151
|
O'Fallon BD. A method to correct for the effects of purifying selection on genealogical inference. Mol Biol Evol 2010; 27:2406-16. [PMID: 20513741 DOI: 10.1093/molbev/msq132] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Accurate reconstruction of the divergence times among individuals is an essential step toward inferring population parameters from genetic data. However, our ability to reconstruct accurate genealogies is often thwarted by the evolutionary forces we hope to detect, most prominently natural selection. Here, I demonstrate that purifying selection acting at many linked sites can systematically bias current methods of genealogical reconstruction, and I present a new method that corrects for this bias by allowing a class of sites to have a time-dependent rate. The parameters influencing the time dependency can be estimated from the data, allowing for a general method to detect the presence of selected sites and correcting for their distortion of the apparent mutation rate. The method works well under a variety of scenarios, including gamma-distributed selection coefficients as well as entirely neutral evolution. I also compare the performance of the new method to relaxed clock models, and I demonstrate the method on a data set from the mitochondrion of the North Atlantic whale-"louse" Cyamus ovalis.
Collapse
|
152
|
Kornobis E, Pálsson S, Kristjánsson BK, Svavarsson J. Molecular evidence of the survival of subterranean amphipods (Arthropoda) during Ice Age underneath glaciers in Iceland. Mol Ecol 2010; 19:2516-30. [PMID: 20465590 DOI: 10.1111/j.1365-294x.2010.04663.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A Two endemic groundwater arthropod crustacean species, Crangonyx islandicus and Crymostygius thingvallensis, were recently discovered on the mid-Atlantic volcanic island of Iceland. The extent of morphological differences from closest relatives, endemism, along with the geographic isolation of Iceland and its complete coverage by glaciers 21,000 years ago, suggests that these two species have survived glaciation periods in sub-glacial refugia. Here we provide strong support for this hypothesis by an analysis of mitochondrial genetic variation within Crangonyx islandicus. Our results show that the species is divided into several distinct monophyletic groups that are found along the volcanic zone in Iceland, which have been separated by 0.5 to around 5 million years. The genetic divergence between groups reflects geographic distances between sampling sites, indicating that divergence occurred after the colonization of Iceland. The genetic patterns, as well as the dependency of genetic variation on distances from the tectonic plate boundary and altitude, points to recent expansion from several refugia within Iceland. This presents the first genetic evidence of multicellular organisms as complex as crustacean amphipods which have survived glaciations beneath an ice sheet. This survival may be explained by geothermal heat linked to volcanic activities, which may have maintained favourable habitats in fissures along the tectonic plate boundary in Iceland during glaciations.
Collapse
Affiliation(s)
- Etienne Kornobis
- Department of Biology, University of Iceland, Askja, Sturlugata 7, 101 Reykjavik, Iceland.
| | | | | | | |
Collapse
|
153
|
Pilot M, Branicki W, Jedrzejewski W, Goszczyński J, Jedrzejewska B, Dykyy I, Shkvyrya M, Tsingarska E. Phylogeographic history of grey wolves in Europe. BMC Evol Biol 2010; 10:104. [PMID: 20409299 PMCID: PMC2873414 DOI: 10.1186/1471-2148-10-104] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 04/21/2010] [Indexed: 02/06/2023] Open
Abstract
Background While it is generally accepted that patterns of intra-specific genetic differentiation are substantially affected by glacial history, population genetic processes occurring during Pleistocene glaciations are still poorly understood. In this study, we address the question of the genetic consequences of Pleistocene glaciations for European grey wolves. Combining our data with data from published studies, we analysed phylogenetic relationships and geographic distribution of mitochondrial DNA haplotypes for 947 contemporary European wolves. We also compared the contemporary wolf sequences with published sequences of 24 ancient European wolves. Results We found that haplotypes representing two haplogroups, 1 and 2, overlap geographically, but substantially differ in frequency between populations from south-western and eastern Europe. A comparison between haplotypes from Europe and other continents showed that both haplogroups are spread throughout Eurasia, while only haplogroup 1 occurs in contemporary North American wolves. All ancient wolf samples from western Europe that dated from between 44,000 and 1,200 years B.P. belonged to haplogroup 2, suggesting the long-term predominance of this haplogroup in this region. Moreover, a comparison of current and past frequencies and distributions of the two haplogroups in Europe suggested that haplogroup 2 became outnumbered by haplogroup 1 during the last several thousand years. Conclusions Parallel haplogroup replacement, with haplogroup 2 being totally replaced by haplogroup 1, has been reported for North American grey wolves. Taking into account the similarity of diets reported for the late Pleistocene wolves from Europe and North America, the correspondence between these haplogroup frequency changes may suggest that they were associated with ecological changes occurring after the Last Glacial Maximum.
Collapse
Affiliation(s)
- Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 00-679 Warszawa, Poland.
| | | | | | | | | | | | | | | |
Collapse
|
154
|
|
155
|
Greenhill SJ, Drummond AJ, Gray RD. How accurate and robust are the phylogenetic estimates of Austronesian language relationships? PLoS One 2010; 5:e9573. [PMID: 20224774 PMCID: PMC2835747 DOI: 10.1371/journal.pone.0009573] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2009] [Accepted: 01/22/2010] [Indexed: 11/30/2022] Open
Abstract
We recently used computational phylogenetic methods on lexical data to test between two scenarios for the peopling of the Pacific. Our analyses of lexical data supported a pulse-pause scenario of Pacific settlement in which the Austronesian speakers originated in Taiwan around 5,200 years ago and rapidly spread through the Pacific in a series of expansion pulses and settlement pauses. We claimed that there was high congruence between traditional language subgroups and those observed in the language phylogenies, and that the estimated age of the Austronesian expansion at 5,200 years ago was consistent with the archaeological evidence. However, the congruence between the language phylogenies and the evidence from historical linguistics was not quantitatively assessed using tree comparison metrics. The robustness of the divergence time estimates to different calibration points was also not investigated exhaustively. Here we address these limitations by using a systematic tree comparison metric to calculate the similarity between the Bayesian phylogenetic trees and the subgroups proposed by historical linguistics, and by re-estimating the age of the Austronesian expansion using only the most robust calibrations. The results show that the Austronesian language phylogenies are highly congruent with the traditional subgroupings, and the date estimates are robust even when calculated using a restricted set of historical calibrations.
Collapse
Affiliation(s)
- Simon J Greenhill
- Department of Psychology, University of Auckland, Auckland, New Zealand.
| | | | | |
Collapse
|
156
|
McCartney MA, Barreto FS. A Mitochondrial DNA Analysis of the Species Status of the Endemic Waccamaw Darter, Etheostoma perlongum. COPEIA 2010. [DOI: 10.1643/cg-07-169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
157
|
Papadopoulou A, Anastasiou I, Vogler AP. Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration. Mol Biol Evol 2010; 27:1659-72. [PMID: 20167609 DOI: 10.1093/molbev/msq051] [Citation(s) in RCA: 484] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Phylogenetic trees in insects are frequently dated by applying a "standard" mitochondrial DNA (mtDNA) clock estimated at 2.3% My(-1), but despite its wide use reliable calibration points have been lacking. Here, we used a well-established biogeographic barrier, the mid-Aegean trench separating the western and eastern Aegean archipelago, to estimate substitution rates in tenebrionid beetles. Cytochrome oxidase I (cox1) for six codistributed genera across 28 islands (444 individuals) on both sides of the mid-Aegean trench revealed 60 independently coalescing entities delimited with a mixed Yule-coalescent model. One representative per entity was used for phylogenetic analysis of mitochondrial (cox1, 16S rRNA) and nuclear (Mp20, 28S rRNA) genes. Six nodes marked geographically congruent east-west splits whose separation was largely contemporaneous and likely to reflect the formation of the mid-Aegean trench at 9-12 Mya. Based on these "known" dates, a divergence rate of 3.54% My(-1) for the cox1 gene (2.69% when combined with the 16S rRNA gene) was obtained under the preferred partitioning scheme and substitution model selected using Bayes factors. An extensive survey suggests that discrepancies in mtDNA substitution rates in the entomological literature can be attributed to the use of different substitution models, the use of different mitochondrial gene regions, mixing of intraspecific with interspecific data, and not accounting for variance in coalescent times or postseparation gene flow. Different treatments of these factors in the literature confound estimates of mtDNA substitution rates in opposing directions and obscure lineage-specific differences in rates when comparing data from various sources.
Collapse
Affiliation(s)
- Anna Papadopoulou
- Department of Entomology, Natural History Museum, London, United Kingdom.
| | | | | |
Collapse
|
158
|
Rebernig CA, Weiss-Schneeweiss H, Schneeweiss GM, Schönswetter P, Obermayer R, Villaseñor JL, Stuessy TF. Quaternary range dynamics and polyploid evolution in an arid brushland plant species (Melampodium cinereum, Asteraceae). Mol Phylogenet Evol 2010; 54:594-606. [DOI: 10.1016/j.ympev.2009.10.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 10/02/2009] [Accepted: 10/06/2009] [Indexed: 12/19/2022]
|
159
|
Ramakrishnan U, Hadly EA. Do complex population histories drive higher estimates of substitution rate in phylogenetic reconstructions? Mol Ecol 2009; 18:4341-3. [PMID: 19845859 DOI: 10.1111/j.1365-294x.2009.04334.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Our curiosity about biodiversity compels us to reconstruct the evolutionary past of species. Molecular evolutionary theory now allows parameterization of mathematically sophisticated and detailed models of DNA evolution, which have resulted in a wealth of phylogenetic histories. But reconstructing how species and population histories have played out is critically dependent on the assumptions we make, such as the clock-like accumulation of genetic differences over time and the rate of accumulation of such differences. An important stumbling block in the reconstruction of evolutionary history has been the discordance in estimates of substitution rate between phylogenetic and pedigree-based studies. Ancient genetic data recovered directly from the past are intermediate in time scale between phylogenetics-based and pedigree-based calibrations of substitution rate. Recent analyses of such ancient genetic data suggest that substitution rates are closer to the higher, pedigree-based estimates. In this issue, Navascués & Emerson (2009) model genetic data from contemporary and ancient populations that deviate from a simple demographic history (including changes in population size and structure) using serial coalescent simulations. Furthermore, they show that when these data are used for calibration, we are likely to arrive at upwardly biased estimates of mutation rate.
Collapse
Affiliation(s)
- Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore 560065, India.
| | | |
Collapse
|
160
|
Gibbs AJ, Fargette D, Garcia-Arenal F, Gibbs MJ. Time - the emerging dimension of plant virus studies. J Gen Virol 2009; 91:13-22. [DOI: 10.1099/vir.0.015925-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
|
161
|
Galtier N, Nabholz B, Glémin S, Hurst GDD. Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Mol Ecol 2009; 18:4541-50. [PMID: 19821901 DOI: 10.1111/j.1365-294x.2009.04380.x] [Citation(s) in RCA: 611] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- N Galtier
- Institut des Sciences de l'Evolution, Université Montpellier 2, C.N.R.S. UMR 5554, Place E. Bataillon, CC 64, 34195 Montpellier, France.
| | | | | | | |
Collapse
|
162
|
NAVASCUÉS MIGUEL, EMERSON BRENTC. Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods. Mol Ecol 2009; 18:4390-7. [DOI: 10.1111/j.1365-294x.2009.04333.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
163
|
Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2. J Virol 2009; 83:12813-21. [PMID: 19812157 DOI: 10.1128/jvi.01719-09] [Citation(s) in RCA: 190] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Porcine circovirus 2 (PCV2) is the primary etiological agent of postweaning multisystemic wasting syndrome (PMWS), one of the most economically important emerging swine diseases worldwide. Virulent PCV2 was first identified following nearly simultaneous outbreaks of PMWS in North America and Europe in the 1990s and has since achieved global distribution. However, the processes responsible for the emergence and spread of PCV2 remain poorly understood. Here, phylogenetic and cophylogenetic inferences were utilized to address key questions on the time scale, processes, and geographic diffusion of emerging PCV2. The results of these analyses suggest that the two genotypes of PCV2 (PCV2a and PCV2b) are likely to have emerged from a common ancestor approximately 100 years ago and have been on independent evolutionary trajectories since that time, despite cocirculating in the same host species and geographic regions. The patterns of geographic movement of PCV2 that we recovered appear to mimic those of the global pig trade and suggest that the movement of asymptomatic animals is likely to have facilitated the rapid spread of virulent PCV2 around the globe. We further estimated the rate of nucleotide substitution for PCV2 to be on the order of 1.2 x 10(-3) substitutions/site/year, the highest yet recorded for a single-stranded DNA virus. This high rate of evolution may allow PCV2 to maintain evolutionary dynamics closer to those of single-stranded RNA viruses than to those of double-stranded DNA viruses, further facilitating the rapid emergence of PCV2 worldwide.
Collapse
|
164
|
Förster DW, Gündüz I, Nunes AC, Gabriel S, Ramalhinho MG, Mathias ML, Britton-Davidian J, Searle JB. Molecular insights into the colonization and chromosomal diversification of Madeiran house mice. Mol Ecol 2009; 18:4477-94. [PMID: 19754514 DOI: 10.1111/j.1365-294x.2009.04344.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The colonization history of Madeiran house mice was investigated by analysing the complete mitochondrial (mt) D-loop sequences of 156 mice from the island of Madeira and mainland Portugal, extending on previous studies. The numbers of mtDNA haplotypes from Madeira and mainland Portugal were substantially increased (17 and 14 new haplotypes respectively), and phylogenetic analysis confirmed the previously reported link between the Madeiran archipelago and northern Europe. Sequence analysis revealed the presence of four mtDNA lineages in mainland Portugal, of which one was particularly common and widespread (termed the 'Portugal Main Clade'). There was no support for population bottlenecks during the formation of the six Robertsonian chromosome races on the island of Madeira, and D-loop sequence variation was not found to be structured according to karyotype. The colonization time of the Madeiran archipelago by Mus musculus domesticus was approached using two molecular dating methods (mismatch distribution and Bayesian skyline plot). Time estimates based on D-loop sequence variation at mainland sites (including previously published data from France and Turkey) were evaluated in the context of the zooarchaeological record of M. m. domesticus. A range of values for mutation rate (mu) and number of mouse generations per year was considered in these analyses because of the uncertainty surrounding these two parameters. The colonization of Portugal and Madeira by house mice is discussed in the context of the best-supported parameter values. In keeping with recent studies, our results suggest that mutation rate estimates based on interspecific divergence lead to gross overestimates concerning the timing of recent within-species events.
Collapse
Affiliation(s)
- D W Förster
- Department of Biology, University of York, York YO10 5YW, UK.
| | | | | | | | | | | | | | | |
Collapse
|
165
|
Endicott P, Ho SY, Metspalu M, Stringer C. Evaluating the mitochondrial timescale of human evolution. Trends Ecol Evol 2009; 24:515-21. [DOI: 10.1016/j.tree.2009.04.006] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 03/27/2009] [Accepted: 04/01/2009] [Indexed: 01/28/2023]
|
166
|
CENTENO-CUADROS A, DELIBES M, GODOY JA. Phylogeography of Southern Water Vole (Arvicola sapidus): evidence for refugia within the Iberian glacial refugium? Mol Ecol 2009; 18:3652-67. [DOI: 10.1111/j.1365-294x.2009.04297.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
167
|
Peterson GI, Masel J. Quantitative prediction of molecular clock and ka/ks at short timescales. Mol Biol Evol 2009; 26:2595-603. [PMID: 19661199 DOI: 10.1093/molbev/msp175] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Recent empirical studies of taxa including humans, fish, and birds have shown elevated rates of molecular evolution between species that diverged recently. Using the Moran model, we calculate expected divergence as a function of time. Our findings suggest that the observed phenomenon of elevated rates at short timescales is consistent with standard population genetics theory. The apparent acceleration of the molecular clock at short timescales can be explained by segregating polymorphisms present at the time of the ancestral population, both neutral and slightly deleterious, and not newly arising slightly deleterious mutations as has been previously hypothesized. Our work also suggests that the duration of the rate elevation depends on the effective population size, providing a method to correct time estimates of recent divergence events. Our model concords with estimates of divergence obtained from African cichlid fish and humans. As an additional application of our model, we calculate that K(a)/K(s) is elevated within a population before decaying slowly to its long-term value. Similar to the molecular clock, the duration and magnitude of K(a)/K(s) elevation depend on the effective population size. Unlike the molecular clock, however, K(a)/K(s) elevation is caused by newly arising slightly deleterious mutations. This elevation, although not as severe in magnitude as had been previously predicted in models neglecting ancestral polymorphism, persists slightly longer.
Collapse
|
168
|
MCDEVITT ALLAND, RAMBAU RAMUGONDOV, O'BRIEN JOHN, MCDEVITT CDAMIEN, HAYDEN THOMASJ, SEARLE JEREMYB. Genetic variation in Irish pygmy shrews Sorex minutus (Soricomorpha: Soricidae): implications for colonization history. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01218.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
169
|
Dixon CJ, Schönswetter P, Vargas P, Ertl S, Schneeweiss GM. Bayesian hypothesis testing supports long-distance Pleistocene migrations in a European high mountain plant (Androsace vitaliana, Primulaceae). Mol Phylogenet Evol 2009; 53:580-91. [PMID: 19622392 DOI: 10.1016/j.ympev.2009.07.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 07/01/2009] [Accepted: 07/06/2009] [Indexed: 11/19/2022]
Abstract
Colonization of the south-western European mountain ranges is suggested to have predominantly progressed from the Iberian Peninsula eastwards, but this hypothesis has never been tested in a statistical framework. Here, we test this hypothesis using Androsace vitaliana, a high elevation species with eight mostly allopatric subspecies, which is widely but disjunctly distributed across all major south-western European mountain ranges. To this end, we use plastid and nuclear sequence data as well as fingerprint (amplified fragment length polymorphisms) data and employ Bayesian methods, which allow co-estimation of genealogy and divergence times using explicit demographic models, as well as hypothesis testing via Bayes factors. Irrespective of the ambiguity concerning where A. vitaliana started to diversify -- both the Alps and the mountain ranges of the Iberian Peninsula outside the Pyrenees were possible -- colonization routes were not simply unidirectional, but involved Pleistocene connections between the Alps and mountain ranges of the Iberian Peninsula bypassing the interjacent Pyrenees via long-distance dispersal. In contrast, the species' post-glacial history is shaped by regional gene pool homogenization resulting in the genetic pattern showing good congruence with geographical proximity in agreement with a vicariance model, but only partly supporting current taxonomy.
Collapse
Affiliation(s)
- Christopher J Dixon
- Department of Biogeography and Botanical Garden, University of Vienna, Vienna, Austria.
| | | | | | | | | |
Collapse
|
170
|
Debruyne R, Poinar HN. Time Dependency of Molecular Rates in Ancient DNA Data Sets, A Sampling Artifact? Syst Biol 2009; 58:348-60. [DOI: 10.1093/sysbio/syp028] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
| | - Hendrik N. Poinar
- Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L9, Canada
| |
Collapse
|
171
|
Rodrigo A, Bertels F, Heled J, Noder R, Shearman H, Tsai P. The perils of plenty: what are we going to do with all these genes? Philos Trans R Soc Lond B Biol Sci 2009; 363:3893-902. [PMID: 18852100 DOI: 10.1098/rstb.2008.0173] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This new century's biology promises more of everything--more genes, more organisms, more species and, in short, more data. The flood of data challenges us to find better and quicker ways to summarize and analyse. Here, we present preliminary results and proofs of concept from three of our research projects that are motivated by our search for solutions to the perils of plenty. First, we discuss how models of evolution can accommodate change to better reflect the dynamics of sequence diversity, particularly when it is becoming a lot easier to obtain sequences at different times and across intervals where the probability of new mutations contributing to this diversity is high. Second, we describe our work on the use of a single locus for species delimitation; this research targets the new DNA-barcoding approach that aims to catalogue the entirety of life. We have developed a single-locus test based on the coalescent that tests the null hypothesis of panmixis. Finally, we discuss new sequencing technologies, the types of data available and the efficacy of alignment-free methods to estimate pairwise distances for phylogenetic analyses.
Collapse
Affiliation(s)
- Allen Rodrigo
- Allan Wilson Centre for Molecular Evolution and Bioinformatics Institute, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | | | | | | | | | | |
Collapse
|
172
|
Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards MB. Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 2009; 84:740-59. [PMID: 19500773 DOI: 10.1016/j.ajhg.2009.05.001] [Citation(s) in RCA: 487] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 04/20/2009] [Accepted: 05/01/2009] [Indexed: 11/15/2022] Open
Abstract
There is currently no calibration available for the whole human mtDNA genome, incorporating both coding and control regions. Furthermore, as several authors have pointed out recently, linear molecular clocks that incorporate selectable characters are in any case problematic. We here confirm a modest effect of purifying selection on the mtDNA coding region and propose an improved molecular clock for dating human mtDNA, based on a worldwide phylogeny of > 2000 complete mtDNA genomes and calibrating against recent evidence for the divergence time of humans and chimpanzees. We focus on a time-dependent mutation rate based on the entire mtDNA genome and supported by a neutral clock based on synonymous mutations alone. We show that the corrected rate is further corroborated by archaeological dating for the settlement of the Canary Islands and Remote Oceania and also, given certain phylogeographic assumptions, by the timing of the first modern human settlement of Europe and resettlement after the Last Glacial Maximum. The corrected rate yields an age of modern human expansion in the Americas at approximately 15 kya that-unlike the uncorrected clock-matches the archaeological evidence, but continues to indicate an out-of-Africa dispersal at around 55-70 kya, 5-20 ky before any clear archaeological record, suggesting the need for archaeological research efforts focusing on this time window. We also present improved rates for the mtDNA control region, and the first comprehensive estimates of positional mutation rates for human mtDNA, which are essential for defining mutation models in phylogenetic analyses.
Collapse
Affiliation(s)
- Pedro Soares
- Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
173
|
KORSTEN MARJU, HO SIMONYW, DAVISON JOHN, PÄHN BERIT, VULLA EGLE, ROHT MARIS, TUMANOV IGORL, KOJOLA ILPO, ANDERSONE-LILLEY ZANETE, OZOLINS JANIS, PILOT MALGORZATA, MERTZANIS YORGOS, GIANNAKOPOULOS ALEXIOS, VOROBIEV ALEXA, MARKOV NIKOLAII, SAVELJEV ALEXANDERP, LYAPUNOVA ELENAA, ABRAMOV ALEXEIV, MÄNNIL PEEP, VALDMANN HARRI, PAZETNOV SERGEIV, PAZETNOV VALENTINS, RÕKOV ALEXANDERM, SAARMA URMAS. Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals? Mol Ecol 2009; 18:1963-79. [DOI: 10.1111/j.1365-294x.2009.04163.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
174
|
Ohnishi N, Uno R, Ishibashi Y, Tamate HB, Oi T. The influence of climatic oscillations during the Quaternary Era on the genetic structure of Asian black bears in Japan. Heredity (Edinb) 2009; 102:579-89. [PMID: 19319151 DOI: 10.1038/hdy.2009.28] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The Asian black bear (Ursus thibetanus) inhabits two of the main islands, Honshu and Shikoku, in Japan. To determine how climatic oscillations during the Quaternary Era affected the genetic structure of the black bear populations in Japan, we examined their phylogeographic relationships and compared their genetic structure. We analysed an approximately 700-bp sequence in the D-loop region of mitochondrial DNA collected from 589 bears in this study with 108 bears from a previous study. We observed a total of 57 haplotypes and categorized them into three clusters (Eastern, Western and Southern) based on the spatial distribution of the haplotypes. All but 2 of the 41 haplotypes in the Eastern cluster were distributed locally. Genetic diversity was generally low in northern Japan and high in central Japan. Demographic tests rejected the expansion model in northern populations. Haplotypes of the Western and Southern clusters were unique to local populations. We conclude that the extant genetic structure of the Asian black bear populations arose as follows: first, populations became small and genetic drift decreased genetic diversity in the northern area during the last glacial period, whereas large continuous populations existed in the southern part of central Japan. These patterns were essentially maintained until the present time. In western and southern Japan, the effects of climatic oscillations were smaller, and thus, local structure was maintained.
Collapse
Affiliation(s)
- N Ohnishi
- Kansai Research Center, Forestry and Forest Products Research Institute, Nagaikyutaro, Kyoto, Japan.
| | | | | | | | | |
Collapse
|
175
|
Gray RD, Drummond AJ, Greenhill SJ. Language phylogenies reveal expansion pulses and pauses in Pacific settlement. Science 2009; 323:479-83. [PMID: 19164742 DOI: 10.1126/science.1166858] [Citation(s) in RCA: 292] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Debates about human prehistory often center on the role that population expansions play in shaping biological and cultural diversity. Hypotheses on the origin of the Austronesian settlers of the Pacific are divided between a recent "pulse-pause" expansion from Taiwan and an older "slow-boat" diffusion from Wallacea. We used lexical data and Bayesian phylogenetic methods to construct a phylogeny of 400 languages. In agreement with the pulse-pause scenario, the language trees place the Austronesian origin in Taiwan approximately 5230 years ago and reveal a series of settlement pauses and expansion pulses linked to technological and social innovations. These results are robust to assumptions about the rooting and calibration of the trees and demonstrate the combined power of linguistic scholarship, database technologies, and computational phylogenetic methods for resolving questions about human prehistory.
Collapse
Affiliation(s)
- R D Gray
- Department of Psychology, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | | |
Collapse
|
176
|
McDEVITT ALLAND, MARIANI STEFANO, HEBBLEWHITE MARK, DECESARE NICHOLASJ, MORGANTINI LUIGI, SEIP DALE, WECKWORTH BYRONV, MUSIANI MARCO. Survival in the Rockies of an endangered hybrid swarm from diverged caribou (Rangifer tarandus) lineages. Mol Ecol 2009; 18:665-79. [DOI: 10.1111/j.1365-294x.2008.04050.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
177
|
Benavides E, Baum R, Snell HM, Snell HL, Sites JW. Island biogeography of Galápagos lava lizards (Tropiduridae: Microlophus): species diversity and colonization of the archipelago. Evolution 2009; 63:1606-26. [PMID: 19154379 DOI: 10.1111/j.1558-5646.2009.00617.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The "lava lizards" (Microlophus) are distributed throughout the Galápagos Archipelago, and consist of radiations derived from two independent colonizations. The "Eastern Radiation" includes M. bivittatus and M. habeli endemic to San Cristobal and Marchena Islands. The "Western Radiation" includes five to seven historically recognized species distributed across almost the entire Archipelago. We combine dense geographic sampling and multilocus sequence data to estimate a phylogenetic hypothesis for the Western Radiation, to delimit species boundaries in this radiation, and to estimate a time frame for colonization events. Our phylogenetic hypothesis rejects two earlier topologies for the Western Radiation and paraphyly of M. albemarlensis, while providing strong support for single colonizations on each island. The colonization history implied by our phylogeny is consistent with general expectations of an east-to-west route predicted by the putative age of island groups, and prevailing ocean currents in the Archipelago. Additionally, combined evidence suggests that M. indefatigabilis from Santa Fe should be recognized as a full species. Finally, molecular divergence estimates suggest that the two colonization events likely occurred on the oldest existing islands, and the Western Radiation represents a recent radiation that, in most cases, has produced species that are considerably younger than the islands they inhabit.
Collapse
Affiliation(s)
- Edgar Benavides
- Department of Biology, Brigham Young University, Provo, Utah 84602, USA.
| | | | | | | | | |
Collapse
|
178
|
Miller HC, Moore JA, Allendorf FW, Daugherty CH. The evolutionary rate of tuatara revisited. Trends Genet 2009; 25:13-5; author reply 16-8. [DOI: 10.1016/j.tig.2008.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 09/18/2008] [Accepted: 09/23/2008] [Indexed: 01/20/2023]
|
179
|
Feng L, Reeves PR, Lan R, Ren Y, Gao C, Zhou Z, Ren Y, Cheng J, Wang W, Wang J, Qian W, Li D, Wang L. A recalibrated molecular clock and independent origins for the cholera pandemic clones. PLoS One 2008; 3:e4053. [PMID: 19115014 PMCID: PMC2605724 DOI: 10.1371/journal.pone.0004053] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 11/18/2008] [Indexed: 01/30/2023] Open
Abstract
Cholera, caused by Vibrio cholerae, erupted globally from South Asia in 7 pandemics, but there were also local outbreaks between the 6(th) (1899-1923) and 7(th) (1961-present) pandemics. All the above are serotype O1, whereas environmental or invertebrate isolates are antigenically diverse. The pre 7th pandemic isolates mentioned above, and other minor pathogenic clones, are related to the 7(th) pandemic clone, while the 6(th) pandemic clone is in the same lineage but more distantly related, and non-pathogenic isolates show no clonal structure. To understand the origins and relationships of the pandemic clones, we sequenced the genomes of a 1937 prepandemic strain and a 6(th) pandemic isolate, and compared them with the published 7(th) pandemic genome. We distinguished mutational and recombinational events, and allocated these and other events, to specific branches in the evolutionary tree. There were more mutational than recombinational events, but more genes, and 44 times more base pairs, changed by recombination. We used the mutational single-nucleotide polymorphisms and known isolation dates of the prepandemic and 7(th) pandemic isolates to estimate the mutation rate, and found it to be 100 fold higher than usually assumed. We then used this to estimate the divergence date of the 6(th) and 7(th) pandemic clones to be about 1880. While there is a large margin of error, this is far more realistic than the 10,000-50,000 years ago estimated using the usual assumptions. We conclude that the 2 pandemic clones gained pandemic potential independently, and overall there were 29 insertions or deletions of one or more genes. There were also substantial changes in the major integron, attributed to gain of individual cassettes including copying from within, or loss of blocks of cassettes. The approaches used open up new avenues for analysing the origin and history of other important pathogens.
Collapse
Affiliation(s)
- Lu Feng
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin Economic-Technological Development Area (TEDA), Tianjin, China
| | - Peter R. Reeves
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Yi Ren
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Chunxu Gao
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Zhemin Zhou
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Yan Ren
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Jiansong Cheng
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Wei Wang
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Nankai University, Tianjin Economic-Technological Development Area (TEDA), Tianjin, China
| | - Jianmei Wang
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Wubin Qian
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Dan Li
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin Economic-Technological Development Area (TEDA), Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Nankai University, Tianjin Economic-Technological Development Area (TEDA), Tianjin, China
- * E-mail:
| |
Collapse
|
180
|
Maggs CA, Castilho R, Foltz D, Henzler C, Jolly MT, Kelly J, Olsen J, Perez KE, Stam W, Väinölä R, Viard F, Wares J. EVALUATING SIGNATURES OF GLACIAL REFUGIA FOR NORTH ATLANTIC BENTHIC MARINE TAXA. Ecology 2008; 89:S108-22. [PMID: 19097488 DOI: 10.1890/08-0257.1] [Citation(s) in RCA: 251] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Christine A Maggs
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
181
|
Millar CD, Dodd A, Anderson J, Gibb GC, Ritchie PA, Baroni C, Woodhams MD, Hendy MD, Lambert DM. Mutation and evolutionary rates in adélie penguins from the antarctic. PLoS Genet 2008; 4:e1000209. [PMID: 18833304 PMCID: PMC2546446 DOI: 10.1371/journal.pgen.1000209] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 08/25/2008] [Indexed: 12/15/2022] Open
Abstract
Precise estimations of molecular rates are fundamental to our understanding of the processes of evolution. In principle, mutation and evolutionary rates for neutral regions of the same species are expected to be equal. However, a number of recent studies have shown that mutation rates estimated from pedigree material are much faster than evolutionary rates measured over longer time periods. To resolve this apparent contradiction, we have examined the hypervariable region (HVR I) of the mitochondrial genome using families of Adélie penguins (Pygoscelis adeliae) from the Antarctic. We sequenced 344 bps of the HVR I from penguins comprising 508 families with 915 chicks, together with both their parents. All of the 62 germline heteroplasmies that we detected in mothers were also detected in their offspring, consistent with maternal inheritance. These data give an estimated mutation rate (micro) of 0.55 mutations/site/Myrs (HPD 95% confidence interval of 0.29-0.88 mutations/site/Myrs) after accounting for the persistence of these heteroplasmies and the sensitivity of current detection methods. In comparison, the rate of evolution (k) of the same HVR I region, determined using DNA sequences from 162 known age sub-fossil bones spanning a 37,000-year period, was 0.86 substitutions/site/Myrs (HPD 95% confidence interval of 0.53 and 1.17). Importantly, the latter rate is not statistically different from our estimate of the mutation rate. These results are in contrast to the view that molecular rates are time dependent.
Collapse
Affiliation(s)
- Craig D. Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Andrew Dodd
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Jennifer Anderson
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Gillian C. Gibb
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Peter A. Ritchie
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Carlo Baroni
- Dipartmento Scienze della Terra, Università di Pisa, Pisa, Italy
- Consiglio Nazionale Ricerche, Centro Studio Geologia Strutturale, Pisa, Italy
| | - Michael D. Woodhams
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Fundamental Sciences, Massey University Palmerston North, Palmerston North, New Zealand
| | - Michael D. Hendy
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Fundamental Sciences, Massey University Palmerston North, Palmerston North, New Zealand
| | - David M. Lambert
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
- * E-mail:
| |
Collapse
|
182
|
GRATTON P, KONOPIŃSKI MK, SBORDONI V. Pleistocene evolutionary history of the Clouded Apollo (Parnassius mnemosyne): genetic signatures of climate cycles and a ‘time-dependent’ mitochondrial substitution rate. Mol Ecol 2008; 17:4248-62. [DOI: 10.1111/j.1365-294x.2008.03901.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
183
|
Smith CI, Godsoe WKW, Tank S, Yoder JB, Pellmyr O. DISTINGUISHING COEVOLUTION FROM COVICARIANCE IN AN OBLIGATE POLLINATION MUTUALISM: ASYNCHRONOUS DIVERGENCE IN JOSHUA TREE AND ITS POLLINATORS. Evolution 2008; 62:2676-87. [DOI: 10.1111/j.1558-5646.2008.00500.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
184
|
Fagundes NJR, Kanitz R, Bonatto SL. A reevaluation of the Native American mtDNA genome diversity and its bearing on the models of early colonization of Beringia. PLoS One 2008; 3:e3157. [PMID: 18797501 PMCID: PMC2527677 DOI: 10.1371/journal.pone.0003157] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 08/08/2008] [Indexed: 11/18/2022] Open
Abstract
The Americas were the last continents to be populated by humans, and their colonization represents a very interesting chapter in our species' evolution in which important issues are still contentious or largely unknown. One difficult topic concerns the details of the early peopling of Beringia, such as for how long it was colonized before people moved into the Americas and the demography of this occupation. A recent work using mitochondrial genome (mtDNA) data presented evidence for a so called "three-stage model" consisting of a very early expansion into Beringia followed by approximately 20,000 years of population stability before the final entry into the Americas. However, these results are in disagreement with other recent studies using similar data and methods. Here, we reanalyze their data to check the robustness of this model and test the ability of Native American mtDNA to discriminate details of the early colonization of Beringia. We apply the Bayesian Skyline Plot approach to recover the past demographic dynamic underpinning these events using different mtDNA data sets. Our results refute the specific details of the "three-stage model", since the early stage of expansion into Beringia followed by a long period of stasis could not be reproduced in any mtDNA data set cleaned from non-Native American haplotypes. Nevertheless, they are consistent with a moderate population bottleneck in Beringia associated with the Last Glacial Maximum followed by a strong population growth around 18,000 years ago as suggested by other recent studies. We suggest that this bottleneck erased the signals of ancient demographic history from recent Native American mtDNA pool, and conclude that the proposed early expansion and occupation of Beringia is an artifact caused by the misincorporation of non-Native American haplotypes.
Collapse
Affiliation(s)
- Nelson J. R. Fagundes
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ricardo Kanitz
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Sandro L. Bonatto
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
| |
Collapse
|
185
|
MORRIS ASHLEYB, ICKERT-BOND STEFANIEM, BRUNSON DBURKE, SOLTIS DOUGLASE, SOLTIS PAMELAS. Phylogeographical structure and temporal complexity in American sweetgum (Liquidambar styraciflua; Altingiaceae). Mol Ecol 2008; 17:3889-900. [DOI: 10.1111/j.1365-294x.2008.03875.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
186
|
YANNIC G, BASSET P, HAUSSER J. Phylogeography and recolonization of the Swiss Alps by the Valais shrew (Sorex antinorii), inferred with autosomal and sex-specific markers. Mol Ecol 2008; 17:4118-33. [DOI: 10.1111/j.1365-294x.2008.03888.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
187
|
Axelsson E, Willerslev E, Gilbert MTP, Nielsen R. The effect of ancient DNA damage on inferences of demographic histories. Mol Biol Evol 2008; 25:2181-7. [PMID: 18653730 DOI: 10.1093/molbev/msn163] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The field of ancient DNA (aDNA) is casting new light on many evolutionary questions. However, problems associated with the postmortem instability of DNA may complicate the interpretation of aDNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates of diversity. In this paper, we examine the effect of DNA damage on population genetic estimates of ancestral population size. We simulate data using standard coalescent simulations that include postmortem damage and show that estimates of effective population sizes are inflated around, or right after, the sampling time of the ancestral DNA sequences. This bias leads to estimates of increasing, and then decreasing, population sizes, as observed in several recently published studies. We reanalyze a recently published data set of DNA sequences from the Bison (Bison bison/Bison priscus) and show that the signal for a change in effective population size in this data set vanishes once the effects of putative damage are removed. Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution.
Collapse
Affiliation(s)
- Erik Axelsson
- Department of Biology, Evolutionary Biology, Copenhagen University, Copenhagen, Denmark
| | | | | | | |
Collapse
|
188
|
Brown R, Terrasa B, Pérez-Mellado V, Castro J, Hoskisson P, Picornell A, Ramon M. Bayesian estimation of post-Messinian divergence times in Balearic Island lizards. Mol Phylogenet Evol 2008; 48:350-8. [DOI: 10.1016/j.ympev.2008.04.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Revised: 03/19/2008] [Accepted: 04/06/2008] [Indexed: 10/22/2022]
|
189
|
The crucial role of calibration in molecular date estimates for the peopling of the Americas. Am J Hum Genet 2008; 83:142-6; author reply 146-7. [PMID: 18606310 DOI: 10.1016/j.ajhg.2008.06.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 06/09/2008] [Accepted: 06/12/2008] [Indexed: 11/22/2022] Open
|
190
|
Molecular clock debate: Time dependency of molecular rate estimates for mtDNA: this is not the time for wishful thinking. Heredity (Edinb) 2008; 101:107-8. [DOI: 10.1038/hdy.2008.52] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
|
191
|
Santos C, Montiel R, Arruda A, Alvarez L, Aluja MP, Lima M. Mutation patterns of mtDNA: empirical inferences for the coding region. BMC Evol Biol 2008; 8:167. [PMID: 18518963 PMCID: PMC2438339 DOI: 10.1186/1471-2148-8-167] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Accepted: 06/02/2008] [Indexed: 01/22/2023] Open
Abstract
Background Human mitochondrial DNA (mtDNA) has been extensively used in population and evolutionary genetics studies. Thus, a valid estimate of human mtDNA evolutionary rate is important in many research fields. The small number of estimations performed for the coding region of the molecule, showed important differences between phylogenetic and empirical approaches. We analyzed a portion of the coding region of mtDNA (tRNALeu, ND1 and tRNAIle genes), using individuals belonging to extended families from the Azores Islands (Portugal) with the main aim of providing empirical estimations of the mutation rate of the coding region of mtDNA under different assumptions, and hence to better understand the mtDNA evolutionary process. Results Heteroplasmy was detected in 6.5% (3/46) of the families analyzed. In all of the families the presence of mtDNA heteroplasmy resulted from three new point mutations, and no cases of insertions or deletions were identified. Major differences were found in the proportion and type of heteroplasmy found in the genes studied when compared to those obtained in a previous report for the D-loop. Our empirical estimation of mtDNA coding region mutation rate, calculated taking into account the sex of individuals carrying new mutations, the probability of intra-individual fixation of mutations present in heteroplasmy and, to the possible extent, the effect of selection, is similar to that obtained using phylogenetic approaches. Conclusion Based on our results, the discrepancy previously reported between the human mtDNA coding region mutation rates observed along evolutionary timescales and estimations obtained using family pedigrees can be resolved when correcting for the previously cited factors.
Collapse
Affiliation(s)
- Cristina Santos
- Center for Research in Natural Resources (CIRN), University of the Azores, 9500 Ponta Delgada, S, Miguel, Azores, Portugal.
| | | | | | | | | | | |
Collapse
|
192
|
Pavlova A, Zink RM, Drovetski SV, Rohwer S. Pleistocene evolution of closely related sand martins Riparia riparia and R. diluta. Mol Phylogenet Evol 2008; 48:61-73. [PMID: 18499482 DOI: 10.1016/j.ympev.2008.03.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Revised: 03/21/2008] [Accepted: 03/26/2008] [Indexed: 11/24/2022]
Abstract
Climatic fluctuations during the Quaternary resulted in a dynamic history of species' range shifts, fragmentations and expansions. Some of these events left traces in the genetic structures of plants and animals. Recent avian phylogeographic studies demonstrated that Holarctic birds responded idiosyncratically to Pleistocene climate fluctuations. We present phylogeographic analyses of the Holarctic collared sand martin (Riparia riparia) and the Asian pale sand martin (Riparia diluta), which were considered conspecific until recently. Mitochondrial and nuclear sequences confirm species status of the pale sand martin; the two species diverged sometime between late Pliocene and middle Pleistocene, but precise dates could not be provided without calibration of the substitution rate. Within the pale sand martin, we found two mitochondrial clades that are likely to have diverged in the Pleistocene, one from Central Siberia, and the other restricted to Mongolia. The two clades were sympatric with the collared sand martin in Buryatiya and Mongolia, respectively. The mitochondrial gene genealogy and phi(st) analysis of the collared sand martin haplotypes indicate recent, but not ongoing, gene exchange between North America and Eurasia, and restricted gene flow between western and eastern Siberia that likely resulted from historic fragmentation of the species' range during the last glacial maximum.
Collapse
|
193
|
Endicott P, Ho SY. A Bayesian evaluation of human mitochondrial substitution rates. Am J Hum Genet 2008; 82:895-902. [PMID: 18371929 DOI: 10.1016/j.ajhg.2008.01.019] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 01/24/2008] [Accepted: 01/29/2008] [Indexed: 01/29/2023] Open
Abstract
Accurate estimates of mitochondrial substitution rates are central to molecular studies of human evolution, but meaningful comparisons of published studies are problematic because of the wide range of methodologies and data sets employed. These differences are nowhere more pronounced than among rates estimated from phylogenies, genealogies, and pedigrees. By using a data set comprising mitochondrial genomes from 177 humans, we estimate substitution rates for various data partitions by using Bayesian phylogenetic analysis with a relaxed molecular clock. We compare the effect of multiple internal calibrations with the customary human-chimpanzee split. The analyses reveal wide variation among estimated substitution rates and divergence times made with different partitions and calibrations, with evidence of substitutional saturation, natural selection, and significant rate heterogeneity among lineages and among sites. Collectively, the results support dates for migration out of Africa and the common mitochondrial ancestor of humans that are considerably more recent than most previous estimates. Our results also demonstrate that human mitochondrial genomes exhibit a number of molecular evolutionary complexities that necessitate the use of sophisticated analytical models for genetic analyses.
Collapse
|
194
|
Rapid molecular evolution in a living fossil. Trends Genet 2008; 24:106-9. [DOI: 10.1016/j.tig.2007.12.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 12/12/2007] [Accepted: 12/13/2007] [Indexed: 02/04/2023]
|
195
|
Page TJ, Humphreys WF, Hughes JM. Shrimps down under: evolutionary relationships of subterranean crustaceans from Western Australia (Decapoda: Atyidae: Stygiocaris). PLoS One 2008; 3:e1618. [PMID: 18286175 PMCID: PMC2229661 DOI: 10.1371/journal.pone.0001618] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2007] [Accepted: 01/18/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND We investigated the large and small scale evolutionary relationships of the endemic Western Australian subterranean shrimp genus Stygiocaris (Atyidae) using nuclear and mitochondrial genes. Stygiocaris is part of the unique cave biota of the coastal, anchialine, limestones of the Cape Range and Barrow Island, most of whose nearest evolutionary relations are found in coastal caves of the distant North Atlantic. The dominance of atyids in tropical waters and their food resources suggest they are pivotal in understanding these groundwater ecosystems. METHODOLOGY/PRINCIPLE FINDINGS Our nuclear and mitochondrial analyses all recovered the Mexican cave genus Typhlatya as the sister taxon of Stygiocaris, rather than any of the numerous surface and cave atyids from Australia or the Indo-Pacific region. The two described Stygiocaris species were recovered as monophyletic, and a third, cryptic, species was discovered at a single site, which has very different physiochemical properties from the sites hosting the two described species. CONCLUSIONS/SIGNIFICANCE Our findings suggest that Stygiocaris and Typhlatya may descend from a common ancestor that lived in the coastal marine habitat of the ancient Tethys Sea, and were subsequently separated by plate tectonic movements. This vicariant process is commonly thought to explain the many disjunct anchialine faunas, but has rarely been demonstrated using phylogenetic techniques. The Cape Range's geological dynamism, which is probably responsible for the speciation of the various Stygiocaris species, has also led to geographic population structure within species. In particular, Stygiocaris lancifera is split into northern and southern groups, which correspond to population splits within other sympatric subterranean taxa.
Collapse
Affiliation(s)
- Timothy J Page
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia.
| | | | | |
Collapse
|
196
|
Ho SYW, Saarma U, Barnett R, Haile J, Shapiro B. The effect of inappropriate calibration: three case studies in molecular ecology. PLoS One 2008; 3:e1615. [PMID: 18286172 PMCID: PMC2229648 DOI: 10.1371/journal.pone.0001615] [Citation(s) in RCA: 185] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2007] [Accepted: 01/22/2008] [Indexed: 12/15/2022] Open
Abstract
Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events.
Collapse
Affiliation(s)
- Simon Y W Ho
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
| | | | | | | | | |
Collapse
|
197
|
Villacorta C, Jaume D, Oromí P, Juan C. Under the volcano: phylogeography and evolution of the cave-dwelling Palmorchestia hypogaea (Amphipoda, Crustacea) at La Palma (Canary Islands). BMC Biol 2008; 6:7. [PMID: 18234125 PMCID: PMC2246103 DOI: 10.1186/1741-7007-6-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Accepted: 01/31/2008] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The amphipod crustacean Palmorchestia hypogaea occurs only in La Palma (Canary Islands) and is one of the few terrestrial amphipods in the world that have adapted to a strictly troglobitic life in volcanic cave habitats. A surface-dwelling closely related species (Palmorchestia epigaea) lives in the humid laurel forest on the same island. Previous studies have suggested that an ancestral littoral Orchestia species colonized the humid forests of La Palma and that subsequent drought episodes in the Canaries reduced the distribution of P. epigaea favouring the colonization of lava tubes through an adaptive shift. This was followed by dispersal via the hypogean crevicular system. RESULTS P. hypogaea and P. epigaea did not form reciprocally monophyletic mitochondrial DNA clades. They showed geographically highly structured and genetically divergent populations with current gene flow limited to geographically close surface locations. Coalescence times using Bayesian estimations assuming a non-correlated relaxed clock with a normal prior distribution of the age of La Palma, together with the lack of association of habitat type with ancestral and recent haplotypes, suggest that their adaptation to cave life is relatively ancient. CONCLUSION The data gathered here provide evidence for multiple invasions of the volcanic cave systems that have acted as refuges. A re-evaluation of the taxonomic status of the extant species of Palmorchestia is needed, as the division of the two species by habitat and ecology is unnatural. The information obtained here, and that from previous studies on hypogean fauna, shows the importance of factors such as the uncoupling of morphological and genetic evolution, the role of climatic change and regressive evolution as key processes in leading to subterranean biodiversity.
Collapse
Affiliation(s)
- Carlos Villacorta
- Departamento Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
| | - Damià Jaume
- IMEDEA (CSIC-UIB) Instituto Mediterráneo de Estudios Avanzados, 07190 Esporles, Mallorca, Spain
| | - Pedro Oromí
- Departamento Biología Animal, Universidad de La Laguna, 38205 La Laguna, Tenerife, Spain
| | - Carlos Juan
- Departamento Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
| |
Collapse
|
198
|
Ho SYW, Kolokotronis SO, Allaby RG. Elevated substitution rates estimated from ancient DNA sequences. Biol Lett 2008; 3:702-5. [PMID: 17785261 PMCID: PMC2391221 DOI: 10.1098/rsbl.2007.0377] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, which are not directly accessible via modern DNA. They are particularly suitable for the estimation of substitution rates because their ages provide calibrating information in phylogenetic analyses, circumventing the difficult task of choosing independent calibration points. The substitution rates obtained from such datasets have typically been high, falling between the rates estimated from pedigrees and species phylogenies. Many of these estimates have been made using a Bayesian phylogenetic method that explicitly accommodates heterochronous data. Stimulated by recent criticism of this method, we present a comprehensive simulation study that validates its performance. For datasets of moderate size, it produces accurate estimates of rates, while appearing robust to assumptions about demographic history. We then analyse a large collection of 749 ancient and 727 modern DNA sequences from 19 species of animals, plants and bacteria. Our new estimates confirm that the substitution rates estimated from ancient DNA sequences are elevated above long-term phylogenetic levels.
Collapse
Affiliation(s)
- Simon Y W Ho
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
| | | | | |
Collapse
|
199
|
RAJABI-MAHAM HASSAN, ORTH ANNIE, BONHOMME FRANÇOIS. Phylogeography and postglacial expansion of Mus musculus domesticus inferred from mitochondrial DNA coalescent, from Iran to Europe. Mol Ecol 2007; 17:627-41. [DOI: 10.1111/j.1365-294x.2007.03601.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
200
|
Bandelt HJ. Clock debate: when times are a-changin': Time dependency of molecular rate estimates: tempest in a teacup. Heredity (Edinb) 2007; 100:1-2. [DOI: 10.1038/sj.hdy.6801054] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|