1
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Nicolaï MPJ, Van Hecke B, Rogalla S, Debruyn G, Bowie RCK, Matzke NJ, Hackett SJ, D'Alba L, Shawkey MD. The evolution of multiple colour mechanisms is correlated with diversification in sunbirds (Nectariniidae). Syst Biol 2024:syae006. [PMID: 38289860 DOI: 10.1093/sysbio/syae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Indexed: 02/01/2024] Open
Abstract
How and why certain groups become speciose is a key question in evolutionary biology. Novel traits that enable diversification by opening new ecological niches are likely important mechanisms. However, ornamental traits can also promote diversification by opening up novel sensory niches and thereby creating novel inter-specific interactions. More specifically, ornamental colours may enable more precise and/or easier species recognition, and may act as key innovations by increasing the number of species-specific patterns and promoting diversification. While the influence of colouration on diversification is well-studied, the influence of the mechanisms that produce those colours (e.g. pigmentary, nanostructural) is less so, even though the ontogeny and evolution of these mechanisms differ. We estimated a new phylogenetic tree for 121 sunbird species and combined colour data of 106 species with a range of phylogenetic tools to test the hypothesis that the evolution of novel colour mechanisms increases diversification in sunbirds, one of the most colourful bird clades. Results suggest that (1) the evolution of novel colour mechanisms expands the visual sensory niche, increasing the number of achievable colours. (2) Structural colouration diverges more readily across the body than pigment-based colouration, enabling an increase in colour complexity. (3) Novel colour mechanisms might minimize trade-offs between natural and sexual selection such that colour can function both as camouflage and conspicuous signal. (4) Despite structural colours being more colourful and mobile, only melanin-based colouration is positively correlated with net diversification. Together, these findings explain why colour distances increase with increasing number of sympatric species, even though packing of colour space would predict otherwise.
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Affiliation(s)
- Michaël P J Nicolaï
- Biology Department, Evolution and Optics of Nanostructures Group, Ghent University, Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Bert Van Hecke
- Biology Department, Evolution and Optics of Nanostructures Group, Ghent University, Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Svana Rogalla
- Biology Department, Evolution and Optics of Nanostructures Group, Ghent University, Ledeganckstraat 35, 9000, Ghent, Belgium
- Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena, 48940 Leioa, Spain
| | - Gerben Debruyn
- Biology Department, Evolution and Optics of Nanostructures Group, Ghent University, Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720, United States of America, Department of Integrative Biology, University of California, Berkeley, CA, 94720, United States of America
| | - Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - S J Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, United States
| | - Liliana D'Alba
- Biology Department, Evolution and Optics of Nanostructures Group, Ghent University, Ledeganckstraat 35, 9000, Ghent, Belgium
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Matthew D Shawkey
- Biology Department, Evolution and Optics of Nanostructures Group, Ghent University, Ledeganckstraat 35, 9000, Ghent, Belgium
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2
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Islam MI, Ridone P, Lin A, Michie KA, Matzke NJ, Hochberg G, Baker MAB. Ancestral reconstruction of the MotA stator subunit reveals that conserved residues far from the pore are required to drive flagellar motility. Microlife 2023; 4:uqad011. [PMID: 37223728 PMCID: PMC10117855 DOI: 10.1093/femsml/uqad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/31/2023] [Accepted: 04/01/2023] [Indexed: 05/25/2023]
Abstract
The bacterial flagellar motor (BFM) is a rotary nanomachine powered by the translocation of ions across the inner membrane through the stator complex. The stator complex consists of two membrane proteins: MotA and MotB (in H+-powered motors), or PomA and PomB (in Na+-powered motors). In this study, we used ancestral sequence reconstruction (ASR) to probe which residues of MotA correlate with function and may have been conserved to preserve motor function. We reconstructed 10 ancestral sequences of MotA and found four of them were motile in combination with contemporary Escherichia coli MotB and in combination with our previously published functional ancestral MotBs. Sequence comparison between wild-type (WT) E. coli MotA and MotA-ASRs revealed 30 critical residues across multiple domains of MotA that were conserved among all motile stator units. These conserved residues included pore-facing, cytoplasm-facing, and MotA-MotA intermolecular facing sites. Overall, this work demonstrates the role of ASR in assessing conserved variable residues in a subunit of a molecular complex.
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Affiliation(s)
- Md Imtiazul Islam
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, Kensington, NSW 2052, Australia
| | - Pietro Ridone
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, Kensington, NSW 2052, Australia
| | - Angela Lin
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, Kensington, NSW 2052, Australia
| | - Katharine A Michie
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, Kensington, NSW 2052, Australia
- Structural Biology Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Kensington, NSW 2052, Australia
| | - Nicholas J Matzke
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Georg Hochberg
- Department of Chemistry and Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Karl-von-Frisch-Str. 14, 11 35043 Marburg, Germany
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
| | - Matthew A B Baker
- Corresponding author. School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, Kensington, NSW 2052, Australia. E-mail:
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3
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Sharma D, Denmat SHL, Matzke NJ, Hannan K, Hannan RD, O'Sullivan JM, Ganley ARD. A new method for determining ribosomal DNA copy number shows differences between Saccharomyces cerevisiae populations. Genomics 2022; 114:110430. [PMID: 35830947 DOI: 10.1016/j.ygeno.2022.110430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/23/2022] [Accepted: 07/04/2022] [Indexed: 11/26/2022]
Abstract
Ribosomal DNA genes (rDNA) encode the major ribosomal RNAs and in eukaryotes typically form tandem repeat arrays. Species have characteristic rDNA copy numbers, but there is substantial intra-species variation in copy number that results from frequent rDNA recombination. Copy number differences can have phenotypic consequences, however difficulties in quantifying copy number mean we lack a comprehensive understanding of how copy number evolves and the consequences. Here we present a genomic sequence read approach to estimate rDNA copy number based on modal coverage to help overcome limitations with existing mean coverage-based approaches. We validated our method using Saccharomyces cerevisiae strains with known rDNA copy numbers. Application of our pipeline to a global sample of S. cerevisiae isolates showed that different populations have different rDNA copy numbers. Our results demonstrate the utility of the modal coverage method, and highlight the high level of rDNA copy number variation within and between populations.
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Affiliation(s)
- Diksha Sharma
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Sylvie Hermann-Le Denmat
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Ecole Normale Supérieure, PSL Research University, F-75005 Paris, France
| | - Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Katherine Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ACT 2601, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ross D Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ACT 2601, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3168, Australia
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Auckland, New Zealand; Maurice Wilkins Center, University of Auckland, New Zealand; MRC Lifecourse Unit, University of Southampton, United Kingdom; Brain Research New Zealand, The University of Auckland, Auckland, New Zealand
| | - Austen R D Ganley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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4
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Patel S, Evans CW, Stuckey A, Matzke NJ, Millar CD. A Unique Mitochondrial Gene Block Inversion in Antarctic Trematomin Fishes: A Cautionary Tale. J Hered 2022; 113:414-420. [PMID: 35657776 PMCID: PMC9308043 DOI: 10.1093/jhered/esac028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/29/2022] [Indexed: 11/29/2022] Open
Abstract
Many Antarctic notothenioid fishes have major rearrangements in their mitochondrial (mt) genomes. Here, we report the complete mt genomes of 3 trematomin notothenioids: the bald notothen (Trematomus (Pagothenia) borchgrevinki), the spotted notothen (T. nicolai), and the emerald notothen (T. bernacchii). The 3 mt genomes were sequenced using next-generation Illumina technology, and the assemblies verified by Sanger sequencing. When compared with the canonical mt gene order of the Antarctic silverfish (Pleuragramma antarctica), we found a large gene inversion in the 3 trematomin mt genomes that included tRNAIle, ND1, tRNALeu2, 16S, tRNAVal, 12S, tRNAPhe, and the control region. The trematomin mt genomes contained 3 intergenic spacers, which are thought to be the remnants of previous gene and control region duplications. All control regions included the characteristic conserved regulatory sequence motifs. Although short-read next-generation DNA sequencing technology has allowed the rapid and cost-effective sequencing of a large number of complete mt genomes, it is essential in all cases to verify the assembly in order to prevent the publication and use of erroneous data.
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Affiliation(s)
- Selina Patel
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Clive W Evans
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Alex Stuckey
- Genomics England, Queen Mary University of London, Dawson Hall, London EC1M 6BQ, United Kingdom
| | - Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Craig D Millar
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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5
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Liddell LG, Lee WG, Dale EE, Meudt HM, Matzke NJ. Pioneering polyploids: the impact of whole-genome duplication on biome shifting in New Zealand Coprosma (Rubiaceae) and Veronica (Plantaginaceae). Biol Lett 2021; 17:20210297. [PMID: 34464540 PMCID: PMC8437022 DOI: 10.1098/rsbl.2021.0297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/02/2021] [Indexed: 12/17/2022] Open
Abstract
The role of whole-genome duplication (WGD) in facilitating shifts into novel biomes remains unknown. Focusing on two diverse woody plant groups in New Zealand, Coprosma (Rubiaceae) and Veronica (Plantaginaceae), we investigate how biome occupancy varies with ploidy level, and test the hypothesis that WGD increases the rate of biome shifting. Ploidy levels and biome occupancy (forest, open and alpine) were determined for indigenous species in both clades. The distribution of low-ploidy (Coprosma: 2x, Veronica: 6x) versus high-ploidy (Coprosma: 4-10x, Veronica: 12-18x) species across biomes was tested statistically. Estimation of the phylogenetic history of biome occupancy and WGD was performed using time-calibrated phylogenies and the R package BioGeoBEARS. Trait-dependent dispersal models were implemented to determine support for an increased rate of biome shifting among high-ploidy lineages. We find support for a greater than random portion of high-ploidy species occupying multiple biomes. We also find strong support for high-ploidy lineages showing a three- to eightfold increase in the rate of biome shifts. These results suggest that WGD promotes ecological expansion into new biomes.
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Affiliation(s)
- Luke G. Liddell
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - William G. Lee
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Ecosystems and Conservation, Manaaki Whenua - Landcare Research Dunedin, Dunedin 9054, New Zealand
| | - Esther E. Dale
- Ecosystems and Conservation, Manaaki Whenua - Landcare Research Dunedin, Dunedin 9054, New Zealand
- Department of Botany, University of Otago, Dunedin 9054, New Zealand
| | - Heidi M. Meudt
- Museum of New Zealand Te Papa Tongarewa, Wellington 6011, New Zealand
| | - Nicholas J. Matzke
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
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6
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Ogilvie HA, Mendes FK, Vaughan TG, Matzke NJ, Stadler T, Welch D, Drummond AJ. Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales. Syst Biol 2021; 71:208-220. [PMID: 34228807 PMCID: PMC8677526 DOI: 10.1093/sysbio/syab054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
Evolutionary models account for either population- or species-level processes but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth–death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.[Caninae; fossilized birth–death; molecular clock; multispecies coalescent; phylogenetics; species trees.]
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Affiliation(s)
- Huw A Ogilvie
- Department of Computer Science, Rice University, Houston TX, 77005, USA
| | - Fábio K Mendes
- Centre for Computational Evolution, The University of Auckland, Auckland, 1010, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Timothy G Vaughan
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, 4058, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Nicholas J Matzke
- Centre for Computational Evolution, The University of Auckland, Auckland, 1010, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, 4058, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - David Welch
- Centre for Computational Evolution, The University of Auckland, Auckland, 1010, New Zealand.,School of Computer Science, The University of Auckland, Auckland, 1010, New Zealand
| | - Alexei J Drummond
- Centre for Computational Evolution, The University of Auckland, Auckland, 1010, New Zealand.,School of Computer Science, The University of Auckland, Auckland, 1010, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
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7
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Matzke NJ, Lin A, Stone M, Baker MAB. Flagellar export apparatus and ATP synthetase: Homology evidenced by synteny predating the Last Universal Common Ancestor. Bioessays 2021; 43:e2100004. [PMID: 33998015 DOI: 10.1002/bies.202100004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 11/07/2022]
Abstract
We report evidence further supporting homology between proteins in the F1 FO -ATP synthetase and the bacterial flagellar motor (BFM). BFM proteins FliH, FliI, and FliJ have been hypothesized to be homologous to FO -b + F1 -δ, F1 -α/β, and F1 -γ, with similar structure and interactions. We conduct a further test by constructing a gene order dataset, examining the order of fliH, fliI, and fliJ genes across the phylogenetic breadth of flagellar and nonflagellar type 3 secretion systems, and comparing this to published surveys of gene order in the F1 FO -ATP synthetase, its N-ATPase relatives, and the bacterial/archaeal V- and A-type ATPases. Strikingly, the fliHIJ gene order was deeply conserved, with the few exceptions appearing derived, and exactly matching the widely conserved F-ATPase gene order atpFHAG, coding for subunits b-δ-α-γ. The V/A-type ATPases have a similar conserved gene order. Our results confirm homology between these systems, and suggest a rare case of synteny conserved over billions of years, predating the Last Universal Common Ancestor (LUCA).
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Affiliation(s)
- Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Angela Lin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Micaella Stone
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew A B Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, Australia
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8
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Islam MI, Lin A, Lai YW, Matzke NJ, Baker MAB. Corrigendum: Ancestral Sequence Reconstructions of MotB Are Proton-Motile and Require MotA for Motility. Front Microbiol 2021; 12:650373. [PMID: 33815339 PMCID: PMC8017333 DOI: 10.3389/fmicb.2021.650373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/11/2021] [Indexed: 11/26/2022] Open
Affiliation(s)
- Md Imtiazul Islam
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
| | - Angela Lin
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
| | - Yu-Wen Lai
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
| | - Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew A B Baker
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD, Australia
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9
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Garcia-R JC, Matzke NJ. Trait-dependent dispersal in rails (Aves: Rallidae): Historical biogeography of a cosmopolitan bird clade. Mol Phylogenet Evol 2021; 159:107106. [PMID: 33601027 DOI: 10.1016/j.ympev.2021.107106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 11/29/2020] [Accepted: 02/03/2021] [Indexed: 11/27/2022]
Abstract
The ability of lineages to disperse over evolutionary timescales may be influenced by the gain or loss of traits after adaptation to new ecological conditions. For example, rails (Aves: Rallidae) have many cases of flightless insular endemic species that presumably evolved after flying ancestors dispersed over large ocean barriers and became isolated. Nonetheless, the details of how flying and its loss have influenced the clade's historical biogeography are unknown, as is the importance of other predictors of dispersal such as the geographic distance between regions. Here, we used a dated phylogeny of 158 species of rails to compare trait-dependent and trait-independent biogeography models in BioGeoBEARS. We evaluated a probabilistic historical biogeographical model that allows geographic range and flight to co-evolve and influence dispersal ability on a phylogeny. The best-fitting dispersal model was a trait-dependent dispersal (DEC + j + x + t21 + m1) that accrued 85.2% of the corrected Akaike Information Criterion (AICc) model weight. The distance-dependence parameter, x was estimated at -0.54, ranging from -0.49 to -0.65 across models, suggesting that a doubling of dispersal distance results in an approximately 31% decrease in dispersal rate (2-0.54 = 0.69). The estimated rate of loss of flight (t21) was similar across all models (~0.029 loss events per lineage per million years). The multiplier on dispersal rate when a lineage is non-flying, m1, is estimated to be 0.38 under this model. Surprisingly, the estimate of m1 was not 0.0, probably because the loss of flight is so common in the rails that entire clades of flightless species are found in the data, forcing the model to attribute some dispersal to flightless lineages. These results indicate that long-distance dispersal over macroevolutionary timespans can be modelled, rather than simply attributed to chance, allowing support for different hypotheses to be quantified and limitations to be identified. Overall, by combining new analytical methods with a comprehensive phylogeny, we use a quantitative framework to show how traits influence dispersal capacity and eventually shape geographical distributions at a macroevolutionary scale.
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Affiliation(s)
- Juan C Garcia-R
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, School of Veterinary Science, Massey University, Private Bag, 11 222, Palmerston North 4442, New Zealand.
| | - Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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10
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Islam MI, Lin A, Lai YW, Matzke NJ, Baker MAB. Ancestral Sequence Reconstructions of MotB Are Proton-Motile and Require MotA for Motility. Front Microbiol 2020; 11:625837. [PMID: 33424826 PMCID: PMC7787011 DOI: 10.3389/fmicb.2020.625837] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/27/2020] [Indexed: 12/23/2022] Open
Abstract
The bacterial flagellar motor (BFM) is a nanomachine that rotates the flagellum to propel many known bacteria. The BFM is powered by ion transit across the cell membrane through the stator complex, a membrane protein. Different bacteria use various ions to run their BFM, but the majority of BFMs are powered by either proton (H+) or sodium (Na+) ions. The transmembrane (TM) domain of the B-subunit of the stator complex is crucial for ion selectivity, as it forms the ion channel in complex with TM3 and TM4 of the A-subunit. In this study, we reconstructed and engineered thirteen ancestral sequences of the stator B-subunit to evaluate the functional properties and ionic power source of the stator proteins at reconstruction nodes to evaluate the potential of ancestral sequence reconstruction (ASR) methods for stator engineering and to test specific motifs previously hypothesized to be involved in ion-selectivity. We found that all thirteen of our reconstructed ancient B-subunit proteins could assemble into functional stator complexes in combination with the contemporary Escherichia coli MotA-subunit to restore motility in stator deleted E. coli strains. The flagellar rotation of the thirteen ancestral MotBs was found to be Na+ independent which suggested that the F30/Y30 residue was not significantly correlated with sodium/proton phenotype, in contrast to what we had reported previously. Additionally, four among the thirteen reconstructed B-subunits were compatible with the A-subunit of Aquifex aeolicus and able to function in a sodium-independent manner. Overall, this work demonstrates the use of ancestral reconstruction to generate novel stators and quantify which residues are correlated with which ionic power source.
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Affiliation(s)
- Md Imtiazul Islam
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
| | - Angela Lin
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
| | - Yu-Wen Lai
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
| | - Nicholas J. Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD, Australia
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11
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Blom MPK, Matzke NJ, Bragg JG, Arida E, Austin CC, Backlin AR, Carretero MA, Fisher RN, Glaw F, Hathaway SA, Iskandar DT, McGuire JA, Karin BR, Reilly SB, Rittmeyer EN, Rocha S, Sanchez M, Stubbs AL, Vences M, Moritz C. Habitat preference modulates trans-oceanic dispersal in a terrestrial vertebrate. Proc Biol Sci 2019; 286:20182575. [PMID: 31161911 DOI: 10.1098/rspb.2018.2575] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The importance of long-distance dispersal (LDD) in shaping geographical distributions has been debated since the nineteenth century. In terrestrial vertebrates, LDD events across large water bodies are considered highly improbable, but organismal traits affecting dispersal capacity are generally not taken into account. Here, we focus on a recent lizard radiation and combine a summary-coalescent species tree based on 1225 exons with a probabilistic model that links dispersal capacity to an evolving trait, to investigate whether ecological specialization has influenced the probability of trans-oceanic dispersal. Cryptoblepharus species that occur in coastal habitats have on average dispersed 13 to 14 times more frequently than non-coastal species and coastal specialization has, therefore, led to an extraordinarily widespread distribution that includes multiple continents and distant island archipelagoes. Furthermore, their presence across the Pacific substantially predates the age of human colonization and we can explicitly reject the possibility that these patterns are solely shaped by human-mediated dispersal. Overall, by combining new analytical methods with a comprehensive phylogenomic dataset, we use a quantitative framework to show how coastal specialization can influence dispersal capacity and eventually shape geographical distributions at a macroevolutionary scale.
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Affiliation(s)
- Mozes P K Blom
- 1 Research School of Biology, The Australian National University , Canberra , Australia.,2 Museum für Naturkunde, Leibniz Institut für Evolutions- und Biodiversitätsforschung , Berlin , Germany
| | - Nicholas J Matzke
- 1 Research School of Biology, The Australian National University , Canberra , Australia.,3 School of Biological Sciences, University of Auckland , Auckland , New Zealand
| | - Jason G Bragg
- 1 Research School of Biology, The Australian National University , Canberra , Australia
| | - Evy Arida
- 4 Research Center for Biology, The Indonesian Institute of Sciences , Cibinong , Indonesia
| | | | - Adam R Backlin
- 6 U.S. Geological Survey, Western Ecological Research Center , Santa Ana, CA , USA
| | | | - Robert N Fisher
- 8 U.S. Geological Survey, Western Ecological Research Center , San Diego, CA , USA
| | - Frank Glaw
- 9 Department of Herpetology, Zoologische Staatssamlung Münich , Munich , Germany
| | - Stacie A Hathaway
- 8 U.S. Geological Survey, Western Ecological Research Center , San Diego, CA , USA
| | - Djoko T Iskandar
- 10 School of Life Sciences and Technology, Institut Teknologi , Bandung , Indonesia
| | - Jimmy A McGuire
- 11 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley , Berkeley, CA , USA
| | - Benjamin R Karin
- 11 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley , Berkeley, CA , USA
| | - Sean B Reilly
- 11 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley , Berkeley, CA , USA
| | - Eric N Rittmeyer
- 1 Research School of Biology, The Australian National University , Canberra , Australia.,5 Museum of Natural Science, Louisiana State University , Baton Rouge, LA , USA
| | - Sara Rocha
- 12 Department of Biochemistry, Genetics and Immunology & Biomedical Research Center (CINBIO), University of Vigo , Vigo , Spain
| | | | - Alexander L Stubbs
- 11 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley , Berkeley, CA , USA
| | - Miguel Vences
- 14 Zoological Institute, Technische Universität Braunschweig , Braunschweig , Germany
| | - Craig Moritz
- 1 Research School of Biology, The Australian National University , Canberra , Australia
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12
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Klaus KV, Matzke NJ. Statistical Comparison of Trait-Dependent Biogeographical Models Indicates That Podocarpaceae Dispersal Is Influenced by Both Seed Cone Traits and Geographical Distance. Syst Biol 2019; 69:61-75. [DOI: 10.1093/sysbio/syz034] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 05/04/2019] [Indexed: 11/12/2022] Open
Abstract
Abstract
The ability of lineages to disperse long distances over evolutionary timescales may be influenced by the gain or loss of traits adapted to enhance local, ecological dispersal. For example, some species in the southern conifer family Podocarpaceae have fleshy cones that encourage bird dispersal, but it is unknown how this trait has influenced the clade’s historical biogeography, or its importance compared with other predictors of dispersal such as the geographic distance between regions. We answer these questions quantitatively by using a dated phylogeny of 197 species of southern conifers (Podocarpaceae and their sister family Araucariaceae) to statistically compare standard, trait-independent biogeography models with new BioGeoBEARS models where an evolving trait can influence dispersal probability, and trait history, biogeographical history, and model parameters are jointly inferred. We validate the method with simulation-inference experiments. Comparing all models, those that include trait-dependent dispersal accrue 87.5% of the corrected Akaike Information Criterion (AICc) model weight. Averaged across all models, lineages with nonfleshy cones had a dispersal probability multiplier of 0.49 compared with lineages with fleshy cones. Distance is included as a predictor of dispersal in all credible models (100% model weight). However, models with changing geography earned only 22.0% of the model weight, and models submerging New Caledonia/New Zealand earned only 0.01%. The importance of traits and distance suggests that long-distance dispersal over macroevolutionary timespans should not be thought of as a highly unpredictable chance event. Instead, long-distance dispersal can be modeled, allowing statistical model comparison to quantify support for different hypotheses.
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Affiliation(s)
- Kristina V Klaus
- Department of Evolution and Biodiversity of Plants, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Nicholas J Matzke
- Moritz Laboratory, Division of Ecology and Evolution, Centre for Biodiversity Analysis, Research School of Biology, RN Robertson Bldg, Level 2, West Wing (W208), 46 Sullivans Creek Rd, Australian National University, Acton ACT 2601, Australia
- School of Biological Sciences, 3A Symonds Street, The University of Auckland, Auckland 1010, New Zealand
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13
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Ishida T, Ito R, Clark J, Matzke NJ, Sowa Y, Baker MAB. Sodium‐powered stators of the bacterial flagellar motor can generate torque in the presence of phenamil with mutations near the peptidoglycan‐binding region. Mol Microbiol 2019; 111:1689-1699. [DOI: 10.1111/mmi.14246] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Tsubasa Ishida
- Department of Frontier Bioscience Hosei University Tokyo Japan
| | - Rie Ito
- Department of Frontier Bioscience Hosei University Tokyo Japan
| | - Jessica Clark
- School of Biotechnology and Biomolecular Science University of New South Wales Kensington NSW Australia
| | - Nicholas J. Matzke
- School of Biological Sciences University of Auckland Auckland New Zealand
| | - Yoshiyuki Sowa
- Department of Frontier Bioscience Hosei University Tokyo Japan
- Research Center for Micro‐Nano Technology Hosei University Tokyo Japan
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Science University of New South Wales Kensington NSW Australia
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14
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Mccann J, Jang TS, Macas J, Schneeweiss GM, Matzke NJ, Novák P, Stuessy TF, Villaseñor JL, Weiss-Schneeweiss H. Dating the Species Network: Allopolyploidy and Repetitive DNA Evolution in American Daisies (Melampodium sect. Melampodium, Asteraceae). Syst Biol 2018; 67:1010-1024. [PMID: 29562303 PMCID: PMC6193527 DOI: 10.1093/sysbio/syy024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 02/17/2018] [Accepted: 03/15/2018] [Indexed: 12/04/2022] Open
Abstract
Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the age of origin of an allopolyploid. Whereas parentage is typically inferred from cytogenetic and phylogenetic data, age inference is hampered by the reticulate nature of the phylogenetic relationships. Treating subgenomes of allopolyploids as if they belonged to different species (i.e., no recombination among subgenomes) and applying cross-bracing (i.e., putting a constraint on the age difference of nodes pertaining to the same event), we can infer the age of allopolyploids within the framework of the multispecies coalescent within BEAST2. Together with a comprehensive characterization of the repetitive DNA fraction using the RepeatExplorer pipeline, we apply the dating approach in a group of closely related allopolyploids and their progenitor species in the plant genus Melampodium (Asteraceae). We dated the origin of both the allotetraploid, Melampodium strigosum, and its two allohexaploid derivatives, Melampodium pringlei and Melampodium sericeum, which share both parentage and the direction of the cross, to the Pleistocene ($<$1.4 Ma). Thus, Pleistocene climatic fluctuations may have triggered formation of allopolyploids possibly in short intervals, contributing to difficulties in inferring the precise temporal order of allopolyploid species divergence of M. sericeum and M. pringlei. The relatively recent origin of the allopolyploids likely played a role in the near-absence of major changes in the repetitive fraction of the polyploids' genomes. The repetitive elements most affected by the postpolyploidization changes represented retrotransposons of the Ty1-copia lineage Maximus and, to a lesser extent, also Athila elements of Ty3-gypsy family.
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Affiliation(s)
- Jamie Mccann
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
- Department of Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Jiři Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Nicholas J Matzke
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Tod F Stuessy
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
- Herbarium and Department of Evolution, Ecology and Organismal Biology, 1315 Kinnear Road, The Ohio State University, Columbus, Ohio, USA
| | - José L Villaseñor
- Department of Botany, UNAM, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, MX-04510 México, D.F., México
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
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15
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Matos-Maraví P, Matzke NJ, Larabee FJ, Clouse RM, Wheeler WC, Sorger DM, Suarez AV, Janda M. Taxon cycle predictions supported by model-based inference in Indo-Pacific trap-jaw ants (Hymenoptera: Formicidae: Odontomachus). Mol Ecol 2018; 27:4090-4107. [PMID: 30106242 DOI: 10.1111/mec.14835] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/01/2018] [Accepted: 08/07/2018] [Indexed: 01/05/2023]
Abstract
Nonequilibrium dynamics and non-neutral processes, such as trait-dependent dispersal, are often missing from quantitative island biogeography models despite their potential explanatory value. One of the most influential nonequilibrium models is the taxon cycle, but it has been difficult to test its validity as a general biogeographical framework. Here, we test predictions of the taxon cycle model using six expected phylogenetic patterns and a time-calibrated phylogeny of Indo-Pacific Odontomachus (Hymenoptera: Formicidae: Ponerinae), one of the ant genera that E.O. Wilson used when first proposing the hypothesis. We used model-based inference and a newly developed trait-dependent dispersal model to jointly estimate ancestral biogeography, ecology (habitat preferences for forest interiors, vs. "marginal" habitats, such as savannahs, shorelines, disturbed areas) and the linkage between ecology and dispersal rates. We found strong evidence that habitat shifts from forest interior to open and disturbed habitats increased macroevolutionary dispersal rate. In addition, lineages occupying open and disturbed habitats can give rise to both island endemics re-occupying only forest interiors and taxa that re-expand geographical ranges. The phylogenetic predictions outlined in this study can be used in future work to evaluate the relative weights of neutral (e.g., geographical distance and area) and non-neutral (e.g., trait-dependent dispersal) processes in historical biogeography and community ecology.
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Affiliation(s)
- Pável Matos-Maraví
- Institute of Entomology, Biology Centre CAS, Ceske Budejovice, Czech Republic.,Department of Zoology, Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.,Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Göteborg, Sweden
| | - Nicholas J Matzke
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Fredrick J Larabee
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia.,Department of Entomology and Department of Animal Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois
| | - Ronald M Clouse
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, New York
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, New York
| | - Daniela Magdalena Sorger
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina.,W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina.,Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, North Carolina
| | - Andrew V Suarez
- Department of Entomology and Department of Animal Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois
| | - Milan Janda
- Institute of Entomology, Biology Centre CAS, Ceske Budejovice, Czech Republic.,Laboratorio Nacional de Análisis y Síntesis Ecológica, ENES, UNAM, Morelia, Mexico
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16
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Flammensbeck CK, Pollerspöck J, Schedel FDB, Matzke NJ, Straube N. Of teeth and trees: A fossil tip‐dating approach to infer divergence times of extinct and extant squaliform sharks. ZOOL SCR 2018. [DOI: 10.1111/zsc.12299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Nicholas J. Matzke
- Division of Ecology, Evolution, and Genetics Research School of Biology The Australian National University Canberra Australia
- School of Biological Sciences University of Auckland Auckland New Zealand
| | - Nicolas Straube
- SNSB – Bavarian State Collection of Zoology (ZSM) Munich Germany
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17
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Ashman LG, Bragg JG, Doughty P, Hutchinson MN, Bank S, Matzke NJ, Oliver P, Moritz C. Diversification across biomes in a continental lizard radiation. Evolution 2018; 72:1553-1569. [PMID: 29972238 DOI: 10.1111/evo.13541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 12/23/2022]
Abstract
Ecological opportunity is a powerful driver of evolutionary diversification, and predicts rapid lineage and phenotypic diversification following colonization of competitor-free habitats. Alternatively, topographic or environmental heterogeneity could be key to generating and sustaining diversity. We explore these hypotheses in a widespread lineage of Australian lizards: the Gehyra variegata group. This clade occurs across two biomes: the Australian monsoonal tropics (AMT), where it overlaps a separate, larger bodied clade of Gehyra and is largely restricted to rocks; and in the larger Australian arid zone (AAZ) where it has no congeners and occupies trees and rocks. New phylogenomic data and coalescent analyses of AAZ taxa resolve lineages and their relationships and reveal high diversity in the western AAZ (Pilbara region). The AMT and AAZ radiations represent separate radiations with no difference in speciation rates. Most taxa occur on rocks, with small geographic ranges relative to widespread generalist taxa across the vast central AAZ. Rock-dwelling and generalist taxa differ morphologically, but only the lineage-poor central AAZ taxa have accelerated evolution. This accords with increasing evidence that lineage and morphological diversity are poorly correlated, and suggests environmental heterogeneity and refugial dynamics have been more important than ecological release in elevating lineage diversity.
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Affiliation(s)
- L G Ashman
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - J G Bragg
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Royal Botanic Garden, Sydney, NSW 2000, Australia
| | - P Doughty
- Department of Terrestrial Zoology, Western Australian Museum, Perth, WA 6016, Australia
| | - M N Hutchinson
- South Australian Museum, Adelaide, SA 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- School of Biological Sciences, Flinders University, Adelaide, SA 5042, Australia
| | - S Bank
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen 37073, Germany
| | - N J Matzke
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - P Oliver
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
- Biodiversity and Geosciences Program, Queensland Museum, Brisbane, QLD 4101, Australia
| | - C Moritz
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
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18
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Matzke NJ, Irmis RB. Including autapomorphies is important for paleontological tip-dating with clocklike data, but not with non-clock data. PeerJ 2018; 6:e4553. [PMID: 29637019 PMCID: PMC5890724 DOI: 10.7717/peerj.4553] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 03/08/2018] [Indexed: 12/01/2022] Open
Abstract
Tip-dating, where fossils are included as dated terminal taxa in Bayesian dating inference, is an increasingly popular method. Data for these studies often come from morphological character matrices originally developed for non-dated, and usually parsimony, analyses. In parsimony, only shared derived characters (synapomorphies) provide grouping information, so many character matrices have an ascertainment bias: they omit autapomorphies (unique derived character states), which are considered uninformative. There has been no study of the effect of this ascertainment bias in tip-dating, but autapomorphies can be informative in model-based inference. We expected that excluding autapomorphies would shorten the morphological branchlengths of terminal branches, and thus bias downwards the time branchlengths inferred in tip-dating. We tested for this effect using a matrix for Carboniferous-Permian eureptiles where all autapomorphies had been deliberately coded. Surprisingly, date estimates are virtually unchanged when autapomorphies are excluded, although we find large changes in morphological rate estimates and small effects on topological and dating confidence. We hypothesized that the puzzling lack of effect on dating was caused by the non-clock nature of the eureptile data. We confirm this explanation by simulating strict clock and non-clock datasets, showing that autapomorphy exclusion biases dating only for the clocklike case. A theoretical solution to ascertainment bias is computing the ascertainment bias correction (Mkparsinf), but we explore this correction in detail, and show that it is computationally impractical for typical datasets with many character states and taxa. Therefore we recommend that palaeontologists collect autapomorphies whenever possible when assembling character matrices.
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Affiliation(s)
- Nicholas J Matzke
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Randall B Irmis
- Department of Geology & Geophysics, University of Utah, Salt Lake City, UT, United States of America.,Natural History Museum of Utah, Salt Lake City, UT, United States of America
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19
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Matzke NJ, Wright A. Inferring node dates from tip dates in fossil Canidae: the importance of tree priors. Biol Lett 2017; 12:rsbl.2016.0328. [PMID: 27512133 DOI: 10.1098/rsbl.2016.0328] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/19/2016] [Indexed: 11/12/2022] Open
Abstract
Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs. Using a canid morphology dataset, we performed tip-dating using BEAST v. 2.1.3 and MrBayes v. 3.2.5. We find that for key nodes (Canis, approx. 3.2 Ma, Caninae approx. 11.7 Ma) a non-mechanistic model using a uniform tree prior produces estimates that are unrealistically old (27.5, 38.9 Ma). Mechanistic models (incorporating lineage birth, death and sampling rates) estimate ages that are closely in line with prior research. We provide a discussion of these two families of models (mechanistic versus non-mechanistic) and their applicability to fossil datasets.
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Affiliation(s)
- Nicholas J Matzke
- Moritz Laboratory, Division of Ecology, Evolution, and Genetics, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - April Wright
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011-4009, USA Department of Ecology, Evolution and Behavior, University of Kansas, Lawrence, KS 66045, USA
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20
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Pérez‐Escobar OA, Chomicki G, Condamine FL, Karremans AP, Bogarín D, Matzke NJ, Silvestro D, Antonelli A. Recent origin and rapid speciation of Neotropical orchids in the world's richest plant biodiversity hotspot. New Phytol 2017; 215:891-905. [PMID: 28631324 PMCID: PMC5575461 DOI: 10.1111/nph.14629] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/07/2017] [Indexed: 05/07/2023]
Abstract
The Andean mountains of South America are the most species-rich biodiversity hotspot worldwide with c. 15% of the world's plant species, in only 1% of the world's land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their origin and diversification. We address this knowledge gap by inferring the biogeographical history and diversification dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using two unparalleled, densely sampled orchid phylogenies (including more than 400 newly generated DNA sequences), comparative phylogenetic methods, geological and biological datasets. We find that the majority of Andean orchid lineages only originated in the last 20-15 million yr. Andean lineages are derived from lowland Amazonian ancestors, with additional contributions from Central America and the Antilles. Species diversification is correlated with Andean orogeny, and multiple migrations and recolonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales. Our study sheds new light on the timing and geography of a major Neotropical diversification, and suggests that mountain uplift promotes species diversification across all elevational zones.
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Affiliation(s)
| | - Guillaume Chomicki
- Systematic Botany and MycologyUniversity of Munich (LMU)67 Menzinger Str.Munich80638Germany
| | - Fabien L. Condamine
- CNRSUMR 5554 Institut des Sciences de l'Evolution (Université de Montpellier)Place Eugène Bataillon34095MontpellierFrance
| | - Adam P. Karremans
- Lankester Botanical GardenUniversity of Costa RicaPO Box 302‐7050CartagoCosta Rica
- Naturalis Biodiversity CenterLeiden2333 CRthe Netherlands
| | - Diego Bogarín
- Lankester Botanical GardenUniversity of Costa RicaPO Box 302‐7050CartagoCosta Rica
- Naturalis Biodiversity CenterLeiden2333 CRthe Netherlands
| | - Nicholas J. Matzke
- Division of Ecology, Evolution, and GeneticsResearch School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Daniele Silvestro
- Department of Biological and Environmental SciencesUniversity of Gothenburg413 19GothenburgSweden
- Department of Computational Biology, BiophoreUniversity of Lausanne1015LausanneSwitzerland
- Gothenburg Global Biodiversity CentreBox 461SE‐405 30GöteborgSweden
| | - Alexandre Antonelli
- Department of Biological and Environmental SciencesUniversity of Gothenburg413 19GothenburgSweden
- Gothenburg Global Biodiversity CentreBox 461SE‐405 30GöteborgSweden
- Gothenburg Botanical GardenCarl Skottsbergs gata 22A41319GothenburgSweden
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21
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Turner AH, Pritchard AC, Matzke NJ. Empirical and Bayesian approaches to fossil-only divergence times: A study across three reptile clades. PLoS One 2017; 12:e0169885. [PMID: 28187191 PMCID: PMC5302793 DOI: 10.1371/journal.pone.0169885] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/23/2016] [Indexed: 11/19/2022] Open
Abstract
Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed to estimate divergences beyond these minimum values. We explore the utility of simultaneous estimation of tree topology and divergence times using BEAST tip-dating on datasets consisting only of fossils by using relaxed morphological clocks and birth-death tree priors that include serial sampling (BDSS) at a constant rate through time. We compare BEAST results to those from the traditional maximum parsimony (MP) and undated Bayesian inference (BI) methods. Three overlapping datasets were used that span 250 million years of archosauromorph evolution leading to crocodylians. The first dataset focuses on early Sauria (31 taxa, 240 chars.), the second on early Archosauria (76 taxa, 400 chars.) and the third on Crocodyliformes (101 taxa, 340 chars.). For each dataset three time-calibrated trees (timetrees) were calculated: a minimum-age timetree with node ages based on earliest occurrences in the fossil record; a 'smoothed' timetree using a range of time added to the root that is then averaged over zero-length internodes; and a tip-dated timetree. Comparisons within datasets show that the smoothed and tip-dated timetrees provide similar estimates. Only near the root node do BEAST estimates fall outside the smoothed timetree range. The BEAST model is not able to overcome limited sampling to correctly estimate divergences considerably older than sampled fossil occurrence dates. Conversely, the smoothed timetrees consistently provide node-ages far older than the strict dates or BEAST estimates for morphologically conservative sister-taxa when they sit on long ghost lineages. In this latter case, the relaxed-clock model appears to be correctly moderating the node-age estimate based on the limited morphological divergence. Topologies are generally similar across analyses, but BEAST trees for crocodyliforms differ when clades are deeply nested but contain very old taxa. It appears that the constant-rate sampling assumption of the BDSS tree prior influences topology inference by disfavoring long, unsampled branches.
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Affiliation(s)
- Alan H. Turner
- Department of Anatomical Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Adam C. Pritchard
- Department of Geology, Yale University, New Haven, Connecticut, United States of America
| | - Nicholas J. Matzke
- Division of Ecology, Evolution, and Genetics, Research School of Biology, The Australian National University, Canberra, Australia
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22
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Shih PM, Hemp J, Ward LM, Matzke NJ, Fischer WW. Crown group Oxyphotobacteria postdate the rise of oxygen. Geobiology 2017; 15:19-29. [PMID: 27392323 DOI: 10.1111/gbi.12200] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/30/2016] [Indexed: 05/24/2023]
Abstract
The rise of oxygen ca. 2.3 billion years ago (Ga) is the most distinct environmental transition in Earth history. This event was enabled by the evolution of oxygenic photosynthesis in the ancestors of Cyanobacteria. However, long-standing questions concern the evolutionary timing of this metabolism, with conflicting answers spanning more than one billion years. Recently, knowledge of the Cyanobacteria phylum has expanded with the discovery of non-photosynthetic members, including a closely related sister group termed Melainabacteria, with the known oxygenic phototrophs restricted to a clade recently designated Oxyphotobacteria. By integrating genomic data from the Melainabacteria, cross-calibrated Bayesian relaxed molecular clock analyses show that crown group Oxyphotobacteria evolved ca. 2.0 billion years ago (Ga), well after the rise of atmospheric dioxygen. We further estimate the divergence between Oxyphotobacteria and Melainabacteria ca. 2.5-2.6 Ga, which-if oxygenic photosynthesis is an evolutionary synapomorphy of the Oxyphotobacteria-marks an upper limit for the origin of oxygenic photosynthesis. Together, these results are consistent with the hypothesis that oxygenic photosynthesis evolved relatively close in time to the rise of oxygen.
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Affiliation(s)
- P M Shih
- Joint BioEnergy Institute, Emeryville, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J Hemp
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - L M Ward
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - N J Matzke
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN, USA
| | - W W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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Bapst DW, Wright AM, Matzke NJ, Lloyd GT. Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria). Biol Lett 2016; 12:20160237. [PMID: 27405380 PMCID: PMC4971167 DOI: 10.1098/rsbl.2016.0237] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/20/2016] [Indexed: 11/12/2022] Open
Abstract
Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian 'tip-dating' methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.
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Affiliation(s)
- D W Bapst
- Department of Geology University of California Davis, One Shields Avenue Davis, CA 94568, USA Geological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - A M Wright
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
| | - N J Matzke
- Division of Evolution, Ecology, and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - G T Lloyd
- Department of Biological Sciences, Faculty of Science, Macquarie University, Sydney, New South Wales 2109, Australia
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Yuan ZY, Zhou WW, Chen X, Poyarkov NA, Chen HM, Jang-Liaw NH, Chou WH, Matzke NJ, Iizuka K, Min MS, Kuzmin SL, Zhang YP, Cannatella DC, Hillis DM, Che J. Spatiotemporal Diversification of the True Frogs (GenusRana): A Historical Framework for a Widely Studied Group of Model Organisms. Syst Biol 2016; 65:824-42. [DOI: 10.1093/sysbio/syw055] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 05/31/2015] [Indexed: 11/12/2022] Open
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Dembo M, Matzke NJ, Mooers AØ, Collard M. Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships. Proc Biol Sci 2016. [PMID: 26202999 DOI: 10.1098/rspb.2015.0943] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The phylogenetic relationships of several hominin species remain controversial. Two methodological issues contribute to the uncertainty-use of partial, inconsistent datasets and reliance on phylogenetic methods that are ill-suited to testing competing hypotheses. Here, we report a study designed to overcome these issues. We first compiled a supermatrix of craniodental characters for all widely accepted hominin species. We then took advantage of recently developed Bayesian methods for building trees of serially sampled tips to test among hypotheses that have been put forward in three of the most important current debates in hominin phylogenetics--the relationship between Australopithecus sediba and Homo, the taxonomic status of the Dmanisi hominins, and the place of the so-called hobbit fossils from Flores, Indonesia, in the hominin tree. Based on our results, several published hypotheses can be statistically rejected. For example, the data do not support the claim that Dmanisi hominins and all other early Homo specimens represent a single species, nor that the hobbit fossils are the remains of small-bodied modern humans, one of whom had Down syndrome. More broadly, our study provides a new baseline dataset for future work on hominin phylogeny and illustrates the promise of Bayesian approaches for understanding hominin phylogenetic relationships.
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Affiliation(s)
- Mana Dembo
- Human Evolutionary Studies Program, Simon Fraser University, Burnaby, British Columbia, Canada Department of Archaeology,, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Nicholas J Matzke
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN, USA
| | - Arne Ø Mooers
- Human Evolutionary Studies Program, Simon Fraser University, Burnaby, British Columbia, Canada Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Mark Collard
- Human Evolutionary Studies Program, Simon Fraser University, Burnaby, British Columbia, Canada Department of Archaeology,, Simon Fraser University, Burnaby, British Columbia, Canada Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada Department of Archaeology, University of Aberdeen, Aberdeen, UK
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Affiliation(s)
- Nicholas J Matzke
- The Australian National University, Canberra, ACT 2601, Australia. Work began at: National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN 37996 USA.
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Gavin DG, Fitzpatrick MC, Gugger PF, Heath KD, Rodríguez-Sánchez F, Dobrowski SZ, Hampe A, Hu FS, Ashcroft MB, Bartlein PJ, Blois JL, Carstens BC, Davis EB, de Lafontaine G, Edwards ME, Fernandez M, Henne PD, Herring EM, Holden ZA, Kong WS, Liu J, Magri D, Matzke NJ, McGlone MS, Saltré F, Stigall AL, Tsai YHE, Williams JW. Climate refugia: joint inference from fossil records, species distribution models and phylogeography. New Phytol 2014; 204:37-54. [PMID: 25039238 DOI: 10.1111/nph.12929] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 06/06/2014] [Indexed: 05/16/2023]
Abstract
Climate refugia, locations where taxa survive periods of regionally adverse climate, are thought to be critical for maintaining biodiversity through the glacial-interglacial climate changes of the Quaternary. A critical research need is to better integrate and reconcile the three major lines of evidence used to infer the existence of past refugia - fossil records, species distribution models and phylogeographic surveys - in order to characterize the complex spatiotemporal trajectories of species and populations in and out of refugia. Here we review the complementary strengths, limitations and new advances for these three approaches. We provide case studies to illustrate their combined application, and point the way towards new opportunities for synthesizing these disparate lines of evidence. Case studies with European beech, Qinghai spruce and Douglas-fir illustrate how the combination of these three approaches successfully resolves complex species histories not attainable from any one approach. Promising new statistical techniques can capitalize on the strengths of each method and provide a robust quantitative reconstruction of species history. Studying past refugia can help identify contemporary refugia and clarify their conservation significance, in particular by elucidating the fine-scale processes and the particular geographic locations that buffer species against rapidly changing climate.
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Affiliation(s)
- Daniel G Gavin
- Department of Geography, University of Oregon, Eugene, OR, 97403, USA
| | - Matthew C Fitzpatrick
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, 21532, USA
| | - Paul F Gugger
- Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois, Urbana, IL, 61801, USA
| | | | - Solomon Z Dobrowski
- Department of Forest Management, College of Forestry and Conservation, University of Montana, Missoula, MT, 59812, USA
| | - Arndt Hampe
- INRA, BIOGECO, UMR 1202, 33610, Cestas, France
- BIOGECO, UMR 1202, University of Bordeaux, 33400, Talence, France
| | - Feng Sheng Hu
- Department of Plant Biology, University of Illinois, Urbana, IL, 61801, USA
| | | | | | - Jessica L Blois
- School of Natural Sciences, University of California, Merced, CA, 95343, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Edward B Davis
- Department of Geological Sciences, University of Oregon, Eugene, OR, 97403, USA
| | - Guillaume de Lafontaine
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Mary E Edwards
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ, UK
| | - Matias Fernandez
- Department of Plant Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Paul D Henne
- Oeschger Centre for Climate Change Research, Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Erin M Herring
- Department of Geography, University of Oregon, Eugene, OR, 97403, USA
| | | | - Woo-Seok Kong
- Department of Geography, Kyung Hee University, Seoul, 130-701, Korea
| | - Jianquan Liu
- College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Donatella Magri
- Dipartimento di Biologia Ambientale, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Nicholas J Matzke
- Department of Ecology and Evolutionary Biology, National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Frédérik Saltré
- Environment Institute, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Alycia L Stigall
- Department of Geological Sciences, OHIO Center for Ecology and Evolutionary Studies, Ohio University, Athens, OH, 45701, USA
| | - Yi-Hsin Erica Tsai
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - John W Williams
- Department of Geography, Nelson Center for Climatic Research, University of Wisconsin, Madison, WI, 53706, USA
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Matzke NJ. Model Selection in Historical Biogeography Reveals that Founder-Event Speciation Is a Crucial Process in Island Clades. Syst Biol 2014; 63:951-70. [DOI: 10.1093/sysbio/syu056] [Citation(s) in RCA: 763] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nicholas J. Matzke
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA; and 2National Institute for Mathematical and Biological Synthesis and Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996-3410, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA; and 2National Institute for Mathematical and Biological Synthesis and Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996-3410, USA
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Matzke NJ, Shih PM, Kerfeld CA. Bayesian analysis of congruence of core genes in Prochlorococcus and Synechococcus and implications on horizontal gene transfer. PLoS One 2014; 9:e85103. [PMID: 24465485 PMCID: PMC3897415 DOI: 10.1371/journal.pone.0085103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 11/22/2013] [Indexed: 01/28/2023] Open
Abstract
It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the pattern of vertical inheritance is oversimplified or even positively misleading. "Universal proteins" have been used to infer the organismal phylogeny, but have been criticized as being only the "tree of one percent." Currently, few options exist for those wishing to rigorously assess how well a universal protein phylogeny, based on a relative handful of well-conserved genes, represents the phylogenetic histories of hundreds of genes. Here, we address this problem by proposing a visualization method and a statistical test within a Bayesian framework. We use the genomes of marine cyanobacteria, a group thought to exhibit substantial amounts of HGT, as a test case. We take 379 orthologous gene families from 28 cyanobacteria genomes and estimate the Bayesian posterior distributions of trees - a "treecloud" - for each, as well as for a concatenated dataset based on putative "universal proteins." We then calculate the average distance between trees within and between all treeclouds on various metrics and visualize this high-dimensional space with non-metric multidimensional scaling (NMMDS). We show that the tree space is strongly clustered and that the universal protein treecloud is statistically significantly closer to the center of this tree space than any individual gene treecloud. We apply several commonly-used tests for incongruence/HGT and show that they agree HGT is rare in this dataset, but make different choices about which genes were subject to HGT. Our results show that the question of the representativeness of the "tree of one percent" is a quantitative empirical question, and that the phylogenetic central tendency is a meaningful observation even if many individual genes disagree due to the various sources of incongruence.
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Affiliation(s)
- Nicholas J. Matzke
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Cheryl A. Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- US Department of Energy-Joint Genome Institute, Walnut Creek, California, United States of America
- * E-mail:
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Alexandrou MA, Swartz BA, Matzke NJ, Oakley TH. Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae. Mol Phylogenet Evol 2013; 69:514-23. [PMID: 23933489 DOI: 10.1016/j.ympev.2013.07.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/21/2013] [Accepted: 07/26/2013] [Indexed: 12/26/2022]
Abstract
Multiple rounds of whole genome duplication have repeatedly marked the evolution of vertebrates, and correlate strongly with morphological innovation. However, less is known about the behavioral, physiological and ecological consequences of genome duplication, and whether these events coincide with major transitions in vertebrate complexity. The complex behavior of anadromy - where adult fishes migrate up rivers from the sea to their natal site to spawn - is well known in salmonid fishes. Some hypotheses suggest that migratory behavior evolved as a consequence of an ancestral genome duplication event, which permitted salinity tolerance and osmoregulatory plasticity. Here we test whether anadromy evolved multiple times within salmonids, and whether genome duplication coincided with the evolution of anadromy. We present a method that uses ancestral character simulation data to plot the frequency of character transitions over a time calibrated phylogenetic tree to provide estimates of the absolute timing of character state transitions. Furthermore, we incorporate extinct and extant taxa to improve on previous estimates of divergence times. We present the first phylogenetic evidence indicating that anadromy evolved at least twice from freshwater salmonid ancestors. Results suggest that genome duplication did not coincide in time with changes in migratory behavior, but preceded a transition to anadromy by 55-50 million years. Our study represents the first attempt to estimate the absolute timing of a complex behavioral trait in relation to a genome duplication event.
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Affiliation(s)
- Markos A Alexandrou
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
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Abstract
Historical biogeography is increasingly studied from an explicitly statistical perspective, using stochastic models to describe the evolution of species range as a continuous-time Markov process of dispersal between and extinction within a set of discrete geographic areas. The main constraint of these methods is the computational limit on the number of areas that can be specified. We propose a Bayesian approach for inferring biogeographic history that extends the application of biogeographic models to the analysis of more realistic problems that involve a large number of areas. Our solution is based on a "data-augmentation" approach, in which we first populate the tree with a history of biogeographic events that is consistent with the observed species ranges at the tips of the tree. We then calculate the likelihood of a given history by adopting a mechanistic interpretation of the instantaneous-rate matrix, which specifies both the exponential waiting times between biogeographic events and the relative probabilities of each biogeographic change. We develop this approach in a Bayesian framework, marginalizing over all possible biogeographic histories using Markov chain Monte Carlo (MCMC). Besides dramatically increasing the number of areas that can be accommodated in a biogeographic analysis, our method allows the parameters of a given biogeographic model to be estimated and different biogeographic models to be objectively compared. Our approach is implemented in the program, BayArea.
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Affiliation(s)
- Michael J Landis
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA; Department of Evolution and Ecology, University of California, Davis, Storer Hall, One Shields Avenue, Davis, CA 95616, USA; and Biology Department, King Abdulaziz University, Jeddah, Saudi Arabia
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Wood HM, Matzke NJ, Gillespie RG, Griswold CE. Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals Ancient Vicariance Patterns in the Palpimanoid Spiders. Syst Biol 2012. [DOI: 10.1093/sysbio/sys092] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Goldsmith GR, Matzke NJ, Dawson TE. The incidence and implications of clouds for cloud forest plant water relations. Ecol Lett 2012; 16:307-14. [DOI: 10.1111/ele.12039] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 10/14/2012] [Accepted: 10/25/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Gregory R. Goldsmith
- Department of Integrative Biology; Valley Life Sciences Building, University of California; Berkeley; California; 94705; USA
| | - Nicholas J. Matzke
- Department of Integrative Biology; Valley Life Sciences Building, University of California; Berkeley; California; 94705; USA
| | - Todd E. Dawson
- Department of Integrative Biology; Valley Life Sciences Building, University of California; Berkeley; California; 94705; USA
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Lippold S, Matzke NJ, Reissmann M, Hofreiter M. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evol Biol 2011; 11:328. [PMID: 22082251 PMCID: PMC3247663 DOI: 10.1186/1471-2148-11-328] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 11/14/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (Equus caballus) were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region) were investigated for larger sample sets. RESULTS In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds and a single Przewalski horse (Equus przewalski) using a recently described multiplex micro-array capture approach. We found 473 variable positions within the domestic horses, 292 of which are parsimony-informative, providing a well resolved phylogenetic tree. Our divergence time estimate suggests that the mitochondrial genomes of modern horse breeds shared a common ancestor around 93,000 years ago and no later than 38,000 years ago. A Bayesian skyline plot (BSP) reveals a significant population expansion beginning 6,000-8,000 years ago with an ongoing exponential growth until the present, similar to other domestic animal species. Our data further suggest that a large sample of wild horse diversity was incorporated into the domestic population; specifically, at least 46 of the mtDNA lineages observed in domestic horses (73%) already existed before the beginning of domestication about 5,000 years ago. CONCLUSIONS Our study provides a window into the maternal origins of extant domestic horses and confirms that modern domestic breeds present a wide sample of the mtDNA diversity found in ancestral, now extinct, wild horse populations. The data obtained allow us to detect a population expansion event coinciding with the beginning of domestication and to estimate both the minimum number of female horses incorporated into the domestic gene pool and the time depth of the domestic horse mtDNA gene pool.
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Affiliation(s)
- Sebastian Lippold
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
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Abstract
Although evolutionary biology is replete with explanations for complex biological structures, scientists concerned about evolution education have been forced to confront "intelligent design" (ID), which rejects a natural origin for biological complexity. The content of ID is a subset of the claims made by the older "creation science" movement. Both creationist views contend that highly complex biological adaptations and even organisms categorically cannot result from natural causes but require a supernatural creative agent. Historically, ID arose from efforts to produce a form of creationism that would be less vulnerable to legal challenges and that would not overtly rely upon biblical literalism. Scientists do not use ID to explain nature, but because it has support from outside the scientific community, ID is nonetheless contributing substantially to a long-standing assault on the integrity of science education.
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Affiliation(s)
- Eugenie C Scott
- National Center for Science Education, Inc., 420 40th Street #2, Oakland, CA 94609-2509, USA.
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Abstract
In the recent Dover trial, and elsewhere, the 'Intelligent Design' movement has championed the bacterial flagellum as an irreducibly complex system that, it is claimed, could not have evolved through natural selection. Here we explore the arguments in favour of viewing bacterial flagella as evolved, rather than designed, entities. We dismiss the need for any great conceptual leaps in creating a model of flagellar evolution and speculate as to how an experimental programme focused on this topic might look.
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Affiliation(s)
- Mark J Pallen
- Division of Immunity & Infection, Medical School, University of Birmingham, Birmingham, B15 2TT UK.
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Affiliation(s)
- Andrea Bottaro
- Department of Medicine, James P. Wilmot Cancer Center, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA.
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