Do clones degenerate over time? Explaining the genetic variability of asexuals through population genetic models

<p>Abstract</p> <p>Background</p> <p>Quest for understanding the nature of mechanisms governing the life span of clonal organisms lasts for several decades. Phylogenetic evidence for recent origins of most clones is usually interpreted as proof that clones suffer from gradual age-dependent fitness decay (e.g. Muller's ratchet). However, we have shown that a neutral drift can also qualitatively explain the observed distribution of clonal ages. This finding was followed by several attempts to distinguish the effects of neutral and non-neutral processes. Most recently, Neiman et al. 2009 (Ann N Y Acad Sci.:1168:185-200.) reviewed the distribution of asexual lineage ages estimated from a diverse array of taxa and concluded that neutral processes alone may not explain the observed data. Moreover, the authors inferred that similar types of mechanisms determine maximum asexual lineage ages in all asexual taxa. In this paper we review recent methods for distinguishing the effects of neutral and non-neutral processes and point at methodological problems related with them.</p> <p>Results and Discussion</p> <p>We found that contemporary analyses based on phylogenetic data are inadequate to provide any clear-cut answer about the nature and generality of processes affecting evolution of clones. As an alternative approach, we demonstrate that sequence variability in asexual populations is suitable to detect age-dependent selection against clonal lineages. We found that asexual taxa with relatively old clonal lineages are characterised by progressively stronger deviations from neutrality.</p> <p>Conclusions</p> <p>Our results demonstrate that some type of age-dependent selection against clones is generally operational in asexual animals, which cover a wide taxonomic range spanning from flatworms to vertebrates. However, we also found a notable difference between the data distribution predicted by available models of sequence evolution and those observed in empirical data. These findings point at the possibility that processes affecting clonal evolution differ from those described in recent studies, suggesting that theoretical models of asexual populations must evolve to address this problem in detail.</p> <p>Reviewers</p> <p>This article was reviewed by Isa Schön (nominated by John Logsdon), Arcady Mushegian and Timothy G. Barraclough (nominated by Laurence Hurst).</p

Macrobiotus polypiformis sp. nov., a new tardigrade (Macrobiotidae; hufelandi group) from the Ecuadorian Pacific coast, with remarks on the claw abnormalities in eutardigrades

From a moss sample collected in the Manabí Province in Ecuador, we extracted 96 specimens of a new species of eutardigrade. No eggs were found. In order to obtain eggs, an in vitro culture was prepared. In total, 136 specimens (including ten simplex), one exuvia and 44 eggs (including two with embryos) of the new species were obtained. In addition to the traditional taxonomic description with morphometrics, light and scanning microscopy imaging, we also provide nucleotide sequences of three nuclear (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial (COI) DNA fragments of the new species. Macrobiotus polypiformis sp. nov. belongs to the hufelandi group and is most similar to Ma. paulinae Stec, Smolak, Kaczmarek & Michalczyk, 2015, but differs from it mainly by the lack of dorso-lateral patches of granulation on the cuticle, egg processes with longer and more numerous filaments and in some morphometric characters of both eggs and adults. Moreover, we provide a short discussion on the modifications/abnormalities of the claws in eutardigrades and the possible consequences on the taxonomic status of Mesobiotus armatus (Pilato & Binda, 1996), suggesting its consideration as species inquirenda (with uncertain taxonomic status)

Did glacial advances during the Pleistocene influence differently the demographic histories of benthic and pelagic Antarctic shelf fishes? – Inferences from intraspecific mitochondrial and nuclear DNA sequence diversity

<p>Abstract</p> <p>Background</p> <p>Circum-Antarctic waters harbour a rare example of a marine species flock – the Notothenioid fish, most species of which are restricted to the continental shelf. It remains an open question as to how they survived Pleistocene climatic fluctuations characterised by repeated advances of continental glaciers as far as the shelf break that probably resulted in a loss of habitat for benthic organisms. Pelagic ecosystems, on the other hand, might have flourished during glacial maxima due to the northward expansion of Antarctic polar waters. In order to better understand the role of ecological traits in Quaternary climatic fluctuations, we performed demographic analyses of populations of four fish species from the tribe Trematominae, including both fully benthic and pelagic species using the mitochondrial cytochrome b gene and an intron from the nuclear S7 gene.</p> <p>Results</p> <p>Nuclear and cytoplasmic markers showed differences in the rate and time of population expansions as well as the likely population structure. Neutrality tests suggest that such discordance comes from different coalescence dynamics of each marker, rather than from selective pressure. Demographic analyses based on intraspecific DNA diversity suggest a recent population expansion in both benthic species, dated by the cyt b locus to the last glacial cycle, whereas the population structure of pelagic feeders either did not deviate from a constant-size model or indicated that the onset of the major population expansion of these species by far predated those of the benthic species. Similar patterns were apparent even when comparing previously published data on other Southern Ocean organisms, but we observed considerable heterogeneity within both groups with regard to the onset of major demographic events and rates.</p> <p>Conclusion</p> <p>Our data suggest benthic and pelagic species reacted differently to the Pleistocene ice-sheet expansions that probably significantly reduced the suitable habitat for benthic species. However, the asynchronous timing of major demographic events observed in different species within both "ecological guilds", imply that the species examined here may have different population and evolutionary histories, and that more species should be analysed in order to more precisely assess the role of life history in the response of organisms to climatic changes.</p

Developmental plasticity of Arabidopsis hypocotyl is dependent on exocyst complex function

The collet (root–hypocotyl junction) region is an important plant transition zone between soil and atmospheric environments. Despite its crucial importance for plant development, little is known about how this transition zone is specified. Here we document the involvement of the exocyst complex in this process. The exocyst, an octameric tethering complex, participates in secretion and membrane recycling and is central to numerous cellular and developmental processes, such as growth of root hairs, cell expansion, recycling of PIN auxin efflux carriers and many others. We show that dark-grown Arabidopsis mutants deficient in exocyst subunits can form a hair-bearing ectopic collet-like structure above the true collet, morphologically resembling the true collet but also retaining some characteristics of the hypocotyl. The penetrance of this phenotypic defect is significantly influenced by cultivation temperature and carbon source, and is related to a defect in auxin regulation. These observations provide new insights into the regulation of collet region formation and developmental plasticity of the hypocotyl

Temperature (latitude) and nutrient (seabird guano) effects on limno-terrestrial Tardigrada (Testechiniscus spitsbergensis and Pilatobius recamieri) body size

Surveys of terrestrial microinvertebrate morphometry, especially spatial patterns of body size at wider geographical scales, including the polar regions, are very scarce. In this study, we focused on Tardigrada, common limno-terrestrial microinvertebrates. Considering Bergmann’s rule, originally formulated for endothermic animals, we tested the hypothesis that body length of limno-terrestrial tardigrades augments with increasing latitude and decreasing temperature. Since some of our sampling areas adjoined seabird colonies, we also explored the effects of nutrients from seabird guano deposits. Individual body length of Testechiniscus spitsbergensis was measured in populations obtained from seven localities distributed along a latitudinal gradient extending from 45^{\circ}N (northern Italy) to 79^{\circ}N (northern Svalbard), and for Pilatobius recamieri from three localities in Svalbard (77^{\circ}N-80^{\circ}N). Considering both latitude and proximity to a seabird colony there were significant effects of locality on the body length of T. spitsbergensis; however, no clear pattern of increasing individual body size with increasing latitude could be detected. Immense differences in body size may be a signal for cryptic species diversity within this genus. No effect of latitude, or proximity to a seabird colony, on the body length of Arctic populations of P. recamieri was documented. Evidently, there is no tendency towards body size increase along the latitudinal gradient in either T. spitsbergensis or P. recamieri. Our study, and recent literature, indicates that larger body size in polar regions reported for several groups of micro-fauna may be a taxon-dependent response, and cannot be taken as a universally applicable rule for limnoterrestrial animals

Distinguishing between Incomplete Lineage Sorting and Genomic Introgressions : Complete Fixation of Allospecific Mitochondrial DNA in a Sexually Reproducing Fish (Cobitis; Teleostei), despite Clonal Reproduction of Hybrids

Peer reviewe

Different Vancomycin Immunoassays Contribute to the Variability in Vancomycin Trough Measurements in Neonates

Substantial interassay variability (up to 20%) has been described for vancomycin immunoassays in adults, but the impact of neonatal matrix is difficult to quantify because of blood volume constraints in neonates. However, we provide circumstantial evidence for a similar extent of variability. Using the same vancomycin dosing regimens and confirming similarity in clinical characteristics, vancomycin trough concentrations measured by PETINIA (2011-2012, n = 400) were 20% lower and the mean difference was 1.93 mg/L compared to COBAS (2012-2014, n = 352) measurements. The impact of vancomycin immunoassays in neonatal matrix was hereby suggested, supporting a switch to more advanced techniques (LC-MS/MS)

Genome fractionation and loss of heterozygosity in hybrids and polyploids: Mechanisms, consequences for selection, and link to gene function

Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. The subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that opens up unexpected evolutionary pathways. To elucidate this problem, we compared published cytogenetic and RNAseq data with exome sequences of asexual diploid and polyploid hybrids between three fish species; Cobitis elongatoides, C taenia, and C tanaitica. Clonal genomes remained generally static at chromosome-scale levels but their heterozygosity gradually deteriorated at the level of individual genes owing to allelic deletions and conversions. Interestingly, the impact of both processes varies among animals and genomic regions depending on ploidy level and the properties of affected genes. Namely, polyploids were more tolerant to deletions than diploid asexuals where conversions prevailed, and genomic restructuring events accumulated preferentially in genes characterized by high transcription levels and GC-content, strong purifying selection and specific functions like interacting with intracellular membranes. Although hybrids were phenotypically more similar to C taenia, we found that they preferentially retained C elongatoides alleles. This demonstrates that favored subgenome is not necessarily the transcriptionally dominant one. This study demonstrated that subgenomes in asexual hybrids and polyploids evolve under a complex interplay of selection and several molecular mechanisms whose efficiency depends on the organism's ploidy level, as well as functional properties and parental ancestry of the genomic region.Web of Science38125274525

Cryophilic Tardigrada have disjunct and bipolar distribution and establish long-term stable, low-density demes

Glaciers are inhabited by various cryophilic organisms ranging from single celled to multicellular, like Tardigrada (water bears). Owing to their scattered distribution, glaciers represent extremely fragmented habitats, and it remains unclear how their inhabitants survive and disperse among such isolated patches. This study investigates the biogeography of the tardigrade genus Cryoconicus, whose distribution, population stability, and interregional connectivity are examined by screening the collections from ~ 60 glaciers worldwide and by a phylogeographic analysis. We found that two Cryoconicus species occur at low densities on two Arctic glaciers in Svalbard, far from their previously reported Antarctic and Central Asian ranges. Screening of worldwide databases and DNA metabarcoding indicated that these species are absent or rare in the intermediate areas, suggesting large disjunctions in their ranges. In particular, the genetic data and multiyear resampling showed that Cryoconicus kaczmareki established a stable population on the Ebba Glacier (Svalbard), which has been isolated from its Asian core range since before the last glacial maximum. Our findings suggest that glacial invertebrates may possess wide yet largely disjunctive ranges. Interpolar- or intercontinental-scale movements of cryophilic meiofauna may occur, but migration connectivity is not sufficient to mitigate the differentiation of the local population. Revealed biogeographic patterns further demonstrate that inhabitants of extreme environments may establish isolated and highly fragmented populations that persist long term, even if at very low densities