Identifying Interpretable Latent Factors with Sparse Component Analysis.

In many neural populations, the computationally relevant signals are posited to be a set of 'latent factors' - signals shared across many individual neurons. Understanding the relationship between neural activity and behavior requires the identification of factors that reflect distinct computational roles. Methods for identifying such factors typically require supervision, which can be suboptimal if one is unsure how (or whether) factors can be grouped into distinct, meaningful sets. Here, we introduce Sparse Component Analysis (SCA), an unsupervised method that identifies interpretable latent factors. SCA seeks factors that are sparse in time and occupy orthogonal dimensions. With these simple constraints, SCA facilitates surprisingly clear parcellations of neural activity across a range of behaviors. We applied SCA to motor cortex activity from reaching and cycling monkeys, single-trial imaging data from C. elegans, and activity from a multitask artificial network. SCA consistently identified sets of factors that were useful in describing network computations.

Automated neuron tracking inside moving and deforming C. elegans using deep learning and targeted augmentation.

Reading out neuronal activity from three-dimensional (3D) functional imaging requires segmenting and tracking individual neurons. This is challenging in behaving animals if the brain moves and deforms. The traditional approach is to train a convolutional neural network with ground-truth (GT) annotations of images representing different brain postures. For 3D images, this is very labor intensive. We introduce 'targeted augmentation', a method to automatically synthesize artificial annotations from a few manual annotations. Our method ('Targettrack') learns the internal deformations of the brain to synthesize annotations for new postures by deforming GT annotations. This reduces the need for manual annotation and proofreading. A graphical user interface allows the application of the method end-to-end. We demonstrate Targettrack on recordings where neurons are labeled as key points or 3D volumes. Analyzing freely moving animals exposed to odor pulses, we uncover rich patterns in interneuron dynamics, including switching neuronal entrainment on and off.

Evolutionarily conserved behavioral plasticity enables context-dependent mating in C. elegans.

Behavioral plasticity helps humans and animals to achieve their goals by adapting their behaviors to different environments.1,2 Although behavioral plasticity is ubiquitous, many innate species-specific behaviors, such as mating, are often assumed to be stereotyped and unaffected by plasticity or learning, especially in invertebrates. Here, we describe a novel case of behavioral plasticity in the nematode C. elegans. Under standard lab conditions (agar plates with bacterial food), the male performs parallel mating,3,4,5 a largely two-dimensional behavioral strategy where his body and tail remain flat on the surface and slide alongside the partner's body from initial contact to copulation. But when placed in liquid media, the male performs spiral mating, a distinctly three-dimensional behavioral strategy where he winds around the partner's body in a helical embrace. The performance of spiral mating does not require a long-term change in growing conditions, but it does improve with experience. This experience-dependent improvement appears to involve a critical period-a time window around the L4 larval stage to the early adult stage-which coincides with the development of most male-specific neurons. We tested several wild isolates of C. elegans and other Caenorhabditis species and found that most were capable of parallel mating on surfaces and spiral mating in liquids. We suggest that two- and three-dimensional mating strategies in Caenorhabditis are plastic, conditionally expressed phenotypes conserved across the genus, which can be genetically "fixed" in some species.

Horizontally Acquired Cellulases Assist the Expansion of Dietary Range in Pristionchus Nematodes.

Horizontal gene transfer (HGT) enables the acquisition of novel traits via non-Mendelian inheritance of genetic material. HGT plays a prominent role in the evolution of prokaryotes, whereas in animals, HGT is rare and its functional significance is often uncertain. Here, we investigate horizontally acquired cellulase genes in the free-living nematode model organism Pristionchus pacificus. We show that these cellulase genes 1) are likely of eukaryotic origin, 2) are expressed, 3) have protein products that are secreted and functional, and 4) result in endo-cellulase activity. Using CRISPR/Cas9, we generated an octuple cellulase mutant, which lacks all eight cellulase genes and cellulase activity altogether. Nonetheless, this cellulase-null mutant is viable and therefore allows a detailed analysis of a gene family that was horizontally acquired. We show that the octuple cellulase mutant has associated fitness costs with reduced fecundity and slower developmental speed. Furthermore, by using various Escherichia coli K-12 strains as a model for cellulosic biofilms, we demonstrate that cellulases facilitate the procurement of nutrients from bacterial biofilms. Together, our analysis of cellulases in Pristionchus provides comprehensive evidence from biochemistry, genetics, and phylogeny, which supports the integration of horizontally acquired genes into the complex life history strategy of this soil nematode.

PEZO-1 and TRP-4 mechanosensors are involved in mating behavior in Caenorhabditis elegans.

Male mating in Caenorhabditis elegans is a complex behavior with a strong mechanosensory component. C. elegans has several characterized mechanotransducer proteins, but few have been shown to contribute to mating. Here, we investigated the roles of PEZO-1, a piezo channel, and TRP-4, a mechanotransducing TRPN channel, in male mating behavior. We show that pezo-1 is expressed in several male-specific neurons with known roles in mating. We show that, among other neurons, trp-4 is expressed in the Post-Cloacal sensilla neuron type A (PCA) sensory neuron, which monitors relative sliding between the male and the hermaphrodite and inhibits neurons involved in vulva detection. Mutations in both genes compromise many steps of mating, including initial response to the hermaphrodite, scanning, turning, and vulva detection. We performed pan-neuronal imaging during mating between freely moving mutant males and hermaphrodites. Both pezo-1 and trp-4 mutants showed spurious activation of the sensory neurons involved in vulva detection. In trp-4 mutants, this spurious activation might be caused by PCA failure to inhibit vulva-detecting neurons during scanning. Indeed, we show that without functional TRP-4, PCA fails to detect the relative sliding between the male and hermaphrodite. Cell-specific TRP-4 expression restores PCA's mechanosensory function. Our results demonstrate new roles for both PEZO-1 and TRP-4 mechanotransducers in C. elegans mating behavior.

Natural sensory context drives diverse brain-wide activity during C. elegans mating.

Natural goal-directed behaviors often involve complex sequences of many stimulus-triggered components. Understanding how brain circuits organize such behaviors requires mapping the interactions between an animal, its environment, and its nervous system. Here, we use brain-wide neuronal imaging to study the full performance of mating by the C. elegans male. We show that as mating unfolds in a sequence of component behaviors, the brain operates similarly between instances of each component but distinctly between different components. When the full sensory and behavioral context is taken into account, unique roles emerge for each neuron. Functional correlations between neurons are not fixed but change with behavioral dynamics. From individual neurons to circuits, our study shows how diverse brain-wide dynamics emerge from the integration of sensory perception and motor actions in their natural context.

Small peptide-mediated self-recognition prevents cannibalism in predatory nematodes.

Self-recognition is observed abundantly throughout the natural world, regulating diverse biological processes. Although ubiquitous, often little is known of the associated molecular machinery, and so far, organismal self-recognition has never been described in nematodes. We investigated the predatory nematode Pristionchus pacificus and, through interactions with its prey, revealed a self-recognition mechanism acting on the nematode surface, capable of distinguishing self-progeny from closely related strains. We identified the small peptide SELF-1, which is composed of an invariant domain and a hypervariable C terminus, as a key component of self-recognition. Modifications to the hypervariable region, including single-amino acid substitutions, are sufficient to eliminate self-recognition. Thus, the P. pacificus self-recognition system enables this nematode to avoid cannibalism while promoting the killing of competing nematodes.

Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes borbonicus 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.

Large-scale diversification without genetic isolation in nematode symbionts of figs.

Diversification is commonly understood to be the divergence of phenotypes accompanying that of lineages. In contrast, alternative phenotypes arising from a single genotype are almost exclusively limited to dimorphism in nature. We report a remarkable case of macroevolutionary-scale diversification without genetic divergence. Upon colonizing the island-like microecosystem of individual figs, symbiotic nematodes of the genus Pristionchus accumulated a polyphenism with up to five discrete adult morphotypes per species. By integrating laboratory and field experiments with extensive genotyping of individuals, including the analysis of 49 genomes from a single species, we show that rapid filling of potential ecological niches is possible without diversifying selection on genotypes. This uncoupling of morphological diversification and speciation in fig-associated nematodes has resulted from a remarkable expansion of discontinuous developmental plasticity.

Predatory feeding behaviour in Pristionchus nematodes is dependent on phenotypic plasticity and induced by serotonin.

Behavioural innovation and morphological adaptation are intrinsically linked but their relationship is often poorly understood. In nematodes, a huge diversity of feeding morphologies and behaviours can be observed to meet their distinctive dietary and environmental demands. Pristionchus and their relatives show varied feeding activities, both consuming bacteria and also predating other nematodes. In addition, Pristionchus nematodes display dimorphic mouth structures triggered by an irreversible developmental switch, which generates a narrower mouthed form with a single tooth and a wider mouthed form with an additional tooth. However, little is known about the specific predatory adaptations of these mouth forms or the associated mechanisms and behaviours. Through a mechanistic analysis of predation behaviours, in particular in the model organism Pristionchus pacificus, we reveal multifaceted feeding modes characterised by dynamic rhythmic switching and tooth stimulation. This complex feeding mode switch is regulated by the neurotransmitter serotonin in a previously uncharacterised role, a process that appears conserved across several predatory nematode species. Furthermore, we investigated the effects of starvation, prey size and prey preference on P. pacificus predatory feeding kinetics, revealing predation to be a fundamental component of the P. pacificus feeding repertoire, thus providing an additional rich source of nutrition in addition to bacteria. Finally, we found that mouth form morphology also has a striking impact on predation, suppressing predatory behaviour in the narrow mouthed form. Our results therefore hint at the regulatory networks involved in controlling predatory feeding and underscore P. pacificus as a model for understanding the evolution of complex behaviours.

Rapid diversification associated with a macroevolutionary pulse of developmental plasticity.

Developmental plasticity has been proposed to facilitate phenotypic diversification in plants and animals, but the macroevolutionary potential of plastic traits remains to be objectively tested. We studied the evolution of feeding structures in a group of 90 nematodes, including Caenorhabditis elegans, some species of which have evolved a mouthpart polyphenism, moveable teeth, and predatory feeding. Comparative analyses of shape and form, using geometric morphometrics, and of structural complexity revealed a rapid process of diversification associated with developmental plasticity. First, dimorphism was associated with a sharp increase in complexity and elevated evolutionary rates, represented by a radiation of feeding-forms with structural novelties. Second, the subsequent assimilation of a single phenotype coincided with a decrease in mouthpart complexity but an even stronger increase in evolutionary rates. Our results suggest that a macroevolutionary 'pulse' of plasticity promotes novelties and, even after the secondary fixation of phenotypes, permits sustained rapid exploration of morphospace.

Leptojacobus dorci n. gen., n. sp. (Nematoda: Diplogastridae), an Associate of Dorcus Stag Beetles (Coleoptera: Lucanidae).

A new species of diplogastrid nematode, Leptojacobus dorci n. gen., n. sp., was isolated from adults of the stag beetle Dorcus ritsemae (Coleoptera: Lucanidae) that were purchased from a pet shop in Japan. Leptojacobus n. gen. is circumscribed by a very thin, delicate body and by a small stoma with minute armature. A combination of other stomatal characters, namely the division of the cheilostom into adradial plates, the symmetry of the subventral stegostomatal sectors, and the presence of a thin, conical dorsal tooth, further distinguishes Leptojacobus n. gen. from other genera of Diplogastridae. Phylogenetic analysis of nearly full-length SSU rRNA sequences support the new species, together with an isolate identified previously as Koerneria luziae, to be excluded from a clade including all other molecularly characterized diplogastrids with teeth and stomatal dimorphism. Therefore, the new species will be of importance for reconstruction of ancestral character histories in Diplogastridae, a family circumscribed by a suite of feeding-related novelties.

Two androdioecious and one dioecious new species of pristionchus (nematoda: diplogastridae): new reference points for the evolution of reproductive mode.

Rhabditid nematodes are one of a few animal taxa in which androdioecious reproduction, involving hermaphrodites and males, is found. In the genus Pristionchus, several cases of androdioecy are known, including the model species P. pacificus. A comprehensive understanding of the evolution of reproductive mode depends on dense taxon sampling and careful morphological and phylogenetic reconstruction. In this article, two new androdioecious species, P. boliviae n. sp. and P. mayeri n. sp., and one gonochoristic outgroup, P. atlanticus n. sp., are described on morphological, molecular, and biological evidence. Their phylogenetic relationships are inferred from 26 ribosomal protein genes and a partial SSU rRNA gene. Based on current representation, the new androdioecious species are sister taxa, indicating either speciation from an androdioecious ancestor or rapid convergent evolution in closely related species. Male sexual characters distinguish the new species, and new characters for six closely related Pristionchus species are presented. Male papillae are unusually variable in P. boliviae n. sp. and P. mayeri n. sp., consistent with the predictions of "selfing syndrome." Description and phylogeny of new androdioecious species, supported by fuller outgroup representation, establish new reference points for mechanistic studies in the Pristionchus system by expanding its comparative context.