Biology subjects

Manica, A.

Publications and source records attributed to Manica, A..

7 recordsLinked to original sources

bioRxiv2018

The jellyfish genome sheds light on the early evolution of active predation

BackgroundUnique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column. One of the first animals to become free-swimming, jellyfish employ pulsed jet propulsion and venomous tentacles to capture prey.\n\nResultsTo understand these key innovations, we sequenced the genome of the giant Nomuras jellyfish (Nemopilema nomurai), the transcriptomes of its bell and tentacles, and transcriptomes across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with expanded Myosin type II family and venom domains; possibly contributing to jellyfish mobility and active predation. We also identified gene family expansions of Wnt and posterior Hox genes, and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, which together may be related to the unique jellyfish body plan (medusa formation).\n\nConclusionsTaken together, the jellyfish genome and transcriptomes genetically confirm their unique morphological and physiological traits that have combined to make these animals one of the worlds earliest and most successful multi-cellular predators.

genomics↗

bioRxiv2018

The role of tactile interactions in flight responses in the Bronze Cory catfish (Corydoras aeneus)

One of the primary functions of animal aggregations is defense against predators. Many social animals enjoy reduced predation risk as a result of grouping, and individuals within groups can benefit from information transferred by their group-mates about a potential predator. We present evidence that a tactile interaction behavior we term nudging substantially modified group responses to a potential threat in a highly social catfish species, Corydoras aeneus. These catfish deployed nudges during flight responses, and these nudges were associated with a greater likelihood of group cohesion following a threat event. Increased nudging behavior resulted in longer flight responses. In addition, individuals that perceived the threat first were more likely to initiate nudges, implying that nudges could be used to alert group-mates to the presence of a threat. Taken together, our results suggest that tactile communication plays an important role in gaining anti-predator benefits from sociality in these fish.

animal behavior and cognition↗

bioRxiv2018

Coping with strangers: how familiarity and active interactions shape group coordination in Corydoras aeneus

Social groups whose members have had sustained prior experience with each other frequently exhibit improved coordination and outperform groups whose members are unfamiliar with one another. The mechanisms by which familiarity assists coordination are not well known. Prior social experience may simply allow individuals to learn the behavioral tendencies of familiar group-mates and coordinate accordingly. In the absence of prior social experience, it would be adaptive for individuals to develop strategies for coping with unfamiliar others to minimize the disadvantage of unfamiliarity. To explore the dynamics of familiarity in shaping group behaviors, we used a highly social catfish, Corydoras aeneus, that utilizes a distinctive, observable tactile interactions. Here we describe this tactile interaction behavior, physical \"nudges\" that are deployed to initiate group movements and maintain contact with group-mates during group movements. We then report the results of two experiments exploring the relationship between nudges and coordination. First, within triplets of two familiar and one unfamiliar individual, we found no individual differences in nudging rate based on familiarity. Despite all individuals interacting at similar rates, however, unfamiliar individuals failed to coordinate as well as their familiar group-mates, and were more frequently absent from group movements. Second, comparing pairs of familiar with pairs of unfamiliar fish, there was no difference in the level of coordination between pairs. Instead, we found that unfamiliar pairs exhibited significantly higher nudging rates, suggesting that unfamiliar pairs could compensate for their unfamiliarity by nudging more frequently. In contrast, familiar individuals coordinated with comparatively little nudging, presumably because they were experienced with each other. Overall, these results suggest that nudges can be used to improve coordination of group activities, but that their usage is reduced in the case of familiar individuals, implying that these potential signals may be costly.

animal behavior and cognition↗

bioRxiv2018

The whale shark genome reveals how genomic and physiological properties scale with body size

The endangered whale shark (Rhincodon typus) is the largest fish on Earth and is a long-lived member of the ancient Elasmobranchii clade. To characterize the relationship between genome features and biological traits, we sequenced and assembled the genome of the whale shark and compared its genomic and physiological features to those of 81 animals and yeast. We examined scaling relationships between body size, temperature, metabolic rates, and genomic features and found both general correlations across the animal kingdom and features specific to the whale shark genome. Among animals, increased lifespan is positively correlated to body size and metabolic rate. Several genomic features also significantly correlated with body size, including intron and gene length. Our large-scale comparative genomic analysis uncovered general features of metazoan genome architecture: GC content and codon adaptation index are negatively correlated, and neural connectivity genes are longer than average genes in most genomes. Focusing on the whale shark genome, we identified multiple features that significantly correlate with lifespan. Among these were very long gene length, due to large introns highly enriched in repetitive elements such as CR1-like LINEs, and considerably longer neural genes of several types, including connectivity, activity, and neurodegeneration genes. The whale sharks genome had an expansion of gene families related to fatty acid metabolism and neurogenesis, with the slowest evolutionary rate observed in vertebrates to date. Our comparative genomics approach uncovered multiple genetic features associated with body size, metabolic rate, and lifespan, and showed that the whale shark is a promising model for studies of neural architecture and lifespan.

genomics↗

bioRxiv2018

Modern wolves trace their origin to a late Pleistocene expansion from Beringia

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain a mystery. Here we analyzed a large dataset of novel modern and ancient mitochondrial wolf genomes, spanning the last 50,000 years, using a spatially and temporally explicit modeling framework to show that contemporary wolf populations across the globe trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum - a process most likely driven by the significant ecological changes that occurred across the Northern Hemisphere during this period. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.

evolutionary biology↗

bioRxiv2018

A metapopulation model of the spread of the Devil Facial Tumour Disease predicts the long term collapse of its host but not its extinction

The Devil Facial Tumour Disease (DFTD), a unique case of a transmissible cancer, had a devastating effect on its host, the Tasmanian Devil. Current estimates of its density are at roughly 20% of the pre-disease state, and single-population epidemiological models have predicted the likely extinction of the host. Here we take advantage of extensive surveys across Tasmania providing data on the spatial and temporal spread of DFTD, and investigate the dynamics of this host-pathogen system using a spatial metapopulation model. We first confirm a most likely origin of DFTD in the north-east corner of the island, and then use the inferred dynamics to predict the fate of the species. We find that our medium-term predictions match additional data not used for fitting, and that on the longterm, Tasmanian Devils are predicted to coexist with the tumour. The key process allowing persistence is the repeated reinvasion of extinct patches from neighbouring areas where the disease has flared up and died out, resulting in a dynamic equilibrium with different levels of spatial heterogeneity. However, this dynamic equilibrium is predicted to keep this apex predator at about 9 % of its original density, with possible dramatic effects on the Tasmanian ecosystem.

ecology↗

bioRxiv2017

Consistent Individual Differences Drive Collective Behaviour And Group Functioning Of Schooling Fish

The ubiquity of consistent inter-individual differences in behaviour ( animal personalities) 1,2, suggests they may constitute a fundamental component of animal groups that may drive their functioning 3,4. Despite increasing evidence that highlights their importance 5-16, we still lack a unified mechanistic frame-work to explain and predict how inter-individual differences may affect collective behaviour. Here we investigate how differences in individual behavioural tendencies affect the group structure, movement dynamics, and foraging behaviour of animal groups using free-swimming stickleback fish (Gasterosteus aculeatus). Analysis of high-resolution tracking data of known individuals demonstrates that, across a range of contexts, consistent inter-individual differences in social proximity were strongly linked to speed and, together with boldness predicted spatial positioning and leadership within groups, differences in structure and movement dynamics between groups, as well as individual and group foraging performance. These effects of inter-individual behavioural variation on group-level states emerged naturally from a generic model of heterogeneous, self-organising groups. Our study combines experimental and theoretical evidence for a simple mechanism to explain variation in the emergence of structure, dynamics, and functional capabilities of groups across social and ecological scales. In addition, we show that individual performance was conditional to the group composition, providing a potential basis for social selection driving behavioural differentiation between individuals.

animal behavior and cognition↗