Optimal time lags from causal prediction model help stratify and forecast nervous system pathology

Traditional clinical approaches diagnose disorders of the nervous system using standardized observational criteria. Although aiming for homogeneity of symptoms, this method often results in highly heterogeneous disorders. A standing question thus is how to automatically stratify a given random cohort of the population, such that treatment can be better tailored to each cluster’s symptoms, and severity of any given group forecasted to provide neuroprotective therapies. In this work we introduce new methods to automatically stratify a random cohort of the population composed of healthy controls of different ages and patients with different disorders of the nervous systems. Using a simple walking task and measuring micro-fluctuations in their biorhythmic motions, we combine non-linear causal network connectivity analyses in the temporal and frequency domains with stochastic mapping. The methods define a new type of internal motor timings. These are amenable to create personalized clinical interventions tailored to self-emerging clusters signaling fundamentally different types of gait pathologies. We frame our results using the principle of reafference and operationalize them using causal prediction, thus renovating the theory of internal models for the study of neuromotor control.

Directed Data-Processing Inequalities for Systems with Feedback

We present novel data-processing inequalities relating the mutual information and the directed information in systems with feedback. The internal deterministic blocks within such systems are restricted only to be causal mappings, but are allowed to be non-linear and time varying, and randomized by their own external random input, can yield any stochastic mapping. These randomized blocks can for example represent source encoders, decoders, or even communication channels. Moreover, the involved signals can be arbitrarily distributed. Our first main result relates mutual and directed information and can be interpreted as a law of conservation of information flow. Our second main result is a pair of data-processing inequalities (one the conditional version of the other) between nested pairs of random sequences entirely within the closed loop. Our third main result introduces and characterizes the notion of in-the-loop (ITL) transmission rate for channel coding scenarios in which the messages are internal to the loop. Interestingly, in this case the conventional notions of transmission rate associated with the entropy of the messages and of channel capacity based on maximizing the mutual information between the messages and the output turn out to be inadequate. Instead, as we show, the ITL transmission rate is the unique notion of rate for which a channel code attains zero error probability if and only if such an ITL rate does not exceed the corresponding directed information rate from messages to decoded messages. We apply our data-processing inequalities to show that the supremum of achievable (in the usual channel coding sense) ITL transmission rates is upper bounded by the supremum of the directed information rate across the communication channel. Moreover, we present an example in which this upper bound is attained. Finally, we further illustrate the applicability of our results by discussing how they make possible the generalization of two fundamental inequalities known in networked control literature.

Mesoamerica is a cradle and the Atlantic Forest is a museum of Neotropical butterfly diversity: insights from the evolution and biogeography of Brassolini (Lepidoptera: Nymphalidae)

Regional species diversity is explained ultimately by speciation, extinction and dispersal. Here, we estimate dispersal and speciation rates of Neotropical butterflies to propose an explanation for the distribution and diversity of extant species. We focused on the tribe Brassolini (owl butterflies and allies), a Neotropical group that comprises 17 genera and 108 species, most of them endemic to rainforest biomes. We inferred a robust species tree using the multispecies coalescent framework and a dataset including molecular and morphological characters. This formed the basis for three changes in Brassolini classification: (1) Naropina syn. nov. is subsumed within Brassolina; (2) Aponarope syn. nov. is subsumed within Narope; and (3) Selenophanes orgetorix comb. nov. is reassigned from Catoblepia to Selenophanes. By applying biogeographical stochastic mapping, we found contrasting species diversification and dispersal dynamics across rainforest biomes, which might be explained, in part, by the geological and environmental history of each bioregion. Our results revealed a mosaic of biome-specific evolutionary histories within the Neotropics, where butterfly species have diversified rapidly (cradles: Mesoamerica), have accumulated gradually (museums: Atlantic Forest) or have diversified and accumulated alternately (Amazonia). Our study contributes evidence from a major butterfly lineage that the Neotropics are a museum and a cradle of species diversity.

Global phylogeography of a pantropical mangrove genus Rhizophora

Rhizophora is a key genus for revealing the formation process of the pantropical distribution of mangroves. In this study, in order to fully understand the historical scenario of Rhizophora that achieved pantropical distribution, we conducted phylogeographic analyses based on nucleotide sequences of chloroplast and nuclear DNA as well as microsatellites for samples collected worldwide. Phylogenetic trees suggested the monophyly of each AEP and IWP lineages respectively except for R. samoensis and R. × selala. The divergence time between the two lineages was 10.6 million years ago on a dated phylogeny, and biogeographic stochastic mapping analyses supported these lineages separated following a vicariant event. These data suggested that the closure of the Tethys Seaway and the reduction in mangrove distribution followed by Mid-Miocene cooling were key factors that caused the linage diversification. Phylogeographic analyses also suggested the formation of the distinctive genetic structure at the AEP region across the American continents around Pliocene. Furthermore, long-distance trans-pacific dispersal occurred from the Pacific coast of American continents to the South Pacific and formed F1 hybrid, resulting in gene exchange between the IWP and AEP lineages after 11 million years of isolation. Considering the phylogeny and phylogeography with divergence time, a comprehensive picture of the historical scenario behind the pantropical distribution of Rhizophora is updated.

Optimal Time Lags from Causal Prediction Model Help Stratify and Forecast Nervous System Pathology

Traditional clinical approaches diagnose disorders of the nervous system using standardized observational criteria. Although aiming for homogeneity of symptoms, this method often results in highly heterogeneous disorders. A standing question thus is how to automatically stratify a given random cohort of the population, such that treatment can be better tailored to each cluster’s symptoms, and severity of any given group forecasted to provide neuroprotective therapies. In this work we introduce new methods to automatically stratify a random cohort of the population composed of healthy controls of different ages and patients with different disorders of the nervous systems. Using a simple walking task and measuring micro-fluctuations in their biorhythmic motions, we show that gait is compromised in healthy aging and that in young FMR1 premutation carriers, gait forecasts, even by 15 years ahead, symptoms resembling those of elderly with Parkinson’s disease. Our methods combine non-linear causal network connectivity analyses in the temporal and frequency domains with stochastic mapping, defining a new type of internal motor timings amenable to create personalized clinical interventions. We frame our results using the principle of reafference and operationalize them using causal prediction, thus renovating the theory of internal models for the study of neuromotor control.

Optimal Time Lags from Causal Prediction Model Help Stratify and Forecast Nervous System Pathology

Traditional clinical approaches diagnose disorders of the nervous system using standardized observational criteria. Although aiming for homogeneity of symptoms, this method often results in highly heterogeneous disorders. A standing question thus is how to automatically stratify a given random cohort of the population, such that treatment can be better tailored to each cluster’s symptoms, and severity of any given group forecasted to provide neuroprotective therapies. In this work we introduce new methods to automatically stratify a random cohort of the population composed of healthy controls of different ages and patients with different disorders of the nervous systems. Using a simple walking task and measuring micro-fluctuations in their biorhythmic motions, we show that gait is compromised in healthy aging and that in young FMR1 premutation carriers, gait forecasts, even by 15 years ahead, symptoms resembling those of elderly with Parkinson’s disease. Our methods combine non-linear causal network connectivity analyses in the temporal and frequency domains with stochastic mapping, defining a new type of internal motor timings amenable to create personalized clinical interventions. We frame our results using the principle of reafference and operationalize them using causal prediction, thus renovating the theory of internal models for the study of neuromotor control.

Laticifers in Sapindaceae: Structure, Evolution and Phylogenetic Importance

Laticifer occurrence and structure are poorly known in Sapindaceae. Occurrence is likely underestimated owing to the low production of latex in most species. We investigated 67 species from 23 genera of Sapindaceae to verify laticifer occurrence and their structural, developmental and chemical features, as well as their evolutionary history in the family. Shoots were collected from herbarium and fresh specimens for histological analyses. Three characters derived from laticifer features were coded and their ancestral states reconstructed through Bayesian stochastic mapping and maximum likelihood estimation. Only articulated non-anastomosing laticifers were found in Sapindaceae. Laticifers differentiate early during shoot development and are found in the cortex, phloem, and pith. Latex is mostly composed of lipids. Callose and suberin were detected in laticifer cell walls in some genera. Reconstruction of laticifer ancestral states showed that laticifers are present in most clades of Sapindaceae with some reversals. Callose in the laticifer cell wall was found exclusively in Serjania and Paullinia (tribe Paullinieae), a character regarded as independently derived. Occurrence of laticifers in Sapindaceae is broader than previously reported. Articulated non-anastomosing laticifers had five independent origins in Sapindaceae with some secondary losses, occurring in five out of six genera of Paullinieae and 10 other genera outside Paullinieae. Particularly, callose in the laticifer cell wall evolved independently twice in the family, and its occurrence may be interpreted as a key-innovation that promoted the diversification of Paullinia and Serjania. Our study suggests that laticifer characters may be useful in understanding the generic relationships within the family.

From scales to armour: scale losses and trunk bony plate gains in ray-finned fishes

Actinopterygians (ray-finned fishes) are the most diversified group of vertebrates and are characterized by a variety of protective structures covering their tegument, the evolution of which has intrigued biologists for decades. Paleontological records showed that the first mineralized vertebrate skeleton was composed of dermal bony plates covering the body, including odontogenic and skeletogenic components. Later in evolution, the exoskeleton of actinopterygian’s trunk was composed of scale structures. Although scales are nowadays a widespread tegument cover, some contemporary lineages do not have scales but bony plates covering their trunk, whereas other lineages are devoid of any such structures. To understand the evolution of the tegument coverage and particularly the transition between different structures, we investigated the pattern of scale loss events along actinopterygian evolution and addressed the functional relationship between the scaleless phenotype and the ecology of fishes. Furthermore, we examined whether the emergence of trunk bony plates was dependent over the presence or absence of scales. To this aim, we used two recently published actinopterygian phylogenies, one including > 11,000 species, and by using stochastic mapping and Bayesian methods, we inferred scale loss events and trunk bony plate acquisitions. Our results reveal that a scaled tegument is the most frequent state in actinopterygians, but multiple independent scale loss events occurred along their phylogeny with essentially no scale re-acquisition. Based on linear mixed models, we found evidence supporting that after a scale loss event, fishes tend to change their ecology and adopt a benthic lifestyle. Furthermore, we show that trunk bony plates appeared independently multiple times along the phylogeny. By using fitted likelihood models for character evolution, we show that trunk bony plate acquisitions were dependent over a previous scale loss event. Overall, our findings support the hypothesis that tegument cover is a key evolutionary trait underlying actinopterygian radiation.Impact SummaryRay-finned fishes (actinopterygians) are the most diverse vertebrate group in the world. The majority of these fishes possess scales as a protective shield covering their trunk. However, several lineages display a body armour composed of trunk bony plates or are devoid of any protective structures. The diversity and the transitions between different tegument coverage types have not been previously studied in an evolutionary framework. Here, we investigate which structure was present at the origin of ray-finned fishes and how the different phenotypes emerged through time.We show that a scaled tegument was the most widespread sate along ray-finned fish evolution, yet scale losses occurred multiple independent times, while acquiring scales again almost never happened. Moreover, we reveal that scaleless teguments most probably led species to change their ecology and colonise the floors of oceans and water bodies. The functional advantages of a scaleless tegument in a benthic environment are yet to be demonstrated, but the increased cutaneous respiration could be an explanation. We show that trunk bony plates also emerged independently multiple times along the evolution of ray-finned fishes but these armours protecting the trunk can only appear after a scale loss event. Therefore, while the acquisitions of trunk bony plates are phylogenetically independent, they need a “common ground” to emerge. All together, our findings provide evidence that the various tegument covers have contributed to the outstanding diversification of ray-finned fishes.

Estimating dispersal and evolutionary dynamics in diploporan blastozoans (Echinodermata) across the great Ordovician biodiversification event

Echinoderms make up a substantial component of Ordovician marine invertebrates, yet their speciation and dispersal history as inferred within a rigorous phylogenetic and statistical framework is lacking. We use biogeographic stochastic mapping (BSM; implemented in the R package BioGeoBEARS) to infer ancestral area relationships and the number and type of dispersal events through the Ordovician for diploporan blastozoans and related species. The BSM analysis was divided into three time slices to analyze how dispersal paths changed before and during the great Ordovician biodiversification event (GOBE) and within the Late Ordovician mass extinction intervals. The best-fit biogeographic model incorporated jump dispersal, indicating this was an important speciation strategy. Reconstructed areas within the phylogeny indicate the first diploporan blastozoans likely originated within Baltica or Gondwana. Dispersal, jump dispersal, and sympatry dominated the BSM inference through the Ordovician, while dispersal paths varied in time. Long-distance dispersal events in the Early Ordovician indicate distance was not a significant predictor of dispersal, whereas increased dispersal events between Baltica and Laurentia are apparent during the GOBE, indicating these areas were important to blastozoan speciation. During the Late Ordovician, there is an increase in dispersal events among all paleocontinents. The drivers of dispersal are attributed to oceanic and epicontinental currents. Speciation events plotted against geochemical data indicate that blastozoans may not have responded to climate cooling events and other geochemical perturbations, but additional data will continue to shed light on the drivers of early Paleozoic blastozoan speciation and dispersal patterns.

Phylogeny and Biogeography of South American Marsh Pitcher Plant Genus Heliamphora (Sarraceniaceae) Endemic to the Guiana Highlands

Heliamphora is a genus of carnivorous pitcher plants endemic to the Guiana Highlands with fragmented distributions. We presented a well resolved, time-calibrated, and nearly comprehensive Heliamphora phylogeny estimated using Bayesian inference and maximum likelihood based on nuclear genes (26S, ITS, and PHYC) and secondary calibration. We used stochastic mapping to infer ancestral states of morphological characters and ecological traits. Our ancestral state estimations revealed that the pitcher drainage structures characteristic of the genus transformed from a hole to a slit in single clade, while other features (scape pubescence and hammock-like growth) have been gained and lost multiple times. Habitat was similarly labile in Heliamphora, with multiple transitions from the ancestral highland habitats into the lowlands. Using Mantel test, we found closely related species tend to be geographically closely distributed. Placing our phylogeny in a historical context, major clades likely emerged through both vicariance and dispersal during Miocene with more recent diversification driven by vertical displacement during the Pleistocene glacial-interglacial thermal oscillations. Despite the dynamic climatic history experienced by Heliamphora, the temperature changes brought by global warming pose a significant threat, particularly for those species at the highest elevations.