scholarly journals Detecting mosaic patterns in macroevolutionary disparity

2018 ◽  
Author(s):  
Caroline Parins-Fukuchi
Keyword(s):  
Evolutionary Dynamics ◽  
Distinct Pattern ◽  
The Body ◽  
Phenotypic Trait ◽  
Multiple Traits ◽  
Mosaic Pattern ◽  
Phenotypic Data ◽  
Evolutionary Patterns ◽  
Multidimensional Datasets ◽  
Evolutionary Distinctiveness

ABSTRACTEvolutionary biologists have long sought to understand the full complexity in pattern and process that shapes organismal diversity. Although phylogenetic comparative methods are often used to reconstruct complex evolutionary dynamics, they are typically limited to a single phenotypic trait. Extensions that accommodate multiple traits lack the ability to partition multidimensional datasets into a set of mosaic suites of evolutionarily linked characters. I introduce a comparative framework that identifies heterogeneity in evolutionary patterns across large datasets of continuous traits. Using a model of continuous trait evolution based on the differential accumulation of disparity across lineages in a phylogeny, the approach algorithmically partitions traits into a set of character suites that best explains the data, where each suite displays a distinct pattern in phylogenetic morphological disparity. When applied to empirical data, the approach revealed a mosaic pattern predicted by developmental biology. The evolutionary distinctiveness of individual suites can be investigated in more detail, either by fitting conventional comparative models or by directly studying the phylogenetic patterns in disparity recovered during the analysis. This framework can supplement existing comparative approaches by inferring the complex, integrated patterns that shape evolution across the body plan from disparate developmental, morphometric, and environmental sources of phenotypic data.

scholarly journals Evolution of correlated complexity in the radically different courtship signals of birds-of-paradise

2018 ◽  
Author(s):  
Russell A. Ligon ◽  
Christopher D. Diaz ◽  
Janelle L. Morano ◽  
Jolyon Troscianko ◽  
Martin Stevens ◽  
...  
Keyword(s):  
Sexual Selection ◽  
Natural Selection ◽  
Evolutionary Biology ◽  
Evolutionary Dynamics ◽  
Functional Integration ◽  
Empirical Support ◽  
Evolutionary Patterns ◽  
Evolutionary Innovation ◽  
Birds Of Paradise ◽  
Analytical Approaches

Ornaments used in courtship often vary wildly among species, reflecting the evolutionary interplay between mate preference functions and the constraints imposed by natural selection. Consequently, understanding the evolutionary dynamics responsible for ornament diversification has been a longstanding challenge in evolutionary biology. However, comparing radically different ornaments across species, as well as different classes of ornaments within species, is a profound challenge to understanding diversification of sexual signals. Using novel methods and a unique natural history dataset, we explore evolutionary patterns of ornament evolution in a group - the birds-of-paradise - exhibiting dramatic phenotypic diversification widely assumed to be driven by sexual selection. Rather than the tradeoff between ornament types originally envisioned by Darwin and Wallace, we found positive correlations among cross-modal (visual/acoustic) signals indicating functional integration of ornamental traits into a composite unit - the courtship phenotype. Furthermore, given the broad theoretical and empirical support for the idea that systemic robustness - functional overlap and interdependency - promotes evolutionary innovation, we posit that birds-of-paradise have radiated extensively through ornamental phenotype space as a consequence of the robustness in the courtship phenotype that we document at a phylogenetic scale. We suggest that the degree of robustness in courtship phenotypes among taxa can provide new insights into the relative influence of sexual and natural selection on phenotypic radiations.Author SummaryAnimals frequently vary widely in ornamentation, even among closely related species. Understanding the patterns that underlie this variation is a significant challenge, requiring comparisons among drastically different traits - like comparing apples to oranges. Here, we use novel analytical approaches to quantify variation in ornamental diversity and richness across the wildly divergent birds-of-paradise, a textbook example of how sexual selection can profoundly shape organismal phenotypes. We find that color and acoustic complexity, along with behavior and acoustic complexity, are positively correlated across evolutionary time-scales. Positive covariation among ornament classes suggests that selection is acting on correlated suites of traits - a composite courtship phenotype - and that this integration may be partially responsible for the extreme variation we see in birds-of-paradise.

Eco-evolutionary adaptations of ochotonids (Mammalia: Lagomorpha) to islands: new insights into Late Miocene pikas from the Gargano palaeo-archipelago (Italy)

2020 ◽  
Author(s):  
Blanca Moncunill-Solé
Keyword(s):  
Climate Change ◽  
Growth Rate ◽  
Late Miocene ◽  
Ecological Niche ◽  
Rate Increase ◽  
The Body ◽  
Evolutionary Patterns ◽  
Selective Pressures ◽  
Extant Species ◽  
Management And Conservation

Abstract Climate change strongly affects the range of ochotonids (Order Lagomorpha), fragmenting their habitats and restricting them to ecological islands. The present paper discusses the adaptations of extinct ochotonids to insular stressors, providing baseline data for the management and conservation of extant species. For this purpose, the body mass (BM) and locomotion of the endemic Prolagus apricenicus and Prolagus imperialis from the Gargano palaeo archipelago (Late Miocene) were assessed. P. apricenicus was a small-sized ochotonid (BM 150–250 g) and P. imperialis was probably the largest Prolagus that ever lived (BM 500–750 g). The eco-evolutionary BM dynamics suggest a targeted ecological niche for P. apricenicus, whereas the BM of P. imperialis rose abruptly as a result of growth-rate increase. In both species, the locomotion was stable and less cursorial, with leaping skills, resembling extant rocky ochotonids. Convergent eco-evolutionary patterns are observed in extinct insular ochotonids, concerning an increase of BM (giants), more efficient chewing, less cursorial and more stable locomotion, leaping skills, as well as a slower life history (longer lifespan). Such adaptations are triggered by the specific selective pressures of insular regimes. The present results point to the long-lasting insular Prolagus species as reference taxa for addressing the management of extant rocky ochotonids.

scholarly journals PRDM9 Diversity at Fine Geographical Scale Reveals Contrasting Evolutionary Patterns and Functional Constraints in Natural Populations of House Mice

2019 ◽  
Vol 36 (8) ◽  
pp. 1686-1700 ◽  
Author(s):  
Covadonga Vara ◽  
Laia Capilla ◽  
Luca Ferretti ◽  
Alice Ledda ◽  
Rosa A Sánchez-Guillén ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Evolutionary Biology ◽  
Evolutionary Dynamics ◽  
Rapid Evolution ◽  
Natural Populations ◽  
Global Scale ◽  
House Mice ◽  
Functional Constraints ◽  
Evolutionary Patterns ◽  
Data Set

Abstract One of the major challenges in evolutionary biology is the identification of the genetic basis of postzygotic reproductive isolation. Given its pivotal role in this process, here we explore the drivers that may account for the evolutionary dynamics of the PRDM9 gene between continental and island systems of chromosomal variation in house mice. Using a data set of nearly 400 wild-caught mice of Robertsonian systems, we identify the extent of PRDM9 diversity in natural house mouse populations, determine the phylogeography of PRDM9 at a local and global scale based on a new measure of pairwise genetic divergence, and analyze selective constraints. We find 57 newly described PRDM9 variants, this diversity being especially high on Madeira Island, a result that is contrary to the expectations of reduced variation for island populations. Our analysis suggest that the PRDM9 allelic variability observed in Madeira mice might be influenced by the presence of distinct chromosomal fusions resulting from a complex pattern of introgression or multiple colonization events onto the island. Importantly, we detect a significant reduction in the proportion of PRDM9 heterozygotes in Robertsonian mice, which showed a high degree of similarity in the amino acids responsible for protein–DNA binding. Our results suggest that despite the rapid evolution of PRDM9 and the variability detected in natural populations, functional constraints could facilitate the accumulation of allelic combinations that maintain recombination hotspot symmetry. We anticipate that our study will provide the basis for examining the role of different PRDM9 genetic backgrounds in reproductive isolation in natural populations.

Phylogenomic analysis of SARS-CoV-2 genomes from western India reveals unique linked mutations

2020 ◽  
Author(s):  
Dhiraj Paul ◽  
Kunal Jani ◽  
Janesh Kumar ◽  
Radha Chauhan ◽  
Vasudevan Seshadri ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Fitness Landscape ◽  
Geographical Location ◽  
Specific Pattern ◽  
Distinct Pattern ◽  
Viral Fitness ◽  
Phylogenomic Analysis ◽  
Western India ◽  
Asymptomatic Patients ◽  
Major Cluster

AbstractIndia has become the third worst-hit nation by the COVID-19 pandemic caused by the SARS-CoV-2 virus. Here, we investigated the molecular, phylogenomic, and evolutionary dynamics of SARS-CoV-2 in western India, the most affected region of the country. A total of 90 genomes were sequenced. Four nucleotide variants, namely C241T, C3037T, C14408T (Pro4715Leu), and A23403G (Asp614Gly), located at 5’UTR, Orf1a, Orf1b, and Spike protein regions of the genome, respectively, were predominant and ubiquitous (90%). Phylogenetic analysis of the genomes revealed four distinct clusters, formed owing to different variants. The major cluster (cluster 4) is distinguished by mutations C313T, C5700A, G28881A are unique patterns and observed in 45% of samples. We thus report a newly emerging pattern of linked mutations. The predominance of these linked mutations suggests that they are likely a part of the viral fitness landscape. A novel and distinct pattern of mutations in the viral strains of each of the districts was observed. The Satara district viral strains showed mutations primarily at the 3′ end of the genome, while Nashik district viral strains displayed mutations at the 5′ end of the genome. Characterization of Pune strains showed that a novel variant has overtaken the other strains. Examination of the frequency of three mutations i.e., C313T, C5700A, G28881A in symptomatic versus asymptomatic patients indicated an increased occurrence in symptomatic cases, which is more prominent in females. The age-wise specific pattern of mutation is observed. Mutations C18877T, G20326A, G24794T, G25563T, G26152T, and C26735T are found in more than 30% study samples in the age group of 10-25. Intriguingly, these mutations are not detected in the higher age range 61-80. These findings portray the prevalence of unique linked mutations in SARS-CoV-2 in western India and their prevalence in symptomatic patients.ImportanceElucidation of the SARS-CoV-2 mutational landscape within a specific geographical location, and its relationship with age and symptoms, is essential to understand its local transmission dynamics and control. Here we present the first comprehensive study on genome and mutation pattern analysis of SARS-CoV-2 from the western part of India, the worst affected region by the pandemic. Our analysis revealed three unique linked mutations, which are prevalent in most of the sequences studied. These may serve as a molecular marker to track the spread of this viral variant to different places.

Effects of pollution on individual size of a single species

2020 ◽  
pp. 2050079
Author(s):  
Bing Liu ◽  
Le Song ◽  
Xin Wang ◽  
Baolin Kang
Keyword(s):  
Growth Rate ◽  
Evolutionary Dynamics ◽  
Function Analysis ◽  
Fitness Function ◽  
Adaptive Dynamics ◽  
Single Species ◽  
Phenotypic Trait ◽  
Evolutionary Branching ◽  
Critical Function ◽  
Individual Size

In this paper, we develop a single species evolutionary model with a continuous phenotypic trait in a pulsed pollution discharge environment and discuss the effects of pollution on the individual size of the species. The invasion fitness function of a monomorphic species is given, which involves the long-term average exponential growth rate of the species. Then the critical function analysis method is used to obtain the evolutionary dynamics of the system, which is related to interspecific competition intensity between mutant species and resident species and the curvature of the trade-off between individual size and the intrinsic growth rate. We conclude that the pollution affects the evolutionary traits and evolutionary dynamics. The worsening of the pollution can lead to rapid stable evolution toward a smaller individual size, while the opposite is more likely to generate evolutionary branching and promote species diversity. The adaptive dynamics of coevolution of dimorphic species is further analyzed when evolutionary branching occurs.

scholarly journals Generalized Mosaic Neurofibromatosis Type 1: A Rare Case Report

2018 ◽  
Vol 3 (1) ◽  
pp. 390-392
Author(s):  
Niraj Parajuli ◽  
Bhaskar MM Kayastha ◽  
Rushma Shrestha ◽  
Anupama Karki ◽  
Laila Lama
Keyword(s):  
Case Report ◽  
Neurofibromatosis Type ◽  
The Body ◽  
Inherited Disorders ◽  
Mosaic Pattern ◽  
Nerve Sheath Tumors ◽  
Nerve Sheath ◽  
Rare Case Report ◽  
Lines Of Blaschko

Neurofibromatosis (NF) consists of group of genetically inherited disorders all of which is characterized by occurrence of nerve sheath tumors. There are eight different subtypes of neurofibromatosis. Segmental NF, a rare mosaic pattern of NF- type1 (NF1) is diagnosed in individuals who have typical features of NF1 restricted to one part of the body and whose parents are both unaffected. But recently the nomenclature has been changed to mosaic NF. We report a case of neurofibromatosis following the lines of blaschko. To the best of our knowledge, no such case report has been published till date of generalized mosaic NF following lines of blaschko's bilaterally symmetrically. BJHS 2018;3(1)5 :390-392

scholarly journals How predation shaped fish: the impact of fin spines on body form evolution across teleosts

2015 ◽  
Vol 282 (1819) ◽  
pp. 20151428 ◽  
Author(s):  
S. A. Price ◽  
S. T. Friedman ◽  
P. C. Wainwright
Keyword(s):  
Evolutionary Dynamics ◽  
Morphological Changes ◽  
Evolutionary Relationship ◽  
Vertical Plane ◽  
The Body ◽  
Body Dimension ◽  
Body Depth ◽  
Body Dimensions ◽  
The Impact ◽  
Fin Spines

It is well known that predators can induce morphological changes in some fish: individuals exposed to predation cues increase body depth and the length of spines. We hypothesize that these structures may evolve synergistically, as together, these traits will further enlarge the body dimensions of the fish that gape-limited predators must overcome. We therefore expect that the orientation of the spines will predict which body dimension increases in the presence of predators. Using phylogenetic comparative methods, we tested this prediction on the macroevolutionary scale across 347 teleost families, which display considerable variation in fin spines, body depth and width. Consistent with our predictions, we demonstrate that fin spines on the vertical plane (dorsal and anal fins) are associated with a deeper-bodied optimum. Lineages with spines on the horizontal plane (pectoral fins) are associated with a wider-bodied optimum. Optimal body dimensions across lineages without spines paralleling the body dimension match the allometric expectation. Additionally, lineages with longer spines have deeper and wider body dimensions. This evolutionary relationship between fin spines and body dimensions across teleosts reveals functional synergy between these two traits and a potential macroevolutionary signature of predation on the evolutionary dynamics of body shape.

scholarly journals Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung

mBio ◽  
2015 ◽  
Vol 6 (5) ◽  
Author(s):  
Julio Diaz Caballero ◽  
Shawn T. Clark ◽  
Bryan Coburn ◽  
Yu Zhang ◽  
Pauline W. Wang ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Evolutionary Dynamics ◽  
Genomic Analysis ◽  
Opportunistic Pathogen ◽  
Ancestral Population ◽  
Selective Sweeps ◽  
Short Term ◽  
Evolutionary Patterns ◽  
Content Type

ABSTRACT Pulmonary infections caused by Pseudomonas aeruginosa are a recalcitrant problem in cystic fibrosis (CF) patients. While the clinical implications and long-term evolutionary patterns of these infections are well studied, we know little about the short-term population dynamics that enable this pathogen to persist despite aggressive antimicrobial therapy. Here, we describe a short-term population genomic analysis of 233 P. aeruginosa isolates collected from 12 sputum specimens obtained over a 1-year period from a single patient. Whole-genome sequencing and antimicrobial susceptibility profiling identified the expansion of two clonal lineages. The first lineage originated from the coalescence of the entire sample less than 3 years before the end of the study and gave rise to a high-diversity ancestral population. The second expansion occurred 2 years later and gave rise to a derived population with a strong signal of positive selection. These events show characteristics consistent with recurrent selective sweeps. While we cannot identify the specific mutations responsible for the origins of the clonal lineages, we find that the majority of mutations occur in loci previously associated with virulence and resistance. Additionally, approximately one-third of all mutations occur in loci that are mutated multiple times, highlighting the importance of parallel pathoadaptation. One such locus is the gene encoding penicillin-binding protein 3, which received three independent mutations. Our functional analysis of these alleles shows that they provide differential fitness benefits dependent on the antibiotic under selection. These data reveal that bacterial populations can undergo extensive and dramatic changes that are not revealed by lower-resolution analyses. IMPORTANCE Pseudomonas aeruginosa is a bacterial opportunistic pathogen responsible for significant morbidity and mortality in cystic fibrosis (CF) patients. Once it has colonized the lung in CF, it is highly resilient and rarely eradicated. This study presents a deep sampling examination of the fine-scale evolutionary dynamics of P. aeruginosa in the lungs of a chronically infected CF patient. We show that diversity of P. aeruginosa is driven by recurrent clonal emergence and expansion within this patient and identify potential adaptive variants associated with these events. This high-resolution sequencing strategy thus reveals important intraspecies dynamics that explain a clinically important phenomenon not evident at a lower-resolution analysis of community structure.

scholarly journals Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering

PLoS Genetics ◽  
2021 ◽  
Vol 17 (4) ◽  
pp. e1009541
Author(s):  
Leonor García-Bayona ◽  
Michael J. Coyne ◽  
Laurie E. Comstock
Keyword(s):  
Evolutionary Dynamics ◽  
Secretion System ◽  
Human Populations ◽  
Trna Genes ◽  
Type Vi Secretion System ◽  
Human Gut ◽  
Evolutionary Patterns ◽  
Integrative And Conjugative Elements ◽  
Type Vi Secretion ◽  
Geographical Clustering

The human gut microbiota is a dense microbial ecosystem with extensive opportunities for bacterial contact-dependent processes such as conjugation and Type VI secretion system (T6SS)-dependent antagonism. In the gut Bacteroidales, two distinct genetic architectures of T6SS loci, GA1 and GA2, are contained on Integrative and Conjugative Elements (ICE). Despite intense interest in the T6SSs of the gut Bacteroidales, there is only a superficial understanding of their evolutionary patterns, and of their dissemination among Bacteroidales species in human gut communities. Here, we combine extensive genomic and metagenomic analyses to better understand their ecological and evolutionary dynamics. We identify new genetic subtypes, document extensive intrapersonal transfer of these ICE to Bacteroidales species within human gut microbiomes, and most importantly, reveal frequent population fixation of these newly armed strains in multiple species within a person. We further show the distribution of each of the distinct T6SSs in human populations and show there is geographical clustering. We reveal that the GA1 T6SS ICE integrates at a minimal recombination site leading to their integration throughout genomes and their frequent interruption of genes, whereas the GA2 T6SS ICE integrate at one of three different tRNA genes. The exclusion of concurrent GA1 and GA2 T6SSs in individual strains is associated with intact T6SS loci and with an ICE-encoded gene. By performing a comprehensive analysis of mobile genetic elements (MGE) in co-resident Bacteroidales species in numerous human gut communities, we identify 74 MGE that transferred to multiple Bacteroidales species within individual gut microbiomes. We further show that only three other MGE demonstrate multi-species spread in several human gut microbiomes to the degree demonstrated by the GA1 and GA2 ICE. These data underscore the ubiquity and dissemination of mobile T6SS loci within Bacteroidales communities and across human populations.

scholarly journals Test Gene-Environment Interactions for Multiple Traits in Sequencing Association Studies

2019 ◽  
Author(s):  
Jianjun Zhang ◽  
Qiuying Sha ◽  
Han Hao ◽  
Shuanglin Zhang ◽  
Xiaoyi Raymond Gao ◽  
...  
Keyword(s):  
Association Studies ◽  
Complex Diseases ◽  
Error Rates ◽  
Phenotypic Trait ◽  
Type I ◽  
Environment Interaction ◽  
Multiple Traits ◽  
Gene Environment ◽  
Variable Weight ◽  
Protective Variants

AbstractThe risk of many complex diseases is determined by a complex interplay of genetic and environmental factors. Data on multiple traits is often collected for many complex diseases in order to obtain a better understanding of the diseases. Examination of gene-environment interactions (GxEs) for multiple traits can yield valuable insights about the etiology of the disease and increase power in detecting disease associated genes. Most existing methods focus on testing gene-environment interaction (GxE) for a single trait. In this study, we develop novel approaches to test GxEs for multiple traits in sequencing association studies. We first perform transformation of multiple traits by using either principle component analysis or standardization analysis. Then, we detect the effect of GxE for each transferred phenotypic trait using novel proposed tests: testing the effect of an optimallyweighted combination of GxE (TOW-GE) and/or variable weight TOW-GE (VW-TOW-GE). Finally, we employ the Fisher’s combination test to combine the p-values of TOW-GE and/or VW-TOW-GE. Extensive simulation studies based on the Genetic Analysis Workshop 17 data show that the type I error rates of the proposed methods are well controlled. Compared to the existing interaction sequence kernel association test (ISKAT), TOW-GE is more powerful when there are only rare risk and protective variants; VW-TOW-GE is more powerful when there are both rare and common risk and protective variants. Both TOW-GE and VW-TOW-GE are robust to directions of effects of causal GxEs. Application to the COPDGene Study demonstrates that our proposed methods are very powerful.

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