| 1. |
- Cervantes, Sandra, et al.
(författare)
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Strong Purifying Selection in Haploid Tissue-Specific Genes of Scots Pine Supports the Masking Theory
- 2023
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Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 40:8
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Tidskriftsartikel (refereegranskat)abstract
- The masking theory states that genes expressed in a haploid stage will be under more efficient selection. In contrast, selection will be less efficient in genes expressed in a diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can be hidden from selection in heterozygous form. This difference can influence several evolutionary processes such as the maintenance of genetic variation, adaptation rate, and genetic load. Masking theory expectations have been confirmed in single-cell haploid and diploid organisms. However, in multicellular organisms, such as plants, the effects of haploid selection are not clear-cut. In plants, the great majority of studies indicating haploid selection have been carried out using male haploid tissues in angiosperms. Hence, evidence in these systems is confounded with the effects of sexual selection and intraspecific competition. Evidence from other plant groups is scarce, and results show no support for the masking theory. Here, we have used a gymnosperm Scots pine megagametophyte, a maternally derived seed haploid tissue, and four diploid tissues to test the strength of purifying selection on a set of genes with tissue-specific expression. By using targeted resequencing data of those genes, we obtained estimates of genetic diversity, the site frequency spectrum of 0-fold and 4-fold sites, and inferred the distribution of fitness effects of new mutations in haploid and diploid tissue-specific genes. Our results show that purifying selection is stronger for tissue-specific genes expressed in the haploid megagametophyte tissue and that this signal of strong selection is not an artifact driven by high expression levels.
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| 2. |
- Dhaygude, Kishor, et al.
(författare)
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Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta
- 2017
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.
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| 3. |
- Helanterä, Heikki, et al.
(författare)
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Different perspectives on non-genetic inheritance illustrate the versatile utility of the Price equation in evolutionary biology
- 2020
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Ingår i: Philosophical Transactions of the Royal Society B: Biological Sciences. - : The Royal Society. - 1471-2970 .- 0962-8436. ; 375:1797
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Tidskriftsartikel (refereegranskat)abstract
- The diversity of genetic and non-genetic processes that make offspring resemble their parents are increasingly well understood. In addition to genetic inheritance, parent-offspring similarity is affected by epigenetic, behavioural and cultural mechanisms that collectively can be referred to as non-genetic inheritance. Given the generality of the Price equation as a description of evolutionary change, is it not surprising that the Price equation has been adopted to model the evolutionary implications of non-genetic inheritance. In this paper, we briefly introduce the heredity perspectives on which those models rely, discuss the extent to which these perspectives make different assumptions and place different emphases on the roles of heredity and development in evolution, and the types of empirical research programmes they motivate. The existence of multiple perspectives and explanatory aims highlight, on the one hand, the versatility of the Price equation and, on the other hand, the importance of understanding how heredity and development can be conceptualized in evolutionary studies. This article is part of the theme issue 'Fifty years of the Price equation'.
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| 4. |
- Helanterä, Heikki, et al.
(författare)
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Neutral and adaptive explanations for an association between caste-biased gene expression and rate of sequence evolution.
- 2014
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Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 5, s. 1-297
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Tidskriftsartikel (refereegranskat)abstract
- The castes of social insects provide outstanding opportunities to address the causes and consequences of evolution of discrete phenotypes, i.e., polymorphisms. Here we focus on recently described patterns of a positive association between the degree of caste-specific gene expression and the rate of sequence evolution. We outline how neutral and adaptive evolution can cause genes that are morph-biased in their expression profiles to exhibit historical signatures of faster or slower sequence evolution compared to unbiased genes. We conclude that evaluation of different hypotheses will benefit from (i) reconstruction of the phylogenetic origin of biased expression and changes in rates of sequence evolution, and (ii) replicated data on gene expression variation within versus between morphs. Although the data are limited at present, we suggest that the observed phylogenetic and intra-population variation in gene expression lends support to the hypothesis that the association between caste-biased expression and rate of sequence evolution largely is a result of neutral processes.
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| 5. |
- Tuominen, Laura S., et al.
(författare)
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Factors promoting hunting groups’ sustainable harvest of moose in a co-management system
- 2023
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Ingår i: Scientific Reports. - 2045-2322. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Collaboration between and within management levels and involvement of local communities (co-management) increases sustainable management of natural resources. In Finland, moose (Alces alces) are harvested by hunting groups within a co-management system, providing meat and social benefits. We computed the 14-year change in moose harvest (2007–2020) for 4320 hunting groups. Moose harvest declined on average 1.1% per year, but with substantial variation in moose harvest changes between the hunting groups. We extracted information describing the collaboration between the hunting groups, their democratic status as well as leader dynamics, and the year of establishment. A hunting group’s moose harvest was more stable (i.e. declined less) when the hunting group was (1) established a longer time ago; (2), had more changes in leadership over time, but did not depend on collaboration with other local hunting groups (in terms of jointly holding moose hunting licenses), whether the hunting group was a registered society (presumed to be more democratic than a non-registered one) or had consecutive leaders that shared a surname (presumed to be related). We conclude that encouraging resource users’ early establishment in groups and groups’ long-term persistence and promoting democratic leadership roles improves stable benefits from a natural resource in a co-management system.
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| 6. |
- Tuominen, Laura S., et al.
(författare)
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Structural equation modeling reveals decoupling of ecological and self-perceived outcomes in a garden box social-ecological system
- 2022
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- It is well known that green urban commons enhance mental and physical well-being and improve local biodiversity. We aim to investigate how these outcomes are related in an urban system and which variables are associated with better outcomes. We model the outcomes of an urban common—box gardening—by applying the Social-Ecological Systems (SES) framework. We expand the SES framework by analyzing it from the perspective of social evolution theory. The system was studied empirically through field inventories and questionnaires and modeled quantitatively by Structural Equation Modeling (SEM). This method offers powerful statistical models of complex social-ecological systems. Our results show that objectively evaluated ecological outcomes and self-perceived outcomes are decoupled: gardening groups that successfully govern the natural resource ecologically do not necessarily report many social, ecological, or individual benefits, and vice versa. Social capital, box location, gardener concerns, and starting year influenced the changes in the outcomes. In addition, the positive association of frequent interactions with higher self-perceived outcomes, and lack of such association with relatedness of group members suggests that reciprocity rather than kin selection explains cooperation. Our findings exemplify the importance of understanding natural resource systems at a very low “grassroot” level.
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| 7. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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