates play a key role in the environment, their conservation and use in environmental monitoring is often considered “too difficult” and consequently ignored. One of the main problems in dealing with invertebrates is that even limited sampling can yield large numbers of specimens and an enormous diversity of species. Other problems include the taxonomic impediment (i.e. high proportions of invertebrate taxa are undescribed and there are few specialists available to identify specimens), the lack of knowledge on species distribution, diversity and ecological roles, and the fact that invertebrates are undervalued by the general public. A number of rapid biodiversity assessment (RBA) approaches have been suggested to overcome these problems. RBA approaches generally fall into four categories: (1) restricted sampling in place of intensive sampling (sampling surrogacy); (2) the use of higher taxonomic levels than species (species surrogacy); (3) the use of recognisable taxonomic units (RTUs) identified by non-specialists (taxonomic surrogacy); and (4) the use of surrogate taxa in place of all taxa (taxon-focusing). Australia has a long history of using invertebrates in terrestrial ecological studies, and in developing and using RBA approaches. Therefore, New Zealand could benefit from the experienced gained in Australia. Potentially one of the most useful RBA approaches to take in New Zealand involves focusing resources and attention on a limited range of taxa. However, this requires substantial communication, discussion, and agreement over which taxa should be selected for conservation priorities and environmental monitoring in terrestrial ecosystems.     

Heat tolerant fungi and applied research: Addition to the previously treated group of strictly thermotolerant species

Heat tolerant fungi are organisms that may perform bioconversion processes and produce industrially important metabolites. They may either be obligate thermophiles or simple thermotolerants. The present document is the continuation of a critical note on thermotolerant fungi erroneously reported in the literature as possessing thermophilic attributes. Fifty strictly thermotolerant taxa are here considered. Some of their binomials have only recently been introduced in the scientific literature. The reported thermotolerant species are grouped according to broad taxonomic categories. The nomenclature of zygomycetous taxa and anamorphic fungi is straightforward, as usually only one binomial is available or only one state is produced in culture respectively. For Ascomycetes regularly producing in culture a conidial state, the name of the sexual state (teleomorph) should be used to designate the organism even when a binomial is available for the anamorph; this prevents the practice of interchangeably using the name of either states of the same fungus. When ascomycetous taxa produce the anamorph regularly and the teleomorph only under specific cultural conditions, the name of the anamorph could be preferentially selected. The goal is to introduce uniformity in name citations of fungi, particularly in the literature of applied research. Each species is reported under its taxonomically correct name, either the original binomial or the latest combined binomial after generic transfer(s). Known synonyms are also specified. Maximum efforts were undertaken to trace updated information on the taxonomic position of these fifty strict thermotolerant species. For each, information on the type material, morphological features distinguishing it from related members of the genus (and when necessary a generic taxonomic assessment) and, finally, salient ecological features including heat tolerance levels are given. For some information on their biotechnological use is also provided. Overall 86 strictly thermotolerant fungi are so far documented in the corresponding published and present contributions; however, this figure should not be regarded as exhaustive for the group. Among these 86 taxa ascomycetous fungi (46) presently outnumber anamorphic microfungi (28) but their relevant figures should be regarded as provisional. Only 12 zygomycetous species proved to be strict thermotolerants. Further cardinal temperature growth values established for these 86 thermotolerants disclose no pattern linked to their broad taxonomic categories. Standardized growth temperature curves at increments smaller than 5 °C have to be performed to assess conclusively variability in growth temperature relationships. Several heat tolerant fungi are widely used in industry; however, more research is needed to explore the applied potential of these particular organisms. An exhaustive document on the biodiversity of heat tolerant fungi also awaits production. It would be informative in relation to the global warming process of the earth.     

On some features of historical morphogenesis

The results of the analysis of the diversity dynamics and phylogenetic schemes of various taxa (from species up to classes) show that taxa of different ranks evolved as separate integral natural systems. The main trends in the diversity dynamics of classes and orders are quite different from those of genera and families. The diversity dynamics of genera and families reflect the adaptive essence of these taxonomic categories in the evolution. About five short episodes of mass appearances of genera and families took place in the Phanerozoic. The taxonomic categories of classes and orders are characterized by the archetypes of these groups, and their diversity decreased in the evolution. The appearance of these taxa is not connected with the mass extinctions and changes in the abiotic environment.     

Ectomycorrhizal fungi are shared between seedlings and adults in a monodominant Gilbertiodendron dewevrei rain forest in Cameroon

Ectomycorrhizal networks may facilitate the establishment and survival of seedlings regenerating under the canopies of tropical forests and are often invoked as a potential contributor to monodominance. We identified ectomycorrhizal fungi in a monodominant Gilbertiodendron dewevrei (Fabaceae) rain forest in Cameroon, using sporocarps and ectomycorrhizae of three age categories (seedlings, intermediate trees, and large trees) and tentatively revealed nutrient transfer through ectomycorrhizal networks by measuring spontaneous isotopic (¹³C and ¹⁵N) abundances in seedlings. Sporocarp surveys revealed fewer ectomycorrhizal fungal taxa (59 species from 1030 sporocarps) than molecular barcoding of ectomycorrhizal roots (75 operational taxonomic units from 828 ectomycorrhizae). Our observations suggest that ectomycorrhizal fungal diversity is similar to that in other mixed tropical forests and provide the first report of the Tuber‐Helvella lineage in a tropical forest. Despite some differences, all age categories of G. dewevrei had overlapping ectomycorrhizal fungal communities, with families belonging to Thelephoraceae, Russulaceae, Sebacinaceae, Boletaceae, and Clavulinaceae. Of the 49 operational taxonomic units shared by the three age categories (65.3% of the ectomycorrhizal fungal community), 19 were the most abundant on root tips of all categories (38.7% of the shared taxa), supporting the likelihood of ectomycorrhizal networks. However, we obtained no evidence for nutrient transfer from trees to seedlings. We discuss the composition of the ectomycorrhizal fungal community among the G. dewevrei age categories and the possible role of common ectomycorrhizal networks in this rain forest.     

The Species Concept as a Cognitive Tool for Biological Anthropology

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

Molecular approach for assessing responses of microbial-feeding nematodes to burning and chronic nitrogen enrichment in a native grassland

A substantial proportion of the primary productivity in grassland ecosystems is allocated belowground, sustaining an abundant and diverse community of microbes and soil invertebrates. These belowground communities drive many important ecosystem functions and are responsive to a variety of environmental changes. Nematodes, an abundant and diverse component of grassland soil communities, are particularly responsive to altered environmental conditions, such as those associated with reduced fire frequency and nitrogen enrichment, with the most consistent responses displayed by microbial-feeding nematodes. However, much of the available research characterizing nematode responses to environmental change has been carried out at the taxonomic level of family or by broad trophic categories (e.g. fungivores, bacterivores). The extent to which differential responses to environmental change occurs at the genus level or below is unclear. Therefore, the objective of this study was to use molecular methods to quantify the response of microbial-feeding nematodes, at the lowest levels of taxonomic resolution, to nitrogen enrichment and changes in fire frequency. Using sequencing and quantitative polymerase chain reaction (PCR) probes for the 18S ribosomal RNA gene and the ITS1 region, we identified 19 microbial-feeding nematode taxa across four families. When nematodes were sampled across treatments, we found that some nematode taxa within a family responded similarly to nitrogen and burning treatments, while other taxa within the same family respond quite differently. Additionally, although nematodes from different families on average responded differently to nitrogen enrichment and burning, similar responses were seen in nematode taxa that span three taxonomic families. Thus, if nematodes are to be used as indicators of environmental change, care should be taken to assess the response at the lowest taxonomic level possible.     

How the sperm lost its tail: the evolution of aflagellate sperm

The typical sperm is comprised of a head, midpiece and flagellum. Around this theme there is an enormous diversity of form--giant sperm, multi-flagellate sperm and also sperm that lack flagella entirely. Explaining this diversity in sperm morphology is a challenging question that evolutionary biologists have only recently engaged in. Nonetheless, one of the selective forces identified as being an important factor in the evolution of sperm form is sperm competition, which occurs when the sperm of two or more males compete to fertilize a female's ova. In species with a truly monandrous mating system, the absence of sperm competition means that the selection pressure on males to produce motile sperm may be relaxed. Potentially aflagellate sperm are less costly to produce, both in terms of energy and time. Thus, selection may therefore favour the loss of the sperm flagellum and any other motile mechanisms in monandrous taxa. A review of the literature revealed that 36 taxonomic groups, from red algae to fish, were found independently to have evolved aflagellate sperm. I review what is known about the mating systems of each of these taxa and their nearest sister taxa. A sister-group analysis using this information provided weak evidence suggesting that the evolution of aflagellate sperm could be linked to the removal of selective pressures generated by sperm competition.     

PHYLOGENYOF THE VLE-14 CHLAMYOMONAS (CHLOROPHYCEAE) GROUP: A STUDY OF 18S rRNA GENE SEQUENCES1

Comparative specificity of sporangial wall autolysins (i.e. vegetative lytic enzymes [VLE]) derived from sporulating cultures has been used to group Chlamydomonas taxa into 15 different VLE types. The VLE-14 group, including isolates of C. geitleri, C. noctigama, C. monoica, C. pinicola, C. terricoia, and C. hindakii, is one of the largest of these VLE groups. Genetic studies have shown that a number of the VLE-14 taxa are interfertile, albeit with little or reduced viability of progeny. A reevaluation of the VLE-14 group suggested that all members should be regarded as distinct isolates of C. noctigama. The present investigation tests the phylogenetic implications of the VLE evidence and examines the validity of the taxonomic reevaluation in a phylogenetic context by analysis of 18S rRNA gene sequence data. Results from analyses of the sequence data are consistent with an interpretation of the VLE evidence as indicative of monophyletic taxa. Phylogenetic analyses of the sequence data are also consistent with the taxonomic reevaluation and reidentification of the group. However, at least some of the VLE-14 isolates studied in this investigation fit criteria for distinct biologic or phylogenetic species. It is concluded that the VLE-14 taxa represent a very closely allied group that includes some isolates that are in the early stages of speciation ly reproductive isolation.     

Aphyly: A Systematic Designation for a Taxonomic Problem

A taxon is aphyletic when it is deemed to be non-monophyletic or unresolved, therefore aphyletic taxa are a taxonomic problem rather than an evolutionary anomaly. A problem arises in systematics when taxonomic names assigned to aphyletic taxa are treated as if they were natural groups. In the absence of a taxonomic and systematic revision, anomalous taxa should be labelled as aphyletic without recourse to phylogenetic inference (i.e., interpretation). Doing so avoids the validation of aphyletic names and the creation of dubious results in fields that rely on systematic and taxonomic data.     

Taxonomic and biological trait differences of stream macroinvertebrate communities between mediterranean and temperate regions: implications for future climatic scenarios

Streams in mediterranean regions have highly seasonal discharge patterns, with predictable torrential floods and severe droughts. In contrast, discharge is less variable in temperate regions and intermittent flow conditions are uncommon. Hydroclimatic models predict that climate change would increase frequency and severity of floods and droughts across Europe, thus increasing the proportion of streams with mediterranean characteristics in actually temperate areas. Correspondingly, understanding actual ecological differences between mediterranean and temperate streams may help to anticipate large‐scale ecological impacts of climate change. Given that large‐scale factors determine local community composition, we hypothesized that climatic differences between mediterranean and temperate regions should affect the taxonomic and biological trait composition in streams. We assembled the abundance of stream macroinvertebrate genera of 265 sites each from the Mediterranean Basin and from temperate Europe and linked these abundances to published information on 61 categories of 11 biological traits reflecting the potential of resilience from and resistance to disturbances. Although regional taxonomic richness was higher in the mediterranean than in the temperate region, local taxonomic richness and diversity did not significantly differ between regions. Local trait richness and diversity were significantly higher in the mediterranean region. Both local taxonomic and trait‐community composition differed between regions, but the former varied much more than the latter, highlighting that climate change could produce large changes in the taxonomic but rather weak changes in the trait composition. The mediterranean region was characterized by macroinvertebrates with higher dispersion and colonization capabilities, suggesting that species loss in the temperate region, by extinction or northward emigration of taxa, would be compensated for by immigration of southern mediterranean taxa. Thus, climate change would likely have stronger implications for the local conservation of taxa than for the trait composition of stream macroinvertebrate communities.     

Temporal and Taxonomic Variability in Response of Fauna to Riparian Restoration

Evaluating the success of restoration projects requires well‐designed studies. Among the decisions that need to be made are what taxonomic groups to study and when to conduct the monitoring. To explore how these decisions can influence assessments of restoration success, we examined species richness and composition data collected over several years on different terrestrial fauna (landbirds, rodents, bees, and beetles) at Sacramento River restoration and remnant riparian sites. Our selection of study organisms enabled us to ask whether variability in species richness among restoration sites is less for vagile taxa than for sedentary taxa, and if invertebrates display greater variability among sites than vertebrates. Our results demonstrate that responses to restoration can vary depending upon the season when it is assessed, and the taxa that are studied. For all taxa except bees, there was considerable variability in the relative performance of taxa at restoration sites from one sampling date to the next, such that the relative ranking of the sites often changed dramatically. Comparisons of β ‐diversity (variability in species richness across sites) revealed that certain taxonomic groups were more spatially variable in their response to restoration than others. Among vertebrates, sedentary taxa (rodents) had significantly higher variability in species richness across sites than highly vagile taxa (birds); however, no such pattern was observed for invertebrates. Overall, vertebrates had lower variability than invertebrates, suggesting that evaluations of restoration success based on a few better‐known taxonomic groups (e.g., birds, rodents) may be inadequate to represent the biodiversity response of other groups (e.g., insects).     

Delimiting species boundaries and the conservation genetics of the endangered maritime ringlet butterfly (Coenonympha nipisiquit McDunnough)

Species delimitation is a difficult problem that has implications across organismal biology, yet no single method has proved wholly satisfactory. We tested the utility of combining species-delimitation methods based on phylogeny and gene flow statistics using two parapatric members of the Coenonympha tullia group as an example: the endangered maritime ringlet butterfly (Coenonympha nipisiquit McDunnough) and the common inornate ringlet butterfly (Coenonympha inornata Edwards). We reconstructed the phylogeny of the nearctic C. tullia-group taxa from mitochondrial DNA (mtDNA) sequences (cytochrome oxidase I and mitochondrial control region) to explore the ancestry of the C. nipisiquit lineage within the group. We investigated the extent of gene flow between the two taxa with F-statistics using 587 nuclear amplified fragment length polymorphism markers, accounting for the effect of potential scoring 'collisions' where a marker may represent more than one DNA fragment. Combining species-delimitation methods was especially effective because it uncovered both historical and recent evolutionary patterns. Phylogenetic analysis of mtDNA revealed the early divergence of C. nipisiquit from other C. tullia-group taxa, including the morphologically similar C. inornata. F-statistics and gene-by-gene introgression profiles demonstrated clear isolation between the two taxa and revealed strong population structure within C. nipisiquit. C. nipisiquit is the first taxon in the nearctic C. tullia group showing strong evidence of genetic isolation. The methods we used are relatively inexpensive and can be widely used to delimit taxonomic boundaries near the species level, both generally and in particular for taxa that may be targets of conservation efforts.