On the reality and recognisability of asexual organisms: morphological analysis of the masticatory apparatus of bdelloid rotifers

Species concepts and definitions have been a long-standing debate in evolutionary biology since before Darwin, and almost all proposed solutions are based upon grouping and clustering, with species conceived as somehow biological distinct entities, originated and maintained mainly by reproductive isolation. Lacking reproductive exchange, asexual organisms such as bdelloid rotifers, the best-supported clade of so-called 'ancient asexuals', pose an interesting challenge to debates over the reality of species. However, few data are available on bdelloid rotifers. The only evidence has been that bdelloid species have been more consistently recognised than in their sister sexual group, the monogonont rotifers, across successive taxonomic treatments, but this is confounded by the much lesser degree of taxonomic interest in bdelloids. We applied geometric morphometrics analyses on shape and size of hard masticatory pieces, named trophi, of 1420 bdelloids, belonging to 48 populations of eight traditional species, to test the hypothesis of recognisability of bdelloids. Our morphological analysis confirms that traditional bdelloid species are separated distinct entities, possessing trophi morphologies divided by gaps between taxa, similar to patterns of morphological features in sexually reproducing organisms. In common with most microscopic understudied organisms, bdelloid rotifers harbour much previously undescribed diversity: we found significant differences in trophi morphology within traditional species, revealing the existence of cryptic taxa, similar to those also found in facultatively sexual monogonont rotifers. We confirm that recognisability in bdelloids is not qualitatively different from other small understudied animals such as monogononts, and that sexual versus asexual reproduction does not lead to differences in morphological diversity patterns, as previously suggested based on interpretation of taxonomic revisions.     

Evolutionary Dynamics of ‘the’ Bdelloid and Monogonont Rotifer Life-history Patterns

Substantial differences in both life-table characteristics and reproductive patterns distinguish bdelloid from monogonont rotifers. Bdelloids reproduce only asexually, whereas most monogononts are cyclical parthenogens. We explore some of the adaptive consequences of these life-history differences using a computer model to simulate the evolutionary acquisition of new beneficial mutations. A one-locus mutation-selection regime based on the life-history characteristics of bdelloids indicates that asexuals can maintain higher levels of both allelic and genotypic diversity over a longer time period than obligate sexuals. These results are produced by differences in the magnitude of random genetic drift (RGD) associated with the different types of reproduction. Cyclical parthenogens have significantly higher evolutionary rates than sexual forms in a single-locus model, but incorporate beneficial mutations more slowly than sexuals in a two-locus simulation. Our results are therefore strongly influenced by the number of loci being evaluated as well as the pattern of reproduction. The asexual life history was found to maintain higher levels of allelic diversity than any pattern including sexual reproduction. This intriguing finding is amplified as the number of loci undergoing selection is increased. We end by considering the adaptive consequences of the remarkably divergent life histories found in typical bdelloid and monogonont rotifers.     

A Mitogenomic Re-Evaluation of the Bdelloid Phylogeny and Relationships among the Syndermata

Molecular and morphological data regarding the relationships among the three classes of Rotifera (Bdelloidea, Seisonidea, and Monogononta) and the phylum Acanthocephala are inconclusive. In particular, Bdelloidea lacks molecular-based phylogenetic appraisal. I obtained coding sequences from the mitochondrial genomes of twelve bdelloids and two monogononts to explore the molecular phylogeny of Bdelloidea and provide insight into the relationships among lineages of Syndermata (Rotifera + Acanthocephala). With additional sequences taken from previously published mitochondrial genomes, the total dataset included nine species of bdelloids, three species of monogononts, and two species of acanthocephalans. A supermatrix of these 10-12 mitochondrial proteins consistently recovered a bdelloid phylogeny that questions the validity of a generally accepted classification scheme despite different methods of inference and various parameter adjustments. Specifically, results showed that neither the family Philodinidae nor the order Philodinida are monophyletic as currently defined. The application of a similar analytical strategy to assess syndermate relationships recovered either a tree with Bdelloidea and Monogononta as sister taxa (Eurotatoria) or Bdelloidea and Acanthocephala as sister taxa (Lemniscea). Both outgroup choice and method of inference affected the topological outcome emphasizing the need for sequences from more closely related outgroups and more sophisticated methods of analysis that can account for the complexity of the data.     

Phenotypic plasticity and genetic isolation-by-distance in the freshwater mussel <Emphasis Type="Italic">Unio pictorum</Emphasis> (Mollusca: Unionoida)

Freshwater mussels (Unionoida) show high intraspecific morphological variability, and some shell morphological traits are believed to be associated with habitat conditions. It is not known whether and which of these ecophenotypic differences reflect underlying genetic differentiation or are the result of phenotypic plasticity. Using 103 amplified fragment length polymorphism (AFLP) markers, we studied population genetics of three paired Unio pictorum populations sampled from two different habitat types (marina and river) along the River Thames. We found genetic differences along the Thames which were consistent with a pattern of isolation by distance and probably reflect limited dispersal via host fish species upon which unionoid larvae are obligate parasites. No consistent genetic differences were found between the two different habitat types suggesting that morphological differences in the degree of shell elongation and the shape of dorso-posterior margin are caused by phenotypic plasticity. Our study provides the first good evidence for phenotypic plasticity of shell shape in a European unionoid and illustrates the need to include genetic data in order properly to interpret geographic patterns of morphological variation.     

SEXUAL SPECIES ARE SEPARATED BY LARGER GENETIC GAPS THAN ASEXUAL SPECIES IN ROTIFERS

Why organisms diversify into discrete species instead of showing a continuum of genotypic and phenotypic forms is an important yet rarely studied question in speciation biology. Does species discreteness come from adaptation to fill discrete niches or from interspecific gaps generated by reproductive isolation? We investigate the importance of reproductive isolation by comparing genetic discreteness, in terms of intra‐ and interspecific variation, between facultatively sexual monogonont rotifers and obligately asexual bdelloid rotifers. We calculated the age (phylogenetic distance) and average pairwise genetic distance (raw distance) within and among evolutionarily significant units of diversity in six bdelloid clades and seven monogonont clades sampled for 4211 individuals in total. We find that monogonont species are more discrete than bdelloid species with respect to divergence between species but exhibit similar levels of intraspecific variation (species cohesiveness). This pattern arises because bdelloids have diversified into discrete genetic clusters at a faster net rate than monogononts. Although sampling biases or differences in ecology that are independent of sexuality might also affect these patterns, the results are consistent with the hypothesis that bdelloids diversified at a faster rate into less discrete species because their diversification does not depend on the evolution of reproductive isolation.     

广东省水库轮虫分布特征

在2000年调查了广东省18座水库的轮虫种类分布特征。在此基础上,于2001～2003年研究了滞留时间对飞来峡水库、流溪河水库和新丰江水库三座典型水库(平均滞留时间分别为14d、172d和644d)轮虫分布的影响。共检到轮虫101种,其中大多数种类来自臂尾轮科(Brachionidae)、腔轮科(Lecanidae)、异尾轮科(Trichcercidae)和疣毛轮科(Synchaetidae)。常见属为龟甲轮属(Keratella)、臂尾轮属(Brachionus)、腔轮属(Lecane)、多肢轮属(Polyarthra)、异尾轮属(Trichocerca)、晶囊轮属(Asplanchna)、聚花轮属(Conochilus)和无柄轮属(Ascomorpha)。从不同生活习性种类组成看．每次采样均以浮游种类为主。在直流型的飞来峡水库中,底栖和着生种类占种类数的41％;而在长滞留时间的新丰江水库中只占18％;中等滞留时间的流溪河水库则介于它们之间。从不同食性种类的丰度看,在新丰江水库和流溪河水库中,轮虫以滤食细小悬浮颗粒物的种类(螺形龟轮虫、独角聚花轮虫和广生多肢轮虫)为优势种;而在直流型的飞来峡水库中,以劫掠粒径较大食物的种类(疣毛轮虫等)为优势种。聚类分析表明,不同营养水平水库轮虫的组成并不是绝然不同的,而是随着营养水平的上升逐渐发生变化的。在营养水平较低水库中以广栖性的螺形龟甲轮虫为优势种,随着营养水平的上升,螺形龟甲轮虫优势度逐渐降低,而异尾轮虫或臂尾轮虫优势度逐渐上升,并在中富营养和富营养水库中成为优势种。     

Evidence for inefficient selection against deleterious mutations in cytochrome oxidase I of asexual bdelloid rotifers

Evolutionary theory predicts that natural selection should be less efficient in asexually than in sexually reproducing organisms. Obligate asexuals are expected to adapt slowly to changing environments and to accumulate mildly deleterious mutations to their genomes, potentially explaining their typically short evolutionary lifespans. One group of animals that appear to challenge these ideas is the bdelloid rotifers, a large and ancient clade of obligate asexuals. Previous work has found no evidence for inefficient selection against deleterious mutations in protein-coding genes of bdelloids. However, these studies relied mostly on between-species comparisons and were therefore unable to detect mildly deleterious mutations that persist within populations but are removed by selection over longer time periods. Here, we test for inefficient purifying selection acting on the cytochrome oxidase I (cox1) mitochondrial gene in 3 clades of bdelloids. Patterns of variation are compared to those of two facultatively sexual clades: a monogonont rotifer (Brachionus) and a branchiopod crustacean (Daphnia). As predicted due to the strict linkage between mitochondrial and nuclear genomes, bdelloids exhibit higher frequencies of putatively deleterious amino acid polymorphism within populations than the two facultatively sexual clades. While the monophyly and age of bdelloids makes it hard to rule out other explanations for the observed differences, several possible confounding factors, such as differences in effective population size or patterns of codon usage, are shown not to explain the observed differences. We therefore conclude that bdelloid mitochondrial DNA variation does display the signature of inefficient selection expected of obligate asexuals.     

Small-sized invertebrates in a gravel stream: community structure and variability of benthic rotifers

1. The Rotifera assemblage inhabiting the streambed surface and the hyporheic zone of a gravel stream was investigated between October 1991 and October 1992. Forty-two species of Monogononta and 27 of Bdelloidea were identified. Within these two classes, dominant species differed between the surface and the hyporheic zone. At the streambed surface, the abundance of monogonont rotifers showed a seasonal pattern with significantly higher densities in pools, whereas bdelloids showed no clear temporal trend and did not differ significantly among sites. In the hyporheic zone, the depth distribution differed among the two rotifer groups, bdelloids occurred in highest densities between 0 and 30 cm sediment depth, while monogononts were most abundant at greater depths.
2. Species composition differed greatly between successive sampling dates (min. 5 to max. 26 days) at both the streambed surface and the hyporheos. At the streambed surface and in the shallow hyporheos a significantly higher percentage of species was replaced in riffles than in pools.
3. Few measured hydrophysical variables were associated with the Rotifera assemblage structure. At the streambed surface, species richness was negatively correlated with water temperature and substratum heterogeneity, and Monogononta rotifer densities declined with water depth and substratum roughness.
4. Permutation tests carried out on temporal serial correlations showed that, at riffle sites at the streambed surface, bdelloid rotifer densities, rotifer species richness and diversity did not differ significantly from a temporal, near-random pattern. The hyporheic rotifer assemblage followed similar near-random patterns.     

Rotifers of the Kalahari Gemsbok National Park,South Africa

The Kalahari Gemsbok National Park in the Northern Cape Province, South Africa, is bounded by two dry river beds in which 39 artificial water sources have been provided for the use of the wild animals. The water in these sources varies from fresh to highly saline and an opportunity is thus provided to determine, not only which rotifer species are able to colonise such sources, but what their salinity tolerances are. The rotifer fauna, studied in summer and winter, is dominated by mixed populations of Brachionus calyciflorus, B. plicatilis and Hexarthra jenkinae, with only a few other monogononts and bdelloids. The most striking feature of the rotifer fauna in these troughs is the very low species diversity encountered.     

Genome‐wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation

Alternanthera philoxeroides (alligator weed) is an invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation in its introduced range. The mechanisms underpinning the wide range of phenotypic variation and rapid adaptation to novel and changing environments remain uncharacterized. In this study, we examined the epigenetic variation and its correlation with phenotypic variation in plants exposed to natural and manipulated environmental variability. Genome‐wide methylation profiling using methylation‐sensitive amplified fragment length polymorphism (MSAP) revealed considerable DNA methylation polymorphisms within and between natural populations. Plants of different source populations not only underwent significant morphological changes in common garden environments, but also underwent a genome‐wide epigenetic reprogramming in response to different treatments. Methylation alterations associated with response to different water availability were detected in 78.2% (169/216) of common garden induced polymorphic sites, demonstrating the environmental sensitivity and flexibility of the epigenetic regulatory system. These data provide evidence of the correlation between epigenetic reprogramming and the reversible phenotypic response of alligator weed to particular environmental factors.     

Multiple scale patterns of shell and anatomy variability in land snails: the case of the Sicilian Marmorana (Gastropoda: Pulmonata, Helicidae)

Certain major aspects of phenotypic diversity are still largely unexplained. When phenotypic patterns do not relate to habitat variables, fine analysis of morphological patterns and their distribution sheds light on the origin of diversity. Among invertebrates, snails are an ideal model for studying the roles of the neutral processes and selection involved in creating diversity. To understand patterns and processes of variability on different scales (regional: areas; local: sites), morphological variability of two sets of characters (shell and genitalia) was quantified in a group of rock-dwelling land snails of the genus Marmorana (Pulmonata, Helicidae). To analyse shell variability, partitioning of the overall variation into size and shape components was analysed by a principal component-based approach. Shell shape and size variability is not significantly influenced by any environmental pressure. Variability at site scale is mainly attributed to shell size, which is a trait demonstrated to have a high degree of phenotypic plasticity. No sharp changes were observed for genitalia. Moreover, allometries between shell size and genitalia measurements involve a few populations. The observed multiple scale patterns are in line with the hypothesis that genital variance may be selectively controlled to maintain function.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 359–370.     

Ecology of bdelloids: how to be successful

Bdelloids inhabit many different environments. The entire taxon is an order belonging to the phylum Rotifera. In spite of its wide distribution, it has a very uniform morphology, suggesting that natural selection has had almost no effect on its morphological characteristics.This paper reviews the geographical and ecological distributions of bdelloids and their ability to tolerate different conditions is discussed. Two characteristics account for the wide distribution of bdelloids, parthenogenetic reproduction and their ability to withstand unfavorable conditions through anhydrobiosis. The former is an apomictic thelytoky which may ensure genetic homogeneity within clones. However, evidence which suggests variability among and within parthenogenetic clones is discussed. Some recent experimental evidence indicates that anhydrobiosis does not affect the life history of the surviving individuals. The effects of anhydrobiosis on bdelloid populations are considered.     

Genetic diversity and population structure detection in sponge gourd ( Luffa cylindrica ) using ISSR,SCoT and morphological markers

Investigation of genetic diversity is essential for the selection of parents for crop breeding and conservation of genetic resources. To estimate the genetic variability and population structure in the midst of 45 accessions of sponge gourd brought together from different geographical areas of India, morphological traits and two molecular markers, ISSR and SCoT markers were compared. Principal components analysis of 20 morphological traits showed 72.70% variability and significant positive correlations between fruit traits. All three marker techniques clustered all accessions into two groups with few outgroups. High level of polymorphism was observed among ISSR (74.6%) and SCoT (71.5%) primers. The Bayesian model revealed the hidden grouping and showed admixture type of population. The diversity pattern is influenced by genetic marker used, as different molecular markers have different polymorphism evaluation efficiency. This study can be helpful in amplifying the genetic base and selection of specific traits for breeding. Thus, ISSR and SCoT markers are potential marker for identification in sponge gourd and provide valuable data on its genetic correlation and structure.     

Musculature of two bdelloid rotifers, Adineta ricciae and Macrotrachela quadricornifera: organization in a functional and evolutionary perspective

Organization of muscles in microinvertebrates has often been studied to answer functional questions and understand phylogenetic relationships among taxa. In this study, the musculature of two bdelloid species, Adineta ricciae and Macrotrachela quadricornifera , was illustrated, and their organization was compared with other rotifer taxa to generate possible hypotheses of evolutionary relationships among Rotifera. The two species share a common habitat but differ from each other in feeding and locomotion. A. ricciae feeds on the biofilm by scraping it, is unable to swim, and slides on the head cilia using the foot to propel over the substratum. M. quadricornifera feeds by filtration, can swim, and advances by looping in a leech-like motion. Their musculature, stained with TRITC-phalloidin, was observed using confocal laser scanning microscopy. Major differences between the two species were observed in the muscles of head and foot, possibly reflecting differences in their life style. Muscles of the trunk were similarly arranged: circular muscles surrounded longitudinal bands, which were inserted at different points on the body wall. In both bdelloids, circular muscles of the trunk were incomplete ventrally, a condition also present in Seison and in soft-bodied monogononts from benthos. Within rotifers, circular muscles in the form of complete rings are present in acanthocephalans and in soft-bodied planktonic monogononts but are absent in loricate monogononts, which generally possess dorsoventral bands. The diversity of muscle organization among rotifers was interpreted and discussed.     

Patterns of diversity in microscopic animals: are they comparable to those in protists or in larger animals?

Aim General patterns of biodiversity, such as latitudinal gradients and species‐area relationships, are found consistently in a wide range of organisms, but recent results for protist diversity suggest that organisms shorter than 2 mm do not display such patterns. We tested this prediction in bdelloid rotifers, pluricellular metazoans smaller than 2 mm, but with size and ecology comparable to protists. Location A single valley in northern Italy was surveyed in detail and compared to all available faunistic data on bdelloids worldwide. Methods We analysed 171 local assemblages of bdelloid rotifers living in 5 systems of dry mosses and submerged mosses in running water and in lakes. We compared patterns of alpha, beta, and gamma diversity, and nestedness of metacommunities, with those known from protists and larger organisms. Results Bdelloid rotifers showed low local species richness (alpha diversity), with strong habitat selection, as observed in larger organisms. The number of species differed among systems, with a higher number of species in dry than in aquatic mosses. There was no hierarchical structure or exclusion of species in the metacommunity pattern within each system. Local diversity for the entire valley was surprisingly high compared with worldwide bdelloid diversity, similar to observed patterns in protists. Main Conclusions Bdelloid rotifers have some of the peculiarities of protist biodiversity, although at slightly different spatial scales, thus confirming the idea of a major change in biodiversity patterns among organisms shorter than 2 mm. However, bdelloids show stronger habitat selection than protists. We suggest two possible explanations for the observed patterns: (1) dispersal is very rare, and not all bdelloid clones are arriving everywhere; and (2) dispersal is effective in displacing propagules, but environmental heterogeneity is very high and prevents many species from colonizing a given patch of moss.     

Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis

One hundred and sixty-four accessions representing Czech and Slovak pea (Pisum sativum L.) varieties bred over the last 50 years were evaluated for genetic diversity using morphological, simple sequence repeat (SSR) and retrotransposon-based insertion polymorphism (RBIP) markers. Polymorphic information content (PIC) values of 10 SSR loci and 31 RBIP markers were on average high at 0.89 and 0.73, respectively. The silhouette method after the Ward clustering produced the most probable cluster estimate, identifying nine clusters from molecular data and five to seven clusters from morphological characters. Principal component analysis of nine qualitative and eight quantitative morphological parameters explain over 90 and 93% of total variability, respectively, in the first three axes. Multidimensional scaling of molecular data revealed a continuous structure for the set. To enable integration and evaluation of all data types, a Bayesian method for clustering was applied. Three clusters identified using morphology data, with clear separation of fodder, dry seed and afila types, were resolved by DNA data into 17, 12 and five sub-clusters, respectively. A core collection of 34 samples was derived from the complete collection by BAPS Bayesian analysis. Values for average gene diversity and allelic richness for molecular marker loci and diversity indexes of phenotypic data were found to be similar between the two collections, showing that this is a useful approach for representative core selection.     

From micro- to macroevolution: brood parasitism as a driver of phenotypic diversity in birds

A fundamental question in biology is how diversity evolves and why some clades are more diverse than others. Phenotypic diversity has often been shown to result from morphological adaptation to different habitats. The role of behavioral interactions as a driver of broadscale phenotypic diversity has received comparatively less attention. Behavioral interactions, however, are a key agent of natural selection. Antagonistic behavioral interactions with predators or with parasites can have significant fitness consequences, and hence act as strong evolutionary forces on the phenotype of species, ultimately generating diversity between species of both victims and exploiters. Avian obligate brood parasites lay their eggs in the nests of other species, their hosts, and this behavioral interaction between hosts and parasites is often considered one of the best examples of coevolution in the natural world. In this review, we use the coevolution between brood parasites and their hosts to illustrate the potential of behavioral interactions to drive evolution of phenotypic diversity at different taxonomic scales. We provide a bridge between behavioral ecology and macroevolution by describing how this interaction has increased avian phenotypic diversity not only in the brood parasitic clades but also in their hosts.     

Genetic diversity and methylation polymorphism analysis of Chrysanthemum nankingense

The diploid species Chrysanthemum nankingense (Anthemideae, Asteraceae) is closely related to the commercially important hexaploid ornamental species Chrysanthemum morifolium and is well adapted to poor environments. In this study, phenotypic variants of C. nankingense were first identified by morphological traits. Using EST-SSR (simple sequence repeat) analysis, we detected some absent EST-SSRs. The percentage of AFLP (amplified fragment length polymorphism) polymorphic fragments was 78.2%, indicating high genetic diversity. To evaluate the genome methylation level and methylation polymorphism, we used the MSAP (methylation-sensitive amplification polymorphism) technique to analyze the 30 C. nankingense lines. The total DNA methylation level ranged from 54.6% to 62.6%. Most of the MSAP-methylated fragments (97%) were polymorphic in the lines. The U-values associated with hemi-methylation were larger than those associated with full methylation in four of the 30 lines, and six individual values were statistically significant (U > 1.96). The high genomic diversity as well as the high methylation polymorphism may be responsible for the morphological polymorphism. There was no significant correlation between the phenotypic and genetic diversity among the lines.     

Populational variability of Proteocephalus longicollis (Cestoda: Proteocephalidae) in the vendace Coregonus albula from lakes of Karelia

Populational variability of Proteocephalus longicollis from the vendace inhabiting various types of Karelian water bodies was studied. High phenotypic diversity of the helminth and polymorphism in the cestode's major functional complexes - attachment, trophic and reproduction - are established. High degree of phenotype pool realization was determined for various P. longicollis populations. Traits belonging to different functional complexes were shown to have different variability patterns. The highest stability was shown for the attachment organs of P. longicollis, which had similar values of qualitative indices and nature of variation. The traits of the trophic and reproduction complexes are more variable. The conclusion was made that the high intrapopulation diversity of P. longicollis is a response to high ecological variability of the vendace, and the distinctions in the phenotype variability of the helminth reflect the differences between population development patterns of the parasite (cestode P. longicollis) and its host (vendace Coregonus albula) in lakes of Karelia.     

Lipid status of fingerlings of the Atlantic salmon <Emphasis Type="Italic">Salmo salar</Emphasis> from different microbiotopes of the Varzuga River

Mechanisms of formation of phenotypic groups of fingerlings of the Atlantic salmon are investigated, related to diversity of embryos and subsequent start possibilities of dispersion of larvae to microbiotopes differing in their life conditions. The fingerlings of salmon, which after hatching and dissolution of the yolk sac moved from the mainstream of the Varzuga River to mouths of its tributaries, had an increased level of triacylglycerols and a higher growth rate than the juveniles remaining in the coastal zone of the river. The revealed differences between the compared groups of fingerlings by the spectrum of stock and structural lipids are mainly connected with distinctions of feeding of juveniles of the same age. The found stable differences by lipid spectra in fingerlings of salmon from the investigated biotopes of the Varzuga in July, August, and October are considered as biochemical prerequisites of the origin of different phenotypic groups of juveniles. Subdivision of fingerlings into phenotypic groups may further on influence the oncoming of the smoltification time of juveniles at the age 2+, 3+, and 4+. Accordingly, this is reflected in formation of the complex age structure (by the number of years spent in the river and in the sea) of the Varzuga population of Atlantic salmon.