scholarly journals Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging

2019 ◽  
Author(s):  
Jamie R. Oaks ◽  
Nadia L’Bahy ◽  
Kerry A. Cobb
Keyword(s):  
Population Size ◽  
Gasterosteus Aculeatus ◽  
Simulated Data ◽  
Genomic Data ◽  
Demographic Changes ◽  
Ecological Interactions ◽  
Approximate Methods ◽  
Full Likelihood ◽  
Threespine Sticklebacks ◽  
Multiple Species

AbstractFactors that influence the distribution, abundance, and diversification of species can simultaneously affect multiple evolutionary lineages within or across communities. These include changes to the environment or inter-specific ecological interactions that cause ranges of multiple species to contract, expand, or fragment. Such processes predict temporally clustered evolutionary events across species, such as synchronous population divergences and/or changes in population size. There have been a number of methods developed to infer shared divergences or changes in population size, but not both, and the latter has been limited to approximate methods. We introduce a full-likelihood Bayesian method that uses genomic data to estimate temporal clustering of an arbitrary mix of population divergences and population-size changes across taxa. Using simulated data, we find that estimating the timing and sharing of demographic changes tends to be inaccurate and sensitive to prior assumptions, which is in contrast to accurate, precise, and robust estimates of shared divergence times. We also show previous estimates of co-expansion among five Alaskan populations of threespine sticklebacks (Gasterosteus aculeatus) were likely driven by prior assumptions and ignoring invariant characters. We conclude by discussing potential avenues to improve the estimation of synchronous demographic changes across populations.

scholarly journals Diversity and sexual dimorphism in the head lateral line system in North Sea populations of threespine sticklebacks, Gasterosteus aculeatus (Teleostei: Gasterosteidae)

Zoomorphology ◽  
2020 ◽  
Author(s):  
Harald Ahnelt ◽  
David Ramler ◽  
Maria Ø. Madsen ◽  
Lasse F. Jensen ◽  
Sonja Windhager
Keyword(s):  
Sexual Dimorphism ◽  
North Sea ◽  
Lateral Line ◽  
Gasterosteus Aculeatus ◽  
Sensory System ◽  
Threespine Stickleback ◽  
Lateral Line System ◽  
Line System ◽  
Marine Population ◽  
Threespine Sticklebacks

AbstractThe mechanosensory lateral line of fishes is a flow sensing system and supports a number of behaviors, e.g. prey detection, schooling or position holding in water currents. Differences in the neuromast pattern of this sensory system reflect adaptation to divergent ecological constraints. The threespine stickleback, Gasterosteus aculeatus, is known for its ecological plasticity resulting in three major ecotypes, a marine type, a migrating anadromous type and a resident freshwater type. We provide the first comparative study of the pattern of the head lateral line system of North Sea populations representing these three ecotypes including a brackish spawning population. We found no distinct difference in the pattern of the head lateral line system between the three ecotypes but significant differences in neuromast numbers. The anadromous and the brackish populations had distinctly less neuromasts than their freshwater and marine conspecifics. This difference in neuromast number between marine and anadromous threespine stickleback points to differences in swimming behavior. We also found sexual dimorphism in neuromast number with males having more neuromasts than females in the anadromous, brackish and the freshwater populations. But no such dimorphism occurred in the marine population. Our results suggest that the head lateral line of the three ecotypes is under divergent hydrodynamic constraints. Additionally, sexual dimorphism points to divergent niche partitioning of males and females in the anadromous and freshwater but not in the marine populations. Our findings imply careful sampling as an important prerequisite to discern especially between anadromous and marine threespine sticklebacks.

Effects of constant and fluctuating temperatures on egg production in the threespine stickleback (Gasterosteus aculeatus)

1989 ◽  
Vol 67 (6) ◽  
pp. 1599-1602 ◽  
Author(s):  
Vital Boulé ◽  
Gerard J. Fitzgerald
Keyword(s):  
Reproductive Performance ◽  
Egg Production ◽  
Egg Size ◽  
Laboratory Experiments ◽  
Gasterosteus Aculeatus ◽  
Reproduction Number ◽  
Temperature Fluctuations ◽  
Spawning Grounds ◽  
Threespine Sticklebacks ◽  
Fluctuating Temperatures

Female threespine sticklebacks (Gasterosteus aculeatus) spend only 9–15 days on the spawning grounds, an intertidal salt marsh at Isle Verte, Quebec, during a 2-month breeding season. Individuals average only one spawning. However, in the laboratory they lay clutches of several hundred eggs every 3–5 days for several months. We designed laboratory experiments to determine (i) whether daily temperature fluctuations similar to those encountered in the marsh affect reproduction (number of clutches, number of eggs per clutch, and size of eggs) and (ii) whether the amplitude of the fluctuations encountered by the fish affects reproduction. We compared the reproduction of females held in fluctuating temperatures with that of females kept at 20 °C. Fish kept under fluctuating conditions produced more eggs per clutch but had longer interspawning intervals than those at 20 °C. Total seasonal egg production and egg size did not differ between the two groups. Fish in fluctuating temperatures survived longer and were in better condition than those at 20 °C. We conclude that the amplitude of the fluctuations is less important than mean temperature in determining reproductive performance. Fluctuating temperatures on the spawning grounds are not responsible for the short residency there.

Burst swimming and its enzymatic correlates in the threespine stickleback (Gasterosteus aculeatus): full-sib heritabilities

1998 ◽  
Vol 76 (4) ◽  
pp. 680-688 ◽  
Author(s):  
Christophe Garenc ◽  
Frederick G Silversides ◽  
Helga Guderley
Keyword(s):  
Gasterosteus Aculeatus ◽  
Genetic Factors ◽  
Creatine Phosphokinase ◽  
Swimming Performance ◽  
Biotic Interactions ◽  
Considerable Influence ◽  
Paternal Effects ◽  
Threespine Sticklebacks ◽  
Burst Swimming ◽  
Intrafamilial Variability

Full-sib heritabilities of burst-swimming capacity and its enzymatic correlates were calculated in juvenile threespine sticklebacks, Gasterosteus aculeatus, from 25 families raised under constant laboratory conditions. Variation among families in burst-swimming performance, enzyme activities, body size, and condition of the juveniles was considerable. Estimates of full-sib heritabilities of absolute and relative burst-swimming performance decreased during ontogenesis, as they were higher for 2-month-old than for 3.6-month-old sticklebacks. This decline may reflect a decrease in the importance of paternal effects with age, as well as an increase in intrafamilial variability due to the existence of feeding or social hierarachies. Enzymatic correlates of burst-swimming performance measured in 3.6-month-old sticklebacks had higher full-sib heritabilities than burst-swimming performance itself, with the highest values found for cytochrome c oxidase, followed by lactate dehydrogenase and then phosphofructokinase and creatine phosphokinase. These results suggest that genetic factors may have a considerable influence upon burst-swimming performance and muscle metabolic capacities of juvenile threespine sticklebacks, but that this influence may be tempered by biotic interactions.

scholarly journals The theory on and software simulating large-scale genomic data for genotype-by-environment interactions

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiujin Li ◽  
Hailiang Song ◽  
Zhe Zhang ◽  
Yunmao Huang ◽  
Qin Zhang ◽  
...  
Keyword(s):  
Large Scale ◽  
Simulated Data ◽  
Genomic Data ◽  
Efficient Tool ◽  
Phenotypic Data ◽  
Genotype By Environment Interactions ◽  
Genotype By Environment ◽  
Threshold Trait ◽  
Genome Wide ◽  
Increasing Demand

Abstract Background With the emphasis on analysing genotype-by-environment interactions within the framework of genomic selection and genome-wide association analysis, there is an increasing demand for reliable tools that can be used to simulate large-scale genomic data in order to assess related approaches. Results We proposed a theory to simulate large-scale genomic data on genotype-by-environment interactions and added this new function to our developed tool GPOPSIM. Additionally, a simulated threshold trait with large-scale genomic data was also added. The validation of the simulated data indicated that GPOSPIM2.0 is an efficient tool for mimicking the phenotypic data of quantitative traits, threshold traits, and genetically correlated traits with large-scale genomic data while taking genotype-by-environment interactions into account. Conclusions This tool is useful for assessing genotype-by-environment interactions and threshold traits methods.

scholarly journals Disentangling environmental effects in microbial association networks

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Ina Maria Deutschmann ◽  
Gipsi Lima-Mendez ◽  
Anders K. Krabberød ◽  
Jeroen Raes ◽  
Sergio M. Vallina ◽  
...  
Keyword(s):  
Data Processing ◽  
Simulated Data ◽  
Potential Interaction ◽  
Microbial Interactions ◽  
Ecological Interactions ◽  
Sign Pattern ◽  
Interaction Information ◽  
Microbial Association ◽  
Environmental Selection ◽  
Data Processing Inequality

Abstract Background Ecological interactions among microorganisms are fundamental for ecosystem function, yet they are mostly unknown or poorly understood. High-throughput-omics can indicate microbial interactions through associations across time and space, which can be represented as association networks. Associations could result from either ecological interactions between microorganisms, or from environmental selection, where the association is environmentally driven. Therefore, before downstream analysis and interpretation, we need to distinguish the nature of the association, particularly if it is due to environmental selection or not. Results We present EnDED (environmentally driven edge detection), an implementation of four approaches as well as their combination to predict which links between microorganisms in an association network are environmentally driven. The four approaches are sign pattern, overlap, interaction information, and data processing inequality. We tested EnDED on networks from simulated data of 50 microorganisms. The networks contained on average 50 nodes and 1087 edges, of which 60 were true interactions but 1026 false associations (i.e., environmentally driven or due to chance). Applying each method individually, we detected a moderate to high number of environmentally driven edges—87% sign pattern and overlap, 67% interaction information, and 44% data processing inequality. Combining these methods in an intersection approach resulted in retaining more interactions, both true and false (32% of environmentally driven associations). After validation with the simulated datasets, we applied EnDED on a marine microbial network inferred from 10 years of monthly observations of microbial-plankton abundance. The intersection combination predicted that 8.3% of the associations were environmentally driven, while individual methods predicted 24.8% (data processing inequality), 25.7% (interaction information), and up to 84.6% (sign pattern as well as overlap). The fraction of environmentally driven edges among negative microbial associations in the real network increased rapidly with the number of environmental factors. Conclusions To reach accurate hypotheses about ecological interactions, it is important to determine, quantify, and remove environmentally driven associations in marine microbial association networks. For that, EnDED offers up to four individual methods as well as their combination. However, especially for the intersection combination, we suggest using EnDED with other strategies to reduce the number of false associations and consequently the number of potential interaction hypotheses.

scholarly journals GeneRax: A tool for species tree-aware maximum likelihood based gene family tree inference under gene duplication, transfer, and loss

2019 ◽  
Author(s):  
Benoit Morel ◽  
Alexey M. Kozlov ◽  
Alexandros Stamatakis ◽  
Gergely J. Szöllősi
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Simulated Data ◽  
Gene Families ◽  
Species Tree ◽  
Homologous Gene ◽  
Sequence Alignments ◽  
Full Likelihood ◽  
True Tree

AbstractInferring phylogenetic trees for individual homologous gene families is difficult because alignments are often too short, and thus contain insufficient signal, while substitution models inevitably fail to capture the complexity of the evolutionary processes. To overcome these challenges species tree-aware methods also leverage information from a putative species tree. However, only few methods are available that implement a full likelihood framework or account for horizontal gene transfers. Furthermore, these methods often require expensive data pre-processing (e.g., computing bootstrap trees), and rely on approximations and heuristics that limit the degree of tree space exploration. Here we present GeneRax, the first maximum likelihood species tree-aware phylogenetic inference software. It simultaneously accounts for substitutions at the sequence level as well as gene level events, such as duplication, transfer, and loss relying on established maximum likelihood optimization algorithms. GeneRax can infer rooted phylogenetic trees for multiple gene families, directly from the per-gene sequence alignments and a rooted, yet undated, species tree. We show that compared to competing tools, on simulated data GeneRax infers trees that are the closest to the true tree in 90% of the simulations in terms of relative Robinson-Foulds distance. On empirical datasets, GeneRax is the fastest among all tested methods when starting from aligned sequences, and it infers trees with the highest likelihood score, based on our model. GeneRax completed tree inferences and reconciliations for 1099 Cyanobacteria families in eight minutes on 512 CPU cores. Thus, its parallelization scheme enables large-scale analyses. GeneRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax.

scholarly journals Frequent birth-and-death events throughout perforin-1 evolution

2020 ◽  
Author(s):  
Miguel Araujo-Voces ◽  
Victor Quesada
Keyword(s):  
Preliminary Analysis ◽  
Large Scale ◽  
Mammalian Species ◽  
Genomic Data ◽  
Start Codon ◽  
High Similarity ◽  
Gene Encoding ◽  
Coding Sequences ◽  
Copy Numbers ◽  
Multiple Species

Abstract Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. Results We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci containing up to twelve copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. Conclusions The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.

scholarly journals Frequent birth-and-death events throughout perforin-1 evolution

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Miguel Araujo-Voces ◽  
Víctor Quesada
Keyword(s):  
Preliminary Analysis ◽  
Large Scale ◽  
Mammalian Species ◽  
Genomic Data ◽  
Start Codon ◽  
High Similarity ◽  
Gene Encoding ◽  
Coding Sequences ◽  
Copy Numbers ◽  
Multiple Species

Abstract Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. Results We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci containing up to twelve copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. Conclusions The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.

scholarly journals Genome Characterization, Prevalence, and Transmission Mode of a Novel Picornavirus Associated with the Threespine Stickleback Fish (Gasterosteus aculeatus)

2019 ◽  
Vol 93 (9) ◽  
Author(s):  
Megan A. Hahn ◽  
Nolwenn M. Dheilly
Keyword(s):  
Gasterosteus Aculeatus ◽  
Rna Virus ◽  
Wide Distribution ◽  
Model System ◽  
Threespine Stickleback ◽  
Tissue Samples ◽  
Content Type ◽  
Threespine Sticklebacks ◽  
The Impact

ABSTRACT The complete genome sequence of an RNA virus was assembled from RNA sequencing of virus particles purified from threespine stickleback intestine tissue samples. This new virus is most closely related to the Eel picornavirus and can be assigned to the genus Potamipivirus in the family Picornaviridae. Its unique genetic properties are enough to establish a new species, dubbed the Threespine Stickleback picornavirus (TSPV). Due to their broad geographic distribution throughout the Northern Hemisphere and parallel adaptation to freshwater, threespine sticklebacks have become a model in evolutionary ecology. Further analysis using diagnostic PCRs revealed that TSPV is highly prevalent in both anadromous and freshwater populations of threespine sticklebacks, infects almost all fish tissues, and is transmitted vertically to offspring obtained from in vitro fertilization in laboratory settings. Finally, TSPV was found in Sequence Reads Archives of transcriptome of Gasterosteus aculeatus, further demonstrating its wide distribution and unsought prevalence in samples. It is thus necessary to test the impact of TSPV on the biology of threespine sticklebacks, as this widespread virus could interfere with the behavioral, physiological, or immunological studies that employ this fish as a model system. IMPORTANCE The threespine stickleback species complex is an important model system in ecological and evolutionary studies because of the large number of isolated divergent populations that are experimentally tractable. For similar reasons, its coevolution with the cestode parasite Schistocephalus solidus, its interaction with gut microbes, and the evolution of its immune system are of growing interest. Herein we describe the discovery of an RNA virus that infects both freshwater and anadromous populations of sticklebacks. We show that the virus is transmitted vertically in laboratory settings and found it in Sequence Reads Archives, suggesting that experiments using sticklebacks were conducted in the presence of the virus. This discovery can serve as a reminder that the presence of viruses in wild-caught animals is possible, even when animals appear healthy. Regarding threespine sticklebacks, the impact of Threespine Stickleback picornavirus (TSPV) on the fish biology should be investigated further to ensure that it does not interfere with experimental results.

Sign in / Sign up

Export Citation Format

Share Document