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.     

Plant responses to climatic extremes: within‐species variation equals among‐species variation

Within‐species and among‐species differences in growth responses to a changing climate have been well documented, yet the relative magnitude of within‐species vs. among‐species variation has remained largely unexplored. This missing comparison impedes our ability to make general predictions of biodiversity change and to project future species distributions using models. We present a direct comparison of among‐ versus within‐species variation in response to three of the main stresses anticipated with climate change: drought, warming, and frost. Two earlier experiments had experimentally induced (i) summer drought and (ii) spring frost for four common European grass species and their ecotypes from across Europe. To supplement existing data, a third experiment was carried out, to compare variation among species from different functional groups to within‐species variation. Here, we simulated (iii) winter warming plus frost for four grasses, two nonleguminous, and two leguminous forbs, in addition to eleven European ecotypes of the widespread grass Arrhenatherum elatius. For each experiment, we measured: (i) C/N ratio and biomass, (ii) chlorophyll content and biomass, and (iii) plant greenness, root ¹⁵N uptake, and live and dead tissue mass. Using coefficients of variation (CVs) for each experiment and response parameter, a total of 156 within‐ vs. among‐species comparisons were conducted, comparing within‐species variation in each of four species with among‐species variation for each seed origin (five countries). Of the six significant differences, within‐species CVs were higher than among‐species CVs in four cases. Partitioning of variance within each treatment in two of the three experiments showed that within‐species variability (ecotypes) could explain an additional 9% of response variation after accounting for the among‐species variation. Our observation that within‐species variation was generally as high as among‐species variation emphasizes the importance of including both within‐ and among‐species variability in ecological theory (e.g., the insurance hypothesis) and for practical applications (e.g., biodiversity conservation).     

<Emphasis Type="Italic">Otidea</Emphasis> species from China,three new species with comments on some previously described species

The genus Otidea was recently monographed and studied phylogenetically, but knowledge of the diversity and distribution of Otidea species in China is fragmentary. In this study, collections from China were examined morphologically and included in phylogenetic analyses. Using LSU, TEF1-α, and RPB2 new species were placed within previously recognized clades in the genus. The results agree with both Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and genetic divergence as previously reported. Three new species, Otidea hanseniae, Otidea korfii and Otidea purpureogrisea are recognized based on phylogenetic reconstruction using ITS, LSU, TEF1- α and RPB2. Comments on some incompletely known species are added. With the discovery of these three new species, the genus Otidea in China proves to be more diverse than previously recognized.     

Gen‐morph species concept—A new and integrative species concept for outbreeding organisms

The present article briefly reviewed the prevailing species concepts, especially biological, genetic, evolutionary, phylogenetic, ecological, and several taxonomic species concepts. The former five reflect the properties of species from diverse aspects and in different degrees, while taxonomic species concepts all contain more or less subjective elements, except for Hedberg's taxonomic method (not species concept). So far, there is no species concept that is both theoretically rational and practically operable. The present article outlined recent studies on the genus Paeonia L. (Paeoniaceae) in biology, particularly in morphology, biogeography, molecular phylogeny, and reproductive behavior, which provided insight into the relationship between variation of morphological characteristics and phylogeny. Taking the study on Paeonia L. as a case, referring to studies on some other plant groups, and incorporating the merits of the prevailing species concepts into our consideration, “gen‐morph species concept” is proposed here formally as new for outbreeding organisms. The new species concept has three special features: (i) a bridge linking morphological aspect with genetic and other aspects of species; (ii) proposal of a concrete morphological criterion for species definition, and (iii) considering quantitative and qualitative characteristics as equally valuable for species definition and introducing statistics into the concept to handle such characteristics. Therefore, the gen‐morph species concept is an integrative species concept, both theoretically objective and practically operable.     

“整合物种概念”和“分化路上的物种”

已有的各个物种概念对物种的认识类似盲人摸象, 只包含了物种的某一个方面; 而一个分化后期的成熟物种应涵盖了所有的物种概念。但是, 尚未到达分化后期的物种往往又已开始新一轮的物种分化; 自然中存在的多数“物种”处于分化路上。这种循环往复连续分化产生的物种, 存在种间生殖隔离不彻底、基因流频繁发生、网状进化突出等现象。此外, 对于不同的物种对, 最早开始分化的基因以及不同物种概念所要求的条件的分化顺序不是统一的, 而是随机的。定义一个适合所有“分化路上的物种”概念存在较大困难。但是, 应采用尽可能多的物种概念来界定分化路上的物种、发表新种和进行分类处理; 也应承认种间可能广泛存在不完全的生殖隔离和有限的基因流, 即有不属于两个物种群体的杂交或回交个体的存在。这样划分的物种比只依据一个物种概念认定的物种具有更高的客观性和科学性。     

The evolution of between‐species reproductive interference capability under different within‐species mating regimes

Sexual selection sometimes favors male traits that benefit their bearers, but harm their mates. The harmful effects of male traits may also extend to females of other species via heterospecific mating interactions. This could affect the coexistence of closely related species during secondary contact. We examined the evolution of the interspecific interfering capability of a beetle (Callosobruchus chinensis) with a congener (C. maculatus) using C. chinensis males reared under conditions of monogamy and polygamy for 17 generations. After experimental evolution, C. chinensis males reared under polygamous conditions imposed greater impacts on offspring production by C. maculatus females than did C. chinensis males reared under monogamous conditions. However, the mechanism by which differential mating regimes altered the effect of C. chinensis males on C. maculatus females was unclear, because we did not find evidence for the expected genital evolution in C. chinensis, despite their body size divergence. Our findings suggest that traits that originally evolved through sexual selection in two allopatric species could influence the coexistence of these species or the likelihood of reinforcement during secondary contact.     

Mixed‐species aggregations in arthropods

This review offers the first synthesis of the research on mixed-species groupings of arthropods and highlights the behavioral and evolutionary questions raised by such behavior.Mixed-species groups are commonly found in mammals and birds.Such groups are also observed in a large range of arthropod taxa independent of their level of sociality. Several examples are presented to highlight the mechanisms underlying such groupings, particularly the evidence for phylogenetie proximity between members that promotes cross-species recognition.The advantages offered by such aggregates are described and discussed.These advantages can be attributed to the increase in group size and could be identical to those of nonmixed groupings,but competition-cooperation dynamics might also be involved,and such effects may differ between homo-and heterospecific groups.We discuss three extreme cases of interspecific recognition that are likely involved in mixed-species groups as vectors for cross-species aggregation:tolerance behavior between two social species,one-way mechanism in which one species is attractive to others and two-way mechanism of mutual attraction.As shown in this review,the study of mixed-species groups offers biologists an interesting way to explore the frontiers of cooperation-competition, including the process of sympatric speciation.     

<Emphasis Type="Italic">Phragmidium</Emphasis> species parasitizing species of Rosaceae in Tibet,China, with descriptions of three new species

Phragmidum spp. are rust fungi that are serious pathogens of plants in the Rosaceae. We characterized 15 Phragmidium species from Tibet, including 12 previously described and 3 new species. All the taxa, including the three new species (Ph. chayuensis, Ph. cibanum, Ph. zangdongii) are described and illustrated based on morphological characteristics. These taxa have multi-celled teliospores with firm pedicels. Phragmidium chayuensis is characterized by (5)7–9-celled teliospores with short papillae. Phragmidium cibanum is characterized by smooth teliospores that are distinctly constricted at the septa. Phragmidium zangdongii is characterized by large uredinia and 11–13-celled teliospores. Five types of urediniospore-surface structures were identified based on the gross shape of ornamentations and their distribution on the urediniospore wall. Molecular sequence data from the LSU rDNA analysis showed that the new taxa formed distinct clades independent from previously recorded species represented by LSU rDNA sequence data. The phylogenetic tree indicated that Phragmidium species are highly host specific.     

The host—parasite relationship of two copepod species and two fish species

A total of 2494 Menidia beryllina and 717 M. peninsulae (Atherinidae) were examined from the Pensacola Bay area for parasitic copepods. M. peninsulae was infested with Bomolochus concinnus (Bomolochidae) and Ergasilus marticatus (Ergasilidae) and had incidences (and intensities) of 12.3% (1.6) and 4.2% (1.3), respectively. Only seven M. peninsulae were infested with both species of parasites. M. beryllina was infested only with E. manicatus and showed different incidences (and intensities) in two areas: Mulatto Bayou, 13.2% (1.9); Catfish Basin, 53.0% (2.3). Fishes with parasites were significantly longer than fishes without parasites and the case of increasing number of parasites with increasing fish length was reinforced. B. concinnus is a warm water parasite on M. peninsulae while E. manicatus acts as a cold water parasite on M. peninsulae and a warm water parasite on M. beryllina . The parasites tended to be overdispersed on their hosts but at the same time showed evidence of negative intraspecific associations within a host. These data suggest intraspecific avoidance by the parasite but active acquisition by the host.     

Guidelines for assigning species rank†

Developments in several fields of study (including bio‐acoustics and the analysis of DNA) together with reappraisals of the nature of species have impacted significantly on avian taxonomy. The BOU's Taxonomic Subcommittee has developed guidelines for the application of species limits to sympatric, parapatric, allopatric and hybridizing taxa. These are published here to assist researchers understand the rationale behind the committee's taxonomic recommendations relating to the British List.     

Are rare species less shade tolerant than common species in fire-prone environments? A test with seven <Emphasis Type="Italic">Amorpha</Emphasis> (Fabaceae) species

Increases in tree density resulting from fire suppression have contributed considerably to the loss of savanna and grassland habitats in North America. Inability to tolerate shade is likely an important cause of species loss in areas that have not maintained historical burning regimes. We conducted an experiment to test whether differences in shade tolerance can explain rarity within the genus Amorpha. Four common and three rare species of Amorpha were grown in a greenhouse for 100 days in direct sun or under 90% shade. Overall, shading significantly reduced growth and survival and affected allocation among species, but these differences did not differ consistently between common and rare species. Ability to tolerate shade was best explained by phenotypic plasticity, with greater shade survival being exhibited by species with the largest changes in leaf area ratio. Furthermore, this study demonstrated that all three of the rare species can be readily cultivated under greenhouse conditions.     

On the integrated frameworks of species concepts: Mayden’s hierarchy of species concepts and de Queiroz’s unified concept of species

Richard L. Mayden and Kevin de Queiroz have devised and developed ‘a hierarchy of species concepts’ and ‘a unified species concept’, respectively. Although their integrated frameworks of species concepts are rather different as to how to integrate the diverse modern concepts of species, the end result is that they are likely to agree on species recognition in nature, because they virtually share the same major components (i.e. evolutionary or lineage concept of species; same way of delimiting species), and have the same important consequences. Both the hierarchical and unified frameworks, however, are interpreted to have shortcoming regarding the way of integrating the modern species concepts. I reformulate these ideas into a framework of species concepts as follows: It treats the idea of species as population‐level evolutionary lineages (sensu Wiley 1978 ) as the concept for species category, and it adopts the contingent biological properties of species (e.g. internal reproductive isolation, diagnosability, monophyly) as operational criteria in delimiting species. I also suggest that existing and revised versions of the integrated framework of species concepts all are not new species concepts, but versions of the evolutionary species concept, because they treat the evolutionary (or lineage) species concept as the concept for species category.     

Effects of tree species composition on within‐forest distribution of understorey species

Question: Do tree species, with different litter qualities, affect the within‐forest distribution of forest understorey species on intermediate to base‐rich soils? Since habitat loss and fragmentation have caused ancient forest species to decline, those species are the main focus of this study. Location: Three ancient forests, along a soil gradient from acidification‐sensitive to base‐rich, were studied: Limbrichterbosch and Savelsbos in The Netherlands and Holtkrat in Denmark. Methods: Canopy and soil surveys along transects generated data for Redundancy Analysis on tree – humus relationships. We analysed the distribution of forest plant species with Canonical Correspondence Analysis. The explanatory factors were soil characteristics (pH, organic matter, loam content and thickness of the humus layers), external crown projection, ground water and canopy data. We further analysed the relationship between forest species and humus characteristics with Spearman correlations. Results: Tree species have a significant impact on humus characteristics through the nature of their litter. Humus characteristics significantly explain the distribution of forest understorey species. The pH of the first 25 cm mineral soil and the thickness of the F‐ (fermentation) layer are the primary factors affecting the distribution of ancient forest species. Conclusion: This study indicates that the species composition of the forest canopy affects the distribution of forest understorey species. Ancient forest species are more abundant and frequent underneath trees with base‐rich litter. On acidification‐sensitive soils these relationships were stronger than on more base‐rich, loamy soils.     

Phylogeny and species delimitation of the C‐genome diploid species in Oryza

Abstract The diploid Oryza species with C‐genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C‐genome (BBCC, CCDD). Despite extensive studies, the phylogenetic relationship among the C‐genome species and the taxonomic status of some taxa remain controversial. In this study, we reconstructed the phylogeny of three diploid species with C‐genome (Oryza officinalis, O. rhizomatis, and O. eichingeri) based on sequences of 68 nuclear single‐copy genes. We obtained a fully resolved phylogenetic tree, clearly indicating the sister relationship of O. officinalis and O. rhizomatis, with O. eichingeri being the more divergent lineage. Incongruent phylogenies of the C‐genome species found in previous studies might result from lineage sorting, introgression/hybridization and limited number of genetic markers used. We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O. eichingeri. Analyses of two datasets (68 genes with a single sample, and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O. eichingeri. In addition, we evaluated the impact of the number of sampled individuals and loci on species delimitation. Our simulation suggests that sampling multiple individuals is critically important for species delimitation, particularly for closely related species.     

Keywords: ornithochory; fleshy fruit; succession; species losses; cultural biotope.

Abandonment of traditional agricultural practices in fruit orchards on hillsides in Central Germany results in successive changes in vegetation. We examined three hypotheses relating to these changes: (1) thickets of fleshy-fruited plants develop around planted trees as a result of ornithochory and local soil and site amelioration, (2) woody plants have long-term effects on soil fertility, and (3) thicket development reduces the plant-species diversity of semi-dry grassland between the trees. Field observations and nursery experiments supported the first and second hypotheses. Increased soil fertility, a seed rain of fleshy-fruited shrubs, and shrub establishment occurred mainly around planted fruit trees. Soils from old tree-planting sites remained fertile after the trees had died and disappeared. The third hypothesis was rejected because no decrease in species' richness or diversity occurred during the initial stages of thicket formation. Nevertheless, herbaceous plant species characteristic of the Festuco-Brometea community were absent from the vegetation and seed bank of shaded, nutrient-enriched sites. Conservation of semi-dry grasslands following orchard abandonment will therefore require active control of woody plants.     

From species distributions to meta‐communities

The extent that biotic interactions and dispersal influence species ranges and diversity patterns across scales remains an open question. Answering this question requires framing an analysis on the frontier between species distribution modelling (SDM), which ignores biotic interactions and dispersal limitation, and community ecology, which provides specific predictions on community and meta‐community structure and resulting diversity patterns such as species richness and functional diversity. Using both empirical and simulated datasets, we tested whether predicted occurrences from fine‐resolution SDMs provide good estimates of community structure and diversity patterns at resolutions ranging from a resolution typical of studies within reserves (250 m) to that typical of a regional biodiversity study (5 km). For both datasets, we show that the imprint of biotic interactions and dispersal limitation quickly vanishes when spatial resolution is reduced, which demonstrates the value of SDMs for tracking the imprint of community assembly processes across scales.