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Rios-Carlos H, Segovia-Ramírez MG, Fujita MK, Rovito SM. Genomic Gigantism is not Associated with Reduced Selection Efficiency in Neotropical Salamanders. J Mol Evol 2024; 92:371-380. [PMID: 38844681 PMCID: PMC11291587 DOI: 10.1007/s00239-024-10177-w] [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: 02/28/2024] [Accepted: 05/16/2024] [Indexed: 08/03/2024]
Abstract
Genome size variation in eukaryotes has myriad effects on organismal biology from the genomic to whole-organism level. Large genome size may be associated with lower selection efficiency because lower effective population sizes allow fixation of deleterious mutations via genetic drift, increasing genome size and decreasing selection efficiency. Because of a hypothesized negative relationship between genome size and recombination rate per base pair, increased genome size could also increase the effect of linked selection in the genome, decreasing the efficiency with which natural selection can fix or remove mutations. We used a transcriptomic dataset of 15 and a subset of six Neotropical salamander species ranging in genome size from 12 to 87 pg to study the relationship between genome size and efficiency of selection. We estimated dN/dS of salamanders with small and large genomes and tested for relaxation of selection in the larger genomes. Contrary to our expectations, we did not find a significant relationship between genome size and selection efficiency or strong evidence for higher dN/dS values in species with larger genomes for either species set. We also found little evidence for relaxation of selection in species with larger genomes. A positive correlation between genome size and range size (a proxy of population size) in this group disagrees with predictions of stronger drift in species with larger genomes. Our results highlight the complex interactions between the many forces shaping genomic variation in organisms with genomic gigantism.
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Affiliation(s)
- Hairo Rios-Carlos
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, México
| | - María Guadalupe Segovia-Ramírez
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, México
| | - Matthew K Fujita
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas, Arlington, TX, USA
| | - Sean M Rovito
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, México.
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2
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Iverson ENK. Conservation Mitonuclear Replacement: Facilitated mitochondrial adaptation for a changing world. Evol Appl 2024; 17:e13642. [PMID: 38468713 PMCID: PMC10925831 DOI: 10.1111/eva.13642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 03/13/2024] Open
Abstract
Most species will not be able to migrate fast enough to cope with climate change, nor evolve quickly enough with current levels of genetic variation. Exacerbating the problem are anthropogenic influences on adaptive potential, including the prevention of gene flow through habitat fragmentation and the erosion of genetic diversity in small, bottlenecked populations. Facilitated adaptation, or assisted evolution, offers a way to augment adaptive genetic variation via artificial selection, induced hybridization, or genetic engineering. One key source of genetic variation, particularly for climatic adaptation, are the core metabolic genes encoded by the mitochondrial genome. These genes influence environmental tolerance to heat, drought, and hypoxia, but must interact intimately and co-evolve with a suite of important nuclear genes. These coadapted mitonuclear genes form some of the important reproductive barriers between species. Mitochondrial genomes can and do introgress between species in an adaptive manner, and they may co-introgress with nuclear genes important for maintaining mitonuclear compatibility. Managers should consider the relevance of mitonuclear genetic variability in conservation decision-making, including as a tool for facilitating adaptation. I propose a novel technique dubbed Conservation Mitonuclear Replacement (CmNR), which entails replacing the core metabolic machinery of a threatened species-the mitochondrial genome and key nuclear loci-with those from a closely related species or a divergent population, which may be better-adapted to climatic changes or carry a lower genetic load. The most feasible route to CmNR is to combine CRISPR-based nuclear genetic editing with mitochondrial replacement and assisted reproductive technologies. This method preserves much of an organism's phenotype and could allow populations to persist in the wild when no other suitable conservation options exist. The technique could be particularly important on mountaintops, where rising temperatures threaten an alarming number of species with almost certain extinction in the next century.
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Affiliation(s)
- Erik N. K. Iverson
- Department of Integrative BiologyThe University of Texas at AustinAustinTexasUSA
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3
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Iverson ENK, Criswell A, Havird JC. Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576402. [PMID: 38328137 PMCID: PMC10849488 DOI: 10.1101/2024.01.20.576402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive, rather than relaxed purifying selection has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.
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Affiliation(s)
- Erik N K Iverson
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
| | - Abby Criswell
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
| | - Justin C Havird
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
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4
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Eliason CM, Mellenthin LE, Hains T, McCullough JM, Pirro S, Andersen MJ, Hackett SJ. Genomic signatures of convergent shifts to plunge-diving behavior in birds. Commun Biol 2023; 6:1011. [PMID: 37875535 PMCID: PMC10598022 DOI: 10.1038/s42003-023-05359-z] [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: 05/17/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023] Open
Abstract
Understanding the genetic basis of convergence at broad phylogenetic scales remains a key challenge in biology. Kingfishers (Aves: Alcedinidae) are a cosmopolitan avian radiation with diverse colors, diets, and feeding behaviors-including the archetypal plunge-dive into water. Given the sensory and locomotor challenges associated with air-water transitions, kingfishers offer a powerful opportunity to explore the effects of convergent behaviors on the evolution of genomes and phenotypes, as well as direct comparisons between continental and island lineages. Here, we use whole-genome sequencing of 30 diverse kingfisher species to identify the genomic signatures associated with convergent feeding behaviors. We show that species with smaller ranges (i.e., on islands) have experienced stronger demographic fluctuations than those on continents, and that these differences have influenced the dynamics of molecular evolution. Comparative genomic analyses reveal positive selection and genomic convergence in brain and dietary genes in plunge-divers. These findings enhance our understanding of the connections between genotype and phenotype in a diverse avian radiation.
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Affiliation(s)
- Chad M Eliason
- Grainger Bioinformatics Center, The Field Museum, Chicago, IL, USA.
- Negaunee Integrative Research Center, The Field Museum, Chicago, IL, USA.
| | - Lauren E Mellenthin
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Taylor Hains
- Grainger Bioinformatics Center, The Field Museum, Chicago, IL, USA
- Negaunee Integrative Research Center, The Field Museum, Chicago, IL, USA
- Committee on Evolution Biology, University of Chicago, Chicago, IL, USA
| | - Jenna M McCullough
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Stacy Pirro
- Iridian Genomes, Inc., 6213 Swords Way, Bethesda, MD, USA
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Shannon J Hackett
- Committee on Evolution Biology, University of Chicago, Chicago, IL, USA
- Negaunee Integrative Research Center, The Field Museum, Chicago, IL, USA
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5
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Zwonitzer KD, Iverson ENK, Sterling JE, Weaver RJ, Maclaine BA, Havird JC. Disentangling Positive Selection from Relaxed Selection in Animal Mitochondrial Genomes. Am Nat 2023; 202:E121-E129. [PMID: 37792916 PMCID: PMC10955554 DOI: 10.1086/725805] [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] [Indexed: 10/06/2023]
Abstract
AbstractDisentangling different types of selection is a common goal in molecular evolution. Elevated dN/dS ratios (the ratio of nonsynonymous to synonymous substitution rates) in focal lineages are often interpreted as signs of positive selection. Paradoxically, relaxed purifying selection can also result in elevated dN/dS ratios, but tests to distinguish these two causes are seldomly implemented. Here, we reevaluated seven case studies describing elevated dN/dS ratios in animal mitochondrial DNA (mtDNA) and their accompanying hypotheses regarding selection. They included flightless lineages versus flighted lineages in birds, bats, and insects and physiological adaptations in snakes, two groups of electric fishes, and primates. We found that elevated dN/dS ratios were often not caused by the predicted mechanism, and we sometimes found strong support for the opposite mechanism. We discuss reasons why energetic hypotheses may be confounded by other selective forces acting on mtDNA and caution against overinterpreting singular molecular signals, including elevated dN/dS ratios.
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Affiliation(s)
- Kendra D. Zwonitzer
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Erik N. K. Iverson
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Jess E. Sterling
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Ryan J. Weaver
- Department of Ecology, Evolution, and Organismal Biology and Department of Natural Resource Ecology and Management, Iowa State University, Ames, Iowa 50011
| | - Bradley A. Maclaine
- Department of Human Development and Family Sciences, University of Texas at Austin, Austin, Texas 78712
| | - Justin C. Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
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6
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Marcionetti A, Salamin N. Insights into the Genomics of Clownfish Adaptive Radiation: The Genomic Substrate of the Diversification. Genome Biol Evol 2023; 15:evad088. [PMID: 37226990 PMCID: PMC10349533 DOI: 10.1093/gbe/evad088] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/01/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023] Open
Abstract
Clownfishes are an iconic group of coral reef fishes that evolved a mutualistic interaction with sea anemones, which triggered the rapid diversification of the group. Following the emergence of this mutualism, clownfishes diversified into different ecological niches and developed convergent phenotypes associated with their host use. The genetic basis of the initial acquisition of the mutualism with host anemones has been described, but the genomic architecture underlying clownfish diversification once the mutualism was established and the extent to which clownfish phenotypic convergence originated through shared genetic mechanisms are still unknown. Here, we investigated these questions by performing comparative genomic analyses on the available genomic data of five pairs of closely related but ecologically divergent clownfish species. We found that clownfish diversification was characterized by bursts of transposable elements, an overall accelerated coding evolution, incomplete lineage sorting, and ancestral hybridization events. Additionally, we detected a signature of positive selection in 5.4% of the clownfish genes. Among them, five presented functions associated with social behavior and ecology, and they represent candidate genes involved in the evolution of the size-based hierarchical social structure so particular to clownfishes. Finally, we found genes with patterns of either relaxation or intensification of purifying selection and signals of positive selection linked with clownfish ecological divergence, suggesting some level of parallel evolution during the diversification of the group. Altogether, this work provides the first insights into the genomic substrate of clownfish adaptive radiation and integrates the growing collection of studies investigating the genomic mechanisms governing species diversification.
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Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Genopode, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Genopode, University of Lausanne, 1015 Lausanne, Switzerland
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7
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Subramanian S, Kumar M. Genomic footprints of bottleneck in landlocked salmon population. Sci Rep 2023; 13:6706. [PMID: 37185620 PMCID: PMC10130149 DOI: 10.1038/s41598-023-34076-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
At the end of the last ice age, several Atlantic salmon populations got caught up in the lakes and ponds of the Northern Hemisphere. Occasionally, the populations also got locked when the flow of rivers terminated from reaching the sea due to land upheaval. Therefore, the pattern of evolution shaping the landlocked salmon populations is different from the other anadromous salmons, which migrate between the sea and rivers. According to the theories of population genetics, the effect of genetic drift is expected to be more pronounced in the former compared to the latter. Here we examined this using the whole genome data of landlocked and anadromous salmon populations of Norway. Our results showed a 50-80% reduction in the genomic heterozygosity in the landlocked compared to anadromous salmon populations. The number and total size of the runs of homozygosity (RoH) segments of landlocked salmons were two to eightfold higher than those of their anadromous counterparts. We found the former had a higher ratio of nonsynonymous-to-synonymous diversities than the latter. The investigation also revealed a significant elevation of homozygous deleterious Single Nucleotide Variants (SNVs) in the landlocked salmon compared to the anadromous populations. All these results point to a significant reduction in the population size of the landlocked salmons. This process of reduction might have started recently as the phylogeny revealed a recent separation of the landlocked from the anadromous population. Previous studies on terrestrial vertebrates observed similar signatures of a bottleneck when the populations from Island and the mainland were compared. Since landlocked waterbody such as ponds and lakes are geographically analogous to Islands for fish populations, the findings of this study suggest the similarity in the patterns of evolution between the two.
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Affiliation(s)
- Sankar Subramanian
- Centre for Bioinnovation, School of Science, Technology, and Engineering, The University of the Sunshine Coast, 1 Moreton Parade, Petrie, Moreton Bay, QLD, 4502, Australia.
| | - Manoharan Kumar
- Centre for Bioinnovation, School of Science, Technology, and Engineering, The University of the Sunshine Coast, 1 Moreton Parade, Petrie, Moreton Bay, QLD, 4502, Australia
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8
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Li Y, Wang D, Wang W, Yang W, Gao J, Zhang W, Shan L, Kang M, Chen Y, Ma T. A chromosome-level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination. Mol Ecol 2023; 32:1366-1380. [PMID: 35712997 DOI: 10.1111/mec.16566] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/24/2022] [Accepted: 06/10/2022] [Indexed: 01/17/2023]
Abstract
Populus species have long been used as model organisms to study the adaptability of trees and the evolution of sex chromosomes. As a species belonging to the section Populus and limited to tropical areas, the P. qiongdaoensis genome contains important information for tropical poplar studies and protection. Here, we report a chromosome-level genome assembly and annotation of a female P. qiongdaoensis. Gene family clustering, positive selection detection and historical reconstruction of population dynamics revealed the tropical adaptation of P. qiongdaoensis, and showed convergent evolution with another tropical poplar, P. ilicifolia, at the molecular level, especially on some functional genes (e.g., PIF3 and PIL1). In addition, we also identified a ZW sex determination system on chromosome 19 of P. qiongdaoensis, and inferred that it seems to have a similar sex determination mechanism to other poplars, controlled by a type-A cytokinin response regulator (RR) gene. However, comparison and phylogenetic analysis of the sex determination regions confirmed a cryptic sex turnover event in the section Populus, which may be caused by the translocation and duplication of the RR gene driven by Helitron-like transposable elements. Our study provides new insights into the environmental adaptation and sex chromosome evolution of poplars, and emphasizes the importance of using long read sequencing in ecological and evolutionary inferences of plants.
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Affiliation(s)
- Yiling Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Deyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Weiwei Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wenlu Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jinwen Gao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wenyan Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lanxing Shan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Minghui Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
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9
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Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes. Nat Commun 2023; 14:617. [PMID: 36739280 PMCID: PMC9899254 DOI: 10.1038/s41467-023-36247-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 01/20/2023] [Indexed: 02/06/2023] Open
Abstract
In lineages of allopolyploid origin, sets of homoeologous chromosomes may coexist that differ in gene content and syntenic structure. Presence or absence of genes and microsynteny along chromosomal blocks can serve to differentiate subgenomes and to infer phylogenies. We here apply genome-structural data to infer relationships in an ancient allopolyploid lineage, the walnut family (Juglandaceae), by using seven chromosome-level genomes, two of them newly assembled. Microsynteny and gene-content analyses yield identical topologies that place Platycarya with Engelhardia as did a 1980s morphological-cladistic study. DNA-alignment-based topologies here and in numerous earlier studies instead group Platycarya with Carya and Juglans, perhaps misled by past hybridization. All available data support a hybrid origin of Juglandaceae from extinct or unsampled progenitors nested within, or sister to, Myricaceae. Rhoiptelea chiliantha, sister to all other Juglandaceae, contains proportionally more DNA repair genes and appears to evolve at a rate 2.6- to 3.5-times slower than the remaining species.
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10
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Wiens BJ, Combe FJ, Dickerson B, Divine LM, Padula VM, Sage GK, Talbot SL, Hope AG. Genetic drift drives rapid speciation of an Arctic insular endemic shrew (Sorex pribilofensis). Mol Ecol 2022; 31:5231-5248. [PMID: 35972323 DOI: 10.1111/mec.16658] [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] [Received: 03/09/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 12/15/2022]
Abstract
Episodes of Quaternary environmental change shaped the genomes of extant species, influencing their response to contemporary environments, which are changing rapidly. Island endemics are among the most vulnerable to such change, accounting for a disproportionate number of recent extinctions. To prevent extinctions and conserve island biodiversity it is vital to combine knowledge of species' ecologies with their complex evolutionary histories. The Bering Sea has a history of cyclical island isolation and reconnection, coupled with modern rates of climate change that exceed global averages. The endangered Pribilof Island shrew (Sorex pribilofensis) is endemic to St. Paul Island, Alaska, which was isolated from mainland Beringia ~14,000 years ago by rising sea levels. Using ~11,000 single nucleotide polymorphisms, 17 microsatellites and mitochondrial sequence data, we test predictions about the evolutionary processes driving shrew speciation across Beringia. Our data show considerable differentiation of S. pribilofensis from mainland sibling species, relative to levels of divergence between mainland shrews. We also find a genome-wide loss of diversity and extremely low Ne for S. pribilofensis. We then show that intraspecific genetic diversity is significantly related to interspecific divergence, and that differentiation between S. pribilofensis and other Beringian shrews is highest across loci that are fixed in S. pribilofensis, indicating that strong drift has driven differentiation of this island species. Our findings show that drift as a consequence of Arctic climate cycling can rapidly reshape insular biodiversity. Arctic island species that lack genomic diversity and have evolved in response to past climate may have limited ability to respond to modern environmental changes.
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Affiliation(s)
- Ben J Wiens
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Fraser J Combe
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | | - Lauren M Divine
- Aleut Community of St. Paul Island, Ecosystem Conservation Office, St. Paul, Alaska, USA
| | - Veronica M Padula
- Aleut Community of St. Paul Island, Ecosystem Conservation Office, St. Paul, Alaska, USA
| | - George K Sage
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Sandra L Talbot
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Andrew G Hope
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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11
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Ohtsuki H, Norimatsu H, Makino T, Urabe J. Invasions of an obligate asexual daphnid species support the nearly neutral theory. Sci Rep 2022; 12:7305. [PMID: 35508526 PMCID: PMC9068809 DOI: 10.1038/s41598-022-11218-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/20/2022] [Indexed: 11/09/2022] Open
Abstract
To verify the "nearly neutral theory (NNT)," the ratio of nonsynonymous to synonymous substitutions (dN/dS) was compared among populations of different species. To determine the validity of NNT, however, populations that are genetically isolated from each other but share the same selection agents and differ in size should be compared. Genetically different lineages of obligate asexual Daphnia pulex invading Japan from North America are an ideal example as they satisfy these prerequisites. Therefore, we analyzed the whole-genome sequences of 18 genotypes, including those of the two independently invaded D. pulex lineages (JPN1 and JPN2) and compared the dN/dS ratio between the lineages. The base substitution rate of each genotype demonstrated that the JPN1 lineage having a larger distribution range diverged earlier and thus was older than the JPN2 lineage. Comparisons of the genotypes within lineages revealed that changes in dN/dS occurred after the divergence and were larger in the younger lineage, JPN2. These results imply that the JPN1 lineage has been more effectively subjected to purification selections, while slightly deteriorating mutations are less purged in JPN2 with smaller population size. Altogether, the lineage-specific difference in the dN/dS ratio for the obligate asexual D. pulex was well explained by the NNT.
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Affiliation(s)
- Hajime Ohtsuki
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Hirotomo Norimatsu
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Jotaro Urabe
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
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12
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Schlis‐Elias MC, Malaney JL. Island biogeography predicts skull gigantism and shape variation in meadow voles
Microtus pennsylvanicus
through ecological release and allometry. OIKOS 2022. [DOI: 10.1111/oik.08777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Mariah C. Schlis‐Elias
- Snyder Museum of Zoology and Dept of Biology, Austin Peay State Univ. Clarksville TN USA
- New Mexico Museum of Natural History and Science, Dept of BioScience Albuquerque NM USA
| | - Jason L. Malaney
- Snyder Museum of Zoology and Dept of Biology, Austin Peay State Univ. Clarksville TN USA
- New Mexico Museum of Natural History and Science, Dept of BioScience Albuquerque NM USA
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13
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Kolařík M, Wei IC, Hsieh SY, Piepenbring M, Kirschner R. Nucleotide composition bias of rDNA sequences as a source of phylogenetic artifacts in Basidiomycota—a case of a new lineage of a uredinicolous Ramularia-like anamorph with affinities to Ustilaginomycotina. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01749-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Walters AD, Cannizzaro AG, Trujillo DA, Berg DJ. Addressing the Linnean shortfall in a cryptic species complex. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Biodiversity is being lost at an alarming rate, but the rate of this loss is likely to be underestimated as a result of a deficit in taxonomic knowledge (i.e. the Linnean shortfall). This knowledge gap is more extensive for morphologically indistinct taxa. The advancement of molecular techniques and delimitation methods has facilitated the identification of such cryptic species, but a majority of these taxa remain undescribed. To investigate the effects of taxonomic uncertainty on understanding of biodiversity, we applied the general lineage concept of species to an amphipod species complex, the Gammaruslacustris lineage that occupies springs of the northern Chihuahuan Desert, which is emerging in contemporary times. We investigated species boundaries using a validation-based approach and examined genetic structure of the lineage using a suite of microsatellite markers to identify independently evolving metapopulations. Our results show that each spring contains a genetically distinct population that is geographically isolated from other springs, suggesting evolutionary independence and status as separate species. Additionally, we observed subtle interspecific morphological variation among the putative species. We used multiple lines of evidence to formally describe four new species (Gammarus langi sp. nov., G. percalacustris sp. nov., G. colei sp. nov. and G. malpaisensis sp. nov.) endemic to the northern Chihuahuan Desert. Cryptic speciation is likely to be high in other aquatic taxa within these ecosystems, and across arid landscapes throughout North America and elsewhere, suggesting that the magnitude of the Linnean shortfall is currently underestimated in desert springs worldwide.
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Affiliation(s)
| | | | | | - David J Berg
- Department of Biology, Miami University, Hamilton, OH USA
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15
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Kutschera VE, Poelstra JW, Botero-Castro F, Dussex N, Gemmell NJ, Hunt GR, Ritchie MG, Rutz C, Wiberg RAW, Wolf JBW. Purifying Selection in Corvids Is Less Efficient on Islands. Mol Biol Evol 2020; 37:469-474. [PMID: 31633794 PMCID: PMC6993847 DOI: 10.1093/molbev/msz233] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Theory predicts that deleterious mutations accumulate more readily in small populations. As a consequence, mutation load is expected to be elevated in species where life-history strategies and geographic or historical contingencies reduce the number of reproducing individuals. Yet, few studies have empirically tested this prediction using genome-wide data in a comparative framework. We collected whole-genome sequencing data for 147 individuals across seven crow species (Corvus spp.). For each species, we estimated the distribution of fitness effects of deleterious mutations and compared it with proxies of the effective population size Ne. Island species with comparatively smaller geographic range sizes had a significantly increased mutation load. These results support the view that small populations have an elevated risk of mutational meltdown, which may contribute to the higher extinction rates observed in island species.
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Affiliation(s)
- Verena E Kutschera
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | - Fidel Botero-Castro
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Nicolas Dussex
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | | | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Christian Rutz
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - R Axel W Wiberg
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, United Kingdom.,Department of Environmental Sciences, Evolutionary Biology, University of Basel, Basel, Switzerland
| | - Jochen B W Wolf
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
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16
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Łukasik P, Chong RA, Nazario K, Matsuura Y, Bublitz DAC, Campbell MA, Meyer MC, Van Leuven JT, Pessacq P, Veloso C, Simon C, McCutcheon JP. One Hundred Mitochondrial Genomes of Cicadas. J Hered 2020; 110:247-256. [PMID: 30590568 DOI: 10.1093/jhered/esy068] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 12/21/2018] [Indexed: 01/10/2023] Open
Abstract
Mitochondrial genomes can provide valuable information on the biology and evolutionary histories of their host organisms. Here, we present and characterize the complete coding regions of 107 mitochondrial genomes (mitogenomes) of cicadas (Insecta: Hemiptera: Auchenorrhyncha: Cicadoidea), representing 31 genera, 61 species, and 83 populations. We show that all cicada mitogenomes retain the organization and gene contents thought to be ancestral in insects, with some variability among cicada clades in the length of a region between the genes nad2 and cox1, which encodes 3 tRNAs. Phylogenetic analyses using these mitogenomes recapitulate a recent 5-gene classification of cicadas into families and subfamilies, but also identify a species that falls outside of the established taxonomic framework. While protein-coding genes are under strong purifying selection, tests of relative evolutionary rates reveal significant variation in evolutionary rates across taxa, highlighting the dynamic nature of mitochondrial genome evolution in cicadas. These data will serve as a useful reference for future research into the systematics, ecology, and evolution of the superfamily Cicadoidea.
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Affiliation(s)
- Piotr Łukasik
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Rebecca A Chong
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI
| | - Katherine Nazario
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - Yu Matsuura
- Tropical Biosphere Research Center, University of the Ryukyus, Japan
| | - De Anna C Bublitz
- Division of Biological Sciences, University of Montana, Missoula, MT
| | | | - Mariah C Meyer
- Division of Biological Sciences, University of Montana, Missoula, MT
| | | | - Pablo Pessacq
- Centro de Investigaciones Esquel de Montaña y Estepa Patagónicas (CIEMEP), Esquel, Chubut, Argentina
| | - Claudio Veloso
- Department of Ecological Sciences, Science Faculty, University of Chile, Santiago, Chile
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, MT
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17
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Elbassiouny AA, Lovejoy NR, Chang BSW. Convergent patterns of evolution of mitochondrial oxidative phosphorylation (OXPHOS) genes in electric fishes. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190179. [PMID: 31787042 PMCID: PMC6939368 DOI: 10.1098/rstb.2019.0179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2019] [Indexed: 12/26/2022] Open
Abstract
The ability to generate and detect electric fields has evolved in several groups of fishes as a means of communication, navigation and, occasionally, predation. The energetic burden required can account for up to 20% of electric fishes' daily energy expenditure. Despite this, molecular adaptations that enable electric fishes to meet the metabolic demands of bioelectrogenesis remain unknown. Here, we investigate the molecular evolution of the mitochondrial oxidative phosphorylation (OXPHOS) complexes in the two most diverse clades of weakly electric fishes-South American Gymnotiformes and African Mormyroidea, using codon-based likelihood approaches. Our analyses reveal that although mitochondrial OXPHOS genes are generally subject to strong purifying selection, this constraint is significantly reduced in electric compared to non-electric fishes, particularly for complexes IV and V. Moreover, analyses of concatenated mitochondrial genes show strong evidence for positive selection in complex I genes on the two branches associated with the independent evolutionary origins of electrogenesis. These results suggest that adaptive evolution of proton translocation in the OXPHOS cellular machinery may be associated with the evolution of bioelectrogenesis. Overall, we find striking evidence for remarkably similar effects of electrogenesis on the molecular evolution of mitochondrial OXPHOS genes in two independently derived clades of electrogenic fishes. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Ahmed A. Elbassiouny
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - Nathan R. Lovejoy
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - Belinda S. W. Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
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18
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Castellano D, James J, Eyre-Walker A. Nearly Neutral Evolution across the Drosophila melanogaster Genome. Mol Biol Evol 2019; 35:2685-2694. [PMID: 30418639 DOI: 10.1093/molbev/msy164] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Under the nearly neutral theory of molecular evolution, the proportion of effectively neutral mutations is expected to depend upon the effective population size (Ne). Here, we investigate whether this is the case across the genome of Drosophila melanogaster using polymorphism data from North American and African lines. We show that the ratio of the number of nonsynonymous and synonymous polymorphisms is negatively correlated to the number of synonymous polymorphisms, even when the nonindependence is accounted for. The relationship is such that the proportion of effectively neutral nonsynonymous mutations increases by ∼45% as Ne is halved. However, we also show that this relationship is steeper than expected from an independent estimate of the distribution of fitness effects from the site frequency spectrum. We investigate a number of potential explanations for this and show, using simulation, that this is consistent with a model of genetic hitchhiking: Genetic hitchhiking depresses diversity at neutral and weakly selected sites, but has little effect on the diversity of strongly selected sites.
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Affiliation(s)
- David Castellano
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Jennifer James
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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19
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An integrative study of island diversification: Insights from the endemic Haemodracon geckos of the Socotra Archipelago. Mol Phylogenet Evol 2019; 133:166-175. [DOI: 10.1016/j.ympev.2019.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 11/22/2022]
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20
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Bolívar P, Guéguen L, Duret L, Ellegren H, Mugal CF. GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes. Genome Biol 2019; 20:5. [PMID: 30616647 PMCID: PMC6322265 DOI: 10.1186/s13059-018-1613-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 12/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in diverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection, such as the dN/dS ratio. Surprisingly, avian taxa are an exception to this theory because correlations between life-history traits and dN/dS are apparently absent. Here we explore the role of GC-biased gene conversion on estimates of substitution rates as a potential driver of these unexpected observations. RESULTS We analyze the relationship between dN/dS estimated from alignments of 47 avian genomes and several proxies for effective population size. To distinguish the impact of GC-biased gene conversion from selection, we use an approach that accounts for non-stationary base composition and estimate dN/dS separately for changes affected or unaffected by GC-biased gene conversion. This analysis shows that the impact of GC-biased gene conversion on substitution rates can explain the lack of correlations between life-history traits and dN/dS. Strong correlations between life-history traits and dN/dS are recovered after accounting for GC-biased gene conversion. The correlations are robust to variation in base composition and genomic location. CONCLUSIONS Our study shows that gene sequence evolution across a wide range of avian lineages meets the prediction of the nearly neutral theory, the efficacy of selection increases with effective population size. Moreover, our study illustrates that accounting for GC-biased gene conversion is important to correctly estimate the strength of selection.
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Affiliation(s)
- Paulina Bolívar
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Laurent Guéguen
- Laboratoire de Biologie et Biométrie Évolutive CNRS UMR 5558, Université Claude Bernard Lyon 1, Lyon, France
| | - Laurent Duret
- Laboratoire de Biologie et Biométrie Évolutive CNRS UMR 5558, Université Claude Bernard Lyon 1, Lyon, France
| | - Hans Ellegren
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Carina F. Mugal
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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21
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Barrera-Redondo J, Ramírez-Barahona S, Eguiarte LE. Rates of molecular evolution in tree ferns are associated with body size, environmental temperature, and biological productivity. Evolution 2018; 72:1050-1062. [PMID: 29604055 DOI: 10.1111/evo.13475] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 03/11/2018] [Indexed: 12/31/2022]
Abstract
Variation in rates of molecular evolution (heterotachy) is a common phenomenon among plants. Although multiple theoretical models have been proposed, fundamental questions remain regarding the combined effects of ecological and morphological traits on rate heterogeneity. Here, we used tree ferns to explore the correlation between rates of molecular evolution in chloroplast DNA sequences and several morphological and environmental factors within a Bayesian framework. We revealed direct and indirect effects of body size, biological productivity, and temperature on substitution rates, where smaller tree ferns living in warmer and less productive environments tend to have faster rates of molecular evolution. In addition, we found that variation in the ratio of nonsynonymous to synonymous substitution rates (dN/dS) in the chloroplast rbcL gene was significantly correlated with ecological and morphological variables. Heterotachy in tree ferns may be influenced by effective population size associated with variation in body size and productivity. Macroevolutionary hypotheses should go beyond explaining heterotachy in terms of mutation rates and instead, should integrate population-level factors to better understand the processes affecting the tempo of evolution at the molecular level.
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Affiliation(s)
- Josué Barrera-Redondo
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad de México 04510, México
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad de México 04510, México
| | - Luis E Eguiarte
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad de México 04510, México
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22
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Puig Giribets M, García Guerreiro MP, Santos M, Ayala FJ, Tarrío R, Rodríguez-Trelles F. Chromosomal inversions promote genomic islands of concerted evolution of Hsp70 genes in the Drosophila subobscura species subgroup. Mol Ecol 2018; 28:1316-1332. [PMID: 29412486 DOI: 10.1111/mec.14511] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/15/2018] [Accepted: 01/17/2018] [Indexed: 01/31/2023]
Abstract
Heat-shock (HS) assays to understand the connection between standing inversion variation and evolutionary response to climate change in Drosophila subobscura found that "warm-climate" inversion O3+4 exhibits non-HS levels of Hsp70 protein like those of "cold-climate" OST after HS induction. This was unexpected, as overexpression of Hsp70 can incur multiple fitness costs. To understand the genetic basis of this finding, we have determined the genomic sequence organization of the Hsp70 family in four different inversions, including OST , O3+4 , O3+4+8 and O3+4+16 , using as outgroups the remainder of the subobscura species subgroup, namely Drosophila madeirensis and Drosophila guanche. We found (i) in all the assayed lines, the Hsp70 family resides in cytological locus 94A and consists of only two genes, each with four HS elements (HSEs) and three GAGA sites on its promoter. Yet, in OST , the family is comparatively more compact; (ii) the two Hsp70 copies evolve in concert through gene conversion, except in D. guanche; (iii) within D. subobscura, the rate of concerted evolution is strongly structured by inversion, being higher in OST than in O3+4 ; and (iv) in D. guanche, the two copies accumulated multiple differences, including a newly evolved "gap-type" HSE2. The absence of concerted evolution in this species may be related to a long-gone-unnoticed observation that it lacks Hsp70 HS response, perhaps because it has evolved within a narrow thermal range in an oceanic island. Our results point to a previously unrealized link between inversions and concerted evolution, with potentially major implications for understanding genome evolution.
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Affiliation(s)
- Marta Puig Giribets
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
| | - María Pilar García Guerreiro
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
| | - Mauro Santos
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
| | - Francisco J Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Rosa Tarrío
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
| | - Francisco Rodríguez-Trelles
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
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23
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Meik JM, Schaack S, Flores-Villela O, Streicher JW. Integrative taxonomy at the nexus of population divergence and speciation in insular speckled rattlesnakes. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1429689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Jesse M. Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR, USA
| | - Oscar Flores-Villela
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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24
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Fulgione A, Koornneef M, Roux F, Hermisson J, Hancock AM. Madeiran Arabidopsis thaliana Reveals Ancient Long-Range Colonization and Clarifies Demography in Eurasia. Mol Biol Evol 2017; 35:564-574. [PMID: 29216397 PMCID: PMC5850838 DOI: 10.1093/molbev/msx300] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The study of model organisms on islands may shed light on rare long-range dispersal events, uncover signatures of local evolutionary processes, and inform demographic inference on the mainland. Here, we sequenced the genomes of Arabidopsis thaliana samples from the oceanic island of Madeira. These samples include the most diverged worldwide, likely a result of long isolation on the island. We infer that colonization of Madeira happened between 70 and 85 ka, consistent with a propagule dispersal model (of size ≥10), or with an ecological window of opportunity. This represents a clear example of a natural long-range dispersal event in A. thaliana. Long-term effective population size on the island, rather than the founder effect, had the greatest impact on levels of diversity, and rates of coalescence. Our results uncover a selective sweep signature on the ancestral haplotype of a known translocation in Eurasia, as well as the possible importance of the low phosphorous availability in volcanic soils, and altitude, in shaping early adaptations to the island conditions. Madeiran genomes, sheltered from the complexities of continental demography, help illuminate ancient demographic events in Eurasia. Our data support a model in which two separate lineages of A. thaliana, one originating in Africa and the other from the Caucasus expanded and met in Iberia, resulting in a secondary contact zone there. Although previous studies inferred that the westward expansion of A. thaliana coincided with the spread of human agriculture, our results suggest that it happened much earlier (20-40 ka).
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Affiliation(s)
- Andrea Fulgione
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Maarten Koornneef
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Wageningen University, Wageningen, The Netherlands
| | - Fabrice Roux
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Joachim Hermisson
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.,Department of Mathematics, University of Vienna, Vienna, Austria
| | - Angela M Hancock
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
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25
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Worsham MLD, Julius EP, Nice CC, Diaz PH, Huffman DG. Geographic isolation facilitates the evolution of reproductive isolation and morphological divergence. Ecol Evol 2017; 7:10278-10288. [PMID: 29238554 PMCID: PMC5723600 DOI: 10.1002/ece3.3474] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 07/17/2017] [Accepted: 08/31/2017] [Indexed: 11/07/2022] Open
Abstract
Geographic isolation is known to contribute to divergent evolution, resulting in unique phenotypes. Oftentimes morphologically distinct populations are found to be interfertile while reproductive isolation is found to exist within nominal morphological species revealing the existence of cryptic species. These disparities can be difficult to predict or explain especially when they do not reflect an inferred history of common ancestry which suggests that environmental factors affect the nature of ecological divergence. A series of laboratory experiments and observational studies were used to address what role biogeographic factors may play in the ecological divergence of Hyalella amphipods. It was found that geographic isolation plays a key role in the evolution of reproductive isolation and divergent morphology and that divergence cannot be explained by molecular genetic variation.
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Affiliation(s)
- McLean L. D. Worsham
- Department of BiologyTexas State UniversitySan MarcosTXUSA
- Department of ZoologyUniversity of HawaiiHonoluluHIUSA
| | - Eric P. Julius
- Department of BiologyTexas State UniversitySan MarcosTXUSA
| | - Chris C. Nice
- Department of BiologyTexas State UniversitySan MarcosTXUSA
| | - Peter H. Diaz
- U.S. Fish and Wildlife ServiceTexas Fish and Wildlife Conservation OfficeSan MarcosTXUSA
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26
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Pellissier L, Kostikova A, Litsios G, Salamin N, Alvarez N. High Rate of Protein Coding Sequence Evolution and Species Diversification in the Lycaenids. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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27
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Wang J, Ai B, Kong H, Kang M. Speciation history of a species complex of Primulina eburnea (Gesneriaceae) from limestone karsts of southern China, a biodiversity hot spot. Evol Appl 2017; 10:919-934. [PMID: 29151883 PMCID: PMC5680421 DOI: 10.1111/eva.12495] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/22/2017] [Indexed: 11/30/2022] Open
Abstract
Limestone karsts in southern China are characterized by high edaphic and topographic heterogeneity and host high levels of species richness and endemism. However, the evolutionary mechanisms for generating such biodiversity remain poorly understood. Here, we performed species delimitation, population genetic analyses, simulations of gene flow and analyses of floral morphological traits to infer the geographic history of speciation in a species complex of Primulina eburnea from limestone karsts of southern China. Using Bayesian species delimitation, we determined that there are seven distinct species that correspond well to the putative morphological species. Species tree reconstruction, Structure and Neighbor‐Net analyses all recovered four lineages in agreement with currently species geographic boundaries. High levels of genetic differentiation were observed both within and among species. Isolation–migration coalescent analysis provides evidence for significant but low gene flow among species. Approximate Bayesian computation (ABC) analysis supports a scenario of historical gene flow rather than recent contemporary gene flow for most species divergences. Finally, we found no evidence of divergent selection contributing to population differentiation of a suite of flower traits. These results support the prevalence of allopatric speciation and highlight the role of geographic isolation in the diversification process. At small geographic scales, limited hybridization occurred in the past between proximate populations but did not eliminate species boundaries. We conclude that limited gene flow might have been the predominant evolutionary force in promoting population differentiation and speciation.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Bin Ai
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China.,Southeast Asia Biodiversity Research Institute Chinese Academy of Sciences Nay Pyi Taw Myanmar
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28
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Hoekstra PH, Wieringa JJ, Smets E, Brandão RD, Lopes JDC, Erkens RHJ, Chatrou LW. Correlated evolutionary rates across genomic compartments in Annonaceae. Mol Phylogenet Evol 2017; 114:63-72. [PMID: 28578201 DOI: 10.1016/j.ympev.2017.05.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 05/29/2017] [Accepted: 05/29/2017] [Indexed: 11/28/2022]
Abstract
The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models. The plant family Annonaceae is an excellent case to study lineage-specific rate heterogeneity. The two major sister subfamilies, Annonoideae and Malmeoideae, have shown great discrepancies in branch lengths. We used high-throughput sequencing data of 72 genes, 99 spacers and 16 introns from 24 chloroplast genomes and nuclear ribosomal DNA of 23 species to study the molecular rate of evolution in Annonaceae. In all analyses, longer branch lengths and/or higher substitution rates were found for the Annonoideae compared to the Malmeoideae. The Annonaceae had wide variability in chloroplast length, ranging from minimal 175,684bp to 201,723 for Annonoideae and minimal 152,357 to 170,985bp in Malmeoideae, mostly reflecting variation in inverted-repeat length. The Annonoideae showed a higher GC-content in the conserved parts of the chloroplast genome and higher omega (dN/dS)-ratios than the Malmeoideae, which could indicate less stringent purifying selection, a pattern that has been found in groups with small population sizes. This study generates new insights into the processes causing lineage-specific rate heterogeneity, which could lead to improved phylogenetic methods.
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Affiliation(s)
- Paul H Hoekstra
- Naturalis Biodiversity Center, National Herbarium of the Netherlands, Darwinweg 2, 2300 RA Leiden, The Netherlands; Wageningen University & Research, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Jan J Wieringa
- Naturalis Biodiversity Center, National Herbarium of the Netherlands, Darwinweg 2, 2300 RA Leiden, The Netherlands; Wageningen University & Research, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Erik Smets
- Naturalis Biodiversity Center, National Herbarium of the Netherlands, Darwinweg 2, 2300 RA Leiden, The Netherlands; Katholieke Universiteit Leuven, Ecology, Evolution and Biodiversity Conservation Section, Kasteelpark Arenberg 31, Box 2435, 3001 Leuven, Belgium.
| | - Rita D Brandão
- Maastricht University, Maastricht Science Programme, Kapoenstraat 2, 6211 KW Maastricht, The Netherlands.
| | - Jenifer de Carvalho Lopes
- Universidade de São Paulo, Instituto de Biociências, Departamento de Botânica, Rua do Matão 277, 05508-090 São Paulo, SP, Brazil.
| | - Roy H J Erkens
- Maastricht University, Maastricht Science Programme, Kapoenstraat 2, 6211 KW Maastricht, The Netherlands.
| | - Lars W Chatrou
- Wageningen University & Research, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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Salvi D, Pinho C, Harris DJ. Digging up the roots of an insular hotspot of genetic diversity: decoupled mito-nuclear histories in the evolution of the Corsican-Sardinian endemic lizard Podarcis tiliguerta. BMC Evol Biol 2017; 17:63. [PMID: 28253846 PMCID: PMC5335832 DOI: 10.1186/s12862-017-0899-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 01/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mediterranean islands host a disproportionately high level of biodiversity and endemisms. Growing phylogeographic evidence on island endemics has unveiled unexpectedly complex patterns of intra-island diversification, which originated at diverse spatial and temporal scales. We investigated multilocus genetic variation of the Corsican-Sardinian endemic lizard Podarcis tiliguerta with the aim of shedding more light on the evolutionary processes underlying the origin of Mediterranean island biodiversity. RESULTS We analysed DNA sequences of mitochondrial (12S and nd4) and nuclear (acm4 and mc1r) gene fragments in 174 individuals of P. tiliguerta from 81 localities across the full range of the species in a geographic and genealogical framework. We found surprisingly high genetic diversity both at mitochondrial and nuclear loci. Seventeen reciprocally monophyletic allopatric mitochondrial haplogroups were sharply divided into four main mitochondrial lineages (two in Corsica and two in Sardinia) of Miocene origin. In contrast, shallow divergence and shared diversity within and between islands was observed at the nuclear loci. We evaluated alternative biogeographic and evolutionary scenarios to explain such profound discordance in spatial and phylogenetic patterning between mitochondrial and nuclear genomes. While neutral models provided unparsimonious explanations for the observed pattern, the hypothesis of environmental selection driving mitochondrial divergence in the presence of nuclear gene flow is favoured. CONCLUSIONS Our study on the genetic variation of P. tiliguerta reveals surprising levels of diversity underlining a complex phylogeographic pattern with a striking example of mito-nuclear discordance. These findings have profound implications, not only for the taxonomy and conservation of P. tiliguerta. Growing evidence on deep mitochondrial breaks in absence of geographic barriers and of climatic factors associated to genetic variation of Corsican-Sardinian endemics warrants additional investigation on the potential role of environmental selection driving the evolution of diversity hotspots within Mediterranean islands.
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Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100 Coppito, L'Aquila, Italy. .,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
| | - Catarina Pinho
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - D James Harris
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
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Hua X, Bromham L. Darwinism for the Genomic Age: Connecting Mutation to Diversification. Front Genet 2017; 8:12. [PMID: 28224003 PMCID: PMC5293951 DOI: 10.3389/fgene.2017.00012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/19/2017] [Indexed: 12/30/2022] Open
Abstract
A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness. Here we draw together empirical studies and theoretical concepts that may help to build links in the explanatory chain that connects mutation to diversification. First we consider the way that mutation rates vary between species. We then explore how differences in mutation rates have flow-through effects to the rate at which populations acquire substitutions, which in turn influences the speed at which populations become reproductively isolated from each other due to the acquisition of genomic incompatibilities. Since diversification rate is commonly measured from phylogenetic analyses, we propose a conceptual approach for relating events of reproductive isolation to bifurcations on molecular phylogenies. As we examine each of these relationships, we consider theoretical models that might shine a light on the observed association between rate of molecular evolution and diversification rate, and critically evaluate the empirical evidence for these links, focusing on phylogenetic comparative studies. Finally, we ask whether we are getting closer to a real understanding of the way that the processes of molecular evolution connect to the observable patterns of diversification.
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Affiliation(s)
- Xia Hua
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
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Hung CM, Drovetski SV, Zink RM. Matching loci surveyed to questions asked in phylogeography. Proc Biol Sci 2016; 283:20152340. [PMID: 26962145 DOI: 10.1098/rspb.2015.2340] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Although mitochondrial DNA (mtDNA) has long been used for assessing genetic variation within and between populations, its workhorse role in phylogeography has been criticized owing to its single-locus nature. The only choice for testing mtDNA results is to survey nuclear loci, which brings into contrast the difference in locus effective size and coalescence times. Thus, it remains unclear how erroneous mtDNA-based estimates of species history might be, especially for evolutionary events in the recent past. To test the robustness of mtDNA and nuclear sequences in phylogeography, we provide one of the largest paired comparisons of summary statistics and demographic parameters estimated from mitochondrial, five Z-linked and 10 autosomal genes of 30 avian species co-distributed in the Caucasus and Europe. The results suggest that mtDNA is robust in estimating inter-population divergence but not in intra-population diversity, which is sensitive to population size change. Here, we provide empirical evidence showing that mtDNA was more likely to detect population divergence than any other single locus owing to its smaller Ne and thus faster coalescent time. Therefore, at least in birds, numerous studies that have based their inferences of phylogeographic patterns solely on mtDNA should not be readily dismissed.
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Affiliation(s)
- Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Sergei V Drovetski
- Division of Birds, National Museum of Natural History, Smithsonian Institution, Washington, DC 20004, USA
| | - Robert M Zink
- Bell Museum and Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, USA
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32
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Mohlhenrich ER, Mueller RL. Genetic drift and mutational hazard in the evolution of salamander genomic gigantism. Evolution 2016; 70:2865-2878. [DOI: 10.1111/evo.13084] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 09/27/2016] [Accepted: 09/27/2016] [Indexed: 12/25/2022]
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Nabholz B, Lanfear R, Fuchs J. Body mass-corrected molecular rate for bird mitochondrial DNA. Mol Ecol 2016; 25:4438-49. [PMID: 27483387 DOI: 10.1111/mec.13780] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 07/22/2016] [Accepted: 07/22/2016] [Indexed: 01/13/2023]
Abstract
Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of ~0.01 substitution per site per million years, that is that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary among bird species and correlate with life history traits such as body mass and generation time. These correlations could cause systematic biases in molecular dating studies that assume a strict molecular clock. In this study, we overcome this issue by estimating corrected molecular rates for birds. Using complete or nearly complete mitochondrial genomes of 475 species, we show that there are strong relationships between body mass and substitution rates across birds. We use this information to build models that use bird species' body mass to estimate their substitution rates across a wide range of common mitochondrial markers. We demonstrate the use of these corrected molecular rates on two recently published data sets. In one case, we obtained molecular dates that are twice as old as the estimates obtained using the strict molecular clock. We hope that this method to estimate molecular rates will increase the accuracy of future molecular dating studies in birds.
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Affiliation(s)
- Benoit Nabholz
- Institut des Sciences de l'Evolution, UMR 5554, Université Montpellier place Eugène Bataillon, Montpellier Cedex 5, 34095, France.
| | - Robert Lanfear
- Department of Biological Sciences, Faculty of Science, Macquarie University, Sydney, NSW, 2109, Australia
| | - Jérome Fuchs
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205 CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Université, 57 rue Cuvier, CP5175005, Paris, France
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34
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Li FW, Kuo LY, Pryer KM, Rothfels CJ. Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content. Genome Biol Evol 2016; 8:2452-8. [PMID: 27401175 PMCID: PMC5010901 DOI: 10.1093/gbe/evw167] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Plant chloroplast genomes (plastomes) are characterized by an inverted repeat (IR) region and two larger single copy (SC) regions. Patterns of molecular evolution in the IR and SC regions differ, most notably by a reduced rate of nucleotide substitution in the IR compared to the SC region. In addition, the organization and structure of plastomes is fluid, and rearrangements through time have repeatedly shuffled genes into and out of the IR, providing recurrent natural experiments on how chloroplast genome structure can impact rates and patterns of molecular evolution. Here we examine four loci (psbA, ycf2, rps7, and rps12 exon 2-3) that were translocated from the SC into the IR during fern evolution. We use a model-based method, within a phylogenetic context, to test for substitution rate shifts. All four loci show a significant, 2- to 3-fold deceleration in their substitution rate following translocation into the IR, a phenomenon not observed in any other, nontranslocated plastid genes. Also, we show that after translocation, the GC content of the third codon position and of the noncoding regions is significantly increased, implying that gene conversion within the IR is GC-biased. Taken together, our results suggest that the IR region not only reduces substitution rates, but also impacts nucleotide composition. This finding highlights a potential vulnerability of correlating substitution rate heterogeneity with organismal life history traits without knowledge of the underlying genome structure.
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Affiliation(s)
- Fay-Wei Li
- University Herbarium and Department of Integrative Biology, University of California, Berkeley Department of Biology, Duke University, Durham
| | - Li-Yaung Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei
| | | | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley
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35
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Mitterboeck TF, Chen AY, Zaheer OA, Ma EYT, Adamowicz SJ. Do saline taxa evolve faster? Comparing relative rates of molecular evolution between freshwater and marine eukaryotes. Evolution 2016; 70:1960-78. [PMID: 27402284 DOI: 10.1111/evo.13000] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 05/24/2016] [Accepted: 06/28/2016] [Indexed: 12/16/2022]
Abstract
The major branches of life diversified in the marine realm, and numerous taxa have since transitioned between marine and freshwaters. Previous studies have demonstrated higher rates of molecular evolution in crustaceans inhabiting continental saline habitats as compared with freshwaters, but it is unclear whether this trend is pervasive or whether it applies to the marine environment. We employ the phylogenetic comparative method to investigate relative molecular evolutionary rates between 148 pairs of marine or continental saline versus freshwater lineages representing disparate eukaryote groups, including bony fish, elasmobranchs, cetaceans, crustaceans, mollusks, annelids, algae, and other eukaryotes, using available protein-coding and noncoding genes. Overall, we observed no consistent pattern in nucleotide substitution rates linked to habitat across all genes and taxa. However, we observed some trends of higher evolutionary rates within protein-coding genes in freshwater taxa-the comparisons mainly involving bony fish-compared with their marine relatives. The results suggest no systematic differences in substitution rate between marine and freshwater organisms.
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Affiliation(s)
- T Fatima Mitterboeck
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada. .,Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
| | - Alexander Y Chen
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Omar A Zaheer
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Eddie Y T Ma
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.,School of Computer Science, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Sarah J Adamowicz
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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36
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James JE, Lanfear R, Eyre-Walker A. Molecular Evolutionary Consequences of Island Colonization. Genome Biol Evol 2016; 8:1876-88. [PMID: 27358424 PMCID: PMC4943191 DOI: 10.1093/gbe/evw120] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Island endemics are expected to have low effective population sizes (Ne), first because some may experience population bottlenecks when they are founded, and second because they have restricted ranges. Therefore, we expect island species to have reduced genetic diversity, inefficient selection, and reduced adaptive potential compared with their mainland counterparts. We used both polymorphism and substitution data to address these predictions, improving on the approach of recent studies that only used substitution data. This allowed us to directly test the assumption that island species have small values of Ne We found that island species had significantly less genetic diversity than mainland species; however, this pattern could be attributed to a subset of island species that appeared to have undergone a recent population bottleneck. When these species were excluded from the analysis, island and mainland species had similar levels of genetic diversity, despite island species occupying considerably smaller areas than their mainland counterparts. We also found no overall difference between island and mainland species in terms of the effectiveness of selection or the mutation rate. Our evidence suggests that island colonization has no lasting impact on molecular evolution. This surprising result highlights gaps in our knowledge of the relationship between census and effective population size.
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Affiliation(s)
- Jennifer E James
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Robert Lanfear
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia Division of Evolution Ecology and Genetics, Research School of Biology, the Australian National University, Canberra, Australian Capital Territory, Australia
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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37
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Aguileta G, Badouin H, Hood ME, Møller AP, Le Prieur S, Snirc A, Siguenza S, Mousseau TA, Shykoff JA, Cuomo CA, Giraud T. Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl. Mol Ecol 2016; 25:3370-83. [PMID: 27136128 DOI: 10.1111/mec.13675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/04/2016] [Accepted: 04/15/2016] [Indexed: 12/24/2022]
Abstract
Nuclear disasters at Chernobyl and Fukushima provide examples of effects of acute ionizing radiation on mutations that can affect the fitness and distribution of species. Here, we investigated the prevalence of Microbotryum lychnidis-dioicae, a pollinator-transmitted fungal pathogen of plants causing anther-smut disease in Chernobyl, its viability, fertility and karyotype variation, and the accumulation of nonsynonymous mutations in its genome. We collected diseased flowers of Silene latifolia from locations ranging by more than two orders of magnitude in background radiation, from 0.05 to 21.03 μGy/h. Disease prevalence decreased significantly with increasing radiation level, possibly due to lower pollinator abundance and altered pollinator behaviour. Viability and fertility, measured as the budding rate of haploid sporidia following meiosis from the diploid teliospores, did not vary with increasing radiation levels and neither did karyotype overall structure and level of chromosomal size heterozygosity. We sequenced the genomes of twelve samples from Chernobyl and of four samples collected from uncontaminated areas and analysed alignments of 6068 predicted genes, corresponding to 1.04 × 10(7) base pairs. We found no dose-dependent differences in substitution rates (neither dN, dS, nor dN/dS). Thus, we found no significant evidence of increased deleterious mutation rates at higher levels of background radiation in this plant pathogen. We even found lower levels of nonsynonymous substitution rates in contaminated areas compared to control regions, suggesting that purifying selection was stronger in contaminated than uncontaminated areas. We briefly discuss the possibilities for a mechanistic basis of radio resistance in this nonmelanized fungus.
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Affiliation(s)
- Gabriela Aguileta
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Helene Badouin
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Michael E Hood
- Biology Department, Amherst College, Amherst, MA 01002, USA
| | - Anders P Møller
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Stephanie Le Prieur
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Alodie Snirc
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Sophie Siguenza
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France.,CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Jacqui A Shykoff
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | | | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
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Fujisawa T, Vogler AP, Barraclough TG. Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles. Proc Biol Sci 2015; 282:20142476. [PMID: 25621335 DOI: 10.1098/rspb.2014.2476] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.
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Weber CC, Nabholz B, Romiguier J, Ellegren H. Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biol 2015; 15:542. [PMID: 25607475 PMCID: PMC4264323 DOI: 10.1186/s13059-014-0542-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/13/2014] [Indexed: 02/02/2023] Open
Abstract
Background The ratio of the rates of non-synonymous and synonymous substitution (dN/dS) is commonly used to estimate selection in coding sequences. It is often suggested that, all else being equal, dN/dS should be lower in populations with large effective size (Ne) due to increased efficacy of purifying selection. As Ne is difficult to measure directly, life history traits such as body mass, which is typically negatively associated with population size, have commonly been used as proxies in empirical tests of this hypothesis. However, evidence of whether the expected positive correlation between body mass and dN/dS is consistently observed is conflicting. Results Employing whole genome sequence data from 48 avian species, we assess the relationship between rates of molecular evolution and life history in birds. We find a negative correlation between dN/dS and body mass, contrary to nearly neutral expectation. This raises the question whether the correlation might be a method artefact. We therefore in turn consider non-stationary base composition, divergence time and saturation as possible explanations, but find no clear patterns. However, in striking contrast to dN/dS, the ratio of radical to conservative amino acid substitutions (Kr/Kc) correlates positively with body mass. Conclusions Our results in principle accord with the notion that non-synonymous substitutions causing radical amino acid changes are more efficiently removed by selection in large populations, consistent with nearly neutral theory. These findings have implications for the use of dN/dS and suggest that caution is warranted when drawing conclusions about lineage-specific modes of protein evolution using this metric. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0542-8) contains supplementary material, which is available to authorized users.
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40
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Pellissier L. Stability and the competition-dispersal trade-off as drivers of speciation and biodiversity gradients. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Bromham L, Hua X, Lanfear R, Cowman PF. Exploring the Relationships between Mutation Rates, Life History, Genome Size, Environment, and Species Richness in Flowering Plants. Am Nat 2015; 185:507-24. [PMID: 25811085 DOI: 10.1086/680052] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A new view is emerging of the interplay between mutation at the genomic level, substitution at the population level, and diversification at the lineage level. Many studies have suggested that rate of molecular evolution is linked to rate of diversification, but few have evaluated competing hypotheses. By analyzing sequences from 130 families of angiosperms, we show that variation in the synonymous substitution rate is correlated among genes from the mitochondrial, chloroplast, and nuclear genomes and linked to differences in traits among families (average height and genome size). Within each genome, synonymous rates are correlated to nonsynonymous substitution rates, suggesting that increasing the mutation rate results in a faster rate of genome evolution. Substitution rates are correlated with species richness in protein-coding sequences from the chloroplast and nuclear genomes. These data suggest that species traits contribute to lineage-specific differences in the mutation rate that drive both synonymous and nonsynonymous rates of change across all three genomes, which in turn contribute to greater rates of divergence between populations, generating higher rates of diversification. These observations link mutation in individuals to population-level processes and to patterns of lineage divergence.
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Affiliation(s)
- Lindell Bromham
- Centre for Macroevolution and Macroecology, Division of Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia
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Eberhart-Phillips LJ, Hoffman JI, Brede EG, Zefania S, Kamrad MJ, Székely T, Bruford MW. Contrasting genetic diversity and population structure among three sympatric Madagascan shorebirds: parallels with rarity, endemism, and dispersal. Ecol Evol 2015; 5:997-1010. [PMID: 25798218 PMCID: PMC4364815 DOI: 10.1002/ece3.1393] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 12/15/2014] [Indexed: 01/12/2023] Open
Abstract
Understanding the relative contributions of intrinsic and extrinsic factors to population structure and genetic diversity is a central goal of conservation and evolutionary genetics. One way to achieve this is through comparative population genetic analysis of sympatric sister taxa, which allows evaluation of intrinsic factors such as population demography and life history while controlling for phylogenetic relatedness and geography. We used ten conserved microsatellites to explore the population structure and genetic diversity of three sympatric and closely related plover species in southwestern Madagascar: Kittlitz's plover (Charadrius pecuarius), white-fronted plover (C. marginatus), and Madagascar plover (C. thoracicus). Bayesian clustering revealed strong population structure in the rare and endemic Madagascar plover, intermediate population structure in the white-fronted plover, and no detectable population structure in the geographically widespread Kittlitz's plover. In contrast, allelic richness and heterozygosity were highest for the Kittlitz's plover, intermediate for the white-fronted plover and lowest for the Madagascar plover. No evidence was found in support of the “watershed mechanism” proposed to facilitate vicariant divergence of Madagascan lemurs and reptiles, which we attribute to the vagility of birds. However, we found a significant pattern of genetic isolation by distance among populations of the Madagascar plover, but not for the other two species. These findings suggest that interspecific variation in rarity, endemism, and dispersal propensity may influence genetic structure and diversity, even in highly vagile species.
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Affiliation(s)
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University Morgenbreede 45, 33615, Bielefeld, Germany
| | - Edward G Brede
- Biodiversity and Ecological Processes Group, Cardiff School of Biosciences, Cardiff University Cardiff, CF10 3AX, U.K
| | - Sama Zefania
- Department of Animal Biology, University of Toliara PO Box 185, Toliara, Madagascar
| | - Martina J Kamrad
- Department of Animal Behaviour, Bielefeld University Morgenbreede 45, 33615, Bielefeld, Germany
| | - Tamás Székely
- Department of Animal Behaviour, Bielefeld University Morgenbreede 45, 33615, Bielefeld, Germany ; Biodiversity Lab, Department of Biology and Biochemistry, University of Bath Bath, BA2 7AY, U.K
| | - Michael W Bruford
- Biodiversity and Ecological Processes Group, Cardiff School of Biosciences, Cardiff University Cardiff, CF10 3AX, U.K
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Currie TE, Mace R. Evolution of cultural traits occurs at similar relative rates in different world regions. Proc Biol Sci 2014; 281:20141622. [PMID: 25297866 PMCID: PMC4213619 DOI: 10.1098/rspb.2014.1622] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 09/09/2014] [Indexed: 02/04/2023] Open
Abstract
A fundamental issue in understanding human diversity is whether or not there are regular patterns and processes involved in cultural change. Theoretical and mathematical models of cultural evolution have been developed and are increasingly being used and assessed in empirical analyses. Here, we test the hypothesis that the rates of change of features of human socio-cultural organization are governed by general rules. One prediction of this hypothesis is that different cultural traits will tend to evolve at similar relative rates in different world regions, despite the unique historical backgrounds of groups inhabiting these regions. We used phylogenetic comparative methods and systematic cross-cultural data to assess how different socio-cultural traits changed in (i) island southeast Asia and the Pacific, and (ii) sub-Saharan Africa. The relative rates of change in these two regions are significantly correlated. Furthermore, cultural traits that are more directly related to external environmental conditions evolve more slowly than traits related to social structures. This is consistent with the idea that a form of purifying selection is acting with greater strength on these more environmentally linked traits. These results suggest that despite contingent historical events and the role of humans as active agents in the historical process, culture does indeed evolve in ways that can be predicted from general principles.
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Affiliation(s)
- Thomas E Currie
- Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Cornwall TR10 9EZ, UK Department of Anthropology, University College London, 14 Taviton St., London WC1H 0BH, UK
| | - Ruth Mace
- Department of Anthropology, University College London, 14 Taviton St., London WC1H 0BH, UK
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Inferring the degree of incipient speciation in secondary contact zones of closely related lineages of Palearctic green toads (Bufo viridis subgroup). Heredity (Edinb) 2014; 113:9-20. [PMID: 24713825 DOI: 10.1038/hdy.2014.26] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 01/31/2014] [Accepted: 02/24/2014] [Indexed: 11/08/2022] Open
Abstract
Reproductive isolation between lineages is expected to accumulate with divergence time, but the time taken to speciate may strongly vary between different groups of organisms. In anuran amphibians, laboratory crosses can still produce viable hybrid offspring >20 My after separation, but the speed of speciation in closely related anuran lineages under natural conditions is poorly studied. Palearctic green toads (Bufo viridis subgroup) offer an excellent system to address this question, comprising several lineages that arose at different times and form secondary contact zones. Using mitochondrial and nuclear markers, we previously demonstrated that in Sicily, B. siculus and B. balearicus developed advanced reproductive isolation after Plio-Pleistocene divergence (2.6 My, 3.3-1.9), with limited historic mtDNA introgression, scarce nuclear admixture, but low, if any, current gene flow. Here, we study genetic interactions between younger lineages of early Pleistocene divergence (1.9 My, 2.5-1.3) in northeastern Italy (B. balearicus, B. viridis). We find significantly more, asymmetric nuclear and wider, differential mtDNA introgression. The population structure seems to be molded by geographic distance and barriers (rivers), much more than by intrinsic genomic incompatibilities. These differences of hybridization between zones may be partly explained by differences in the duration of previous isolation. Scattered research on other anurans suggests that wide hybrid zones with strong introgression may develop when secondary contacts occur <2 My after divergence, whereas narrower zones with restricted gene flow form when divergence exceeds 3 My. Our study strengthens support for this rule of thumb by comparing lineages with different divergence times within the same radiation.
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45
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Goldstein RA. Population size dependence of fitness effect distribution and substitution rate probed by biophysical model of protein thermostability. Genome Biol Evol 2014; 5:1584-93. [PMID: 23884461 PMCID: PMC3787666 DOI: 10.1093/gbe/evt110] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The predicted effect of effective population size on the distribution of fitness effects and substitution rate is critically dependent on the relationship between sequence and fitness. This highlights the importance of using models that are informed by the molecular biology, biochemistry, and biophysics of the evolving systems. We describe a computational model based on fundamental aspects of biophysics, the requirement for (most) proteins to be thermodynamically stable. Using this model, we find that differences in population size have minimal impact on the distribution of population-scaled fitness effects, as well as on the rate of molecular evolution. This is because larger populations result in selection for more stable proteins that are less affected by mutations. This reduction in the magnitude of the fitness effects almost exactly cancels the greater selective pressure resulting from the larger population size. Conversely, changes in the population size in either direction cause transient increases in the substitution rate. As differences in population size often correspond to changes in population size, this makes comparisons of substitution rates in different lineages difficult to interpret.
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Affiliation(s)
- Richard A Goldstein
- Division of Infection and Immunity, University College London, United Kingdom
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46
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Thomson CE, Gilbert JDJ, Brooke MDL. Cytochrome b divergence between avian sister species is linked to generation length and body mass. PLoS One 2014; 9:e85006. [PMID: 24505250 PMCID: PMC3914784 DOI: 10.1371/journal.pone.0085006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 11/28/2013] [Indexed: 11/19/2022] Open
Abstract
It is increasingly realised that the molecular clock does not tick at a constant rate. Rather, mitochondrial mutation rates are influenced by factors such as generation length and body mass. This has implications for the use of genetic data in species delimitation. It could be that speciation, as recognised by avian taxonomists, is associated with a certain minimum genetic distance between sister taxa, in which case we would predict no difference in the cytochrome b divergence of sister taxa according to the species' body size or generation time. Alternatively, if what taxonomists recognise as speciation has tended to be associated with the passage of a minimum amount of time since divergence, then there might be less genetic divergence between sister taxa with slower mutation rates, namely those that are heavier and/or with longer generation times. After excluding non-flying species, we analysed a database of over 600 avian sister species pairs, and found that species pairs with longer generation lengths (which tend to be the larger species) showed less cytochrome b divergence. This finding cautions against using any simple unitary criterion of genetic divergence to delimit species.
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Affiliation(s)
- Caroline E. Thomson
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - James D. J. Gilbert
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- School of Biological Sciences, University of Sydney, New South Wales, Australia
| | - M. de L Brooke
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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Moray C, Lanfear R, Bromham L. Domestication and the mitochondrial genome: comparing patterns and rates of molecular evolution in domesticated mammals and birds and their wild relatives. Genome Biol Evol 2014; 6:161-9. [PMID: 24459286 PMCID: PMC3914681 DOI: 10.1093/gbe/evu005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2013] [Indexed: 11/14/2022] Open
Abstract
Studies of domesticated animals have led to the suggestion that domestication could have significant effects on patterns of molecular evolution. In particular, analyses of mitochondrial genome sequences from domestic dogs and yaks have yielded higher ratios of non-synonymous to synonymous substitutions in the domesticated lineages than in their wild relatives. These results are important because they imply that changes to selection or population size operating over a short timescale can cause significant changes to the patterns of mitochondrial molecular evolution. In this study, our aim is to test whether the impact on mitochondrial genome evolution is a general feature of domestication or whether it is specific to particular examples. We test whether domesticated mammals and birds have consistently different patterns of molecular evolution than their wild relatives for 16 phylogenetically independent comparisons of mitochondrial genome sequences. We find no consistent difference in branch lengths or dN/dS between domesticated and wild lineages. We also find no evidence that our failure to detect a consistent pattern is due to the short timescales involved or low genetic distance between domesticated lineages and their wild relatives. However, removing comparisons where the wild relative may also have undergone a bottleneck does reveal a pattern consistent with reduced effective population size in domesticated lineages. Our results suggest that, although some domesticated lineages may have undergone changes to selective regime or effective population size that could have affected mitochondrial evolution, it is not possible to generalize these patterns over all domesticated mammals and birds.
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Affiliation(s)
- Camile Moray
- Centre for Macroevolution and Macroecology, Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Robert Lanfear
- Centre for Macroevolution and Macroecology, Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- National Evolutionary Synthesis Center, Durham, NC
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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48
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Robertson JM, Langin KM, Sillett TS, Morrison SA, Ghalambor CK, Funk WC. Identifying Evolutionarily Significant Units and Prioritizing Populations for Management on Islands. ACTA ACUST UNITED AC 2014. [DOI: 10.3398/042.007.0130] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Loire E, Chiari Y, Bernard A, Cahais V, Romiguier J, Nabholz B, Lourenço JM, Galtier N. Population genomics of the endangered giant Galápagos tortoise. Genome Biol 2013; 14:R136. [PMID: 24342523 PMCID: PMC4053747 DOI: 10.1186/gb-2013-14-12-r136] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 12/16/2013] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The giant Galápagos tortoise, Chelonoidis nigra, is a large-sized terrestrial chelonian of high patrimonial interest. The species recently colonized a small continental archipelago, the Galápagos Islands, where it has been facing novel environmental conditions and limited resource availability. To explore the genomic consequences of this ecological shift, we analyze the transcriptomic variability of five individuals of C. nigra, and compare it to similar data obtained from several continental species of turtles. RESULTS Having clarified the timing of divergence in the Chelonoidis genus, we report in C. nigra a very low level of genetic polymorphism, signatures of a weakened efficacy of purifying selection, and an elevated mutation load in coding and regulatory sequences. These results are consistent with the hypothesis of an extremely low long-term effective population size in this insular species. Functional evolutionary analyses reveal a reduced diversity of immunity genes in C. nigra, in line with the hypothesis of attenuated pathogen diversity in islands, and an increased selective pressure on genes involved in response to stress, potentially related to the climatic instability of its environment and its elongated lifespan. Finally, we detect no population structure or homozygosity excess in our five-individual sample. CONCLUSIONS These results enlighten the molecular evolution of an endangered taxon in a stressful environment and point to island endemic species as a promising model for the study of the deleterious effects on genome evolution of a reduced long-term population size.
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Affiliation(s)
- Etienne Loire
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Ylenia Chiari
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Aurélien Bernard
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Vincent Cahais
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Jonathan Romiguier
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Benoît Nabholz
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Joao Miguel Lourenço
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Nicolas Galtier
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
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50
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Nylinder S, Lemey P, De Bruyn M, Suchard MA, Pfeil BE, Walsh N, Anderberg AA. On the biogeography of Centipeda: a species-tree diffusion approach. Syst Biol 2013; 63:178-91. [PMID: 24335493 DOI: 10.1093/sysbio/syt102] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reconstructing the biogeographic history of groups present in continuous arid landscapes is challenging due to the difficulties in defining discrete areas for analyses, and even more so when species largely overlap both in terms of geography and habitat preference. In this study, we use a novel approach to estimate ancestral areas for the small plant genus Centipeda. We apply continuous diffusion of geography by a relaxed random walk where each species is sampled from its extant distribution on an empirical distribution of time-calibrated species-trees. Using a distribution of previously published substitution rates of the internal transcribed spacer (ITS) for Asteraceae, we show how the evolution of Centipeda correlates with the temporal increase of aridity in the arid zone since the Pliocene. Geographic estimates of ancestral species show a consistent pattern of speciation of early lineages in the Lake Eyre region, with a division in more northerly and southerly groups since ∼840 ka. Summarizing the geographic slices of species-trees at the time of the latest speciation event (∼20 ka), indicates no presence of the genus in Australia west of the combined desert belt of the Nullabor Plain, the Great Victoria Desert, the Gibson Desert, and the Great Sandy Desert, or beyond the main continental shelf of Australia. The result indicates all western occurrences of the genus to be a result of recent dispersal rather than ancient vicariance. This study contributes to our understanding of the spatiotemporal processes shaping the flora of the arid zone, and offers a significant improvement in inference of ancestral areas for any organismal group distributed where it remains difficult to describe geography in terms of discrete areas.
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Affiliation(s)
- Stephan Nylinder
- Department of Botany, Swedish Museum of Natural History, Svante Arrhenius väg 7, SE-104 05 Stockholm, Sweden; Department of Microbiology and Immunology, KU Leuven, Minderbroederstraat 10 blok x, box 1030 BE-3000 Leuven, Belgium; School of Biological Sciences, Bangor University, Deiniol Road Bangor Gwynedd, Bangor, LL57 2UW UK; Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, BOX 951766, University of California, Los Angeles, CA 90095-1766, USA; Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 90095-1772, USA; Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22 B, SE-413 19 Gothenburg, Sweden; and National Herbarium of Victoria, Birdwood Avenue, South Yarra 3141, Australia
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