151
|
Shirley MH, Vliet KA, Carr AN, Austin JD. Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation. Proc Biol Sci 2013; 281:20132483. [PMID: 24335982 DOI: 10.1098/rspb.2013.2483] [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] [Indexed: 11/12/2022] Open
Abstract
Accurate species delimitation is a central assumption of biology that, in groups such as the Crocodylia, is often hindered by highly conserved morphology and frequent introgression. In Africa, crocodilian systematics has been hampered by complex regional biogeography and confounded taxonomic history. We used rigorous molecular and morphological species delimitation methods to test the hypothesis that the slender-snouted crocodile (Mecistops cataphractus) is composed of multiple species corresponding to the Congolian and Guinean biogeographic zones. Speciation probability was assessed by using 11 mitochondrial and nuclear genes, and cranial morphology for over 100 specimens, representing the full geographical extent of the species distribution. Molecular Bayesian and phylogenetic species delimitation showed unanimous support for two Mecistops species isolated to the Upper Guinean and Congo (including Lower Guinean) biomes that were supported by 13 cranial characters capable of unambiguously diagnosing each species. Fossil-calibrated phylogenetic reconstruction estimated that the species split ± 6.5-7.5 Ma, which is congruent with intraspecies divergence within the sympatric crocodile genus Osteolaemus and the formation of the Cameroon Volcanic Line. Our results underscore the necessity of comprehensive phylogeographic analyses within currently recognized taxa to detect cryptic species within the Crocodylia. We recommend that the community of crocodilian researchers reconsider the conceptualization of crocodilian species especially in the light of the conservation ramifications for this economically and ecologically important group.
Collapse
Affiliation(s)
- Matthew H Shirley
- Department of Wildlife Ecology and Conservation, University of Florida, , 110 Newins-Ziegler Hall, Gainesville, FL 32611, USA, SFM Safari Gabon, , BP 1107, Libreville, Gabon, Department of Biology, University of Florida, , 220 Bartram Hall, Gainesville, FL 32611, USA
| | | | | | | |
Collapse
|
152
|
Dellicour S, Mardulyn P. spads 1.0: a toolbox to perform spatial analyses on DNA sequence data sets. Mol Ecol Resour 2013; 14:647-51. [PMID: 24215429 DOI: 10.1111/1755-0998.12200] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 10/21/2013] [Accepted: 11/07/2013] [Indexed: 11/27/2022]
Abstract
SPADS 1.0 (for 'Spatial and Population Analysis of DNA Sequences') is a population genetic toolbox for characterizing genetic variability within and among populations from DNA sequences. In view of the drastic increase in genetic information available through sequencing methods, spads was specifically designed to deal with multilocus data sets of DNA sequences. It computes several summary statistics from populations or groups of populations, performs input file conversions for other population genetic programs and implements locus-by-locus and multilocus versions of two clustering algorithms to study the genetic structure of populations. The toolbox also includes two MATLAB and r functions, GDISPAL and GDIVPAL, to display differentiation and diversity patterns across landscapes. These functions aim to generate interpolating surfaces based on multilocus distance and diversity indices. In the case of multiple loci, such surfaces can represent a useful alternative to multiple pie charts maps traditionally used in phylogeography to represent the spatial distribution of genetic diversity. These coloured surfaces can also be used to compare different data sets or different diversity and/or distance measures estimated on the same data set.
Collapse
Affiliation(s)
- Simon Dellicour
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, av. FD Roosevelt 50, Brussels, 1050, Belgium
| | | |
Collapse
|
153
|
Chaillon A, Gianella S, Wertheim JO, Richman DD, Mehta SR, Smith DM. HIV migration between blood and cerebrospinal fluid or semen over time. J Infect Dis 2013; 209:1642-52. [PMID: 24302756 DOI: 10.1093/infdis/jit678] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Previous studies reported associations between neuropathogenesis and human immunodeficiency virus (HIV) compartmentalization in cerebrospinal fluid (CSF) and between sexual transmission and human immunodeficiency virus type 1 (HIV) compartmentalization in semen. It remains unclear, however, how compartmentalization dynamics change over time. To address this, we used statistical methods and Bayesian phylogenetic approaches to reconstruct temporal dynamics of HIV migration between blood and CSF and between blood and the male genital tract. We investigated 11 HIV-infected individuals with paired semen and blood samples and 4 individuals with paired CSF and blood samples. Aligned partial HIV env sequences were analyzed by (1) phylogenetic reconstruction, using a Bayesian Markov-chain Monte Carlo approach; (2) evaluation of viral compartmentalization, using tree-based and distance-based methods; and (3) analysis of migration events, using a discrete Bayesian asymmetric phylogeographic approach of diffusion with Markov jump counts estimation. Finally, we evaluated potential correlates of viral gene flow across anatomical compartments. We observed bidirectional replenishment of viral compartments and asynchronous peaks of viral migration from and to blood over time, suggesting that disruption of viral compartment is transient and directionally selected. These findings imply that viral subpopulations in anatomical sites are an active part of the whole viral population and that compartmental reservoirs could have implications in future eradication studies.
Collapse
|
154
|
Multi-locus species tree for the Amazonian peacock basses (Cichlidae: Cichla): Emergent phylogenetic signal despite limited nuclear variation. Mol Phylogenet Evol 2013; 69:479-90. [DOI: 10.1016/j.ympev.2013.07.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 07/31/2013] [Accepted: 07/31/2013] [Indexed: 11/18/2022]
|
155
|
Abdalla S, Al-Hadeethi Y. Genes alternations with exposure time of environmental factors. Gene 2013; 528:256-60. [PMID: 23860326 DOI: 10.1016/j.gene.2013.06.065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 01/01/2023]
Abstract
A theoretical model discussing the environmental factors (EFs) effect of exposure time on genes, which leads to human diseases, is presented using multi-logistic model. The advantages and limitations of this model are discussed in terms of its usefulness for simulating genetic samples. It has been shown that EFs affect genes with the same degree both at high exposure level, low exposure time and at low exposure level, high exposure time.
Collapse
Affiliation(s)
- S Abdalla
- Department of Physics, Faculty of Science, King Abdulaziz University Jeddah, P.O. Box 80203, Jeddah 21589, Saudi Arabia.
| | | |
Collapse
|
156
|
Abstract
Transmission events are the fundamental building blocks of the dynamics of any infectious disease. Much about the epidemiology of a disease can be learned when these individual transmission events are known or can be estimated. Such estimations are difficult and generally feasible only when detailed epidemiological data are available. The genealogy estimated from genetic sequences of sampled pathogens is another rich source of information on transmission history. Optimal inference of transmission events calls for the combination of genetic data and epidemiological data into one joint analysis. A key difficulty is that the transmission tree, which describes the transmission events between infected hosts, differs from the phylogenetic tree, which describes the ancestral relationships between pathogens sampled from these hosts. The trees differ both in timing of the internal nodes and in topology. These differences become more pronounced when a higher fraction of infected hosts is sampled. We show how the phylogenetic tree of sampled pathogens is related to the transmission tree of an outbreak of an infectious disease, by the within-host dynamics of pathogens. We provide a statistical framework to infer key epidemiological and mutational parameters by simultaneously estimating the phylogenetic tree and the transmission tree. We test the approach using simulations and illustrate its use on an outbreak of foot-and-mouth disease. The approach unifies existing methods in the emerging field of phylodynamics with transmission tree reconstruction methods that are used in infectious disease epidemiology.
Collapse
|
157
|
Fujisawa T, Barraclough TG. Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets. Syst Biol 2013; 62:707-24. [PMID: 23681854 PMCID: PMC3739884 DOI: 10.1093/sysbio/syt033] [Citation(s) in RCA: 849] [Impact Index Per Article: 77.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 11/19/2012] [Accepted: 05/03/2013] [Indexed: 11/13/2022] Open
Abstract
DNA barcoding-type studies assemble single-locus data from large samples of individuals and species, and have provided new kinds of data for evolutionary surveys of diversity. An important goal of many such studies is to delimit evolutionarily significant species units, especially in biodiversity surveys from environmental DNA samples. The Generalized Mixed Yule Coalescent (GMYC) method is a likelihood method for delimiting species by fitting within- and between-species branching models to reconstructed gene trees. Although the method has been widely used, it has not previously been described in detail or evaluated fully against simulations of alternative scenarios of true patterns of population variation and divergence between species. Here, we present important reformulations to the GMYC method as originally specified, and demonstrate its robustness to a range of departures from its simplifying assumptions. The main factor affecting the accuracy of delimitation is the mean population size of species relative to divergence times between them. Other departures from the model assumptions, such as varying population sizes among species, alternative scenarios for speciation and extinction, and population growth or subdivision within species, have relatively smaller effects. Our simulations demonstrate that support measures derived from the likelihood function provide a robust indication of when the model performs well and when it leads to inaccurate delimitations. Finally, the so-called single-threshold version of the method outperforms the multiple-threshold version of the method on simulated data: we argue that this might represent a fundamental limit due to the nature of evidence used to delimit species in this approach. Together with other studies comparing its performance relative to other methods, our findings support the robustness of GMYC as a tool for delimiting species when only single-locus information is available.
Collapse
Affiliation(s)
- Tomochika Fujisawa
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK; and Department of Entomology, Natural History Museum, London SW7 5BD, UK
| | - Timothy G. Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK; and Department of Entomology, Natural History Museum, London SW7 5BD, UK
| |
Collapse
|
158
|
Akkarathamrongsin S, Hacharoen P, Tangkijvanich P, Theamboonlers A, Tanaka Y, Mizokami M, Poovorawan Y. Molecular epidemiology and genetic history of hepatitis C virus subtype 3a infection in Thailand. Intervirology 2013; 56:284-294. [PMID: 23838334 DOI: 10.1159/000351621] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 04/22/2013] [Indexed: 10/10/2023] Open
Abstract
OBJECTIVE Among all hepatitis C virus (HCV) infections, subtype 3a is the most common genotype in Thailand. This study investigates the molecular epidemiology and epidemic history of HCV subtype 3a in Thailand. METHODS Three hundred and fifty-six serum samples were collected from HCV-infected Thai patients. The virus was isolated, after which the core and NS5B regions were sequenced. Subsequently, the HCV genotype was classified by phylogenetic analysis based on the core and NS5B regions. Molecular evolution analysis of HCV subtype 3a was estimated using BEAST (Bayesian Evolutionary Analysis by Sampling Trees) v.1.5.4. RESULTS Based on our phylogenetic analyses, subtype 3a (38.5%) was the most prevalent, followed by 1a (21%), 1b (13.8%), genotype 6 (19.9%) [comprised of subtypes 6e (0.3%), 6f (11%), 6i (1.9%), 6j (1.9%) and 6n (4.8%)] and 3b (5.6%). Our phylogenetic tree indicates the existence of a specific group of HCV subtype 3a strains in the Thai population. Molecular evolutionary analysis dated the most recent common ancestor of the Thai HCV subtype 3a strains as existing approximately 200 ago, and a Bayesian skyline plot showed that this particular strain spread to Thailand during the mid-1970s and early 1980s. This period overlaps with the Vietnam War (1955-1975) and the widespread use of injection stimulants introduced by the US Army during this time. CONCLUSION The estimated history of HCV subtype 3a infection in Thailand may help to predict the future burden of HCV-related diseases and facilitate better public health control and surveillance.
Collapse
Affiliation(s)
- S Akkarathamrongsin
- Inter-Department of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand
| | | | | | | | | | | | | |
Collapse
|
159
|
Iacchei M, Ben-Horin T, Selkoe KA, Bird CE, García-Rodríguez FJ, Toonen RJ. Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations. Mol Ecol 2013; 22:3476-94. [PMID: 23802550 PMCID: PMC3749441 DOI: 10.1111/mec.12341] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 03/10/2013] [Accepted: 03/12/2013] [Indexed: 11/28/2022]
Abstract
We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; D(est_Chao) = 0.025) and seven nuclear microsatellites (F(ST) = 0.004, P < 0.001; D(est_Chao) = 0.03), despite the species' 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F(16,988) = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (D(est_Chao), R(2) = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R(2) = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low F(ST) and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal.
Collapse
Affiliation(s)
- Matthew Iacchei
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96744, USA.
| | | | | | | | | | | |
Collapse
|
160
|
Smith KC, Castro-Nallar E, Fisher JN, Breakwell DP, Grose JH, Burnett SH. Phage cluster relationships identified through single gene analysis. BMC Genomics 2013; 14:410. [PMID: 23777341 PMCID: PMC3698066 DOI: 10.1186/1471-2164-14-410] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 06/12/2013] [Indexed: 12/16/2022] Open
Abstract
Background Phylogenetic comparison of bacteriophages requires whole genome approaches such as dotplot analysis, genome pairwise maps, and gene content analysis. Currently mycobacteriophages, a highly studied phage group, are categorized into related clusters based on the comparative analysis of whole genome sequences. With the recent explosion of phage isolation, a simple method for phage cluster prediction would facilitate analysis of crude or complex samples without whole genome isolation and sequencing. The hypothesis of this study was that mycobacteriophage-cluster prediction is possible using comparison of a single, ubiquitous, semi-conserved gene. Tape Measure Protein (TMP) was selected to test the hypothesis because it is typically the longest gene in mycobacteriophage genomes and because regions within the TMP gene are conserved. Results A single gene, TMP, identified the known Mycobacteriophage clusters and subclusters using a Gepard dotplot comparison or a phylogenetic tree constructed from global alignment and maximum likelihood comparisons. Gepard analysis of 247 mycobacteriophage TMP sequences appropriately recovered 98.8% of the subcluster assignments that were made by whole-genome comparison. Subcluster-specific primers within TMP allow for PCR determination of the mycobacteriophage subcluster from DNA samples. Using the single-gene comparison approach for siphovirus coliphages, phage groupings by TMP comparison reflected relationships observed in a whole genome dotplot comparison and confirm the potential utility of this approach to another widely studied group of phages. Conclusions TMP sequence comparison and PCR results support the hypothesis that a single gene can be used for distinguishing phage cluster and subcluster assignments. TMP single-gene analysis can quickly and accurately aid in mycobacteriophage classification.
Collapse
Affiliation(s)
- Kyle C Smith
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, UT, USA
| | | | | | | | | | | |
Collapse
|
161
|
Ikeda H, Setoguchi H. A multilocus sequencing approach reveals the cryptic phylogeographical history ofPhyllodoce nipponica Makino (Ericaceae). Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Hajime Ikeda
- Department of Botany; National Museum of Nature and Science; 4-1-1 Amakubo; Tsukuba; Ibaraki; 305-0005; Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida-nihonmatsu-cho; Sakyo-ku; Kyoto; 606-8501; Japan
| |
Collapse
|
162
|
Heller R, Chikhi L, Siegismund HR. The confounding effect of population structure on Bayesian skyline plot inferences of demographic history. PLoS One 2013; 8:e62992. [PMID: 23667558 PMCID: PMC3646956 DOI: 10.1371/journal.pone.0062992] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 04/01/2013] [Indexed: 11/19/2022] Open
Abstract
Many coalescent-based methods aiming to infer the demographic history of populations assume a single, isolated and panmictic population (i.e. a Wright-Fisher model). While this assumption may be reasonable under many conditions, several recent studies have shown that the results can be misleading when it is violated. Among the most widely applied demographic inference methods are Bayesian skyline plots (BSPs), which are used across a range of biological fields. Violations of the panmixia assumption are to be expected in many biological systems, but the consequences for skyline plot inferences have so far not been addressed and quantified. We simulated DNA sequence data under a variety of scenarios involving structured populations with variable levels of gene flow and analysed them using BSPs as implemented in the software package BEAST. Results revealed that BSPs can show false signals of population decline under biologically plausible combinations of population structure and sampling strategy, suggesting that the interpretation of several previous studies may need to be re-evaluated. We found that a balanced sampling strategy whereby samples are distributed on several populations provides the best scheme for inferring demographic change over a typical time scale. Analyses of data from a structured African buffalo population demonstrate how BSP results can be strengthened by simulations. We recommend that sample selection should be carefully considered in relation to population structure previous to BSP analyses, and that alternative scenarios should be evaluated when interpreting signals of population size change.
Collapse
|
163
|
Rovito SM, Parra-Olea G, Hanken J, Bonett RM, Wake DB. Adaptive radiation in miniature: the minute salamanders of the Mexican highlands (Amphibia: Plethodontidae:Thorius). Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12083] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Gabriela Parra-Olea
- Departamento de Zoología; Instituto de Biología; Universidad Nacional Autónoma de México; AP 70-153, CP 04510, Ciudad Universitaria; México; D.F.; México
| | - James Hanken
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology; Harvard University; 26 Oxford St.; Cambridge; MA; 02138; USA
| | - Ronald M. Bonett
- Department of Biological Science; University of Tulsa; 800 S Tucker Drive; Tulsa; OK; 74104; USA
| | - David B. Wake
- Department of Integrative Biology and Museum of Vertebrate Zoology; University of California; Berkeley; CA; 94720-3160; USA
| |
Collapse
|
164
|
Shea K, Metaxas A, Young CR, Fisher CR. Processes and Interactions in Macrofaunal Assemblages at Hydrothermal Vents: A Modeling Perspective. MAGMA TO MICROBE: MODELING HYDROTHERMAL PROCESSES AT OCEAN SPREADING CENTERS 2013. [DOI: 10.1029/178gm13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
165
|
Mendez F, Krahn T, Schrack B, Krahn AM, Veeramah K, Woerner A, Fomine F, Bradman N, Thomas M, Karafet T, Hammer M. An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am J Hum Genet 2013; 92:454-9. [PMID: 23453668 DOI: 10.1016/j.ajhg.2013.02.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/01/2013] [Accepted: 02/06/2013] [Indexed: 12/31/2022] Open
Abstract
We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237-581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.
Collapse
|
166
|
Palacios JA, Minin VN. Gaussian Process-Based Bayesian Nonparametric Inference of Population Size Trajectories from Gene Genealogies. Biometrics 2013; 69:8-18. [DOI: 10.1111/biom.12003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Julia A. Palacios
- Department of Statistics, University of Washington; Seattle Washington 98195-4322 U.S.A
| | - Vladimir N. Minin
- Department of Statistics, University of Washington; Seattle Washington 98195-4322 U.S.A
| |
Collapse
|
167
|
Shi CM, Ji YJ, Liu L, Wang L, Zhang DX. Impact of climate changes from Middle Miocene onwards on evolutionary diversification in Eurasia: insights from the mesobuthid scorpions. Mol Ecol 2013; 22:1700-16. [PMID: 23356513 DOI: 10.1111/mec.12205] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 11/30/2012] [Accepted: 12/04/2012] [Indexed: 11/30/2022]
Abstract
The aridification from Middle Miocene onwards has transformed the Asian interior into an arid environment, and the Pleistocene glacial-interglacial oscillations exerted further ecological impact. Therefore, both aridification and glaciation would have considerably influenced the evolution of many mid-latitude species in temperate Asia. Here, we tested this perspective by a phylogeographic study of the mesobuthid scorpions across temperate Asia using one mitochondrial and three nuclear genes. Concordant mitochondrial and nuclear gene trees were obtained, which are consistent with species tree inferred using a Bayesian approach. The age of the most recent common ancestor (MRCA) of all the studied scorpions was estimated to be 12.49 Ma (late Middle Miocene); Mesobuthus eupeus diverged from the clade composing Mesobuthus caucasicus and Mesobuthus martensii in early Late Miocene (10.21 Ma); M. martensii diverged from M. caucasicus at 5.53 Ma in Late Miocene. The estimated MRCA ages of M. martensii and the Chinese lineage of M. eupeus were 2.37 and 0.68 Ma, respectively. Central Asia was identified as the ancestral area for the lineage leading to M. martensii and M. caucasicus and the Chinese lineage of M. eupeus. The ancestral habitat of the genus Mesobuthus is likely to have been characterized by an arid environment; a shift towards more humid habitat occurred in the MRCA of M. martensii and a lineage of M. caucasicus, finally leading to the adaptation of M. martensii to humid environment. Our data strongly support the idea that the stepwise intensified aridifications from Mid-Miocene onwards drove the diversification of mesobuthid scorpions, and suggest that M. martensii and M. eupeus observed today in China originated from an ancestral lineage distributed in Central Asia. Both the colonization and the ensuing evolution of these species in East Asia appear to have been further moulded by Quaternary glaciations.
Collapse
Affiliation(s)
- Cheng-Min Shi
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | | | | | | | | |
Collapse
|
168
|
Kitchen JL, Allaby RG. Systems Modeling at Multiple Levels of Regulation: Linking Systems and Genetic Networks to Spatially Explicit Plant Populations. PLANTS (BASEL, SWITZERLAND) 2013; 2:16-49. [PMID: 27137364 PMCID: PMC4844292 DOI: 10.3390/plants2010016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/21/2012] [Accepted: 01/16/2013] [Indexed: 11/16/2022]
Abstract
Selection and adaptation of individuals to their underlying environments are highly dynamical processes, encompassing interactions between the individual and its seasonally changing environment, synergistic or antagonistic interactions between individuals and interactions amongst the regulatory genes within the individual. Plants are useful organisms to study within systems modeling because their sedentary nature simplifies interactions between individuals and the environment, and many important plant processes such as germination or flowering are dependent on annual cycles which can be disrupted by climate behavior. Sedentism makes plants relevant candidates for spatially explicit modeling that is tied in with dynamical environments. We propose that in order to fully understand the complexities behind plant adaptation, a system that couples aspects from systems biology with population and landscape genetics is required. A suitable system could be represented by spatially explicit individual-based models where the virtual individuals are located within time-variable heterogeneous environments and contain mutable regulatory gene networks. These networks could directly interact with the environment, and should provide a useful approach to studying plant adaptation.
Collapse
Affiliation(s)
- James L Kitchen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Robin G Allaby
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
| |
Collapse
|
169
|
Ardila NE, Giribet G, Sánchez JA. A time-calibrated molecular phylogeny of the precious corals: reconciling discrepancies in the taxonomic classification and insights into their evolutionary history. BMC Evol Biol 2012; 12:246. [PMID: 23249327 PMCID: PMC3565870 DOI: 10.1186/1471-2148-12-246] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 11/26/2012] [Indexed: 12/02/2022] Open
Abstract
Background Seamount-associated faunas are often considered highly endemic but isolation and diversification processes leading to such endemism have been poorly documented at those depths. Likewise, species delimitation and phylogenetic studies in deep-sea organisms remain scarce, due to the difficulty in obtaining samples, and sometimes controversial. The phylogenetic relationships within the precious coral family Coralliidae remain largely unexplored and the monophyly of its two constituent genera, Corallium Cuvier and Paracorallium Bayer & Cairns, has not been resolved. As traditionally recognized, the diversity of colonial forms among the various species correlates with the diversity in shape of their supporting axis, but the phylogenetic significance of these characters remains to be tested. We thus used mitochondrial sequence data to evaluate the monophyly of Corallium and Paracorallium and the species boundaries for nearly all named taxa in the family. Species from across the coralliid range, including material from Antarctica, Hawaii, Japan, New Zealand, Taiwan, Tasmania, the eastern Pacific and the western Atlantic were examined. Results The concatenated analysis of five mitochondrial regions (COI, 16S rRNA, ND2, and ND3-ND6) recovered two major coralliid clades. One clade is composed of two subgroups, the first including Corallium rubrum, the type species of the genus, together with a small group of Paracorallium species (P. japonicum and P. tortuosum) and C. medea (clade I-A); the other subgroup includes a poorly-resolved assemblage of six Corallium species (C. abyssale, C. ducale, C. imperiale, C. laauense, C. niobe, and C. sulcatum; clade I-B). The second major clade is well resolved and includes species of Corallium and Paracorallium (C. elatius, C. kishinouyei, C. konojoi, C. niveum, C. secundum, Corallium sp., Paracorallium nix, Paracorallium thrinax and Paracorallium spp.). A traditional taxonomic study of this clade delineated 11 morphospecies that were congruent with the general mixed Yule-coalescent (GMYC) model. A multilocus species-tree approach also identified the same two well-supported clades, being Clade I-B more recent in the species tree (18.0-15.9 mya) than in the gene tree (35.2-15.9 mya). In contrast, the diversification times for Clade II were more ancient in the species tree (136.4-41.7 mya) than in the gene tree (66.3-16.9 mya). Conclusions Our results provide no support for the taxonomic status of the two currently recognized genera in the family Coralliidae. Given that Paracorallium species were all nested within Corallium, we recognize the coralliid genus Corallium, which includes the type species of the family, and thus consider Paracorallium a junior synonym of Corallium. We propose the use of the genus Hemicorallium Gray for clade I-B (species with long rod sclerites, cylindrical autozooids and smooth axis). Species delimitation in clade I-B remains unclear and the molecular resolution for Coralliidae species is inconsistent in the two main clades. Some species have wide distributions, recent diversification times and low mtDNA divergence whereas other species exhibit narrower allopatric distributions, older diversification times and greater levels of mtDNA resolution.
Collapse
Affiliation(s)
- Néstor E Ardila
- Departamento de Ciencias Biológicas-Facultad de Ciencias, Laboratorio de Biología Molecular Marina, Universidad de los Andes, Carrera 1E No 18A-10, Bogotá, Colombia
| | | | | |
Collapse
|
170
|
Long-term population size of the North Atlantic humpback whale within the context of worldwide population structure. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0432-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
171
|
Xu Y, Wu Y, Song C, Zhang H. Simulating realistic genomic data with rare variants. Genet Epidemiol 2012; 37:163-72. [PMID: 23161487 DOI: 10.1002/gepi.21696] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/09/2012] [Accepted: 10/15/2012] [Indexed: 01/05/2023]
Abstract
Increasing evidence suggests that rare and generally deleterious genetic variants might have a strong impact on disease risks of not only Mendelian disease, but also many common diseases. However, identifying such rare variants remains challenging, and novel statistical methods and bioinformatic software must be developed. Hence, we have to extensively evaluate various methods under reasonable genetic models. Although there are abundant genomic data, they are not most helpful for the evaluation of the methods because the disease mechanism is unknown. Thus, it is imperative that we simulate genomic data that mimic the real data containing rare variants and that enable us to impose a known disease penetrance model. Although resampling simulation methods have shown their advantages in computational efficiency and in preserving important properties such as linkage disequilibrium (LD) and allele frequency, they still have limitations as we demonstrated. We propose an algorithm that combines a regression-based imputation with resampling to simulate genetic data with both rare and common variants. Logistic regression model was employed to fit the relationship between a rare variant and its nearby common variants in the 1000 Genomes Project data and then applied to the real data to fill in one rare variant at a time using the fitted logistic model based on common variants. Individuals then were simulated using the real data with imputed rare variants. We compared our method with existing simulators and demonstrated that our method performed well in retaining the real sample properties, such as LD and minor allele frequency, qualitatively.
Collapse
Affiliation(s)
- Yaji Xu
- Department of Biostatistics, Yale University, New Haven, CT 06511, USA
| | | | | | | |
Collapse
|
172
|
Gonçalves da Silva A, Cunha ICL, Santos WS, Luz SLB, Ribolla PEM, Abad-Franch F. Gene flow networks among American Aedes aegypti populations. Evol Appl 2012; 5:664-76. [PMID: 23144654 PMCID: PMC3492893 DOI: 10.1111/j.1752-4571.2012.00244.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 01/09/2012] [Indexed: 12/01/2022] Open
Abstract
The mosquito Aedes aegypti, the dengue virus vector, has spread throughout the tropics in historical times. While this suggests man-mediated dispersal, estimating contemporary connectivity among populations has remained elusive. Here, we use a large mtDNA dataset and a Bayesian coalescent framework to test a set of hypotheses about gene flow among American Ae. aegypti populations. We assessed gene flow patterns at the continental and subregional (Amazon basin) scales. For the Americas, our data favor a stepping-stone model in which gene flow is higher among adjacent populations but in which, at the same time, North American and southeastern Brazilian populations are directly connected, likely via sea trade. Within Amazonia, the model with highest support suggests extensive gene flow among major cities; Manaus, located at the center of the subregional transport network, emerges as a potentially important connecting hub. Our results suggest substantial connectivity across Ae. aegypti populations in the Americas. As long-distance active dispersal has not been observed in this species, our data support man-mediated dispersal as a major determinant of the genetic structure of American Ae. aegypti populations. The inferred topology of interpopulation connectivity can inform network models of Ae. aegypti and dengue spread.
Collapse
Affiliation(s)
- Anders Gonçalves da Silva
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Division of Marine and Atmospheric Research Hobart, TAS, Australia
| | | | | | | | | | | |
Collapse
|
173
|
Kohnen A, Richter I, Brandl R. No concordant phylogeographies of the rose gall wasp Diplolepis rosae (Hymenoptera, Cynipidae) and two associated parasitoids across Europe. PLoS One 2012; 7:e47156. [PMID: 23071742 PMCID: PMC3469489 DOI: 10.1371/journal.pone.0047156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 09/12/2012] [Indexed: 11/18/2022] Open
Abstract
According to the Host-tracking Hypothesis, species of higher trophic levels with a close relationship to their hosts, such as parasites or parasitoids, are expected to show spatio-temporal phylogeographic patterns similar to those of their host. Alternatively, with ecological sorting, a subset of the local species pools might shift to a related host species, thereby disengaging common phylogeographic patterns. Here, we compare the phylogeographic structures of the cynipid rose gall wasp Diplolepis rosae across Europe and of two of its most common parasitoids, the wasps Orthopelma mediator and Glyphomerus stigma, by analysing the sequences of two gene fragments (COI and ITS 2). The phylogeographic structures of the three species associated with roses were incongruent. D. rosae had the lowest genetic diversity with one major clade, O. mediator showed the classical phylogeographic structure for Europe with one eastern and one western clade, and G. stigma had the highest diversity but no geographical structuring. This discordance of geographical patterns may be explained by 1) the dispersal propensity of adult parasitoids or 2) the parasitoids having the ability to switch to another host, while the primary host becomes rare or is even not available. Furthermore there was no indication that phylogenetic patterns were affected by Wolbachia infections. Our results document that communities of closely interacting species may be the result of idiosyncratic biogeographic histories.
Collapse
Affiliation(s)
- Annette Kohnen
- Department of Animal Ecology, Philipps-Universität Marburg, Marburg, Germany.
| | | | | |
Collapse
|
174
|
Via S, Conte G, Mason-Foley C, Mills K. Localizing F(ST) outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow. Mol Ecol 2012; 21:5546-60. [PMID: 23057835 DOI: 10.1111/mec.12021] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Revised: 06/24/2012] [Accepted: 07/11/2012] [Indexed: 12/15/2022]
Abstract
Populations that maintain phenotypic divergence in sympatry typically show a mosaic pattern of genomic divergence, requiring a corresponding mosaic of genomic isolation (reduced gene flow). However, mechanisms that could produce the genomic isolation required for divergence-with-gene-flow have barely been explored, apart from the traditional localized effects of selection and reduced recombination near centromeres or inversions. By localizing F(ST) outliers from a genome scan of wild pea aphid host races on a Quantitative Trait Locus (QTL) map of key traits, we test the hypothesis that between-population recombination and gene exchange are reduced over large 'divergence hitchhiking' (DH) regions. As expected under divergence hitchhiking, our map confirms that QTL and divergent markers cluster together in multiple large genomic regions. Under divergence hitchhiking, the nonoutlier markers within these regions should show signs of reduced gene exchange relative to nonoutlier markers in genomic regions where ongoing gene flow is expected. We use this predicted difference among nonoutliers to perform a critical test of divergence hitchhiking. Results show that nonoutlier markers within clusters of F(ST) outliers and QTL resolve the genetic population structure of the two host races nearly as well as the outliers themselves, while nonoutliers outside DH regions reveal no population structure, as expected if they experience more gene flow. These results provide clear evidence for divergence hitchhiking, a mechanism that may dramatically facilitate the process of speciation-with-gene-flow. They also show the power of integrating genome scans with genetic analyses of the phenotypic traits involved in local adaptation and population divergence.
Collapse
Affiliation(s)
- Sara Via
- Department of Biology, University of Maryland, College Park, MD 21042, USA.
| | | | | | | |
Collapse
|
175
|
Phylogeography. Mol Ecol 2012. [DOI: 10.1002/9780470979365.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
176
|
References. Mol Ecol 2012. [DOI: 10.1002/9780470979365.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
177
|
Honda M, Matsui M, Tominaga A, Ota H, Tanaka S. Phylogeny and biogeography of the Anderson's crocodile newt, Echinotriton andersoni (Amphibia: Caudata), as revealed by mitochondrial DNA sequences. Mol Phylogenet Evol 2012; 65:642-53. [PMID: 22846685 DOI: 10.1016/j.ympev.2012.07.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/19/2012] [Accepted: 07/20/2012] [Indexed: 11/16/2022]
Abstract
The Anderson's crocodile newt, Echinotriton andersoni, is considered a relic and endangered species distributed in the Central Ryukyus. To elucidate phylogenetic relationships and detailed genetic structures among populations, we analyzed variation in the mitochondrial cytochrome b gene. Results strongly support a primary dichotomy between populations from the Amami and Okinawa Island Groups with substantial genetic divergence, favoring a primary divergence between the two island groups. Within the latter, populations from the southern part of Okinawajima Island are shown to be more closely related to those from Tokashikijima Island than to those from the northern and central parts of Okinawajima. The prominent genetic divergence between the two island groups of the Central Ryukyus seems to have initiated in the Miocene, i.e., prior to formation of the strait that has consistently separated these island groups since the Pleistocene. The ancestor of the southern Okinawajima-Tokashikijima is estimated to have migrated from the northern and central parts of Okinawajima into southern Okinawajima at the Pleistocene, and dispersed into Tokashikijima subsequently.
Collapse
Affiliation(s)
- Masanao Honda
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | | | | | | | | |
Collapse
|
178
|
Blanco-Pastor JL, Vargas P, Pfeil BE. Coalescent simulations reveal hybridization and incomplete lineage sorting in Mediterranean Linaria. PLoS One 2012; 7:e39089. [PMID: 22768061 PMCID: PMC3387178 DOI: 10.1371/journal.pone.0039089] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 05/18/2012] [Indexed: 11/21/2022] Open
Abstract
We examined the phylogenetic history of Linaria with special emphasis on the Mediterranean sect. Supinae (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (rpl32-trnLUAG, trnS-trnG). Coalescent simulations, a hybrid detection test and species tree inference in *BEAST revealed that incomplete lineage sorting and hybridization may both be responsible for the incongruent pattern observed. Additionally, we present a multilabelled *BEAST species tree as an alternative approach that allows the possibility of observing multiple placements in the species tree for the same taxa. That permitted the incorporation of processes such as hybridization within the tree while not violating the assumptions of the *BEAST model. This methodology is presented as a functional tool to disclose the evolutionary history of species complexes that have experienced both hybridization and incomplete lineage sorting. The drastic climatic events that have occurred in the Mediterranean since the late Miocene, including the Quaternary-type climatic oscillations, may have made both processes highly recurrent in the Mediterranean flora.
Collapse
Affiliation(s)
- José Luis Blanco-Pastor
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC), Madrid, Spain.
| | | | | |
Collapse
|
179
|
JACKSON NATHAND, AUSTIN CHRISTOPHERC. Inferring the evolutionary history of divergence despite gene flow in a lizard species, Scincella lateralis (Scincidae), composed of cryptic lineages. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01929.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
180
|
Human influence on the population decline and loss of genetic diversity in a small and isolated population of Sichuan snub-nosed monkeys (Rhinopithecus roxellana). Genetica 2012; 140:105-14. [DOI: 10.1007/s10709-012-9662-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 06/07/2012] [Indexed: 10/28/2022]
|
181
|
Tollis M, Ausubel G, Ghimire D, Boissinot S. Multi-locus phylogeographic and population genetic analysis of Anolis carolinensis: historical demography of a genomic model species. PLoS One 2012; 7:e38474. [PMID: 22685573 PMCID: PMC3369884 DOI: 10.1371/journal.pone.0038474] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 05/07/2012] [Indexed: 11/19/2022] Open
Abstract
The green anole (Anolis carolinensis) has been widely used as an animal model in physiology and neurobiology but has recently emerged as an important genomic model. The recent sequencing of its genome has shed new light on the evolution of vertebrate genomes and on the process that govern species diversification. Surprisingly, the patterns of genetic diversity within natural populations of this widespread and abundant North American lizard remain relatively unknown. In the present study, we use 10 novel nuclear DNA sequence loci (N = 62 to 152) and one mitochondrial locus (N = 226) to delimit green anole populations and infer their historical demography. We uncovered four evolutionarily distinct and geographically restricted lineages of green anoles using phylogenetics, bayesian clustering, and genetic distance methods. Molecular dating indicates that these lineages last shared a common ancestor ∼2 million years ago. Summary statistics and analysis of the frequency distributions of DNA polymorphisms strongly suggest range-wide expansions in population size. Using Bayesian Skyline Plots, we inferred the timing of population size expansions, which differ across lineages, and found evidence for a relatively recent and rapid westward expansion of green anoles across the Gulf Coastal Plain during the mid-Pleistocene. One surprising result is that the distribution of genetic diversity is not consistent with a latitudinal shift caused by climatic oscillations as is observed for many co-distributed taxa. This suggests that the most recent Pleistocene glacial cycles had a limited impact on the geographic distribution of the green anole at the northern limits of its range.
Collapse
Affiliation(s)
- Marc Tollis
- Biology Department, Queens College, City University of New York, Flushing, New York, United States of America
- Biology Program: Ecology, Evolutionary Biology and Behavior, Graduate Center, City University of New York, New York, New York, United States of America
| | - Gavriel Ausubel
- Biology Department, Queens College, City University of New York, Flushing, New York, United States of America
| | - Dhruba Ghimire
- Biology Department, Queens College, City University of New York, Flushing, New York, United States of America
| | - Stéphane Boissinot
- Biology Department, Queens College, City University of New York, Flushing, New York, United States of America
- Biology Program: Ecology, Evolutionary Biology and Behavior, Graduate Center, City University of New York, New York, New York, United States of America
| |
Collapse
|
182
|
Eldon B, Degnan JH. Multiple merger gene genealogies in two species: Monophyly, paraphyly, and polyphyly for two examples of Lambda coalescents. Theor Popul Biol 2012; 82:117-30. [PMID: 22613063 DOI: 10.1016/j.tpb.2012.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 05/07/2012] [Accepted: 05/09/2012] [Indexed: 10/28/2022]
Abstract
Probabilities of monophyly, paraphyly, and polyphyly of two-species gene genealogies are computed for modest sample sizes and compared for two different Λ coalescent processes. Coalescent processes belonging to the Λ coalescent family admit asynchronous multiple mergers of active ancestral lineages. Assigning a timescale to the time of divergence becomes a central issue when different populations have different coalescent processes running on different timescales. Clade probabilities in single populations are also computed, which can be useful for testing for taxonomic distinctiveness of an observed set of monophyletic lineages. The coalescence rates of multiple merger coalescent processes are functions of coalescent parameters. The effect of coalescent parameters on the probabilities studied depends on the coalescent process, and if the population is ancestral or derived. The probability of reciprocal monophyly tends to be somewhat lower, when associated with a Λ coalescent, under the null hypothesis that two groups come from the same population. However, even for fairly recent divergence times, the probability of monophyly tends to be higher as a function of the number of generations for coalescent processes that admit multiple mergers, and is sensitive to the parameter of one of the example processes.
Collapse
Affiliation(s)
- Bjarki Eldon
- Department of Statistics, University of Oxford, One South Parks Road, Oxford OX1 3TG, UK.
| | | |
Collapse
|
183
|
Karl SA, Toonen RJ, Grant WS, Bowen BW. Common misconceptions in molecular ecology: echoes of the modern synthesis. Mol Ecol 2012; 21:4171-89. [PMID: 22574714 DOI: 10.1111/j.1365-294x.2012.05576.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The field of molecular ecology has burgeoned into a large discipline spurred on by technical innovations that facilitate the rapid acquisition of large amounts of genotypic data, by the continuing development of theory to interpret results, and by the availability of computer programs to analyse data sets. As the discipline grows, however, misconceptions have become enshrined in the literature and are perpetuated by routine citations to other articles in molecular ecology. These misconceptions hamper a better understanding of the processes that influence genetic variation in natural populations and sometimes lead to erroneous conclusions. Here, we consider eight misconceptions commonly appearing in the literature: (i) some molecular markers are inherently better than other markers; (ii) mtDNA produces higher F(ST) values than nDNA; (iii) estimated population coalescences are real; (iv) more data are always better; (v) one needs to do a Bayesian analysis; (vi) selective sweeps influence mtDNA data; (vii) equilibrium conditions are critical for estimating population parameters; and (viii) having better technology makes us smarter than our predecessors. This is clearly not an exhaustive list and many others can be added. It is, however, sufficient to illustrate why we all need to be more critical of our own understanding of molecular ecology and to be suspicious of self-evident truths.
Collapse
Affiliation(s)
- Stephen A Karl
- Hawai'i Institute of Marine Biology, University of Hawai'i, Mānoa, Kāne'ohe, HI 96744, USA.
| | | | | | | |
Collapse
|
184
|
Cuthill JH, Charleston M. Phylogenetic codivergence supports coevolution of mimetic Heliconius butterflies. PLoS One 2012; 7:e36464. [PMID: 22586474 PMCID: PMC3346731 DOI: 10.1371/journal.pone.0036464] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 04/06/2012] [Indexed: 11/18/2022] Open
Abstract
The unpalatable and warning-patterned butterflies Heliconius erato and Heliconius melpomene provide the best studied example of mutualistic Müllerian mimicry, thought-but rarely demonstrated-to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of H. erato and H. melpomene, and this was initially hailed as one of the most striking known cases of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of H. erato and H. melpomene, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of H. erato and H. melpomene. Cophylogenetic historical reconstructions support repeated codivergence of mimetic populations, from the base of the sampled radiations. Pairwise distance correlation tests, based on our coalescent analyses plus recently published AFLP and wing colour pattern gene data, also suggest that the phylogenies of H. erato and H. melpomene show significant topological congruence. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of H. erato and H. melpomene occurred over the same time period, and are compatible with a series of temporally congruent codivergence events. Our results suggest that differences in within-species genetic divergence are the result of a greater overall effective population size for H. erato relative to H. melpomene and do not imply incongruence in the timing of their phylogenetic radiations. Repeated codivergence between Müllerian co-mimics, predicted to exert mutual selection pressures, strongly suggests coevolution. Our results therefore support a history of reciprocal coevolution between Müllerian co-mimics characterised by phylogenetic codivergence and parallel phenotypic change.
Collapse
Affiliation(s)
- Jennifer Hoyal Cuthill
- School of Information Technologies, University of Sydney, Sydney, New South Wales, Australia.
| | | |
Collapse
|
185
|
Enard W. Functional primate genomics—leveraging the medical potential. J Mol Med (Berl) 2012; 90:471-80. [DOI: 10.1007/s00109-012-0901-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 04/04/2012] [Accepted: 04/05/2012] [Indexed: 10/28/2022]
|
186
|
VERKUIL YVONNEI, PIERSMA THEUNIS, JUKEMA JOOP, HOOIJMEIJER JOSCEW, ZWARTS LEO, BAKER ALLANJ. The interplay between habitat availability and population differentiation: a case study on genetic and morphological structure in an inland wader (Charadriiformes). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01878.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
187
|
Henn BM, Hon L, Macpherson JM, Eriksson N, Saxonov S, Pe'er I, Mountain JL. Cryptic distant relatives are common in both isolated and cosmopolitan genetic samples. PLoS One 2012; 7:e34267. [PMID: 22509285 PMCID: PMC3317976 DOI: 10.1371/journal.pone.0034267] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 02/24/2012] [Indexed: 12/19/2022] Open
Abstract
Although a few hundred single nucleotide polymorphisms (SNPs) suffice to infer close familial relationships, high density genome-wide SNP data make possible the inference of more distant relationships such as 2nd to 9th cousinships. In order to characterize the relationship between genetic similarity and degree of kinship given a timeframe of 100–300 years, we analyzed the sharing of DNA inferred to be identical by descent (IBD) in a subset of individuals from the 23andMe customer database (n = 22,757) and from the Human Genome Diversity Panel (HGDP-CEPH, n = 952). With data from 121 populations, we show that the average amount of DNA shared IBD in most ethnolinguistically-defined populations, for example Native American groups, Finns and Ashkenazi Jews, differs from continentally-defined populations by several orders of magnitude. Via extensive pedigree-based simulations, we determined bounds for predicted degrees of relationship given the amount of genomic IBD sharing in both endogamous and ‘unrelated’ population samples. Using these bounds as a guide, we detected tens of thousands of 2nd to 9th degree cousin pairs within a heterogenous set of 5,000 Europeans. The ubiquity of distant relatives, detected via IBD segments, in both ethnolinguistic populations and in large ‘unrelated’ populations samples has important implications for genetic genealogy, forensics and genotype/phenotype mapping studies.
Collapse
Affiliation(s)
- Brenna M. Henn
- 23andMe, Inc., Mountain View, California, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
- * E-mail: (BMH); (JLM)
| | - Lawrence Hon
- 23andMe, Inc., Mountain View, California, United States of America
| | | | - Nick Eriksson
- 23andMe, Inc., Mountain View, California, United States of America
| | - Serge Saxonov
- 23andMe, Inc., Mountain View, California, United States of America
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, New York, United States of America
| | - Joanna L. Mountain
- 23andMe, Inc., Mountain View, California, United States of America
- * E-mail: (BMH); (JLM)
| |
Collapse
|
188
|
Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, RoyChoudhury A. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol 2012; 29:1917-32. [PMID: 22422763 DOI: 10.1093/molbev/mss086] [Citation(s) in RCA: 590] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove).
Collapse
Affiliation(s)
- David Bryant
- Department of Mathematics and Statistics and the Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand.
| | | | | | | | | |
Collapse
|
189
|
Peters JL, Roberts TE, Winker K, McCracken KG. Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history. PLoS One 2012; 7:e31972. [PMID: 22384117 PMCID: PMC3285185 DOI: 10.1371/journal.pone.0031972] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 01/17/2012] [Indexed: 12/26/2022] Open
Abstract
Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to test for deviations from selective neutrality in the gadwall (Anas strepera), a Holarctic duck. Nucleotide diversity among these loci varied by nearly two orders of magnitude (from 0.0004 to 0.029), and this heterogeneity could not be explained by differences in substitution rates alone. Using two different coalescent methods to infer models of population history and then simulating neutral genetic diversity under these models, we found that the observed among-locus heterogeneity in nucleotide diversity was significantly higher than expected for these simple models. Defining more complex models of population history demonstrated that a pre-divergence bottleneck was also unlikely to explain this heterogeneity. However, both selection and interspecific hybridization could account for the heterogeneity observed among loci. Regardless of the cause of the deviation, our results illustrate that violating key assumptions of coalescent models can mislead inferences of population history.
Collapse
Affiliation(s)
- Jeffrey L Peters
- Department of Biological Sciences, Wright State University, Dayton, Ohio, United States of America.
| | | | | | | |
Collapse
|
190
|
|
191
|
Vidal MA, Ortiz JC, Marín JC, Poulin E, Moreno PI. Comparative phylogeography of two co-distributed species of lizards of the genus Liolaemus (Squamata: Tropiduridae) from Southern Chile. AMPHIBIA-REPTILIA 2012. [DOI: 10.1163/156853811x622039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Comparative phylogeography describes the patterns of evolutionary divergence and whether or not they are congruent, in co-distributed populations of different taxa. If the populations of these taxa have been co-distributed for a prolonged time, and if the times between processes of perturbation or vicariance have been more or less stable, it is expected that patterns of divergence will be congruent in closely related species, for example because of similar biological and demographic characteristics.Liolaemus pictusandL. cyanogasterare widely co-distributed lizard species in southern Chile, occurring in a region with a complex topology. We analyzed the phylogeographic structure of the two lizard species usingCytochromebDNA sequences to estimate their genetic structure in response to historical events. Our results suggest an evolutionary pattern of genetic diversity for each species that is consistent with the geomorphological history of the region, suggesting a complex phylogeographic history inLiolaemusspecies. Also, the high levels of divergence among haplotypes in several populations suggest the possibility that their origin might predate the middle Pleistocene in both species. Finally, our results are consistent with our hypothesis that two species have responded to historical events in parallel, where historical process have been sufficient to influence their phylogeographical structure (0.80 congruency between topologies).
Collapse
Affiliation(s)
- Marcela A. Vidal
- 1Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Casilla 447, Chillán, Chile
| | - Juan Carlos Ortiz
- 2Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Juan Carlos Marín
- 1Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Casilla 447, Chillán, Chile
| | - Elie Poulin
- 3Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
| | - Patricio I. Moreno
- 3Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
| |
Collapse
|
192
|
Review of genetic diversity in malaria vectors (Culicidae: Anophelinae). INFECTION GENETICS AND EVOLUTION 2012; 12:1-12. [DOI: 10.1016/j.meegid.2011.08.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 08/05/2011] [Accepted: 08/07/2011] [Indexed: 12/27/2022]
|
193
|
|
194
|
Malaney JL, Frey JK, Cook JA. The biogeographic legacy of an imperilled taxon provides a foundation for assessing lineage diversification, demography and conservation genetics. DIVERS DISTRIB 2011. [DOI: 10.1111/j.1472-4642.2011.00866.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
195
|
de Gruijter JM, Lao O, Vermeulen M, Xue Y, Woodwark C, Gillson CJ, Coffey AJ, Ayub Q, Mehdi SQ, Kayser M, Tyler-Smith C. Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing. INVESTIGATIVE GENETICS 2011; 2:24. [PMID: 22133426 PMCID: PMC3287149 DOI: 10.1186/2041-2223-2-24] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 12/01/2011] [Indexed: 01/21/2023]
Abstract
Background Numerous genome-wide scans conducted by genotyping previously ascertained single-nucleotide polymorphisms (SNPs) have provided candidate signatures for positive selection in various regions of the human genome, including in genes involved in pigmentation traits. However, it is unclear how well the signatures discovered by such haplotype-based test statistics can be reproduced in tests based on full resequencing data. Four genes (oculocutaneous albinism II (OCA2), tyrosinase-related protein 1 (TYRP1), dopachrome tautomerase (DCT), and KIT ligand (KITLG)) implicated in human skin-color variation, have shown evidence for positive selection in Europeans and East Asians in previous SNP-scan data. In the current study, we resequenced 4.7 to 6.7 kb of DNA from each of these genes in Africans, Europeans, East Asians, and South Asians. Results Applying all commonly used neutrality-test statistics for allele frequency distribution to the newly generated sequence data provided conflicting results regarding evidence for positive selection. Previous haplotype-based findings could not be clearly confirmed. Although some tests were marginally significant for some populations and genes, none of them were significant after multiple-testing correction. Combined P values for each gene-population pair did not improve these results. Application of Approximate Bayesian Computation Markov chain Monte Carlo based to these sequence data using a simple forward simulator revealed broad posterior distributions of the selective parameters for all four genes, providing no support for positive selection. However, when we applied this approach to published sequence data on SLC45A2, another human pigmentation candidate gene, we could readily confirm evidence for positive selection, as previously detected with sequence-based and some haplotype-based tests. Conclusions Overall, our data indicate that even genes that are strong biological candidates for positive selection and show reproducible signatures of positive selection in SNP scans do not always show the same replicability of selection signals in other tests, which should be considered in future studies on detecting positive selection in genetic data.
Collapse
Affiliation(s)
- Johanna Maria de Gruijter
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands.,Netherlands Forensic Institute, Postbus 24044, The Hague, 2490 AA, The Netherlands
| | - Oscar Lao
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Mark Vermeulen
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Yali Xue
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Cara Woodwark
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Christopher J Gillson
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Alison J Coffey
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Qasim Ayub
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - S Qasim Mehdi
- Sindh Institute of Urology and Transplantation (SIUT) Karachi, Civil Hospital Karachi 74200, Pakistan
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Chris Tyler-Smith
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| |
Collapse
|
196
|
Novembre J, Ramachandran S. Perspectives on human population structure at the cusp of the sequencing era. Annu Rev Genomics Hum Genet 2011; 12:245-74. [PMID: 21801023 DOI: 10.1146/annurev-genom-090810-183123] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human groups show structured levels of genetic similarity as a consequence of factors such as geographical subdivision and genetic drift. Surveying this structure gives us a scientific perspective on human origins, sheds light on evolutionary processes that shape both human adaptation and disease, and is integral to effectively carrying out the mission of global medical genetics and personalized medicine. Surveys of population structure have been ongoing for decades, but in the past three years, single-nucleotide-polymorphism (SNP) array technology has provided unprecedented detail on human population structure at global and regional scales. These studies have confirmed well-known relationships between distantly related populations and uncovered previously unresolvable relationships among closely related human groups. SNPs represent the first dense genome-wide markers, and as such, their analysis has raised many challenges and insights relevant to the study of population genetics with whole-genome sequences. Here we draw on the lessons from these studies to anticipate the directions that will be most fruitful to pursue during the emerging whole-genome sequencing era.
Collapse
Affiliation(s)
- John Novembre
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90403, USA.
| | | |
Collapse
|
197
|
WEGIER A, PIÑEYRO-NELSON A, ALARCÓN J, GÁLVEZ-MARISCAL A, ÁLVAREZ-BUYLLA ER, PIÑERO D. Recent long-distance transgene flow into wild populations conforms to historical patterns of gene flow in cotton (Gossypium hirsutum) at its centre of origin. Mol Ecol 2011; 20:4182-94. [DOI: 10.1111/j.1365-294x.2011.05258.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
198
|
Bell RC, MacKenzie JB, Hickerson MJ, Chavarría KL, Cunningham M, Williams S, Moritz C. Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs. Proc Biol Sci 2011; 279:991-9. [PMID: 21900325 DOI: 10.1098/rspb.2011.1229] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Though Pleistocene refugia are frequently cited as drivers of species diversification, comparisons of molecular divergence among sister species typically indicate a continuum of divergence times from the Late Miocene, rather than a clear pulse of speciation events at the Last Glacial Maximum. Community-scale inference methods that explicitly test for multiple vicariance events, and account for differences in ancestral effective population size and gene flow, are well suited for detecting heterogeneity of species' responses to past climate fluctuations. We apply this approach to multi-locus sequence data from five co-distributed frog species endemic to the Wet Tropics rainforests of northeast Australia. Our results demonstrate at least two episodes of vicariance owing to climate-driven forest contractions: one in the Early Pleistocene and the other considerably older. Understanding how repeated cycles of rainforest contraction and expansion differentially affected lineage divergence among co-distributed species provides a framework for identifying evolutionary processes that underlie population divergence and speciation.
Collapse
Affiliation(s)
- Rayna C Bell
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.
| | | | | | | | | | | | | |
Collapse
|
199
|
Falahati-Anbaran M, Lundemo S, Ågren J, Stenøien HK. Genetic consequences of seed banks in the perennial herb Arabidopsis lyrata subsp. petraea (Brassicaceae). AMERICAN JOURNAL OF BOTANY 2011; 98:1475-1485. [PMID: 21875972 DOI: 10.3732/ajb.1100021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Seed banks may increase the effective population size (N(e)) of plants as a result of elevated coalescence times for alleles residing in the populations. This has been empirically demonstrated in populations of the annual Arabidopsis thaliana, whereas comparable data for perennial species are currently lacking. We studied the contribution of seed banks to effective sizes of natural populations of the self-incompatible, perennial Arabidopsis lyrata subsp. petraea, a close relative of A. thaliana. • METHODS Fourteen populations of A. lyrata collected throughout the Norwegian distribution range were analyzed using microsatellite markers. • KEY RESULTS The genetic composition of seed-bank and aboveground cohorts was found to be highly similar, with little genetic differentiation between cohorts in most populations. However, the proportion of private alleles was higher in aboveground than in seed-bank cohorts. The presence of seed banks significantly increased total N(e), but the contribution from seed banks to overall N(e) were lower than the contribution from aboveground cohorts in most populations. Estimated historical N(e) values, reflecting the effective sizes of populations throughout the history of the species, were considerably higher than estimates of contemporary N(e), reflecting number of reproducing individuals within the past few generations. • CONCLUSIONS The results show that the seed bank contributes to total N(e) in the perennial herb A. lyrata. However, the contribution is similar to or lower than that of the above-ground fraction of the population and markedly weaker than that previously documented in the annual A. thaliana.
Collapse
Affiliation(s)
- Mohsen Falahati-Anbaran
- Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
| | | | | | | |
Collapse
|
200
|
Garnica S, Spahn P, Oertel B, Ammirati J, Oberwinkler F. Tracking the evolutionary history of Cortinarius species in section Calochroi, with transoceanic disjunct distributions. BMC Evol Biol 2011; 11:213. [PMID: 21771336 PMCID: PMC3161008 DOI: 10.1186/1471-2148-11-213] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 07/19/2011] [Indexed: 01/08/2023] Open
Abstract
Background Cortinarius species in section Calochroi display local, clinal and circumboreal patterns of distribution across the Northern Hemisphere where these ectomycorrhizal fungi occur with host trees throughout their geographical range within a continent, or have disjunct intercontinental distributions, the origins of which are not understood. We inferred evolutionary histories of four species, 1) C. arcuatorum, 2) C. aureofulvus, 3) C. elegantior and 4) C. napus, from populations distributed throughout the Old World, and portions of the New World (Central- and North America) based on genetic variation of 154 haplotype internal transcribed spacer (ITS) sequences from 83 population samples. By describing the population structure of these species across their geographical distribution, we attempt to identify their historical migration and patterns of diversification. Results Models of population structure from nested clade, demographic and coalescent-based analyses revealed genetically differentiated and geographically structured haplotypes in C. arcuatorum and C. elegantior, while C. aureofulvus showed considerably less population structure and C. napus lacked sufficient genetic differentiation to resolve any population structure. Disjunct populations within C. arcuatorum, C. aureofulvus and C. elegantior show little or no morphological differentiation, whereas in C. napus there is a high level of homoplasy and phenotypic plasticity for veil and lamellae colour. The ITS sequences of the type specimens of C. albobrunnoides and C. albobrunnoides var. violaceovelatus were identical to one another and are treated as one species with a wider range of geographic distribution under C. napus. Conclusions Our results indicate that each of the Calochroi species has undergone a relatively independent evolutionary history, hypothesised as follows: 1) a widely distributed ancestral population of C. arcuatorum diverged into distinctive sympatric populations in the New World; 2) two divergent lineages in C. elegantior gave rise to the New World and Old World haplotypes, respectively; and 3) the low levels of genetic divergence within C. aureofulvus and C. napus may be the result of more recent demographic population expansions. The scenario of migration via the Bering Land Bridge provides the most probable explanation for contemporaneous disjunct geographic distributions of these species, but it does not offer an explanation for the low degree of genetic divergence between populations of C. aureofulvus and C. napus. Our findings are mostly consistent with the designation of New World allopatric populations as separate species from the European counterpart species C. arcuatorum and C. elegantior. We propose the synonymy of C. albobrunnoides, C. albobrunnoides var. violaceovelatus and C. subpurpureophyllus var. sulphureovelatus with C. napus. The results also reinforce previous observations that linked C. arcuatorum and C. aureofulvus displaying distributions in parts of North America and Europe. Interpretations of the population structure of these fungi suggest that host tree history has heavily influenced their modern distributions; however, the complex issues related to co-migration of these fungi with their tree hosts remain unclear at this time.
Collapse
Affiliation(s)
- Sigisfredo Garnica
- Organismic Botany, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany.
| | | | | | | | | |
Collapse
|