1
|
Mekbib KY, Muñoz W, Allington G, McGee S, Mehta NH, Shofi JP, Fortes C, Le HT, Nelson-Williams C, Nanda P, Dennis E, Kundishora AJ, Khanna A, Smith H, Ocken J, Greenberg ABW, Wu R, Moreno-De-Luca A, DeSpenza T, Zhao S, Marlier A, Jin SC, Alper SL, Butler WE, Kahle KT. Human genetics and molecular genomics of Chiari malformation type 1. Trends Mol Med 2023; 29:1059-1075. [PMID: 37802664 DOI: 10.1016/j.molmed.2023.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 10/08/2023]
Abstract
Chiari malformation type 1 (CM1) is the most common structural brain disorder involving the craniocervical junction, characterized by caudal displacement of the cerebellar tonsils below the foramen magnum into the spinal canal. Despite the heterogeneity of CM1, its poorly understood patho-etiology has led to a 'one-size-fits-all' surgical approach, with predictably high rates of morbidity and treatment failure. In this review we present multiplex CM1 families, associated Mendelian syndromes, and candidate genes from recent whole exome sequencing (WES) and other genetic studies that suggest a significant genetic contribution from inherited and de novo germline variants impacting transcription regulation, craniovertebral osteogenesis, and embryonic developmental signaling. We suggest that more extensive WES may identify clinically relevant, genetically defined CM1 subtypes distinguished by unique neuroradiographic and neurophysiological endophenotypes.
Collapse
Affiliation(s)
- Kedous Y Mekbib
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA; Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA; Harvard Center for Hydrocephalus and Neurodevelopmental Disorders, Massachusetts General Hospital, Boston, MA, USA
| | - William Muñoz
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA; Harvard Center for Hydrocephalus and Neurodevelopmental Disorders, Massachusetts General Hospital, Boston, MA, USA
| | - Garrett Allington
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Neel H Mehta
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - John P Shofi
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Carla Fortes
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Hao Thi Le
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | | | - Pranav Nanda
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Evan Dennis
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Adam J Kundishora
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Arjun Khanna
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Hannah Smith
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Jack Ocken
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Ana B W Greenberg
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Rui Wu
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Andres Moreno-De-Luca
- Department of Radiology, Autism and Developmental Medicine Institute, Genomic Medicine Institute, Geisinger, Danville, PA, USA
| | - Tyrone DeSpenza
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Shujuan Zhao
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Seth L Alper
- Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - William E Butler
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA; Harvard Center for Hydrocephalus and Neurodevelopmental Disorders, Massachusetts General Hospital, Boston, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
2
|
Human mitochondrial DNA diversity is compatible with the multiregional continuity theory of the origin of Homo sapiens. ANTHROPOLOGICAL REVIEW 2022. [DOI: 10.2478/anre-2021-0032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Confidence intervals for estimates of human mtDNA sequence diversity, chimpanzee-human mtDNA sequence divergence, and the time of splitting of the pongid-hominid lineages are presented. Consistent with all the data used in estimating the coalescence time for human mitochondrial lineages to a common ancestral mitochondrion is a range of dates from less than 79,000 years ago to more than 1,139,000 years ago. Consequently, the hypothesis that a migration of modern humans (Homo sapiens) out of Africa in the range of 140,000 to 280,000 years ago resulted in the complete replacement, without genetic interchange, of earlier Eurasian hominid populations (Homo erectus) is but one of several possible interpretations of the mtDNA data. The data are also compatible with the hypothesis, suggested earlier and supported by fossil evidence, of a single, more ancient expansion of the range of Homo erectus from Africa, followed by a gradual transition to Homo sapiens in Europe, Asia, and Africa.
Collapse
|
3
|
Smith S, Sandoval-Castellanos E, Lagerholm VK, Napierala H, Sablin M, Von Seth J, Fladerer FA, Germonpré M, Wojtal P, Miller R, Stewart JR, Dalén L. Nonreceding hare lines: genetic continuity since the Late Pleistocene in European mountain hares (Lepus timidus). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
4
|
Lombaert E, Guillemaud T, Lundgren J, Koch R, Facon B, Grez A, Loomans A, Malausa T, Nedved O, Rhule E, Staverlokk A, Steenberg T, Estoup A. Complementarity of statistical treatments to reconstruct worldwide routes of invasion: the case of the Asian ladybirdHarmonia axyridis. Mol Ecol 2014; 23:5979-97. [DOI: 10.1111/mec.12989] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/18/2014] [Accepted: 10/28/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Eric Lombaert
- Inra; UMR 1355 ISA; Sophia-Antipolis 06903 France
- Université de Nice Sophia Antipolis; UMR ISA; Sophia-Antipolis 06903 France
- CNRS; UMR 7254 ISA; Sophia-Antipolis 06903 France
| | - Thomas Guillemaud
- Inra; UMR 1355 ISA; Sophia-Antipolis 06903 France
- Université de Nice Sophia Antipolis; UMR ISA; Sophia-Antipolis 06903 France
- CNRS; UMR 7254 ISA; Sophia-Antipolis 06903 France
| | - Jonathan Lundgren
- USDA-ARS; North Central Agricultural Research Laboratory; Brookings SD 57006 USA
| | - Robert Koch
- Department of Entomology; University of Minnesota; Saint Paul MN 55108 USA
| | - Benoît Facon
- Inra; UMR CBGP (INRA/IRD/CIRAD/Montpellier SupAgro); Montferrier-sur-Lez 34988 France
| | - Audrey Grez
- Facultad de Ciencias Veterinarias y Pecuarias; Universidad de Chile; Casilla 2, Correo 15 La Granja Santiago Chile
| | - Antoon Loomans
- National Reference Centre; Netherlands Food and Consumer Product Safety Authority; Wageningen 6706 EA The Netherlands
| | - Thibaut Malausa
- Inra; UMR 1355 ISA; Sophia-Antipolis 06903 France
- Université de Nice Sophia Antipolis; UMR ISA; Sophia-Antipolis 06903 France
- CNRS; UMR 7254 ISA; Sophia-Antipolis 06903 France
| | - Oldrich Nedved
- University of South Bohemia; Ceske Budejovice 37005 Czech Republic
| | - Emma Rhule
- Department of Genetics; University of Cambridge; Cambridge CB2 3EH UK
| | - Arnstein Staverlokk
- Department of Terrestrial Ecology; Norwegian Institute for Nature Research; Trondheim NO-7485 Norway
| | - Tove Steenberg
- Department of Agroecology; Aarhus University; Slagelse DK-4200 Denmark
| | - Arnaud Estoup
- Inra; UMR CBGP (INRA/IRD/CIRAD/Montpellier SupAgro); Montferrier-sur-Lez 34988 France
| |
Collapse
|
5
|
Dating human cultural capacity using phylogenetic principles. Sci Rep 2014; 3:1785. [PMID: 23648831 PMCID: PMC3646280 DOI: 10.1038/srep01785] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 04/16/2013] [Indexed: 11/16/2022] Open
Abstract
Humans have genetically based unique abilities making complex culture possible; an assemblage of traits which we term “cultural capacity”. The age of this capacity has for long been subject to controversy. We apply phylogenetic principles to date this capacity, integrating evidence from archaeology, genetics, paleoanthropology, and linguistics. We show that cultural capacity is older than the first split in the modern human lineage, and at least 170,000 years old, based on data on hyoid bone morphology, FOXP2 alleles, agreement between genetic and language trees, fire use, burials, and the early appearance of tools comparable to those of modern hunter-gatherers. We cannot exclude that Neanderthals had cultural capacity some 500,000 years ago. A capacity for complex culture, therefore, must have existed before complex culture itself. It may even originated long before. This seeming paradox is resolved by theoretical models suggesting that cultural evolution is exceedingly slow in its initial stages.
Collapse
|
6
|
Almendra AL, Rogers DS, González-Cózatl FX. Molecular phylogenetics of theHandleyomys chapmanicomplex in Mesoamerica. J Mammal 2014. [DOI: 10.1644/13-mamm-a-044.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
7
|
Fernandes YB, Ramina R, Campos-Herrera CR, Borges G. Evolutionary hypothesis for Chiari type I malformation. Med Hypotheses 2013; 81:715-9. [DOI: 10.1016/j.mehy.2013.07.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 07/10/2013] [Accepted: 07/19/2013] [Indexed: 12/28/2022]
|
8
|
Abstract
Approximation Bayesian computation [ABC] is an analysis approach that has arisen in response to the recent trend to collect data that is of a magnitude far higher than has been historically the case. This has led to many existing methods become intractable because of difficulties in calculating the likelihood function. ABC circumvents this issue by replacing calculation of the likelihood with a simulation step in which it is estimated in one way or another. In this review we give an overview of the ABC approach, giving examples of some of the more popular specific forms of ABC. We then discuss some of the areas of most active research and application in the field, specifically, choice of low-dimensional summaries of complex datasets and metrics for measuring similarity between observed and simulated data. Next, we consider the question of how to do model selection in an ABC context. Finally, we discuss an area of growing prominence in the ABC world, use of ABC methods in genetic pathway inference.
Collapse
Affiliation(s)
- Paul Marjoram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| |
Collapse
|
9
|
Abstract
Approximate Bayesian computation has become an essential tool for the analysis of complex stochastic models when the likelihood function is numerically unavailable. However, the well-established statistical method of empirical likelihood provides another route to such settings that bypasses simulations from the model and the choices of the approximate Bayesian computation parameters (summary statistics, distance, tolerance), while being convergent in the number of observations. Furthermore, bypassing model simulations may lead to significant time savings in complex models, for instance those found in population genetics. The Bayesian computation with empirical likelihood algorithm we develop in this paper also provides an evaluation of its own performance through an associated effective sample size. The method is illustrated using several examples, including estimation of standard distributions, time series, and population genetics models.
Collapse
Affiliation(s)
- Kerrie L. Mengersen
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Pierre Pudlo
- Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier-sur-Lez Cedex, France
- Université Montpellier 2, Institut de Mathématiques et de Modélisation de Montpellier, 34095 Montpellier Cedex 5, France
- Institut de Biologie Computationnelle, Montpellier, France
| | - Christian P. Robert
- Université Paris Dauphine, Centre de Recherche en Mathematiques de la Decision, 75775 Paris Cedex 16, France
- Institut Universitaire de France, Paris, France; and
- Centre de Recherche en Statistique et Economie, 92245 Malakoff Cedex, France
| |
Collapse
|
10
|
Abstract
Approximate Bayesian computation (ABC) constitutes a class of computational methods rooted in Bayesian statistics. In all model-based statistical inference, the likelihood function is of central importance, since it expresses the probability of the observed data under a particular statistical model, and thus quantifies the support data lend to particular values of parameters and to choices among different models. For simple models, an analytical formula for the likelihood function can typically be derived. However, for more complex models, an analytical formula might be elusive or the likelihood function might be computationally very costly to evaluate. ABC methods bypass the evaluation of the likelihood function. In this way, ABC methods widen the realm of models for which statistical inference can be considered. ABC methods are mathematically well-founded, but they inevitably make assumptions and approximations whose impact needs to be carefully assessed. Furthermore, the wider application domain of ABC exacerbates the challenges of parameter estimation and model selection. ABC has rapidly gained popularity over the last years and in particular for the analysis of complex problems arising in biological sciences (e.g., in population genetics, ecology, epidemiology, and systems biology).
Collapse
|
11
|
A multidisciplinary reconstruction of Palaeolithic nutrition that holds promise for the prevention and treatment of diseases of civilisation. Nutr Res Rev 2012; 25:96-129. [PMID: 22894943 DOI: 10.1017/s0954422412000017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evolutionary medicine acknowledges that many chronic degenerative diseases result from conflicts between our rapidly changing environment, our dietary habits included, and our genome, which has remained virtually unchanged since the Palaeolithic era. Reconstruction of the diet before the Agricultural and Industrial Revolutions is therefore indicated, but hampered by the ongoing debate on our ancestors' ecological niche. Arguments and their counterarguments regarding evolutionary medicine are updated and the evidence for the long-reigning hypothesis of human evolution on the arid savanna is weighed against the hypothesis that man evolved in the proximity of water. Evidence from various disciplines is discussed, including the study of palaeo-environments, comparative anatomy, biogeochemistry, archaeology, anthropology, (patho)physiology and epidemiology. Although our ancestors had much lower life expectancies, the current evidence does neither support the misconception that during the Palaeolithic there were no elderly nor that they had poor health. Rather than rejecting the possibility of 'healthy ageing', the default assumption should be that healthy ageing posed an evolutionary advantage for human survival. There is ample evidence that our ancestors lived in a land-water ecosystem and extracted a substantial part of their diets from both terrestrial and aquatic resources. Rather than rejecting this possibility by lack of evidence, the default assumption should be that hominins, living in coastal ecosystems with catchable aquatic resources, consumed these resources. Finally, the composition and merits of so-called 'Palaeolithic diets', based on different hominin niche-reconstructions, are evaluated. The benefits of these diets illustrate that it is time to incorporate this knowledge into dietary recommendations.
Collapse
|
12
|
Neves AGM, Serva M. Extremely rare interbreeding events can explain neanderthal DNA in living humans. PLoS One 2012; 7:e47076. [PMID: 23112810 PMCID: PMC3480414 DOI: 10.1371/journal.pone.0047076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 09/11/2012] [Indexed: 11/18/2022] Open
Abstract
Considering the recent experimental discovery of Green et al that present-day non-Africans have 1 to of their nuclear DNA of Neanderthal origin, we propose here a model which is able to quantify the genetic interbreeding between two subpopulations with equal fitness, living in the same geographic region. The model consists of a solvable system of deterministic ordinary differential equations containing as a stochastic ingredient a realization of the neutral Wright-Fisher process. By simulating the stochastic part of the model we are able to apply it to the interbreeding ofthe African ancestors of Eurasians and Middle Eastern Neanderthal subpopulations and estimate the only parameter of the model, which is the number of individuals per generation exchanged between subpopulations. Our results indicate that the amount of Neanderthal DNA in living non-Africans can be explained with maximum probability by the exchange of a single pair of individuals between the subpopulations at each 77 generations, but larger exchange frequencies are also allowed with sizeable probability. The results are compatible with a long coexistence time of 130,000 years, a total interbreeding population of order individuals, and with all living humans being descendants of Africans both for mitochondrial DNA and Y chromosome.
Collapse
Affiliation(s)
- Armando G M Neves
- Departamento de Matemática, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | | |
Collapse
|
13
|
Werneck FP, Gamble T, Colli GR, Rodrigues MT, Sites Jr JW. DEEP DIVERSIFICATION AND LONG-TERM PERSISTENCE IN THE SOUTH AMERICAN ‘DRY DIAGONAL’: INTEGRATING CONTINENT-WIDE PHYLOGEOGRAPHY AND DISTRIBUTION MODELING OF GECKOS. Evolution 2012; 66:3014-34. [DOI: 10.1111/j.1558-5646.2012.01682.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
14
|
Camargo A, Morando M, Avila LJ, Sites JW. SPECIES DELIMITATION WITH ABC AND OTHER COALESCENT-BASED METHODS: A TEST OF ACCURACY WITH SIMULATIONS AND AN EMPIRICAL EXAMPLE WITH LIZARDS OF THE LIOLAEMUS DARWINII COMPLEX (SQUAMATA: LIOLAEMIDAE). Evolution 2012; 66:2834-49. [PMID: 22946806 DOI: 10.1111/j.1558-5646.2012.01640.x] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Arley Camargo
- Department of Biology & Monte L Bean Museum, Brigham Young University, Provo, Utah 84602, USA.
| | | | | | | |
Collapse
|
15
|
Manolopoulou I, Legarreta L, Emerson BC, Brooks S, Tavaré S. A Bayesian approach to phylogeographic clustering. Interface Focus 2011; 1:909-21. [PMID: 23226589 DOI: 10.1098/rsfs.2011.0054] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 09/12/2011] [Indexed: 11/12/2022] Open
Abstract
Phylogeographic methods have attracted a lot of attention in recent years, stressing the need to provide a solid statistical framework for many existing methodologies so as to draw statistically reliable inferences. Here, we take a flexible fully Bayesian approach by reducing the problem to a clustering framework, whereby the population distribution can be explained by a set of migrations, forming geographically stable population clusters. These clusters are such that they are consistent with a fixed number of migrations on the corresponding (unknown) subdivided coalescent tree. Our methods rely upon a clustered population distribution, and allow for inclusion of various covariates (such as phenotype or climate information) at little additional computational cost. We illustrate our methods with an example from weevil mitochondrial DNA sequences from the Iberian peninsula.
Collapse
|
16
|
Abstract
Approximate Bayesian computation (ABC) have become an essential tool for the analysis of complex stochastic models. Grelaud et al. [(2009) Bayesian Anal 3:427-442] advocated the use of ABC for model choice in the specific case of Gibbs random fields, relying on an intermodel sufficiency property to show that the approximation was legitimate. We implemented ABC model choice in a wide range of phylogenetic models in the Do It Yourself-ABC (DIY-ABC) software [Cornuet et al. (2008) Bioinformatics 24:2713-2719]. We now present arguments as to why the theoretical arguments for ABC model choice are missing, because the algorithm involves an unknown loss of information induced by the use of insufficient summary statistics. The approximation error of the posterior probabilities of the models under comparison may thus be unrelated with the computational effort spent in running an ABC algorithm. We then conclude that additional empirical verifications of the performances of the ABC procedure as those available in DIY-ABC are necessary to conduct model choice.
Collapse
|
17
|
Bloomquist EW, Lemey P, Suchard MA. Three roads diverged? Routes to phylogeographic inference. Trends Ecol Evol 2010; 25:626-32. [PMID: 20863591 PMCID: PMC2956787 DOI: 10.1016/j.tree.2010.08.010] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 08/25/2010] [Accepted: 08/26/2010] [Indexed: 11/29/2022]
Abstract
Phylogeographic methods facilitate inference of the geographical history of genetic lineages. Recent examples explore human migration and the origins of viral pandemics. There is longstanding disagreement over the use and validity of certain phylogeographic inference methodologies. In this paper, we highlight three distinct frameworks for phylogeographic inference to give a taste of this disagreement. Each of the three approaches presents a different viewpoint on phylogeography, most fundamentally on how we view the relationship between the inferred history of a sample and the history of the population the sample is embedded in. Satisfactory resolution of this relationship between history of the tree and history of the population remains a challenge for all but the most trivial models of phylogeographic processes. Intriguingly, we believe that some recent methods that entirely avoid inference about the history of the population will eventually help to reach a resolution.
Collapse
Affiliation(s)
- Erik W. Bloomquist
- Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Leuven 3000, Belgium
| | - Marc A. Suchard
- Department of Biostatistics, UCLA School of Public Health, Los Angeles, CA 90095, USA
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA, Phone: (310) 825-7442, Fax: (310) 825-8685,
| |
Collapse
|
18
|
Reply to Berger et al.: Improving ABC. Proc Natl Acad Sci U S A 2010. [DOI: 10.1073/pnas.1009012107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
19
|
|
20
|
Csilléry K, Blum MG, Gaggiotti OE, François O. Invalid arguments against ABC: Reply to A.R. Templeton. Trends Ecol Evol 2010. [DOI: 10.1016/j.tree.2010.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
21
|
CAMARGO ARLEY, SINERVO BARRY, SITES JACKW. Lizards as model organisms for linking phylogeographic and speciation studies. Mol Ecol 2010; 19:3250-70. [DOI: 10.1111/j.1365-294x.2010.04722.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
22
|
Templeton AR. Correcting approximate Bayesian computation. Trends Ecol Evol 2010; 25:488-9; author reply 490-1. [PMID: 20619480 DOI: 10.1016/j.tree.2010.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 06/15/2010] [Accepted: 06/16/2010] [Indexed: 11/25/2022]
|
23
|
Bertorelle G, Benazzo A, Mona S. ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Mol Ecol 2010; 19:2609-25. [PMID: 20561199 DOI: 10.1111/j.1365-294x.2010.04690.x] [Citation(s) in RCA: 290] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The analysis of genetic variation to estimate demographic and historical parameters and to quantitatively compare alternative scenarios recently gained a powerful and flexible approach: the Approximate Bayesian Computation (ABC). The likelihood functions does not need to be theoretically specified, but posterior distributions can be approximated by simulation even assuming very complex population models including both natural and human-induced processes. Prior information can be easily incorporated and the quality of the results can be analysed with rather limited additional effort. ABC is not a statistical analysis per se, but rather a statistical framework and any specific application is a sort of hybrid between a simulation and a data-analysis study. Complete software packages performing the necessary steps under a set of models and for specific genetic markers are already available, but the flexibility of the method is better exploited combining different programs. Many questions relevant in ecology can be addressed using ABC, but adequate amount of time should be dedicated to decide among alternative options and to evaluate the results. In this paper we will describe and critically comment on the different steps of an ABC analysis, analyse some of the published applications of ABC and provide user guidelines.
Collapse
Affiliation(s)
- G Bertorelle
- Department of Biology and Evolution, University of Ferrara, Via Borsari 46, 44100 Ferrara, Italy.
| | | | | |
Collapse
|