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Glover AN, Sousa VC, Ridenbaugh RD, Sim SB, Geib SM, Linnen CR. Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow. Mol Ecol 2024:e17509. [PMID: 39165007 DOI: 10.1111/mec.17509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/16/2024] [Accepted: 08/02/2024] [Indexed: 08/22/2024]
Abstract
Understanding the genetics of adaptation and speciation is critical for a complete picture of how biodiversity is generated and maintained. Heterogeneous genomic differentiation between diverging taxa is commonly documented, with genomic regions of high differentiation interpreted as resulting from differential gene flow, linked selection and reduced recombination rates. Disentangling the roles of each of these non-exclusive processes in shaping genome-wide patterns of divergence is challenging but will enhance our knowledge of the repeatability of genomic landscapes across taxa. Here, we combine whole-genome resequencing and genome feature data to investigate the processes shaping the genomic landscape of differentiation for a sister-species pair of haplodiploid pine sawflies, Neodiprion lecontei and Neodiprion pinetum. We find genome-wide correlations between genome features and summary statistics are consistent with pervasive linked selection, with patterns of diversity and divergence more consistently predicted by exon density and recombination rate than the neutral mutation rate (approximated by dS). We also find that both global and local patterns of FST, dXY and π provide strong support for recurrent selection as the primary selective process shaping variation across pine sawfly genomes, with some contribution from balancing selection and lineage-specific linked selection. Because inheritance patterns for haplodiploid genomes are analogous to those of sex chromosomes, we hypothesize that haplodiploids may be especially prone to recurrent selection, even if gene flow occurred throughout divergence. Overall, our study helps fill an important taxonomic gap in the genomic landscape literature and contributes to our understanding of the processes that shape genome-wide patterns of genetic variation.
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Affiliation(s)
- Ashleigh N Glover
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Vitor C Sousa
- Department of Animal Biology, CE3C - Center for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Lisbon, Lisboa, Portugal
| | - Ryan D Ridenbaugh
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Sheina B Sim
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, Hawaii, USA
| | - Scott M Geib
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, Hawaii, USA
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2
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Mulim HA, Pedrosa VB, Pinto LFB, Tiezzi F, Maltecca C, Schenkel FS, Brito LF. Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data. BMC Genomics 2024; 25:726. [PMID: 39060982 PMCID: PMC11282608 DOI: 10.1186/s12864-024-10642-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND A heterozygous-enriched region (HER) is a genomic region with high variability generated by factors such as balancing selection, introgression, and admixture processes. In this study, we evaluated the genomic background of HERs and the impact of different parameters (i.e., minimum number of SNPs in a HER, maximum distance between two consecutive SNPs, minimum length of a HER, maximum number of homozygous allowed in a HER) and scenarios [i.e., different SNP panel densities and whole-genome sequence (WGS)] on the detection of HERs. We also compared HERs characterized in Holstein cattle with those identified in Angus, Jersey, and Norwegian Red cattle using WGS data. RESULTS The parameters used for the identification of HERs significantly impact their detection. The maximum distance between two consecutive SNPs did not impact HERs detection as the same average of HERs (269.31 ± 787.00) was observed across scenarios. However, the minimum number of markers, maximum homozygous markers allowed inside a HER, and the minimum length size impacted HERs detection. For the minimum length size, the 10 Kb scenario showed the highest average number of HERs (1,364.69 ± 1,483.64). The number of HERs decreased as the minimum number of markers increased (621.31 ± 1,271.83 to 6.08 ± 21.94), and an opposite pattern was observed for the maximum homozygous markers allowed inside a HER (54.47 ± 195.51 to 494.89 ± 1,169.35). Forty-five HER islands located in 23 chromosomes with high Tajima's D values and differential among the observed and estimated heterozygosity were detected in all evaluated scenarios, indicating their ability to potentially detect regions under balancing selection. In total, 3,440 markers and 28 genes previously related to fertility (e.g., TP63, ZSCAN23, NEK5, ARHGAP44), immunity (e.g., TP63, IGC, ARHGAP44), residual feed intake (e.g., MAYO9A), stress sensitivity (e.g., SERPINA6), and milk fat percentage (e.g., NOL4) were identified. When comparing HER islands among breeds, there were substantial overlaps between Holstein with Angus (95.3%), Jersey (94.3%), and Norwegian Red cattle (97.1%), indicating conserved HER across taurine breeds. CONCLUSIONS The detection of HERs varied according to the parameters used, but some HERs were consistently identified across all scenarios. Heterozygous genotypes observed across generations and breeds appear to be conserved in HERs. The results presented could serve as a guide for defining HERs detection parameters and further investigating their biological roles in future studies.
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Affiliation(s)
- Henrique A Mulim
- Department of Animal Sciences, Federal University of Bahia, Salvador, Bahia, 40110-909, Brazil.
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, 47907, USA.
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, Parana, 84010-330, Brazil
| | | | - Francesco Tiezzi
- Department of Agriculture, Food, Environment and Forestry, University of Florence, 50121, Florence, Italy
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Ontario, N1G 2W1, Canada
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, 47907, USA.
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3
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De Gasperin O, Blacher P, Sarton-Lohéac S, Grasso G, Corliss MK, Nicole S, Chérasse S, Aron S, Chapuisat M. A supergene-controlling social structure in Alpine ants also affects the dispersal ability and fecundity of each sex. Proc Biol Sci 2024; 291:20240494. [PMID: 38864332 DOI: 10.1098/rspb.2024.0494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/18/2024] [Indexed: 06/13/2024] Open
Abstract
Social organization, dispersal and fecundity coevolve, but whether they are genetically linked remains little known. Supergenes are prime candidates for coupling adaptive traits and mediating sex-specific trade-offs. Here, we test whether a supergene that controls social structure in Formica selysi also influences dispersal-related traits and fecundity within each sex. In this ant species, single-queen colonies contain only the ancestral supergene haplotype M and produce MM queens and M males, while multi-queen colonies contain the derived haplotype P and produce MP queens, PP queens and P males. By combining multiple experiments, we show that the M haplotype induces phenotypes with higher dispersal potential and higher fecundity in both sexes. Specifically, MM queens, MP queens and M males are more aerodynamic and more fecund than PP queens and P males, respectively. Differences between MP and PP queens from the same colonies reveal a direct genetic effect of the supergene on dispersal-related traits and fecundity. The derived haplotype P, associated with multi-queen colonies, produces queens and males with reduced dispersal abilities and lower fecundity. More broadly, similarities between the Formica and Solenopsis systems reveal that supergenes play a major role in linking behavioural, morphological and physiological traits associated with intraspecific social polymorphisms.
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Affiliation(s)
- Ornela De Gasperin
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
- Red de Ecoetología, Instituto de Ecología, A. C. , Xalapa, Veracruz 91073, Mexico
| | - Pierre Blacher
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
| | - Solenn Sarton-Lohéac
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
| | - Guglielmo Grasso
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
- University of Manchester , Manchester M13 9PL, UK
| | - Mia Kotur Corliss
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
| | - Sidonie Nicole
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
| | | | - Serge Aron
- Universite libre de Bruxelles , Brussels 1050, Belgium
| | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
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4
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Glaser-Schmitt A, Ramnarine TJS, Parsch J. Rapid evolutionary change, constraints and the maintenance of polymorphism in natural populations of Drosophila melanogaster. Mol Ecol 2024; 33:e17024. [PMID: 37222070 DOI: 10.1111/mec.17024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/25/2023]
Abstract
Allele frequencies can shift rapidly within natural populations. Under certain conditions, repeated rapid allele frequency shifts can lead to the long-term maintenance of polymorphism. In recent years, studies of the model insect Drosophila melanogaster have suggested that this phenomenon is more common than previously believed and is often driven by some form of balancing selection, such as temporally fluctuating or sexually antagonistic selection. Here we discuss some of the general insights into rapid evolutionary change revealed by large-scale population genomic studies, as well as the functional and mechanistic causes of rapid adaptation uncovered by single-gene studies. As an example of the latter, we consider a regulatory polymorphism of the D. melanogaster fezzik gene. Polymorphism at this site has been maintained at intermediate frequency over an extended period of time. Regular observations from a single population over a period of 7 years revealed significant differences in the frequency of the derived allele and its variance across collections between the sexes. These patterns are highly unlikely to arise from genetic drift alone or from the action of sexually antagonistic or temporally fluctuating selection individually. Instead, the joint action of sexually antagonistic and temporally fluctuating selection can best explain the observed rapid and repeated allele frequency shifts. Temporal studies such as those reviewed here further our understanding of how rapid changes in selection can lead to the long-term maintenance of polymorphism as well as improve our knowledge of the forces driving and limiting adaptation in nature.
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Affiliation(s)
- Amanda Glaser-Schmitt
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Timothy J S Ramnarine
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
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5
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Herrick J. DNA Damage, Genome Stability, and Adaptation: A Question of Chance or Necessity? Genes (Basel) 2024; 15:520. [PMID: 38674454 PMCID: PMC11049855 DOI: 10.3390/genes15040520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/14/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
DNA damage causes the mutations that are the principal source of genetic variation. DNA damage detection and repair mechanisms therefore play a determining role in generating the genetic diversity on which natural selection acts. Speciation, it is commonly assumed, occurs at a rate set by the level of standing allelic diversity in a population. The process of speciation is driven by a combination of two evolutionary forces: genetic drift and ecological selection. Genetic drift takes place under the conditions of relaxed selection, and results in a balance between the rates of mutation and the rates of genetic substitution. These two processes, drift and selection, are necessarily mediated by a variety of mechanisms guaranteeing genome stability in any given species. One of the outstanding questions in evolutionary biology concerns the origin of the widely varying phylogenetic distribution of biodiversity across the Tree of Life and how the forces of drift and selection contribute to shaping that distribution. The following examines some of the molecular mechanisms underlying genome stability and the adaptive radiations that are associated with biodiversity and the widely varying species richness and evenness in the different eukaryotic lineages.
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Affiliation(s)
- John Herrick
- Independent Researcher at 3, Rue des Jeûneurs, 75002 Paris, France
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6
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Häfker NS, Holcik L, Mat AM, Ćorić A, Vadiwala K, Beets I, Stockinger AW, Atria CE, Hammer S, Revilla-i-Domingo R, Schoofs L, Raible F, Tessmar-Raible K. Molecular circadian rhythms are robust in marine annelids lacking rhythmic behavior. PLoS Biol 2024; 22:e3002572. [PMID: 38603542 PMCID: PMC11008795 DOI: 10.1371/journal.pbio.3002572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/29/2024] [Indexed: 04/13/2024] Open
Abstract
The circadian clock controls behavior and metabolism in various organisms. However, the exact timing and strength of rhythmic phenotypes can vary significantly between individuals of the same species. This is highly relevant for rhythmically complex marine environments where organismal rhythmic diversity likely permits the occupation of different microenvironments. When investigating circadian locomotor behavior of Platynereis dumerilii, a model system for marine molecular chronobiology, we found strain-specific, high variability between individual worms. The individual patterns were maintained for several weeks. A diel head transcriptome comparison of behaviorally rhythmic versus arrhythmic wild-type worms showed that 24-h cycling of core circadian clock transcripts is identical between both behavioral phenotypes. While behaviorally arrhythmic worms showed a similar total number of cycling transcripts compared to their behaviorally rhythmic counterparts, the annotation categories of their transcripts, however, differed substantially. Consistent with their locomotor phenotype, behaviorally rhythmic worms exhibit an enrichment of cycling transcripts related to neuronal/behavioral processes. In contrast, behaviorally arrhythmic worms showed significantly increased diel cycling for metabolism- and physiology-related transcripts. The prominent role of the neuropeptide pigment-dispersing factor (PDF) in Drosophila circadian behavior prompted us to test for a possible functional involvement of Platynereis pdf. Differing from its role in Drosophila, loss of pdf impacts overall activity levels but shows only indirect effects on rhythmicity. Our results show that individuals arrhythmic in a given process can show increased rhythmicity in others. Across the Platynereis population, rhythmic phenotypes exist as a continuum, with no distinct "boundaries" between rhythmicity and arrhythmicity. We suggest that such diel rhythm breadth is an important biodiversity resource enabling the species to quickly adapt to heterogeneous or changing marine environments. In times of massive sequencing, our work also emphasizes the importance of time series and functional tests.
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Affiliation(s)
- N. Sören Häfker
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Laurenz Holcik
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Audrey M. Mat
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Aida Ćorić
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Karim Vadiwala
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Isabel Beets
- Division of animal Physiology and Neurobiology, KU Leuven, Leuven, Belgium
| | - Alexander W. Stockinger
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Carolina E. Atria
- Department of Neuro- and Developmental Biology, University of Vienna, Vienna, Austria
- Research Platform Single-Cell Regulation of Stem Cells, University of Vienna, Vienna, Austria
| | - Stefan Hammer
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Roger Revilla-i-Domingo
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Department of Neuro- and Developmental Biology, University of Vienna, Vienna, Austria
- Research Platform Single-Cell Regulation of Stem Cells, University of Vienna, Vienna, Austria
| | - Liliane Schoofs
- Division of animal Physiology and Neurobiology, KU Leuven, Leuven, Belgium
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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7
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Jay P, Aubier TG, Joron M. The interplay of local adaptation and gene flow may lead to the formation of supergenes. Mol Ecol 2024:e17297. [PMID: 38415327 DOI: 10.1111/mec.17297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/28/2023] [Accepted: 01/10/2024] [Indexed: 02/29/2024]
Abstract
Supergenes are genetic architectures resulting in the segregation of alternative combinations of alleles underlying complex phenotypes. The co-segregation of alleles at linked loci is often facilitated by polymorphic chromosomal rearrangements suppressing recombination locally. Supergenes are involved in many complex polymorphisms, including sexual, colour or behavioural polymorphisms in numerous plants, fungi, mammals, fish, and insects. Despite a long history of empirical and theoretical research, the formation of supergenes remains poorly understood. Here, using a two-island population genetic model, we explore how gene flow and the evolution of overdominant chromosomal inversions may jointly lead to the formation of supergenes. We show that the evolution of inversions in differentiated populations, both under disruptive selection, leads to an increase in frequency of poorly adapted, immigrant haplotypes. Indeed, rare allelic combinations, such as immigrant haplotypes, are more frequently reshuffled by recombination than common allelic combinations, and therefore benefit from the recombination suppression generated by inversions. When an inversion capturing a locally adapted haplotype spreads but is associated with a fitness cost hampering its fixation (e.g. a recessive mutation load), the maintenance of a non-inverted haplotype in the population is enhanced; under certain conditions, the immigrant haplotype persists alongside the inverted local haplotype, while the standard local haplotype disappears. This establishes a stable, local polymorphism with two non-recombining haplotypes encoding alternative adaptive strategies, that is, a supergene. These results bring new light to the importance of local adaptation, overdominance, and gene flow in the formation of supergenes and inversion polymorphisms in general.
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Affiliation(s)
- Paul Jay
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Thomas G Aubier
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, France
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
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8
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Meyer L, Barry P, Riquet F, Foote A, Der Sarkissian C, Cunha RL, Arbiol C, Cerqueira F, Desmarais E, Bordes A, Bierne N, Guinand B, Gagnaire PA. Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long-snouted seahorse. Mol Ecol 2024:e17277. [PMID: 38279695 DOI: 10.1111/mec.17277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/18/2023] [Accepted: 01/04/2024] [Indexed: 01/28/2024]
Abstract
Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion polymorphisms arise, how they are maintained over the long term, and ultimately, whether and how they contribute to speciation. The long-snouted seahorse (Hippocampus guttulatus) is genetically subdivided into geographic lineages and marine-lagoon ecotypes, with shared structural variation underlying lineage and ecotype divergence. Here, we aim to characterize structural variants and to reconstruct their history and suspected role in ecotype formation. We generated a near chromosome-level genome assembly and described genome-wide patterns of diversity and divergence through the analysis of 112 whole-genome sequences from Atlantic, Mediterranean, and Black Sea populations. By also analysing linked-read sequencing data, we found evidence for two chromosomal inversions that were several megabases in length and showed contrasting allele frequency patterns between lineages and ecotypes across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one likely being maintained by divergent selection and the other by pseudo-overdominance. A possible selective coupling between the two inversions was further supported by the absence of specific haplotype combinations and a putative functional interaction between the two inversions in reproduction. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels for the two inversions, with a likely impact on their dynamics and contribution to divergence and speciation.
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Affiliation(s)
- Laura Meyer
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Pierre Barry
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto, Vairão, Portugal
| | | | - Andrew Foote
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Clio Der Sarkissian
- Centre for Anthropobiology and Genomics of Toulouse, CNRS, University of Toulouse Paul Sabatier, Toulouse, France
| | - Regina L Cunha
- Centre of Marine Sciences-CCMAR, University of Algarve, Faro, Portugal
| | | | | | - Erick Desmarais
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Anaïs Bordes
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Bruno Guinand
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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9
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Richard-St-Hilaire A, Gamache I, Pelletier J, Grenier JC, Poujol R, Hussin JG. Signatures of Co-evolution and Co-regulation in the CYP3A and CYP4F Genes in Humans. Genome Biol Evol 2024; 16:evad236. [PMID: 38207129 PMCID: PMC10805436 DOI: 10.1093/gbe/evad236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024] Open
Abstract
Cytochromes P450 (CYP450) are hemoproteins generally involved in the detoxification of the body of xenobiotic molecules. They participate in the metabolism of many drugs and genetic polymorphisms in humans have been found to impact drug responses and metabolic functions. In this study, we investigate the genetic diversity of CYP450 genes. We found that two clusters, CYP3A and CYP4F, are notably differentiated across human populations with evidence for selective pressures acting on both clusters: we found signals of recent positive selection in CYP3A and CYP4F genes and signals of balancing selection in CYP4F genes. Furthermore, an extensive amount of unusual linkage disequilibrium is detected in this latter cluster, indicating co-evolution signatures among CYP4F genes. Several of the selective signals uncovered co-localize with expression quantitative trait loci (eQTL), which could suggest epistasis acting on co-regulation in these gene families. In particular, we detected a potential co-regulation event between CYP3A5 and CYP3A43, a gene whose function remains poorly characterized. We further identified a causal relationship between CYP3A5 expression and reticulocyte count through Mendelian randomization analyses, potentially involving a regulatory region displaying a selective signal specific to African populations. Our findings linking natural selection and gene expression in CYP3A and CYP4F subfamilies are of importance in understanding population differences in metabolism of nutrients and drugs.
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Affiliation(s)
- Alex Richard-St-Hilaire
- Département de biochimie et médecine moléculaire, Université de Montréal, Montreal, QC, Canada
- Sainte-Justine Hospital, Research Center, Montreal, QC, Canada
| | - Isabel Gamache
- Département de biochimie et médecine moléculaire, Université de Montréal, Montreal, QC, Canada
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Justin Pelletier
- Département de biochimie et médecine moléculaire, Université de Montréal, Montreal, QC, Canada
- McGill CERC in Genomic Medicine, McGill University, Montreal, Canada
| | | | - Raphaël Poujol
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Julie G Hussin
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
- Département de médecine, Université de Montréal, Montreal, QC, Canada
- Mila-Quebec AI institute, Montreal, QC, Canada
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10
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Wellenreuther M. Environmental change unlinks a gene from its trait. Mol Ecol 2024; 33:e17254. [PMID: 38146910 DOI: 10.1111/mec.17254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
In Atlantic salmon (Salmo salar), sea age is a major life history trait governed by a sex-specific trade-off between reproductive success and survival. In this issue of Molecular Ecology, Besnier et al. (Molecular Ecology, 2023) found evidence to suggest that the disassociation between sea age and major effect loci, including the previously identified candidate genes vgll3 and six6, may be related to the recently observed trend towards slower growth and later maturation. These results are of importance because they challenge the prevailing view that evolution moves in a slow shuffle, and they provide a pertinent example of how an optimal phenotype can change due to growth-driven plasticity and lead to contemporary molecular and phenotypic evolution.
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Affiliation(s)
- Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd, Nelson, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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11
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Busoms S, Fischer S, Yant L. Chasing the mechanisms of ecologically adaptive salinity tolerance. PLANT COMMUNICATIONS 2023; 4:100571. [PMID: 36883005 PMCID: PMC10721451 DOI: 10.1016/j.xplc.2023.100571] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/12/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Plants adapted to challenging environments offer fascinating models of evolutionary change. Importantly, they also give information to meet our pressing need to develop resilient, low-input crops. With mounting environmental fluctuation-including temperature, rainfall, and soil salinity and degradation-this is more urgent than ever. Happily, solutions are hiding in plain sight: the adaptive mechanisms from natural adapted populations, once understood, can then be leveraged. Much recent insight has come from the study of salinity, a widespread factor limiting productivity, with estimates of 20% of all cultivated lands affected. This is an expanding problem, given increasing climate volatility, rising sea levels, and poor irrigation practices. We therefore highlight recent benchmark studies of ecologically adaptive salt tolerance in plants, assessing macro- and microevolutionary mechanisms, and the recently recognized role of ploidy and the microbiome on salinity adaptation. We synthesize insight specifically on naturally evolved adaptive salt-tolerance mechanisms, as these works move substantially beyond traditional mutant or knockout studies, to show how evolution can nimbly "tweak" plant physiology to optimize function. We then point to future directions to advance this field that intersect evolutionary biology, abiotic-stress tolerance, breeding, and molecular plant physiology.
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Affiliation(s)
- Silvia Busoms
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Bellaterra, Barcelona E-08193, Spain
| | - Sina Fischer
- Future Food Beacon of Excellence, University of Nottingham, Nottingham NG7 2RD, UK; School of Biosciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Levi Yant
- Future Food Beacon of Excellence, University of Nottingham, Nottingham NG7 2RD, UK; School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
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12
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Llaurens V. A colourful duplication. eLife 2023; 12:e92763. [PMID: 37917141 PMCID: PMC10622141 DOI: 10.7554/elife.92763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
A genetic duplication event during evolution allowed male wood tiger moths to have either yellow or white patterns on their wings.
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Affiliation(s)
- Violaine Llaurens
- Centre national de la recherche scientifique (CNRS)ParisFrance
- Muséum national d'Histoire naturelleParisFrance
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13
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Santos WB, Pereira CB, Maiorano AM, Arce CDS, Baldassini WA, Pereira GL, Chardulo LAL, Neto ORM, Oliveira HN, Curi RA. Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line. J Anim Breed Genet 2023; 140:583-595. [PMID: 37282810 DOI: 10.1111/jbg.12812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 03/30/2023] [Accepted: 05/28/2023] [Indexed: 06/08/2023]
Abstract
With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (FROH ), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, and to map selection signatures in relevant chromosomal regions in the Quarter Horse racing line. A total of 336 animals registered with the Brazilian Association of Quarter Horse Breeders (ABQM) were genotyped. One hundred and twelve animals were genotyped using the Equine SNP50 BeadChip (Illumina, USA), with 54,602 single nucleotide polymorphisms (SNPs; 54K). The remaining 224 samples were genotyped using the Equine SNP70 BeadChip (Illumina, USA) with 65,157 SNPs (65K). To ensure data quality, we excluded animals with a call rate below 0.9. We also excluded SNPs located on non-autosomal chromosomes, as well as those with a call rate below 0.9 or a p-value below 1 × 10-5 for Hardy-Weinberg equilibrium. The results indicate moderate to high genomic inbreeding, with 46,594 ROH and 16,101 ROHet detected. In total, 30 and 14 candidate genes overlap with ROH and ROHet regions, respectively. The ROH islands showed genes linked to crucial biological processes, such as cell differentiation (CTBP1, WNT5B, and TMEM120B), regulation of glucose metabolic process (MAEA and NKX1-1), heme transport (PGRMC2), and negative regulation of calcium ion import (VDAC1). In ROHet, the islands showed genes related to respiratory capacity (OR7D19, OR7D4G, OR7D4E, and OR7D4J) and muscle repair (EGFR and BCL9). These findings could aid in selecting animals with greater regenerative capacity and developing treatments for muscle disorders in the QH breed. This study serves as a foundation for future research on equine breeds. It can contribute to developing reproductive strategies in animal breeding programs to improve and preserve the Quarter Horse breed.
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Affiliation(s)
- Wellington B Santos
- Department of Animal Science, São Paulo State University, Jaboticabal, Brazil
| | - Camila B Pereira
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Amanda M Maiorano
- Department of Animal Science, Federal University of Uberlândia, Uberlândia, Brazil
| | | | - Welder A Baldassini
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Guilherme L Pereira
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Luis Artur L Chardulo
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Otávio R M Neto
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Henrique N Oliveira
- Department of Animal Science, São Paulo State University, Jaboticabal, Brazil
| | - Rogério A Curi
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
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14
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Tong X, Chen D, Hu J, Lin S, Ling Z, Ai H, Zhang Z, Huang L. Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences. Nat Commun 2023; 14:5126. [PMID: 37612277 PMCID: PMC10447580 DOI: 10.1038/s41467-023-40434-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/27/2023] [Indexed: 08/25/2023] Open
Abstract
High-quality whole-genome resequencing in large-scale pig populations with pedigree structure and multiple breeds would enable accurate construction of haplotype and robust selection-signature detection. Here, we sequence 740 pigs, combine with 149 of our previously published resequencing data, retrieve 207 resequencing datasets, and form a panel of worldwide distributed wild boars, aboriginal and highly selected pigs with pedigree structures, amounting to 1096 genomes from 43 breeds. Combining with their haplotype-informative reads and pedigree structure, we accurately construct a panel of 1874 haploid genomes with 41,964,356 genetic variants. We further demonstrate its valuable applications in GWAS by identifying five novel loci for intramuscular fat content, and in genomic selection by increasing the accuracy of estimated breeding value by 36.7%. In evolutionary selection, we detect MUC13 gene under a long-term balancing selection, as well as NPR3 gene under positive selection for pig stature. Our study provides abundant genomic variations for robust selection-signature detection and accurate haplotypes for deciphering complex traits in pigs.
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Affiliation(s)
- Xinkai Tong
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China
- College of Life Sciences, Jiangxi Normal University, NanChang, Jiangxi Province, PR China
| | - Dong Chen
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China
| | - Jianchao Hu
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China
| | - Shiyao Lin
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China
| | - Ziqi Ling
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China
| | - Huashui Ai
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China
| | - Zhiyan Zhang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China.
| | - Lusheng Huang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China.
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15
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Coupé S, Giantsis IA, Vázquez Luis M, Scarpa F, Foulquié M, Prévot J, Casu M, Lattos A, Michaelidis B, Sanna D, García‐March JR, Tena‐Medialdea J, Vicente N, Bunet R. The characterization of toll-like receptor repertoire in Pinna nobilis after mass mortality events suggests adaptive introgression. Ecol Evol 2023; 13:e10383. [PMID: 37546570 PMCID: PMC10401143 DOI: 10.1002/ece3.10383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 08/08/2023] Open
Abstract
The fan mussel Pinna nobilis is currently on the brink of extinction due to a multifactorial disease mainly caused to the highly pathogenic parasite Haplosporidium pinnae, meaning that the selection pressure outweighs the adaptive potential of the species. Hopefully, rare individuals have been observed somehow resistant to the parasite, stretching the need to identify the traits underlying this better fitness. Among the candidate to explore at first intention are fast-evolving immune genes, of which toll-like receptor (TLR). In this study, we examined the genetic diversity at 14 TLR loci across P. nobilis, Pinna rudis and P. nobilis × P. rudis hybrid genomes, collected at four physically distant regions, that were found to be either resistant or sensitive to the parasite H. pinnae. We report a high genetic diversity, mainly observed at cell surface TLRs compared with that of endosomal TLRs. However, the endosomal TLR-7 exhibited unexpected level of diversity and haplotype phylogeny. The lack of population structure, associated with a high genetic diversity and elevated dN/dS ratio, was interpreted as balancing selection, though both directional and purifying selection were detected. Interestingly, roughly 40% of the P. nobilis identified as resistant to H. pinnae were introgressed with P. rudis TLR. Specifically, they all carried a TLR-7 of P. rudis origin, whereas sensitive P. nobilis were not introgressed, at least at TLR loci. Small contributions of TLR-6 and TLR-4 single-nucleotide polymorphisms to the clustering of resistant and susceptible individuals could be detected, but their specific role in resistance remains highly speculative. This study provides new information on the diversity of TLR genes within the P. nobilis species after MME and additional insights into adaptation to H. pinnae that should contribute to the conservation of this Mediterranean endemic species.
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Affiliation(s)
- Stéphane Coupé
- Université de Toulon, Aix Marseille Univ, CNRS, IRD, MIOMarseilleFrance
| | | | - Maite Vázquez Luis
- Instituto Español de Oceanografía (IEO, CSIC), Centro Oceanográfico de BalearesPalma de MallorcaSpain
| | - Fabio Scarpa
- Department of Biomedical SciencesFabio Scarpa, Daria Sanna: University of SassariSassariItaly
| | - Mathieu Foulquié
- Université de Toulon, Aix Marseille Univ, CNRS, IRD, MIOMarseilleFrance
- Institut océanographique Paul RicardIle des Embiez, VarFrance
| | | | - Marco Casu
- Department of Veterinary MedicineUniversity of SassariSassariItaly
| | - Athanasios Lattos
- Faculty of Agricultural SciencesUniversity of Western MacedoniaKozaniGreece
| | - Basile Michaelidis
- Faculty of Agricultural SciencesUniversity of Western MacedoniaKozaniGreece
| | - Daria Sanna
- Department of Biomedical SciencesFabio Scarpa, Daria Sanna: University of SassariSassariItaly
| | - José Rafa García‐March
- IMEDMAR‐UCV, Institute of Environment and Marine Science ResearchUniversidad Católica de Valencia SVMCalpe, AlicanteSpain
| | - José Tena‐Medialdea
- IMEDMAR‐UCV, Institute of Environment and Marine Science ResearchUniversidad Católica de Valencia SVMCalpe, AlicanteSpain
| | - Nardo Vicente
- Institut Méditerranéen de Biodiversité et Ecologie marine et continentale (IMBE), Aix‐Marseille Université, CNRS, IRD, Avignon UniversitéAvignonFrance
| | - Robert Bunet
- Institut océanographique Paul RicardIle des Embiez, VarFrance
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16
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Guo L, Wang X, Wang R, Li P. Characterization and Comparative Analysis of Chloroplast Genomes of Medicinal Herb Scrophularia ningpoensis and Its Common Adulterants (Scrophulariaceae). Int J Mol Sci 2023; 24:10034. [PMID: 37373180 DOI: 10.3390/ijms241210034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Scrophularia ningpoensis, a perennial medicinal plant from the Scrophulariaceae family, is the original species of Scrophulariae Radix (SR) in the Chinese Pharmacopoeia. This medicine is usually deliberately substituted or accidentally contaminated with other closely related species including S. kakudensis, S. buergeriana, and S. yoshimurae. Given the ambiguous identification of germplasm and complex evolutionary relationships within the genus, the complete chloroplast genomes of the four mentioned Scrophularia species were sequenced and characterized. Comparative genomic studies revealed a high degree of conservation in genomic structure, gene arrangement, and content within the species, with the entire chloroplast genome spanning 153,016-153,631 bp in full length, encoding 132 genes, including 80 protein-coding genes, 4 rRNA genes, 30 tRNA genes, and 18 duplicated genes. We identified 8 highly variable plastid regions and 39-44 SSRs as potential molecular markers for further species identification in the genus. The consistent and robust phylogenetic relationships of S. ningpoensis and its common adulterants were firstly established using a total of 28 plastid genomes from the Scrophulariaceae family. In the monophyletic group, S. kakudensis was determined to be the earliest diverging species, succeeded by S. ningpoensis. Meanwhile, S. yoshimurae and S. buergeriana were clustered together as sister clades. Our research manifestly illustrates the efficacy of plastid genomes in identifying S. ningpoensis and its counterfeits and will also contribute to a deeper understanding of the evolutionary processes within Scrophularia.
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Affiliation(s)
- Lei Guo
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xia Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Ruihong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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17
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Tunström K, Woronik A, Hanly JJ, Rastas P, Chichvarkhin A, Warren AD, Kawahara AY, Schoville SD, Ficarrotta V, Porter AH, Watt WB, Martin A, Wheat CW. Evidence for a single, ancient origin of a genus-wide alternative life history strategy. SCIENCE ADVANCES 2023; 9:eabq3713. [PMID: 36947619 PMCID: PMC10032607 DOI: 10.1126/sciadv.abq3713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Understanding the evolutionary origins and factors maintaining alternative life history strategies (ALHS) within species is a major goal of evolutionary research. While alternative alleles causing discrete ALHS are expected to purge or fix over time, one-third of the ~90 species of Colias butterflies are polymorphic for a female-limited ALHS called Alba. Whether Alba arose once, evolved in parallel, or has been exchanged among taxa is currently unknown. Using comparative genome-wide association study (GWAS) and population genomic analyses, we placed the genetic basis of Alba in time-calibrated phylogenomic framework, revealing that Alba evolved once near the base of the genus and has been subsequently maintained via introgression and balancing selection. CRISPR-Cas9 mutagenesis was then used to verify a putative cis-regulatory region of Alba, which we identified using phylogenetic foot printing. We hypothesize that this cis-regulatory region acts as a modular enhancer for the induction of the Alba ALHS, which has likely facilitated its long evolutionary persistence.
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Affiliation(s)
- Kalle Tunström
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Alyssa Woronik
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Biology, Sacred Heart University, Fairfield, CT, USA
| | - Joseph J. Hanly
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Anton Chichvarkhin
- National Scientific Center of Marine Biology, Far Eastern Branch of Russian Academy of Sciences, Palchevskogo 17, Vladivostok 690022, Russia
| | - Andrew D. Warren
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Sean D. Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Vincent Ficarrotta
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Adam H. Porter
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Ward B. Watt
- Department of Biology, University of South Carolina, Columbia, SC 29208, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO 81224, USA
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
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18
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Chapuisat M. Evolution: A social parasite was born from a virgin. Curr Biol 2023; 33:R225-R228. [PMID: 36977384 DOI: 10.1016/j.cub.2023.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The sudden appearance of small winged queens within a lineage of asexually reproducing ant workers reveals that such social parasites can appear abruptly. The parasitic queens differ in a large genomic region, suggesting that a supergene instantly equipped the social parasite with a suite of co-adapted traits.
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Affiliation(s)
- Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
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19
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Blacher P, De Gasperin O, Grasso G, Sarton-Lohéac S, Allemann R, Chapuisat M. Cryptic recessive lethality of a supergene controlling social organization in ants. Mol Ecol 2023; 32:1062-1072. [PMID: 36504171 DOI: 10.1111/mec.16821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/23/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
Supergenes are clusters of linked loci that control complex phenotypes, such as alternative forms of social organization in ants. Explaining the long-term maintenance of supergenes is challenging, particularly when the derived haplotype lacks homozygous lethality and causes gene drive. In the Alpine silver ant, Formica selysi, a large and ancient social supergene with two haplotypes, M and P, controls colony social organization. Single-queen colonies only contain MM females, while multiqueen colonies contain MP and PP females. The derived P haplotype, found only in multiqueen colonies, selfishly enhances its transmission through maternal effect killing, which could have led to its fixation. A population genetic model showed that a stable social polymorphism can only be maintained under a narrow set of conditions, which includes partial assortative mating by social form (which is known to occur in the wild), and low fitness of PP queens. With a combination of field and laboratory experiments, we show that the P haplotype has deleterious effects on female fitness. The survival rate of PP queens and workers was around half that of other genotypes. Moreover, P-carrying queens had lower fertility and fecundity compared to other queens. We discuss how cryptic lethal effects of the P haplotype help stabilize this ancient polymorphism.
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Affiliation(s)
- Pierre Blacher
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ornela De Gasperin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Red de Ecoetología, Instituto de Ecología A. C., Veracruz, Mexico
| | - Guglielmo Grasso
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,University of Manchester, Manchester, UK
| | - Solenn Sarton-Lohéac
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Roxane Allemann
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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20
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Prazdnikov DV. Chromosome complements of Channalucius and C.striata from Phu Quoc Island and karyotypic evolution in snakehead fishes (Actinopterygii, Channidae). COMPARATIVE CYTOGENETICS 2023; 17:1-12. [PMID: 36761446 PMCID: PMC9836404 DOI: 10.3897/compcytogen.v17.i1.94943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Snakehead fishes of the family Channidae are obligatory air-breathers freshwater predators, the vast majority of which belong to the genus Channa Scopoli, 1777. Channa species are characterized by high karyotypic diversity due to various types of chromosomal rearrangements. It is assumed that, in addition to the lifestyle, fragmentation and isolation of snakehead populations contribute to an increase in karyotypic diversity. However, the chromosome complements of many isolated populations of widespread Channa species remain unknown, and the direction of karyotype transformations is poorly understood. This paper describes the previously unstudied karyotypes of Channalucius (Cuvier, 1831) and C.striata (Bloch, 1793) from Phu Quoc Island and analyzes the trends of karyotypic evolution in the genus Channa. In C.lucius, the karyotypes are differed in the number of chromosome arms (2n = 48, NF = 50 and 51), while in C.striata, the karyotypes are differed in the diploid chromosome number (2n = 44 and 43, NF = 48). A comparative cytogenetic analysis showed that the main trend of karyotypic evolution of Channa species is associated with a decrease in the number of chromosomes and an increase in the number of chromosome arms, mainly due to fusions and pericentric inversions. The data obtained support the assumption that fragmentation and isolation of populations, especially of continental islands, contribute to the karyotypic diversification of snakeheads and are of interest for further cytogenetic studies of Channidae.
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Affiliation(s)
- Denis V Prazdnikov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russia Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Moscow Russia
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21
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Vallier M, Suwandi A, Ehrhardt K, Belheouane M, Berry D, Čepić A, Galeev A, Johnsen JM, Grassl GA, Baines JF. Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice. Gut Microbes 2023; 15:2164448. [PMID: 36683151 PMCID: PMC9872957 DOI: 10.1080/19490976.2022.2164448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/15/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Infectious disease is widely considered to be a major driver of evolution. A preponderance of signatures of balancing selection at blood group-related genes is thought to be driven by inherent trade-offs in susceptibility to disease. B4galnt2 is subject to long-term balancing selection in house mice, where two divergent allele classes direct alternative tissue-specific expression of a glycosyltransferase in the intestine versus blood vessels. The blood vessel allele class leads to prolonged bleeding times similar to von Willebrand disease in humans, yet has been maintained for millions of years. Based on in vivo functional studies in inbred lab strains, it is hypothesized that the cost of prolonged bleeding times may be offset by an evolutionary trade-off involving susceptibility to a yet unknown pathogen(s). To identify candidate pathogens for which resistance could be mediated by B4galnt2 genotype, we here employed a novel "pathometagenomic" approach in a wild mouse population, which combines bacterial 16S rRNA gene-based community profiling with histopathology of gut tissue. Through subsequent isolation, genome sequencing and controlled experiments in lab mice, we show that the presence of the blood vessel allele is associated with resistance to a newly identified subspecies of Morganella morganii, a clinically important opportunistic pathogen. Given the increasing importance of zoonotic events, the approach outlined here may find useful application in the detection of emerging diseases in wild animal populations.
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Affiliation(s)
- Marie Vallier
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Abdulhadi Suwandi
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover, Germany
| | - Katrin Ehrhardt
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover, Germany
| | - Meriem Belheouane
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Aleksa Čepić
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Alibek Galeev
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jill M. Johnsen
- Bloodworks Research Institute, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Guntram A. Grassl
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover, Germany
| | - John F. Baines
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
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22
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Dubin CA, Voorhies M, Sil A, Teixeira MM, Barker BM, Brem RB. Genome Organization and Copy-Number Variation Reveal Clues to Virulence Evolution in Coccidioides posadasii. J Fungi (Basel) 2022; 8:jof8121235. [PMID: 36547568 PMCID: PMC9782707 DOI: 10.3390/jof8121235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
The human fungal pathogen Coccidioides spp. causes valley fever, a treatment-refractory and sometimes deadly disease prevalent in arid regions of the western hemisphere. Fungal virulence in the mammalian host hinges on a switch between growth as hyphae and as large spherules containing infectious spores. How these virulence programs are encoded in the genome remains poorly understood. Drawing on Coccidioides genomic resources, we first discovered a new facet of genome organization in this system: spherule-gene islands, clusters of genes physically linked in the genome that exhibited specific mRNA induction in the spherule phase. Next, we surveyed copy-number variation genome-wide among strains of C. posadasii. Emerging from this catalog were spherule-gene islands with striking presence-absence differentiation between C. posadasii populations, a pattern expected from virulence factors subjected to different selective pressures across habitats. Finally, analyzing single-nucleotide differences across C. posadasii strains, we identified signatures of natural selection in spherule-expressed genes. Together, our data establish spherule-gene islands as candidate determinants of virulence and targets of selection in Coccidioides.
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Affiliation(s)
- Claire A. Dubin
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720-3102, USA
| | - Mark Voorhies
- Department of Microbiology and Immunology, UC San Francisco, San Francisco, CA 94143, USA
| | - Anita Sil
- Department of Microbiology and Immunology, UC San Francisco, San Francisco, CA 94143, USA
| | - Marcus M. Teixeira
- The Translational Genomics Research Institute (TGen)-Affiliate of City of Hope, Flagstaff, AZ 85004, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Bridget M. Barker
- The Translational Genomics Research Institute (TGen)-Affiliate of City of Hope, Flagstaff, AZ 85004, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Rachel B. Brem
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720-3102, USA
- Correspondence:
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23
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De Pasqual C, Suisto K, Kirvesoja J, Gordon S, Ketola T, Mappes J. Heterozygote advantage and pleiotropy contribute to intraspecific color trait variability. Evolution 2022; 76:2389-2403. [PMID: 35984008 PMCID: PMC9805086 DOI: 10.1111/evo.14597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/23/2022] [Accepted: 06/29/2022] [Indexed: 01/22/2023]
Abstract
The persistence of intrapopulation phenotypic variation typically requires some form of balancing selection because drift and directional selection eventually erode genetic variation. Heterozygote advantage remains a classic explanation for the maintenance of genetic variation in the face of selection. However, examples of heterozygote advantage, other than those associated with disease resistance, are rather uncommon. Across most of its distribution, males of the aposematic moth Arctia plantaginis have two hindwing phenotypes determined by a heritable one locus-two allele polymorphism (genotypes: WW/Wy = white morph, yy = yellow morph). Using genotyped moths, we show that the presence of one or two copies of the yellow allele affects several life-history traits. Reproductive output of both males and females and female mating success are negatively affected by two copies of the yellow allele. Females carrying one yellow allele (i.e., Wy) have higher fertility, hatching success, and offspring survival than either homozygote, thus leading to strong heterozygote advantage. Our results indicate strong female contribution especially at the postcopulatory stage in maintaining the color polymorphism. The interplay between heterozygote advantage, yellow allele pleiotropic effect, and morph-specific predation pressure may exert balancing selection on the color locus, suggesting that color polymorphism may be maintained through complex interactions between natural and sexual selection.
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Affiliation(s)
- Chiara De Pasqual
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40014, Finland.,Organismal and Evolutionary Biology Research Program, University of Helsinki, Helsinki, 00014, Finland
| | - Kaisa Suisto
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Jimi Kirvesoja
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Swanne Gordon
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Tarmo Ketola
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Johanna Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40014, Finland.,Organismal and Evolutionary Biology Research Program, University of Helsinki, Helsinki, 00014, Finland
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24
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Schield DR, Perry BW, Adams RH, Holding ML, Nikolakis ZL, Gopalan SS, Smith CF, Parker JM, Meik JM, DeGiorgio M, Mackessy SP, Castoe TA. The roles of balancing selection and recombination in the evolution of rattlesnake venom. Nat Ecol Evol 2022; 6:1367-1380. [PMID: 35851850 PMCID: PMC9888523 DOI: 10.1038/s41559-022-01829-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 06/15/2022] [Indexed: 02/02/2023]
Abstract
The origin of snake venom involved duplication and recruitment of non-venom genes into venom systems. Several studies have predicted that directional positive selection has governed this process. Venom composition varies substantially across snake species and venom phenotypes are locally adapted to prey, leading to coevolutionary interactions between predator and prey. Venom origins and contemporary snake venom evolution may therefore be driven by fundamentally different selection regimes, yet investigations of population-level patterns of selection have been limited. Here, we use whole-genome data from 68 rattlesnakes to test hypotheses about the factors that drive genomic diversity and differentiation in major venom gene regions. We show that selection has resulted in long-term maintenance of genetic diversity within and between species in multiple venom gene families. Our findings are inconsistent with a dominant role of directional positive selection and instead support a role of long-term balancing selection in shaping venom evolution. We also detect rapid decay of linkage disequilibrium due to high recombination rates in venom regions, suggesting that venom genes have reduced selective interference with nearby loci, including other venom paralogues. Our results provide an example of long-term balancing selection that drives trans-species polymorphism and help to explain how snake venom keeps pace with prey resistance.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Richard H Adams
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA, USA
| | | | | | | | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Joshua M Parker
- Life Science Department, Fresno City College, Fresno, CA, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.
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25
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Reid JM. Intrinsic emergence and modulation of sex-specific dominance reversals in threshold traits. Evolution 2022; 76:1924-1941. [PMID: 35803581 PMCID: PMC9541474 DOI: 10.1111/evo.14563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/24/2022] [Accepted: 06/30/2022] [Indexed: 01/22/2023]
Abstract
Sex-specific dominance reversals (SSDRs) in fitness-related traits, where heterozygotes' phenotypes resemble those of alternative homozygotes in females versus males, can simultaneously maintain genetic variation in fitness and resolve sexual conflict and thereby shape key evolutionary outcomes. However, the full implications of SSDRs will depend on how they arise and the resulting potential for evolutionary, ecological and environmental modulation. Recent field and laboratory studies have demonstrated SSDRs in threshold(-like) traits with dichotomous or competitive phenotypic outcomes, implying that such traits could promote the emergence of SSDRs. However, such possibilities have not been explicitly examined. I show how phenotypic SSDRs can readily emerge in threshold traits given genetic architectures involving large-effect loci alongside sexual dimorphism in the mean and variance in polygenic liability. I also show how multilocus SSDRs can arise in line-cross experiments, especially given competitive reproductive systems that generate nonlinear fitness outcomes. SSDRs can consequently emerge in threshold(-like) traits as functions of sexual antagonism, sexual dimorphism and reproductive systems, even with purely additive underlying genetic effects. Accordingly, I identify theoretical and empirical advances that are now required to discern the basis and occurrence of SSDRs in nature, probe forms of (co-)evolutionary, ecological and environmental modulation, and evaluate net impacts on sexual conflict.
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Affiliation(s)
- Jane M. Reid
- Centre for Biodiversity DynamicsNTNUTrondheimNorway,School of Biological SciencesUniversity of AberdeenAberdeenUK
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26
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Tafreshi AG, Otto SP, Chapuisat M. Unbalanced selection: the challenge of maintaining a social polymorphism when a supergene is selfish. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210197. [PMID: 35694754 PMCID: PMC9189496 DOI: 10.1098/rstb.2021.0197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Supergenes often have multiple phenotypic effects, including unexpected detrimental ones, because recombination suppression maintains associations among co-adapted alleles but also allows the accumulation of recessive deleterious mutations and selfish genetic elements. Yet, supergenes often persist over long evolutionary periods. How are such polymorphisms maintained in the face of selection, drive and drift? We present a population genetic model that investigates the conditions necessary for a stable polymorphic equilibrium when one of the supergene haplotypes is a selfish genetic element. The model fits the characteristics of the Alpine silver ant, Formica selysi, in which a large supergene underlies colony social organization, and one haplotype distorts Mendelian transmission by killing progeny that did not inherit it. The model shows that such maternal-effect killing strongly limits the maintenance of social polymorphism. Under random mating, transmission ratio distortion prevents rare single-queen colonies from invading populations of multiple-queen colonies, regardless of the fitness of each genotype. A stable polymorphic equilibrium can, however, be reached when high rates of assortative mating are combined with large fitness differences among supergene genotypes. The model reveals that the persistence of the social polymorphism is non-trivial and expected to occur only under restrictive conditions that deserve further empirical investigation. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Alireza G Tafreshi
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Sarah P Otto
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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27
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Berdan EL, Blanckaert A, Butlin RK, Flatt T, Slotte T, Wielstra B. Mutation accumulation opposes polymorphism: supergenes and the curious case of balanced lethals. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210199. [PMID: 35694750 PMCID: PMC9189497 DOI: 10.1098/rstb.2021.0199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Supergenes offer spectacular examples of long-term balancing selection in nature, but their origin and maintenance remain a mystery. Reduced recombination between arrangements, a critical aspect of many supergenes, protects adaptive multi-trait phenotypes but can lead to mutation accumulation. Mutation accumulation can stabilize the system through the emergence of associative overdominance (AOD), destabilize the system, or lead to new evolutionary outcomes. One outcome is the formation of maladaptive balanced lethal systems, where only heterozygotes remain viable and reproduce. We investigated the conditions under which these different outcomes occur, assuming a scenario of introgression after divergence. We found that AOD aided the invasion of a new supergene arrangement and the establishment of a polymorphism. However, this polymorphism was easily destabilized by further mutation accumulation, which was often asymmetric, disrupting the quasi-equilibrium state. Mechanisms that accelerated degeneration tended to amplify asymmetric mutation accumulation between the supergene arrangements and vice-versa. As the evolution of balanced lethal systems requires symmetric degeneration of both arrangements, this leaves only restricted conditions for their evolution, namely small population sizes and low rates of gene conversion. The dichotomy between the persistence of polymorphism and degeneration of supergene arrangements likely underlies the rarity of balanced lethal systems in nature. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
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Affiliation(s)
- Emma L Berdan
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands.,Tjarnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, 45296 Stromstad, Sweden
| | - Alexandre Blanckaert
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Roger K Butlin
- Tjarnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, 45296 Stromstad, Sweden.,Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, 106 91 Stockholm, Sweden
| | - Ben Wielstra
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands
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28
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Parrett JM, Chmielewski S, Aydogdu E, Łukasiewicz A, Rombauts S, Szubert-Kruszyńska A, Babik W, Konczal M, Radwan J. Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load. Nat Ecol Evol 2022; 6:1330-1342. [DOI: 10.1038/s41559-022-01816-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/26/2022] [Indexed: 10/17/2022]
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29
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Kumar H, Panigrahi M, Panwar A, Rajawat D, Nayak SS, Saravanan KA, Kaisa K, Parida S, Bhushan B, Dutt T. Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data. J Comput Biol 2022; 29:943-960. [PMID: 35639362 DOI: 10.1089/cmb.2021.0447] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Natural selection has been given a lot of attention because it relates to the adaptation of populations to their environments, both biotic and abiotic. An allele is selected when it is favored by natural selection. Consequently, the favored allele increases in frequency in the population and neighboring linked variation diminishes, causing so-called selective sweeps. A high-throughput genomic sequence allows one to disentangle the evolutionary forces at play in populations. With the development of high-throughput genome sequencing technologies, it has become easier to detect these selective sweeps/selection signatures. Various methods can be used to detect selective sweeps, from simple implementations using summary statistics to complex statistical approaches. One of the important problems of these statistical models is the potential to provide inaccurate results when their assumptions are violated. The use of machine learning (ML) in population genetics has been introduced as an alternative method of detecting selection by treating the problem of detecting selection signatures as a classification problem. Since the availability of population genomics data is increasing, researchers may incorporate ML into these statistical models to infer signatures of selection with higher predictive accuracy and better resolution. This article describes how ML can be used to aid in detecting and studying natural selection patterns using population genomic data.
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Affiliation(s)
- Harshit Kumar
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Manjit Panigrahi
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Anuradha Panwar
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Divya Rajawat
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Sonali Sonejita Nayak
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - K A Saravanan
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Kaiho Kaisa
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Subhashree Parida
- Divisions of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Bharat Bhushan
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, India
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30
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Chotard A, Ledamoisel J, Decamps T, Herrel A, Chaine AS, Llaurens V, Debat V. Evidence of attack deflection suggests adaptive evolution of wing tails in butterflies. Proc Biol Sci 2022; 289:20220562. [PMID: 35611535 PMCID: PMC9130794 DOI: 10.1098/rspb.2022.0562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Predation is a powerful selective force shaping many behavioural and morphological traits in prey species. The deflection of predator attacks from vital parts of the prey usually involves the coordinated evolution of prey body shape and colour. Here, we test the deflection effect of hindwing (HW) tails in the swallowtail butterfly Iphiclides podalirius. In this species, HWs display long tails associated with a conspicuous colour pattern. By surveying the wings within a wild population of I. podalirius, we observed that wing damage was much more frequent on the tails. We then used a standardized behavioural assay employing dummy butterflies with real I. podalirius wings to study the location of attacks by great tits Parus major. Wing tails and conspicuous coloration of the HWs were struck more often than the rest of the body by birds. Finally, we characterized the mechanical properties of fresh wings and found that the tail vein was more fragile than the others, suggesting facilitated escape ability of butterflies attacked at this location. Our results clearly support the deflective effect of HW tails and suggest that predation is an important selective driver of the evolution of wing tails and colour pattern in butterflies.
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Affiliation(s)
- Ariane Chotard
- Institut de Systématique, Evolution, Biodiversité (ISYEB, UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France
| | - Joséphine Ledamoisel
- Institut de Systématique, Evolution, Biodiversité (ISYEB, UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France
| | - Thierry Decamps
- Unité Mixte de Recherche Mécanismes Adaptatifs et Evolution (MECADEV, UMR 7179), Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - Anthony Herrel
- Unité Mixte de Recherche Mécanismes Adaptatifs et Evolution (MECADEV, UMR 7179), Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - Alexis S. Chaine
- Station d'Ecologie Theorique et Experimentale du CNRS (SETE, UAR 2029), Moulis, France
| | - Violaine Llaurens
- Institut de Systématique, Evolution, Biodiversité (ISYEB, UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France
| | - Vincent Debat
- Institut de Systématique, Evolution, Biodiversité (ISYEB, UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France
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31
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Jay P, Joron M. The double game of chromosomal inversions in a neotropical butterfly. C R Biol 2022; 345:57-73. [DOI: 10.5802/crbiol.73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/24/2022]
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32
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Contiguously hydrophobic sequences are functionally significant throughout the human exome. Proc Natl Acad Sci U S A 2022; 119:e2116267119. [PMID: 35294280 PMCID: PMC8944643 DOI: 10.1073/pnas.2116267119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
SignificanceProteins rely on the hydrophobic effect to maintain structure and interactions with the environment. Surprisingly, natural selection on amino acid hydrophobicity has not been detected using modern genetic data. Analyses that treat each amino acid separately do not reveal significant results, which we confirm here. However, because the hydrophobic effect becomes more powerful as more hydrophobic molecules are introduced, we tested whether unbroken stretches of hydrophobic amino acids are under selection. Using genetic variant data from across the human genome, we find evidence that selection increases with the length of the unbroken hydrophobic sequence. These results could lead to improvements in a wide range of genomic tools as well as insights into protein-aggregation disease etiology and protein evolutionary history.
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33
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Fark SN, Gerber S, Alonzo SH, Kindsvater HK, Meier JI, Seehausen O. Multispecies colour polymorphisms associated with contrasting microhabitats in two Mediterranean wrasse radiations. J Evol Biol 2022; 35:633-647. [PMID: 35304789 PMCID: PMC9311657 DOI: 10.1111/jeb.13999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/14/2022] [Accepted: 02/20/2022] [Indexed: 12/01/2022]
Abstract
Intraspecific colour polymorphisms (CPs) present unique opportunities to study fundamental evolutionary questions, such as the link between ecology and phenotype, mechanisms maintaining genetic diversity and their putative role in speciation. Wrasses are highly diverse in ecology and morphology and harbour a variety of colour‐polymorphic species. In the Mediterranean Sea, wrasses of the tribe Labrini evolved two species radiations each harbouring several species with a brown and a green morph. The colour morphs occur in complete sympatry in mosaic habitats with rocky outcrops and Neptune grass patches. Morph‐specific differences had not been characterized yet and the evolutionary forces maintaining them remained unknown. With genome‐wide data for almost all Labrini species, we show that species with CPs are distributed across the phylogeny, but show evidence of hybridization. This suggests that the colour morphs are either ancient and have been lost repeatedly, that they have evolved repeatedly or have been shared via hybridization. Focusing on two polymorphic species, we find that each colour morph is more common in the microhabitat providing the best colour match and that the morphs exhibit additional behavioural and morphological differences further improving crypsis in their respective microhabitats. We find little evidence for genetic differentiation between the morphs in either species. Therefore, we propose that these colour morphs represent a multi‐niche polymorphism as an adaptation to the highly heterogeneous habitat. Our study highlights how colour polymorphism (CP) can be advantageous in mosaic habitats and that Mediterranean wrasses are an ideal system to study trans‐species polymorphisms, i.e. polymorphisms maintained across several species, in adaptive radiations.
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Affiliation(s)
- Sarya N Fark
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Steve Gerber
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Suzanne H Alonzo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA
| | - Holly K Kindsvater
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Joana I Meier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Zoology, University of Cambridge, Cambridge, UK.,Center of Ecology, Evolution & Biogeochemistry, Swiss Institute for Environmental Sciences and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Center of Ecology, Evolution & Biogeochemistry, Swiss Institute for Environmental Sciences and Technology (EAWAG), Kastanienbaum, Switzerland
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34
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Giraldo-Deck LM, Loveland JL, Goymann W, Tschirren B, Burke T, Kempenaers B, Lank DB, Küpper C. Intralocus conflicts associated with a supergene. Nat Commun 2022; 13:1384. [PMID: 35296671 PMCID: PMC8927407 DOI: 10.1038/s41467-022-29033-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/23/2022] [Indexed: 11/12/2022] Open
Abstract
Chromosomal inversions frequently underlie major phenotypic variation maintained by divergent selection within and between sexes. Here we examine whether and how intralocus conflicts contribute to balancing selection stabilizing an autosomal inversion polymorphism in the ruff Calidris pugnax. In this lekking shorebird, three male mating morphs (Independents, Satellites and Faeders) are controlled by an inversion-based supergene. We show that in a captive population, Faeder females, who are smaller and whose inversion haplotype has not undergone recombination, have lower average reproductive success in terms of laying rate, egg size, and offspring survival than Independent females, who lack the inversion. Satellite females, who carry a recombined inversion haplotype and have intermediate body size, more closely resemble Independent than Faeder females in reproductive performance. We inferred that the lower reproductive output of Faeder females is most likely balanced by higher than average reproductive success of individual Faeder males. These findings suggest that intralocus conflicts may play a major role in the evolution and maintenance of supergene variants.
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Affiliation(s)
- Lina M Giraldo-Deck
- Research Group Behavioural Genetics and Evolutionary Ecology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str., 82319, Seewiesen, Germany.
| | - Jasmine L Loveland
- Research Group Behavioural Genetics and Evolutionary Ecology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str., 82319, Seewiesen, Germany
| | - Wolfgang Goymann
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str., 82319, Seewiesen, Germany
| | - Barbara Tschirren
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
| | - Terry Burke
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str., 82319, Seewiesen, Germany
| | - David B Lank
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
| | - Clemens Küpper
- Research Group Behavioural Genetics and Evolutionary Ecology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str., 82319, Seewiesen, Germany.
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35
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Potente G, Léveillé-Bourret É, Yousefi N, Choudhury RR, Keller B, Diop SI, Duijsings D, Pirovano W, Lenhard M, Szövényi P, Conti E. Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism. Mol Biol Evol 2022; 39:msac035. [PMID: 35143659 PMCID: PMC8859637 DOI: 10.1093/molbev/msac035] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula?
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Affiliation(s)
- Giacomo Potente
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- BaseClear BV, Leiden, The Netherlands
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Étienne Léveillé-Bourret
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Narjes Yousefi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Rimjhim Roy Choudhury
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Seydina Issa Diop
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- BaseClear BV, Leiden, The Netherlands
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | | | | | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Elena Conti
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
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36
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Cavedon M, vonHoldt B, Hebblewhite M, Hegel T, Heppenheimer E, Hervieux D, Mariani S, Schwantje H, Steenweg R, Theoret J, Watters M, Musiani M. Genomic legacy of migration in endangered caribou. PLoS Genet 2022; 18:e1009974. [PMID: 35143486 PMCID: PMC8830729 DOI: 10.1371/journal.pgen.1009974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 12/01/2021] [Indexed: 11/18/2022] Open
Abstract
Wide-ranging animals, including migratory species, are significantly threatened by the effects of habitat fragmentation and habitat loss. In the case of terrestrial mammals, this results in nearly a quarter of species being at risk of extinction. Caribou are one such example of a wide-ranging, migratory, terrestrial, and endangered mammal. In populations of caribou, the proportion of individuals considered as "migrants" can vary dramatically. There is therefore a possibility that, under the condition that migratory behavior is genetically determined, those individuals or populations that are migratory will be further impacted by humans, and this impact could result in the permanent loss of the migratory trait in some populations. However, genetic determination of migration has not previously been studied in an endangered terrestrial mammal. We examined migratory behavior of 139 GPS-collared endangered caribou in western North America and carried out genomic scans for the same individuals. Here we determine a genetic subdivision of caribou into a Northern and a Southern genetic cluster. We also detect >50 SNPs associated with migratory behavior, which are in genes with hypothesized roles in determining migration in other organisms. Furthermore, we determine that propensity to migrate depends upon the proportion of ancestry in individual caribou, and thus on the evolutionary history of its migratory and sedentary subspecies. If, as we report, migratory behavior is influenced by genes, caribou could be further impacted by the loss of the migratory trait in some isolated populations already at low numbers. Our results indicating an ancestral genetic component also suggest that the migratory trait and their associated genetic mutations could not be easily re-established when lost in a population.
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Affiliation(s)
- Maria Cavedon
- Faculty of Environmental Design, University of Calgary, Calgary, Alberta, Canada
| | - Bridgett vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Mark Hebblewhite
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
| | - Troy Hegel
- Yukon Department of Environment, Whitehorse, Yukon, Canada
| | - Elizabeth Heppenheimer
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Dave Hervieux
- Fish and Wildlife Stewardship Branch, Alberta Environment and Parks, Grande Prairie, Alberta, Canada
| | - Stefano Mariani
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom
| | - Helen Schwantje
- Wildlife and Habitat Branch, Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, Nanaimo, British Columbia, Canada
| | - Robin Steenweg
- Pacific Region, Canadian Wildlife Service, Environment and Climate Change Canada, Delta, British Columbia, Canada
| | - Jessica Theoret
- Faculty of Environmental Design, University of Calgary, Calgary, Alberta, Canada
| | - Megan Watters
- Land and Resource Specialist, Fort St. John, British Columbia, Canada
| | - Marco Musiani
- Department of Biological Sciences, Faculty of Science and Veterinary Medicine (Joint Appointment), University of Calgary, Calgary, Alberta, Canada
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37
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Ebel ER, Uricchio LH, Petrov DA, Egan ES. Revisiting the malaria hypothesis: accounting for polygenicity and pleiotropy. Trends Parasitol 2022; 38:290-301. [PMID: 35065882 PMCID: PMC8916997 DOI: 10.1016/j.pt.2021.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 10/19/2022]
Abstract
The malaria hypothesis predicts local, balancing selection of deleterious alleles that confer strong protection from malaria. Three protective variants, recently discovered in red cell genes, are indeed more common in African than European populations. Still, up to 89% of the heritability of severe malaria is attributed to many genome-wide loci with individually small effects. Recent analyses of hundreds of genome-wide association studies (GWAS) in humans suggest that most functional, polygenic variation is pleiotropic for multiple traits. Interestingly, GWAS alleles and red cell traits associated with small reductions in malaria risk are not enriched in African populations. We propose that other selective and neutral forces, in addition to malaria prevalence, explain the global distribution of most genetic variation impacting malaria risk.
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38
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Ogilvie JG, Van Belleghem S, Range R, Papa R, McMillan OW, Chouteau M, Counterman BA. Balanced polymorphisms and their divergence in a Heliconius butterfly. Ecol Evol 2021; 11:18319-18330. [PMID: 35003675 PMCID: PMC8717333 DOI: 10.1002/ece3.8423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022] Open
Abstract
The evolution of mimicry in similarly defended prey is well described by the Müllerian mimicry theory, which predicts the convergence of warning patterns in order to gain the most protection from predators. However, despite this prediction, we can find great diversity of color patterns among Müllerian mimics such as Heliconius butterflies in the neotropics. Furthermore, some species have evolved the ability to maintain multiple distinct warning patterns in single populations, a phenomenon known as polymorphic mimicry. The adaptive benefit of these polymorphisms is questionable since variation from the most common warning patterns is expected to be disadvantageous as novel signals are punished by predators naive to them. In this study, we use artificial butterfly models throughout Central and South America to characterize the selective pressures maintaining polymorphic mimicry in Heliconius doris. Our results highlight the complexity of positive frequency-dependent selection, the principal selective pressure driving convergence among Müllerian mimics, and its impacts on interspecific variation of mimetic warning coloration. We further show how this selection regime can both limit and facilitate the diversification of mimetic traits.
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Affiliation(s)
- James G. Ogilvie
- Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
- Smithsonian Tropical Research InstitutePanama CityPanama
| | | | - Ryan Range
- Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
| | - Riccardo Papa
- Department of BiologyUniversity of Puerto RicoRio PiedrasPuerto Rico
| | | | - Mathieu Chouteau
- Laboratoire Écologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA)Université de GuyaneCNRSIFREMERCayenneFrench Guiana
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39
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Enbody ED, Sprehn CG, Abzhanov A, Bi H, Dobreva MP, Osborne OG, Rubin CJ, Grant PR, Grant BR, Andersson L. A multispecies BCO2 beak color polymorphism in the Darwin's finch radiation. Curr Biol 2021; 31:5597-5604.e7. [PMID: 34687609 DOI: 10.1016/j.cub.2021.09.085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/25/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
Carotenoid-based polymorphisms are widespread in populations of birds, fish, and reptiles,1 but generally little is known about the factors affecting their maintenance in populations.2 We report a combined field and molecular-genetic investigation of a nestling beak color polymorphism in Darwin's finches. Beaks are pink or yellow, and yellow is recessive.3 Here we show that the polymorphism arose in the Galápagos half a million years ago through a mutation associated with regulatory change in the BCO2 gene and is shared by 14 descendant species. The polymorphism is probably a balanced polymorphism, maintained by ecological selection associated with survival and diet. In cactus finches, the frequency of the yellow genotype is correlated with cactus fruit abundance and greater hatching success and may be altered by introgressive hybridization. Polymorphisms that are hidden as adults, as here, may be far more common than is currently recognized, and contribute to diversification in ways that are yet to be discovered.
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Affiliation(s)
- Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.
| | - C Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Arhat Abzhanov
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Huijuan Bi
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Mariya P Dobreva
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Owen G Osborne
- School of Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor LL57 2UW, UK
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Peter R Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - B Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA.
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40
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Durland E, De Wit P, Langdon C. Temporally balanced selection during development of larval Pacific oysters ( Crassostrea gigas) inherently preserves genetic diversity within offspring. Proc Biol Sci 2021; 288:20203223. [PMID: 34465244 PMCID: PMC8437028 DOI: 10.1098/rspb.2020.3223] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Balancing selection is one of the mechanisms which has been proposed to explain the maintenance of genetic diversity in species across generations. For species with large populations and complex life histories, however, heterogeneous selection pressures may create a scenario in which the net effects of selection are balanced across developmental stages. With replicated cultures and a pooled sequencing approach, we show that genotype-dependent mortality in larvae of the Pacific oyster (Crassostrea gigas) is largely temporally dynamic and inconsistently in favour of a single genotype or allelic variant at each locus. Overall, the patterns of genetic change we observe to be taking place are more complex than what would be expected under classical examples of additive or dominant genetic interactions. They are also not easily explained by our current understanding of the effects of genetic load. Collectively, temporally heterogeneous selection pressures across different larval developmental stages may act to maintain genetic diversity, while also inherently sheltering genetic load within oyster populations.
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Affiliation(s)
- Evan Durland
- Department of Fisheries and Wildlife and Coastal Oregon Marine Experiment Station, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA.,Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Pierre De Wit
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Chris Langdon
- Department of Fisheries and Wildlife and Coastal Oregon Marine Experiment Station, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
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41
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Tepolt CK, Grosholz ED, de Rivera CE, Ruiz GM. Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity. Mol Ecol 2021; 31:55-69. [PMID: 34431151 DOI: 10.1111/mec.16143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/24/2021] [Accepted: 08/13/2021] [Indexed: 12/30/2022]
Abstract
Adaptation across environmental gradients has been demonstrated in numerous systems with extensive dispersal, despite high gene flow and consequently low genetic structure. The speed and mechanisms by which such adaptation occurs remain poorly resolved, but are critical to understanding species spread and persistence in a changing world. Here, we investigate these mechanisms in the European green crab Carcinus maenas, a globally distributed invader. We focus on a northwestern Pacific population that spread across >12 degrees of latitude in 10 years from a single source, following its introduction <35 years ago. Using six locations spanning >1500 km, we examine genetic structure using 9376 single nucleotide polymorphisms (SNPs). We find high connectivity among five locations, with significant structure between these locations and an enclosed lagoon with limited connectivity to the coast. Among the five highly connected locations, the only structure observed was a cline driven by a handful of SNPs strongly associated with latitude and winter temperature. These SNPs are almost exclusively found in a large cluster of genes in strong linkage disequilibrium that was previously identified as a candidate for cold tolerance adaptation in this species. This region may represent a balanced polymorphism that evolved to promote rapid adaptation in variable environments despite high gene flow, and which now contributes to successful invasion and spread in a novel environment. This research suggests an answer to the paradox of genetically depauperate yet successful invaders: populations may be able to adapt via a few variants of large effect despite low overall diversity.
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Affiliation(s)
- Carolyn K Tepolt
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Edwin D Grosholz
- Department of Environmental Science and Policy, University of California, Davis, California, USA
| | - Catherine E de Rivera
- Department of Environmental Science and Management, Portland State University, Portland, Oregon, USA
| | - Gregory M Ruiz
- Smithsonian Environmental Research Center, Smithsonian Institution, Edgewater, Maryland, USA
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42
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Billiard S, Castric V, Llaurens V. The integrative biology of genetic dominance. Biol Rev Camb Philos Soc 2021; 96:2925-2942. [PMID: 34382317 PMCID: PMC9292577 DOI: 10.1111/brv.12786] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/29/2022]
Abstract
Dominance is a basic property of inheritance systems describing the link between a diploid genotype at a single locus and the resulting phenotype. Models for the evolution of dominance have long been framed as an opposition between the irreconcilable views of Fisher in 1928 supporting the role of largely elusive dominance modifiers and Wright in 1929, who viewed dominance as an emerging property of the structure of enzymatic pathways. Recent theoretical and empirical advances however suggest that these opposing views can be reconciled, notably using models investigating the regulation of gene expression and developmental processes. In this more comprehensive framework, phenotypic dominance emerges from departures from linearity between any levels of integration in the genotype‐to‐phenotype map. Here, we review how these different models illuminate the emergence and evolution of dominance. We then detail recent empirical studies shedding new light on the diversity of molecular and physiological mechanisms underlying dominance and its evolution. By reconciling population genetics and functional biology, we hope our review will facilitate cross‐talk among research fields in the integrative study of dominance evolution.
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Affiliation(s)
- Sylvain Billiard
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | - Vincent Castric
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | - Violaine Llaurens
- Institut de Systématique, Evolution et Biodiversité, CNRS/MNHN/Sorbonne Université/EPHE, Museum National d'Histoire Naturelle, CP50, 57 rue Cuvier, 75005, Paris, France
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43
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O'Connor TK, Sandoval MC, Wang J, Hans JC, Takenaka R, Child M, Whiteman NK. Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti). Evolution 2021; 75:2441-2459. [PMID: 34370317 DOI: 10.1111/evo.14321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/09/2021] [Accepted: 07/20/2021] [Indexed: 11/28/2022]
Abstract
Color polymorphic species can offer exceptional insight into the ecology and genetics of adaptation. Although the genetic architecture of animal coloration is diverse, many color polymorphisms are associated with large structural variants and maintained by biotic interactions. Grasshoppers are notably polymorphic in both color and karyotype, which makes them excellent models for understanding the ecological drivers and genetic underpinnings of color variation. Banded and uniform morphs of the desert clicker grasshopper (Ligurotettix coquilletti) are found across the western deserts of North America. To address the hypothesis that predation maintains local color polymorphism and shapes regional crypsis variation, we surveyed morph frequencies and tested for covariation with two predation environments. Morphs coexisted at intermediate frequencies at most sites, consistent with local balancing selection. Morph frequencies covaried with the appearance of desert substrate-an environment used only by females-suggesting that ground-foraging predators are major agents of selection on crypsis. We next addressed the hypothesized link between morph variation and genome structure. To do so, we designed an approach for detecting inversions and indels using only RADseq data. The banded morph was perfectly correlated with a large putative indel. Remarkably, indel dominance differed among populations, a rare example of dominance evolution in nature.
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Affiliation(s)
- Timothy K O'Connor
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720.,Current Address: Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, 60637
| | - Marissa C Sandoval
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
| | - Jiarui Wang
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
| | - Jacob C Hans
- Department of Entomology, University of California, Riverside, Riverside, California, 92521
| | - Risa Takenaka
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, 98195.,Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109
| | - Myron Child
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, 84112
| | - Noah K Whiteman
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
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44
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Ameline C, Bourgeois Y, Vögtli F, Savola E, Andras J, Engelstädter J, Ebert D. A Two-Locus System with Strong Epistasis Underlies Rapid Parasite-Mediated Evolution of Host Resistance. Mol Biol Evol 2021; 38:1512-1528. [PMID: 33258959 PMCID: PMC8042741 DOI: 10.1093/molbev/msaa311] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Parasites are a major evolutionary force, driving adaptive responses in host populations. Although the link between phenotypic response to parasite-mediated natural selection and the underlying genetic architecture often remains obscure, this link is crucial for understanding the evolution of resistance and predicting associated allele frequency changes in the population. To close this gap, we monitored the response to selection during epidemics of a virulent bacterial pathogen, Pasteuria ramosa, in a natural host population of Daphnia magna. Across two epidemics, we observed a strong increase in the proportion of resistant phenotypes as the epidemics progressed. Field and laboratory experiments confirmed that this increase in resistance was caused by selection from the local parasite. Using a genome-wide association study, we built a genetic model in which two genomic regions with dominance and epistasis control resistance polymorphism in the host. We verified this model by selfing host genotypes with different resistance phenotypes and scoring their F1 for segregation of resistance and associated genetic markers. Such epistatic effects with strong fitness consequences in host–parasite coevolution are believed to be crucial in the Red Queen model for the evolution of genetic recombination.
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Affiliation(s)
- Camille Ameline
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Yann Bourgeois
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Felix Vögtli
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Eevi Savola
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | - Jason Andras
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,Department of Biological Sciences, Clapp Laboratory, Mount Holyoke College, South Hadley, MA, USA
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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45
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Paccard A, Hanson D, Stuart YE, von Hippel FA, Kalbe M, Klepaker T, Skúlason S, Kristjánsson BK, Bolnick DI, Hendry AP, Barrett RDH. Repeatability of Adaptive Radiation Depends on Spatial Scale: Regional Versus Global Replicates of Stickleback in Lake Versus Stream Habitats. J Hered 2021; 111:43-56. [PMID: 31690947 DOI: 10.1093/jhered/esz056] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/30/2019] [Indexed: 11/13/2022] Open
Abstract
The repeatability of adaptive radiation is expected to be scale-dependent, with determinism decreasing as greater spatial separation among "replicates" leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation-their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on levels of parallel evolution by quantifying phenotypic and genetic divergence between lake and stream stickleback pairs sampled at regional (Vancouver Island) and global (North America and Europe) scales. We measured phenotypes known to show lake-stream divergence and used reduced representation genome-wide sequencing to estimate genetic divergence. We assessed the scale dependence of parallel evolution by comparing effect sizes from multivariate models and also the direction and magnitude of lake-stream divergence vectors. At the phenotypic level, parallelism was greater at the regional than the global scale. At the genetic level, putative selected loci showed greater lake-stream parallelism at the regional than the global scale. Generally, the level of parallel evolution was low at both scales, except for some key univariate traits. Divergence vectors were often orthogonal, highlighting possible ecological and genetic constraints on parallel evolution at both scales. Overall, our results confirm that the repeatability of adaptive radiation decreases at increasing spatial scales. We suggest that greater environmental heterogeneity at larger scales imposes different selection regimes, thus generating lower repeatability of adaptive radiation at larger spatial scales.
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Affiliation(s)
- Antoine Paccard
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Dieta Hanson
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Frank A von Hippel
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
| | - Martin Kalbe
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tom Klepaker
- University of Bergen, Department of Biology, Bergen, Norway
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Bjarni K Kristjánsson
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Daniel I Bolnick
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
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46
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Jardine MD, Ruzicka F, Diffley C, Fowler K, Reuter M. A non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster exhibits antagonistically pleiotropic fitness effects. Proc Biol Sci 2021; 288:20202958. [PMID: 33975471 PMCID: PMC8113896 DOI: 10.1098/rspb.2020.2958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/14/2021] [Indexed: 11/12/2022] Open
Abstract
The amount of genetic variation for fitness within populations tends to exceed that expected under mutation-selection-drift balance. Several mechanisms have been proposed to actively maintain polymorphism and account for this discrepancy, including antagonistic pleiotropy (AP), where allelic variants have opposing effects on different components of fitness. Here, we identify a non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster and measure survival and reproductive components of fitness in males and females of replicate lines carrying each respective allele. Expressing the fruitless region in a hemizygous state reveals a pattern of AP, with one allele generating greater reproductive fitness and the other conferring greater survival to adulthood. Different fitness effects were observed in an alternative genetic background, which may reflect dominance reversal and/or epistasis. Our findings link sequence-level variation at a single locus with complex effects on a range of fitness components, thus helping to explain the maintenance of genetic variation for fitness. Transcription factors, such as fruitless, may be prime candidates for targets of balancing selection since they interact with multiple target loci and their associated phenotypic effects.
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Affiliation(s)
- Michael D. Jardine
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Centre for Life's Origins and Evolution, University College London, London, UK
| | - Filip Ruzicka
- School of Biological Sciences and Centre for Geometric Biology, Monash University, Clayton, Australia
| | - Charlotte Diffley
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Kevin Fowler
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Centre for Life's Origins and Evolution, University College London, London, UK
| | - Max Reuter
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Centre for Life's Origins and Evolution, University College London, London, UK
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47
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Andras JP, Fields PD, Du Pasquier L, Fredericksen M, Ebert D. Genome-Wide Association Analysis Identifies a Genetic Basis of Infectivity in a Model Bacterial Pathogen. Mol Biol Evol 2021; 37:3439-3452. [PMID: 32658956 PMCID: PMC7743900 DOI: 10.1093/molbev/msaa173] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/22/2020] [Accepted: 07/08/2020] [Indexed: 12/22/2022] Open
Abstract
Knowledge of the genetic architecture of pathogen infectivity and host resistance is essential for a mechanistic understanding of coevolutionary processes, yet the genetic basis of these interacting traits remains unknown for most host-pathogen systems. We used a comparative genomic approach to explore the genetic basis of infectivity in Pasteuria ramosa, a Gram-positive bacterial pathogen of planktonic crustaceans that has been established as a model for studies of Red Queen host-pathogen coevolution. We sequenced the genomes of a geographically, phenotypically, and genetically diverse collection of P. ramosa strains and performed a genome-wide association study to identify genetic correlates of infection phenotype. We found multiple polymorphisms within a single gene, Pcl7, that correlate perfectly with one common and widespread infection phenotype. We then confirmed this perfect association via Sanger sequencing in a large and diverse sample set of P. ramosa clones. Pcl7 codes for a collagen-like protein, a class of adhesion proteins known or suspected to be involved in the infection mechanisms of a number of important bacterial pathogens. Consistent with expectations under Red Queen coevolution, sequence variation of Pcl7 shows evidence of balancing selection, including extraordinarily high diversity and absence of geographic structure. Based on structural homology with a collagen-like protein of Bacillus anthracis, we propose a hypothesis for the structure of Pcl7 and the physical location of the phenotype-associated polymorphisms. Our results offer strong evidence for a gene governing infectivity and provide a molecular basis for further study of Red Queen dynamics in this model host-pathogen system.
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Affiliation(s)
- Jason P Andras
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA
| | - Peter D Fields
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Louis Du Pasquier
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Maridel Fredericksen
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Dieter Ebert
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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48
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Kardos M, Luikart G. The Genetic Architecture of Fitness Drives Population Viability during Rapid Environmental Change. Am Nat 2021; 197:511-525. [DOI: 10.1086/713469] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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49
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Bougie TC, Brelsford A, Hedin M. Evolutionary impacts of introgressive hybridization in a rapidly evolving group of jumping spiders (F. Salticidae, Habronattus americanus group). Mol Phylogenet Evol 2021; 161:107165. [PMID: 33798670 DOI: 10.1016/j.ympev.2021.107165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/11/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Introgressive hybridization can be a powerful force impacting patterns of evolution at multiple taxonomic levels. We aimed to understand how introgression has affected speciation and diversification within a species complex of jumping spiders. The Habronattus americanus subgroup is a recently radiating group of jumping spiders, with species now in contact after hypothesized periods of isolation during glaciation cycles of the Pleistocene. Effects of introgression on genomes and morphology were investigated using phylogenomic and clustering methods using RADseq, ultraconserved elements (UCEs), and morphological data. We characterized 14 unique species/morphs using non-metric multidimensional scaling of morphological data, a majority of which were not recovered as monophyletic in our phylogenomic analyses. Morphological clusters and genetic lineages are highly incongruent, such that geographic region was a greater predictor of phylogenetic relatedness and genomic similarity than species or morph identity. STRUCTURE analyses support this pattern, revealing clusters corresponding to larger geographic regions. A history of rapid radiation in combination with frequent introgression seems to have mostly homogenized the genomes of species in this system, while selective forces maintain distinct male morphologies. GEMMA analyses support this idea by identifying SNPs correlated with distinct male morphologies. Overall, we have uncovered a system at odds with a typical bifurcating evolutionary model, instead supporting one where closely related species evolve together connected through multiple introgression events, creating a reticulate evolutionary history.
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Affiliation(s)
- T C Bougie
- Dept. of Biology, San Diego State University, San Diego, CA 92182, United States; Evolution, Ecology, and Organismal Biology Department, University of California Riverside, Riverside, CA 92521, United States.
| | - A Brelsford
- Evolution, Ecology, and Organismal Biology Department, University of California Riverside, Riverside, CA 92521, United States
| | - M Hedin
- Dept. of Biology, San Diego State University, San Diego, CA 92182, United States
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50
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DePasquale AN, Webb SE, Williamson RE, Fedigan LM, Melin AD. Testing the niche differentiation hypothesis in wild capuchin monkeys with polymorphic color vision. Behav Ecol 2021. [DOI: 10.1093/beheco/arab001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
The polymorphic color vision system present in most North, Central, and South American monkeys is a textbook case of balancing selection, yet the mechanism behind it remains poorly understood. Previous work has established task-specific foraging advantages to different color vision phenotypes: dichromats (red-green colorblind) are more efficient foraging for invertebrates, while trichromats (color “normal” relative to humans) are more efficient foraging for “reddish” ripe fruit, suggesting that niche differentiation may underlie the maintenance of color vision variation. We explore a prediction of the niche differentiation hypothesis by asking whether dichromatic and trichromatic capuchin monkeys (Cebus imitator) diverge in their foraging activity budget, specifically testing whether dichromats forage more frequently for invertebrates and trichromats forage more frequently for “reddish” ripe fruit. To assess this, we analyze a large data set of behavioral scan samples (n = 21 984) from 48 wild adult female capuchins of known color vision genotype, dominance rank, and reproductive status, together with models of food conspicuity. We find no significant differences between dichromats and trichromats in the frequency of scans spent foraging for different food types but do find that nursing females forage less overall than cycling females. Our results suggest that the potential for color-vision-based niche differentiation in foraging time may be curtailed by the energetic requirements of reproduction, behavioral synchrony caused by group living, and/or individual preferences. While niche differentiation in activity budgets by color vision type is not apparent, fine-scale niche differentiation may be occurring. This research enhances our understanding of the evolutionary processes maintaining sensory polymorphisms.
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Affiliation(s)
- Allegra N DePasquale
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Shasta E Webb
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Rachel E Williamson
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Linda M Fedigan
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB T2N 4N1, Canada
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