Phylogenetic species recognition and species concepts in fungi

The operational species concept, i.e., the one used to recognize species, is contrasted to the theoretical species concept. A phylogenetic approach to recognize fungal species based on concordance of multiple gene genealogies is compared to those based on morphology and reproductive behavior. Examples where Phylogenetic Species Recognition has been applied to fungi are reviewed and concerns regarding Phylogenetic Species Recognition are discussed.     

Finding unknown species in the genomes of extant species

Although many species have gone extinct, their genetic components might exist in extant species because of ancient hybridization. Via advances in genome sequencing and development of modern population genetics, one can find the legacy of unknown or extinct species in the context of available genomes from extant species. Such discovery can be used as a strategy to search for hidden species or fossils in conservation biology and archeology, gain novel insight into complex evolutionary history, and provide the new sources of genetic variation for breeding and trait improvement in agriculture.     

Associations between Trichinella species and host species in Finland

Examination of 627 wild animals--raccoon dogs (Nyctereutes procyonoides), red foxes (Vulpes vulpes), European lynxes (Lynx lynx), brown bears (Ursus arctos), wolves (Canis lupus), and badgers (Meles meles)--revealed Trichinella spp. The prevalence varied according to geographical region of Finland (north; southwest, SW; and southeast, SE) and was the highest among lynxes (70%, SW). The risk of trichinellosis was higher in the SE (odds ratio, OR, 19.4) and SW regions (OR 14.3), as compared with the northern region (OR 1), with no difference between the former 2 regions. Foxes (OR 2.1) and lynxes (OR 1.9) had a higher risk than raccoon dogs (OR 1) of being infected. The distribution of different Trichinella species was evaluated in 87 wild and domestic mammals by multiplex polymerase chain reaction. Trichinella spiralis was detected more often in domestic and synanthropic animals than in sylvatic hosts. Trichinella nativa was detected only in wildlife. Trichinella pseudospiralis was found both in sylvatic and synanthropic hosts. Trichinella britovi was detected only in mixed infections with other Trichinella species. The raccoon dog was the sole host for all 4 Trichinella species and also carried the most intense infections.     

Inferring species roles in metacommunity structure from species co-occurrence networks

A long-standing question in community ecology is what determines the identity of species that coexist across local communities or metacommunity assembly. To shed light upon this question, we used a network approach to analyse the drivers of species co-occurrence patterns. In particular, we focus on the potential roles of body size and trophic status as determinants of metacommunity cohesion because of their link to resource use and dispersal ability. Small-sized individuals at low-trophic levels, and with limited dispersal potential, are expected to form highly linked subgroups, whereas large-size individuals at higher trophic positions, and with good dispersal potential, will foster the spatial coupling of subgroups and the cohesion of the whole metacommunity. By using modularity analysis, we identified six modules of species with similar responses to ecological conditions and high co-occurrence across local communities. Most species either co-occur with species from a single module or are connectors of the whole network. Among the latter are carnivorous species of intermediate body size, which by virtue of their high incidence provide connectivity to otherwise isolated communities playing the role of spatial couplers. Our study also demonstrates that the incorporation of network tools to the analysis of metacommunity ecology can help unveil the mechanisms underlying patterns and processes in metacommunity assembly.     

Multiple species effects and spatial autocorrelation in detecting species associations

Abstract. The traditional approach to the analysis of species association within a community, based upon co-occurrence in sampling units such as quadrats, has been to test all pairs of species, using a 2 × 2 contingency table for each pair. It has long been recognised that all these tests are not independent of each other, but there is an additional problem in that the association between any particular pair may depend on the combination of the other species that are present or on the environmental factors that determine that combination. We use a 2^k contingency table to examine this problem and find that pairwise associations are not independent of the other species. The second problem that we consider is the effect of spatial autocorrelation in the data which makes the statistical tests too liberal. In the absence of a derived solution for a deflation factor to correct the test statistic calculated from a 2^k table, we describe a Monte Carlo approach that provides an approximate solution to this problem. In our data the amount of deflation that is necessary for a 2^k table is small compared to the amount required for the 2 × 2 tables used to test pairwise association.     

Neurospora species in bakeries

S. YASSIN AND A. WHEALS. 1992. Neurospora species may occur as spoilage organisms in bakeries and bakery products. A survey of two bakeries over a 4 month period produced 315 individually isolated strains which were characterized with respect to six features: conidial colour, protoperitheciality, mating type and percentage dark-coloured (fertile) ascospores in crosses with type specimens of Neurospora crassa, N. sitophila and N. intermedia. We concluded that (i) N: crassa of both mating types was by far the most abundant but N. sitophila and N. intermedia were also represented; (ii) conidial colour was not a good species criterion; (iii) the percentage of fertile ascospores produced in crosses with several type specimens provided a reliable and simple species indicator; (iv) identification of individuals based on these six characteristics suggested that a large number of genetically different organisms were present in the collection; and (v) bakery infection was not due to endemic contamination in the bakery or in raw materials but from repeated external infection, perhaps on contaminated returned goods.     

Delimitating species in paleoanthropology

Evolutionary biologists created a large twentieth‐century literature about delimiting biological species. Paleontologists contributed the unique complications of deep time. Toward century's end, one participant wrote: “In all probability more paper has been consumed on the questions of the nature and definition of the species than any other subject in evolutionary and systematic biology.” 1     

New species in Cienfuegosia

Cienfuegosia hearnii (from Aden, Arabian peninsula),C. somaliana (from Somalia and Ethiopia),C. ulmifolia (from Argentina and Paraguay), andC. intermedia (from Mexico) are described as new.     

The species in primatology

Biologists of the late eighteenth and early nineteenth centuries all bandied about the term “species,” but very rarely actually said what they meant by it. Often, however, one can get inside their thinking by piecing together some of their remarks. One of the most nearly explicit‐appropriately, for the man who wrote a book called The Origin of Species – was Charles Darwin 1 : “Practically, when a naturalist can unite two forms together by others having intermediate characters, he treats the one as a variety of the other… He later translated this into evolutionary terms: “Hereafter, we shall be compelled to acknowledge that the only distinction between species and well‐marked varieties is, that the latter are known, or believed, to be connected at the present day by intermediate gradations, whereas species were formerly thus connected”^1:484‐5     

Cephalosporium maydis is a distinct species in the Gaeumannomyces-Harpophora species complex

Cephalosporium maydis is an important plant pathogen whose phylogenetic position relative to other fungi has not been established clearly. We compared strains of C. maydis, strains from several other plant-pathogenic Cephalosporium spp. and several possible relatives within the Gaeumannomyces-Harpophora species complex, to which C. maydis has been suggested to belong based on previous preliminary DNA sequence analyses. DNA sequences of the nuclear genes encoding the rDNA ITS region, β-tubulin, histone H3, and MAT-2 support the hypothesis that C. maydis is a distinct taxon within the Gaeumannomyces-Harpophora species complex. Based on amplified fragment length polymorphism (AFLP) profiles, C. maydis also is distinct from the other tested species of Cephalosporium, Phialophora sensu lato and members of Gaeumannomyces-Harpophora species complex, which supports its classification as Harpophora maydis. Oligonucleotide primers for H. maydis were developed that can be used in a PCR diagnostic protocol to rapidly and reliably detect and identify this pathogen. These diagnostic PCR primers will aid the detection of H. maydis in diseased maize because this fungus can be difficult to detect and isolate, and the movement of authentic cultures may be limited by quarantine restrictions.     

Light partitioning among species and species replacement in early successional grasslands

Abstract. We studied canopy structure, shoot architecture and light harvesting efficiencies of the species (photon flux captured per unit above‐ground plant mass) in a series of exclosures of different age (up to 4.5 yr) in originally heavily grazed grassland in N Japan.Vegetation height and Leaf Area Index (LAI) increased in the series and Zoysia japonica, the dominant in the beginning, was replaced by the much taller Miscanthus sinensis. We showed how this displacement in dominance can be explained by inherent constraints on the above‐ground architecture of these two species. In all stands light capture of plants increased with their above‐ground biomass but taller species were not necessarily more efficient in light harvesting. Some subordinate species grew disproportionally large leaf areas and persisted in the shady undergrowth. Some other species first grew taller and managed to stay in the better‐lit parts of the canopy, but ultimately failed to match the height growth of their neighbours in this early successional series. Their light harvesting efficiencies declined and this probably led to their exclusion. By contrast, species that maintained their position high in the canopy managed to persist in the vegetation despite their relatively low light harvesting efficiencies. In the tallest stands ‘later successional’ species had higher light harvesting efficiencies for the same plant height than ‘early successional’ species which was mostly the result of the greater area to mass ratio (specific leaf area, SLA) of their leaves. This shows how plant stature, plasticity in above‐ground biomass partitioning, and architectural constraints determine the ability of plants to efficiently capture light, which helps to explain species replacement in this early successional series.     

Freakish patterns – species and species concepts in apomicts

Apomict groups keep challenging taxonomists, in classifications as well as in more fundamental question about the nature of apomictic species. The latter question is not just an academic one, because the outcome influences practical decisions on biodiversity and conservation. A historical overview over the species problem shows that a period of confusion and proliferation of species concepts between 1940 and 1990 was followed by an increasing consensus at the end of the 20th century that the species category is heterogeneous. Species come in kinds, which is understandable in light of their different evolutional histories. Recently, Wilkins stated that we do not need a generally applicable species concept, because species are not an a priori category into which all biological organisms must fit, but salient phenomena that are to be explained. Not only biparental, but also asexual organisms often form such species‐as‐phenomena, explained as some combination of adaptation to an ecological niche and reproductive compatibility. The above is illustrated by historical and current studies in three well‐studied apomict groups, viz. Ranunculus cassubicus agg., Rubus subgen. Rubus and Hieracium (subgen. Hieracium and Pilosella). Species in the Ranunculus cassubicus aggregate are the few existing sexuals, which are surrounded by a hybrid swarm of only partial apomictic forms, whereas in Rubus subgen. Rubus and Hieracium s.s. sexuals as well as numerous apomicts form well defined species. How species should be circumscribed in Pilosella is yet to be clarified. Largely, the differences between these groups can be contributed to their different modes of apomixis and the associated retained sexuality. From this review it is clear that the question is not so much ‘What is a species?‘, but ‘What is a species in this particular group?‘ To answer this question a thorough knowledge and understanding of the biology of the genus in question is required.