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Bare EA, Bogart JP, Wilson C, Murray DL, Hossie TJ. Diversity and composition of mixed-ploidy unisexual salamander assemblages reflect the key influence of host species. Oecologia 2023; 202:807-818. [PMID: 37615743 DOI: 10.1007/s00442-023-05440-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023]
Abstract
Understanding processes that govern and sustain biological diversity is a central goal of community ecology. Unisexual complexes, where reproduction depends on sperm from males of one or more bisexual host species, are rare and the processes driving their diversity and structure remain poorly understood. Unisexual Ambystoma salamanders produce distinct biotypes ('genomotypes') depending on which bisexual species they 'steal' sperm from. This reproductive mode should generate distinct assemblages depending on the locally available bisexual host species. Yet, how availability and relative abundance of multiple bisexual hosts influences composition and diversity of natural unisexual assemblages at local or regional scales remains unknown. We hypothesize that host identity most directly drives local assemblage composition, with host variation associated with increased beta and gamma diversity within unisexuals. We collected genetic samples from Ambystoma salamanders across Pelee Island, Ontario, Canada (2015-2022). Two host species were identified (A. texanum and A. laterale) with nine sites having a single host and one site having both. Unisexual assemblages were grouped into four clusters by similarity, with host identity being a key determinant. Gamma diversity increased as a result of distinct host-specific assemblages forming at different sites on the island (i.e., high beta diversity). Assemblage composition, but not diversity, was correlated with relative host abundance, which may reflect matching niche requirements between host and unisexual forms they produce. Our results demonstrate that diversity and structure of unisexual assemblages are clearly shaped by their host(s) and such systems may serve as models for studying how biotic interactions shape ecological communities.
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Affiliation(s)
- Evan A Bare
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, K9L 0G2, Canada.
| | - Jim P Bogart
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Chris Wilson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, K9L 0G2, Canada
- Aquatic Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, ON, Canada
| | - Dennis L Murray
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, K9L 0G2, Canada
- Biology Department, Trent University, Peterborough, ON, K9L 1Z8, Canada
| | - Thomas J Hossie
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, K9L 0G2, Canada
- Biology Department, Trent University, Peterborough, ON, K9L 1Z8, Canada
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Affiliation(s)
- J.P. Bogart
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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Bogart JP. A family study to examine clonal diversity in unisexual salamanders (genus Ambystoma). Genome 2019; 62:549-561. [DOI: 10.1139/gen-2019-0034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Unisexual Ambystoma are the oldest known unisexual vertebrates and comprise a lineage of eastern North American all female salamanders that reproduce by stealing sperm from as many as five normally bisexual congeneric species. The sperm may be used to only stimulate egg development by gynogenesis but can be incorporated in the zygote to elevate the ploidy level or to replace one of the female’s haploid genomes. This flexible and unique reproductive system, termed kleptogenesis, is investigated using a microsatellite examination of 988 offspring from 14 unisexual mothers. All mothers produced clonal and ploidy-elevated offspring. Genome replacement and multiple paternity are confirmed for the first time in unisexual Ambystoma. Microsatellite mutations were found in all five microsatellite loci and the estimated microsatellite mutation rate varied by locus and by genome. Clonal variation is attributed to the inclusion of sperm donors’ haploid genomes for ploidy elevation, genome replacement, mutations, and natural selection.
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Affiliation(s)
- James P. Bogart
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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Duclos KK, Hendrikse JL, Jamniczky HA. Investigating the evolution and development of biological complexity under the framework of epigenetics. Evol Dev 2019; 21:247-264. [PMID: 31268245 PMCID: PMC6852014 DOI: 10.1111/ede.12301] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Biological complexity is a key component of evolvability, yet its study has been hampered by a focus on evolutionary trends of complexification and inconsistent definitions. Here, we demonstrate the utility of bringing complexity into the framework of epigenetics to better investigate its utility as a concept in evolutionary biology. We first analyze the existing metrics of complexity and explore the link between complexity and adaptation. Although recently developed metrics allow for a unified framework, they omit developmental mechanisms. We argue that a better approach to the empirical study of complexity and its evolution includes developmental mechanisms. We then consider epigenetic mechanisms and their role in shaping developmental and evolutionary trajectories, as well as the development and organization of complexity. We argue that epigenetics itself could have emerged from complexity because of a need to self‐regulate. Finally, we explore hybridization complexes and hybrid organisms as potential models for studying the association between epigenetics and complexity. Our goal is not to explain trends in biological complexity but to help develop and elucidate novel questions in the investigation of biological complexity and its evolution. This manuscript argues that biological complexity is better understood under the framework of epigenetics and that the epigenetic interactions emerge from the self‐regulation of complex systems. Hybrids are offered as models to study these properties.
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Affiliation(s)
- Kevin K Duclos
- Department of Cell Biology and Anatomy, The University of Calgary, Calgary, Alberta, Canada
| | - Jesse L Hendrikse
- Department of Community Health Sciences, The University of Calgary, Calgary, Alberta, Canada
| | - Heather A Jamniczky
- Department of Cell Biology and Anatomy, The University of Calgary, Calgary, Alberta, Canada
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Beauregard F, Angers B. Effect of a locally adapted genome on environmentally induced epigenetic variation. ENVIRONMENTAL EPIGENETICS 2018; 4:dvy025. [PMID: 30505465 PMCID: PMC6255975 DOI: 10.1093/eep/dvy025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/02/2018] [Accepted: 10/16/2018] [Indexed: 06/09/2023]
Abstract
Both genetic variation and environmentally induced epigenetic changes allow organisms to persist through the heterogeneity of their habitats. Selection on genetic variation can promote local adaptation of populations. However, in absence of genetic variation, clonal organisms mostly rely on epigenetics to respond to environmental heterogeneity. We used the potential of unisexual organisms in incorporating their host genome, to empirically assess whether the presence of a locally adapted genome affects environmentally induced epigenetic changes in clonal organisms. We addressed this problematic by using unisexual lineages of the kleptogen vertebrate Ambystoma laterale-jeffersonianum complex that can optionally incorporate genetic material from locally adapted sexual hosts through genomic exchanges. More specifically, we compared environmentally induced epigenetic changes between lineages strictly reproducing clonally vs. those incorporating a locally adapted genome. The results revealed that both lineage and sample site components, as well as their interaction, affected epigenetic variation. When lineages were analysed separately, differences among sample sites were only detected in lineages impervious to genomic exchanges. Sample sites had no significant effect on the epigenetic variation of lineages that performed genomic exchanges. These results suggest that environmentally induced epigenetic variation among sites depends more on the lack of locally adapted alleles than on the level of genetic variation.
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Affiliation(s)
- France Beauregard
- Departement of Biological Sciences, Université de Montréal, Montréal, Canada
| | - Bernard Angers
- Departement of Biological Sciences, Université de Montréal, Montréal, Canada
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Denton RD, Morales AE, Gibbs HL. Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species. Evolution 2018; 72:1689-1700. [PMID: 29926914 DOI: 10.1111/evo.13528] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/07/2018] [Accepted: 06/14/2018] [Indexed: 02/06/2023]
Abstract
Quantifying introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what drives the longevity of putatively asexual groups. Here, we capitalize on three recent innovations-ultraconserved element (UCE) sequencing, bioinformatic techniques for identifying genome-specific variation in polyploids, and model-based methods for evaluating historical gene flow-to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all-female salamanders and two ancestral sexual species. Our analyses support a scenario in which the genomes sampled in unisexual salamanders last shared a common ancestor with genomes in their parental species ∼3.4 million years ago, followed by a period of divergence between homologous genomes. Recently, secondary introgression has occurred at different times with each sexual species during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage is the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have undergone long periods of divergence without introgression. Unlike other sperm-dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could explain why these salamanders are among the oldest described unisexual animals.
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Affiliation(s)
- Robert D Denton
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, Ohio 43210
- Ohio Biodiversity Conservation Partnership, Columbus, Ohio 43210
- Current Address: Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Ariadna E Morales
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, Ohio 43210
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, Ohio 43210
- Ohio Biodiversity Conservation Partnership, Columbus, Ohio 43210
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Beauregard F, Angers B. Influence of genome and bio-ecology on the prevalence of genome exchange in unisexuals of the Ambystoma complex. BMC Evol Biol 2018; 18:82. [PMID: 29855267 PMCID: PMC5984407 DOI: 10.1186/s12862-018-1200-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 05/21/2018] [Indexed: 11/15/2022] Open
Abstract
Background Unisexuals of the blue-spotted salamander complex are thought to reproduce by kleptogenesis. Genome exchanges associated with this sperm-dependent mode of reproduction are expected to result in a higher genetic variation and multiple ploidy levels compared to clonality. However, the existence of some populations exclusively formed of genetically identical individuals suggests that factors could prevent genome exchanges. This study aimed at assessing the prevalence of genome exchange among unisexuals of the Ambystoma laterale-jeffersonianum complex from 10 sites in the northern part of their distribution. Results A total of 235 individuals, including 207 unisexuals, were genotyped using microsatellite loci and AFLP. Unisexual individuals could be sorted in five genetically distinct groups, likely derived from the same paternal A. jeffersonianum haplome. One of these groups exclusively reproduced clonally, even when found in sympatry with lineages presenting signature of genome exchange. Genome exchange was site-dependent for another group. Genome exchange was detected at all sites for the three remaining groups. Conclusion Prevalence of genome exchange appears to be associated with ecological conditions such as availability of effective sperm donors. Intrinsic genomic factors may also affect this process, since different lineages in sympatry present highly variable rate of genome exchange. The coexistence of clonal and genetically diversified lineages opens the door to further research on alternatives to genetic variation. Electronic supplementary material The online version of this article (10.1186/s12862-018-1200-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- France Beauregard
- Departement of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, QC, H3C 317, Canada
| | - Bernard Angers
- Departement of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, QC, H3C 317, Canada.
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Denton RD, Greenwald KR, Gibbs HL. Locomotor endurance predicts differences in realized dispersal between sympatric sexual and unisexual salamanders. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12813] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Robert D. Denton
- Department of Evolution, Ecology and Organismal Biology Ohio State University, 300 Aronoff Laboratory, 318 West 12th Avenue Columbus OH 43210 USA
- Ohio Biodiversity Conservation Partnership Ohio State University, 300 Aronoff Laboratory, 318 West 12th Avenue Columbus OH 43210 USA
| | - Katherine R. Greenwald
- Department of Biology Eastern Michigan University, 441 Mark Jefferson Science Complex Ypsilanti MI 48197 USA
| | - H. Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology Ohio State University, 300 Aronoff Laboratory, 318 West 12th Avenue Columbus OH 43210 USA
- Ohio Biodiversity Conservation Partnership Ohio State University, 300 Aronoff Laboratory, 318 West 12th Avenue Columbus OH 43210 USA
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Teltser C, Greenwald KR. Survivorship of Ploidy-variable UnisexualAmbystomaSalamanders Across Developmental Stages. HERPETOLOGICA 2015. [DOI: 10.1655/herpetologica-d-14-00007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Bogart JP, Bi K. Genetic and genomic interactions of animals with different ploidy levels. Cytogenet Genome Res 2013; 140:117-36. [PMID: 23751376 DOI: 10.1159/000351593] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Polyploid animals have independently evolved from diploids in diverse taxa across the tree of life. We review a few polyploid animal species or biotypes where recently developed molecular and cytogenetic methods have significantly improved our understanding of their genetics, reproduction and evolution. Mitochondrial sequences that target the maternal ancestor of a polyploid show that polyploids may have single (e.g. unisexual salamanders in the genus Ambystoma) or multiple (e.g. parthenogenetic polyploid lizards in the genus Aspidoscelis) origins. Microsatellites are nuclear markers that can be used to analyze genetic recombinations, reproductive modes (e.g. Ambystoma) and recombination events (e.g. polyploid frogs such as Pelophylax esculentus). Hom(e)ologous chromosomes and rare intergenomic exchanges in allopolyploids have been distinguished by applying genome-specific fluorescent probes to chromosome spreads. Polyploids arise, and are maintained, through perturbations of the 'normal' meiotic program that would include pre-meiotic chromosome replication and genomic integrity of homologs. When possible, asexual, unisexual and bisexual polyploid species or biotypes interact with diploid relatives, and genes are passed from diploid to polyploid gene pools, which increase genetic diversity and ultimately evolutionary flexibility in the polyploid. When diploid relatives do not exist, polyploids can interact with another polyploid (e.g. species of African Clawed Frogs in the genus Xenopus). Some polyploid fish (e.g. salmonids) and frogs (Xenopus) represent independent lineages whose ancestors experienced whole genome duplication events. Some tetraploid frogs (P. esculentus) and fish (Squaliusalburnoides) may be in the process of becoming independent species, but diploid and triploid forms of these 'species' continue to genetically interact with the comparatively few tetraploid populations. Genetic and genomic interaction between polyploids and diploids is a complex and dynamic process that likely plays a crucial role for the evolution and persistence of polyploid animals. See also other articles in this themed issue.
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Affiliation(s)
- J P Bogart
- Department of Integrative Biology, University of Guelph, Guelph, Ont., Canada. jbogart @ uoguelph.ca
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