Mitonuclear interactions and introgression genomics of macaque monkeys ( Macaca ) highlight the influence of behaviour on genome evolution

2021 ◽  
Vol 288 (1960) ◽  
Author(s):  
Ben J. Evans ◽  
Benjamin M. Peter ◽  
Don J. Melnick ◽  
Noviar Andayani ◽  
Jatna Supriatna ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Indirect Effects ◽  
Genomic Data ◽  
Species Boundaries ◽  
Mitochondrial Genomes ◽  
Runs Of Homozygosity ◽  
Interaction Partners ◽  
Significant Enrichment ◽  
Compensatory Mutations ◽  
Multiple Species

In most macaques, females are philopatric and males migrate from their natal ranges, which results in pronounced divergence of mitochondrial genomes within and among species. We therefore predicted that some nuclear genes would have to acquire compensatory mutations to preserve compatibility with diverged interaction partners from the mitochondria. We additionally expected that these sex-differences would have distinctive effects on gene flow in the X and autosomes. Using new genomic data from 29 individuals from eight species of Southeast Asian macaque, we identified evidence of natural selection associated with mitonuclear interactions, including extreme outliers of interspecies differentiation and metrics of positive selection, low intraspecies polymorphism and atypically long runs of homozygosity associated with nuclear-encoded genes that interact with mitochondria-encoded genes. In one individual with introgressed mitochondria, we detected a small but significant enrichment of autosomal introgression blocks from the source species of her mitochondria that contained genes which interact with mitochondria-encoded loci. Our analyses also demonstrate that sex-specific demography sculpts genetic exchange across multiple species boundaries. These findings show that behaviour can have profound but indirect effects on genome evolution by influencing how interacting components of different genomic compartments (mitochondria, the autosomes and the sex chromosomes) move through time and space.

scholarly journals Crying wolf to a predator: deceptive vocal mimicry by a bird protecting young

2015 ◽  
Vol 282 (1809) ◽  
pp. 20150798 ◽  
Author(s):  
Branislav Igic ◽  
Jessica McLachlan ◽  
Inkeri Lehtinen ◽  
Robert D. Magrath
Keyword(s):  
Indirect Effects ◽  
Trophic Levels ◽  
Alarm Calls ◽  
Toxic Species ◽  
Vocal Mimicry ◽  
Primary Nest ◽  
Defence Strategy ◽  
Multiple Species ◽  
Defensive Mimicry ◽  
As If

Animals often mimic dangerous or toxic species to deter predators; however, mimicry of such species may not always be possible and mimicry of benign species seems unlikely to confer anti-predator benefits. We reveal a system in which a bird mimics the alarm calls of harmless species to fool a predator 40 times its size and protect its offspring against attack. Our experiments revealed that brown thornbills ( Acanthiza pusilla ) mimic a chorus of other species' aerial alarm calls, a cue of an Accipiter hawk in flight, when predators attack their nest. The absence of any flying predators in this context implies that these alarms convey deceptive information about the type of danger present. Experiments on the primary nest predators of thornbills, pied currawongs ( Strepera graculina ), revealed that the predators treat these alarms as if they themselves are threatened by flying hawks, either by scanning the sky for danger or fleeing, confirming a deceptive function. In turn, these distractions delay attack and provide thornbill nestlings with an opportunity to escape. This sophisticated defence strategy exploits the complex web of interactions among multiple species across several trophic levels, and in particular exploits a predator's ability to eavesdrop on and respond appropriately to heterospecific alarm calls. Our findings demonstrate that prey can fool predators by deceptively mimicking alarm calls of harmless species, suggesting that defensive mimicry could be more widespread because of indirect effects on predators within a web of eavesdropping.

scholarly journals Bridging the Gap between Vertebrate Cytogenetics and Genomics with Single-Chromosome Sequencing (ChromSeq)

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 124
Author(s):  
Alessio Iannucci ◽  
Alexey I. Makunin ◽  
Artem P. Lisachov ◽  
Claudio Ciofi ◽  
Roscoe Stanyon ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Karyotype Evolution ◽  
Genomic Data ◽  
Anolis Carolinensis ◽  
Vertebrate Genome ◽  
Single Chromosome ◽  
Sequencing Technologies ◽  
Novel Approaches ◽  
Genome Assemblies ◽  
Generation Sequencing

The study of vertebrate genome evolution is currently facing a revolution, brought about by next generation sequencing technologies that allow researchers to produce nearly complete and error-free genome assemblies. Novel approaches however do not always provide a direct link with information on vertebrate genome evolution gained from cytogenetic approaches. It is useful to preserve and link cytogenetic data with novel genomic discoveries. Sequencing of DNA from single isolated chromosomes (ChromSeq) is an elegant approach to determine the chromosome content and assign genome assemblies to chromosomes, thus bridging the gap between cytogenetics and genomics. The aim of this paper is to describe how ChromSeq can support the study of vertebrate genome evolution and how it can help link cytogenetic and genomic data. We show key examples of ChromSeq application in the refinement of vertebrate genome assemblies and in the study of vertebrate chromosome and karyotype evolution. We also provide a general overview of the approach and a concrete example of genome refinement using this method in the species Anolis carolinensis.

scholarly journals Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

2019 ◽  
Vol 67 (6) ◽  
pp. 1457-1463 ◽  
Author(s):  
Radovan Kasarda ◽  
Nina Moravčíková ◽  
Ondrej Kadlečík ◽  
Anna Trakovická ◽  
Marko Halo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quality Control ◽  
Genomic Analysis ◽  
Genomic Data ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Snp Markers ◽  
Runs Of Homozygosity ◽  
Current Generation ◽  
Genomic Inbreeding

The objective of this study was to analyse the level of pedigree and genomic inbreeding in a herd of the Norik of Muran horses. The pedigree file included 1374 animals (603 stallions and 771 mares), while the reference population consisted of animals that were genotyped by using 70k SNP platform (n = 25). The trend of pedigree inbreeding was expressed as the probability that an animal has two identical alleles by descent according to classical formulas. The trend of genomic inbreeding was derived from the distribution of runs of homozygosity (ROHs) with various length in the genome based on the assumption that these regions reflect the autozygosity originated from past generations of ancestors. A maximum of 19 generations was found in pedigree file. As expected, the highest level of pedigree completeness was found in first five generations. Subsequent quality control of genomic data resulted in totally 54432 SNP markers covering 2.242 Mb of the autosomal genome. The pedigree analysis showed that in current generation can be expected the pedigree inbreeding at level 0.23% (ΔFPEDi = 0.19 ± 1.17%). Comparable results was obtained also by the genomic analysis, when the inbreeding in current generation reached level 0.11%. Thus, in term of genetic diversity both analyses reflected sufficient level of variability across analysed population of Norik of Muran horses.

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 Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps

2020 ◽  
Author(s):  
Solomon T C Chak ◽  
Juan Antonio Baeza ◽  
Phillip Barden
Keyword(s):  
Molecular Evolution ◽  
Genome Evolution ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Mitochondrial Genomes ◽  
Comparative Genomic ◽  
Effective Population ◽  
Protein Coding ◽  
Marine Realm ◽  
Snapping Shrimps

Abstract Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm—lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits—extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.

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.

SIZE DISTRIBUTION OF GENE FAMILIES IN A GENOME

2014 ◽  
Vol 24 (04) ◽  
pp. 697-717 ◽  
Author(s):  
RYSZARD RUDNICKI ◽  
JERZY TIURYN
Keyword(s):  
Size Distribution ◽  
Genome Evolution ◽  
Gene Mutation ◽  
Probabilistic Model ◽  
Gene Loss ◽  
Genomic Data ◽  
Gene Families ◽  
Paralogous Gene ◽  
A Genome ◽  
Theoretical Results

We consider a probabilistic model of genome evolution. We are interested in size distribution of gene families. The model is based on three fundamental evolutionary events: gene loss, duplication and accumulated change. We assume that the probability of gene loss and duplication is constant and the probability of gene mutation mi depends on the size i of a family. We prove that size distribution of paralogous gene families in a genome converges to the equilibrium as time goes to infinity. Moreover, we show how this equilibrium depends on the sequence (mi). Theoretical results are compared with the available genomic data.

scholarly journals Fine-scale resolution and analysis of runs of homozygosity in domestic dogs

2018 ◽  
Author(s):  
Aaron J. Sams ◽  
Adam R. Boyko
Keyword(s):  
Inbreeding Depression ◽  
Genetic Architecture ◽  
Domestic Dogs ◽  
Selective Sweeps ◽  
Runs Of Homozygosity ◽  
Identical By Descent ◽  
Density Maps ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Significant Enrichment

Abstract/SummaryInbreeding and consanguinity leave distinct genomic traces, most notably long genomic tracts that are identical by descent and completely homozygous. These runs of homozygosity (ROH) can contribute to inbreeding depression if they contain deleterious variants that are fully or partially recessive. Several lines of evidence have been used to show that long (> 5 megabase (Mb)) ROH are disproportionately likely to harbor deleterious variation, but the extent to which long versus short tracts contribute to autozygosity at loci known to be deleterious and recessive has not been studied.In domestic dogs, nearly 200 mutations are known to cause recessive diseases, most of which can be efficiently assayed using SNP arrays. By examining genome-wide data from over 200,000 markers, including 150 recessive disease variants, we built high-resolution ROH density maps for nearly 2,500 dogs, recording ROH down to 500 kilobases. We observed over 500 homozygous deleterious recessive genotypes in the panel, 90% of which overlapped with ROH inferred by GERMLINE. Although most of these genotypes were contained in ROH over 5 Mb in length, 14% were contained in short (0.5 - 2.5 Mb) tracts, a significant enrichment compared to the genetic background, suggesting that even short tracts are useful for computing inbreeding metrics like the coefficient of inbreeding estimated from ROH (FROH).In our dataset, FROH differed significantly both within and among dog breeds. All breeds harbored some regions of reduced genetic diversity due to drift or selective sweeps, but the degree of inbreeding and the proportion of inbreeding caused by short versus long tracts differed between breeds, reflecting their different population histories. Although only available for a few species, large genome-wide datasets including recessive disease variants hold particular promise not only for disentangling the genetic architecture of inbreeding depression, but also evaluating and improving upon current approaches for detecting ROH.

scholarly journals Population genetics of Paramecium mitochondrial genomes: recombination, mutational spectrum, and efficacy of selection

2018 ◽  
Author(s):  
Parul Johri ◽  
Georgi K. Marinov ◽  
Thomas G. Doak ◽  
Michael Lynch
Keyword(s):  
Gc Content ◽  
Purifying Selection ◽  
Mitochondrial Genomes ◽  
Unique Combination ◽  
Protein Coding ◽  
Unicellular Eukaryotes ◽  
Population Genomic ◽  
Outgroup Species ◽  
Multiple Species ◽  
Mutation Spectra

ABSTRACTThe evolution of mitochondrial genomes and their population-genetic environment among unicellular eukaryotes are understudied. Ciliate mitochondrial genomes exhibit a unique combination of characteristics, including a linear organization and the presence of multiple genes with no known function or detectable homologs in other eukaryotes. Here we study the variation of ciliate mitochondrial genomes both within and across thirteen highly diverged Paramecium species, including multiple species from the P. aurelia species complex, with four outgroup species: P. caudatum, P. multimicronucleatum, and two strains that may represent novel related species. We observe extraordinary conservation of gene order and protein-coding content in Paramecium mitochondria across species. In contrast, significant differences are observed in tRNA content and copy number, which is highly conserved in species belonging to the P. aurelia complex but variable among and even within the other Paramecium species. There is an increase in GC content from ~20% to ~40% on the branch leading to the P. aurelia complex. Patterns of polymorphism in population-genomic data and mutation-accumulation experiments suggest that the increase in GC content is primarily due to changes in the mutation spectra in the P. aurelia species. Finally, we find no evidence of recombination in Paramecium mitochondria and find that the mitochondrial genome appears to experience either similar or stronger efficacy of purifying selection than the nucleus.

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