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Glascock A, Waltari E, Dudas G, Wong J, Ahyong V. PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes. BMC Bioinformatics 2024; 25:49. [PMID: 38291430 PMCID: PMC10829301 DOI: 10.1186/s12859-024-05640-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Genome streamlining, the process by which genomes become smaller and encode fewer genes over time, is a common phenomenon among pathogenic bacteria. This reduction is driven by selection for minimized energy expenditure in a nutrient-rich environment. As pathogens evolve to become more reliant on the host, metabolic genes and resulting capabilities are lost in favor of siphoning metabolites from the host. Characterizing genome streamlining, gene loss, and metabolic pathway degradation can be useful in assessing pathogen dependency on host metabolism and identifying potential targets for host-directed therapeutics. RESULTS PoMeLo (Predictor of Metabolic Loss) is a novel evolutionary genomics-guided computational approach for identifying metabolic gaps in the genomes of pathogenic bacteria. PoMeLo leverages a centralized public database of high-quality genomes and annotations and allows the user to compare an unlimited number of genomes across individual genes and pathways. PoMeLo runs locally using user-friendly prompts in a matter of minutes and generates tabular and visual outputs for users to compare predicted metabolic capacity between groups of bacteria and individual species. Each pathway is assigned a Predicted Metabolic Loss (PML) score to assess the magnitude of genome streamlining. Optionally, PoMeLo places the results in an evolutionary context by including phylogenetic relationships in visual outputs. It can also initially compute phylogenetically-weighted mean genome sizes to identify genome streamlining events. Here, we describe PoMeLo and demonstrate its use in identifying metabolic gaps in genomes of pathogenic Treponema species. CONCLUSIONS PoMeLo represents an advance over existing methods for identifying metabolic gaps in genomic data, allowing comparison across large numbers of genomes and placing the resulting data in a phylogenetic context. PoMeLo is freely available for academic and non-academic use at https://github.com/czbiohub-sf/pomelo .
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Affiliation(s)
| | | | - Gytis Dudas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Joan Wong
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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Grzywacz B, Skórka P. Genome size versus geographic range size in birds. PeerJ 2021; 9:e10868. [PMID: 33614292 PMCID: PMC7881720 DOI: 10.7717/peerj.10868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/10/2021] [Indexed: 11/20/2022] Open
Abstract
Why do some species occur in small, restricted areas, while others are distributed globally? Environmental heterogeneity increases with area and so does the number of species. Hence, diverse biotic and abiotic conditions across large ranges may lead to specific adaptations that are often linked to a species' genome size and chromosome number. Therefore, a positive association between genome size and geographic range is anticipated. Moreover, high cognitive ability in organisms would be favored by natural selection to cope with the dynamic conditions within large geographic ranges. Here, we tested these hypotheses in birds-the most mobile terrestrial vertebrates-and accounted for the effects of various confounding variables, such as body mass, relative brain mass, and geographic latitude. Using phylogenetic generalized least squares and phylogenetic confirmatory path analysis, we demonstrated that range size is positively associated with bird genome size but probably not with chromosome number. Moreover, relative brain mass had no effect on range size, whereas body mass had a possible weak and negative effect, and range size was larger at higher geographic latitudes. However, our models did not fully explain the overall variation in range size. Hence, natural selection may impose larger genomes in birds with larger geographic ranges, although there may be additional explanations for this phenomenon.
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Affiliation(s)
- Beata Grzywacz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Piotr Skórka
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
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Lanszki J, Heltai M, Kövér G, Zalewski A. Non-linear relationship between body size of terrestrial carnivores and their trophic niche breadth and overlap. Basic Appl Ecol 2019. [DOI: 10.1016/j.baae.2019.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Lacava M, Camargo A, Garcia LF, Benamú MA, Santana M, Fang J, Wang X, Blamires SJ. Web building and silk properties functionally covary among species of wolf spider. J Evol Biol 2018; 31:968-978. [DOI: 10.1111/jeb.13278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/18/2018] [Accepted: 04/04/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Mariángeles Lacava
- Centro Universitario de Rivera Universidad de la República Rivera Uruguay
- Centro Universitario Regional del Este (CURE) Universidad de la República Treinta y Tres Uruguay
| | - Arley Camargo
- Centro Universitario de Rivera Universidad de la República Rivera Uruguay
| | - Luis F. Garcia
- Centro Universitario Regional del Este (CURE) Universidad de la República Treinta y Tres Uruguay
- Laboratorio Ecología del Comportamiento (IIBCE) Montevideo Uruguay
| | - Marco A. Benamú
- Centro Universitario de Rivera Universidad de la República Rivera Uruguay
- Laboratorio Ecología del Comportamiento (IIBCE) Montevideo Uruguay
| | - Martin Santana
- Laboratorio Ecología del Comportamiento (IIBCE) Montevideo Uruguay
| | - Jian Fang
- Institute for Frontier Materials (IFM) Deakin University Geelong Vic. Australia
| | - Xungai Wang
- Institute for Frontier Materials (IFM) Deakin University Geelong Vic. Australia
| | - Sean J. Blamires
- Evolution & Ecology Research Centre School of Biological, Earth & Environmental Sciences The University of New South Wales Sydney NSW Australia
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Lower SS, Johnston JS, Stanger-Hall KF, Hjelmen CE, Hanrahan SJ, Korunes K, Hall D. Genome Size in North American Fireflies: Substantial Variation Likely Driven by Neutral Processes. Genome Biol Evol 2017; 9:1499-1512. [PMID: 28541478 PMCID: PMC5499882 DOI: 10.1093/gbe/evx097] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2017] [Indexed: 12/11/2022] Open
Abstract
Eukaryotic genomes show tremendous size variation across taxa. Proximate explanations for genome size variation include differences in ploidy and amounts of noncoding DNA, especially repetitive DNA. Ultimate explanations include selection on physiological correlates of genome size such as cell size, which in turn influence body size, resulting in the often-observed correlation between body size and genome size. In this study, we examined body size and repetitive DNA elements in relationship to the evolution of genome size in North American representatives of a single beetle family, the Lampyridae (fireflies). The 23 species considered represent an excellent study system because of the greater than 5-fold range of genome sizes, documented here using flow cytometry, and the 3-fold range in body size, measured using pronotum width. We also identified common genomic repetitive elements using low-coverage sequencing. We found a positive relationship between genome size and repetitive DNA, particularly retrotransposons. Both genome size and these elements were evolving as expected given phylogenetic relatedness. We also tested whether genome size varied with body size and found no relationship. Together, our results suggest that genome size is evolving neutrally in fireflies.
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Affiliation(s)
| | | | | | | | | | | | - David Hall
- Department of Genetics, University of Georgia
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Schultheis EH, Berardi AE, Lau JA. No release for the wicked: enemy release is dynamic and not associated with invasiveness. Ecology 2015; 96:2446-57. [PMID: 26594701 DOI: 10.1890/14-2158.1] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The enemy release hypothesis predicts that invasive species will receive less damage from enemies, compared to co-occurring native and noninvasive exotic species in their introduced range. However, release operating early in invasion could be lost over time and with increased range size as introduced species acquire new enemies. We used three years of data, from 61 plant species planted into common gardens, to determine whether (1) invasive, noninvasive exotic, and native species experience differential damage from insect herbivores. and mammalian browsers, and (2) enemy release is lost with increased residence time and geographic spread in the introduced range. We find no evidence suggesting enemy release is a general mechanism contributing to invasiveness in this region. Invasive species received the most insect herbivory, and damage increased with longer residence times and larger range sizes at three spatial scales. Our results show that invasive and exotic species fail to escape enemies, particularly over longer temporal and larger spatial scales.
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Polishchuk LV, Popadin KY, Baranova MA, Kondrashov AS. A genetic component of extinction risk in mammals. OIKOS 2015. [DOI: 10.1111/oik.01734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Leonard V. Polishchuk
- Dept of General Ecology; Biological Faculty, M.V. Lomonosov Moscow State Univ.; RU-119992 Moscow Russia
| | - Konstantin Y. Popadin
- Dept of Genetic Medicine and Development; Univ. of Geneva Medical School; 1 rue Michel-Servet CH-1211 Geneva Switzerland
- Inst. of Genetics and Genomics in Geneva (iGE3); CH-1211 Geneva Switzerland
- Inst. for Information Transmission Problems (Kharkevich Inst.), Russian Academy of Sciences; RU-127994 Moscow Russia
| | - Maria A. Baranova
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State Univ.; RU-119992 Moscow Russia
| | - Aleksey S. Kondrashov
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State Univ.; RU-119992 Moscow Russia
- Life Sciences Inst. and Dept of Ecology and Evolutionary Biology; Univ. of Michigan; Ann Arbor MI 48109 USA
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White CR, Seymour RS. The role of gravity in the evolution of mammalian blood pressure. Evolution 2014; 68:901-8. [PMID: 24152198 DOI: 10.1111/evo.12298] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 04/19/2013] [Indexed: 11/30/2022]
Abstract
Understanding of the factors involved in determining the level of central arterial blood pressure in mammals has been clouded by inappropriate allometric analyses that fail to account for phylogenetic relationships among species, and require pressure to approach 0 as body size decreases. The present study analyses systolic, mean arterial, and diastolic blood pressure in 47 species of mammal with phylogenetically informed techniques applied to two-parameter equations. It also sets nonlinear, three-parameter equations to the data to remove the assumption of the two-parameter power equation that the smallest animals must have negligible blood pressure. These analyses show that blood pressure increases with body size. Nonlinear analyses show that mean blood pressure increases from 93 mmHg in a 10 g mouse to 156 mmHg in a 4 tonne elephant. The scaling exponent of blood pressure is generally lower than, though not significantly different from, the exponent predicted on the basis of the expected scaling of the vertical distance between the head and the heart. This indicates that compensation for the vertical distance above the heart is not perfect and suggests that the pressure required to perfuse the capillaries at the top of the body may decrease in larger species.
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Affiliation(s)
- Craig R White
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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Dyer RJ, Pellicer J, Savolainen V, Leitch IJ, Schneider H. Genome size expansion and the relationship between nuclear DNA content and spore size in the Asplenium monanthes fern complex (Aspleniaceae). BMC PLANT BIOLOGY 2013; 13:219. [PMID: 24354467 PMCID: PMC3930065 DOI: 10.1186/1471-2229-13-219] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/10/2013] [Indexed: 05/07/2023]
Abstract
BACKGROUND Homosporous ferns are distinctive amongst the land plant lineages for their high chromosome numbers and enigmatic genomes. Genome size measurements are an under exploited tool in homosporous ferns and show great potential to provide an overview of the mechanisms that define genome evolution in these ferns. The aim of this study is to investigate the evolution of genome size and the relationship between genome size and spore size within the apomictic Asplenium monanthes fern complex and related lineages. RESULTS Comparative analyses to test for a relationship between spore size and genome size show that they are not correlated. The data do however provide evidence for marked genome size variation between species in this group. These results indicate that Asplenium monanthes has undergone a two-fold expansion in genome size. CONCLUSIONS Our findings challenge the widely held assumption that spore size can be used to infer ploidy levels within apomictic fern complexes. We argue that the observed genome size variation is likely to have arisen via increases in both chromosome number due to polyploidy and chromosome size due to amplification of repetitive DNA (e.g. transposable elements, especially retrotransposons). However, to date the latter has not been considered to be an important process of genome evolution within homosporous ferns. We infer that genome evolution, at least in some homosporous fern lineages, is a more dynamic process than existing studies would suggest.
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Affiliation(s)
- Robert J Dyer
- Department of Botany, Natural History Museum, London SW7 5BD, UK
- Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Centre for Ecology and Hydrology, Wallingford, Oxfordshire OX10 8BB, UK
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Vincent Savolainen
- Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Harald Schneider
- Department of Botany, Natural History Museum, London SW7 5BD, UK
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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De Lisle SP, Rowe L. Correlated Evolution of Allometry and Sexual Dimorphism across Higher Taxa. Am Nat 2013; 182:630-9. [DOI: 10.1086/673282] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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In contrast to many other mammals, cetaceans have relatively small hippocampi that appear to lack adult neurogenesis. Brain Struct Funct 2013; 220:361-83. [PMID: 24178679 DOI: 10.1007/s00429-013-0660-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 10/15/2013] [Indexed: 12/16/2022]
Abstract
The hippocampus is essential for the formation and retrieval of memories and is a crucial neural structure sub-serving complex cognition. Adult hippocampal neurogenesis, the birth, migration and integration of new neurons, is thought to contribute to hippocampal circuit plasticity to augment function. We evaluated hippocampal volume in relation to brain volume in 375 mammal species and examined 71 mammal species for the presence of adult hippocampal neurogenesis using immunohistochemistry for doublecortin, an endogenous marker of immature neurons that can be used as a proxy marker for the presence of adult neurogenesis. We identified that the hippocampus in cetaceans (whales, dolphins and porpoises) is both absolutely and relatively small for their overall brain size, and found that the mammalian hippocampus scaled as an exponential function in relation to brain volume. In contrast, the amygdala was found to scale as a linear function of brain volume, but again, the relative size of the amygdala in cetaceans was small. The cetacean hippocampus lacks staining for doublecortin in the dentate gyrus and thus shows no clear signs of adult hippocampal neurogenesis. This lack of evidence of adult hippocampal neurogenesis, along with the small hippocampus, questions current assumptions regarding cognitive abilities associated with hippocampal function in the cetaceans. These anatomical features of the cetacean hippocampus may be related to the lack of postnatal sleep, causing a postnatal cessation of hippocampal neurogenesis.
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Nomura F, De Marco P, Carvalho A, Rossa-Feres DC. Does background colouration affect the behaviour of tadpoles? An experimental approach with an odonate predator. ETHOL ECOL EVOL 2013. [DOI: 10.1080/03949370.2012.742465] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Hardenberg AV, Gonzalez-Voyer A. DISENTANGLING EVOLUTIONARY CAUSE-EFFECT RELATIONSHIPS WITH PHYLOGENETIC CONFIRMATORY PATH ANALYSIS. Evolution 2012; 67:378-87. [DOI: 10.1111/j.1558-5646.2012.01790.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pointer MA, Kamilar JM, Warmuth V, Chester SGB, Delsuc F, Mundy NI, Asher RJ, Bradley BJ. RUNX2 tandem repeats and the evolution of facial length in placental mammals. BMC Evol Biol 2012; 12:103. [PMID: 22741925 PMCID: PMC3438065 DOI: 10.1186/1471-2148-12-103] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 06/28/2012] [Indexed: 01/21/2023] Open
Abstract
Background When simple sequence repeats are integrated into functional genes, they can potentially act as evolutionary ‘tuning knobs’, supplying abundant genetic variation with minimal risk of pleiotropic deleterious effects. The genetic basis of variation in facial shape and length represents a possible example of this phenomenon. Runt-related transcription factor 2 (RUNX2), which is involved in osteoblast differentiation, contains a functionally-important tandem repeat of glutamine and alanine amino acids. The ratio of glutamines to alanines (the QA ratio) in this protein seemingly influences the regulation of bone development. Notably, in domestic breeds of dog, and in carnivorans in general, the ratio of glutamines to alanines is strongly correlated with facial length. Results In this study we examine whether this correlation holds true across placental mammals, particularly those mammals for which facial length is highly variable and related to adaptive behavior and lifestyle (e.g., primates, afrotherians, xenarthrans). We obtained relative facial length measurements and RUNX2 sequences for 41 mammalian species representing 12 orders. Using both a phylogenetic generalized least squares model and a recently-developed Bayesian comparative method, we tested for a correlation between genetic and morphometric data while controlling for phylogeny, evolutionary rates, and divergence times. Non-carnivoran taxa generally had substantially lower glutamine-alanine ratios than carnivorans (primates and xenarthrans with means of 1.34 and 1.25, respectively, compared to a mean of 3.1 for carnivorans), and we found no correlation between RUNX2 sequence and face length across placental mammals. Conclusions Results of our diverse comparative phylogenetic analyses indicate that QA ratio does not consistently correlate with face length across the 41 mammalian taxa considered. Thus, although RUNX2 might function as a ‘tuning knob’ modifying face length in carnivorans, this relationship is not conserved across mammals in general.
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Affiliation(s)
- Marie A Pointer
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
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Variation in seed germination of 86 subalpine forest species from the eastern Tibetan Plateau: phylogeny and life-history correlates. Ecol Res 2012. [DOI: 10.1007/s11284-011-0916-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Hopkins MJ. HOW SPECIES LONGEVITY, INTRASPECIFIC MORPHOLOGICAL VARIATION, AND GEOGRAPHIC RANGE SIZE ARE RELATED: A COMPARISON USING LATE CAMBRIAN TRILOBITES. Evolution 2011; 65:3253-73. [DOI: 10.1111/j.1558-5646.2011.01379.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Arnold C, Nunn C. Phylogenetic Targeting of Research Effort in Evolutionary Biology. Am Nat 2010; 176:601-12. [DOI: 10.1086/656490] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Codron D, Clauss M. Rumen physiology constrains diet niche: linking digestive physiology and food selection across wild ruminant species. CAN J ZOOL 2010. [DOI: 10.1139/z10-077] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We propose a hypothesis for digestive constraints on the browsing and grazing options available to ruminants: that the diet-niche range (maximum and minimum grass intake) of a species is dependent upon its predisposition to stratified rumen contents, based on observations that this characteristic is a critical step towards enhanced fibre digestion and greater fluid throughput. We compare a physiological (heterogeneity of ingesta fluid content) and an anatomical (the intraruminal papillation pattern) measure with dietary evidence for a range of African and temperate species. Both measures are strongly related to the mean percentage of grass in species’ natural diets, as well as to the maximum and minimum levels of grass intake, respectively. The nature of these effects implies a stratification-level threshold, below which a species will not use a grass-based diet, but above which grass consumption can increase exponentially. However, above this threshold, a minimum percentage of grass in the diet is a prerequisite for optimal performance. We argue that this second constraint is crucial, as it depicts how a greater fluid throughput reduces potential for detoxification of plant secondary compounds, and therefore limits the maximum amount of browse a stratifying species will consume.
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Affiliation(s)
- Daryl Codron
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Winterthurerstr. 260, CH-8057 Zurich, Switzerland
- School of Biological and Conservation Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
- Florisbad Quaternary Research, National Museum, Bloemfontein, 9300, South Africa
| | - Marcus Clauss
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Winterthurerstr. 260, CH-8057 Zurich, Switzerland
- School of Biological and Conservation Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
- Florisbad Quaternary Research, National Museum, Bloemfontein, 9300, South Africa
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Lang D, Weiche B, Timmerhaus G, Richardt S, Riaño-Pachón DM, Corrêa LGG, Reski R, Mueller-Roeber B, Rensing SA. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol 2010; 2:488-503. [PMID: 20644220 PMCID: PMC2997552 DOI: 10.1093/gbe/evq032] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Evolutionary retention of duplicated genes encoding transcription-associated proteins (TAPs, comprising transcription factors and other transcriptional regulators) has been hypothesized to be positively correlated with increasing morphological complexity and paleopolyploidizations, especially within the plant kingdom. Here, we present the most comprehensive set of classification rules for TAPs and its application for genome-wide analyses of plants and algae. Using a dated species tree and phylogenetic comparative (PC) analyses, we define the timeline of TAP loss, gain, and expansion among Viridiplantae and find that two major bursts of gain/expansion occurred, coinciding with the water-to-land transition and the radiation of flowering plants. For the first time, we provide PC proof for the long-standing hypothesis that TAPs are major driving forces behind the evolution of morphological complexity, the latter in Plantae being shaped significantly by polyploidization and subsequent biased paleolog retention. Principal component analysis incorporating the number of TAPs per genome provides an alternate and significant proxy for complexity, ideally suited for PC genomics. Our work lays the ground for further interrogation of the shaping of gene regulatory networks underlying the evolution of organism complexity.
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Affiliation(s)
- Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- These authors contributed equally to this work
| | - Benjamin Weiche
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Present address: Life & Medical Sciences Institute, Laboratory of Chemical Biology, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
- These authors contributed equally to this work
| | - Gerrit Timmerhaus
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Present address: Nofima Marin, Postboks 5010, 1432 Ås, Norway
| | - Sandra Richardt
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Present address: QIAGEN, Qiagen Strasse 1, 40724 Hilden, Germany
| | - Diego M. Riaño-Pachón
- GabiPD team, Bioinformatics Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Luiz G. G. Corrêa
- Department of Molecular Biology, Institute of Biochemistry and Biology, GoFORSYS, University of Potsdam, Potsdam-Golm, Germany
- Present address: Fermentas, Opelstraße 9, 68789 St. Leon-Rot, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Freiburg Initiative for Systems Biology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Bernd Mueller-Roeber
- Department of Molecular Biology, Institute of Biochemistry and Biology, GoFORSYS, University of Potsdam, Potsdam-Golm, Germany
- Cooperative Research Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Stefan A. Rensing
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Freiburg Initiative for Systems Biology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Corresponding author: E-mail:
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MacLeod CD. Assessing the shape and topology of allometric relationships with body mass: a case study using testes mass allometry. Methods Ecol Evol 2010. [DOI: 10.1111/j.2041-210x.2010.00037.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Moya-Laraño J, Vinković D, Allard CM, Foellmer MW. Optimal climbing speed explains the evolution of extreme sexual size dimorphism in spiders. J Evol Biol 2009; 22:954-63. [PMID: 19243487 DOI: 10.1111/j.1420-9101.2009.01707.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Several hypotheses have been put forward to explain the evolution of extreme sexual size dimorphism (SSD). Among them, the gravity hypothesis (GH) explains that extreme SSD has evolved in spiders because smaller males have a mating or survival advantage by climbing faster. However, few studies have supported this hypothesis thus far. Using a wide span of spider body sizes, we show that there is an optimal body size (7.4 mm) for climbing and that extreme SSD evolves only in spiders that: (1) live in high-habitat patches and (2) in which females are larger than the optimal size. We report that the evidence for the GH across studies depends on whether the body size of individuals expands beyond the optimal climbing size. We also present an ad hoc biomechanical model that shows how the higher stride frequency of small animals predicts an optimal body size for climbing.
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Affiliation(s)
- J Moya-Laraño
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Aridas, Consejo Superior de Investigaciones Científicas, General Segura 1, Almería, Spain.
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22
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Purvis A. Phylogenetic Approaches to the Study of Extinction. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2008. [DOI: 10.1146/annurev-ecolsys-063008-102010] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Species extinction is both a key process throughout the history of life and a pressing concern in the conservation of present-day biodiversity. These two facets have largely been studied by separate communities using different approaches. This article illustrates with examples some of the ways that considering the evolutionary relationships among species—phylogenies—has helped the study of both past and present species extinction. The focus is on three topics: extinction rates and severities, phylogenetic nonrandomness of extinction, and the testing of hypotheses relating extinction-proneness to attributes of organisms or species. Phylogenetic and taxic approaches to extinction have not fully fused, largely because of the difficulties of relating discrete taxa to the underlying continuity of phylogeny. Phylogeny must be considered in comparative tests of hypotheses about extinction, but care must be taken to avoid overcorrecting for phylogenetic nonindependence among taxa.
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Affiliation(s)
- Andy Purvis
- Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, United Kingdom
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23
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Using neural networks to detect patterns in inter-specific data: An example from net-spinning caddisflies (Trichoptera: Annulipalpia). ECOL INFORM 2008. [DOI: 10.1016/j.ecoinf.2008.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Mangel M, Kindsvater HK, Bonsall MB. Evolutionary analysis of life span, competition, and adaptive radiation, motivated by the Pacific rockfishes (Sebastes). Evolution 2007; 61:1208-24. [PMID: 17492972 DOI: 10.1111/j.1558-5646.2007.00094.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Pacific rockfishes (Sebastes spp) are remarkable for both their diversity (on the order of 100 species) and range of maximum life span ( approximately 10 years for Calico rockfish to approximately 200 years for Rougheye rockfish). We describe the natural history and patterns of diversity and life span in these species and then use independent contrasts to explore correlates of these. When phylogenetic history is taken into account, maximum life span is explained by age at maturity, size at maturity, and the interaction of these two. We introduce a life-history model that allows insight into the origin of these correlations. We then describe a variety of mechanisms that may increase lifepans and diversity. These include fluctuating environments (in which organisms basically have to "wait out" bad periods to reproduce successfully), diversity, and longevity inspired by interspecific competition and physiological complexity in growth and accumulation of cellular damage. All of the results point toward the importance of flat or "indifferent" fitness surfaces as a key element in the evolution of diversity. We conclude that further development of the theory of flat or indifferent fitness surfaces as applied to diversity and life span is clearly warranted.
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Affiliation(s)
- Marc Mangel
- Center for Stock Assessment Research and Department of Applied Mathematics and Statistics, University of California, Santa Cruz, California 95064, USA.
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25
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Ottaviani D, Cairns SC, Oliverio M, Boitani L. Body mass as a predictive variable of home-range size among Italian mammals and birds. J Zool (1987) 2006. [DOI: 10.1111/j.1469-7998.2006.00060.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Phillimore AB, Freckleton RP, Orme CDL, Owens IPF. Ecology predicts large-scale patterns of phylogenetic diversification in birds. Am Nat 2006; 168:220-9. [PMID: 16874631 DOI: 10.1086/505763] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Accepted: 04/26/2006] [Indexed: 11/03/2022]
Abstract
One of the most striking patterns in evolutionary biology is that clades may differ greatly in the number of species they contain. Numerous hypotheses have been put forward to explain this phenomenon, and several have been tested using phylogenetic methods. Remarkably, however, all such tests performed to date have been characterized by modest explanatory power, which has generated an interest in explanations stressing the importance of random processes. Here we make use of phylogenetic methods to test whether ecological variables, typically ignored in previous models, may explain phylogenetic tree imbalance in birds. We show that diversification rate possesses an intermediate phylogenetic signal across families. Using phylogenetic comparative methods, we then build a multipredictor model that explains more than 50% of the variation in diversification rate among clades. High annual dispersal is identified as the strongest predictor of high rates of diversification. In addition, high diversification rate is strongly associated with feeding generalization. In all but one instance, these key findings remain qualitatively unchanged when we use an alternative phylogeny and methodology and when small clades, containing five species or less, are excluded. Taken together, these results suggest that large-scale patterns in avian diversification can be explained by variation in intrinsic biology.
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Affiliation(s)
- Albert B Phillimore
- Division of Biology and Natural Environment Research Council Centre for Population Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, United Kingdom.
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Garland T, Bennett AF, Rezende EL. Phylogenetic approaches in comparative physiology. ACTA ACUST UNITED AC 2006; 208:3015-35. [PMID: 16081601 DOI: 10.1242/jeb.01745] [Citation(s) in RCA: 444] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Over the past two decades, comparative biological analyses have undergone profound changes with the incorporation of rigorous evolutionary perspectives and phylogenetic information. This change followed in large part from the realization that traditional methods of statistical analysis tacitly assumed independence of all observations, when in fact biological groups such as species are differentially related to each other according to their evolutionary history. New phylogenetically based analytical methods were then rapidly developed, incorporated into ;the comparative method', and applied to many physiological, biochemical, morphological and behavioral investigations. We now review the rationale for including phylogenetic information in comparative studies and briefly discuss three methods for doing this (independent contrasts, generalized least-squares models, and Monte Carlo computer simulations). We discuss when and how to use phylogenetic information in comparative studies and provide several examples in which it has been helpful, or even crucial, to a comparative analysis. We also consider some difficulties with phylogenetically based statistical methods, and of comparative approaches in general, both practical and theoretical. It is our personal opinion that the incorporation of phylogeny information into comparative studies has been highly beneficial, not only because it can improve the reliability of statistical inferences, but also because it continually emphasizes the potential importance of past evolutionary history in determining current form and function.
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Affiliation(s)
- Theodore Garland
- Department of Biology, University of California, Riverside, CA 92521, USA
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Seddon N. ECOLOGICAL ADAPTATION AND SPECIES RECOGNITION DRIVES VOCAL EVOLUTION IN NEOTROPICAL SUBOSCINE BIRDS. Evolution 2005. [DOI: 10.1554/04-300] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Seddon N. ECOLOGICAL ADAPTATION AND SPECIES RECOGNITION DRIVES VOCAL EVOLUTION IN NEOTROPICAL SUBOSCINE BIRDS. Evolution 2005. [DOI: 10.1111/j.0014-3820.2005.tb00906.x] [Citation(s) in RCA: 223] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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