Biology subjects

Manica, A.

Publications and source records attributed to Manica, A..

50 records · Page 3Linked to original sources

bioRxiv2019

mtDNA-based reconstructions of change in effective population sizes of Holarctic birds do not agree with their reconstructed range sizes based on paleoclimates

During the Quaternary, large climate oscillations had profound impacts on the distribution, demography and diversity of species globally. Birds offer a special opportunity for studying these impacts because surveys of geographical distributions, publicly-available genetic sequence data, and the existence of species with adaptations to life in structurally different habitats, permit large-scale comparative analyses. We use Bayesian Skyline Plot (BSP) analysis of mitochondrial DNA to reconstruct profiles depicting how effective population size (Ne) may have changed over time, focussing on variation in the effect of the last deglaciation among 102 Holarctic species. Only 3 species showed a decline in Ne since the Last Glacial Maximum (LGM) and 7 showed no sizeable change, whilst 92 profiles revealed an increase in Ne. Using bioclimatic Species Distribution Models (SDMs), we also estimated changes in species potential range extent since the LGM. Whilst most modelled ranges also increased, we found no correlation across species between the magnitude of change in range size and change in Ne. The lack of correlation between SDM and BSP reconstructions could not be reconciled even when range shifts were considered. We suggest the lack of agreement between these measures might be linked to changes in population densities which can be independent of range changes. We caution that interpreting either SDM or BSPs independently is problematic and potentially misleading. Additionally, we found that Ne of wetland species tended to increase later than species from terrestrial habitats, possibly reflecting a delayed increase in the extent of this habitat type after the LGM.

evolutionary biology↗

bioRxiv2019

Removing reference bias in ancient DNA data analysis by mapping to a sequence variation graph

BackgroundDuring the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Recently, alternative approaches for read mapping and genetic variation analysis have been developed that replace the linear reference by a variation graph which includes known alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for ancient DNA and compare our approach to existing methods. ResultsWe used vg to align simulated and real aDNA samples to a variation graph containing 1000 Genome Project variants, and compared these with the same data aligned with bwa to the human linear reference genome. We show that use of vg leads to a balanced allelic representation at polymorphic sites, effectively removing reference bias, and more sensitive variant detection in comparison with bwa, especially for insertions and deletions (indels). Alternative approaches that use relaxed bwa parameter settings or filter bwa alignments can also reduce bias, but can have lower sensitivity than vg, particularly for indels. ConclusionsOur findings demonstrate that aligning aDNA sequences to variation graphs effectively mitigates the impact of reference bias when analysing aDNA, while retaining mapping sensitivity and allowing detection of variation, in particular indel variation, that was previously missed.

genomics↗

bioRxiv2019

Global range contractions of mammals, birds and amphibians from 10,000 BC to 2100 AD.

Species vulnerability to extinction is strongly impacted by their geographical range size. Formulating effective conservation strategies therefore requires a better understanding of how the ranges of the worlds species have changed in the past, and how they will change under alternative future scenarios. Here, we used reconstructions of global land use and biomes of the past 7,000 years, and 16 possible climatic and socio-economic scenarios until the year 2100, to map the habitat ranges of 16,511 individual mammal, bird, and amphibian species through time. We estimate that extant species have lost an average of 19% of their natural range sizes thus far, and may lose up to 32% by 2100. Changes in range size vary greatly between species, with tropical, small-ranged, and threatened species being especially impacted. Our data reveal that range losses have been increasing disproportionately in relation to the size of destroyed habitat, driven by a long-term increase of land use in tropical biodiversity hotspots. The outcomes of different future land use and climate trajectories for global habitat ranges vary considerably, providing important quantitative evidence for conservation planners and policy makers of the costs and benefits of alternative pathways for the future of global biodiversity.

ecology↗

bioRxiv2019

Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information

BackgroundLong DNA reads produced by single molecule and pore-based sequencers are more suitable for assembly and structural variation discovery than short read DNA fragments. For de novo assembly, PacBio and Oxford Nanopore Technologies (ONT) are favorite options. However, PacBios SMRT sequencing is expensive for a full human genome assembly and costs over 40,000 USD for 30x coverage as of 2019. ONT PromethION sequencing, on the other hand, is one-twelfth the price of PacBio for the same coverage. This study aimed to compare the cost-effectiveness of ONT PromethION and PacBios SMRT sequencing in relation to the quality.\n\nFindingsWe performed whole genome de novo assemblies and comparison to construct an improved version of KOREF, the Korean reference genome, using sequencing data produced by PromethION and PacBio. With PromethION, an assembly using sequenced reads with 64x coverage (193 Gb, 3 flowcell sequencing) resulted in 3,725 contigs with N50s of 16.7 Mbp and a total genome length of 2.8 Gbp. It was comparable to a KOREF assembly constructed using PacBio at 62x coverage (188 Gbp, 2,695 contigs and N50s of 17.9 Mbp). When we applied Hi-C-derived long-range mapping data, an even higher quality assembly for the 64x coverage was achieved, resulting in 3,179 scaffolds with an N50 of 56.4 Mbp.\n\nConclusionThe pore-based PromethION approach provides a good quality chromosome-scale human genome assembly at a low cost with long maximum contig and scaffold lengths and is more cost-effective than PacBio at comparable quality measurements.

genomics↗

bioRxiv2019

Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles

BackgroundBirds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day, and owls (Strigiformes) hunting by night.\n\nResultsHere, we report new genomes and transcriptomes for 20 species of birds, including 16 species of birds of prey, and high-quality reference genomes for the Eurasian eagle-owl (Bubo bubo), oriental scops-owl (Otus sunia), eastern buzzard (Buteo japonicus), and common kestrel (Falco tinnunculus). Our extensive genomic analysis and comparisons with non-raptor genomes identified common molecular signatures that underpin anatomical structure and sensory, muscle, circulatory, and respiratory systems related to a predatory lifestyle. Compared with diurnal birds, owls exhibit striking adaptations to the nocturnal environment, including functional trade-offs in the sensory systems (e.g., loss of color vision genes and selection for enhancement of nocturnal vision and other sensory systems) that are probably convergent with other nocturnal avian orders. Additionally, we found that a suite of genes associated with vision and circadian rhythm were differentially expressed between nocturnal and diurnal raptors, indicating adaptive expression change during the transition to nocturnality.\n\nConclusionsOverall, raptor genomes showed genomic signatures associated with the origin and maintenance of several specialized physiological and morphological features essential to be apex predators.

genomics↗

bioRxiv2018

Relocating agriculture could drastically reduce humanity’s ecological footprint

Agriculture is a major driver of global biodiversity loss 1,2, accounts for one quarter of greenhouse gas emissions 3, and is responsible for 70% of freshwater use 4,5. How can land be used for agriculture in a way that minimises the impact on the worlds natural resources while maintaining current production levels? Here, we solved this more than 10 million dimensional optimisation problem and find that moving current croplands and pastures to optimal locations, while allowing then-abandoned areas to regenerate, could simultaneously decrease the current carbon, biodiversity and water footprint of global agriculture by up to 71%, 91% and 100%, respectively. This would offset current net CO2 emissions for half a century, massively alleviate pressure on global biodiversity and greatly reduce freshwater shortages. Whilst these achievements would require global coordination of agricultural policies, reductions of up to 59%, 78% and close to 100% are achievable by relocating production within national borders, with the greatest potential for carbon footprint reduction held by the worlds top three CO2 emitting countries.

ecology↗

bioRxiv2018

The development of social interactions in Corydoras aeneus larvae

Very young animals develop life skills as they mature, and for social animals this includes the acquisition of social abilities such as communication. Many animals exhibit changeable patterns of social behavior based on development, and social experience during the juvenile period can be vital for the development of necessary social behaviors in adulthood. We investigated the development of a distinctive tactile interaction behavior in Corydoras aeneus, the Bronze Cory catfish. Adults use this behavior to coordinate group activities during foraging and flight responses from predators, and the development of this behavior in larvae is of interest in investigating how communication and social behaviors develop as an individual matures, and which factors affect their development. We found that larvae respond to applied tactile stimulation with a flight response far less often as larvae matured, implying that larvae become less sensitive to tactile stimulation with age. Given that adults frequently interact with one another tactilely, this development is consistent with developing appropriate social behavior in adulthood. We also found that social exposure affects the development of the larval response to tactile interactions with conspecifics, and that isolation in the earliest larval stage leads to a greater likelihood of responding to a tactile interaction with a conspecific with a flight response. This suggests that social exposure is important for developing an appropriate response to tactile stimulation in social settings and underscores the particular importance of early life experiences in the development of sociality.

animal behavior and cognition↗

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↗