Developmental Plasticity, Ecology, and Evolutionary Radiation of Nematodes of Diplogastridae

Explaining organismal diversity and adaptation are the two central aims of evolutionary biology. In this thesis, I address these questions using a comparative evolutionary approach and nematodes of the family Diplogastridae as a study system. Systematic sampling of diplogastrid nematodes resulted in the discovery of numerous nematode species, their novel traits and ecological associations, providing reference points for consequent comparative evolutionary analyses. I first studied forces that drive evolutionary radiation and speciation in a host-symbiont system, specifically in a diverse group of predatory nematodes of the genus Micoletzkya, which are associated with bark beetles. I showed that nematode evolutionary radiation resulted from parallel divergence with their beetle hosts and was also shaped by preferential hosts shifts among closely related hosts, thus highlighting the roles of isolation and adaptation in the evolution of host-symbiont systems. I then built a new phylogenetic framework for the family Diplogastridae and used it to investigate the evolutionary implications of discrete phenotypic plasticity (polyphenism), specifically its impact on evolutionary tempo and the evolution of novelties. As a result, I identified that the origin of polyphenism coincided with a sharp increase in phenotypic complexity, which surprisingly decreased after secondary loss of plasticity; the rates of evolution, however, became even higher after phenotype fixation, which provided evidence for developmental character release. These results gave original support for a role of developmental plasticity in evolutionary diversification. Finally, I have discovered several new species of Pristionchus, which live in symbiosis with figs and fig wasps and show an extreme polyphenism with up to five discrete eco-morphotypes per species. This study revealed that adaptive radiation, or the rapid filling of contrasting ecological niches need not to be associated with diversifying selection on genotypes and can be based on discontinuous phenotypic plasticity

Preferential host switching and codivergence shaped radiation of bark beetle symbionts, nematodes of Micoletzkya (Nematoda: Diplogastridae)

Host-symbiont systems are of particular interest to evolutionary biology because they allow testable inferences of diversification processes while also providing both a historical basis and an ecological context for studies of adaptation. Our investigations of bark beetle symbionts, predatory nematodes of the genus Micoletzkya, have revealed remarkable diversity of the group along with a high level of host specificity. Cophylogenetic analyses suggest that evolution of the nematodes was largely influenced by the evolutionary history of beetles. The diversification of the symbionts, however, could not be attributed to parallel divergence alone; our results indicate that adaptive radiation of the nematodes was shaped by preferential host shifts among closely related beetles along with codivergence. Whereas ecological and geographic isolation have played a major role in the diversification of Micoletzkya at shallow phylogenetic depths, adaptations towards related hosts have played a role in shaping cophylogenetic structure at a larger evolutionary scale

Validation of Rhabditolaimus Fuchs, 1914 (Nematoda: Diplogastridae) supported by integrative taxonomic evidence

Rhabditolaimus leuckarti, type species of Rhabditolaimus, was isolated from its type host, Hylobius abietis (Coleoptera: Curculionidae), at several locations in central Europe. The position of the species among other diplogastrid nematodes was revised using morphological characters and molecular phylogenetic analysis. The revealed common apomorphic features and the inferred evolutionary tree strongly indicates a close relationship between R. leuckarti and Myctolaimus. Our findings suggest that the historical classifications do not reflect the natural relationships of some diplogastrid taxa. Therefore, we reject all previous synonymisations of Rhabditolaimus and consider it to be valid within the Diplogastridae. Five species are transferred from Diplogasteroides to Rhabditolaimus. Myctolaimus sensu lato is regarded as a junior synonym of Rhabditolaimus and the following new combinations are proposed: R. anoplophorae comb. n., R. carolinensis comb. n., R. curzii comb. n., R. dendrophilus comb. n., R. erectus comb. n., R. goodeyi comb. n., R. inevectus, comb. n., R. kishtwarensis comb. n., R. macrolaimus comb. n., R. nacogdochensis comb. n., R. neolongistoma comb. n., R. pellucidus comb. n., R. platypi comb. n., R. rifflei comb. n., R. robiniae comb. n., R. ulmi comb. n., R. vitautasi comb. n., R. walkeri comb. n. and R. zamithi comb. n

microbiome

The data contains tables in txt format with read counts for bacterial phyla (Phylum_level_readsCountTable.txt) and families (Family_level_readsCountTable.txt) in pooled samples from five different environments (nematodes, beetle gut, decaying beetle, native soil, and decaying beetle). Zero read counts (no reads mapping to a taxonomic group) has been replaced by a value of 1e-5 to facilitate downstream analysis, such as taking the logarithm. We pooled the reads of technical replicates into one single sample by adding up the read counts, including 1e-5 values. For this reason some entries are floating point values rather than integers. Tables contain detailed information about each sample such as environment, sequencing year, decaying status, species and beetle parts information for nematode gut samples

Data from: Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes beetles on La Réunion Island

Insects and nematodes represent the most species-rich animal taxa and they occur together in a variety of associations. Necromenic nematodes of the genus Pristionchus are found on scarab beetles with more than 30 species known from worldwide samplings. However, little is known about the dynamics and succession of nematodes and bacteria during the decomposition of beetle carcasses. Here, we study nematode and bacterial succession of the decomposing rhinoceros beetle Oryctes borbonicus on La Réunion Island. We show that Pristionchus pacificus exits the arrested dauer stage seven days after the beetles´ deaths. Surprisingly, new dauers are seen after 11 days, suggesting that some worms return to the dauer stage after one reproductive cycle. We used high-throughput sequencing of the 16S rRNA genes of decaying beetles, beetle guts and nematodes to study bacterial communities in comparison to soil. We find that soil environments have the most diverse bacterial communities. The bacterial community of living and decaying beetles are more stable but one single bacterial family dominates the microbiome of decaying beetles. In contrast, the microbiome of nematodes is relatively similar even across different families. This study represents the first characterization of the dynamics of nematode-bacterial interactions during the decomposition of insects