1
|
Johnson MTJ, Arif I, Marchetti F, Munshi-South J, Ness RW, Szulkin M, Verrelli BC, Yauk CL, Anstett DN, Booth W, Caizergues AE, Carlen EJ, Dant A, González J, Lagos CG, Oman M, Phifer-Rixey M, Rennison DJ, Rosenberg MS, Winchell KM. Effects of urban-induced mutations on ecology, evolution and health. Nat Ecol Evol 2024; 8:1074-1086. [PMID: 38641700 DOI: 10.1038/s41559-024-02401-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/13/2024] [Indexed: 04/21/2024]
Abstract
Increasing evidence suggests that urbanization is associated with higher mutation rates, which can affect the health and evolution of organisms that inhabit cities. Elevated pollution levels in urban areas can induce DNA damage, leading to de novo mutations. Studies on mutations induced by urban pollution are most prevalent in humans and microorganisms, whereas studies of non-human eukaryotes are rare, even though increased mutation rates have the potential to affect organisms and their populations in contemporary time. Our Perspective explores how higher mutation rates in urban environments could impact the fitness, ecology and evolution of populations. Most mutations will be neutral or deleterious, and higher mutation rates associated with elevated pollution in urban populations can increase the risk of cancer in humans and potentially other species. We highlight the potential for urban-driven increased deleterious mutational loads in some organisms, which could lead to a decline in population growth of a wide diversity of organisms. Although beneficial mutations are expected to be rare, we argue that higher mutation rates in urban areas could influence adaptive evolution, especially in organisms with short generation times. Finally, we explore avenues for future research to better understand the effects of urban-induced mutations on the fitness, ecology and evolution of city-dwelling organisms.
Collapse
Affiliation(s)
- Marc T J Johnson
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada.
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada.
| | - Irtaqa Arif
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Jason Munshi-South
- Department of Biology and Louis Calder Center, Fordham University, Armonk, NY, USA
| | - Rob W Ness
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Marta Szulkin
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Brian C Verrelli
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel N Anstett
- Department of Plant Biology, Department of Entomology, Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Warren Booth
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Aude E Caizergues
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Elizabeth J Carlen
- Living Earth Collaborative, Washington University in St. Louis, St. Louis, MO, USA
| | - Anthony Dant
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Josefa González
- Institute of Evolutionary Biology, CSIC, UPF, Barcelona, Spain
| | - César González Lagos
- Departamento de Ciencias, Facultad de Artes Liberales, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Madeleine Oman
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | | | - Diana J Rennison
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Michael S Rosenberg
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
| | | |
Collapse
|
2
|
Vu GTH, Cao HX, Hofmann M, Steiner W, Gailing O. Uncovering epigenetic and transcriptional regulation of growth in Douglas-fir: identification of differential methylation regions in mega-sized introns. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:863-875. [PMID: 37984804 PMCID: PMC10955500 DOI: 10.1111/pbi.14229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023]
Abstract
Tree growth performance can be partly explained by genetics, while a large proportion of growth variation is thought to be controlled by environmental factors. However, to what extent DNA methylation, a stable epigenetic modification, contributes to phenotypic plasticity in the growth performance of long-lived trees remains unclear. In this study, a comparative analysis of targeted DNA genotyping, DNA methylation and mRNAseq profiling for needles of 44-year-old Douglas-fir trees (Pseudotsuga menziesii (Mirb.) Franco) having contrasting growth characteristics was performed. In total, we identified 195 differentially expressed genes (DEGs) and 115 differentially methylated loci (DML) that are associated with genes involved in fitness-related processes such as growth, stress management, plant development and energy resources. Interestingly, all four intronic DML were identified in mega-sized (between 100 and 180 kbp in length) and highly expressed genes, suggesting specialized regulation mechanisms of these long intron genes in gymnosperms. DNA repetitive sequences mainly comprising long-terminal repeats of retroelements are involved in growth-associated DNA methylation regulation (both hyper- and hypomethylation) of 99 DML (86.1% of total DML). Furthermore, nearly 14% of the DML was not tagged by single nucleotide polymorphisms, suggesting a unique contribution of the epigenetic variation in tree growth.
Collapse
Affiliation(s)
- Giang Thi Ha Vu
- Forest Genetics and Forest Tree BreedingUniversity of GöttingenGöttingenGermany
- Center for Integrated Breeding Research (CiBreed)University of GöttingenGöttingenGermany
| | - Hieu Xuan Cao
- Forest Genetics and Forest Tree BreedingUniversity of GöttingenGöttingenGermany
- Center for Integrated Breeding Research (CiBreed)University of GöttingenGöttingenGermany
| | - Martin Hofmann
- Nordwestdeutsche Forstliche VersuchsanstaltAbteilung WaldgenressourcenHann. MündenGermany
| | - Wilfried Steiner
- Nordwestdeutsche Forstliche VersuchsanstaltAbteilung WaldgenressourcenHann. MündenGermany
| | - Oliver Gailing
- Forest Genetics and Forest Tree BreedingUniversity of GöttingenGöttingenGermany
- Center for Integrated Breeding Research (CiBreed)University of GöttingenGöttingenGermany
| |
Collapse
|
3
|
Galtier N. Half a Century of Controversy: The Neutralist/Selectionist Debate in Molecular Evolution. Genome Biol Evol 2024; 16:evae003. [PMID: 38311843 PMCID: PMC10839204 DOI: 10.1093/gbe/evae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/01/2024] [Indexed: 02/06/2024] Open
Abstract
The neutral and nearly neutral theories, introduced more than 50 yr ago, have raised and still raise passionate discussion regarding the forces governing molecular evolution and their relative importance. The debate, initially focused on the amount of within-species polymorphism and constancy of the substitution rate, has spread, matured, and now underlies a wide range of topics and questions. The neutralist/selectionist controversy has structured the field and influences the way molecular evolutionary scientists conceive their research.
Collapse
Affiliation(s)
- Nicolas Galtier
- ISEM, CNRS, IRD, Université de Montpellier, Montpellier, France
| |
Collapse
|
4
|
Kang JS, Giang VNL, Park HS, Park YS, Cho W, Nguyen VB, Shim H, Waminal NE, Park JY, Kim HH, Yang TJ. Evolution of the Araliaceae family involved rapid diversification of the Asian Palmate group and Hydrocotyle specific mutational pressure. Sci Rep 2023; 13:22325. [PMID: 38102332 PMCID: PMC10724125 DOI: 10.1038/s41598-023-49830-7] [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: 04/04/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023] Open
Abstract
The Araliaceae contain many valuable species in medicinal and industrial aspects. We performed intensive phylogenomics using the plastid genome (plastome) and 45S nuclear ribosomal DNA sequences. A total of 66 plastome sequences were used, 13 of which were newly assembled in this study, 12 from new sequences, and one from existing data. While Araliaceae plastomes showed conserved genome structure, phylogenetic reconstructions based on four different plastome datasets revealed phylogenetic discordance within the Asian Palmate group. The divergence time estimation revealed that splits in two Araliaceae subfamilies and the clades exhibiting phylogenetic discordances in the Asian Palmate group occurred at two climatic optima, suggesting that global warming events triggered species divergence, particularly the rapid diversification of the Asian Palmate group during the Middle Miocene. Nucleotide substitution analyses indicated that the Hydrocotyloideae plastomes have undergone accelerated AT-biased mutations (C-to-T transitions) compared with the Aralioideae plastomes, and the acceleration may occur in their mitochondrial and nuclear genomes as well. This implies that members of the genus Hydrocotyle, the only aquatic plants in the Araliaceae, have experienced a distinct evolutionary history from the other species. We also discussed the intercontinental disjunction in the genus Panax and proposed a hypothesis to complement the previously proposed hypothesis. Our results provide the evolutionary trajectory of Araliaceae and advance our current understanding of the evolution of Araliaceae species.
Collapse
Affiliation(s)
- Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Vo Ngoc Linh Giang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000, Vietnam
| | - Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, South Korea
| | - Young Sang Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Woohyeon Cho
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Van Binh Nguyen
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Faculty of Biology, Dalat University, Dalat, 670000, Vietnam
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Nomar Espinosa Waminal
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, 01795, South Korea
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Seeland, Gatersleben, Germany
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hyun Hee Kim
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, 01795, South Korea.
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
| |
Collapse
|
5
|
Amin MR, Hasan M, Arnab SP, DeGiorgio M. Tensor Decomposition-based Feature Extraction and Classification to Detect Natural Selection from Genomic Data. Mol Biol Evol 2023; 40:msad216. [PMID: 37772983 PMCID: PMC10581699 DOI: 10.1093/molbev/msad216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/10/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023] Open
Abstract
Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under nonconvex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data although preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termed T-REx, which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance of T-REx on simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore, T-REx is a powerful addition to the toolkit for detecting adaptive processes from genomic data.
Collapse
Affiliation(s)
- Md Ruhul Amin
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Mahmudul Hasan
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Sandipan Paul Arnab
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| |
Collapse
|
6
|
Beichman AC, Robinson J, Lin M, Moreno-Estrada A, Nigenda-Morales S, Harris K. Evolution of the Mutation Spectrum Across a Mammalian Phylogeny. Mol Biol Evol 2023; 40:msad213. [PMID: 37770035 PMCID: PMC10566577 DOI: 10.1093/molbev/msad213] [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: 06/01/2023] [Revised: 08/21/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023] Open
Abstract
Although evolutionary biologists have long theorized that variation in DNA repair efficacy might explain some of the diversity of lifespan and cancer incidence across species, we have little data on the variability of normal germline mutagenesis outside of humans. Here, we shed light on the spectrum and etiology of mutagenesis across mammals by quantifying mutational sequence context biases using polymorphism data from thirteen species of mice, apes, bears, wolves, and cetaceans. After normalizing the mutation spectrum for reference genome accessibility and k-mer content, we use the Mantel test to deduce that mutation spectrum divergence is highly correlated with genetic divergence between species, whereas life history traits like reproductive age are weaker predictors of mutation spectrum divergence. Potential bioinformatic confounders are only weakly related to a small set of mutation spectrum features. We find that clock-like mutational signatures previously inferred from human cancers cannot explain the phylogenetic signal exhibited by the mammalian mutation spectrum, despite the ability of these signatures to fit each species' 3-mer spectrum with high cosine similarity. In contrast, parental aging signatures inferred from human de novo mutation data appear to explain much of the 1-mer spectrum's phylogenetic signal in combination with a novel mutational signature. We posit that future models purporting to explain the etiology of mammalian mutagenesis need to capture the fact that more closely related species have more similar mutation spectra; a model that fits each marginal spectrum with high cosine similarity is not guaranteed to capture this hierarchy of mutation spectrum variation among species.
Collapse
Affiliation(s)
- Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Meixi Lin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity, Advanced Genomics Unit (UGA-LANGEBIO), CINVESTAV, Irapuato, Mexico
| | - Sergio Nigenda-Morales
- Department of Biological Sciences, California State University, San Marcos, San Marcos, CA, USA
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| |
Collapse
|
7
|
Lan L, Zhao H, Xu S, Kan S, Zhang X, Liu W, Liao X, Tembrock LR, Ren Y, Reeve W, Yang J, Wu Z. A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales. HORTICULTURE RESEARCH 2023; 10:uhad124. [PMID: 37554346 PMCID: PMC10405137 DOI: 10.1093/hr/uhad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/05/2023] [Indexed: 08/10/2023]
Abstract
Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the world. However, the absence of genome data limits our understanding of the pathways involved in bract coloration and breeding. Here, we report a chromosome-level assembly of the giga-genome of Bougainvillea × buttiana 'Mrs Butt', a cultivar thought to be the origin of many other Bougainvillea cultivars. The assembled genome is ~5 Gb with a scaffold N50 of 151 756 278 bp and contains 86 572 genes which have undergone recent whole-genome duplication. We confirmed that multiple rounds of whole-genome multiplication have occurred in the evolutionary history of the Caryophyllales, reconstructed the relationship in the Caryophyllales at whole genome level, and found discordance between species and gene trees as the result of complex introgression events. We investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryophyllales species. To explore the potential formation mechanism of diverse bract colors in Bougainvillea, we analyzed the genes involved in betalain and anthocyanin biosynthesis and found extremely low expression of ANS and DFR genes in all cultivars, which may limit anthocyanin biosynthesis. Our findings indicate that the expression pattern of the betalain biosynthetic pathway did not directly correlate with bract color, and a higher expression level in the betalain biosynthetic pathway is required for colored bracts. This improved understanding of the correlation between gene expression and bract color allows plant breeding outcomes to be predicted with greater certainty.
Collapse
Affiliation(s)
- Lan Lan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- School of Medical, Molecularand Forensic Sciences, Murdoch University, 6150, Western Australia, 90 South Street, Murdoch, Australia
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Huiqi Zhao
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, 572025, China
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Suxia Xu
- Fujian Key Laboratory of Subtropical Plant Physiology & Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, China
| | - Shenglong Kan
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiaoni Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Weichao Liu
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Yonglin Ren
- School of Medical, Molecularand Forensic Sciences, Murdoch University, 6150, Western Australia, 90 South Street, Murdoch, Australia
| | - Wayne Reeve
- School of Medical, Molecularand Forensic Sciences, Murdoch University, 6150, Western Australia, 90 South Street, Murdoch, Australia
| | - Jun Yang
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, 572025, China
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| |
Collapse
|
8
|
Bartish IV, Bonnefoi S, Aïnouche A, Bruelheide H, Bartish M, Prinzing A. Fewer chromosomes, more co-occurring species within plant lineages: A likely effect of local survival and colonization. AMERICAN JOURNAL OF BOTANY 2023; 110:e16139. [PMID: 36758168 DOI: 10.1002/ajb2.16139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Plant lineages differ markedly in species richness globally, regionally, and locally. Differences in whole-genome characteristics (WGCs) such as monoploid chromosome number, genome size, and ploidy level may explain differences in global species richness through speciation or global extinction. However, it is unknown whether WGCs drive species richness within lineages also in a recent, postglacial regional flora or in local plant communities through local extinction or colonization and regional species turnover. METHODS We tested for relationships between WGCs and richness of angiosperm families across the Netherlands/Germany/Czechia as a region, and within 193,449 local vegetation plots. RESULTS Families that are species-rich across the region have lower ploidy levels and small monoploid chromosomes numbers or both (interaction terms), but the relationships disappear after accounting for continental and local richness of families. Families that are species-rich within occupied localities have small numbers of polyploidy and monoploid chromosome numbers or both, independent of their own regional richness and the local richness of all other locally co-occurring species in the plots. Relationships between WGCs and family species-richness persisted after accounting for niche characteristics and life histories. CONCLUSIONS Families that have few chromosomes, either monoploid or holoploid, succeed in maintaining many species in local communities and across a continent and, as indirect consequence of both, across a region. We suggest evolutionary mechanisms to explain how small chromosome numbers and ploidy levels might decrease rates of local extinction and increase rates of colonization. The genome of a macroevolutionary lineage may ultimately control whether its species can ecologically coexist.
Collapse
Affiliation(s)
- Igor V Bartish
- Université de Rennes 1, CNRS Research Unit Ecosystèmes Biodiversité Evolution (ECOBIO), Campus de Beaulieu, 35042, Rennes, France
- Department of Genetic Ecology, Institute of Botany, Academy of Sciences, CZ-25243 Pruhonice 1, Czech Republic
| | - Salomé Bonnefoi
- Université de Rennes 1, CNRS Research Unit Ecosystèmes Biodiversité Evolution (ECOBIO), Campus de Beaulieu, 35042, Rennes, France
| | - Abdelkader Aïnouche
- Université de Rennes 1, CNRS Research Unit Ecosystèmes Biodiversité Evolution (ECOBIO), Campus de Beaulieu, 35042, Rennes, France
| | - Helge Bruelheide
- Institute of Biology/Geobotany & Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103, Leipzig, Germany
| | - Mark Bartish
- Royal Institute of Technology, Stockholm, SE-100 44, Sweden
| | - Andreas Prinzing
- Université de Rennes 1, CNRS Research Unit Ecosystèmes Biodiversité Evolution (ECOBIO), Campus de Beaulieu, 35042, Rennes, France
| |
Collapse
|
9
|
Fujiwara T, Liu H, Meza-Torres EI, Morero RE, Vega AJ, Liang Z, Ebihara A, Leitch IJ, Schneider H. Evolution of genome space occupation in ferns: linking genome diversity and species richness. ANNALS OF BOTANY 2023; 131:59-70. [PMID: 34259813 PMCID: PMC9904345 DOI: 10.1093/aob/mcab094] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/10/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The dynamics of genome evolution caused by whole genome duplications and other processes are hypothesized to shape the diversification of plants and thus contribute to the astonishing variation in species richness among the main lineages of land plants. Ferns, the second most species-rich lineage of land plants, are highly suitable to test this hypothesis because of several unique features that distinguish fern genomes from those of seed plants. In this study, we tested the hypothesis that genome diversity and disparity shape fern species diversity by recording several parameters related to genome size and chromosome number. METHODS We conducted de novo measurement of DNA C-values across the fern phylogeny to reconstruct the phylogenetic history of the genome space occupation in ferns by integrating genomic parameters such as genome size, chromosome number and average DNA amount per chromosome into a time-scaled phylogenetic framework. Using phylogenetic generalized least square methods, we determined correlations between chromosome number and genome size, species diversity and evolutionary rates of their transformation. KEY RESULTS The measurements of DNA C-values for 233 species more than doubled the taxon coverage from ~2.2 % in previous studies to 5.3 % of extant diversity. The dataset not only documented substantial differences in the accumulation of genomic diversity and disparity among the major lineages of ferns but also supported the predicted correlation between species diversity and the dynamics of genome evolution. CONCLUSIONS Our results demonstrated substantial genome disparity among different groups of ferns and supported the prediction that alterations of reproductive modes alter trends of genome evolution. Finally, we recovered evidence for a close link between the dynamics of genome evolution and species diversity in ferns for the first time.
Collapse
Affiliation(s)
- Tao Fujiwara
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, Japan
| | - Hongmei Liu
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Esteban I Meza-Torres
- Instituto de Botánica del Nordeste, Universidad Nacional del Nordeste, Consejo Nacional de Investigaciones Científicas y Técnicas, Corrientes, Argentina
| | - Rita E Morero
- Instituto Multidiscipinario de Biologia Vegetal, Universidad Nacional de Cordoba, Consejo Nacional de Investigaciones Científicas y Tecnicas, Cordoba, Argentina
| | - Alvaro J Vega
- Instituto de Botánica del Nordeste, Universidad Nacional del Nordeste, Consejo Nacional de Investigaciones Científicas y Técnicas, Corrientes, Argentina
| | - Zhenlong Liang
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Sciences, Tsukuba, Japan
| | | | | |
Collapse
|
10
|
Ten Plastomes of Crassula (Crassulaceae) and Phylogenetic Implications. BIOLOGY 2022; 11:biology11121779. [PMID: 36552287 PMCID: PMC9775174 DOI: 10.3390/biology11121779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
The genus Crassula is the second-largest genus in the family Crassulaceae, with about 200 species. As an acknowledged super-barcode, plastomes have been extensively utilized for plant evolutionary studies. Here, we first report 10 new plastomes of Crassula. We further focused on the structural characterizations, codon usage, aversion patterns, and evolutionary rates of plastomes. The IR junction patterns-IRb had 110 bp expansion to rps19-were conservative among Crassula species. Interestingly, we found the codon usage patterns of matK gene in Crassula species are unique among Crassulaceae species with elevated ENC values. Furthermore, subgenus Crassula species have specific GC-biases in the matK gene. In addition, the codon aversion motifs from matK, pafI, and rpl22 contained phylogenetic implications within Crassula. The evolutionary rates analyses indicated all plastid genes of Crassulaceae were under the purifying selection. Among plastid genes, ycf1 and ycf2 were the most rapidly evolving genes, whereas psaC was the most conserved gene. Additionally, our phylogenetic analyses strongly supported that Crassula is sister to all other Crassulaceae species. Our findings will be useful for further evolutionary studies within the Crassula and Crassulaceae.
Collapse
|
11
|
Montoya P, Cadena CD, Claramunt S, Duchêne DA. Environmental niche and flight intensity are associated with molecular evolutionary rates in a large avian radiation. BMC Ecol Evol 2022; 22:95. [PMID: 35918644 PMCID: PMC9347078 DOI: 10.1186/s12862-022-02047-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/20/2022] [Indexed: 11/27/2022] Open
Abstract
Background Metabolic activity and environmental energy are two of the most studied putative drivers of molecular evolutionary rates. Their extensive study, however, has resulted in mixed results and has rarely included the exploration of interactions among various factors impacting molecular evolutionary rates across large clades. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with proxies of metabolic demands imposed by flight (wing loading and wing shape) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation). Results We found weak evidence of a positive effect of environmental and morphological variables on mitochondrial substitution rates. Additionally, we found that temperature and UV radiation interact to explain molecular rates at nucleotide sites affected by selection and population size (non-synonymous substitutions), contrary to the expectation of their impact on sites associated with mutation rates (synonymous substitutions). We also found a negative interaction between wing shape (as described by the hand-wing index) and body mass explaining mitochondrial molecular rates, suggesting molecular signatures of positive selection or reduced population sizes in small-bodied species with greater flight activity. Conclusions Our results suggest that the demands of flight and environmental energy pose multiple evolutionary pressures on the genome either by driving mutation rates or via their association with natural selection or population size. Data from whole genomes and detailed physiology across taxa will bring a more complete picture of the impact of metabolism, population size, and the environment on avian genome evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02047-0.
Collapse
|
12
|
Vidal-Russell R, Tadey M, Urfusová R, Urfus T, Souto CP. Evolutionary importance of the relationship between cytogeography and climate: New insights on creosote bushes from North and South America. PLANT DIVERSITY 2022; 44:492-498. [PMID: 36187552 PMCID: PMC9512640 DOI: 10.1016/j.pld.2021.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/18/2021] [Accepted: 11/21/2021] [Indexed: 06/16/2023]
Abstract
Relationships between genome size and environmental variables suggest that DNA content might be adaptive and of evolutionary importance in plants. The genus Larrea provides an interesting system to test this hypothesis, since it shows both intra- and interspecific variation in genome size. Larrea has an amphitropical distribution in North and South American deserts, where it is most speciose. Larrea tridentata in North America shows a gradient of increasing autopolyploidy; while three of the four studied South American species are diploids, Larrea divaricata, Larrea nitida, Larrea ameghinoi, and the fourth is an allopolyploid, Larrea cuneifolia. We downloaded available focal species' georeferenced records from seven data reservoirs. We used these records to extract biologically relevant environmental variables from WorldClim at 30 arc seconds scale, to have a broad characterization of the variable climatic conditions of both regions, and a climatic envelope for each species. We estimated relative DNA content index and relative monoploid genome values, by flow cytometry, of four most abundant Larrea species throughout their respective ranges. Then we winnow the bioclimatic dataset down to uncorrelated variables and sampled locales, to analyse the degree of association between both intra- and interspecific relative DNA content and climatic variables that are functionally relevant in arid environments using Pearson correlations, general linear and mixed effects models. Within the genus Larrea, relative DNA content increases with rising temperature and decreases with rising precipitation. At the intraspecific level, all four species show relative DNA content variation across climatic conditions. Larrea is a genus that shows genome size variation correlated with climate. Our results are also consistent with the hypothesis that extreme environmental pressures may have facilitated repeated whole genome duplication events in North America, while in South America, reticulate evolution, as allopolyploidization, and speciation might have been climate-dependent since the Oligocene.
Collapse
Affiliation(s)
- Romina Vidal-Russell
- Laboratorio Ecotono- INIBIOMA (CONICET-UNComahue), Quintral, 1250, Bariloche, Río Negro, Argentina
| | - Mariana Tadey
- Laboratorio Ecotono- INIBIOMA (CONICET-UNComahue), Quintral, 1250, Bariloche, Río Negro, Argentina
| | - Romana Urfusová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 00, Prague, Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 00, Prague, Czech Republic
| | - Cintia Paola Souto
- Laboratorio Ecotono- INIBIOMA (CONICET-UNComahue), Quintral, 1250, Bariloche, Río Negro, Argentina
| |
Collapse
|
13
|
Skeels A, Bach W, Hagen O, Jetz W, Pellissier L. Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations. Syst Biol 2022:6637530. [PMID: 35809070 DOI: 10.1093/sysbio/syac048] [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: 10/08/2021] [Revised: 06/21/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Biodiversity varies predictably with environmental energy around the globe, but the underlaying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental kinetic energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 million years of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modelled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modelling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time.
Collapse
Affiliation(s)
- A Skeels
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
| | - W Bach
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
| | - O Hagen
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 04103, Germany
| | - W Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.,Center for Biodiversity and Global Change, Yale University, New Haven, CT 06520, USA
| | - L Pellissier
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
| |
Collapse
|
14
|
Liedtke HC, Cruz F, Gómez-Garrido J, Fuentes Palacios D, Marcet-Houben M, Gut M, Alioto T, Gabaldón T, Gomez-Mestre I. Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad. DNA Res 2022; 29:6588074. [PMID: 35583263 PMCID: PMC9164646 DOI: 10.1093/dnares/dsac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/12/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Genomic resources for amphibians are still hugely under-represented in vertebrate genomic research, despite being a group of major interest for ecology, evolution and conservation. Amphibians constitute a highly threatened group of vertebrates, present a vast diversity in reproductive modes, are extremely diverse in morphology, occupy most ecoregions of the world, and present the widest range in genome sizes of any major group of vertebrates. We combined Illumina, Nanopore and Hi-C sequencing technologies to assemble a chromosome-level genome sequence for an anuran with a moderate genome size (assembly span 3.09 Gb); Pelobates cultripes, the western spadefoot toad. The genome has an N50 length of 330 Mb with 98.6% of the total sequence length assembled into 14 super scaffolds, and 87.7% complete BUSCO genes. We use published transcriptomic data to provide annotations, identifying 32,684 protein-coding genes. We also reconstruct the P. cultripes phylome and identify 2,527 gene expansions. We contribute the first draft of the genome of the western spadefoot toad, P. cultripes. This species represents a relatively basal lineage in the anuran tree with an interesting ecology and a high degree of developmental plasticity, and thus is an important resource for amphibian genomic research.
Collapse
Affiliation(s)
- Hans Christoph Liedtke
- Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC) , 41092 Sevilla, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
| | - Diego Fuentes Palacios
- Barcelona Supercomputing Centre (BSC-CNS) , 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
| | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS) , 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF) , Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS) , 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA) , Barcelona, Spain
| | - Ivan Gomez-Mestre
- Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC) , 41092 Sevilla, Spain
| |
Collapse
|
15
|
Ritchie AM, Hua X, Bromham L. Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary. BMC Ecol Evol 2022; 22:61. [PMID: 35538412 PMCID: PMC9088092 DOI: 10.1186/s12862-022-02015-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 04/14/2022] [Indexed: 11/17/2022] Open
Abstract
Background An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used methods rely on idealised models of rate variation, such as the uncorrelated and autocorrelated clocks, and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as current evidence suggests, they may have a significant influence on molecular dates. Results We simulate phylogenies and molecular sequences under three different realistic rate variation models—one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test three commonly used “relaxed clock” molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior using BEAST 2, to up to 91% when sequences evolved under the punctuated model are reconstructed under an autocorrelated prior using PAML. Conclusions We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02015-8.
Collapse
|
16
|
Dong W, Li E, Liu Y, Xu C, Wang Y, Liu K, Cui X, Sun J, Suo Z, Zhang Z, Wen J, Zhou S. Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family. BMC Biol 2022; 20:92. [PMID: 35468824 PMCID: PMC9040247 DOI: 10.1186/s12915-022-01297-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/13/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Deep-branching phylogenetic relationships are often difficult to resolve because phylogenetic signals are obscured by the long history and complexity of evolutionary processes, such as ancient introgression/hybridization, polyploidization, and incomplete lineage sorting (ILS). Phylogenomics has been effective in providing information for resolving both deep- and shallow-scale relationships across all branches of the tree of life. The olive family (Oleaceae) is composed of 25 genera classified into five tribes with tribe Oleeae consisting of four subtribes. Previous phylogenetic analyses showed that ILS and/or hybridization led to phylogenetic incongruence in the family. It was essential to distinguish phylogenetic signal conflicts, and explore mechanisms for the uncertainties concerning relationships of the olive family, especially at the deep-branching nodes. RESULTS We used the whole plastid genome and nuclear single nucleotide polymorphism (SNP) data to infer the phylogenetic relationships and to assess the variation and rates among the main clades of the olive family. We also used 2608 and 1865 orthologous nuclear genes to infer the deep-branching relationships among tribes of Oleaceae and subtribes of tribe Oleeae, respectively. Concatenated and coalescence trees based on the plastid genome, nuclear SNPs and multiple nuclear genes suggest events of ILS and/or ancient introgression during the diversification of Oleaceae. Additionally, there was extreme heterogeneity in the substitution rates across the tribes. Furthermore, our results supported that introgression/hybridization, rather than ILS, is the main factor for phylogenetic discordance among the five tribes of Oleaceae. The tribe Oleeae is supported to have originated via ancient hybridization and polyploidy, and its most likely parentages are the ancestral lineage of Jasmineae or its sister group, which is a "ghost lineage," and Forsythieae. However, ILS and ancient introgression are mainly responsible for the phylogenetic discordance among the four subtribes of tribe Oleeae. CONCLUSIONS This study showcases that using multiple sequence datasets (plastid genomes, nuclear SNPs and thousands of nuclear genes) and diverse phylogenomic methods such as data partition, heterogeneous models, quantifying introgression via branch lengths (QuIBL) analysis, and species network analysis can facilitate untangling long and complex evolutionary processes of ancient introgression, paleopolyploidization, and ILS.
Collapse
Affiliation(s)
- Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yushuang Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Xingyong Cui
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Zhili Suo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA.
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| |
Collapse
|
17
|
Ritchie AM, Hua X, Bromham L. Diversification Rate is Associated with Rate of Molecular Evolution in Ray-Finned Fish (Actinopterygii). J Mol Evol 2022; 90:200-214. [PMID: 35262772 PMCID: PMC8975766 DOI: 10.1007/s00239-022-10052-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 02/24/2022] [Indexed: 10/27/2022]
Abstract
Understanding the factors that drive diversification of taxa across the tree of life is a key focus of macroevolutionary research. While the effects of life history, ecology, climate and geography on diversity have been studied for many taxa, the relationship between molecular evolution and diversification has received less attention. However, correlations between rates of molecular evolution and diversification rate have been detected in a range of taxa, including reptiles, plants and birds. A correlation between rates of molecular evolution and diversification rate is a prediction of several evolutionary theories, including the evolutionary speed hypothesis which links variation in mutation rates to differences in speciation rates. If it is widespread, such correlations could also have significant practical impacts, if they are not adequately accounted for in phylogenetic inference of evolutionary rates and timescales. Ray-finned fish (Actinopterygii) offer a prime target to test for this relationship due to their extreme variation in clade size suggesting a wide range of diversification rates. We employ both a sister-pairs approach and a whole-tree approach to test for correlations between substitution rate and net diversification. We also collect life history and ecological trait data and account for potential confounding factors including body size, latitude, max depth and reef association. We find evidence to support a relationship between diversification and synonymous rates of nuclear evolution across two published backbone phylogenies, as well as weak evidence for a relationship between mitochondrial nonsynonymous rates and diversification at the genus level.
Collapse
Affiliation(s)
- Andrew M Ritchie
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia. .,Research School of Biological Sciences, Australian National University, Robertson Building, 134 Linnaeus Way, Canberra, ACT 2600, Australia.
| | - Xia Hua
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia.,Mathematical Sciences Institute, Australian National University, Canberra, ACT 2600, Australia
| | - Lindell Bromham
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia
| |
Collapse
|
18
|
Cao HX, Vu GTH, Gailing O. From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees. Int J Mol Sci 2022; 23:966. [PMID: 35055150 PMCID: PMC8780650 DOI: 10.3390/ijms23020966] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 12/11/2022] Open
Abstract
Due to the economic and ecological importance of forest trees, modern breeding and genetic manipulation of forest trees have become increasingly prevalent. The CRISPR-based technology provides a versatile, powerful, and widely accepted tool for analyzing gene function and precise genetic modification in virtually any species but remains largely unexplored in forest species. Rapidly accumulating genetic and genomic resources for forest trees enabled the identification of numerous genes and biological processes that are associated with important traits such as wood quality, drought, or pest resistance, facilitating the selection of suitable gene editing targets. Here, we introduce and discuss the latest progress, opportunities, and challenges of genome sequencing and editing for improving forest sustainability.
Collapse
Affiliation(s)
- Hieu Xuan Cao
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
| | - Giang Thi Ha Vu
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
- Center for Integrated Breeding Research (CiBreed), Georg-August University of Göttingen, 37073 Gottingen, Germany
| |
Collapse
|
19
|
Janzen T, Bokma F, Etienne RS. Nucleotide substitutions during speciation may explain substitution rate variation. Syst Biol 2021; 71:1244-1254. [PMID: 34672354 PMCID: PMC9366449 DOI: 10.1093/sysbio/syab085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/11/2021] [Accepted: 10/16/2021] [Indexed: 11/14/2022] Open
Abstract
Although molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which is a statistical distribution of mutation rates without much underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life. [Molecular clock; phylogenetic reconstruction; speciation; substitution rate variation.]
Collapse
Affiliation(s)
- Thijs Janzen
- Correspondence to be sent to: Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands; E-mail:
| | - Folmer Bokma
- Department of BioSciences, Center for Ecological and Evolutionary Synthesis (CEES), University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands
| |
Collapse
|
20
|
Li X, Li Y, Sylvester SP, Zang M, El‐Kassaby YA, Fang Y. Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus. Ecol Evol 2021; 11:13401-13414. [PMID: 34646478 PMCID: PMC8495791 DOI: 10.1002/ece3.8063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular evolution, including nucleotide substitutions, plays an important role in understanding the dynamics and mechanisms of species evolution. Here, we sequenced whole plastid genomes (plastomes) of Quercus fabri, Quercus semecarpifolia, Quercus engleriana, and Quercus phellos and compared them with 14 other Quercus plastomes to explore their evolutionary relationships using 67 shared protein-coding sequences. While many previously identified evolutionary relationships were found, our findings do not support previous research which retrieve Quercus subg. Cerris sect. Ilex as a monophyletic group, with sect. Ilex found to be polyphyletic and composed of three strongly supported lineages inserted between sections Cerris and Cyclobalanposis. Compared with gymnosperms, Quercus plastomes showed higher evolutionary rates (Dn/Ds = 0.3793). Most protein-coding genes experienced relaxed purifying selection, and the high Dn value (0.1927) indicated that gene functions adjusted to environmental changes effectively. Our findings suggest that gene interval regions play an important role in Quercus evolution. We detected greater variation in the intergenic regions (trnH-psbA, trnK_UUU-rps16, trnfM_CAU-rps14, trnS_GCU-trnG_GCC, and atpF-atpH), intron losses (petB and petD), and pseudogene loss and degradation (ycf15). Additionally, the loss of some genes suggested the existence of gene exchanges between plastid and nuclear genomes, which affects the evolutionary rate of the former. However, the connective mechanism between these two genomes is still unclear.
Collapse
Affiliation(s)
- Xuan Li
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- Department of Forest and Conservation Sciences Faculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Yongfu Li
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Steven Paul Sylvester
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Mingyue Zang
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Yousry A. El‐Kassaby
- Department of Forest and Conservation Sciences Faculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Yanming Fang
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| |
Collapse
|
21
|
Linde AM, Eklund DM, Cronberg N, Bowman JL, Lagercrantz U. Rates and patterns of molecular evolution in bryophyte genomes, with focus on complex thalloid liverworts, Marchantiopsida. Mol Phylogenet Evol 2021; 165:107295. [PMID: 34438050 DOI: 10.1016/j.ympev.2021.107295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/30/2021] [Accepted: 08/19/2021] [Indexed: 10/20/2022]
Abstract
Plants commonly referred to as "bryophytes" belong to three major lineages of non-vascular plants: the liverworts, the hornworts and the mosses. They are unique among land plants in having a dominant haploid generation and a short-lived diploid sporophytic generation. The dynamics of selection acting on a haploid genome differs from those acting on a diploid genome: new mutations are directly exposed to selection. The general aim of this paper is to investigate the diversification rateof bryophytes - measured as silent site substitution rate representing neutral evolution (mutation rate) and the nonsynonymous to synonymous substitution rate ratio (dN/dS) representing selective evolution - and compare it with earlier studies on vascular plants. Results show that the silent site substitution rate is lower for liverworts as compared to angiosperms, but not as low as for gymnosperms. The selection pressure, measured as dN/dS, isnot remarkably lower for bryophytes as compared to other diploid dominant plants as would be expected by the masking hypothesis, indicating that other factors are more important than ploidy.
Collapse
Affiliation(s)
- Anna-Malin Linde
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - D Magnus Eklund
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - Nils Cronberg
- Biodiversity, Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden.
| | - John L Bowman
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Ulf Lagercrantz
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| |
Collapse
|
22
|
McGaughran A, Laver R, Fraser C. Evolutionary Responses to Warming. Trends Ecol Evol 2021; 36:591-600. [PMID: 33726946 DOI: 10.1016/j.tree.2021.02.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 12/24/2022]
Abstract
Climate change is predicted to dramatically alter biological diversity and distributions, driving extirpations, extinctions, and extensive range shifts across the globe. Warming can also, however, lead to phenotypic or behavioural plasticity, as species adapt to new conditions. Recent genomic research indicates that some species are capable of rapid evolution as selection favours adaptive responses to environmental change and altered or novel niche spaces. New advances are providing mechanistic insights into how temperature might accelerate evolution in the Anthropocene. These discoveries highlight intriguing new research directions - such as using geothermal and polar systems combined with powerful genomic tools - that will help us to understand the processes underpinning adaptive evolution and better project how ecosystems will change in a warming world.
Collapse
Affiliation(s)
- Angela McGaughran
- Te Aka Mātuatua - School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.
| | - Rebecca Laver
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Ceridwen Fraser
- Department of Marine Science, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| |
Collapse
|
23
|
Ritchie AM, Hua X, Cardillo M, Yaxley KJ, Dinnage R, Bromham L. Phylogenetic diversity metrics from molecular phylogenies: modelling expected degree of error under realistic rate variation. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Andrew M. Ritchie
- Research School of Biological Sciences Australian National University Canberra ACT Australia
| | - Xia Hua
- Research School of Biological Sciences Australian National University Canberra ACT Australia
- Mathematical Sciences Institute Australian National University Canberra ACT Australia
| | - Marcel Cardillo
- Research School of Biological Sciences Australian National University Canberra ACT Australia
| | - Keaghan J. Yaxley
- Research School of Biological Sciences Australian National University Canberra ACT Australia
| | - Russell Dinnage
- Research School of Biological Sciences Australian National University Canberra ACT Australia
| | - Lindell Bromham
- Research School of Biological Sciences Australian National University Canberra ACT Australia
| |
Collapse
|
24
|
May JA, Feng Z, Orton MG, Adamowicz SJ. The Effects of Ecological Traits on the Rate of Molecular Evolution in Ray-Finned Fishes: A Multivariable Approach. J Mol Evol 2020; 88:689-702. [PMID: 33009923 DOI: 10.1007/s00239-020-09967-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 09/22/2020] [Indexed: 11/25/2022]
Abstract
Myriad environmental and biological traits have been investigated for their roles in influencing the rate of molecular evolution across various taxonomic groups. However, most studies have focused on a single trait, while controlling for additional factors in an informal way, generally by excluding taxa. This study utilized a dataset of cytochrome c oxidase subunit I (COI) barcode sequences from over 7000 ray-finned fish species to test the effects of 27 traits on molecular evolutionary rates. Environmental traits such as temperature were considered, as were traits associated with effective population size including body size and age at maturity. It was hypothesized that these traits would demonstrate significant correlations with substitution rate in a multivariable analysis due to their associations with mutation and fixation rates, respectively. A bioinformatics pipeline was developed to assemble and analyze sequence data retrieved from the Barcode of Life Data System (BOLD) and trait data obtained from FishBase. For use in phylogenetic regression analyses, a maximum likelihood tree was constructed from the COI sequence data using a multi-gene backbone constraint tree covering 71% of the species. A variable selection method that included both single- and multivariable analyses was used to identify traits that contribute to rate heterogeneity estimated from different codon positions. Our analyses revealed that molecular rates associated most significantly with latitude, body size, and habitat type. Overall, this study presents a novel and systematic approach for integrative data assembly and variable selection methodology in a phylogenetic framework.
Collapse
Affiliation(s)
- Jacqueline A May
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - Zeny Feng
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Matthew G Orton
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| |
Collapse
|
25
|
Nucleotide substitution rates of diatom plastid encoded protein genes are positively correlated with genome architecture. Sci Rep 2020; 10:14358. [PMID: 32873883 PMCID: PMC7462845 DOI: 10.1038/s41598-020-71473-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 08/17/2020] [Indexed: 01/02/2023] Open
Abstract
Diatoms are the largest group of heterokont algae with more than 100,000 species. As one of the single-celled photosynthetic organisms that inhabit marine, aquatic and terrestrial ecosystems, diatoms contribute ~ 45% of global primary production. Despite their ubiquity and environmental significance, very few diatom plastid genomes (plastomes) have been sequenced and studied. This study explored patterns of nucleotide substitution rates of diatom plastids across the entire suite of plastome protein-coding genes for 40 taxa representing the major clades. The highest substitution rate was lineage-specific within the araphid 2 taxon Astrosyne radiata and radial 2 taxon Proboscia sp. Rate heterogeneity was also evident in different functional classes and individual genes. Similar to land plants, proteins genes involved in photosynthetic metabolism have lower synonymous and nonsynonymous substitutions rates than those involved in transcription and translation. Significant positive correlations were identified between substitution rates and measures of genomic rearrangements, including indels and inversions, which is a similar result to what was found in legume plants. This work advances the understanding of the molecular evolution of diatom plastomes and provides a foundation for future studies.
Collapse
|
26
|
Hernández-Hernández T, Wiens JJ. Why Are There So Many Flowering Plants? A Multiscale Analysis of Plant Diversification. Am Nat 2020; 195:948-963. [DOI: 10.1086/708273] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
27
|
Naciri Y, Linder HP. The genetics of evolutionary radiations. Biol Rev Camb Philos Soc 2020; 95:1055-1072. [PMID: 32233014 DOI: 10.1111/brv.12598] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 02/06/2023]
Abstract
With the realization that much of the biological diversity on Earth has been generated by discrete evolutionary radiations, there has been a rapid increase in research into the biotic (key innovations) and abiotic (key environments) circumstances in which such radiations took place. Here we focus on the potential importance of population genetic structure and trait genetic architecture in explaining radiations. We propose a verbal model describing the stages of an evolutionary radiation: first invading a suitable adaptive zone and expanding both spatially and ecologically through this zone; secondly, diverging genetically into numerous distinct populations; and, finally, speciating. There are numerous examples of the first stage; the difficulty, however, is explaining how genetic diversification can take place from the establishment of a, presumably, genetically depauperate population in a new adaptive zone. We explore the potential roles of epigenetics and transposable elements (TEs), of neutral process such as genetic drift in combination with trait genetic architecture, of gene flow limitation through isolation by distance (IBD), isolation by ecology and isolation by colonization, the possible role of intra-specific competition, and that of admixture and hybridization in increasing the genetic diversity of the founding populations. We show that many of the predictions of this model are corroborated. Most radiations occur in complex adaptive zones, which facilitate the establishment of many small populations exposed to genetic drift and divergent selection. We also show that many radiations (especially those resulting from long-distance dispersal) were established by polyploid lineages, and that many radiating lineages have small genome sizes. However, there are several other predictions which are not (yet) possible to test: that epigenetics has played a role in radiations, that radiations occur more frequently in clades with small gene flow distances, or that the ancestors of radiations had large fundamental niches. At least some of these may be testable in the future as more genome and epigenome data become available. The implication of this model is that many radiations may be hard polytomies because the genetic divergence leading to speciation happens within a very short time, and that the divergence history may be further obscured by hybridization. Furthermore, it suggests that only lineages with the appropriate genetic architecture will be able to radiate, and that such a radiation will happen in a meta-population environment. Understanding the genetic architecture of a lineage may be an essential part of accounting for why some lineages radiate, and some do not.
Collapse
Affiliation(s)
- Yamama Naciri
- Plant Systematics and Biodiversity Laboratory, Department of Botany and Plant biology of the University of Geneva, 1 Chemin de l'Impératrice, CH-1292, Chambésy, Geneva, Switzerland
| | - H Peter Linder
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| |
Collapse
|
28
|
Iglesias-Carrasco M, Jennions MD, Ho SYW, Duchêne DA. Sexual selection, body mass and molecular evolution interact to predict diversification in birds. Proc Biol Sci 2020; 286:20190172. [PMID: 30890097 DOI: 10.1098/rspb.2019.0172] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sexual selection is a powerful agent of evolution, driving microevolutionary changes in the genome and macroevolutionary rates of lineage diversification. The mechanisms by which sexual selection might influence macroevolution remain poorly understood. For example, sexual selection might drive positive selection for key adaptations that facilitate diversification. Furthermore, sexual selection might be a general driver of molecular evolutionary rate. We lay out some of the potential mechanisms that create a link between sexual selection and diversification, based on causal effects on other life-history traits such as body mass and the rate of molecular evolution. Birds are ideally suited for testing the importance of these relationships because of their diverse reproductive systems and the multiple evolutionary radiations that have produced their astounding modern diversity. We show that sexual selection (measured as the degree of polygyny) interacts with the rate of molecular evolution and with body mass to predict species richness at the genus level. A high degree of polygyny and rapid molecular evolution are positively associated with the net rate of diversification, with the two factors being especially important for explaining diversification in large-bodied taxa. Our findings further suggest that mutation rates underpin some of the macroevolutionary effects of sexual selection. We synthesize the existing theory on sexual selection as a force for diversity and propose avenues for exploring this association using genome data.
Collapse
Affiliation(s)
- Maider Iglesias-Carrasco
- 1 Research School of Biology, Australian National University , Canberra, Australian Capital Territory 2601 , Australia
| | - Michael D Jennions
- 1 Research School of Biology, Australian National University , Canberra, Australian Capital Territory 2601 , Australia
| | - Simon Y W Ho
- 2 School of Life and Environmental Sciences, University of Sydney , Sydney, New South Wales 2006 , Australia
| | - David A Duchêne
- 1 Research School of Biology, Australian National University , Canberra, Australian Capital Territory 2601 , Australia.,2 School of Life and Environmental Sciences, University of Sydney , Sydney, New South Wales 2006 , Australia
| |
Collapse
|
29
|
Schaack S, Ho EKH, Macrae F. Disentangling the intertwined roles of mutation, selection and drift in the mitochondrial genome. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190173. [PMID: 31787045 PMCID: PMC6939366 DOI: 10.1098/rstb.2019.0173] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2019] [Indexed: 12/31/2022] Open
Abstract
Understanding and quantifying the rates of change in the mitochondrial genome is a major component of many areas of biological inquiry, from phylogenetics to human health. A critical parameter in understanding rates of change is estimating the mitochondrial mutation rate (mtDNA MR). Although the first direct estimates of mtDNA MRs were reported almost 20 years ago, the number of estimates has not grown markedly since that time. This is largely owing to the challenges associated with time- and labour-intensive mutation accumulation (MA) experiments. But even MA experiments do not solve a major problem with estimating mtDNA MRs-the challenge of disentangling the role of mutation from other evolutionary forces acting within the cell. Now that it is widely understood that any newly generated mutant allele in the mitochondria will initially be at very low frequency (1/N, where N is the number of mtDNA molecules in the cell), the importance of understanding the effective population size (Ne) of the mtDNA and the size of genetic bottlenecks during gametogenesis and development has come into the spotlight. In addition to these factors regulating the role of genetic drift, advances in our understanding of mitochondrial replication and turnover allow us to more easily envision how natural selection within the cell might favour or purge mutations in multi-copy organellar genomes. Here, we review the unique features of the mitochondrial genome that pose a challenge for accurate MR estimation and discuss ways to overcome those challenges. Estimates of mtDNA MRs remain one of the most widely used parameters in biology, thus accurate quantification and a deeper understanding of how and why they may vary within and between individuals, populations and species is an important goal. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
Collapse
Affiliation(s)
- Sarah Schaack
- Department of Biology, Reed College, Portland, OR 97202, USA
| | - Eddie K H Ho
- Department of Biology, Reed College, Portland, OR 97202, USA
| | - Fenner Macrae
- Department of Biology, Reed College, Portland, OR 97202, USA
| |
Collapse
|
30
|
Marchant DB, Sessa EB, Wolf PG, Heo K, Barbazuk WB, Soltis PS, Soltis DE. The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly. Sci Rep 2019; 9:18181. [PMID: 31796775 PMCID: PMC6890710 DOI: 10.1038/s41598-019-53968-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 11/04/2019] [Indexed: 01/04/2023] Open
Abstract
Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.
Collapse
Affiliation(s)
- D Blaine Marchant
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Paul G Wolf
- Department of Biology, Utah State University, Logan, UT, 84322, USA
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Kweon Heo
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 24341, Korea
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
- The Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
- The Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| |
Collapse
|
31
|
Schoen DJ, Schultz ST. Somatic Mutation and Evolution in Plants. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110218-024955] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Somatic mutations are common in plants, and they may accumulate and be passed on to gametes. The determinants of somatic mutation accumulation include the intraorganismal selective effect of mutations, the number of cell divisions that separate the zygote from the formation of gametes, and shoot apical meristem structure and branching. Somatic mutations can promote the evolution of diploidy, polyploidy, sexual recombination, outcrossing, clonality, and separate sexes, and they may contribute genetic variability in many other traits. The amplification of beneficial mutations via intraorganismal selection may relax selection to reduce the genomic mutation rate or to protect the germline in plants. The total rate of somatic mutation, the distribution of selective effects and fates in the plant body, and the degree to which the germline is sheltered from somatic mutations are still poorly understood. Our knowledge can be improved through empirical estimates of mutation rates and effects on cell lineages and whole organisms, such as estimates of the reduction in fitness of progeny produced by within- versus between-flower crosses on the same plant, mutation coalescent studies within the canopy, and incorporation of somatic mutation into theoretical models of plant evolutionary genetics.
Collapse
Affiliation(s)
- Daniel J. Schoen
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Stewart T. Schultz
- Department of Ecology, Agronomy, and Aquaculture, University of Zadar, 23000 Zadar, Croatia
| |
Collapse
|
32
|
Bedoya AM, Ruhfel BR, Philbrick CT, Madriñán S, Bove CP, Mesterházy A, Olmstead RG. Plastid Genomes of Five Species of Riverweeds (Podostemaceae): Structural Organization and Comparative Analysis in Malpighiales. FRONTIERS IN PLANT SCIENCE 2019; 10:1035. [PMID: 31481967 PMCID: PMC6710714 DOI: 10.3389/fpls.2019.01035] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/24/2019] [Indexed: 05/21/2023]
Abstract
With the advent of next-generation sequencing technologies, whole-plastome data can be obtained as a byproduct of low-coverage sequencing of the plant genomic DNA. This provides an opportunity to study plastid evolution across groups, as well as testing phylogenetic relationships among taxa. Within the order Malpighiales (∼16,000 spp.), the Podostemaceae (∼300 spp.) stand out for their unique habit, living attached to rocks in fast-flowing aquatic habitats, and displaying highly modified morphologies that confound our understanding of their classification, biology, and evolution. In this study, we used genome skimming data to assemble the full plastid genome of 5 species within Podostemaceae. We analyzed our data in a comparative framework within Malpighiales to determine the structure, gene content, and rearrangements in the plastomes of the family. The Podostemaceae have one of the smallest plastid genomes reported so far for the Malpighiales, possibly due to variation in length of inverted repeat (IR) regions, gene loss, and intergenic region variation. We also detected a major inversion in the large single-copy region unique to the family. The uncommon loss or pseudogenization of ycf1 and ycf2 in angiosperms and in land plants in general is also found to be characteristic of Podostemaceae, but the compensatory mechanisms and implications of this and of the pseudogenization of accD, rpl22, and clpP and loss of rps16 remain to be explained in this group. In addition, we estimated a phylogenetic tree among selected species in Malpighiales. Our findings indicate that the Podostemaceae are a distinct lineage with long branches that suggest faster rates of evolution in the plastome of the group, compared with other taxa in the order. This study lays the foundations for future phylogenomic studies in the family.
Collapse
Affiliation(s)
- Ana M. Bedoya
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, United States
| | - Bradley R. Ruhfel
- University of Michigan Herbarium, University of Michigan, Ann Arbor, MI, United States
| | - C. Thomas Philbrick
- Department of Biological and Environmental Sciences, Western Connecticut State University, Danbury, CT, United States
| | - Santiago Madriñán
- Laboratorio de Botánica y Sistemática, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Claudia P. Bove
- Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Richard G. Olmstead
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, United States
| |
Collapse
|
33
|
Yu Y, Yang J, Ma W, Pressel S, Liu H, Wu Y, Schneider H. Chloroplast phylogenomics of liverworts: a reappraisal of the backbone phylogeny of liverworts with emphasis on Ptilidiales. Cladistics 2019; 36:184-193. [DOI: 10.1111/cla.12396] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2019] [Indexed: 01/20/2023] Open
Affiliation(s)
- Ying Yu
- College of Life and Environmental Sciences Hangzhou Normal University Hangzhou 311121 China
| | - Jun‐Bo Yang
- CAS Plant Germplasm and Genomics Center Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
| | - Wen‐Zhang Ma
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
| | - Silvia Pressel
- Department of Life Sciences Natural History Museum London SW7 5BD UK
| | - Hong‐Mei Liu
- Key Laboratory of Tropical Plant Resources and Sustainable Use Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Menglun Yunnan 666303 China
| | - Yu‐Huan Wu
- College of Life and Environmental Sciences Hangzhou Normal University Hangzhou 311121 China
| | - Harald Schneider
- Center of Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Menglun Yunnan 666303 China
| |
Collapse
|
34
|
Lin G, Huang Z, Wang L, Chen Z, Zhang T, Gillman LN, Zhao F. Evolutionary Rates of Bumblebee Genomes Are Faster at Lower Elevations. Mol Biol Evol 2019; 36:1215-1219. [PMID: 30865278 PMCID: PMC6526908 DOI: 10.1093/molbev/msz057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The importance of climate in determining biodiversity patterns has been well documented. However, the relationship between climate and rates of genetic evolution remains controversial. Latitude and elevation have been associated with rates of change in genetic markers such as cytochrome b. What is not known, however, is the strength of such associations and whether patterns found among these genes apply across entire genomes. Here, using bumblebee genetic data from seven subgenera of Bombus, we demonstrate that all species occupying warmer elevations have undergone faster genome-wide evolution than those in the same subgenera occupying cooler elevations. Our findings point to a critical biogeographic role in the relative rates of whole species evolution, potentially influencing global biodiversity patterns.
Collapse
Affiliation(s)
- Gonghua Lin
- School of Life Sciences, Jinggangshan University, Ji'an, China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Zuhao Huang
- School of Life Sciences, Jinggangshan University, Ji'an, China
| | - Lei Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Zhenhua Chen
- Qinghai-CAS Institute of Apicultural Research, Xining, Qinghai, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Lennard N Gillman
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Fang Zhao
- School of Life Sciences, Jinggangshan University, Ji'an, China
| |
Collapse
|
35
|
He T, Lamont BB, Pausas JG. Fire as a key driver of Earth's biodiversity. Biol Rev Camb Philos Soc 2019; 94:1983-2010. [PMID: 31298472 DOI: 10.1111/brv.12544] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 12/21/2022]
Abstract
Many terrestrial ecosystems are fire prone, such that their composition and structure are largely due to their fire regime. Regions subject to regular fire have exceptionally high levels of species richness and endemism, and fire has been proposed as a major driver of their diversity, within the context of climate, resource availability and environmental heterogeneity. However, current fire-management practices rarely take into account the ecological and evolutionary roles of fire in maintaining biodiversity. Here, we focus on the mechanisms that enable fire to act as a major ecological and evolutionary force that promotes and maintains biodiversity over numerous spatiotemporal scales. From an ecological perspective, the vegetation, topography and local weather conditions during a fire generate a landscape with spatial and temporal variation in fire-related patches (pyrodiversity), and these produce the biotic and environmental heterogeneity that drives biodiversity across local and regional scales. There have been few empirical tests of the proposition that 'pyrodiversity begets biodiversity' but we show that biodiversity should peak at moderately high levels of pyrodiversity. Overall species richness is greatest immediately after fire and declines monotonically over time, with postfire successional pathways dictated by animal habitat preferences and varying lifespans among resident plants. Theory and data support the 'intermediate disturbance hypothesis' when mean patch species diversity is correlated with mean fire intervals. Postfire persistence, recruitment and immigration allow species with different life histories to coexist. From an evolutionary perspective, fire drives population turnover and diversification by promoting a wide range of adaptive responses to particular fire regimes. Among 39 comparisons, the number of species in 26 fire-prone lineages is much higher than that in their non-fire-prone sister lineages. Fire and its byproducts may have direct mutagenic effects, producing novel genotypes that can lead to trait innovation and even speciation. A paradigm shift aimed at restoring biodiversity-maintaining fire regimes across broad landscapes is required among the fire research and management communities. This will require ecologists and other professionals to spread the burgeoning fire-science knowledge beyond scientific publications to the broader public, politicians and media.
Collapse
Affiliation(s)
- Tianhua He
- School of Molecular and Life Sciences, Curtin University, Perth, Australia.,College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Australia
| | - Byron B Lamont
- School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | | |
Collapse
|
36
|
Hanlon VCT, Otto SP, Aitken SN. Somatic mutations substantially increase the per-generation mutation rate in the conifer Picea sitchensis. Evol Lett 2019; 3:348-358. [PMID: 31388445 PMCID: PMC6675141 DOI: 10.1002/evl3.121] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/14/2019] [Accepted: 05/21/2019] [Indexed: 12/11/2022] Open
Abstract
The rates and biological significance of somatic mutations have long been a subject of debate. Somatic mutations in plants are expected to accumulate with vegetative growth and time, yet rates of somatic mutations are unknown for conifers, which can reach exceptional sizes and ages. We investigated somatic mutation rates in the conifer Sitka spruce (Picea sitchensis (Bong.) Carr.) by analyzing a total of 276 Gb of nuclear DNA from the tops and bottoms of 20 old‐growth trees averaging 76 m in height. We estimate a somatic base substitution rate of 2.7 × 10−8 per base pair within a generation. To date, this is one of the highest estimated per‐generation rates of mutation among eukaryotes, indicating that somatic mutations contribute substantially to the total per‐generation mutation rate in conifers. Nevertheless, as the sampled trees are centuries old, the per‐year rate is low in comparison with nontree taxa. We argue that although somatic mutations raise genetic load in conifers, they generate important genetic variation and enable selection both among cell lineages within individual trees and among offspring.
Collapse
Affiliation(s)
- Vincent C T Hanlon
- Faculty of Forestry Department of Forest and Conservation Sciences University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Sarah P Otto
- Department of Zoology & Biodiversity Research Centre University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Sally N Aitken
- Faculty of Forestry Department of Forest and Conservation Sciences University of British Columbia Vancouver BC V6T 1Z4 Canada
| |
Collapse
|
37
|
Six Impossible Things before Breakfast: Assumptions, Models, and Belief in Molecular Dating. Trends Ecol Evol 2019; 34:474-486. [PMID: 30904189 DOI: 10.1016/j.tree.2019.01.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 01/16/2023]
Abstract
Confidence in molecular dating analyses has grown with the increasing sophistication of the methods. Some problematic cases where molecular dates disagreed with paleontological estimates appear to have been resolved with a growing agreement between molecules and fossils. But we cannot relax just yet. The growing analytical sophistication of many molecular dating methods relies on an increasingly large number of assumptions about evolutionary history and processes. Many of these assumptions are based on statistical tractability rather than being informed by improved understanding of molecular evolution, yet changing the assumptions can influence molecular dates. How can we tell if the answers we get are driven more by the assumptions we make than by the molecular data being analyzed?
Collapse
|
38
|
Qiu F, Baack EJ, Whitney KD, Bock DG, Tetreault HM, Rieseberg LH, Ungerer MC. Phylogenetic trends and environmental correlates of nuclear genome size variation in Helianthus sunflowers. THE NEW PHYTOLOGIST 2019; 221:1609-1618. [PMID: 30368824 DOI: 10.1111/nph.15465] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Flowering plants serve as a powerful model for studying the evolution of nuclear genome size (GS) given the tremendous GS variation that exists both within and across angiosperm lineages. Helianthus sunflowers consist of c. 50 species native to North America that occupy diverse habitats and vary in ploidy level. In the current study, we generated a comprehensive GS database for 49 Helianthus species using flow cytometric approaches. We examined variability across the genus and present a comparative phylogenetic analysis of GS evolution in diploid Helianthus species. Results demonstrated that different clades of diploid Helianthus species showed evolutionary patterns of GS contraction, expansion and relative stasis, with annual diploid species evolving smaller GS with the highest rate of evolution. Phylogenetic comparative analyses of diploids revealed significant negative associations of GS with temperature seasonality and cell production rate, indicating that the evolution of larger GS in Helianthus diploids may be more permissible in habitats with longer growing seasons where selection for more rapid growth may be relaxed. The Helianthus GS database presented here and corresponding analyses of environmental and phenotypic correlates will facilitate ongoing and future research on the ultimate drivers of GS evolution in this well-studied North American plant genus.
Collapse
Affiliation(s)
- Fan Qiu
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Eric J Baack
- Department of Biology, Luther College, Decorah, IA, 52101, USA
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Dan G Bock
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark C Ungerer
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| |
Collapse
|
39
|
Abstract
A major current molecular evolution challenge is to link comparative genomic patterns to species' biology and ecology. Breeding systems are pivotal because they affect many population genetic processes and thus genome evolution. We review theoretical predictions and empirical evidence about molecular evolutionary processes under three distinct breeding systems-outcrossing, selfing, and asexuality. Breeding systems may have a profound impact on genome evolution, including molecular evolutionary rates, base composition, genomic conflict, and possibly genome size. We present and discuss the similarities and differences between the effects of selfing and clonality. In reverse, comparative and population genomic data and approaches help revisiting old questions on the long-term evolution of breeding systems.
Collapse
Affiliation(s)
- Sylvain Glémin
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Clémentine M François
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France.
| |
Collapse
|
40
|
Dornburg A, Su Z, Townsend JP. Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets. Syst Biol 2018; 68:145-156. [PMID: 29939341 DOI: 10.1093/sysbio/syy047] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/13/2018] [Indexed: 02/02/2023] Open
Abstract
With the rise of genome-scale data sets, there has been a call for increased data scrutiny and careful selection of loci that are appropriate to use in an attempt to resolve a phylogenetic problem. Such loci should maximize phylogenetic information content while minimizing the risk of homoplasy. Theory posits the existence of characters that evolve at an optimum rate, and efforts to determine optimal rates of inference have been a cornerstone of phylogenetic experimental design for over two decades. However, both theoretical and empirical investigations of optimal rates have varied dramatically in their conclusions: spanning no relationship to a tight relationship between the rate of change and phylogenetic utility. Herein, we synthesize these apparently contradictory views, demonstrating both empirical and theoretical conditions under which each is correct. We find that optimal rates of characters-not genes-are generally robust to most experimental design decisions. Moreover, consideration of site rate heterogeneity within a given locus is critical to accurate predictions of utility. Factors such as taxon sampling or the targeted number of characters providing support for a topology are additionally critical to the predictions of phylogenetic utility based on the rate of character change. Further, optimality of rates and predictions of phylogenetic utility are not equivalent, demonstrating the need for further development of comprehensive theory of phylogenetic experimental design. [Divergence time; GC bias; homoplasy; incongruence; information content; internode length; optimal rates; phylogenetic informativeness; phylogenetic theory; phylogenetic utility; phylogenomics; signal and noise; subtending branch length; state space; taxon and character sampling.].
Collapse
Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, 1671 Goldstar Drive, NC 27601, USA
| | - Zhuo Su
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, 165 Prospect Street, CT 06525, USA
| | - Jeffrey P Townsend
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, 165 Prospect Street, CT 06525, USA
- Department of Biostatistics, Yale University, New Haven, 60 College Street, CT 06510, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, 300 George Street, CT 06511, USA
| |
Collapse
|
41
|
Gerhold P, Carlucci MB, Procheş Ş, Prinzing A. The Deep Past Controls the Phylogenetic Structure of Present, Local Communities. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062348] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coexisting species may be evolutionarily proximate or distant, resulting in phylogenetically poor or rich communities. This variation is often considered to result from present assembly processes. We argue that, under certain conditions, deep-past processes might control the phylogenetic diversity of communities. First, deep-past effects involve macroevolutionary processes, such as diversification rate, niche conservatism, or dispersal, in the lineages that constitute communities. Second, deep-past processes in the respective region or in the habitat type play a role, for instance, through age, area, stability, or connectivity. Third, the deep past may affect communities via trophic interactions (i.e., communities of enemies or mutualists or communities of hosts). We suggest that deep-past effects can be identified in local communities by measuring phylogenetic diversity in different species pools. We also show how community phylogenetic diversity results in positive or negative eco-evolutionary feedback, and we identify present-day conservation challenges that may profit from a deep-time perspective.
Collapse
Affiliation(s)
- Pille Gerhold
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 51014, Estonia
| | - Marcos B. Carlucci
- Department of Botany, Federal University of Paraná, Curitiba, PR 81531–980, Brazil
| | - Şerban Procheş
- Discipline of Geography, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Andreas Prinzing
- Research Unit “Ecosystèmes Biodiversité, Evolution,” University of Rennes 1, CNRS UMR 6553 “Ecobio,” Rennes 35042, France
| |
Collapse
|
42
|
Saclier N, François CM, Konecny-Dupré L, Lartillot N, Guéguen L, Duret L, Malard F, Douady CJ, Lefébure T. Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods. Mol Biol Evol 2018; 35:2900-2912. [DOI: 10.1093/molbev/msy184] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Nathanaëlle Saclier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - Clémentine M François
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - Lara Konecny-Dupré
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - Nicolas Lartillot
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Laurent Guéguen
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Laurent Duret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Florian Malard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - Christophe J Douady
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
- Institut Universitaire de France, Paris, France
| | - Tristan Lefébure
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| |
Collapse
|
43
|
Orton MG, May JA, Ly W, Lee DJ, Adamowicz SJ. Is molecular evolution faster in the tropics? Heredity (Edinb) 2018; 122:513-524. [PMID: 30202084 PMCID: PMC6461915 DOI: 10.1038/s41437-018-0141-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 11/30/2022] Open
Abstract
The evolutionary speed hypothesis (ESH) suggests that molecular evolutionary rates are higher among species inhabiting warmer environments. Previously, the ESH has been investigated using small numbers of latitudinally-separated sister lineages; in animals, these studies typically focused on subsets of Chordata and yielded mixed support for the ESH. This study analyzed public DNA barcode sequences from the cytochrome c oxidase subunit I (COI) gene for six of the largest animal phyla (Arthropoda, Chordata, Mollusca, Annelida, Echinodermata, and Cnidaria) and paired latitudinally-separated taxa together informatically. Of 8037 lineage pairs, just over half (51.6%) displayed a higher molecular rate in the lineage inhabiting latitudes closer to the equator, while the remainder (48.4%) displayed a higher rate in the higher-latitude lineage. To date, this study represents the most comprehensive analysis of latitude-related molecular rate differences across animals. While a statistically-significant pattern was detected from our large sample size, our findings suggest that the EHS may not serve as a strong universal mechanism underlying the latitudinal diversity gradient and that COI molecular clocks may generally be applied across latitudes. This study also highlights the merits of using automation to analyze large DNA barcode datasets.
Collapse
Affiliation(s)
- Matthew G Orton
- Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.,School of Biological Sciences and Applied Chemistry, Seneca College, 1750 Finch Ave E, North York, ON, M2J 2X5, Canada
| | - Jacqueline A May
- Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Winfield Ly
- School of Biological Sciences and Applied Chemistry, Seneca College, 1750 Finch Ave E, North York, ON, M2J 2X5, Canada
| | - David J Lee
- School of Biological Sciences and Applied Chemistry, Seneca College, 1750 Finch Ave E, North York, ON, M2J 2X5, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| |
Collapse
|
44
|
Gaouda H, Hamaji T, Yamamoto K, Kawai-Toyooka H, Suzuki M, Noguchi H, Minakuchi Y, Toyoda A, Fujiyama A, Nozaki H, Smith DR. Exploring the Limits and Causes of Plastid Genome Expansion in Volvocine Green Algae. Genome Biol Evol 2018; 10:2248-2254. [PMID: 30102347 PMCID: PMC6128376 DOI: 10.1093/gbe/evy175] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2018] [Indexed: 12/25/2022] Open
Abstract
Plastid genomes are not normally celebrated for being large. But researchers are steadily uncovering algal lineages with big and, in rare cases, enormous plastid DNAs (ptDNAs), such as volvocine green algae. Plastome sequencing of five different volvocine species has revealed some of the largest, most repeat-dense plastomes on record, including that of Volvox carteri (∼525 kb). Volvocine algae have also been used as models for testing leading hypotheses on organelle genome evolution (e.g., the mutational hazard hypothesis), and it has been suggested that ptDNA inflation within this group might be a consequence of low mutation rates and/or the transition from a unicellular to multicellular existence. Here, we further our understanding of plastome size variation in the volvocine line by examining the ptDNA sequences of the colonial species Yamagishiella unicocca and Eudorina sp. NIES-3984 and the multicellular Volvox africanus, which are phylogenetically situated between species with known ptDNA sizes. Although V. africanus is closely related and similar in multicellular organization to V. carteri, its ptDNA was much less inflated than that of V. carteri. Synonymous- and noncoding-site nucleotide substitution rate analyses of these two Volvox ptDNAs suggest that there are drastically different plastid mutation rates operating in the coding versus intergenic regions, supporting the idea that error-prone DNA repair in repeat-rich intergenic spacers is contributing to genome expansion. Our results reinforce the idea that the volvocine line harbors extremes in plastome size but ultimately shed doubt on some of the previously proposed hypotheses for ptDNA inflation within the lineage.
Collapse
Affiliation(s)
- Hager Gaouda
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Takashi Hamaji
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, Kyoto University, Japan
| | - Kayoko Yamamoto
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
| | - Hiroko Kawai-Toyooka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
| | - Masahiro Suzuki
- Kobe University Research Center for Inland Seas, Awaji, Hyogo, Japan
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yohei Minakuchi
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
| | - David Roy Smith
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| |
Collapse
|
45
|
Chira AM, Cooney CR, Bright JA, Capp EJR, Hughes EC, Moody CJA, Nouri LO, Varley ZK, Thomas GH. Correlates of rate heterogeneity in avian ecomorphological traits. Ecol Lett 2018; 21:1505-1514. [PMID: 30133084 PMCID: PMC6175488 DOI: 10.1111/ele.13131] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/22/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022]
Abstract
Heterogeneity in rates of trait evolution is widespread, but it remains unclear which processes drive fast and slow character divergence across global radiations. Here, we test multiple hypotheses for explaining rate variation in an ecomorphological trait (beak shape) across a globally distributed group (birds). We find low support that variation in evolutionary rates of species is correlated with life history, environmental mutagenic factors, range size, number of competitors, or living on islands. Indeed, after controlling for the negative effect of species' age, 80% of variation in species‐specific evolutionary rates remains unexplained. At the clade level, high evolutionary rates are associated with unusual phenotypes or high species richness. Taken together, these results imply that macroevolutionary rates of ecomorphological traits are governed by both ecological opportunity in distinct adaptive zones and niche differentiation among closely related species.
Collapse
Affiliation(s)
- A M Chira
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - C R Cooney
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - J A Bright
- School of Geosciences, University of South Florida, Tampa, FL, USA
| | - E J R Capp
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - E C Hughes
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - C J A Moody
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - L O Nouri
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Z K Varley
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - G H Thomas
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.,Bird Group, Department of Life Sciences, The Natural History Museum, Tring, Hertfordshire, UK
| |
Collapse
|
46
|
Schelkunov MI, Penin AA, Logacheva MD. RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants. BMC Genomics 2018; 19:602. [PMID: 30092758 PMCID: PMC6085651 DOI: 10.1186/s12864-018-4968-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While photosynthesis is the most notable trait of plants, several lineages of plants (so-called full heterotrophs) have adapted to obtain organic compounds from other sources. The switch to heterotrophy leads to profound changes at the morphological, physiological and genomic levels. RESULTS Here, we characterize the transcriptomes of three species representing two lineages of mycoheterotrophic plants: orchids (Epipogium aphyllum and Epipogium roseum) and Ericaceae (Hypopitys monotropa). Comparative analysis is used to highlight the parallelism between distantly related fully heterotrophic plants. In both lineages, we observed genome-wide elimination of nuclear genes that encode proteins related to photosynthesis, while systems associated with protein import to plastids as well as plastid transcription and translation remain active. Genes encoding components of plastid ribosomes that have been lost from the plastid genomes have not been transferred to the nuclear genomes; instead, some of the encoded proteins have been substituted by homologs. The nuclear genes of both Epipogium species accumulated nucleotide substitutions twice as rapidly as their photosynthetic relatives; in contrast, no increase in the substitution rate was observed in H. monotropa. CONCLUSIONS Full heterotrophy leads to profound changes in nuclear gene content. The observed increase in the rate of nucleotide substitutions is lineage specific, rather than a universal phenomenon among non-photosynthetic plants.
Collapse
Affiliation(s)
- Mikhail I Schelkunov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
| | - Aleksey A Penin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,A.N Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia. .,Skolkovo Institute of Science and Technology, Moscow, Russia. .,Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.
| |
Collapse
|
47
|
Casola C, Koralewski TE. Pinaceae show elevated rates of gene turnover that are robust to incomplete gene annotation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:862-876. [PMID: 29901849 DOI: 10.1111/tpj.13994] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 05/22/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Gene duplications and gene losses are major determinants of genome evolution and phenotypic diversity. The frequency of gene turnover (gene gains and gene losses combined) is known to vary between organisms. Comparative genomic analyses of gene families can highlight such variation; however, estimates of gene turnover may be biased when using highly fragmented genome assemblies resulting in poor gene annotations. Here, we address potential biases introduced by gene annotation errors in estimates of gene turnover frequencies in a dataset including both well-annotated angiosperm genomes and the incomplete gene sets of four Pinaceae, including two pine species, Norway spruce and Douglas-fir. We show that Pinaceae experienced higher gene turnover rates than angiosperm lineages lacking recent whole-genome duplications. This finding is robust to both known major issues in Pinaceae gene sets: missing gene models and erroneous annotation of pseudogenes. A separate analysis limited to the four Pinaceae gene sets pointed to an accelerated gene turnover rate in pines compared with Norway spruce and Douglas-fir. Our results indicate that gene turnover significantly contributes to genome variation and possibly to speciation in Pinaceae, particularly in pines. Moreover, these findings indicate that reliable estimates of gene turnover frequencies can be discerned in incomplete and potentially inaccurate gene sets. Because gymnosperms are known to exhibit low overall substitution rates compared with angiosperms, our results suggest that the rate of single-base pair mutations is uncoupled from the rate of large DNA duplications and deletions associated with gene turnover in Pinaceae.
Collapse
Affiliation(s)
- Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, 77843-2138, USA
| | - Tomasz E Koralewski
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, 77843-2138, USA
| |
Collapse
|
48
|
Greenhill SJ, Hua X, Welsh CF, Schneemann H, Bromham L. Population Size and the Rate of Language Evolution: A Test Across Indo-European, Austronesian, and Bantu Languages. Front Psychol 2018; 9:576. [PMID: 29755387 PMCID: PMC5934942 DOI: 10.3389/fpsyg.2018.00576] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 04/05/2018] [Indexed: 12/25/2022] Open
Abstract
What role does speaker population size play in shaping rates of language evolution? There has been little consensus on the expected relationship between rates and patterns of language change and speaker population size, with some predicting faster rates of change in smaller populations, and others expecting greater change in larger populations. The growth of comparative databases has allowed population size effects to be investigated across a wide range of language groups, with mixed results. One recent study of a group of Polynesian languages revealed greater rates of word gain in larger populations and greater rates of word loss in smaller populations. However, that test was restricted to 20 closely related languages from small Oceanic islands. Here, we test if this pattern is a general feature of language evolution across a larger and more diverse sample of languages from both continental and island populations. We analyzed comparative language data for 153 pairs of closely-related sister languages from three of the world's largest language families: Austronesian, Indo-European, and Niger-Congo. We find some evidence that rates of word loss are significantly greater in smaller languages for the Indo-European comparisons, but we find no significant patterns in the other two language families. These results suggest either that the influence of population size on rates and patterns of language evolution is not universal, or that it is sufficiently weak that it may be overwhelmed by other influences in some cases. Further investigation, for a greater number of language comparisons and a wider range of language features, may determine which of these explanations holds true.
Collapse
Affiliation(s)
- Simon J Greenhill
- ARC Centre of Excellence for the Dynamics of Language, Australian National University, Canberra, ACT, Australia.,Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History (MPG), Jena, Germany
| | - Xia Hua
- ARC Centre of Excellence for the Dynamics of Language, Australian National University, Canberra, ACT, Australia.,Research School of Biology, Macroevolution and Macroecology, Australian National University, Canberra, ACT, Australia
| | - Caela F Welsh
- Research School of Biology, Macroevolution and Macroecology, Australian National University, Canberra, ACT, Australia
| | - Hilde Schneemann
- ARC Centre of Excellence for the Dynamics of Language, Australian National University, Canberra, ACT, Australia.,Research School of Biology, Macroevolution and Macroecology, Australian National University, Canberra, ACT, Australia
| | - Lindell Bromham
- ARC Centre of Excellence for the Dynamics of Language, Australian National University, Canberra, ACT, Australia.,Research School of Biology, Macroevolution and Macroecology, Australian National University, Canberra, ACT, Australia
| |
Collapse
|
49
|
Pellicer J, Hidalgo O, Dodsworth S, Leitch IJ. Genome Size Diversity and Its Impact on the Evolution of Land Plants. Genes (Basel) 2018; 9:E88. [PMID: 29443885 PMCID: PMC5852584 DOI: 10.3390/genes9020088] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/02/2018] [Accepted: 02/05/2018] [Indexed: 01/09/2023] Open
Abstract
Genome size is a biodiversity trait that shows staggering diversity across eukaryotes, varying over 64,000-fold. Of all major taxonomic groups, land plants stand out due to their staggering genome size diversity, ranging ca. 2400-fold. As our understanding of the implications and significance of this remarkable genome size diversity in land plants grows, it is becoming increasingly evident that this trait plays not only an important role in shaping the evolution of plant genomes, but also in influencing plant community assemblages at the ecosystem level. Recent advances and improvements in novel sequencing technologies, as well as analytical tools, make it possible to gain critical insights into the genomic and epigenetic mechanisms underpinning genome size changes. In this review we provide an overview of our current understanding of genome size diversity across the different land plant groups, its implications on the biology of the genome and what future directions need to be addressed to fill key knowledge gaps.
Collapse
Affiliation(s)
- Jaume Pellicer
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew TW9 3DS, UK.
| | - Oriane Hidalgo
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew TW9 3DS, UK.
| | - Steven Dodsworth
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew TW9 3DS, UK.
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew TW9 3DS, UK.
| |
Collapse
|
50
|
Bromham L, Duchêne S, Hua X, Ritchie AM, Duchêne DA, Ho SYW. Bayesian molecular dating: opening up the black box. Biol Rev Camb Philos Soc 2017; 93:1165-1191. [DOI: 10.1111/brv.12390] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 11/13/2017] [Accepted: 11/17/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Lindell Bromham
- Macroevolution & Macroecology, Division of Ecology & Evolution, Research School of Biology; Australian National University; Canberra ACT 2601 Australia
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute; The University of Melbourne; Melbourne VIC 3010 Australia
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Xia Hua
- Macroevolution & Macroecology, Division of Ecology & Evolution, Research School of Biology; Australian National University; Canberra ACT 2601 Australia
| | - Andrew M. Ritchie
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - David A. Duchêne
- Macroevolution & Macroecology, Division of Ecology & Evolution, Research School of Biology; Australian National University; Canberra ACT 2601 Australia
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
| |
Collapse
|