1
|
Yusuf LH, Lemus YS, Thorpe P, Garcia CM, Ritchie MG. Evidence for gene flow and trait reversal during radiation of Mexican Goodeid fish. Heredity (Edinb) 2024:10.1038/s41437-024-00694-1. [PMID: 38858547 DOI: 10.1038/s41437-024-00694-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/12/2024] Open
Abstract
Understanding the phylogeographic history of a group and identifying the factors contributing to speciation is an important challenge in evolutionary biology. The Goodeinae are a group of live-bearing fishes endemic to Mexico. Here, we develop genomic resources for species within the Goodeinae and use phylogenomic approaches to characterise their evolutionary history. We sequenced, assembled and annotated the genomes of four Goodeinae species, including Ataeniobius toweri, the only matrotrophic live-bearing fish without a trophotaenia in the group. We estimated timings of species divergence and examined the extent and timing of introgression between the species to assess if this may have occurred during an early radiation, or in more recent episodes of secondary contact. We used branch-site models to detect genome-wide positive selection across Goodeinae, and we specifically asked whether this differs in A. toweri, where loss of placental viviparity has recently occurred. We found evidence of gene flow between geographically isolated species, suggesting vicariant speciation was supplemented by limited post-speciation gene flow, and gene flow may explain previous uncertainties about Goodeid phylogeny. Genes under positive selection in the group are likely to be associated with the switch to live-bearing. Overall, our studies suggest that both volcanism-driven vicariance and changes in reproductive mode influenced radiation in the Goodeinae.
Collapse
Affiliation(s)
- Leeban H Yusuf
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK.
| | - Yolitzi Saldívar Lemus
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
- Department of Biology, Texas State University, San Marcos, TX, USA
| | - Peter Thorpe
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Constantino Macías Garcia
- Instituto de Ecologia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito exterior s/n anexo al Jardín Botánico C. P. 04510, Mexico City CdMx, Mexico
| | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| |
Collapse
|
2
|
Yusuf LH, Saldívar Lemus Y, Thorpe P, Macías Garcia C, Ritchie MG. Genomic Signatures Associated with Transitions to Viviparity in Cyprinodontiformes. Mol Biol Evol 2023; 40:msad208. [PMID: 37789509 PMCID: PMC10568250 DOI: 10.1093/molbev/msad208] [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: 02/23/2023] [Revised: 08/23/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
The transition from oviparity to viviparity has occurred independently over 150 times across vertebrates, presenting one of the most compelling cases of phenotypic convergence. However, whether the repeated, independent evolution of viviparity is driven by redeployment of similar genetic mechanisms and whether these leave a common signature in genomic divergence remains largely unknown. Although recent investigations into the evolution of viviparity have demonstrated striking similarity among the genes and molecular pathways involved across disparate vertebrate groups, quantitative tests for genome-wide convergent have provided ambivalent answers. Here, we investigate the potential role of molecular convergence during independent transitions to viviparity across an order of ray-finned freshwater fish (Cyprinodontiformes). We assembled de novo genomes and utilized publicly available genomes of viviparous and oviparous species to test for molecular convergence across both coding and noncoding regions. We found no evidence for an excess of molecular convergence in amino acid substitutions and in rates of sequence divergence, implying independent genetic changes are associated with these transitions. However, both statistical power and biological confounds could constrain our ability to detect significant correlated evolution. We therefore identified candidate genes with potential signatures of molecular convergence in viviparous Cyprinodontiformes lineages. Motif enrichment and gene ontology analyses suggest transcriptional changes associated with early morphogenesis, brain development, and immunity occurred alongside the evolution of viviparity. Overall, however, our findings indicate that independent transitions to viviparity in these fish are not strongly associated with an excess of molecular convergence, but a few genes show convincing evidence of convergent evolution.
Collapse
Affiliation(s)
- Leeban H Yusuf
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - Yolitzi Saldívar Lemus
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
- Department of Biology, Texas State University, San Marcos, TX, USA
| | - Peter Thorpe
- The Data Analysis Group, School of Life Sciences, University of Dundee, Dundee, UK
- School of Medicine, University of North Haugh, St Andrews KY16 9TF, UK
| | - Constantino Macías Garcia
- Instituto de Ecologia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City CdMx, Mexico
| | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| |
Collapse
|
3
|
Pituitary-Gland-Based Genes Participates in Intrauterine Growth Restriction in Piglets. Genes (Basel) 2022; 13:genes13112141. [DOI: 10.3390/genes13112141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Intrauterine growth restriction (IUGR) is a major problem associated with piglet growth performance. The incidence of IUGR is widespread in Rongchang pigs. The pituitary gland is important for regulating growth and metabolism, and research has identified genes associated with growth and development. The pituitary gland of newborn piglets with normal birth weight (NBW group, n = 3) and (IUGR group, n = 3) was collected for transcriptome analysis. A total of 323 differentially expression genes (DEGs) were identified (|log2(fold-change)| > 1 and q value < 0.05), of which 223 were upregulated and 100 were downregulated. Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that the DEGs were mainly related to the extracellular matrix, regulation of the multicellular organismal process, tissue development and angiogenesis, which participate in the growth and immune response in IUGR piglets. Moreover, 7 DEGs including IGF2, THBS1, ITGA1, ITGA8, EPSTI1, FOSB, and UCP2 were associated with growth and immune response. Furthermore, based on the interaction network analysis of the DEGs, two genes, IGF2 and THBS1, participated in cell proliferation, embryonic development and angiogenesis. IGF2 and THBS1 were also the main genes participating in the IUGR. This study identified the core genes involved in IUGR in piglets and provided a reference for exploring the effect of the pituitary gland on piglet growth.
Collapse
|
4
|
Daigneault BW. Insights to maternal regulation of the paternal genome in mammalian livestock embryos: A mini-review. Front Genet 2022; 13:909804. [PMID: 36061209 PMCID: PMC9437210 DOI: 10.3389/fgene.2022.909804] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/22/2022] [Indexed: 11/25/2022] Open
Abstract
This mini-review focuses on current knowledge regarding maternal regulation of the paternal genome in early embryos of mammalian livestock species. Emphasis has been placed on regulatory events described for maternally imprinted genes and further highlights transcriptional regulation of the post-fertilization paternal genome by maternal factors. Specifically, the included content aims to summarize genomic and epigenomic contributions of paternally expressed genes, their regulation by the maternal embryo environment, and chromatin structure that are indispensable for early embryo development. The accumulation of current knowledge will summarize conserved allelic function among species to include molecular and genomic studies across large domestic animals and humans with reference to founding experimental animal models.
Collapse
|
5
|
Conflict and the evolution of viviparity in vertebrates. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03171-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
6
|
Du K, Pippel M, Kneitz S, Feron R, da Cruz I, Winkler S, Wilde B, Avila Luna EG, Myers E, Guiguen Y, Macias Garcia C, Schartl M. Genome biology of the Darkedged Splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation. Genome Res 2022; 32:583-594. [PMID: 35082141 PMCID: PMC8896457 DOI: 10.1101/gr.275826.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 01/10/2022] [Indexed: 11/24/2022]
Abstract
Viviparity evolved independently about 150 times in vertebrates and more than 20 times in fish. Several lineages added to the protection of the embryo inside the body of the mother, the provisioning of nutrients, and physiological exchange. This often led to the evolution of a placenta. Among fish, one of the most complex systems serving the function of the placenta is the embryonal trophotaenia/ovarian luminal epithelium of the goodeid fishes. For a better understanding of this feature and others of this group of fishes, high-quality genomic resources are essential. We have sequenced the genome of the darkedged splitfin, Girardinichthys multiradiatus. The assembly is chromosome level and includes the X and Y Chromosomes. A large male-specific region on the Y was identified covering 80% of Chromosome 20, allowing some first inferences on the recent origin and a candidate male sex determining gene. Genome-wide transcriptomics uncovered sex-specific differences in brain gene expression with an enrichment for neurosteroidogenesis and testis genes in males. The expression signatures of the splitfin embryonal and maternal placenta showed overlap with homologous tissues including human placenta, the ovarian follicle epithelium of matrotrophic poeciliid fish species and the brood pouch epithelium of the seahorse. Our comparative analyses on the evolution of embryonal and maternal placenta indicate that the evolutionary novelty of maternal provisioning development repeatedly made use of genes that already had the same function in other tissues. In this way, preexisting modules are assembled and repurposed to provide the molecular changes for this novel trait.
Collapse
Affiliation(s)
| | - Martin Pippel
- Max-Planck Institute of Molecular Cell Biology and Genetics
| | | | - Romain Feron
- University of Lausanne, Swiss Institute of Bioinformatics, INRAE, LPGP
| | | | - Sylke Winkler
- Max-Planck Institute of Molecular Cell Biology and Genetics
| | | | - Edgar G Avila Luna
- Instituto de Ecologia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito exterior s/n anexo al Jardín Botánico
| | - Eugene Myers
- Max-Planck Institute of Molecular Cell Biology and Genetics
| | | | - Constantino Macias Garcia
- Instituto de Ecologia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito exterior s/n anexo al Jardín Botánico
| | | |
Collapse
|
7
|
Hellmann JK, Bukhari SA, Deno J, Bell AM. Sex-specific plasticity across generations I: Maternal and paternal effects on sons and daughters. J Anim Ecol 2020; 89:2788-2799. [PMID: 33191518 PMCID: PMC7902357 DOI: 10.1111/1365-2656.13364] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023]
Abstract
Intergenerational plasticity or parental effects-when parental environments alter the phenotype of future generations-can influence how organisms cope with environmental change. An intriguing, underexplored possibility is that sex-of both the parent and the offspring-plays an important role in driving the evolution of intergenerational plasticity in both adaptive and non-adaptive ways. Here, we evaluate the potential for sex-specific parental effects in a freshwater population of three-spined sticklebacks Gasterosteus aculeatus by independently and jointly manipulating maternal and paternal experiences and separately evaluating their phenotypic effects in sons versus daughters. We tested the adaptive hypothesis that daughters are more responsive to cues from their mother, whereas sons are more responsive to cues from their father. We exposed mothers, fathers or both parents to visual cues of predation risk and measured offspring antipredator traits and brain gene expression. Predator-exposed fathers produced sons that were more risk-prone, whereas predator-exposed mothers produced more anxious sons and daughters. Furthermore, maternal and paternal effects on offspring survival were non-additive: offspring with a predator-exposed father, but not two predator-exposed parents, had lower survival against live predators. There were also strong sex-specific effects on brain gene expression: exposing mothers versus fathers to predation risk activated different transcriptional profiles in their offspring, and sons and daughters strongly differed in the ways in which their brain gene expression profiles were influenced by parental experience. We found little evidence to support the hypothesis that offspring prioritize their same-sex parent's experience. Parental effects varied with both the sex of the parent and the offspring in complicated and non-additive ways. Failing to account for these sex-specific patterns (e.g. by pooling sons and daughters) would have underestimated the magnitude of parental effects. Altogether, these results draw attention to the potential for sex to influence patterns of intergenerational plasticity and raise new questions about the interface between intergenerational plasticity and sex-specific selective pressures, sexual conflict and sexual selection.
Collapse
Affiliation(s)
- Jennifer K Hellmann
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA, 61801
| | - Syed Abbas Bukhari
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA, 61801
| | - Jack Deno
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA, 61801
| | - Alison M Bell
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA, 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA, 61801
- Program in Ecology, Evolution and Conservation, University of Illinois Urbana-Champaign, Urbana, Illinois, USA, 61801
| |
Collapse
|
8
|
Mokkonen M, Koskela E, Procyshyn T, Crespi B. Socio-reproductive Conflicts and the Father's Curse Dilemma. Am Nat 2018; 192:250-262. [PMID: 30016171 DOI: 10.1086/698216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Evolutionary conflicts between males and females can manifest over sexually antagonistic interactions at loci or over sexually antagonistic interests within a locus. The latter form of conflict, intralocus sexual conflict, arises from sexually antagonistic selection and constrains the fitness of individuals through a phenotypic compromise. These conflicts, and socio-reproductive interactions in general, are commonly mediated by hormones, and thus predictive insights can be gained from studying their mediating effects. Here, we integrate several lines of evidence to describe a novel, hormonally mediated reproductive dilemma that we call the father's curse, which results from an intralocus conflict between mating and parental efforts. Essentially, a genetic locus exerts pleiotropic and antagonistic effects on the mating effort of one individual and the parental effort of a related individual who is the primary provider of parental care. We outline the criteria for operation of the father's curse dilemma, provide evidence of the phenomenon, and discuss the predictions and outcomes arising from its dynamics. By integrating the effects of hormones into socio-reproductive conflicts and socio-reproductive effort, clearer links between genotypes, phenotypes, and fitness can be established.
Collapse
|
9
|
Saldivar Lemus Y, Vielle-Calzada JP, Ritchie MG, Macías Garcia C. Asymmetric paternal effect on offspring size linked to parent-of-origin expression of an insulin-like growth factor. Ecol Evol 2017. [PMID: 28649356 PMCID: PMC5478053 DOI: 10.1002/ece3.3025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Sexual reproduction brings together reproductive partners whose long‐term interests often differ, raising the possibility of conflict over their reproductive investment. Males that enhance maternal investment in their offspring gain fitness benefits, even if this compromises future reproductive investment by iteroparous females. When the conflict occurs at a genomic level, it may be uncovered by crossing divergent populations, as a mismatch in the coevolved patterns of paternal manipulation and maternal resistance may generate asymmetric embryonic growth. We report such an asymmetry in reciprocal crosses between populations of the fish Girardinichthys multiradiatus. We also show that a fragment of a gene which can influence embryonic growth (Insulin‐Like Growth Factor 2; igf2) exhibits a parent‐of‐origin methylation pattern, where the maternally inherited igf2 allele has much more 5′ cytosine methylation than the paternally inherited allele. Our findings suggest that male manipulation of maternal investment may have evolved in fish, while the parent‐of‐origin methylation pattern appears to be a potential candidate mechanism modulating this antagonistic coevolution process. However, disruption of other coadaptive processes cannot be ruled out, as these can lead to similar effects as conflict.
Collapse
|