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Fonseca EM, Carstens BC. Artificial intelligence enables unified analysis of historical and landscape influences on genetic diversity. Mol Phylogenet Evol 2024; 198:108116. [PMID: 38871263 DOI: 10.1016/j.ympev.2024.108116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 04/04/2024] [Accepted: 06/04/2024] [Indexed: 06/15/2024]
Abstract
While genetic variation in any species is potentially shaped by a range of processes, phylogeography and landscape genetics are largely concerned with inferring how environmental conditions and landscape features impact neutral intraspecific diversity. However, even as both disciplines have come to utilize SNP data over the last decades, analytical approaches have remained for the most part focused on either broad-scale inferences of historical processes (phylogeography) or on more localized inferences about environmental and/or landscape features (landscape genetics). Here we demonstrate that an artificial intelligence model-based analytical framework can consider both deeper historical factors and landscape-level processes in an integrated analysis. We implement this framework using data collected from two Brazilian anurans, the Brazilian sibilator frog (Leptodactylus troglodytes) and granular toad (Rhinella granulosa). Our results indicate that historical demographic processes shape most the genetic variation in the sibulator frog, while landscape processes primarily influence variation in the granular toad. The machine learning framework used here allows both historical and landscape processes to be considered equally, rather than requiring researchers to make an a priori decision about which factors are important.
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Affiliation(s)
- Emanuel M Fonseca
- Museum of Biological Diversity & Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 1315 Kinnear Rd., Columbus OH 43212, USA
| | - Bryan C Carstens
- Museum of Biological Diversity & Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 1315 Kinnear Rd., Columbus OH 43212, USA.
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Sethuraman A, Nunziata SO, Jones A, Obrycki J, Weisrock DW. Go west: Population genomics reveals unexpected population fluctuations and little gene flow in Western hemisphere populations of the predatory lady beetle, Hippodamia convergens. Evol Appl 2024; 17:e13631. [PMID: 38283604 PMCID: PMC10810170 DOI: 10.1111/eva.13631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 11/22/2023] [Accepted: 11/30/2023] [Indexed: 01/30/2024] Open
Abstract
Hippodamia convergens-the convergent lady beetle, has been used extensively in augmentative biological control of aphids, thrips, and whiteflies across its native range in North America, and was introduced into South America in the 1950s. Overwintering H. convergens populations from its native western range in the United States are commercially collected and released across its current range in the eastern USA, with little knowledge of the effectiveness of its augmentative biological control. Here we use a novel ddRADseq-based SNP/haplotype discovery approach to estimate its range-wide population diversity, differentiation, and recent evolutionary history. Our results indicate (1) significant population differentiation among eastern USA, western USA, and South American populations of H. convergens, with (2) little to no detectable recent admixture between them, despite repeated population augmentation, and (3) continued recent population size expansion across its range. These results contradict previous findings using microsatellite markers. In light of these new findings, the implications for the effectiveness of augmentative biological control using H. convergens are discussed. Additionally, because quantifying the non-target effects of augmentative biological control is a difficult problem in migratory beetles, our results could serve as a cornerstone in improving and predicting the efficacy of future releases of H. convergens across its range.
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Affiliation(s)
- Arun Sethuraman
- Department of BiologySan Diego State UniversitySan DiegoCaliforniaUSA
| | - Schyler O. Nunziata
- Department of BiologyUniversity of KentuckyLexingtonKentuckyUSA
- Present address:
United States Department of AgricultureWashingtonDCUSA
| | - Angela Jones
- Department of BiologyUniversity of KentuckyLexingtonKentuckyUSA
- Present address:
Duke UniversityDurhamNorth CarolinaUSA
| | - John Obrycki
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
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3
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Anyasodor AE, Nwose EU, Bwititi PT, Richards RS. Cost-effectiveness of community diabetes screening: Application of Akaike information criterion in rural communities of Nigeria. Front Public Health 2022; 10:932631. [PMID: 35958851 PMCID: PMC9357922 DOI: 10.3389/fpubh.2022.932631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Background The prevalence of diabetes mellitus (DM) is increasing globally, and this requires several approaches to screening. There are reports of alternative indices for prediction of DM, besides fasting blood glucose (FBG) level. This study, investigated the ability of combination of biochemical and anthropometric parameters and orodental disease indicators (ODIs) to generate models for DM prediction, using Akaike information criterion (AIC) to substantiate health economics of diabetes screening. Methods Four hundred and thirty-three subjects were enrolled in the study in Ndokwa communities, Delta State, Nigeria, and their glycaemic status was determined, using the CardioChek analyser® and previous data from the Prediabetes and Cardiovascular Complications Study were also used. The cost of screening for diabetes (NGN 300 = $0.72) in a not-for-profit organization/hospital was used as basis to calculate the health economics of number of individuals with DM in 1,000 participants. Data on the subjects' anthropometric, biochemical and ODI parameters were used to generate different models, using R statistical software (version 4.0.0). The different models were evaluated for their AIC values. Lowest AIC was considered as best model. Microsoft Excel software (version 2020) was used in preliminary analysis. Result The cost of identifying <2 new subjects with hyperglycemia, in 1,000 people was ≥NGN 300,000 ($ 716). A total of 4,125 models were generated. AIC modeling indicates FBG test as the best model (AIC = 4), and the least being combination of random blood sugar + waist circumference + hip circumference (AIC ≈ 34). Models containing ODI parameters had AIC values >34, hence considered as not recommendable. Conclusion The cost of general screening for diabetes in rural communities may appear high and burdensome in terms of health economics. However, the use of prediction models involving AIC is of value in terms of cost-benefit and cost-effectiveness to the healthcare consumers, which favors health economics.
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Affiliation(s)
- Anayochukwu Edward Anyasodor
- School of Dentistry and Medical Sciences, Charles Sturt University, Orange, NSW, Australia
- *Correspondence: Anayochukwu Edward Anyasodor
| | - Ezekiel Uba Nwose
- School of Dentistry and Medical Sciences, Charles Sturt University, Orange, NSW, Australia
- Department of Public and Community Health, Novena University, Kwale, Nigeria
| | | | - Ross Stuart Richards
- School of Dentistry and Medical Sciences, Charles Sturt University, Orange, NSW, Australia
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Carstens BC, Moshier SP. Giant tree frogs exemplify the promise of integrating multiple types of data in phylogeographic investigations. Mol Ecol 2022; 31:3971-3974. [PMID: 35779007 DOI: 10.1111/mec.16593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/13/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022]
Abstract
Hugall et al. (2022) is one of the seminal publications from the single locus era of phylogeographic research. These authors were among the first to argue that genetic data are ideally suited to test hypotheses that are ultimately derived from other sources of information. While the testing of predictions from the fossil record has long been important to molecular systematics (e.g., Donoghue et al., 1989), phylogeographic investigations into the more recent evolutionary past lack a fossil record in most focal taxa. In lieu of fossils, which were not available for the small snails that served as the focal taxon, Hugall et al. (2002) applied the (then) new technique of environmental modelling to identify regions within the species range with habitat that was predicted to be stable throughout the Holocene. They then present data that suggests that these regions correspond to the areas with high genetic diversity. Apart from the inferences about snail evolutionary history, the core argument of Hugall et al. (2002) is that consilience (i.e., agreement between inferences drawn from different sources of data) is an important goal for phylogeographic investigation. Consilience in the inferences drawn from independent types of data has a multiplicative effect; when present the researcher is likely to have more confidence in their inference than would be possible to have in an inference from any one source of data. The manuscript by Jaynes et al. (2022) is a splendid illustration of this principle.
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Affiliation(s)
- Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - Shelby P Moshier
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
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Nottingham S, Pelletier TA. The impact of climate change on western Plethodon salamanders' distribution. Ecol Evol 2021; 11:9370-9384. [PMID: 34306628 PMCID: PMC8293714 DOI: 10.1002/ece3.7735] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/07/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023] Open
Abstract
AIM Given that salamanders have experienced large shifts in their distributions over time, we determined how each species of Plethodon in the Pacific Northwest would respond to climate change. We incorporated several greenhouse scenarios both on a species-by-species basis, and also using phylogenetic groups, with the aim to determine the best course of action in managing land area to conserve diversity in this group. LOCATION Pacific Northwest of the United States (northern CA, OR, WA, ID, and MT). MAJOR TAXA STUDIED Western Plethodon salamanders. METHODS Species distribution models were estimated using MaxEnt for the current time period and for several future climate scenarios using bioclimatic data layers. We used several methods to quantify the change in habitat suitability over time from the models. We explored aspects of the climate layers to determine whether we can expect a concerted response to climate change due to similarity in ecological niche or independent responses that could be harder to manage. RESULTS The distribution of western Plethodon salamander species is strongly influenced by precipitation and less so by temperature. Species responses to climate change resulted in both increases and decreases in predicted suitable habitat, though most species ranges do not contract, especially when taken as a phylogenetic group. MAIN CONCLUSIONS While some established habitats may become more or less climatically suitable, the overall distribution of species in this group is unlikely to be significantly affected. Clades of Plethodon species are unlikely to be in danger of extirpation despite the possibility that individual species may be threatened as a result of limited distributions. Grouping species into lineages with similar geographic ranges can be a viable method of determining conservation needs. More biotic and dispersal information is needed to determine the true impact that changes in climate will have on the distribution of Plethodon species.
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Fonseca EM, Colli GR, Werneck FP, Carstens BC. Phylogeographic model selection using convolutional neural networks. Mol Ecol Resour 2021; 21:2661-2675. [PMID: 33973350 DOI: 10.1111/1755-0998.13427] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 04/02/2021] [Accepted: 04/28/2021] [Indexed: 11/26/2022]
Abstract
The discipline of phylogeography has evolved rapidly in terms of the analytical toolkit used to analyse large genomic data sets. Despite substantial advances, analytical tools that could potentially address the challenges posed by increased model complexity have not been fully explored. For example, deep learning techniques are underutilized for phylogeographic model selection. In non-model organisms, the lack of information about their ecology and evolution can lead to uncertainty about which demographic models are appropriate. Here, we assess the utility of convolutional neural networks (CNNs) for assessing demographic models in South American lizards in the genus Norops. Three demographic scenarios (constant, expansion, and bottleneck) were considered for each of four inferred population-level lineages, and we found that the overall model accuracy was higher than 98% for all lineages. We then evaluated a set of 26 models that accounted for evolutionary relationships, gene flow, and changes in effective population size among the four lineages, identifying a single model with an estimated overall accuracy of 87% when using CNNs. The inferred demography of the lizard system suggests that gene flow between non-sister populations and changes in effective population sizes through time, probably in response to Pleistocene climatic oscillations, have shaped genetic diversity in this system. Approximate Bayesian computation (ABC) was applied to provide a comparison to the performance of CNNs. ABC was unable to identify a single model among the larger set of 26 models in the subsequent analysis. Our results demonstrate that CNNs can be easily and usefully incorporated into the phylogeographer's toolkit.
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Affiliation(s)
- Emanuel M Fonseca
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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da Silva R, Pedraza-Marrón CDR, Sampaio I, Betancur-R R, Gomes G, Schneider H. New insights about species delimitation in red snappers (Lutjanus purpureus and L. campechanus) using multilocus data. Mol Phylogenet Evol 2020; 147:106780. [PMID: 32135307 DOI: 10.1016/j.ympev.2020.106780] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 01/29/2020] [Accepted: 02/26/2020] [Indexed: 01/08/2023]
Abstract
Lutjanus campechanus and Lutjanus purpureus are two commercially important lutjanid fishes (snappers) with non-sympatric distribution throughout Western Atlantic. Even though both taxa have traditionally been regarded as valid species, their taxonomic status remains under debate. In the present study, we used phylogeographic approaches and molecular methods of species delimitation to elucidate the taxonomic issues between both species, based on 1478 base pairs from four genomic regions. We found haplotypes shared between the two species, particularly in relation to nuclear DNA (nuDNA) sequences. The molecular delimitation of species supported the discrimination of L. purpureus and L. campechanus as distinct evolutionary units. Nonetheless, a unidirectional gene flow was found from L. campechanus towards L. purpureus. Therefore, it seems plausible to infer that L. campechanus and L. purpureus are two evolutionary units in which the apparent sharing of haplotypes should be driven by introgression.
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Affiliation(s)
- Raimundo da Silva
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | | | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | | | - Grazielle Gomes
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil; Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil.
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Bessa-Silva A, Vallinoto M, Sampaio I, Flores-Villela OA, Smith EN, Sequeira F. The roles of vicariance and dispersal in the differentiation of two species of the Rhinella marina species complex. Mol Phylogenet Evol 2019; 145:106723. [PMID: 31891757 DOI: 10.1016/j.ympev.2019.106723] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 12/23/2019] [Accepted: 12/23/2019] [Indexed: 11/19/2022]
Abstract
The high levels of Neotropical biodiversity are commonly associated with the intense Neogene-Quaternary geological events and climate dynamics. Here, we investigate the evolutionary history of two species of Neotropical closely related amphibians (R. horribilis and R. marina). We combine published data with new mitochondrial DNA sequences and multiple nuclear markers, including 12 microsatellites. The phylogenetic analyses showed support for grouping the samples in two main clades; R. horribilis (Central America and Mexico) and R. marina (South America east of the Andes). However, the phylogenetic inferences also show an evident mito-nuclear discordance. We use Approximate Bayesian Computation (ABC) to test the role of different events in the diversification between the two groups recovered. We found that both species were affected primarily by a recent Pleistocene divergence, which was similar to the divergence estimate revealed by the Isolation-with-Migration model, under persistent bidirectional gene flow through time. We provide the first evidence that R. horribilis is differentiated from the South American R. marina at the nuclear level supporting the taxonomic status of R. horribilis, which has been controversial for more than a century.
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Affiliation(s)
- Adam Bessa-Silva
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, 68 600-000 Pará, Brazil; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Marcelo Vallinoto
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, 68 600-000 Pará, Brazil; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.
| | - Iracilda Sampaio
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, 68 600-000 Pará, Brazil
| | - Oscar A Flores-Villela
- Museo de Zoología, Department of Evolutionary Biology, Facultad de Ciencias, Universidad Nacional Autónoma de México, External Circuit of Ciudad Universitaria, Mexico City 04510, Mexico
| | - Eric N Smith
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA; The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | - Fernando Sequeira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
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Myers EA, Xue AT, Gehara M, Cox CL, Davis Rabosky AR, Lemos‐Espinal J, Martínez‐Gómez JE, Burbrink FT. Environmental heterogeneity and not vicariant biogeographic barriers generate community‐wide population structure in desert‐adapted snakes. Mol Ecol 2019; 28:4535-4548. [DOI: 10.1111/mec.15182] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/23/2019] [Accepted: 07/08/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Edward A. Myers
- Department of Vertebrate Zoology Smithsonian Institution National Museum of Natural History Washington DC USA
- Department of Herpetology The American Museum of Natural History New York NY USA
| | | | - Marcelo Gehara
- Department of Herpetology The American Museum of Natural History New York NY USA
| | - Christian L. Cox
- Department of Biology Georgia Southern University Statesboro GA USA
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
| | - Julio Lemos‐Espinal
- Laboratorio de Ecología, UBIPRO, FES Iztacala Universidad Nacional Autónoma de México Tlalnepantla Mexico
| | | | - Frank T. Burbrink
- Department of Herpetology The American Museum of Natural History New York NY USA
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Ruffley M, Smith ML, Espíndola A, Carstens BC, Sullivan J, Tank DC. Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections. Mol Ecol 2018; 27:1012-1024. [PMID: 29334417 PMCID: PMC5878120 DOI: 10.1111/mec.14491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 01/25/2023]
Abstract
Model selection approaches in phylogeography have allowed researchers to evaluate the support for competing demographic histories, which provides a mode of inference and a measure of uncertainty in understanding climatic and spatial influences on intraspecific diversity. Here, to rank all models in the comparison set and determine what proportion of the total support the top-ranked model garners, we conduct model selection using two analytical approaches-allele frequency-based, implemented in fastsimcoal2, and gene tree-based, implemented in phrapl. We then expand this model selection framework by including an assessment of absolute fit of the models to the data. For this, we utilize DNA isolated from existing natural history collections that span the distribution of red alder (Alnus rubra) in the Pacific Northwest of North America to generate genomic data for the evaluation of 13 demographic scenarios. The quality of DNA recovered from herbarium specimen leaf tissue was assessed for its utility and effectiveness in demographic model selection, specifically in the two approaches mentioned. We present strong support for the use of herbarium tissue in the generation of genomic DNA, albeit with the inclusion of additional quality control checks prior to library preparation and analyses with multiple approaches that incorporate various data. Analyses with allele frequency spectra and gene trees predominantly support A. rubra having experienced an ancient vicariance event with intermittent and frequent gene flow between the disjunct populations. Additionally, the data consistently fit the most frequently selected model, corroborating the model selection techniques. Finally, these results suggest that the A. rubra disjunct populations do not represent separate species.
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Affiliation(s)
- Megan Ruffley
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, Moscow, ID, USA
- Stillinger Herbarium, University of Idaho, Moscow, ID, USA
| | - Megan L Smith
- Department of Evolution, Ecology, & Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Anahí Espíndola
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, Moscow, ID, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, & Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, Moscow, ID, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, Moscow, ID, USA
- Stillinger Herbarium, University of Idaho, Moscow, ID, USA
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Oswald JA, Overcast I, Mauck WM, Andersen MJ, Smith BT. Isolation with asymmetric gene flow during the nonsynchronous divergence of dry forest birds. Mol Ecol 2017; 26:1386-1400. [PMID: 28100029 DOI: 10.1111/mec.14013] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/30/2016] [Accepted: 12/29/2016] [Indexed: 01/17/2023]
Abstract
Dry forest bird communities in South America are often fragmented by intervening mountains and rainforests, generating high local endemism. The historical assembly of dry forest communities likely results from dynamic processes linked to numerous population histories among codistributed species. Nevertheless, species may diversify in the same way through time if landscape and environmental features, or species ecologies, similarly structure populations. Here we tested whether six co-distributed taxon pairs that occur in the dry forests of the Tumbes and Marañón Valley of northwestern South America show concordant patterns and modes of diversification. We employed a genome reduction technique, double-digest restriction site-associated DNA sequencing, and obtained 4407-7186 genomewide SNPs. We estimated demographic history in each taxon pair and inferred that all pairs had the same best-fit demographic model: isolation with asymmetric gene flow from the Tumbes into the Marañón Valley, suggesting a common diversification mode. Overall, we also observed congruence in effective population size (Ne ) patterns where ancestral Ne were 2.9-11.0× larger than present-day Marañón Valley populations and 0.3-2.0× larger than Tumbesian populations. Present-day Marañón Valley Ne was smaller than Tumbes. In contrast, we found simultaneous population isolation due to a single event to be unlikely as taxon pairs diverged over an extended period of time (0.1-2.9 Ma) with multiple nonoverlapping divergence periods. Our results show that even when populations of codistributed species asynchronously diverge, the mode of their differentiation can remain conserved over millions of years. Divergence by allopatric isolation due to barrier formation does not explain the mode of differentiation between these two bird assemblages; rather, migration of individuals occurred before and after geographic isolation.
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Affiliation(s)
- Jessica A Oswald
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611-7800, USA.,Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA, 70803, USA
| | - Isaac Overcast
- Subprogram in Ecology, Evolution and Behavior, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - William M Mauck
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Michael J Andersen
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.,Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
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Riginos C, Crandall ED, Liggins L, Bongaerts P, Treml EA. Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies. Curr Zool 2016; 62:581-601. [PMID: 29491947 PMCID: PMC5804261 DOI: 10.1093/cz/zow067] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 05/25/2016] [Indexed: 11/21/2022] Open
Abstract
Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region (e.g., geographical distance, average sea surface temperature, average salinity). We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water (experienced by most marine taxa at some point in their life cycle), require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for landscape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations.
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Affiliation(s)
- Cynthia Riginos
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Eric D. Crandall
- Division of Science and Environmental Policy, California State University, Seaside, CA 93955, USA
| | - Libby Liggins
- Institute of Natural and Mathematical Sciences, Massey University, Auckland 0745, New Zealand
| | - Pim Bongaerts
- Global Change Institute, The University of Queensland, QLD 4072, St Lucia, Australia
| | - Eric A. Treml
- School of BioSciences, The University of Melbourne, VIC, 3010, Australia
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Demos TC, Achmadi AS, Giarla TC, Handika H, Maharadatunkamsi, Rowe KC, Esselstyn JA. Local endemism and within-island diversification of shrews illustrate the importance of speciation in building Sundaland mammal diversity. Mol Ecol 2016; 25:5158-5173. [PMID: 27552382 DOI: 10.1111/mec.13820] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 08/09/2016] [Accepted: 08/16/2016] [Indexed: 01/15/2023]
Abstract
Island systems are important models for evolutionary biology because they provide convenient, discrete biogeographic units of study. Continental islands with a history of intermittent dry land connections confound the discrete definitions of islands and have led zoologists to predict (1) little differentiation of terrestrial organisms among continental shelf islands and (2) extinction, rather than speciation, to be the main cause of differences in community composition among islands. However, few continental island systems have been subjected to well-sampled phylogeographic studies, leaving these biogeographic assumptions of connectivity largely untested. We analyzed nine unlinked loci from shrews of the genus Crocidura from seven mountains and two lowland localities on the Sundaic continental shelf islands of Sumatra and Java. Coalescent species delimitation strongly supported all currently recognized Crocidura species from Sumatra (six species) and Java (five species), as well as one undescribed species endemic to each island. We find that nearly all species of Crocidura in the region are endemic to a single island and several of these have their closest relative(s) on the same island. Intra-island genetic divergence among allopatric, conspecific populations is often substantial, perhaps indicating species-level diversity remains underestimated. One recent (Pleistocene) speciation event generated two morphologically distinct, syntopic species on Java, further highlighting the prevalence of within-island diversification. Our results suggest that both between- and within-island speciation processes generated local endemism in Sundaland, supplementing the traditional view that the region's fauna is relictual and primarily governed by extinction. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Terrence C Demos
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.,Science and Education, Field Museum of Natural History, Chicago, IL, 60605, USA
| | - Anang S Achmadi
- Museum Zoologicum Bogoriense, Research Center for Biology-LIPI, Cibinong, Bogor, 16911, Indonesia
| | - Thomas C Giarla
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.,Department of Biology, Siena College, Loudonville, NY, 12211, USA
| | - Heru Handika
- Sciences Department, Museum Victoria, Melbourne, 3001, VIC, Australia.,School of Biosciences, The University of Melbourne, Melbourne, 3001, VIC, Australia
| | - Maharadatunkamsi
- Museum Zoologicum Bogoriense, Research Center for Biology-LIPI, Cibinong, Bogor, 16911, Indonesia
| | - Kevin C Rowe
- Sciences Department, Museum Victoria, Melbourne, 3001, VIC, Australia.,School of Biosciences, The University of Melbourne, Melbourne, 3001, VIC, Australia
| | - Jacob A Esselstyn
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
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14
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Thomé MTC, Carstens BC. Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs. Proc Natl Acad Sci U S A 2016; 113:8010-7. [PMID: 27432969 PMCID: PMC4961127 DOI: 10.1073/pnas.1601064113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Phylogeographic research investigates biodiversity at the interface between populations and species, in a temporal and geographic context. Phylogeography has benefited from analytical approaches that allow empiricists to estimate parameters of interest from the genetic data (e.g., θ = 4Neμ, population divergence, gene flow), and the widespread availability of genomic data allow such parameters to be estimated with greater precision. However, the actual inferences made by phylogeographers remain dependent on qualitative interpretations derived from these parameters' values and as such may be subject to overinterpretation and confirmation bias. Here we argue in favor of using an objective approach to phylogeographic inference that proceeds by calculating the probability of multiple demographic models given the data and the subsequent ranking of these models using information theory. We illustrate this approach by investigating the diversification of two sister species of four-eyed frogs of northeastern Brazil using single nucleotide polymorphisms obtained via restriction-associated digest sequencing. We estimate the composite likelihood of the observed data given nine demographic models and then rank these models using Akaike information criterion. We demonstrate that estimating parameters under a model that is a poor fit to the data is likely to produce values that lead to spurious phylogeographic inferences. Our results strongly imply that identifying which parameters to estimate from a given system is a key step in the process of phylogeographic inference and is at least as important as being able to generate precise estimates of these parameters. They also illustrate that the incorporation of model uncertainty should be a component of phylogeographic hypothesis tests.
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Affiliation(s)
- Maria Tereza C Thomé
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Campus Rio Claro, 13506900 Rio Claro, SP, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
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15
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Perez MF, Bonatelli IAS, Moraes EM, Carstens BC. Model-based analysis supports interglacial refugia over long-dispersal events in the diversification of two South American cactus species. Heredity (Edinb) 2016; 116:550-7. [PMID: 27071846 DOI: 10.1038/hdy.2016.17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 01/26/2016] [Accepted: 02/02/2016] [Indexed: 02/06/2023] Open
Abstract
Pilosocereus machrisii and P. aurisetus are cactus species within the P. aurisetus complex, a group of eight cacti that are restricted to rocky habitats within the Neotropical savannas of eastern South America. Previous studies have suggested that diversification within this complex was driven by distributional fragmentation, isolation leading to allopatric differentiation, and secondary contact among divergent lineages. These events have been associated with Quaternary climatic cycles, leading to the hypothesis that the xerophytic vegetation patches which presently harbor these populations operate as refugia during the current interglacial. However, owing to limitations of the standard phylogeographic approaches used in these studies, this hypothesis was not explicitly tested. Here we use Approximate Bayesian Computation to refine the previous inferences and test the role of different events in the diversification of two species within P. aurisetus group. We used molecular data from chloroplast DNA and simple sequence repeats loci of P. machrisii and P. aurisetus, the two species with broadest distribution in the complex, in order to test if the diversification in each species was driven mostly by vicariance or by long-dispersal events. We found that both species were affected primarily by vicariance, with a refuge model as the most likely scenario for P. aurisetus and a soft vicariance scenario most probable for P. machrisii. These results emphasize the importance of distributional fragmentation in these species, and add support to the hypothesis of long-term isolation in interglacial refugia previously proposed for the P. aurisetus species complex diversification.
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Affiliation(s)
- M F Perez
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, São Paulo, Brazil
| | - I A S Bonatelli
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, São Paulo, Brazil
| | - E M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, São Paulo, Brazil
| | - B C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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16
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Kerhoulas NJ, Gunderson AM, Olson LE. Complex history of isolation and gene flow in hoary, Olympic, and endangered Vancouver Island marmots. J Mammal 2015. [DOI: 10.1093/jmammal/gyv089] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Climate change resulting in a reduction of alpine habitat is believed to pose a considerable risk to alpine-dependent species, including many marmots. Hoary marmots (Marmota caligata) range throughout much of the mountainous Pacific Northwest (PNW) and Rocky Mountains while the closely related Olympic and Vancouver Island marmots (M. olympus and M. vancouverensis, respectively) are restricted to small isolated regions of the PNW. The endemic Vancouver Island marmot is currently classified as Critically Endangered and the Olympic marmot has recently experienced dramatic population declines. Previous phylogenetic studies of PNW marmot species have had limited power as they focused on resolving interspecific relationships, implicitly assumed an absence of gene flow among currently recognized species, included relatively few individuals, and relied heavily or entirely on mitochondrial DNA. We sequenced 2 mitochondrial and 4 nuclear markers from 167 hoary, 4 Vancouver Island, and 5 Olympic marmots in order to investigate phylogenetic relationships and historic gene flow among these species. We recovered 2 monophyletic (and predominantly allopatric) mitochondrial clades of hoary marmots that are not sister groups. Instead, Vancouver Island marmots formed a monophyletic mitochondrial sister clade to 1 of the hoary marmot clades. Nuclear loci did not recover the 2 mitochondrial clades of hoary marmots and suggest that Vancouver Island marmots may have experienced mitochondrial introgression from coastal mainland hoary marmots. Additionally, our nuclear results suggest possible gene flow between hoary and Olympic marmots despite different chromosomal formulas. Rather than resolving what has previously been considered a straightforward 3-taxon phylogenetic question, our findings suggest a complicated history of rapid divergence of the 3 species followed by intermittent and possibly ongoing gene flow between hoary marmots and both Olympic and Vancouver Island marmots. These results therefore have significant implications for the conservation of the latter 2 species, both of which are conservation concerns.
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17
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Leydet KP, Hellberg ME. The invasive coral Oculina patagonica has not been recently introduced to the Mediterranean from the western Atlantic. BMC Evol Biol 2015; 15:79. [PMID: 25940207 PMCID: PMC4418043 DOI: 10.1186/s12862-015-0356-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 04/21/2015] [Indexed: 11/23/2022] Open
Abstract
Background Effective policies, management, and scientific research programs depend on the correct identification of invasive species as being either native or introduced. However, many species continue to be misidentified. Oculina patagonica, first recorded in the Mediterranean Sea in 1966, is believed to have been introduced in anthropogenic times and expanding in a west to east direction. However, its present identification and status as a recently introduced species remain to be explored. In this study, we used multi-locus genetic data to test whether O. patagonica in the Mediterranean has been recently introduced from the western North Atlantic. Results We found no genetic or historical demographic evidence to support a recent introduction of O. patagonica from the western North Atlantic or an expansion across the Mediterranean. Instead, Mediterranean and Atlantic populations are genetically distinct and appear to have begun diverging about 5 Mya. We also found evidence of a fossil record of Oculina spp. existing in the eastern North Atlantic millions of years before the present. Conclusions Our results suggest that Mediterranean populations of O. patagonica have long been isolated from the western Atlantic, either in undetectable numbers or overlooked and undersampled sites and habitats, and have only recently been expanding to invasive levels as a result of environmental changes. Accurate identification of species’ invasive statuses will enable more effective research programs aimed at better understanding the mechanisms promoting the invasive nature of species, which can then lead to the implementation of efficient management plans. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0356-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karine Posbic Leydet
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
| | - Michael E Hellberg
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
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18
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Rittmeyer EN, Austin CC. Combined next-generation sequencing and morphology reveal fine-scale speciation in Crocodile Skinks (Squamata: Scincidae: Tribolonotus). Mol Ecol 2015; 24:466-83. [PMID: 25470077 DOI: 10.1111/mec.13030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 11/17/2014] [Accepted: 11/28/2014] [Indexed: 02/03/2023]
Abstract
Next-generation sequencing has vast potential to revolutionize the fields of phylogenetics and population genetics through its ability to collect genomic scale data sets of thousands of orthologous loci. Despite this potential, other types of data (e.g. morphology, ecology) remain important, particularly for studies endeavouring to delimit species. Here, we integrate next-generation sequencing with morphology to examine divergence between populations of Tribolonotus pseudoponceleti on the islands of Buka and Bougainville in the Solomon Archipelago. We used the Ion Torrent PGM to collect over 648 Mbp of sequence data for 12 samples, representing 1526 loci recovered from all samples, and 3342 were recovered from at least six samples. Genetic structure analyses strongly support the distinctiveness of these two populations, and Bayes factor delimitations decisively select speciation between Buka and Bougainville. Principal components and discriminant function analyses reveal concordant morphological divergence. Finally, demographic analyses via diffusion approximation and approximate Bayesian computation prefer a complex model of mid-Pleistocene divergence with migration, and a later decrease or cessation of migration and population size shift, suggesting a scenario in which migration was enabled by Pleistocene merging of these two islands, and limited when isolated by higher sea levels. Further analysis of four Sanger sequenced loci in IMa2 had limited power to distinguish among models including and excluding migration, but resulted in similar population size and divergence time estimates, although with much broader confidence intervals. This study represents a framework for how next-generation sequencing and morphological data can be combined and leveraged towards validating putative species and testing demographic scenarios for speciation.
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Affiliation(s)
- Eric N Rittmeyer
- Department of Biological Sciences, Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA, 70803, USA
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19
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Pelletier TA, Crisafulli C, Wagner S, Zellmer AJ, Carstens BC. Historical Species Distribution Models Predict Species Limits in WesternPlethodonSalamanders. Syst Biol 2014; 64:909-25. [DOI: 10.1093/sysbio/syu090] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/10/2014] [Indexed: 11/12/2022] Open
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20
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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. THE NEW PHYTOLOGIST 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] [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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21
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Chavez AS, Kenagy GJ. Clinal colour variation within a panmictic population of tree squirrels,Tamiasciurus douglasii(Rodentia: Sciuridae), across an ecological gradient. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andreas S. Chavez
- Burke Museum and Department of Biology; University of Washington; Seattle WA 98195 USA
| | - G. J. Kenagy
- Burke Museum and Department of Biology; University of Washington; Seattle WA 98195 USA
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22
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Leaché AD, Harris RB, Maliska ME, Linkem CW. Comparative species divergence across eight triplets of spiny lizards (Sceloporus) using genomic sequence data. Genome Biol Evol 2014; 5:2410-9. [PMID: 24259316 PMCID: PMC3879974 DOI: 10.1093/gbe/evt186] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Species divergence is typically thought to occur in the absence of gene flow, but many empirical studies are discovering that gene flow may be more pervasive during species formation. Although many examples of divergence with gene flow have been identified, few clades have been investigated in a comparative manner, and fewer have been studied using genome-wide sequence data. We contrast species divergence genetic histories across eight triplets of North American Sceloporus lizards using a maximum likelihood implementation of the isolation–migration (IM) model. Gene flow at the time of species divergence is modeled indirectly as variation in species divergence time across the genome or explicitly using a migration rate parameter. Likelihood ratio tests (LRTs) are used to test the null model of no gene flow at speciation against these two alternative gene flow models. We also use the Akaike information criterion to rank the models. Hundreds of loci are needed for the LRTs to have statistical power, and we use genome sequencing of reduced representation libraries to obtain DNA sequence alignments at many loci (between 340 and 3,478; mean = 1,678) for each triplet. We find that current species distributions are a poor predictor of whether a species pair diverged with gene flow. Interrogating the genome using the triplet method expedites the comparative study of species divergence history and the estimation of genetic parameters associated with speciation.
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23
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Hickerson MJ. All models are wrong. Mol Ecol 2014; 23:2887-9. [DOI: 10.1111/mec.12794] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 01/25/2023]
Affiliation(s)
- Michael J. Hickerson
- Department of Biology; City College of New York; 160 Convent Ave.; MR 526, New York, NY 10031 USA
- The Graduate Center of the City University of New York; Subprogram in Ecology, Evolution and Behavior; 365 5th Ave, New York, NY 10016 USA
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24
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Rohwer S, Harris RB, Walsh HE. Rape and the prevalence of hybrids in broadly sympatric species: a case study using albatrosses. PeerJ 2014; 2:e409. [PMID: 24949232 PMCID: PMC4060039 DOI: 10.7717/peerj.409] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 05/12/2014] [Indexed: 11/20/2022] Open
Abstract
Conspecific rape often increases male reproductive success. However, the haste and aggression of forced copulations suggests that males may sometimes rape heterospecific females, thus making rape a likely, but undocumented, source of hybrids between broadly sympatric species. We present evidence that heterospecific rape may be the source of hybrids between Black-footed and Laysan Albatrosses (Phoebastria nigripes, and P. immutabilis, respectively). Extensive field studies have shown that paired (but not unpaired) males of both of these albatross species use rape as a supplemental reproductive strategy. Between species differences in size, timing of laying, and aggressiveness suggest that Black-footed Albatrosses should be more successful than Laysan Albatrosses in heteropspecific rape attempts, and male Black-footed Albatrosses have been observed attempting to force copulations on female Laysan Albatrosses. Nuclear markers showed that the six hybrids we studied were F1s and mitochondrial markers showed that male Black-footed Albatrosses sired all six hybrids. Long-term gene exchange between these species has been from Black-footed Albatrosses into Laysan Albatrosses, suggesting that the siring asymmetry found in our hybrids has long persisted. If hybrids are sired in heterospecific rapes, they presumably would be raised and sexually imprinted on Laysan Albatrosses, and two unmated hybrids in a previous study courted only Laysan Albatrosses.
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Affiliation(s)
- Sievert Rohwer
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington , Seattle, WA , USA
| | - Rebecca B Harris
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington , Seattle, WA , USA
| | - Hollie E Walsh
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington , Seattle, WA , USA
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25
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Gottscho AD, Marks SB, Jennings WB. Speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a species of conservation concern. Ecol Evol 2014; 4:2546-62. [PMID: 25360285 PMCID: PMC4203297 DOI: 10.1002/ece3.1111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/20/2014] [Accepted: 04/23/2014] [Indexed: 11/16/2022] Open
Abstract
The North American deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard (Uma scoparia), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA sequences for 14 nuclear loci, and found that U. scoparia has low genetic diversity relative to the U. notata species complex, comparable to that of chimpanzees and southern elephant seals. Analyses of genotypes using Bayesian clustering algorithms did not identify discrete populations within U. scoparia. Using isolation-with-migration (IM) models and a novel coalescent-based hypothesis testing approach, we estimated that U. scoparia diverged from U. notata in the Pleistocene epoch. The likelihood ratio test and the Akaike Information Criterion consistently rejected nested speciation models that included parameters for migration and population growth of U. scoparia. We reject the Neogene vicariance hypothesis for the speciation of U. scoparia and define this species as a single evolutionarily significant unit for conservation purposes.
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Affiliation(s)
- Andrew D Gottscho
- Department of Biological Sciences, Humboldt State University 1 Harpst Street, Arcata, California, 95521 ; Department of Biology, University of California Riverside, California, 92521
| | - Sharyn B Marks
- Department of Biological Sciences, Humboldt State University 1 Harpst Street, Arcata, California, 95521
| | - W Bryan Jennings
- Department of Biological Sciences, Humboldt State University 1 Harpst Street, Arcata, California, 95521
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26
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Pelletier TA, Carstens BC. Model choice for phylogeographic inference using a large set of models. Mol Ecol 2014; 23:3028-43. [PMID: 24650161 DOI: 10.1111/mec.12722] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 02/14/2014] [Accepted: 02/25/2014] [Indexed: 12/01/2022]
Abstract
Model-based analyses are common in phylogeographic inference because they parameterize processes such as population division, gene flow and expansion that are of interest to biologists. Approximate Bayesian computation is a model-based approach that can be customized to any empirical system and used to calculate the relative posterior probability of several models, provided that suitable models can be identified for comparison. The question of how to identify suitable models is explored using data from Plethodon idahoensis, a salamander that inhabits the North American inland northwest temperate rainforest. First, we conduct an ABC analysis using five models suggested by previous research, calculate the relative posterior probabilities and find that a simple model of population isolation has the best fit to the data (PP=0.70). In contrast to this subjective choice of models to include in the analysis, we also specify models in a more objective manner by simulating prior distributions for 143 models that included panmixia, population isolation, change in effective population size, migration and range expansion. We then identify a smaller subset of models for comparison by generating an expectation of the highest posterior probability that a false model is likely to achieve due to chance and calculate the relative posterior probabilities of only those models that exceed this expected level. A model that parameterized divergence with population expansion and gene flow in one direction offered the best fit to the P. idahoensis data (in contrast to an isolation-only model from the first analysis). Our investigation demonstrates that the determination of which models to include in ABC model choice experiments is a vital component of model-based phylogeographic analysis.
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Affiliation(s)
- Tara A Pelletier
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W 12th Avenue, Columbus, OH, 43210-1293, USA
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Chavez AS, Maher SP, Arbogast BS, Kenagy GJ. DIVERSIFICATION AND GENE FLOW IN NASCENT LINEAGES OF ISLAND AND MAINLAND NORTH AMERICAN TREE SQUIRRELS (TAMIASCIURUS). Evolution 2014; 68:1094-109. [DOI: 10.1111/evo.12336] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 11/29/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Andreas S. Chavez
- Burke Museum and Department of Biology; University of Washington; Seattle Washington 98195
| | - Sean P. Maher
- Museum of Vertebrate Zoology; University of California; Berkeley California 94720
| | - Brian S. Arbogast
- Department of Biology and Marine Biology; University of North Carolina Wilmington; Wilmington North Carolina 28403
| | - G. J. Kenagy
- Burke Museum and Department of Biology; University of Washington; Seattle Washington 98195
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Hearn J, Stone GN, Bunnefeld L, Nicholls JA, Barton NH, Lohse K. Likelihood-based inference of population history from low-coveragede novogenome assemblies. Mol Ecol 2013; 23:198-211. [DOI: 10.1111/mec.12578] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 09/16/2013] [Accepted: 09/20/2013] [Indexed: 01/15/2023]
Affiliation(s)
- Jack Hearn
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh EH9 3JT UK
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh EH9 3JT UK
| | - Lynsey Bunnefeld
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh EH9 3JT UK
| | - James A. Nicholls
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh EH9 3JT UK
| | - Nicholas H. Barton
- Institute of Science and Technology; Am Campus 1 A-3400 Klosterneuburg Austria
| | - Konrad Lohse
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh EH9 3JT UK
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Carstens BC, Brennan RS, Chua V, Duffie CV, Harvey MG, Koch RA, McMahan CD, Nelson BJ, Newman CE, Satler JD, Seeholzer G, Posbic K, Tank DC, Sullivan J. Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsis. Mol Ecol 2013; 22:4014-28. [PMID: 23848064 DOI: 10.1111/mec.12347] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 04/09/2013] [Accepted: 04/09/2013] [Indexed: 12/29/2022]
Abstract
Phylogeographic inference has typically relied on analyses of data from one or a few genes to provide estimates of demography and population histories. While much has been learned from these studies, all phylogeographic analysis is conditioned on the data, and thus, inferences derived from data that represent a small sample of the genome are unavoidably tenuous. Here, we demonstrate one approach for moving beyond classic phylogeographic research. We use sequence capture probes and Illumina sequencing to generate data from >400 loci in order to infer the phylogeographic history of Salix melanopsis, a riparian willow with a disjunct distribution in coastal and the inland Pacific Northwest. We evaluate a priori phylogeographic hypotheses using coalescent models for parameter estimation, and the results support earlier findings that identified post-Pleistocene dispersal as the cause of the disjunction in S. melanopsis. We also conduct a series of model selection exercises using IMa2, Migrate-n and ∂a∂i. The resulting ranking of models indicates that refugial dynamics were complex, with multiple regions in the inland regions serving as the source for postglacial colonization. Our results demonstrate that new sources of data and new approaches to data analysis can rejuvenate phylogeographic research by allowing for the identification of complex models that enable researchers to both identify and estimate the most relevant parameters for a given system.
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Affiliation(s)
- Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA.
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30
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Leite RN, Rogers DS. Revisiting Amazonian phylogeography: insights into diversification hypotheses and novel perspectives. ORG DIVERS EVOL 2013. [DOI: 10.1007/s13127-013-0140-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Andrew RL, Bernatchez L, Bonin A, Buerkle CA, Carstens BC, Emerson BC, Garant D, Giraud T, Kane NC, Rogers SM, Slate J, Smith H, Sork VL, Stone GN, Vines TH, Waits L, Widmer A, Rieseberg LH. A road map for molecular ecology. Mol Ecol 2013; 22:2605-26. [DOI: 10.1111/mec.12319] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rose L. Andrew
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Louis Bernatchez
- DInstitut de Biologie Intégrative et des Systémes; Département de Biologie; 1030, Avenue de la Médecine Université Laval; Québec QC G1V 0A6 Canada
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553 Université Joseph Fourier; BP 53, 38041 Grenoble Cedex 9 France
| | - C. Alex. Buerkle
- Department of Botany; University of Wyoming; 1000 E. University Ave. Laramie WY 82071 USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology; 318 W. 12th Ave. The Ohio State University; Columbus OH 43210 USA
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife; Canary Islands 38206 Spain
| | - Dany Garant
- Département de Biologie; Université de Sherbrooke; Sherbrooke QC J1K 2R1 Canada
| | - Tatiana Giraud
- Laboratoire Ecologie, Systématique et Evolution; UMR 8079 CNRS-UPS-AgroParisTech, Bâtiment 360 Univ. Paris Sud; 91405 Orsay cedex France
| | - Nolan C. Kane
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Sean M. Rogers
- Department of Biological Sciences; University of Calgary; 2500 University Drive N.W., Calgary AB T2N 1N4 Canada
| | - Jon Slate
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | - Harry Smith
- 79 Melton Road Burton-on-the-Wolds Loughborough LE12 5TQ UK
| | - Victoria L. Sork
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; 4139 Terasaki Life Sciences Building, 610 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road, Edinburgh EH9 3JT UK
| | - Timothy H. Vines
- Molecular Ecology Editorial Office; 6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Lisette Waits
- Department of Fish and Wildlife Sciences; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
| | - Alex Widmer
- ETH Zurich; Institute of Integrative Biology; Universitätstrasse 16 Zurich 8092 Switzerland
| | - Loren H. Rieseberg
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
- Department of Biology; Indiana University; 1001 E. 3 St., Bloomington IN 47405 USA
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32
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Rakotoarisoa JE, Raheriarisena M, Goodman SM. Late Quaternary climatic vegetational shifts in an ecological transition zone of northern Madagascar: insights from genetic analyses of two endemic rodent species. J Evol Biol 2013; 26:1019-34. [DOI: 10.1111/jeb.12116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 12/30/2012] [Indexed: 02/01/2023]
Affiliation(s)
- J.-E. Rakotoarisoa
- School of Biological Sciences; Illinois State University; Normal IL USA
- Ecology and Evolutionary Biology Department; Yale University; New Haven CT USA
| | - M. Raheriarisena
- Département de Biologie Animale; Université d'Antananarivo; Antananarivo Madagascar
- Association Vahatra; Antananarivo Madagascar
| | - S. M. Goodman
- Association Vahatra; Antananarivo Madagascar
- Department of Zoology; Field Museum of Natural History; Chicago IL USA
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33
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Collevatti RG, Terribile LC, Lima-Ribeiro MS, Nabout JC, de Oliveira G, Rangel TF, Rabelo SG, Diniz-Filho JAF. A coupled phylogeographical and species distribution modelling approach recovers the demographical history of a Neotropical seasonally dry forest tree species. Mol Ecol 2012; 21:5845-63. [PMID: 23094833 DOI: 10.1111/mec.12071] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/23/2012] [Accepted: 08/28/2012] [Indexed: 11/29/2022]
Abstract
We investigated here the demographical history of Tabebuia impetiginosa (Bignoniaceae) to understand the dynamics of the disjunct geographical distribution of South American seasonally dry forests (SDFs), based on coupling an ensemble approach encompassing hindcasting species distribution modelling and statistical phylogeographical analysis. We sampled 17 populations (280 individuals) in central Brazil and analysed the polymorphisms at chloroplast (trnS-trnG, psbA-trnH, and ycf6-trnC intergenic spacers) and nuclear (ITS nrDNA) genomes. Phylogenetic analyses based on median-joining network showed no haplotype sharing among population but strong evidence of incomplete lineage sorting. Coalescent analyses showed historical constant populations size, negligible gene flow among populations, and an ancient time to most recent common ancestor dated from ~4.7 ± 1.1 Myr BP. Most divergences dated from the Lower Pleistocene, and no signal of important population size reduction was found in coalescent tree and tests of demographical expansion. Demographical scenarios were built based on past geographical range dynamic models, using two a priori biogeographical hypotheses ('Pleistocene Arc' and 'Amazonian SDF expansion') and on two additional hypotheses suggested by the palaeodistribution modelling built with several algorithms for distribution modelling and palaeoclimatic data. The simulation of these demographical scenarios showed that the pattern of diversity found so far for T. impetiginosa is in consonance with a palaeodistribution expansion during the last glacial maximum (LGM, 21 kyr BP), strongly suggesting that the current disjunct distribution of T. impetiginosa in SDFs may represent a climatic relict of a once more wide distribution.
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Affiliation(s)
- Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás, Cx.P. 131, 74001-970 Goiânia, GO, Brasil.
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Barber BR, Xu J, Pérez-Losada M, Jara CG, Crandall KA. Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis. PLoS One 2012; 7:e37105. [PMID: 22685541 PMCID: PMC3369872 DOI: 10.1371/journal.pone.0037105] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 04/17/2012] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Multiple loci and population genetic methods were employed to study the phylogeographic history of the Patagonian freshwater crab Aegla neuquensis (Aeglidae: Decopoda). This taxon occurs in two large river systems in the Patagonian Steppe, from the foothills of the Andes Mountains east to the Atlantic Ocean. METHODOLOGY/PRINCIPAL FINDINGS A nuclear phylogeny and multilocus nested clade phylogeographic analysis detected a fragmentation event between the Negro and Chico-Chubut river systems. This event occurred approximately 137 thousand years ago. An isolation-with-migration analysis and maximum-likelihood estimates of gene flow showed asymmetrical exchange of genetic material between these two river systems exclusively in their headwaters. We used information theory to determine the best-fit demographic history between these two river systems under an isolation-with-migration model. The best-fit model suggests that the Negro and the ancestral populations have the same effective population sizes; whereas the Chico-Chubut population is smaller and shows that gene flow from the Chico-Chubut into the Negro is four times higher than in the reverse direction. Much of the Chico-Chubut system appears to have only been recently colonized while the Negro populations appear to have been in place for most of the evolutionary history of this taxon. CONCLUSIONS/SIGNIFICANCE Due to mitochondrial introgression, three nuclear loci provided different phylogeographic resolution than the three mitochondrial genes for an ancient fragmentation event observed in the nuclear phylogeny. However, the mitochondrial locus provided greater resolution on more recent evolutionary events. Our study, therefore, demonstrates the need to include both nuclear and mitochondrial loci for a more complete understanding of evolutionary histories and associated phylogeographic events. Our results suggest that gene flow between these systems, before and after fragmentation was through periodic paleolakes that formed in the headwaters region. Fragmentation between the Negro and Chico-Chubut systems was driven by the disappearance of these paleolakes during the Patagonian Glaciation.
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Affiliation(s)
- Brian R Barber
- Department of Biology, Brigham Young University, Provo, Utah, United States of America.
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Smith G, Lohse K, Etges WJ, Ritchie MG. Model-based comparisons of phylogeographic scenarios resolve the intraspecific divergence of cactophilic Drosophila mojavensis. Mol Ecol 2012; 21:3293-307. [PMID: 22571504 DOI: 10.1111/j.1365-294x.2012.05604.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The cactophilic fly Drosophila mojavensis exhibits considerable intraspecific genetic structure across allopatric geographic regions and shows associations with different host cactus species across its range. The divergence between these populations has been studied for more than 60years, yet their exact historical relationships have not been resolved. We analysed sequence data from 15 intronic X-linked loci across populations from Baja California, mainland Sonora-Arizona and Mojave Desert regions under an isolation-with-migration model to assess multiple scenarios of divergence. We also compared the results with a pre-existing sequence data set of eight autosomal loci. We derived a population tree with Baja California placed at its base and link their isolation to Pleistocene climatic oscillations. Our estimates suggest the Baja California population diverged from an ancestral Mojave Desert/mainland Sonora-Arizona group around 230,000-270,000years ago, while the split between the Mojave Desert and mainland Sonora-Arizona populations occurred one glacial cycle later, 117,000-135,000years ago. Although we found these three populations to be effectively allopatric, model ranking could not rule out the possibility of a low level of gene flow between two of them. Finally, the Mojave Desert population showed a small effective population size, consistent with a historical population bottleneck. We show that model-based inference from multiple loci can provide accurate information on the historical relationships of closely related groups allowing us to set into historical context a classic system of incipient ecological speciation.
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Affiliation(s)
- Gilbert Smith
- School of Biology, University of St. Andrews, St. Andrews KY16 9TH, UK.
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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.
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Nielsen JT, Eghbalnia HR, Nielsen NC. Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2012; 60:1-28. [PMID: 22293396 PMCID: PMC3270304 DOI: 10.1016/j.pnmrs.2011.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 05/09/2011] [Indexed: 05/05/2023]
Abstract
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction of NMR chemical shifts from protein structures. Our approach, shAIC (shift prediction guided by Akaikes Information Criterion), capitalizes on mathematical ideas and an information-theoretic principle, to represent the functional form of the relationship between structure and chemical shift as a parsimonious sum of smooth analytical potentials which optimally takes into account short-, medium-, and long-range parameters in a nuclei-specific manner to capture potential chemical shift perturbations caused by distant nuclei. shAIC outperforms the state-of-the-art methods that use analytical formulations. Moreover, for structures derived by NMR or structures with novel folds, shAIC delivers better overall results; even when it is compared to sophisticated machine learning approaches. shAIC provides for a computationally lightweight implementation that is unimpeded by molecular size, making it an ideal for use as a force field.
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Affiliation(s)
- Jakob T. Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Hamid R. Eghbalnia
- Department of Molecular and Cellular Physiology, University of Cincinnati, 231 Albert B. Sabin Way, Cincinnati, OH 45267-0576, United States
| | - Niels Chr. Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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Aguirre-Planter É, Jaramillo-Correa JP, Gómez-Acevedo S, Khasa DP, Bousquet J, Eguiarte LE. Phylogeny, diversification rates and species boundaries of Mesoamerican firs (Abies, Pinaceae) in a genus-wide context. Mol Phylogenet Evol 2012; 62:263-74. [DOI: 10.1016/j.ympev.2011.09.021] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 09/26/2011] [Accepted: 09/28/2011] [Indexed: 11/27/2022]
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Walstrom VW, Klicka J, Spellman GM. Speciation in the White-breasted Nuthatch (Sitta carolinensis): a multilocus perspective. Mol Ecol 2011; 21:907-20. [PMID: 22192449 DOI: 10.1111/j.1365-294x.2011.05384.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inferring the evolutionary and ecological processes that have shaped contemporary species distributions using the geographic distribution of gene lineages is the principal goal of phylogeographic research. Researchers in the field have recognized that inferences made from a single gene, often mitochondrial, can be informative regarding the pattern of diversification but lack conclusive information regarding the evolutionary mechanisms that led to the observed patterns. Here, we use a multilocus (20 loci) data set to explore the evolutionary history of the White-breasted Nuthatch (Sitta carolinensis). A previous single-locus study found S. carolinensis is comprised of four reciprocally monophyletic clades geographically restricted to the pine and oak forests of: (i) eastern North America, (ii) southern Rocky Mountain and Mexican Mountain ranges, (iii) Eastern Sierra Nevada and Northern Rocky Mountains and (iv) Pacific slope of North America. The diversification of the clades was attributed to the fragmentation of North American pine and oak woodlands in the Pliocene with subsequent divergences owing to the Pleistocene glacial cycles. Principal component, clustering and species tree analyses of the multilocus data resolved the same four groups or lineages found in the single-locus study. Coalescent analyses and hypothesis testing of nested isolation and migration models indicate that isolation and not gene flow has been the major evolutionary mechanism responsible for shaping genetic variation, and all the divergence events within S. carolinensis have occurred in response to the Pleistocene glacial cycles.
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Affiliation(s)
- Veryl Woody Walstrom
- Center for the Conservation of Biological Resources, Department of Biology, Black Hills State University, Spearfish, SD 57799, USA.
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40
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Predator mediated selection and the impact of developmental stage on viability in wood frog tadpoles (Rana sylvatica). BMC Evol Biol 2011; 11:353. [PMID: 22151372 PMCID: PMC3283531 DOI: 10.1186/1471-2148-11-353] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 12/07/2011] [Indexed: 11/25/2022] Open
Abstract
Background Complex life histories require adaptation of a single organism for multiple ecological niches. Transitions between life stages, however, may expose individuals to an increased risk of mortality, as the process of metamorphosis typically includes developmental stages that function relatively poorly in both the pre- and post-metamorphic habitat. We studied predator-mediated selection on tadpoles of the wood frog, Rana sylvatica, to identify this hypothesized period of differential predation risk and estimate its ontogenetic onset. We reared tadpoles in replicated mesocosms in the presence of the larval odonate Anax junius, a known tadpole predator. Results The probability of tadpole survival increased with increasing age and size, but declined steeply at the point in development where hind limbs began to erupt from the body wall. Selection gradient analyses indicate that natural selection favored tadpoles with short, deep tail fins. Tadpoles resorb their tails as they progress toward metamorphosis, which may have led to the observed decrease in survivorship. Path models revealed that selection acted directly on tail morphology, rather than through its indirect influence on swimming performance. Conclusions This is consistent with the hypothesis that tail morphology influences predation rates by reducing the probability a predator strikes the head or body.
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Gutiérrez-García TA, Vázquez-Domínguez E. Comparative Phylogeography: Designing Studies while Surviving the Process. Bioscience 2011. [DOI: 10.1525/bio.2011.61.11.5] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Manthey JD, Klicka J, Spellman GM. Isolation-driven divergence: speciation in a widespread North American songbird (Aves: Certhiidae). Mol Ecol 2011; 20:4371-84. [PMID: 21933295 PMCID: PMC3256251 DOI: 10.1111/j.1365-294x.2011.05270.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lineage, or true 'species', trees may differ from gene trees because of stochastic processes in molecular evolution leading to gene-tree heterogeneity. Problems with inferring species trees because of excessive incomplete lineage sorting may be exacerbated in lineages with rapid diversification or recent divergences necessitating the use of multiple loci and individuals. Many recent multilocus studies that investigate divergence times identify lineage splitting to be more recent than single-locus studies, forcing the revision of biogeographic scenarios driving divergence. Here, we use 21 nuclear loci from regional populations to re-evaluate hypotheses identified in an mtDNA phylogeographic study of the Brown Creeper (Certhia americana), as well as identify processes driving divergence. Nuclear phylogeographic analyses identified hierarchical genetic structure, supporting a basal split at approximately 32°N latitude, splitting northern and southern populations, with mixed patterns of genealogical concordance and discordance between data sets within the major lineages. Coalescent-based analyses identify isolation, with little to no gene flow, as the primary driver of divergence between lineages. Recent isolation appears to have caused genetic bottlenecks in populations in the Sierra Madre Oriental and coastal mountain ranges of California, which may be targets for conservation concerns.
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Affiliation(s)
- Joseph D Manthey
- Center for the Conservation of Biological Resources, Department of Biology, Black Hills State University, Spearfish, SD 57799, USA.
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DOUGLAS NORMANA, WALL WADEA, XIANG QIUYUNJENNY, HOFFMANN WILLIAMA, WENTWORTH THOMASR, GRAY JANETB, HOHMANN MATTHEWG. Recent vicariance and the origin of the rare, edaphically specialized Sandhills lily, Lilium pyrophilum (Liliaceae): evidence from phylogenetic and coalescent analyses. Mol Ecol 2011; 20:2901-15. [DOI: 10.1111/j.1365-294x.2011.05151.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Morris-Pocock JA, Anderson DJ, Friesen VL. Mechanisms of global diversification in the brown booby (Sula leucogaster) revealed by uniting statistical phylogeographic and multilocus phylogenetic methods. Mol Ecol 2011; 20:2835-50. [PMID: 21615811 DOI: 10.1111/j.1365-294x.2011.05132.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- J A Morris-Pocock
- Department of Biology, Queen's University, Kingston, Ontario, Canada.
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GRUEBER CE, NAKAGAWA S, LAWS RJ, JAMIESON IG. Multimodel inference in ecology and evolution: challenges and solutions. J Evol Biol 2011; 24:699-711. [DOI: 10.1111/j.1420-9101.2010.02210.x] [Citation(s) in RCA: 1549] [Impact Index Per Article: 119.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Carstens BC, Knowles LL. Navigating the unknown: model selection in phylogeography. Models of population structure: tools for thinkers. Mol Ecol 2011; 19:4581-2. [PMID: 20958809 DOI: 10.1111/j.1365-294x.2010.04851.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite the widespread use and obvious strengths of model-based methods for phylogeographic study, a persistent concern for such analyses is related to the definition of the model itself. The study by Peter et al. (2010) in this issue of Molecular Ecology demonstrates an approach for overcoming such hurdles. The authors were motivated by a deceptively simple goal; they sought to infer whether a population has remained at a low and stable size or has undergone a decline, and certainly there is no shortage of software packages for such a task (e.g., see list of programs in Excoffier & Heckel 2006). However, each of these software packages makes basic assumptions about the underling population (e.g., is the population subdivided or panmictic); these assumptions are explicit to any model-based approach but can bias parameter estimates and produce misleading inferences if the model does not approximate the actual demographic history in a reasonable manner. Rather than guessing which model might be best for analyzing the data (microsatellite data from samples of chimpanzees), Peter et al. (2010) quantify the relative fit of competing models for estimating the population genetic parameters of interest. Complemented by a revealing simulation study, the authors highlight the peril inherent to model-based inferences that lack a statistical evaluation of the fit of a model to the data, while also demonstrating an approach for model selection with broad applicability to phylogeographic analysis.
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Affiliation(s)
- Bryan C Carstens
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70808, USA.
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ETTER RONJ, BOYLE ELIZABETHE, GLAZIER AMANDA, JENNINGS ROBERTM, DUTRA EDIANE, CHASE MIKER. Phylogeography of a pan-Atlantic abyssal protobranch bivalve: implications for evolution in the Deep Atlantic. Mol Ecol 2011; 20:829-43. [DOI: 10.1111/j.1365-294x.2010.04978.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Huang W, Takebayashi N, Qi Y, Hickerson MJ. MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity. BMC Bioinformatics 2011; 12:1. [PMID: 21199577 PMCID: PMC3031198 DOI: 10.1186/1471-2105-12-1] [Citation(s) in RCA: 328] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 01/03/2011] [Indexed: 11/19/2022] Open
Abstract
Background MTML-msBayes uses hierarchical approximate Bayesian computation (HABC) under a coalescent model to infer temporal patterns of divergence and gene flow across codistributed taxon-pairs. Under a model of multiple codistributed taxa that diverge into taxon-pairs with subsequent gene flow or isolation, one can estimate hyper-parameters that quantify the mean and variability in divergence times or test models of migration and isolation. The software uses multi-locus DNA sequence data collected from multiple taxon-pairs and allows variation across taxa in demographic parameters as well as heterogeneity in DNA mutation rates across loci. The method also allows a flexible sampling scheme: different numbers of loci of varying length can be sampled from different taxon-pairs. Results Simulation tests reveal increasing power with increasing numbers of loci when attempting to distinguish temporal congruence from incongruence in divergence times across taxon-pairs. These results are robust to DNA mutation rate heterogeneity. Estimating mean divergence times and testing simultaneous divergence was less accurate with migration, but improved if one specified the correct migration model. Simulation validation tests demonstrated that one can detect the correct migration or isolation model with high probability, and that this HABC model testing procedure was greatly improved by incorporating a summary statistic originally developed for this task (Wakeley's ΨW). The method is applied to an empirical data set of three Australian avian taxon-pairs and a result of simultaneous divergence with some subsequent gene flow is inferred. Conclusions To retain flexibility and compatibility with existing bioinformatics tools, MTML-msBayes is a pipeline software package consisting of Perl, C and R programs that are executed via the command line. Source code and binaries are available for download at http://msbayes.sourceforge.net/ under an open source license (GNU Public License).
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Affiliation(s)
- Wen Huang
- Biology Department, City University of New York, Queens College, 65-30 Kissena Blvd, Flushing, NY 11367-1597, USA.
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LOHSE KONRAD, NICHOLLS JAMESA, STONE GRAHAMN. Inferring the colonization of a mountain range-refugia vs. nunatak survival in high alpine ground beetles. Mol Ecol 2010; 20:394-408. [DOI: 10.1111/j.1365-294x.2010.04929.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Koopman MM, Carstens BC. Conservation genetic inferences in the carnivorous pitcher plant Sarracenia alata (Sarraceniaceae). CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0095-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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