scholarly journals Is there convergence of gut microbes in blood-feeding vertebrates?

2019 ◽  
Vol 374 (1777) ◽  
pp. 20180249 ◽  
Author(s):  
Se Jin Song ◽  
Jon G. Sanders ◽  
Daniel T. Baldassarre ◽  
Jaime A. Chaves ◽  
Nicholas S. Johnson ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Parallel Evolution ◽  
Blood Feeding ◽  
Metagenomic Data ◽  
Independent Contrasts ◽  
Theme Issue ◽  
Dietary Adaptation ◽  
The Poor ◽  
Genome Databases ◽  
Alternative Hypotheses

Animal microbiomes play an important role in dietary adaptation, yet the extent to which microbiome changes exhibit parallel evolution is unclear. Of particular interest is an adaptation to extreme diets, such as blood, which poses special challenges in its content of proteins and lack of essential nutrients. In this study, we assessed taxonomic signatures (by 16S rRNA amplicon profiling) and potential functional signatures (inferred by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt)) of haematophagy in birds and bats. Our goal was to test three alternative hypotheses: no convergence of microbiomes, convergence in taxonomy and convergence in function. We find a statistically significant effect of haematophagy in terms of microbial taxonomic convergence across the blood-feeding bats and birds, although this effect is small compared to the differences found between haematophagous and non-haematophagous species within the two host clades. We also find some evidence of convergence at the predicted functional level, although it is possible that the lack of metagenomic data and the poor representation of microbial lineages adapted to haematophagy in genome databases limit the power of this approach. The results provide a paradigm for exploring convergent microbiome evolution replicated with independent contrasts in different host lineages. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.

scholarly journals Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay

2018 ◽  
Vol 115 (5) ◽  
pp. 968-973 ◽  
Author(s):  
Bronwyn A. Lucas ◽  
Eitan Lavi ◽  
Lily Shiue ◽  
Hana Cho ◽  
Sol Katzman ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Regulatory Networks ◽  
Parallel Evolution ◽  
Orthologous Gene ◽  
Control Networks ◽  
Short Interspersed Elements ◽  
Gene Pairs ◽  
Sine Insertion ◽  
Rapid Divergence ◽  
Species Specific

Primate-specific Alu short interspersed elements (SINEs) as well as rodent-specific B and ID (B/ID) SINEs can promote Staufen-mediated decay (SMD) when present in mRNA 3′-untranslated regions (3′-UTRs). The transposable nature of SINEs, their presence in long noncoding RNAs, their interactions with Staufen, and their rapid divergence in different evolutionary lineages suggest they could have generated substantial modification of posttranscriptional gene-control networks during mammalian evolution. Some of the variation in SMD regulation produced by SINE insertion might have had a similar regulatory effect in separate mammalian lineages, leading to parallel evolution of the Staufen network by independent expansion of lineage-specific SINEs. To explore this possibility, we searched for orthologous gene pairs, each carrying a species-specific 3′-UTR SINE and each regulated by SMD, by measuring changes in mRNA abundance after individual depletion of two SMD factors, Staufen1 (STAU1) and UPF1, in both human and mouse myoblasts. We identified and confirmed orthologous gene pairs with 3′-UTR SINEs that independently function in SMD control of myoblast metabolism. Expanding to other species, we demonstrated that SINE-directed SMD likely emerged in both primate and rodent lineages >20–25 million years ago. Our work reveals a mechanism for the convergent evolution of posttranscriptional gene regulatory networks in mammals by species-specific SINE transposition and SMD.

scholarly journals A Metagenomic Analysis of Mosquito Virome Collected From Different Animal Farms at Yunnan–Myanmar Border of China

2021 ◽  
Vol 11 ◽  
Author(s):  
Muddassar Hameed ◽  
Abdul Wahaab ◽  
Tongling Shan ◽  
Xin Wang ◽  
Sawar Khan ◽  
...  
Keyword(s):  
Yunnan Province ◽  
Blood Feeding ◽  
Metagenomic Analysis ◽  
Metagenomic Data ◽  
Armigeres Subalbatus ◽  
Comprehensive Knowledge ◽  
Animal Farms ◽  
Veterinary Importance ◽  
Vertebrate Hosts ◽  
Generation Sequencing

Metagenomic analysis of mosquito-borne and mosquito-specific viruses is useful to understand the viral diversity and for the surveillance of pathogens of medical and veterinary importance. Yunnan province is located at the southwest of China and has rich abundance of mosquitoes. Arbovirus surveillance is not conducted regularly in this province particularly at animal farms, which have public health as well as veterinary importance. Here, we have analyzed 10 pools of mosquitoes belonging to Culex tritaeniorhyncus, Aedes aegypti, Anopheles sinensis, and Armigeres subalbatus species, collected from different animal farms located at Yunnan province of China by using metagenomic next-generation sequencing technique. The generated viral metagenomic data reveal that the viral community matched by the reads was highly diverse and varied in abundance among animal farms, which contained more than 19 viral taxonomic families, specific to vertebrates, invertebrates, fungi, plants, protozoa, and bacteria. Additionally, a large number of viral reads were related to viruses that are non-classified. The viral reads related to animal viruses included parvoviruses, anelloviruses, circoviruses, flaviviruses, rhabdoviruses, and seadornaviruses, which might be taken by mosquitoes from viremic animal hosts during blood feeding. Notably, the presence of viral reads matched with Japanese encephalitis virus, Getah virus, and porcine parvoviruses in mosquitoes collected from different geographic sites suggested a potential circulation of these viruses in their vertebrate hosts. Overall, this study provides a comprehensive knowledge of diverse viral populations present at animal farms of Yunnan province of China, which might be a potential source of diseases for humans and domestic animals.

scholarly journals Synchrony and rhythm interaction: from the brain to behavioural ecology

2021 ◽  
Vol 376 (1835) ◽  
pp. 20200324
Author(s):  
Michael D. Greenfield ◽  
Henkjan Honing ◽  
Sonja A. Kotz ◽  
Andrea Ravignani
Keyword(s):  
Convergent Evolution ◽  
Animal Communication ◽  
Empirical Work ◽  
Emergent Properties ◽  
Behavioural Ecology ◽  
Biological Clocks ◽  
Theme Issue ◽  
Coupled Oscillator ◽  
Wide Range ◽  
The Brain

This theme issue assembles current studies that ask how and why precise synchronization and related forms of rhythm interaction are expressed in a wide range of behaviour. The studies cover human activity, with an emphasis on music, and social behaviour, reproduction and communication in non-human animals. In most cases, the temporally aligned rhythms have short—from several seconds down to a fraction of a second—periods and are regulated by central nervous system pacemakers, but interactions involving rhythms that are 24 h or longer and originate in biological clocks also occur. Across this spectrum of activities, species and time scales, empirical work and modelling suggest that synchrony arises from a limited number of coupled-oscillator mechanisms with which individuals mutually entrain. Phylogenetic distribution of these common mechanisms points towards convergent evolution. Studies of animal communication indicate that many synchronous interactions between the signals of neighbouring individuals are specifically favoured by selection. However, synchronous displays are often emergent properties of entrainment between signalling individuals, and in some situations, the very signallers who produce a display might not gain any benefit from the collective timing of their production. This article is part of the theme issue ‘Synchrony and rhythm interaction: from the brain to behavioural ecology’.

scholarly journals Molecular convergent and parallel evolution among four high-elevation anuran species from the Tibetan region

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Bin Lu ◽  
Hong Jin ◽  
Jinzhong Fu
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Convergent Evolution ◽  
Parallel Evolution ◽  
Amino Acid Level ◽  
High Elevation ◽  
Acid Sites ◽  
Anuran Species ◽  
Close Relatives ◽  
Relative Prevalence

Abstract Background To date, evidence for the relative prevalence or rarity of molecular convergent and parallel evolution is conflicting, and understanding of how these processes contribute to adaptation is limited. We compared four high-elevation anuran species (Bufo tibetanus, Nanorana parkeri, Rana kukunoris and Scutiger boulengeri) from the Tibetan region, and examined convergent and parallel amino acid substitutions between them and how they may have contributed to high-elevation adaptation. Results Genomic data of the four high-elevation species and eight of their low-elevation close relatives were gathered. A total of 1098 orthologs shared by all species were identified. We first conducted pairwise comparisons using Zhang and Kumar’s test. Then, the Rconv index was calculated and convergence/divergence correlation plotting was conducted. Furthermore, genes under positive selection and with elevated evolutionary rate were examined. We detected a large number of amino acid sites with convergent or parallel substitutions. Several pairs of high-elevation species, in particular, R. kukunoris vs N. parkeri and B. tibetanus vs S. boulengeri, had excessive amounts of convergent substitutions compared to neutral expectation. Nevertheless, these sites were mostly concentrated in a small number of genes (3–32), and no genome-wide convergence was detected. Furthermore, the majority of these convergent genes were neither under detectable positive selection nor had elevated evolutionary rates, although functional prediction analysis suggested some of the convergent genes could potentially contribute to high-elevation adaptation. Conclusions There is a substantial amount of convergent evolution at the amino-acid level among high-elevation amphibians, although these sites are concentrated in a few genes, not widespread across the genomes. This may attribute to the fact that all the target species are from the same environment. The relative prevalence of convergent substitutions among high-elevation amphibians provides an excellent opportunity for further study of molecular convergent evolution.

scholarly journals Convergent evolution in human and domesticate adaptation to high-altitude environments

2019 ◽  
Vol 374 (1777) ◽  
pp. 20180235 ◽  
Author(s):  
Kelsey E. Witt ◽  
Emilia Huerta-Sánchez
Keyword(s):  
High Altitude ◽  
Convergent Evolution ◽  
Domestic Animal ◽  
Theme Issue ◽  
Adaptive Introgression ◽  
Selective Pressures ◽  
Animal Populations ◽  
Hypoxic Environment ◽  
Genomic Studies ◽  
Altitude Adaptation

Humans and their domestic animals have lived and thrived in high-altitude environments worldwide for thousands of years. These populations have developed a number of adaptations to survive in a hypoxic environment, and several genomic studies have been conducted to identify the genes that drive these adaptations. Here, we discuss the various adaptations and genetic variants that have been identified as adaptive in human and domestic animal populations and the ways in which convergent evolution has occurred as these populations have adapted to high-altitude environments. We found that human and domesticate populations have adapted to hypoxic environments in similar ways. Specific genes and biological pathways have been involved in high-altitude adaptation for multiple populations, although the specific variants differ between populations. Additionally, we found that the gene EPAS1 is often a target of selection in hypoxic environments and has been involved in multiple adaptive introgression events. High-altitude environments exert strong selective pressures, and human and animal populations have evolved in convergent ways to cope with a chronic lack of oxygen. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions'.

scholarly journals Phylogenetic origins of biological cognition: convergent patterns in the early evolution of learning

2017 ◽  
Vol 7 (3) ◽  
pp. 20160158 ◽  
Author(s):  
Marc van Duijn
Keyword(s):  
Nervous System ◽  
Classical Conditioning ◽  
Convergent Evolution ◽  
Parallel Evolution ◽  
Early Evolution ◽  
Learning Abilities ◽  
Nervous Systems ◽  
Multicellular Organisms ◽  
Basic Learning

Various forms of elementary learning have recently been discovered in organisms lacking a nervous system, such as protists, fungi and plants. This finding has fundamental implications for how we view the role of convergent evolution in biological cognition. In this article, I first review the evidence for basic forms of learning in aneural organisms, focusing particularly on habituation and classical conditioning and considering the plausibility for convergent evolution of these capacities. Next, I examine the possible role of convergent evolution regarding these basic learning abilities during the early evolution of nervous systems. The evolution of nervous systems set the stage for at least two major events relevant to convergent evolution that are central to biological cognition: (i) nervous systems evolved, perhaps more than once, because of strong selection pressures for sustaining sensorimotor strategies in increasingly larger multicellular organisms and (ii) associative learning was a subsequent adaptation that evolved multiple times within the neuralia. Although convergent evolution of basic forms of learning among distantly related organisms such as protists, plants and neuralia is highly plausible, more research is needed to verify whether these forms of learning within the neuralia arose through convergent or parallel evolution.

Constraints in cancer evolution

2017 ◽  
Vol 45 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Subramanian Venkatesan ◽  
Nicolai J. Birkbak ◽  
Charles Swanton
Keyword(s):  
Natural Selection ◽  
Genome Sequencing ◽  
Convergent Evolution ◽  
Parallel Evolution ◽  
Survival Outcomes ◽  
Next Generation ◽  
Cancer Evolution ◽  
Therapeutic Approaches ◽  
Biological Impact ◽  
Intratumour Heterogeneity

Next-generation deep genome sequencing has only recently allowed us to quantitatively dissect the extent of heterogeneity within a tumour, resolving patterns of cancer evolution. Intratumour heterogeneity and natural selection contribute to resistance to anticancer therapies in the advanced setting. Recent evidence has also revealed that cancer evolution might be constrained. In this review, we discuss the origins of intratumour heterogeneity and subsequently focus on constraints imposed upon cancer evolution. The presence of (1) parallel evolution, (2) convergent evolution and (3) the biological impact of acquiring mutations in specific orders suggest that cancer evolution may be exploitable. These constraints on cancer evolution may help us identify cancer evolutionary rule books, which could eventually inform both diagnostic and therapeutic approaches to improve survival outcomes.

scholarly journals Detecting adaptive convergent amino acid evolution

2019 ◽  
Vol 374 (1777) ◽  
pp. 20180234 ◽  
Author(s):  
Carine Rey ◽  
Vincent Lanore ◽  
Philippe Veber ◽  
Laurent Guéguen ◽  
Nicolas Lartillot ◽  
...  
Keyword(s):  
Amino Acid ◽  
Convergent Evolution ◽  
Evolutionary Genomics ◽  
Theme Issue ◽  
Coding Sequences ◽  
Difficult Question ◽  
Adaptive Processes ◽  
Definition Of

In evolutionary genomics, researchers have taken an interest in identifying substitutions that subtend convergent phenotypic adaptations. This is a difficult question that requires distinguishing foreground convergent substitutions that are involved in the convergent phenotype from background convergent substitutions. Those may be linked to other adaptations, may be neutral or may be the consequence of mutational biases. Furthermore, there is no generally accepted definition of convergent substitutions. Various methods that use different definitions have been proposed in the literature, resulting in different sets of candidate foreground convergent substitutions. In this article, we first describe the processes that can generate foreground convergent substitutions in coding sequences, separating adaptive from non-adaptive processes. Second, we review methods that have been proposed to detect foreground convergent substitutions in coding sequences and expose the assumptions that underlie them. Finally, we examine their power on simulations of convergent changes—including in the presence of a change in the efficacy of selection—and on empirical alignments. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions'.

A Multivariate View of Parallel Evolution

2020 ◽  
Author(s):  
Stephen P. De Lisle ◽  
Daniel I. Bolnick
Keyword(s):  
Convergent Evolution ◽  
Empirical Studies ◽  
Parallel Evolution ◽  
Covariance Matrices ◽  
Evolutionary Change ◽  
Multiple Traits ◽  
Eigen Analysis ◽  
Definition Of ◽  
Degree Of Convergence ◽  
Alternative Set

AbstractA growing number of empirical studies have quantified the degree to which evolution is geometrically parallel, by estimating and interpreting pairwise angles between evolutionary change vectors in multiple replicate lineages. Similar comparisons, of distance in trait space, are used to assess the degree of convergence. These approaches amount to element-by-element interpretation of distance matrices, and can fail to capture the true extent of multivariate parallelism when evolution involves multiple traits sampled across multiple lineages. We suggest an alternative set of approaches, co-opted from evolutionary quantitative genetics, involving eigen analysis and comparison of among-lineage covariance matrices. Such approaches not only allow the full extent of multivariate parallelism to be revealed and interpreted, but also allow for the definition of biologically tenable null hypotheses against which empirical patterns can be tested. Reanalysis of a dataset of multivariate evolution across a replicated lake/stream gradient in threespine stickleback reveals that most of the variation in the direction of evolutionary change can be captured in just a few dimensions, indicating a greater extent of parallelism than previously appreciated. We suggest that applying such multivariate approaches may often be necessary to fully understand the extent and form of parallel and convergent evolution.

scholarly journals Population genomics perspectives on convergent adaptation

2019 ◽  
Vol 374 (1777) ◽  
pp. 20180236 ◽  
Author(s):  
Kristin M. Lee ◽  
Graham Coop
Keyword(s):  
Gene Flow ◽  
Molecular Basis ◽  
Convergent Evolution ◽  
Population Genomics ◽  
Evolutionary Change ◽  
Theme Issue ◽  
Fitness Advantage ◽  
Standing Variation ◽  
Independent Replication ◽  
Genetics And Genomics

Convergent adaptation is the independent evolution of similar traits conferring a fitness advantage in two or more lineages. Cases of convergent adaptation inform our ideas about the ecological and molecular basis of adaptation. In judging the degree to which putative cases of convergent adaptation provide an independent replication of the process of adaptation, it is necessary to establish the degree to which the evolutionary change is unexpected under null models and to show that selection has repeatedly, independently driven these changes. Here, we discuss the issues that arise from these questions particularly for closely related populations, where gene flow and standing variation add additional layers of complexity. We outline a conceptual framework to guide intuition as to the extent to which evolutionary change represents the independent gain of information owing to selection and show that this is a measure of how surprised we should be by convergence. Additionally, we summarize the ways population and quantitative genetics and genomics may help us address questions related to convergent adaptation, as well as open new questions and avenues of research. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.

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