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355 results for “Asexuality”
Centennial clonal stability of asexual Daphnia in Greenland lakes despite climate variability
<p><strong>Daphnia_microsatellite_data_Dane_etal.2020.csv: </strong></p> <p><strong>Microsatellite genotypes from three study lakes (SS4, SS1381, and SS1590) in the Kangerlussuaq area, West Greenland. </strong>Microsatellite loci were amplified in single, 12.5 µl multiplex reactions (Type-it PCR kit, Qiagen Inc, Valencia, CA, USA), using an Eppendorf Nexus Thermal Cycler with thermal cycle conditions recommended in the Type-it PCR kit manual. Ten microsatellite primers representing genome-wide loci were used for genotyping; details in (Colbourne et al. 2004; Frisch et al., 2014). Two primers (Dp90, Dp377) failed to amplify in a consistent manner and were therefore excluded from further analysis. Amplified microsatellites were genotyped on an Applied Biosystems 3730 genetic analyser. We used the microsatellite plugin for Geneious 7.0.6 (https://www.geneious.com) for peak calling and binning. Called peaks were visually inspected and manually adjusted when necessary. </p> <p><strong>SS4_sediment.core_data_Fig2_Dane_et_al2020.xlsx</strong>: </p> <p><strong>Information on various parameters of sediment cores collected in Lake SS4, Kangerlussuq area, West Greenland. </strong>Data used in Dane et al. 2020, Figure 2 (panels B and C) are derived from two sediment cores: one for fluorescence (section at 0.5 cm intervals, <em>Depth</em>) and one for <em>Daphnia </em>ephippia analyses (1-cm intervals). Percentage organic matter content (loss-on-ignition at 550 °C,<em>OM%</em>) was used to correlate the two cores to each other and to a previously-dated sediment core (see Dane et al. 2020, Methods). The fluorescence derived parameter Parafac component C2 was used as an indicator of the abundance of purple sulphur bacteria. The organic carbon burial rate (<em>OC AR</em>, g C m–2 yr–1) was also calculated for this core (see Anderson et al. 2019). The <em>Daphnia</em> core was used for the microsatellite analyses and the accumulation rate of ephippia (<em>ephippia AR</em>) at the core site was estimated.</p> <p>For further details please see associated publication in Ecology and Evolution.</p> <p> </p>
Data from: Do pheromones contribute to the persistence of asexual populations in a facultatively parthenogenetic stick insect?
<p>Facultative parthenogenesis is a form of reproduction in which females can either lay unfertilised eggs that typically develop into female offspring only, or mate and lay fertilised eggs that develop into male and female offspring. Facultative parthenogens often occur in mixed-sex populations where reproduction is mostly sexual, and all-female populations where reproduction is asexual. How all-female populations avoid invasion by males remains unknown. Here, we investigated the role of volatile and non-volatile (cuticular hydrocarbons, CHCs) pheromones in the persistence of all-female populations in the facultatively parthenogenetic stick insect, <em>Megacrania </em><em>batesii</em>. We found that <em>M. batesii</em> exhibits slight sexual dimorphism in antenna morphology, and behavioural assays provided little evidence that males could locate females solely by volatile pheromones. However, CHC profiles differed substantially between different types of females. Analysis of CHC structure and abundance indicated a clear genetic difference between females from all-female versus mixed-sex populations, as well as a maternal effect of female parthenogenesis versus sexual development. Together, our results suggest that males might rely more on close-range chemical cues to differentiate females, and chemical communication could play a role in the persistence of all-female populations.</p>
Asymmetric density-dependent competition does not contribute to the maintenance of sex in a mixed population of sexual and asexual Potamopyrgus antipodarum
<p>Asexual reproduction is expected to have a two-fold reproductive advantage over sexual reproduction, owing to the cost of producing males in sexual subpopulations. The persistence of sexual females thus requires an advantage to sexual reproduction, at least periodically. Here we tested the hypothesis that asexual females are more sensitive to limited resources. Under this idea, fluctuations in the availability of resources (<em>per capita</em>) could periodically favor sexual females when resources become limited. We combined sexual and asexual freshwater snails (<em>Potamopyrgus antipodarum</em>) together in nylon mesh enclosures at three different densities in an outdoor mesocosm. After one month, we counted the brood size of fertile female snails. We found that fecundity declined significantly with increasing density. However, sexual females did not produce more offspring than asexual females at any of the experimental densities. Our results thus suggest that the cost of sexual reproduction in <em>P. antipodarum</em> is not ameliorated by periods of intense resource competition.</p>
Greater reproductive assurance of asexual plant compared to sexual relative in a low density sympatric population – experimental evidence for pollen limitation
<p class="western"><span><span><span><span><span><span><span>This dataset contains data from a common garden experiment described in the paper: "</span></span></span></span></span></span><span><span><span><span>Mráz P</span><span><span>, Mrázová V. </span></span></span><span><span><span>2021. </span></span></span><span><span><span>Greater</span></span></span><span><span><span> reproductive assurance of asexual plant compared to sexual relative in a low density sympatric population – experimental evidence for pollen limitation. </span></span></span><i><span><span>Journal of Evolutionary Ecology</span></span></i> </span></span><span><span><span><span><span><span>". </span></span></span></span></span></span></span></p> <p class="western"><span><span><span>We compared the level and stability of reproductive assurance between sexual self-incompatible and asexual autonomously apomictic plants of <i>Hieracium alpinum</i> (Asteraceae) cultivated in a sympatric low-density population with two levels of spatial clumping of sexual plants. </span></span></span><span><span><span>Overall, we found that the realized seed set (i.e. proportion of well developed seeds per capitulum) of asexuals was ca. 3-times greater than that of sexuals (83% <i>versus</i> 27%), while the variance of this trait expressed as coefficient of variation was ca. 4-times smaller in asexuals compared to sexuals (19% <i>versus </i><span>83%)</span>. Solitary sexual plants had more than 2-times lower realized seed set when compared to clumps composed of two spatially close (20-30 cm) sexual plants (13% <i>versus</i> 34%). </span></span></span><span><span><span>Our study provides experimental evidence for benefit of uniparental reproduction of asexuals in a sympatric situation when the availability of mates is limited. This, together with unpredictability of pollinator environment could provide autonomous apomicts with an ultimate demographic superiority during colonization reflected in geographical parthenogenesis observed in this species. </span></span></span></p>
Part 1: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'
<p>Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory.</p> <p>The file Data.One.Focb-2.tar contains 22 files of paired-end reads from F. oxysporum f.sp. cubense tropical race 1 isolate N2 (SRA accession: SRR550150, SRR550151), and F. oxysporum f.sp. cubense TR4 isolates Hainan.B2 (SRR550152), My-1 (SRR7226877), La-2 (SRR7226878), Vn-2 (SRR7226879), Leb1.2C (SRR7226880), JV11 (SRR7226881), Phi2.6C (SRR7226882), Pak1.1A (SRR7226883), UK0001 (SRR9733598).</p>
Part 2: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'
<p>Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory.</p> <p>The file Data.One.Focb.tar contains 16 files of paired-end reads from F. oxysporum f.sp. cubense TR4 isolates II-5 (SRA accession: SRR10054446), S1B8 (SRR10054447), JV14 (SRR10054448), FOC.TR4-5 (SRR10054449), FOC.TR4-1 (SRR10054450), Col2 (SRR10103605), Col4 (SRR10125423), Col17 (SRR10747097).</p> <p> </p>
Part 4: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogen
<p>Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory.</p> <p>The file reads.tar contains 44 files of paired-end reads from <em>F. oxysporum </em>f.sp. <em>lycopersici</em> isolate Fol069 (SRA accession: SRR307106, SRR307107, SRR307113, SRR307115, SRR307123, SRR307257, SRR307266), isolate Fol072 (SRR307122, SRR307092, SRR307091, SRR307090, SRR307086, SRR307281, SRR307250), isolate Fol4287 (SRR7690004, SRR3139043), and F. oxysporum f.sp. radicis-cucumerinum isolate Forc016 (SRR3139027, SRR3139028), isolate Forc024 (SRR3139029, SRR3139030), isolate Forc031 (SRR3139031, SRR3139032).</p>
Asymmetric density-dependent competition does not contribute to the maintenance of sex in a mixed population of sexual and asexual Potamopyrgus antipodarum
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Can sexual conflict drive transitions to asexuality? Female resistance to fertilization in a facultatively parthenogenetic insect
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Greater reproductive assurance of asexual plant compared to sexual relative in a low density sympatric population – experimental evidence for pollen limitation
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After a catastrophe, a little bit of sex is better than nothing: genetic consequences of a major earthquake on asexual and sexual populations
<p>Catastrophic events can have profound effects on the demography of a population and consequently, on genetic diversity. The dynamics of post-catastrophic recovery as well as the role of sexual versus asexual reproduction in buffering the effects of massive perturbations remain poorly understood, in part because the opportunity to document genetic diversity before and after such events is rare. Six natural (purely sexual) and seven cultivated (mainly clonal due to farming practices) populations of the red alga Agarophyton chilense were surveyed along the Chilean coast before, in the days after and two years after the 8.8 magnitude earthquake in 2010. The genetic diversity of sexual populations appeared sensitive to this massive perturbation, notably through the loss of rare alleles immediately after the earthquake. By 2012, the levels of diversity returned to those observed before the catastrophe, probably due to migration. In contrast, enhanced rates of clonality in cultivated populations conferred a surprising ability to buffer the instantaneous loss of diversity. After the earthquake, farmers increased the already high rate of clonality to maintain the few surviving beds, but most of them collapsed rapidly. Contrasting fates between sexual and clonal populations suggest that betting on strict clonality to sustain production is risky, probably because this extreme strategy hampered adaptation to the brutal environmental perturbation induced by the catastrophe.</p>
Data from: Ecological differentiation facilitates fine-scale coexistence of sexual and asexual Boechera
Premise of the study: Ecological differentiation (ED) between sexual and asexual organisms may permit the maintenance of reproductive polymorphism. Several studies of sexual/asexual ED in plants have shown that the geographic ranges of asexuals extend beyond those of sexuals, often in areas of higher latitude or elevation. But very little is known about ED at fine scales, wherein coexistence of sexuals and asexuals may be permitted by differential niche occupation. Methods: We used 149 populations of sexual and apomictic lineages in the genus Boechera (rock cress) collected across a portion of this mustard's vast range. We characterized reproductive mode, ploidy, and species identity or hybrid parentage of each individual, and then used a multi-pronged statistical approach to 1) identify ED between sexuals and asexuals; 2) investigate the impacts of two confounding factors, polyploidy and hybridization, on ED; and 3) determine the environmental variables underlying ED. Key results: We found that sexuals and asexuals are significantly ecologically differentiated across the landscape, despite fine-scale interdigitation of these two reproductive forms. Asexual reproduction was strongly associated with greater disturbance, reduced slope, and greater environmental variability. Although ploidy had little effect on the patterns observed, hybridization has a unique impact on the relationships between asexual reproduction and specific environmental variables. Conclusions: Ecological differentiation along the axes of disturbance, slope, and climatic variability, as well as the effects of heterozygosity, may contribute to the maintenance of sexuality and asexuality across the landscape, ultimately impacting the establishment and spread of asexual lineages.
Phylogenetic distribution of regeneration and asexual reproduction in Annelida: fission evolves in regenerative clades
<p>Supplementary Data</p> <p>Invertebrate Biology 2016</p> <p>Includes annelid regeneration and fission database (comma separated text table), 2 PDF documents containing field descriptions and full references, 1 Nexus formatted file containing multiple-sequence alignment and RAxML tree, and 1 Geneious formatted file containing multiple-sequence alignment and RAxML tree</p>
Investment in regeneration versus asexual reproduction is resource-dependent in a freshwater annelid
<ol> <li>The post-embryonic developmental processes of regeneration and asexual agametic reproduction are widespread and often co-occur in animals. These traits are of great ecological significance, but their physiological dynamics within species are not well understood. In naid annelids, regeneration and asexual reproduction via fission are evolutionarily related and mechanistically similar yet distinct, making these animals useful systems in which to study resource allocation strategies between the two processes.</li> <li>How asexual reproductive investment varies as a function of somatic investment demands was tested in the naid <em>Pristina</em> <em>leidyi</em> by repeatedly amputating the heads of individual worms, allowing regeneration to proceed, and measuring reproductive output over time. Treatments were replicated under high and low food levels to determine to what extent the investment dynamic between regeneration and fission is affected by the resource pool.</li> <li>Reproductive output was affected by injury and regeneration frequency in a resource-dependent manner, such that only worms with less food availability exhibited reproductive deficits; injury and regeneration did not affect reproductive output of worms under the high food condition. When reproductive output was decreased, this occurred not through a reduction in offspring quantity but a reduction in offspring quality. In the offspring of experimental animals, body size and fission speed were dependent on parental feeding level and to a lesser and inconsistent extent on parental injury history, but regeneration speed was unaffected by parental treatment.</li> <li>These findings suggest that in a species capable of both regeneration and asexual reproduction: 1) the resource pool is a key factor mediating the resource investment pattern between regeneration and fission; 2) sacrificing per-offspring investment rather than fecundity may be an optimal strategy if resources are limiting; 3) regeneration and fission have evolved distinct resource allocation pathways. This work prompts further questions about the physiological dynamics between regeneration and asexual reproduction in animals, such as whether and to what extent these have evolved adaptively, including in response to injury and resource pressures.</li> </ol>
Data from: To lose is to win: long-term co-occurrence of two asexual populations realized by a dormant strategy of the inferior competitor
<p><span>Asexual organisms are ubiquitous. While they are the same single species with the same ecological requirements, multiple asexual genotypes within a species are often found in a single habitat. Niche partitioning in time and space among genotypes has been proposed to explain this phenomenon. However, it is not clear whether these different genotypes co-occur in the long term. </span><span>Therefore, we examined the population dynamics of two asexual <em>Daphnia</em> cf. <em>pulex</em> genotypes (JPN1 and JPN2) over nine years in a small mountain lake. These two genotypes consistently occurred in the same seasons and layers, suggesting that niche partitioning cannot explain their long-term co-occurrence. The abundance of JPN1 was typically higher in most years. However, the abundance of dormant eggs in lake sediments was at the same level between the genotypes. </span><span>The laboratory experiment showed that JPN1 excluded JPN2. However, many JPN2 individuals produced the dormant eggs before JPN1 competitively excluded them from the experiment. Furthermore, the competitively inferior JPN2 produced the dormant eggs abundantly in the medium containing a crowding cue from JPN1. However, no such trend was observed for JPN1. </span><span>These results showed that the competitively inferior asexual genotype could maintain the population with the competitively superior genotype for a long period of time because it had the ability to detect the increase in competitors and produce the dormant eggs each year before being competitively eliminated. </span><span>Based on these results, we suggest that the variation in the genotype-specific response in dormant egg production to environmental change plays a key role in t</span><span>he long-term co-occurrence of different asexual genotypes in single habitats.</span></p>
Data from: Reduced mitochondrial respiration in hybrid asexual lizards
<p><span>The scarcity of asexual reproduction in vertebrates alludes to an inherent cost. Several groups of asexual vertebrates exhibit lower endurance capacity (a trait predominantly sourced by mitochondrial respiration) compared to congeneric sexual species. Here we measure endurance capacity in five species of <i>Aspidoscelis </i>lizards and examine mitochondrial respiration between sexual and asexual species using mitochondrial respirometry. Our results show reduced endurance capacity, mitochondrial respiration, and phenotypic variability in asexual species compared to parental sexual species along with a positive relationship between endurance capacity and mitochondrial respiration. Results of lower endurance capacity and lower mitochondrial respiration in asexual <i>Aspidoscelis </i>are consistent with hypotheses involving mitonuclear incompatibility.</span></p> <p><span>This repository includes files with DNA sequence alignments, evolutionary relationships, mitochondrial respiration, and endurance measurements for five species of whiptail lizards. Code used to analyze the data in the context of the study is also included.</span></p>
The origins of asexual brine shrimps
<p>Determining how and how often asexual lineages emerge within sexual species is central to our understanding of sex-asex transitions and the long-term maintenance of sex. Asexuality can arise "by transmission" from an existing asexual lineage to a new one, through different types of crosses. The occurrence of these crosses, cryptic sex, variation in ploidy and recombination within asexuals greatly complicates the study of sex-asex transitions, as they preclude the use of standard phylogenetic methods and genetic distance metrics. In this study we show how to overcome these challenges by developing new approaches to investigate the origin of the various asexual lineages of the brine shrimp <em>Artemia parthenogenetica</em>. We use a large sample of asexuals, including all known polyploids, and their sexual relatives. We combine flow cytometry with mitochondrial and nuclear DNA data. We develop new genetic distance measures and methods to compare various scenarios describing the origin of the different lineages. We find that all diploid and polyploid <em>A. parthenogenetica</em> likely arose within the last 80,000 years through successive and nested hybridization events that involved backcrosses with different sexual species. All <em>A. parthenogenetica</em> have the same common ancestor and therefore likely carry the same asexuality gene(s) and reproduce by automixis. These findings radically change our view of sex-asex transitions in this group, and show the importance of considering asexuality "by transmission" scenarios. The methods developed are applicable to many other asexual taxa.</p>
Data from: Invasions of an obligate asexual daphnid species support the nearly neutral theory
<p><span>To verify the "nearly neutral theory (NNT)," the ratio of nonsynonymous to synonymous substitutions (<em>dN/dS</em>) was compared among populations of different species. To determine the validity of NNT, however, populations that are genetically isolated from each other but share the same selection agents and differ in size should be compared. Genetically different lineages of obligate asexual <em>Daphnia pulex</em> invading Japan from North America are an ideal example as they satisfy these prerequisites. Therefore, we analyzed the whole-genome sequences of 18 genotypes, including those of the two independently invaded <em>D. pulex</em> lineages (JPN1 and JPN2) and compared the <em>dN/dS</em> ratio between the lineages. The base substitution rate of each genotype demonstrated that the JPN1 lineage having a larger distribution range diverged earlier and thus was older than the JPN2 lineage. Comparisons of the genotypes within lineages revealed that changes in <em>dN/dS</em> occurred after the divergence and were larger in the younger lineage, JPN2. These results imply that the JPN1 lineage has been more effectively subjected to purification selections, while slightly deteriorating mutations are less purged in JPN2 with smaller population size. Altogether, the lineage-specific difference in the <em>dN/dS</em> ratio for the obligate asexual <em>D. pulex</em> was well explained by the NNT.</span></p>
Data from: Joint evolution of asexuality and queen number in an ant
Ants exhibit a striking diversity of reproductive systems, varying in traits such as the number of reproductives per colony [1], the mode of daughter production (sexual or asexual) [2], and the mode of caste determination (genetic or environmental) [3]. Species employing mixed reproductive systems present a unique opportunity to explore the causes and consequences of alternative breeding strategies. Mixed reproductive systems in ants include social polymorphism in colony queen number, whereby single-queen (monogyne) and multiple-queen (polygyne) colonies co-occur within species [4, 5, 6, 7], and facultative asexuality, in which female offspring may be produced sexually or asexually within colonies [8, 9, 10, 11, 12, 13]. Here, we document a remarkable confluence of multiple mixed reproductive systems in the tropical fire ant, Solenopsis geminata, in a population with three important features: (1) polygyne colonies produce workers sexually but queens asexually, whereas monogyne colonies produce both castes sexually; (2) polygyne queens mate with monogyne males to produce workers, but monogyne queens do not mate with polygyne males; and (3) different asexual/polygyne lineages evidently were founded separately by genetically distinct founder queens, which appear to have originated from the same neighboring monogyne population. Multiple asexual/polygyne genomes are transmitted undiluted in this system, but sterile workers produced with sperm from a sexually-reproducing/monogyne population are necessary for the persistence of these lineages. The intersection of social polymorphism, facultative asexuality, and genetic caste determination marks this population of S. geminata as an embodiment of the diversity of ant reproductive systems and suggests previously unknown connections between these phenomena.
Range expansions of sexual versus asexual organisms: Effects of reproductive assurance and migration load
<p>It is generally considered that sexual organisms show faster evolutionary adaptation than asexual organisms because sexuals can accumulate adaptive mutations through recombination. Yet empirical evidence often shows that the geographic range size of sexual species is narrower than that of closely-related asexual species, which may seem as if asexuals can adapt to more varied environments. Two potential explanations for this apparent contradiction considered by existing theory are reproduction assurance and migration load. Here, we consider both reproductive assurance and migration load within a single model to comparatively examine their effects on range expansions of sexuals and asexuals across an environmental gradient. The model shows that higher dispersal propensity decreases sexuals' disadvantage in reproductive assurance while increasing their disadvantage in migration load. Moreover, lower mutation rate constrains adaptation more strongly in asexuals than in sexuals. Thus, high dispersal propensity and high mutation rates promote that asexuals have wider range sizes than sexuals. Intriguingly, our model reveals that sexuals can have wider geographic range sizes than asexuals under low dispersal propensity and low mutation rates, a pattern consistent with a few exceptional empirical cases. Combining reproductive assurance and migration load provides a useful perspective to better understand the relationships between species' mating systems and their geographic ranges.<span><br></span></p>
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