Meiosis genes in Daphnia pulex and the role of parthenogenesis in genome evolution

Background  

Thousands of parthenogenetic animal species have been described and cytogenetic manifestations of this reproductive mode are well known. However, little is understood about the molecular determinants of parthenogenesis. The Daphnia pulex genome must contain the molecular machinery for different reproductive modes: sexual (both male and female meiosis) and parthenogenetic (which is either cyclical or obligate). This feature makes D. pulex an ideal model to investigate the genetic basis of parthenogenesis and its consequences for gene and genome evolution. Here we describe the inventory of meiotic genes and their expression patterns during meiotic and parthenogenetic reproduction to help address whether parthenogenesis uses existing meiotic and mitotic machinery, or whether novel processes may be involved.     

Food quality triggers the reproductive mode in the cyclical parthenogen <Emphasis Type="Italic">Daphnia</Emphasis> (Cladocera)

Cyclic parthenogenesis (heterogony) is a widespread reproductive mode found in diverse taxa such as digenean trematodes, gall wasps, gall midges, aphids, cladocerans and rotifers. It is of particular interest as it combines the advantages of asexual reproduction (rapid population growth) and sexual reproduction (recombination). Usually sexual reproduction is initiated when, or slightly before, environmental conditions deteriorate, and often results in the production of resting stages. The optimal timing of diapause induction must thus be under strong natural selection. Using the cladoceran Daphnia as a model system, we show here for the first time that the switch from parthenogenetic to sexual reproduction in a cyclical parthenogenetic organism can be influenced by the chemical composition of food. Under crowding conditions Daphnia reproduced parthenogenetically with subitaneous eggs when fed the algal species Cryptomonas sp., but started the production of resting eggs when fed with the green algal species Scenedesmus obliquus. Supplementation experiments with lipids and especially proteins showed that the induction of resting egg production in two clones of different Daphnia species was due to a dietary deficiency in the green alga. Hence, the low food quality induced a switch in the reproductive mode that may contribute to optimal timing of the sexual reproduction of Daphnia in nature. Furthermore, our results have two other major implications: first, they suggest that protein compounds should be added to the list of diet constituents potentially limiting or influencing Daphnia reproduction. Second, we show that the role of food quality goes far beyond the up to now documented effects of food quality on somatic growth and trophic transfer efficiency of herbivores: due to its effects on sexual reproduction and the production of resting eggs, food quality might influence genetic diversity and long-term persistence of Daphnia in lakes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The costs of crest induction for Daphnia carinata

The effects of notonectid-induced crests on growth and reproduction, and resource allocation to crest construction, moult losses and eggs of Daphnia carinata were measured. An attempt was made to elucidate the mechanisms of physiological costs of crest induction for this species. The crested morph of d. carinata reached a significantly larger size than the uncrested form. Reproductive output was similar in early instars, but the crested morph produced more eggs in latter broods. Instar duration was longer for the crested morph and age at first reproduction was delayed. Survival was also lower in this form. Crest construction required significant resources (equivalent to 60 eggs over a life time) but evidence is presented that these resources were obtained primarily by re-allocation of available material rather than collection of extra resources. The crested morph allocated significantly more resources to moulting than its uncrested counter-parts. The uncrested morph produced large eggs in early instars and progressively smaller ones in later instars. The crested morph produced only small eggs. The hypothesis is presented that the crest-induction strategy of D. carinata involves at least two separate sets of responses, each with its own costs and trade-offs. The first response is production of the crest. The cost of crest production is an increased cost of moulting. D. carinata off sets this cost by increasing instar duration and thus age at reproduction. The second response is increased size. D. carinata achieves this by reducing the fraction of available resources allocated to reproduction. The cost is lower reproductive output.     

A Genomic Comparison of Faster-Sex, Faster-X, and Faster-Male Evolution Between Drosophila melanogaster and Drosophila pseudoobscura

A genomic comparison of Drosophila melanogaster and Drosophila pseudoobscura provides a unique opportunity to investigate factors involved in sequence divergence. The chromosomal arrangements of these species include an autosomal segment in D. melanogaster which is homologous to part of the X chromosome in D. pseudoobscura. Using orthologues to calculate rates of nonsynonymous (d_N) substitutions, we found genes on the X chromosome to be significantly more diverged than those on the autosomes, but it is not true for segment 3L-XR which is autosomal in D. melanogaster (3L) and X-linked in D. pseudoobscura (XR). We also found that the median d_N values for genes having reproductive functions in either the male, the female, or both sexes are higher than those for sequences without reproductive function and even higher for sequences involved in male-specific function. These estimates of divergence for male sex-related sequences are most likely underestimates, as the very rapidly evolving reproductive genes would tend to lose homology sooner and thus not be included in the comparison of orthologues. We also noticed a high proportion of male reproductive genes among the othologous genes with the highest rates of d_N. Reproductive genes with and without an orthologue in D. pseudoobscura were compared among D. melanogaster, D. simulans, and D. yakuba and it was found that there were in fact higher rates of divergence in the group without a D. pseudoobscura orthologue. These results, from widely separated taxa, bolster the thesis that sexual system genes experience accelerated rates of change in comparison to nonsexual genes in evolution and speciation. [Reviewing Editor: Dr. Willie J. Swanson]     

Cloning,expression and cellular localization of the Doublesex gene in the water flea, Daphnia carinata, during different developmental stages

In this study, one of Doublesex genes from the common freshwater cladoceran Daphnia carinata, designated DapcaDsx1, was cloned using primers based on homologous sequences and rapid amplification of cDNA ends (RACE). qPCR was employed to quantify differences in DapcaDsx1 expression between the different sexual phases, with expression levels being higher in sexual females. The role of DapcaDsx1 in the reproductive transformation was further investigated in parthenogenetic-phase females and sexual-phase females using whole-mount in situ hybridization. This cellular localization study showed specific expression of DapcaDsx1 in the thoracic segments, second antenna and part of the ventral carapace. Higher expression levels were exhibited in sexual females compared to parthenogenetic females. This suggests that the DapcaDsx1 gene plays significant roles in switching modes of reproduction and during sexual differentiation.     

Geographic parthenogenesis and the common tea‐tree stick insect of New Zealand

Worldwide, parthenogenetic reproduction has evolved many times in the stick insects (Phasmatidae). Many parthenogenetic stick insects show the distribution pattern known as geographic parthenogenesis, in that they occupy habitats that are at higher altitude or latitude compared with their sexual relatives. Although it is often assumed that, in the short term, parthenogenetic populations will have a reproductive advantage over sexual populations; this is not necessarily the case. We present data on the distribution and evolutionary relationships of sexual and asexual populations of the New Zealand stick insect, Clitarchus hookeri. Males are common in the northern half of the species’ range but rare or absent elsewhere, and we found that most C. hookeri from putative‐parthenogenetic populations share a common ancestor. Female stick insects from bisexual populations of Clitarchus hookeri are capable of parthenogenetic reproduction, but those insects from putative‐parthenogenetic populations produced few offspring via sexual reproduction when males were available. We found similar fertility (hatching success) in mated and virgin females. Mated females produce equal numbers of male and female offspring, with most hatching about 9–16 weeks after laying. In contrast, most eggs from unmated females took longer to hatch (21–23 weeks), and most offspring were female. It appears that all C. hookeri females are capable of parthenogenetic reproduction, and thus could benefit from the numerical advantage this yields. Nevertheless, our phylogeographic evidence shows that the majority of all‐female populations over a wide geographic area originate from a single loss of sexual reproduction.     

A study on the effects of food quantity and quality on glutathione S-transferase (GST) activity and growth rate parameters of <Emphasis Type="Italic">Daphnia</Emphasis><Emphasis Type="Italic">carinata</Emphasis> varying in age

The adverse influences of insufficient food and toxins on Daphnia carinata’s body growth, reproduction and tolerance were investigated in the laboratory. Different concentrations of Scendesmus obliquus and a mixture of S. obliquus and microcystin (MC)-containing Microcystis aeruginosa PCC7820 were used to feed D. carinata. Glutathione S-transferase (GST) activity towards five chemical compounds (substrates) was measured and used as an indicator of their tolerance. Body growth rate and clutch size of D. carinata decreased with declined concentration or decreased proportion of S. obliquus in the diet. GST activity decreased with ageing in D. carinata. However, GST activity to several chemical compounds increased when food quantity or food quality decreased. Adult D. carinata had a lower GST activity towards p-nitrophenenzyl chloride (PNBC) than juveniles and exhibited a sharp decline (P < 0.001) in GST activity towards PNBC as the animals aged. It is suggested that the age-specific decrease in GST activity is a possible mechanism for the high morality of adult D. carinata in the summer of eutrophic lakes.     

Effect of the epizoic rotifer Brachionus rubens on the population growth of three cladoceran species

Using population densities and growth rates as criteria, we studied interactions between the epizoic rotifer Brachionus rubens and each of three cladoceran species differing in size and reproductive rates — Daphnia carinata, Moina macrocopa and Ceriodaphnia rigaudi. In all mixed — species experiments, B. rubens existed in both the epizoic mode, attached to the cladoceran host, and in the free-swimming mode. Rotifer population growth rates were significantly depressed in the presence of M. macrocopa, presumably as a consequence of exploitative and interference competition. The largest cladoceran, D. carinata probably did not suppress B. rubens, because the epizoic component of the rotifer population escaped from the deleterious effects of mechanical interference. Peak population numbers and initial population growth rates reached by all three cladocerans were lower in the presence of B. rubens, probably because of the adverse effects of the epizoic infestation, which was maximal on D. carinata and least on C. rigaudi. In mixed-species cultures of D. carinata and M. macrocopa, the presence of B. rubens helped D. carinata coexist with M. macrocopa, which otherwise would have suppressed the Daphnia.     

Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the <Emphasis Type="Italic">amoCAB</Emphasis> operon

The genes and intergenic regions of the amoCAB operon were analyzed to establish their potential as molecular markers for analyzing ammonia-oxidizing betaproteobacterial (beta-AOB) communities. Initially, sequence similarity for related taxa, evolutionary rates from linear regressions, and the presence of conserved and variable regions were analyzed for all available sequences of the complete amoCAB operon. The gene amoB showed the highest sequence variability of the three amo genes, suggesting that it might be a better molecular marker than the most frequently used amoA to resolve closely related AOB species. To test the suitability of using the amoCAB genes for community studies, a strategy involving nested PCR was employed. Primers to amplify the whole amoCAB operon and each individual gene were tested. The specificity of the products generated was analyzed by denaturing gradient gel electrophoresis, cloning, and sequencing. The fragments obtained showed different grades of sequence identity to amoCAB sequences in the GenBank database. The nested PCR approach provides a possibility to increase the sensitivity of detection of amo genes in samples with low abundance of AOB. It also allows the amplification of the almost complete amoA gene, with about 300 bp more sequence information than the previous approaches. The coupled study of all three amo genes and the intergenic spacer regions that are under different selection pressure might allow a more detailed analysis of the evolutionary processes, which are responsible for the differentiation of AOB communities in different habitats. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Pilar Junier and Ok-Sun Kim contributed equally to this work.     

Birth and Death of Genes and Functions in the β-Esterase Cluster of <Emphasis Type="Italic">Drosophila</Emphasis>

Here we analyze the molecular evolution of the β-esterase gene cluster in the Drosophila genus using the recently released genome sequences of 12 Drosophila species. Molecular evolution in this small cluster is noteworthy because it contains contrasting examples of the types and stages of loss of gene function. Specifically, missing orthologs, pseudogenes, and null alleles are all inferred. Phylogenetic analyses also suggest a minimum of 9 gene gain–loss events; however, the exact number and age of these events is confounded by interparalog recombination. A previous enigma, in which allozyme loci were mapped to β-esterase genes that lacked catalytically essential amino acids, was resolved through the identification of neighbouring genes that contain the canonical catalytic residues and thus presumably encode the mapped allozymes. The originally identified genes are evolving with selective constraint, suggesting that they have a “noncatalytic” function. Curiously, 3 of the 4 paralogous β-esterase genes in the D. ananassae genome sequence have single inactivating (frame-shift or nonsense) mutations. To determine whether these putatively inactivating mutations were fixed, we sequenced other D. ananassae alleles of these four loci. We did not find any of the 3 inactivating mutations of the sequenced strain in 12 other strains; however, other inactivating mutations were observed in the same 3 genes. This is reminiscent of the high frequency of null alleles observed in one of the β-esterase genes (Est7/EstP) of D. melanogaster. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Diversity and geographical distribution of rhizobia associated with <Emphasis Type="Italic">Lespedeza</Emphasis> spp. in temperate and subtropical regions of China

Eighty-eight root-nodule isolates from Lespedeza spp. grown in temperate and subtropical regions of China were characterized by a polyphasic approach. Nine clusters were defined in numerical taxonomy and SDS-PAGE analysis of whole cell proteins. Based upon further characterizations of amplified 16S rDNA restriction analysis (ARDRA), PCR-based restriction fragment length polymorphism of ribosomal IGS, 16S rDNA sequence analysis and DNA-DNA hybridization, these isolates were identified as Bradyrhizobium japonicum, B. elkanii, B. yuanmingense, Mesorhizobium amorphae, M. huakuii, Sinorhizobium meliloti and three genomic species related to B. yuanmingense, Rhizobium gallicum and R. tropici. The Bradyrhizobium species and R. tropici-related rhizobia were mainly isolated from the subtropical region and the species of Mesorhizobium, S. meliloti and R. gallicum-related species were all isolated from the temperate region. Phylogenetic analyses of nifH and nodC indicated that the symbiotic genes of distinct rhizobial species associated with Lespedeza spp. might have different origins and there was no evidence for lateral gene transfer of symbiotic genes. The results obtained in the present study and in a previous report demonstrated that Lespedeza spp. are nodulated by rhizobia with diverse genomic backgrounds and these Lespedeza-nodulating rhizobia were not specific to the host species, but specific to their geographic origins. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. GenBank sequence accession numbers: The GenBank accession numbers were EF61095 through EF061114 and EF051240 for acquired 16S rDNA sequences; EF153395 through EF153402 for nifH sequences; and EF153403 through EF153410 for nodC sequences.     

The evolution of the reproductive system of Urodasys (Gastrotricha: Macrodasyida)

Macrodasyidan gastrotrichs are hermaphrodites with complex reproductive organs that function in sperm transfer and receipt, but homology among the organs of members of different clades remains undetermined, as does a broader understanding of evolutionary trends in the reproductive biology of macrodasyidans. In this study, we investigate the evolution of reproduction in Urodasys, a clade of 15 macrodasyidan species that shows variability in reproductive mode (hermaphroditic and parthenogenetic) and sexual anatomy. We use partial 18S rDNA sequence data from 30 specimens representing five described species, sequence data from one undescribed species in GenBank, and sequence data from a potentially new species found at Capron Shoal, Florida, to gain insight into the phylogeny of the clade and clarify evolutionary trends in reproductive modality. Based on a total of 33 specimens of seven potential species, we found that members of Urodasys can be separated into three clades reflective of different reproductive modalities: Clade I, species with paired male and female gonads but without accessory sexual organs; Clade II, species with a single left testis, paired ova, and accessory organs including a sclerotic stylet; and Clade III, parthenogenetic species without testes or accessory organs. In addition, we find that the potentially new species from Florida can form spermatophores, a condition shared with another species in Clade I. Herein, we describe this novel spermatophore‐bearing species and discuss the significance of spermatophore formation in the genus.     

High-resolution mapping of the <Emphasis Type="Italic">S</Emphasis>-locus in <Emphasis Type="Italic">Turnera</Emphasis> leads to the discovery of three genes tightly associated with the <Emphasis Type="Italic">S</Emphasis>-alleles

While the breeding system known as distyly has been used as a model system in genetics, and evolutionary biology for over a century, the genes determining this system remain unknown. To positionally clone genes determining distyly, a high-resolution map of the S-locus region of Turnera has been constructed using segregation data from 2,013 backcross progeny. We discovered three putative genes tightly linked with the S-locus. An N-acetyltransferase (TkNACE) flanks the S-locus at 0.35 cM while a sulfotransferase (TkST1) and a non-LTR retroelement (TsRETRO) show complete linkage to the S-locus. An assay of population samples of six species revealed that TsRETRO, initially discovered in diploid Turnera subulata, is also associated with the S-allele in tetraploid T. subulata and diploid Turnera scabra. The sulfotransferase gene shows some level of differential expression in long versus short styles, indicating it might be involved in some aspect of distyly. The complete linkage of TkST1 and TsRETRO to the S-locus suggests that both genes may reside within, or in the immediate vicinity of the S-locus. Chromosome walking has been initiated using one of the genes discovered in the present study to identify the genes determining distyly. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Inter-genotype variation in reproductive response to crowding among Daphnia pulex

Crowding is known to have a major influence on reproduction in the freshwater microcrustacean Daphnia pulex. We analyzed reproductive output of six different D. pulex genotypes under two different density regimes in the laboratory. Four of these genotypes reproduce via obligate parthenogenesis, allowing thorough analysis of the life history strategies of some asexual lines. Among 30,109 neonate offspring and 1041 resting egg ephippia collected, several trends were evident. Crowding induced increased resting egg production and reduced neonate offspring production among all genotypes. Offspring sex ratios grew more male-biased with maternal age. The extent, but not direction, of each of these trends varied among genotypes. Offspring sex ratios, and the very direction in which they changed in response to crowding, differed significantly among genotypes with some genotypes producing more and others fewer males in response to crowding. Obligately parthenogenetic genotypes seemed to respond to the crowding stimulus in similar ways as the facultatively parthenogenetic genotypes, as expected from the sexual origins of their genomes. The inter-genotype variation in life-history traits observed in this and other investigations calls into question the common practice of extrapolating results from a single Daphnia genotype to an entire species. Our findings are considered in the context of other research in the field of environmental influences on Daphnia reproduction with a review of representative literature.     

Reproduction strategies of <Emphasis Type="Italic">Daphnia pulicaria</Emphasis> population in a high mountain lake of Southern Spain

For three consecutive years, a population study of Daphnia pulicaria was undertaken in Río Seco Lake, a small high-mountain lake, in order to elucidate the reproductive strategies adopted by Daphnia in this system. Daphnia appears to colonize this lake every spring by hatching from ephippia and reproduce by means of subitaneous (non-diapausing) and ephippial (diapausing) eggs. D. pulicaria in this lake is an obligate parthenogenetic population. There is a short time period for subitaneous egg production and a much longer period for ephippial egg production. The contribution of subitaneous eggs to Daphnia population density and structure appears to be low. Diapause onset showed a high temporal synchronization in the three studied years in Río Seco Lake, and day-length emerged as the main cue triggering diapause onset and the main explanatory factor for the proportion of ephippial females observed. The development and reproduction of D. pulicaria in Río Seco Lake involves taking a gamble on resting forms to guarantee inter-annual Daphnia persistence in the lake, giving priority to investment in future generations. Guest editor: Piet Spaak Cladocera: Proceedings of the 7th International Symposium on Cladocera