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Harmon LJ, Pennell MW, Henao-Diaz LF, Rolland J, Sipley BN, Uyeda JC. Causes and Consequences of Apparent Timescaling Across All Estimated Evolutionary Rates. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-011921-023644] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evolutionary rates play a central role in connecting micro- and macroevolution. All evolutionary rate estimates, including rates of molecular evolution, trait evolution, and lineage diversification, share a similar scaling pattern with time: The highest rates are those measured over the shortest time interval. This creates a disconnect between micro- and macroevolution, although the pattern is the opposite of what some might expect: Patterns of change over short timescales predict that evolution has tremendous potential to create variation and that potential is barely tapped by macroevolution. In this review, we discuss this shared scaling pattern across evolutionary rates. We break down possible explanations for scaling into two categories, estimation error and model misspecification, and discuss how both apply to each type of rate. We also discuss the consequences of this ubiquitous pattern, which can lead to unexpected results when comparing ratesover different timescales. Finally, after addressing purely statistical concerns, we explore a few possibilities for a shared unifying explanation across the three types of rates that results from a failure to fully understand and account for how biological processes scale over time.
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Affiliation(s)
- Luke J. Harmon
- Institute for Bioinformatics and Evolutionary Studies (IBEST) and Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, USA
| | - Matthew W. Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - L. Francisco Henao-Diaz
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jonathan Rolland
- Laboratoire Evolution et Diversité Biologique, CNRS, UMR5174, Université Toulouse III–Paul Sabatier, 31062 Toulouse, France
| | - Breanna N. Sipley
- Program for Bioinformatics and Computational Biology, University of Idaho, Moscow, Idaho 83844, USA
| | - Josef C. Uyeda
- Department of Biological Sciences, Virginia Tech University, Blacksburg, Virginia 24061, USA
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2
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Arnedo MA, Hormiga G. Repeated colonization, adaptive radiation and convergent evolution in the sheet-weaving spiders (Linyphiidae) of the south Pacific Archipelago of Juan Fernandez. Cladistics 2021; 37:317-342. [PMID: 34478200 DOI: 10.1111/cla.12437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2020] [Indexed: 12/25/2022] Open
Abstract
We report on the colonization and diversification of linyphiid spiders in the Pacific oceanic archipelago of Juan Fernandez. About 50 spider species occur naturally in these islands, most of them endemic and about half of them are linyphiids. Linyphiidae includes no fewer than 15 species of Laminacauda and three of Neomaso (with several additional undescribed species in the latter genus), all of them single island endemics. There are three additional linyphiid endemic genera, two monotypic and one, Juanfernandezia, with two species. Unlike the rather uniform somatic morphology and small ground sheet webs of the continental Laminacauda and Neomaso species, the Juan Fernandez endemics exhibit morphological features and life history traits that are very rare or unknown in any other linyphiids. A multi-locus phylogenetic analysis confirms at least five independent Juan Fernandez colonizations of Linyphiidae, two within the same genus, and three of which underwent subsequent local diversification. Different calibrations suggest alternative colonization timelines, some at odds with island ages, but all agree on similar diversification timings of the endemic lineages. Rare phenotypic traits (e.g. gigantism, massive chelicerae or elongated legs) evolved multiple times independently within the islands. Based on the remarkable levels of eco-phenotypic differentiation in locally diversified species showing densely packed distributions, we propose that Laminacauda, and probably Neomaso, constitute a case of adaptive radiation.
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Affiliation(s)
- Miquel A Arnedo
- Department of Evolutionary Biology, Ecology & Environmental Sciences and Biodiversity Research Institute (IRBio), Universitat de Barcelona, Barcelona, Catalonia, 08028, Spain
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, Washington, D.C., 20052, USA
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3
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Morga B, Jacquot M, Pelletier C, Chevignon G, Dégremont L, Biétry A, Pepin JF, Heurtebise S, Escoubas JM, Bean TP, Rosani U, Bai CM, Renault T, Lamy JB. Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species. Front Microbiol 2021; 12:711377. [PMID: 34326830 PMCID: PMC8313985 DOI: 10.3389/fmicb.2021.711377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/21/2021] [Indexed: 11/15/2022] Open
Abstract
The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. This is particularly true for pathogens with low per-site mutation rates, such as DNA viruses, that do not exhibit a large amount of evolutionary change among genetic sequences sampled at different time points. However, whole-genome sequencing can reveal the accumulation of novel genetic variation between samples, promising to render most, if not all, microbial pathogens measurably evolving and suitable for analytical techniques derived from population genetic theory. Here, we aim to assess the measurability of evolution on epidemiological time scales of the Ostreid herpesvirus 1 (OsHV-1), a double stranded DNA virus of which a new variant, OsHV-1 μVar, emerged in France in 2008, spreading across Europe and causing dramatic economic and ecological damage. We performed phylogenetic analyses of heterochronous (n = 21) OsHV-1 genomes sampled worldwide. Results show sufficient temporal signal in the viral sequences to proceed with phylogenetic molecular clock analyses and they indicate that the genetic diversity seen in these OsHV-1 isolates has arisen within the past three decades. OsHV-1 samples from France and New Zealand did not cluster together suggesting a spatial structuration of the viral populations. The genome-wide study of simple and complex polymorphisms shows that specific genomic regions are deleted in several isolates or accumulate a high number of substitutions. These contrasting and non-random patterns of polymorphism suggest that some genomic regions are affected by strong selective pressures. Interestingly, we also found variant genotypes within all infected individuals. Altogether, these results provide baseline evidence that whole genome sequencing could be used to study population dynamic processes of OsHV-1, and more broadly herpesviruses.
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Affiliation(s)
| | | | | | | | | | | | - Jean-François Pepin
- Ifremer, ODE-Littoral-Laboratoire Environnement Ressources des Pertuis Charentais (LER-PC), La Tremblade, France
| | | | - Jean-Michel Escoubas
- IHPE, CNRS, Ifremer, Université de Montpellier - Université de Perpignan Via Domitia, Montpellier, France
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom.,Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom
| | - Umberto Rosani
- Department of Biology, University of Padua, Padua, Italy
| | - Chang-Ming Bai
- Yellow Sea Fisheries Research Institute, CAFS, Qingdao, China
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4
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Late Pleistocene Expansion of Small Murid Rodents across the Palearctic in Relation to the Past Environmental Changes. Genes (Basel) 2021; 12:genes12050642. [PMID: 33925980 PMCID: PMC8145813 DOI: 10.3390/genes12050642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022] Open
Abstract
We investigated the evolutionary history of the striped field mouse to identify factors that initiated its past demographic changes and to shed light on the causes of its current genetic structure and trans-Eurasian distribution. We sequenced mitochondrial cyt b from 184 individuals, obtained from 35 sites in central Europe and eastern Mongolia. We compared genetic analyses with previously published historical distribution models and data on environmental and climatic changes. The past demographic changes displayed similar population trends in the case of recently expanded clades C1 and C3, with the glacial (MIS 3–4) expansion and postglacial bottleneck preceding the recent expansion initiated in the late Holocene and were related to environmental changes during the upper Pleistocene and Holocene. The past demographic trends of the eastern Asian clade C3 were correlated with changes in sea level and the formation of new land bridges formed by the exposed sea shelf during the glaciations. These data were supported by reconstructed historical distribution models. The results of our genetic analyses, supported by the reconstruction of the historical spatial distributions of the distinct clades, confirm that over time the local populations mixed as a consequence of environmental and climatic changes resulting from cyclical glaciation and the interglacial period during the Pleistocene.
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Marko PB, Zaslavskaya NI. Geographic origin and timing of colonization of the Pacific Coast of North America by the rocky shore gastropod Littorina sitkana. PeerJ 2019; 7:e7987. [PMID: 31720112 PMCID: PMC6836758 DOI: 10.7717/peerj.7987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/04/2019] [Indexed: 11/20/2022] Open
Abstract
The demographic history of a species can have a lasting impact on its contemporary population genetic structure. Northeastern Pacific (NEP) populations of the rocky shore gastropod Littorina sitkana have very little mitochondrial DNA (mtDNA) sequence diversity and show no significant population structure despite lacking dispersive planktonic larvae. A contrasting pattern of high mtDNA diversity in the northwestern Pacific (NWP) suggests that L. sitkana may have recently colonized the NEP from the NWP via stepping-stone colonization through the Aleutian-Commander Archipelago (ACA) following the end of the last glacial 20,000 years ago. Here, we use multi-locus sequence data to test that hypothesis using a combination of descriptive statistics and population divergence modeling aimed at resolving the timing and the geographic origin of NEP populations. Our results show that NEP populations share a common ancestor with a population of L. sitkana on the Kamchatka Peninsula ∼46,900 years ago and that NEP populations diverged from each other ∼21,400 years ago. A more recent population divergence between Kamchatka and NEP populations, than between Kamchatka and other populations in the NWP, suggests that the ACA was the most probable dispersal route. Taking into account the confidence intervals for the estimates, we conservatively estimate that L. sitkana arrived in the NEP between 107,400 and 4,100 years ago, a range of dates that is compatible with post-glacial colonization of the NEP. Unlike other congeners that are relatively abundant in the Pleistocene fossil record of the NEP, only one report of L. sitkana exists from the NEP fossil record. Although broadly consistent with the molecular data, the biogeographic significance of these fossils is difficult to evaluate, as the shells cannot be distinguished from the closely-related congener L. subrotundata.
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Affiliation(s)
- Peter B Marko
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
| | - Nadezhda I Zaslavskaya
- National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russian Federation
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6
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Appropriate Assignment of Fossil Calibration Information Minimizes the Difference between Phylogenetic and Pedigree Mutation Rates in Humans. Life (Basel) 2018; 8:life8040049. [PMID: 30360410 PMCID: PMC6316143 DOI: 10.3390/life8040049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/18/2018] [Accepted: 10/18/2018] [Indexed: 12/24/2022] Open
Abstract
Studies that measured mutation rates in human populations using pedigrees have reported values that differ significantly from rates estimated from the phylogenetic comparison of humans and chimpanzees. Consequently, exchanges between mutation rate values across different timescales lead to conflicting divergence time estimates. It has been argued that this variation of mutation rate estimates across hominoid evolution is in part caused by incorrect assignment of calibration information to the mean coalescent time among loci, instead of the true genetic isolation (speciation) time between humans and chimpanzees. In this study, we investigated the feasibility of estimating the human pedigree mutation rate using phylogenetic data from the genomes of great apes. We found that, when calibration information was correctly assigned to the human⁻chimpanzee speciation time (and not to the coalescent time), estimates of phylogenetic mutation rates were statistically equivalent to the estimates previously reported using studies of human pedigrees. We conclude that, within the range of biologically realistic ancestral generation times, part of the difference between whole-genome phylogenetic and pedigree mutation rates is due to inappropriate assignment of fossil calibration information to the mean coalescent time instead of the speciation time. Although our results focus on the human⁻chimpanzee divergence, our findings are general, and relevant to the inference of the timescale of the tree of life.
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7
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Emerson BC, Alvarado-Serrano DF, Hickerson MJ. Model misspecification confounds the estimation of rates and exaggerates their time dependency. Mol Ecol 2016; 24:6013-20. [PMID: 26769403 DOI: 10.1111/mec.13451] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/27/2015] [Accepted: 11/02/2015] [Indexed: 12/18/2022]
Abstract
While welcoming the comment of Ho et al. (2015), we find little that undermines the strength of our criticism, and it would appear they have misunderstood our central argument. Here we respond with the purpose of reiterating that we are (i) generally critical of much of the evidence presented in support of the time-dependent molecular rate (TDMR) hypothesis and (ii) specifically critical of estimates of μ derived from tip-dated sequences that exaggerate the importance of purifying selection as an explanation for TDMR over extended timescales. In response to assertions put forward by Ho et al. (2015), we use panmictic coalescent simulations of temporal data to explore a fundamental assumption for tip-dated tree shape and associated mutation rate estimates, and the appropriateness and utility of the date randomization test. The results reveal problems for the joint estimation of tree topology, effective population size and μ with tip-dated sequences using BEAST. Given the simulations, BEAST consistently obtains incorrect topological tree structures that are consistent with the substantial overestimation of μ and underestimation of effective population size. Data generated from lower effective population sizes were less likely to fail the date randomization test yet still resulted in substantially upwardly biased estimates of rates, bringing previous estimates of μ from temporally sampled DNA sequences into question. We find that our general criticisms of both the hypothesis of time-dependent molecular evolution and Bayesian methods to estimate μ from temporally sampled DNA sequences are further reinforced.
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Affiliation(s)
- Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, 38206, Spain.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Michael J Hickerson
- Biology Department, City College of New York, New York, NY, 10031, USA.,The Graduate Center, City University of New York, New York, NY, 10016, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
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8
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Enk J, Devault A, Widga C, Saunders J, Szpak P, Southon J, Rouillard JM, Shapiro B, Golding GB, Zazula G, Froese D, Fisher DC, MacPhee RDE, Poinar H. Mammuthus Population Dynamics in Late Pleistocene North America: Divergence, Phylogeography, and Introgression. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00042] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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9
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Hoareau TB. Late Glacial Demographic Expansion Motivates a Clock Overhaul for Population Genetics. Syst Biol 2015; 65:449-64. [PMID: 26683588 DOI: 10.1093/sysbio/syv120] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 12/10/2015] [Indexed: 12/18/2022] Open
Abstract
The molecular clock hypothesis is fundamental in evolutionary biology as by assuming constancy of the molecular rate it provides a timeframe for evolution. However, increasing evidence shows time dependence of inferred molecular rates with inflated values obtained using recent calibrations. As recent demographic calibrations are virtually non-existent in most species, older phylogenetic calibration points (>1 Ma) are commonly used, which overestimate demographic parameters. To obtain more reliable rates of molecular evolution for population studies, I propose the calibration of demographic transition (CDT) method, which uses the timing of climatic changes over the late glacial warming period to calibrate expansions in various species. Simulation approaches and empirical data sets from a diversity of species (from mollusk to humans) confirm that, when compared with other genealogy-based calibration methods, the CDT provides a robust and broadly applicable clock for population genetics. The resulting CDT rates of molecular evolution also confirm rate heterogeneity over time and among taxa. Comparisons of expansion dates with ecological evidence confirm the inaccuracy of phylogenetically derived divergence rates when dating population-level events. The CDT method opens opportunities for addressing issues such as demographic responses to past climate change and the origin of rate heterogeneity related to taxa, genes, time, and genetic information content.
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Affiliation(s)
- Thierry B Hoareau
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private bag X20, Hatfield, Pretoria 0028, South Africa
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10
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Suzuki Y, Tomozawa M, Koizumi Y, Tsuchiya K, Suzuki H. Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary ice age events with inferred population expansions and dispersals in Japanese Apodemus. BMC Evol Biol 2015; 15:187. [PMID: 26373638 PMCID: PMC4571126 DOI: 10.1186/s12862-015-0463-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 08/21/2015] [Indexed: 11/22/2022] Open
Abstract
Background Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. Results We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16 % and 22–32 %, respectively, for A. argenteus, and 12–17 % and 17–24 %, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1 %/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17 %/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1 %/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. Conclusions The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.
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Affiliation(s)
- Yutaro Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | | | - Yuki Koizumi
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | - Kimiyuki Tsuchiya
- Laboratory of Bioresources, Ooyo Seibutsu Co. Ltd., Tokyo, 107-0062, Japan.
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan.
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11
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Aiewsakun P, Katzourakis A. Time dependency of foamy virus evolutionary rate estimates. BMC Evol Biol 2015; 15:119. [PMID: 26111824 PMCID: PMC4480597 DOI: 10.1186/s12862-015-0408-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/02/2015] [Indexed: 12/19/2022] Open
Abstract
Background It appears that substitution rate estimates co-vary very strongly with their timescale of measurement; the shorter the timescale, the higher the estimated value. Foamy viruses have a long history of co-speciation with their hosts, and one of the lowest estimated rates of evolution among viruses. However, when their rate of evolution is estimated over short timescales, it is more reminiscent of the rapid rates seen in other RNA viruses. This discrepancy between their short-term and long-term rates could be explained by the time-dependency of substitution rate estimates. Several empirical models have been proposed and used to correct for the time-dependent rate phenomenon (TDRP), such as a vertically-translated exponential rate decay model and a power-law rate decay model. Nevertheless, at present, it is still unclear which model best describes the rate dynamics. Here, we use foamy viruses as a case study to empirically describe the phenomenon and to determine how to correct rate estimates for its effects. Four empirical models were investigated: (i) a vertically-translated exponential rate decay model, (ii) a simple exponential rate decay model, (iii) a vertically-translated power-law rate decay model, and (iv) a simple power-law rate decay model. Results Our results suggest that the TDRP is likely responsible for the large discrepancy observed in foamy virus short-term and long-term rate estimates, and the simple power-law rate decay model is the best model for inferring evolutionary timescales. Furthermore, we demonstrated that, within the Bayesian phylogenetic framework, currently available molecular clocks can severely bias evolutionary date estimates, indicating that they are inadequate for correcting for the TDRP. Our analyses also suggest that different viral lineages may have different TDRP dynamics, and this may bias date estimates if it is unaccounted for. Conclusions As evolutionary rate estimates are dependent on their measurement timescales, their values must be used and interpreted under the context of the timescale of rate estimation. Extrapolating rate estimates across large timescales for evolutionary inferences can severely bias the outcomes. Given that the TDRP is widespread in nature but has been noted only recently the estimated timescales of many viruses may need to be reconsidered and re-estimated. Our models could be used as a guideline to further improve current phylogenetic inference tools. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0408-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pakorn Aiewsakun
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
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12
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Osinov AG, Senchukova AL, Mugue NS, Pavlov SD, Chereshnev IA. Speciation and genetic divergence of three species of charr from ancient Lake El'gygytgyn (Chukotka) and their phylogenetic relationships with other representatives of the genusSalvelinus. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12559] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - Anna L. Senchukova
- Biological Faculty; Lomonosov Moscow State University; Moscow 119991 Russia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences; Moscow Russia
| | - Nikolai S. Mugue
- Russian Federal Research Institute of Fisheries and Oceanography (VNIRO); Moscow 107140 Russia
| | - Sergei D. Pavlov
- Biological Faculty; Lomonosov Moscow State University; Moscow 119991 Russia
| | - Igor A. Chereshnev
- Institute of Biological Problems of the Far North; Far East Branch; Russian Academy of Sciences; Magadan 685000 Russia
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13
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Grant WS. Problems and Cautions With Sequence Mismatch Analysis and Bayesian Skyline Plots to Infer Historical Demography. J Hered 2015; 106:333-46. [DOI: 10.1093/jhered/esv020] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 03/24/2015] [Indexed: 12/11/2022] Open
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14
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Aiewsakun P, Katzourakis A. Endogenous viruses: Connecting recent and ancient viral evolution. Virology 2015; 479-480:26-37. [PMID: 25771486 DOI: 10.1016/j.virol.2015.02.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/15/2014] [Accepted: 02/04/2015] [Indexed: 12/17/2022]
Abstract
The rapid rates of viral evolution allow us to reconstruct the recent history of viruses in great detail. This feature, however, also results in rapid erosion of evolutionary signal within viral molecular data, impeding studies of their deep history. Thus, the further back in time, the less accurate the inference becomes. Furthermore, reconstructing complex histories of transmission can be challenging, especially where extinct viral lineages are concerned. This problem has been partially solved by the discovery of viruses embedded in host genomes, known as endogenous viral elements (EVEs). Some of these endogenous viruses are derived from ancient relatives of extant viruses, allowing us to better examine ancient viral host range, geographical distribution and transmission routes. Moreover, our knowledge of viral evolutionary timescales and rate dynamics has also been greatly improved by their discovery, thereby bridging the gap between recent and ancient viral evolution.
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Affiliation(s)
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
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15
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Molak M, Ho SYW. Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA. PeerJ 2015; 3:e821. [PMID: 25780773 PMCID: PMC4358697 DOI: 10.7717/peerj.821] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/16/2015] [Indexed: 01/07/2023] Open
Abstract
Evolutionary timescales can be estimated from genetic data using the molecular clock, often calibrated by fossil or geological evidence. However, estimates of molecular rates in mitochondrial DNA appear to scale negatively with the age of the clock calibration. Although such a pattern has been observed in a limited range of data sets, it has not been studied on a large scale in metazoans. In addition, there is uncertainty over the temporal extent of the time-dependent pattern in rate estimates. Here we present a meta-analysis of 239 rate estimates from metazoans, representing a range of timescales and taxonomic groups. We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied. The negative relationship between the estimated rate and time persisted across a much wider range of calibration times than previously suggested. This indicates that, over long time frames, purifying selection gives way to mutational saturation as the main driver of time-dependent biases in rate estimates. The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are inferred.
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Affiliation(s)
- Martyna Molak
- School of Biological Sciences, University of Sydney , Sydney , Australia ; Museum and Institute of Zoology, Polish Academy of Sciences , Warsaw , Poland
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney , Sydney , Australia
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16
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Emerson BC, Hickerson MJ. Lack of support for the time-dependent molecular evolution hypothesis. Mol Ecol 2015; 24:702-9. [DOI: 10.1111/mec.13070] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 12/17/2014] [Accepted: 12/30/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC); C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife, Canary Islands 38206 Spain
| | - Michael J. Hickerson
- Biology Department; City College of New York; New York NY 10031 USA
- The Graduate Center; City University of New York; New York NY 10016 USA
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Opatova V, Arnedo MA. Spiders on a Hot Volcanic Roof: Colonisation Pathways and Phylogeography of the Canary Islands Endemic Trap-Door Spider Titanidiops canariensis (Araneae, Idiopidae). PLoS One 2014; 9:e115078. [PMID: 25494329 PMCID: PMC4262472 DOI: 10.1371/journal.pone.0115078] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 11/03/2014] [Indexed: 11/19/2022] Open
Abstract
Studies conducted on volcanic islands have greatly contributed to our current understanding of how organisms diversify. The Canary Islands archipelago, located northwest of the coast of northern Africa, harbours a large number of endemic taxa. Because of their low vagility, mygalomorph spiders are usually absent from oceanic islands. The spider Titanidiops canariensis, which inhabits the easternmost islands of the archipelago, constitutes an exception to this rule. Here, we use a multi-locus approach that combines three mitochondrial and four nuclear genes to investigate the origins and phylogeography of this remarkable trap-door spider. We provide a timeframe for the colonisation of the Canary Islands using two alternative approaches: concatenation and species tree inference in a Bayesian relaxed clock framework. Additionally, we investigate the existence of cryptic species on the islands by means of a Bayesian multi-locus species delimitation method. Our results indicate that T. canariensis colonised the Canary Islands once, most likely during the Miocene, although discrepancies between the timeframes from different approaches make the exact timing uncertain. A complex evolutionary history for the species in the archipelago is revealed, which involves two independent colonisations of Fuerteventura from the ancestral range of T. canariensis in northern Lanzarote and a possible back colonisation of southern Lanzarote. The data further corroborate a previously proposed volcanic refugium, highlighting the impact of the dynamic volcanic history of the island on the phylogeographic patterns of the endemic taxa. T. canariensis includes at least two different species, one inhabiting the Jandia peninsula and central Fuerteventura and one spanning from central Fuerteventura to Lanzarote. Our data suggest that the extant northern African Titanidiops lineages may have expanded to the region after the islands were colonised and, hence, are not the source of colonisation. In addition, T. maroccanus may harbour several cryptic species.
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Affiliation(s)
- Vera Opatova
- Institut de Recerca de la Biodiversitat & Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
- * E-mail:
| | - Miquel A. Arnedo
- Institut de Recerca de la Biodiversitat & Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
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18
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Jing M, Yu HT, Bi X, Lai YC, Jiang W, Huang L. Phylogeography of Chinese house mice (Mus musculus musculus/castaneus): distribution, routes of colonization and geographic regions of hybridization. Mol Ecol 2014; 23:4387-405. [PMID: 25065953 DOI: 10.1111/mec.12873] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 07/22/2014] [Accepted: 07/23/2014] [Indexed: 11/27/2022]
Abstract
House mice (Mus musculus) are human commensals and have served as a primary model in biomedical, ecological and evolutionary research. Although there is detailed knowledge of the biogeography of house mice in Europe, little is known of the history of house mice in China, despite the fact that China encompasses an enormous portion of their range. In the present study, 535 house mice caught from 29 localities in China were studied by sequencing the mitochondrial D-loop and genotyping 10 nuclear microsatellite markers distributed on 10 chromosomes. Phylogenetic analyses revealed two evolutionary lineages corresponding to Mus musculus castaneus and Mus musculus musculus in the south and north, respectively, with the Yangtze River approximately representing the boundary. More detailed analyses combining published sequence data from mice sampled in neighbouring countries revealed the migration routes of the two subspecies into China: M. m. castaneus appeared to have migrated through a southern route (Yunnan and Guangxi), whereas M. m. musculus entered China from Kazakhstan through the north-west border (Xinjiang). Bayesian analysis of mitochondrial sequences indicated rapid population expansions in both subspecies, approximately 4650-9300 and 7150-14 300 years ago for M. m. castaneus and M. m. musculus, respectively. Interestingly, the migration routes of Chinese house mice coincide with the colonization routes of modern humans into China, and the expansion times of house mice are consistent with the development of agriculture in southern and northern China, respectively. Finally, our study confirmed the existence of a hybrid zone between M. m. castaneus and M. m. musculus in China. Further study of this hybrid zone will provide a useful counterpart to the well-studied hybrid zone between M. m. musculus and Mus musculus domesticus in central Europe.
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Affiliation(s)
- Meidong Jing
- College of Life Sciences, Ludong University, Yantai, Shandong, 264025, China
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19
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Rieux A, Eriksson A, Li M, Sobkowiak B, Weinert LA, Warmuth V, Ruiz-Linares A, Manica A, Balloux F. Improved calibration of the human mitochondrial clock using ancient genomes. Mol Biol Evol 2014; 31:2780-92. [PMID: 25100861 PMCID: PMC4166928 DOI: 10.1093/molbev/msu222] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Reliable estimates of the rate at which DNA accumulates mutations (the substitution rate) are crucial for our understanding of the evolution and past demography of virtually any species. In humans, there are considerable uncertainties around these rates, with substantial variation among recent published estimates. Substitution rates have traditionally been estimated by associating dated events to the root (e.g., the divergence between humans and chimpanzees) or to internal nodes in a phylogenetic tree (e.g., first entry into the Americas). The recent availability of ancient mitochondrial DNA sequences allows for a more direct calibration by assigning the age of the sequenced samples to the tips within the human phylogenetic tree. But studies also vary greatly in the methodology employed and in the sequence panels analyzed, making it difficult to tease apart the causes for the differences between previous estimates. To clarify this issue, we compiled a comprehensive data set of 350 ancient and modern human complete mitochondrial DNA genomes, among which 146 were generated for the purpose of this study and estimated substitution rates using calibrations based both on dated nodes and tips. Our results demonstrate that, for the same data set, estimates based on individual dated tips are far more consistent with each other than those based on nodes and should thus be considered as more reliable.
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Affiliation(s)
- Adrien Rieux
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Sobkowiak
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Lucy A Weinert
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Vera Warmuth
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Andres Ruiz-Linares
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - François Balloux
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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20
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Burg T, Taylor S, Lemmen K, Gaston A, Friesen V. Postglacial population genetic differentiation potentially facilitated by a flexible migratory strategy in Golden-crowned Kinglets (Regulussatrapa). CAN J ZOOL 2014. [DOI: 10.1139/cjz-2013-0217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Relatively recently, temperate regions in North America were covered by extensive ice sheets, making them inhospitable to contemporary flora and fauna. Since the retreat of the ice sheets, these regions have been recolonized by a diversity of taxa, some of which have undergone rapid postglacial divergence. Evidence supports the hypothesis that some taxa persisted in unglaciated refugia during the Last Glacial Maximum, such as on Haida Gwaii (formerly the Queen Charlotte Islands). Many taxa on Haida Gwaii are genetically distinct from mainland populations at neutral molecular markers possibly as the result of isolation in refugia or postglacial colonization. The Golden-crowned Kinglet (Regulus satrapa Lichtenstein, 1823) is a continentally distributed, short-distance migratory passerine inhabiting mature conifer forests including those on Haida Gwaii. We used five microsatellite markers and a 568 base-pair fragment of the mitochondrial control region to determine the likelihood that Haida Gwaii region acted as a refugium for this species during the last ice age. We report significant gene flow between Haida Gwaii and the western North American mainland from mitochondrial markers, but significant population genetic differentiation at nuclear markers. We also report genetic divergence between eastern and western Golden-crowned Kinglets, as well as higher genetic diversity and population substructuring within the western population than within the eastern population. The east–west differentiation probably arose due to isolation in separate Pleistocene refugia south of the ice sheets. However, population differences within the west are likely caused by more recent processes; contemporary differentiation of Haida Gwaii Golden-crowned Kinglets most likely occurred postglacially.
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Affiliation(s)
- T.M. Burg
- Department of Biology, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - S.A. Taylor
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA; Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - K.D. Lemmen
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - A.J. Gaston
- Environment Canada, National Wildlife Research Centre, Carleton University, Ottawa, ON K1A 0H3, Canada
| | - V.L. Friesen
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada
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21
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Moura AE, Nielsen SCA, Vilstrup JT, Moreno-Mayar JV, Gilbert MTP, Gray HWI, Natoli A, Möller L, Hoelzel AR. Recent diversification of a marine genus (Tursiops spp.) tracks habitat preference and environmental change. Syst Biol 2013; 62:865-77. [PMID: 23929779 DOI: 10.1093/sysbio/syt051] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the evolution of diversity and the resulting systematics in marine systems is confounded by the lack of clear boundaries in oceanic habitats, especially for highly mobile species like marine mammals. Dolphin populations and sibling species often show differentiation between coastal and offshore habitats, similar to the pelagic/littoral or benthic differentiation seen for some species of fish. Here we test the hypothesis that lineages within the polytypic genus Tursiops track past changes in the environment reflecting ecological drivers of evolution facilitated by habitat release. We used a known recent time point for calibration (the opening of the Bosphorus) and whole mitochondrial genome (mitogenome) sequences for high phylogenetic resolution. The pattern of lineage formation suggested an origin in Australasia and several early divisions involving forms currently inhabiting coastal habitats. Radiation in pelagic environments was relatively recent, and was likely followed by a return to coastal habitat in some regions. The timing of some nodes defining different ecotypes within the genus clustered near the two most recent interglacial transitions. A signal for an increase in diversification was also seen for dates after the last glacial maximum. Together these data suggest the tracking of habitat preference during geographic expansions, followed by transition points reflecting habitat shifts, which were likely associated with periods of environmental change.
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Affiliation(s)
- Andre E Moura
- School of Biological and Biomedical Sciences, Durham University, South Road, DH1 3LE, UK; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark; Biological Department, UAE University, P.O.Box 17551, Al Ain, UAE; and School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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22
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Sanna D, Cossu P, Dedola GL, Scarpa F, Maltagliati F, Castelli A, Franzoi P, Lai T, Cristo B, Curini-Galletti M, Francalacci P, Casu M. Mitochondrial DNA reveals genetic structuring of Pinna nobilis across the Mediterranean Sea. PLoS One 2013; 8:e67372. [PMID: 23840684 PMCID: PMC3696058 DOI: 10.1371/journal.pone.0067372] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 05/18/2013] [Indexed: 11/18/2022] Open
Abstract
Pinna nobilis is the largest endemic Mediterranean marine bivalve. During past centuries, various human activities have promoted the regression of its populations. As a consequence of stringent standards of protection, demographic expansions are currently reported in many sites. The aim of this study was to provide the first large broad-scale insight into the genetic variability of P. nobilis in the area that encompasses the western Mediterranean, Ionian Sea, and Adriatic Sea marine ecoregions. To accomplish this objective twenty-five populations from this area were surveyed using two mitochondrial DNA markers (COI and 16S). Our dataset was then merged with those obtained in other studies for the Aegean and Tunisian populations (eastern Mediterranean), and statistical analyses (Bayesian model-based clustering, median-joining network, AMOVA, mismatch distribution, Tajima's and Fu's neutrality tests and Bayesian skyline plots) were performed. The results revealed genetic divergence among three distinguishable areas: (1) western Mediterranean and Ionian Sea; (2) Adriatic Sea; and (3) Aegean Sea and Tunisian coastal areas. From a conservational point of view, populations from the three genetically divergent groups found may be considered as different management units.
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Affiliation(s)
- Daria Sanna
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Piero Cossu
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Gian Luca Dedola
- Dipartimento di Medicina Veterinaria - Sezione di Anatomia, Università di Sassari, Sassari, Italy
| | - Fabio Scarpa
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | | | | | - Piero Franzoi
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Cà Foscari, Venezia, Italy
| | - Tiziana Lai
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Benedetto Cristo
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Marco Curini-Galletti
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Paolo Francalacci
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Marco Casu
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
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23
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Igea J, Aymerich P, Fernández-González A, González-Esteban J, Gómez A, Alonso R, Gosálbez J, Castresana J. Phylogeography and postglacial expansion of the endangered semi-aquatic mammal Galemys pyrenaicus. BMC Evol Biol 2013; 13:115. [PMID: 23738626 PMCID: PMC3682870 DOI: 10.1186/1471-2148-13-115] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 05/28/2013] [Indexed: 01/20/2023] Open
Abstract
Background Species with strict ecological requirements may provide new insights into the forces that shaped the geographic variation of genetic diversity. The Pyrenean desman, Galemys pyrenaicus, is a small semi-aquatic mammal that inhabits clean streams of the northern half of the Iberian Peninsula and is endangered in most of its geographic range, but its genetic structure is currently unknown. While the stringent ecological demands derived from its aquatic habitat might have caused a partition of the genetic diversity among river basins, Pleistocene glaciations would have generated a genetic pattern related to glacial refugia. Results To study the relative importance of historical and ecological factors in the genetic structure of G. pyrenaicus, we used mitochondrial and intronic sequences of specimens covering most of the species range. We show, first, that the Pyrenean desman has very low levels of genetic diversity compared to other mammals. In addition, phylogenetic and dating analyses of the mitochondrial sequences reveal a strong phylogeographic structure of a Middle Pleistocene origin, suggesting that the main lineages arose during periods of glacial isolation. Furthermore, both the spatial distribution of nuclear and mitochondrial diversity and the results of species distribution modeling suggest the existence of a major glacial refugium in the northwestern part of the Iberian Peninsula. Finally, the main mitochondrial lineages show a striking parapatric distribution without any apparent exchange of mitochondrial haplotypes between the lineages that came into secondary contact (although with certain permeability to nuclear genes), indicating incomplete mixing after the post-glacial recolonization. On the other hand, when we analyzed the partition of the genetic diversity among river basins, the Pyrenean desman showed a lower than expected genetic differentiation among main rivers. Conclusions The analysis of mitochondrial and intronic markers in G. pyrenaicus showed the predominant effects of Pleistocene glaciations on the genetic structure of this species, while the distribution of the genetic diversity was not greatly influenced by the main river systems. These results and, particularly, the discovery of a marked phylogeographic structure, may have important implications for the conservation of the Pyrenean desman.
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Affiliation(s)
- Javier Igea
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37, Barcelona 08003, Spain
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24
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Subramanian S, Lambert DM. Selective constraints determine the time dependency of molecular rates for human nuclear genomes. Genome Biol Evol 2013; 4:1127-32. [PMID: 23059453 PMCID: PMC3514959 DOI: 10.1093/gbe/evs092] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In contrast to molecular rates for neutral mitochondrial sequences, rates for constrained sites (including nonsynonymous sites, D-loop, and RNA) in the mitochondrial genome are known to vary with the time frame used for their estimation. Here, we examined this issue for the nuclear genomes using single-nucleotide polymorphisms (SNPs) from six complete human genomes of individuals belonging to different populations. We observed a strong time-dependent distribution of nonsynonymous SNPs (nSNPs) in highly constrained genes. Typically, the proportion of young nSNPs specific to a single population was found to be up to three times higher than that of the ancient nSNPs shared between diverse human populations. In contrast, this trend disappeared, and a uniform distribution of young and old nSNPs was observed in genes under relaxed selective constraints. This suggests that because mutations in constrained genes are highly deleterious, they are removed over time, resulting in a relative overabundance of young nSNPs. In contrast, mutations in genes under relaxed constraints are nearly neutral, which leads to similar proportions of young and old SNPs. These results could be useful to researchers aiming to select appropriate genes or genomic regions for estimating evolutionary rates and species or population divergence times.
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25
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Maintenance of genetic variation and panmixia in the commercially exploited western rock lobster (Panulirus cygnus). CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0433-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Palsbøll PJ, Zachariah Peery M, Olsen MT, Beissinger SR, Bérubé M. Inferring recent historic abundance from current genetic diversity. Mol Ecol 2012. [PMID: 23181682 DOI: 10.1111/mec.12094] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recent historic abundance is an elusive parameter of great importance for conserving endangered species and understanding the pre-anthropogenic state of the biosphere. The number of studies that have used population genetic theory to estimate recent historic abundance from contemporary levels of genetic diversity has grown rapidly over the last two decades. Such assessments often yield unexpectedly large estimates of historic abundance. We review the underlying theory and common practices of estimating recent historic abundance from contemporary genetic diversity, and critically evaluate the potential issues at various estimation steps. A general issue of mismatched spatio-temporal scales between the estimation itself and the objective of the estimation emerged from our assessment; genetic diversity-based estimates of recent historic abundance represent long-term averages, whereas the objective typically is an estimate of recent abundance for a specific population. Currently, the most promising approach to estimate the difference between recent historic and contemporary abundance requires that genetic data be collected from samples of similar spatial and temporal duration. Novel genome-enabled inference methods may be able to utilize additional information of dense genome-wide distributions of markers, such as of identity-by-descent tracts, to infer recent historic abundance from contemporary samples only.
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Affiliation(s)
- Per J Palsbøll
- Marine Evolution and Conservation, Centre of Evolutionary and Ecological Studies, University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.
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27
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Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species). Mol Phylogenet Evol 2012; 65:203-12. [DOI: 10.1016/j.ympev.2012.06.006] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 06/08/2012] [Accepted: 06/12/2012] [Indexed: 11/20/2022]
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Hung CM, Drovetski SV, Zink RM. Recent allopatric divergence and niche evolution in a widespread Palearctic bird, the common rosefinch (Carpodacus erythrinus). Mol Phylogenet Evol 2012; 66:103-11. [PMID: 23022139 DOI: 10.1016/j.ympev.2012.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 09/08/2012] [Accepted: 09/14/2012] [Indexed: 10/27/2022]
Abstract
A previously published phylogeographic analysis of mtDNA sequences from the widespread Palearctic common rosefinch (Carpodacus erythrinus) suggested the existence of three recently diverged groups, corresponding to the Caucasus, central-western Eurasia, and northeastern Eurasia. We re-evaluated the mtDNA data using coalescence methods and added sequence data from a sex-linked gene. The mtDNA gene tree and SAMOVA supported the distinctiveness of the Caucasian group but not the other two groups. However, UPGMA clustering of mtDNA Φ(ST)-values among populations recovered the three groups. The sex-linked gene tree recovered no phylogeographic signal, which was attributed to recent divergence and insufficient time for sorting of alleles. Overall, coalescence methods indicated a lack of gene flow among the three groups, and population expansion in the central-western and northeastern Eurasia groups. These three groups corresponded to named subspecies, further supporting their validity. A species distribution model revealed potential refugia at the Last Glacial Maximum. These three groups, which we hypothesized are in the early stages of speciation, provided an opportunity for testing tenets of ecological speciation. We showed that the early stages of speciation were not accompanied by ecological niche divergence, consistent with other avian studies.
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Affiliation(s)
- Chih-Ming Hung
- Bell Museum, University of Minnesota, St Paul, MN 55108, USA.
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29
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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.
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Affiliation(s)
- Stephen A Karl
- Hawai'i Institute of Marine Biology, University of Hawai'i, Mānoa, Kāne'ohe, HI 96744, USA.
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30
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Madrigal L, Posthumously LC, Melendez-Obando M, Villegas-Palma R, Barrantes R, Raventos H, Pereira R, Luiselli D, Pettener D, Barbujani G. High mitochondrial mutation rates estimated from deep-rooting Costa Rican pedigrees. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 148:327-33. [PMID: 22460349 DOI: 10.1002/ajpa.22052] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 02/10/2012] [Indexed: 11/07/2022]
Abstract
Estimates of mutation rates for the noncoding hypervariable Region I (HVR-I) of mitochondrial DNA vary widely, depending on whether they are inferred from phylogenies (assuming that molecular evolution is clock-like) or directly from pedigrees. All pedigree-based studies so far were conducted on populations of European origin. In this article, we analyzed 19 deep-rooting pedigrees in a population of mixed origin in Costa Rica. We calculated two estimates of the HVR-I mutation rate, one considering all apparent mutations, and one disregarding changes at sites known to be mutational hot spots and eliminating genealogy branches which might be suspected to include errors, or unrecognized adoptions along the female lines. At the end of this procedure, we still observed a mutation rate equal to 1.24 × 10(-6) , per site per year, i.e., at least threefold as high as estimates derived from phylogenies. Our results confirm that mutation rates observed in pedigrees are much higher than estimated assuming a neutral model of long-term HVRI evolution. We argue that until the cause of these discrepancies will be fully understood, both lower estimates (i.e., those derived from phylogenetic comparisons) and higher, direct estimates such as those obtained in this study, should be considered when modeling evolutionary and demographic processes.
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Affiliation(s)
- Lorena Madrigal
- Department of Anthropology, University of South Florida, Tampa, FL 3360, USA
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31
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Delaney NF, Balenger S, Bonneaud C, Marx CJ, Hill GE, Ferguson-Noel N, Tsai P, Rodrigo A, Edwards SV. Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum. PLoS Genet 2012; 8:e1002511. [PMID: 22346765 PMCID: PMC3276549 DOI: 10.1371/journal.pgen.1002511] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Accepted: 12/09/2011] [Indexed: 12/19/2022] Open
Abstract
Measureable rates of genome evolution are well documented in human pathogens but are less well understood in bacterial pathogens in the wild, particularly during and after host switches. Mycoplasma gallisepticum (MG) is a pathogenic bacterium that has evolved predominantly in poultry and recently jumped to wild house finches (Carpodacus mexicanus), a common North American songbird. For the first time we characterize the genome and measure rates of genome evolution in House Finch isolates of MG, as well as in poultry outgroups. Using whole-genome sequences of 12 House Finch isolates across a 13-year serial sample and an additional four newly sequenced poultry strains, we estimate a nucleotide diversity in House Finch isolates of only ∼2% of ancestral poultry strains and a nucleotide substitution rate of 0.8-1.2×10(-5) per site per year both in poultry and in House Finches, an exceptionally fast rate rivaling some of the highest estimates reported thus far for bacteria. We also found high diversity and complete turnover of CRISPR arrays in poultry MG strains prior to the switch to the House Finch host, but after the invasion of House Finches there is progressive loss of CRISPR repeat diversity, and recruitment of novel CRISPR repeats ceases. Recent (2007) House Finch MG strains retain only ∼50% of the CRISPR repertoire founding (1994-95) strains and have lost the CRISPR-associated genes required for CRISPR function. Our results suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied by apparent functional loss of CRISPRs.
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Affiliation(s)
- Nigel F. Delaney
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Susan Balenger
- Department of Biological Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Camille Bonneaud
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Christopher J. Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Geoffrey E. Hill
- Department of Biological Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Naola Ferguson-Noel
- Poultry Diagnostic and Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Peter Tsai
- Bioinformatics Institute, University of Auckland, Auckland, New Zealand
| | - Allen Rodrigo
- Bioinformatics Institute, University of Auckland, Auckland, New Zealand
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
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Patrício AR, Herbst LH, Duarte A, Vélez-Zuazo X, Santos Loureiro N, Pereira N, Tavares L, Toranzos GA. Global phylogeography and evolution of chelonid fibropapilloma-associated herpesvirus. J Gen Virol 2012; 93:1035-1045. [PMID: 22258862 DOI: 10.1099/vir.0.038950-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A global phylogeny for chelonid fibropapilloma-associated herpesvirus (CFPHV), the most likely aetiological agent of fibropapillomatosis (FP) in sea turtles, was inferred, using dated sequences, through Bayesian Markov chain Monte Carlo analysis and used to estimate the virus evolutionary rate independent of the evolution of the host, and to resolve the phylogenetic positions of new haplotypes from Puerto Rico and the Gulf of Guinea. Four phylogeographical groups were identified: eastern Pacific, western Atlantic/eastern Caribbean, mid-west Pacific and Atlantic. The latter comprises the Gulf of Guinea and Puerto Rico, suggesting recent virus gene flow between these two regions. One virus haplotype from Florida remained elusive, representing either an independent lineage sharing a common ancestor with all other identified virus variants or an Atlantic representative of the lineage giving rise to the eastern Pacific group. The virus evolutionary rate ranged from 1.62×10(-4) to 2.22×10(-4) substitutions per site per year, which is much faster than what is expected for a herpesvirus. The mean time for the most recent common ancestor of the modern virus variants was estimated at 192.90-429.71 years ago, which, although more recent than previous estimates, still supports an interpretation that the global FP pandemic is not the result of a recent acquisition of a virulence mutation(s). The phylogeographical pattern obtained seems partially to reflect sea turtle movements, whereas altered environments appear to be implicated in current FP outbreaks and in the modern evolutionary history of CFPHV.
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Affiliation(s)
- A R Patrício
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, PR 00931, Puerto Rico
| | - L H Herbst
- Department of Pathology and Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - A Duarte
- Interdisciplinary Centre of Research in Animal Health, Faculty of Veterinary Medicine of the Technical University of Lisbon, 1300-477 Lisbon, Portugal
| | - X Vélez-Zuazo
- ecOceanica, Lima 41, Peru.,Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, PR 00931, Puerto Rico
| | - N Santos Loureiro
- Faculty of Sciences and Technology (DCTMA) of the University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal
| | - N Pereira
- Lisbon Oceanarium, 1999-005 Lisbon, Portugal
| | - L Tavares
- Interdisciplinary Centre of Research in Animal Health, Faculty of Veterinary Medicine of the Technical University of Lisbon, 1300-477 Lisbon, Portugal
| | - G A Toranzos
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, PR 00931, Puerto Rico
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Phylogeographic patterns of decapod crustaceans at the Atlantic-Mediterranean transition. Mol Phylogenet Evol 2011; 62:664-72. [PMID: 22138160 DOI: 10.1016/j.ympev.2011.11.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 09/23/2011] [Accepted: 11/14/2011] [Indexed: 11/21/2022]
Abstract
Comparative multispecies studies allow contrasting the effect of past and present oceanographic processes on phylogeographic patterns. In the present study, a fragment of the COI gene was analyzed in seven decapod crustacean species from five families and with different bathymetric distributions. A total of 769 individuals were sampled along the Atlantic-Mediterranean transition area in order to test the effect of three putative barriers to gene flow: Strait of Gibraltar, Almeria-Oran Front and Ibiza Channel. A significant effect of the Strait of Gibraltar was found in the crabs Liocarcinus depurator and Macropipus tuberculatus. The Ibiza Channel had a significant effect for L. depurator. However, the Almeria-Oran front was not found to have a significant effect on any of the studied species. Higher levels of population structure were found in shallow-water species, although the number of species sampled should be increased to obtain a conclusive pattern. The haplotypes within the different species coalesced at times that could be related with past climatic events occurring before, during and after the last glacial maximum. Given the large diversity of phylogeographic patterns obtained within decapods, it is concluded that both historical and contemporary processes (marine current patterns, bathymetry and life-history traits) shape the phylogeographic patterns of these crustaceans.
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Bidegaray-Batista L, Arnedo MA. Gone with the plate: the opening of the Western Mediterranean basin drove the diversification of ground-dweller spiders. BMC Evol Biol 2011; 11:317. [PMID: 22039781 PMCID: PMC3273451 DOI: 10.1186/1471-2148-11-317] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 10/31/2011] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The major islands of the Western Mediterranean--Corsica, Sardinia, and the Balearic Islands--are continental terrenes that drifted towards their present day location following a retreat from their original position on the eastern Iberian Peninsula about 30 million years ago. Several studies have taken advantage of this well-dated geological scenario to calibrate molecular rates in species for which distributions seemed to match this tectonic event. Nevertheless, the use of external calibration points has revealed that most of the present-day fauna on these islands post-dated the opening of the western Mediterranean basin. In this study, we use sequence information of the cox1, nad1, 16S, L1, and 12S mitochondrial genes and the 18S, 28S, and h3 nuclear genes, along with relaxed clock models and a combination of biogeographic and fossil external calibration points, to test alternative historical scenarios of the evolutionary history of the ground-dweller spider genus Parachtes (Dysderidae), which is endemic to the region. RESULTS We analyse 49 specimens representing populations of most Parachtes species and close relatives. Our results reveal that both the sequence of species formation in Parachtes and the estimated divergence times match the geochronological sequence of separation of the main islands, suggesting that the diversification of the group was driven by Tertiary plate tectonics. In addition, the confirmation that Parachtes diversification matches well-dated geological events provides a model framework to infer substitution rates of molecular markers. Divergence rates estimates ranged from 3.5% My(-1) (nad1) to 0.12% My(-1) (28S), and the average divergence rate for the mitochondrial genes was 2.25% My(-1), very close to the "standard" arthropod mitochondrial rate (2.3% My(-1)). CONCLUSIONS Our study provides the first unequivocal evidence of terrestrial endemic fauna of the major western Mediterranean islands, whose origin can be traced back to the Oligocene separation of these islands from the continent. Moreover, our study provides useful information on the divergence rate estimates of the most commonly used genes for phylogenetic inference in non-model arthropods.
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Affiliation(s)
- Leticia Bidegaray-Batista
- Institut de Recerca de la Biodiversitat & Departament de Biologia Animal, Universitat de Barcelona, Av. Diagonal 643, 08020, Barcelona, Spain
| | - Miquel A Arnedo
- Institut de Recerca de la Biodiversitat & Departament de Biologia Animal, Universitat de Barcelona, Av. Diagonal 643, 08020, Barcelona, Spain
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Abstract
Some previous studies have suggested that rates of evolution inferred using molecular sequences vary substantially depending on the time frame over which they are measured, whereas a number of other studies have argued against this proposition. We examined this issue by separating positions of primate mitochondrial genomes that are under different levels of selection constraints. Our results revealed an order of magnitude variation in the evolutionary rates at constrained sites (including nonsynonymous sites, D-loop, and RNA) and virtually an identical rate of evolution at synonymous sites, independent of the timescales over which they were estimated. Although the evolutionary rate at nonsynonymous sites obtained using the European (H1 haplogroup) mitogenomes is 9–15 times higher than that estimated using the human–chimpanzee pair, in contrast, the rates at synonymous sites are similar between these comparisons. We also show that the ratio of divergence at nonsynonymous to synonymous sites estimated using intra- and interspecific comparisons vary up to nine times, which corroborates our results independent of calibration times.
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Huey JA, Baker AM, Hughes JM. Evidence for multiple historical colonizations of an endoreic drainage basin by an Australian freshwater fish. JOURNAL OF FISH BIOLOGY 2011; 79:1047-1067. [PMID: 21967589 DOI: 10.1111/j.1095-8649.2011.03088.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The contemporary and historical colonization capacity of an Australian freshwater fish, north-west glassfish Ambassis sp., was tested using mtDNA sequence data and six newly developed microsatellite loci in an endoreic basin in central Australia. Overall, Ambassis sp. exhibited weak genetic structure within catchments, suggesting some capacity to recolonize extirpated waterholes after disturbance. Genetic structure revealed that the historical pattern of connectivity among catchments in the Lake Eyre Basin was dramatically different from other species studied in this region. Two highly divergent clades were detected in separate catchments in the basin. mtDNA from individuals sampled in catchments north of the Lake Eyre Basin suggest that Ambassis sp. has colonized on two separate occasions from catchments in northern Australia, subsequently generating two highly divergent lineages.
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Affiliation(s)
- J A Huey
- Griffith University, Australian Rivers Institute, Griffith School of Environment, 170 Kessels Road, Nathan, Qld 4111, Australia.
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Crandall ED, Sbrocco EJ, DeBoer TS, Barber PH, Carpenter KE. Expansion Dating: Calibrating Molecular Clocks in Marine Species from Expansions onto the Sunda Shelf Following the Last Glacial Maximum. Mol Biol Evol 2011; 29:707-19. [DOI: 10.1093/molbev/msr227] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Dornburg A, Brandley MC, McGowen MR, Near TJ. Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea). Mol Biol Evol 2011; 29:721-36. [PMID: 21926070 DOI: 10.1093/molbev/msr228] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed "uncorrelated relaxed clock" and "random local clock" (RLC) models allow decoupling of nucleotide substitution rates between descendant lineages and are thus predicted to perform better in the presence of lineage-specific rate heterogeneity. However, it is uncertain how these models perform in the presence of punctuated shifts in substitution rate, especially between closely related clades. Using cetaceans (whales and dolphins) as a case study, we test the performance of these two substitution models in estimating both molecular rates and divergence times in the presence of substantial lineage-specific rate heterogeneity. Our RLC analyses of whole mitochondrial genome alignments find evidence for up to ten clade-specific nucleotide substitution rate shifts in cetaceans. We provide evidence that in the uncorrelated relaxed clock framework, a punctuated shift in the rate of molecular evolution within a subclade results in posterior rate estimates that are either misled or intermediate between the disparate rate classes present in baleen and toothed whales. Using simulations, we demonstrate abrupt changes in rate isolated to one or a few lineages in the phylogeny can mislead rate and age estimation, even when the node of interest is calibrated. We further demonstrate how increasing prior age uncertainty can bias rate and age estimates, even while the 95% highest posterior density around age estimates decreases; in other words, increased precision for an inaccurate estimate. We interpret the use of external calibrations in divergence time studies in light of these results, suggesting that rate shifts at deep time scales may mislead inferences of absolute molecular rates and ages.
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Affiliation(s)
- Alex Dornburg
- Department of Ecology and Evolutionary Biology, Yale University, USA.
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Liu JX, Tatarenkov A, Beacham TD, Gorbachev V, Wildes S, Avise JC. Effects of Pleistocene climatic fluctuations on the phylogeographic and demographic histories of Pacific herring (Clupea pallasii). Mol Ecol 2011; 20:3879-93. [PMID: 21824211 DOI: 10.1111/j.1365-294x.2011.05213.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We gathered mitochondrial DNA sequences (557 bp from the control region in 935 specimens and 668 bp of the cytochrome b gene in 139 specimens) of Pacific herring collected from 20 nearshore localities spanning the species' extensive range along the North Pacific coastlines of Asia and North America. Haplotype diversity and nucleotide diversity were high, and three major phylogeographic lineages (sequence divergences ca. 1.5%) were detected. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidence, we infer that the genetic make-up of extant populations of C. pallasii was shaped by Pleistocene environmental impacts on the historical demography of this species. A deep genealogical split that cleanly distinguishes populations in the western vs. eastern North Pacific probably originated as a vicariant separation associated with a glacial cycle that drove the species southward and isolated two ancestral populations in Asia and North America. Another deep genealogical split may have involved either a vicariant isolation of a third herring lineage (perhaps originally in the Gulf of California) or it may have resulted simply from the long coalescent times that are possible in large populations. Coalescent analyses showed that all the three evolutionary lineages of C. pallasii experienced major expansions in their most recent histories after having remained more stable in the preceding periods. Independent of the molecular calibration chosen, populations of C. pallasii appear to have remained stable or grown throughout the periods that covered at least two major glaciations, and probably more.
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Affiliation(s)
- Jin-Xian Liu
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA.
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40
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de Bruyn M, Hoelzel AR, Carvalho GR, Hofreiter M. Faunal histories from Holocene ancient DNA. Trends Ecol Evol 2011; 26:405-13. [PMID: 21529992 DOI: 10.1016/j.tree.2011.03.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/24/2011] [Accepted: 03/28/2011] [Indexed: 02/05/2023]
Abstract
Recent studies using ancient DNA have been instrumental in advancing understanding of the impact of Holocene climate change on biodiversity. Ancient DNA has been used to track demography, migration and diversity, and is providing new insights into the long-term dynamics of species and population distributions. The Holocene is key to understanding how the past has impacted on the present, as it bridges the gap between contemporary phylogeographic studies and those with inference on Pleistocene patterns, based on ancient DNA studies. Here, we examine the major patterns of Holocene faunal population dynamics and connectivity; highlighting the dynamic nature of species and population responses to Holocene climatic change, thereby providing an 'analogue' for understanding potential impacts of future change.
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Affiliation(s)
- Mark de Bruyn
- Molecular Ecology & Fisheries Genetics Laboratory, Environment Centre for Wales, School of Biological Sciences, Bangor University, Bangor, UK, LL57 2UW.
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Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A. Time-dependent rates of molecular evolution. Mol Ecol 2011; 20:3087-101. [PMID: 21740474 DOI: 10.1111/j.1365-294x.2011.05178.x] [Citation(s) in RCA: 350] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, it has been suggested that rates of molecular evolution are also time dependent, with the estimated rate depending on the timescale of measurement. This followed surprising observations that estimates of mutation rates, obtained in studies of pedigrees and laboratory mutation-accumulation lines, exceeded long-term substitution rates by an order of magnitude or more. Although a range of studies have provided evidence for such a pattern, the hypothesis remains relatively contentious. Furthermore, there is ongoing discussion about the factors that can cause molecular rate estimates to be dependent on time. Here we present an overview of our current understanding of time-dependent rates. We provide a summary of the evidence for time-dependent rates in animals, bacteria and viruses. We review the various biological and methodological factors that can cause rates to be time dependent, including the effects of natural selection, calibration errors, model misspecification and other artefacts. We also describe the challenges in calibrating estimates of molecular rates, particularly on the intermediate timescales that are critical for an accurate characterization of time-dependent rates. This has important consequences for the use of molecular-clock methods to estimate timescales of recent evolutionary events.
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Affiliation(s)
- Simon Y W Ho
- Centre for Macroevolution and Macroecology, Evolution Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia.
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Miraldo A, Hewitt GM, Paulo OS, Emerson BC. Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: multiple refugia, range expansions and secondary contact zones. BMC Evol Biol 2011; 11:170. [PMID: 21682856 PMCID: PMC3141430 DOI: 10.1186/1471-2148-11-170] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 06/17/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Iberian Peninsula is recognized as an important refugial area for species survival and diversification during the climatic cycles of the Quaternary. Recent phylogeographic studies have revealed Iberia as a complex of multiple refugia. However, most of these studies have focused either on species with narrow distributions within the region or species groups that, although widely distributed, generally have a genetic structure that relates to pre-Quaternary cladogenetic events. In this study we undertake a detailed phylogeographic analysis of the lizard species, Lacerta lepida, whose distribution encompasses the entire Iberian Peninsula. We attempt to identify refugial areas, recolonization routes, zones of secondary contact and date demographic events within this species. RESULTS Results support the existence of 6 evolutionary lineages (phylogroups) with a strong association between genetic variation and geography, suggesting a history of allopatric divergence in different refugia. Diversification within phylogroups is concordant with the onset of the Pleistocene climatic oscillations. The southern regions of several phylogroups show a high incidence of ancestral alleles in contrast with high incidence of recently derived alleles in northern regions. All phylogroups show signs of recent demographic and spatial expansions. We have further identified several zones of secondary contact, with divergent mitochondrial haplotypes occurring in narrow zones of sympatry. CONCLUSIONS The concordant patterns of spatial and demographic expansions detected within phylogroups, together with the high incidence of ancestral haplotypes in southern regions of several phylogroups, suggests a pattern of contraction of populations into southern refugia during adverse climatic conditions from which subsequent northern expansions occurred. This study supports the emergent pattern of multiple refugia within Iberia but adds to it by identifying a pattern of refugia coincident with the southern distribution limits of individual evolutionary lineages. These areas are important in terms of long-term species persistence and therefore important areas for conservation.
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Affiliation(s)
- Andreia Miraldo
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7J, UK.
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Sen L, Fares MA, Liang B, Gao L, Wang B, Wang T, Su YJ. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns. Biol Direct 2011; 6:29. [PMID: 21639885 PMCID: PMC3129321 DOI: 10.1186/1745-6150-6-29] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 06/03/2011] [Indexed: 11/10/2022] Open
Abstract
Background The chloroplast-localized ribulose-1, 5-biphosphate carboxylase/oxygenase (Rubisco), the primary enzyme responsible for autotrophy, is instrumental in the continual adaptation of plants to variations in the concentrations of CO2. The large subunit (LSU) of Rubisco is encoded by the chloroplast rbcL gene. Although adaptive processes have been previously identified at this gene, characterizing the relationships between the mutational dynamics at the protein level may yield clues on the biological meaning of such adaptive processes. The role of such coevolutionary dynamics in the continual fine-tuning of RbcL remains obscure. Results We used the timescale and phylogenetic analyses to investigate and search for processes of adaptive evolution in rbcL gene in three gymnosperm families, namely Podocarpaceae, Taxaceae and Cephalotaxaceae. To understand the relationships between regions identified as having evolved under adaptive evolution, we performed coevolutionary analyses using the software CAPS. Importantly, adaptive processes were identified at amino acid sites located on the contact regions among the Rubisco subunits and on the interface between Rubisco and its activase. Adaptive amino acid replacements at these regions may have optimized the holoenzyme activity. This hypothesis was pinpointed by evidence originated from our analysis of coevolution that supported the correlated evolution between Rubisco and its activase. Interestingly, the correlated adaptive processes between both these proteins have paralleled the geological variation history of the concentration of atmospheric CO2. Conclusions The gene rbcL has experienced bursts of adaptations in response to the changing concentration of CO2 in the atmosphere. These adaptations have emerged as a result of a continuous dynamic of mutations, many of which may have involved innovation of functional Rubisco features. Analysis of the protein structure and the functional implications of such mutations put forward the conclusion that this evolutionary scenario has been possible through a complex interplay between adaptive mutations, often structurally destabilizing, and compensatory mutations. Our results unearth patterns of evolution that have likely optimized the Rubisco activity and uncover mutational dynamics useful in the molecular engineering of enzymatic activities. Reviewers This article was reviewed by Prof. Christian Blouin (nominated by Dr W Ford Doolittle), Dr Endre Barta (nominated by Dr Sandor Pongor), and Dr Nicolas Galtier.
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Affiliation(s)
- Lin Sen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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Herman JS, Searle JB. Post-glacial partitioning of mitochondrial genetic variation in the field vole. Proc Biol Sci 2011; 278:3601-7. [PMID: 21508032 DOI: 10.1098/rspb.2011.0321] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genetic markers are often used to examine population history. There is considerable debate about the behaviour of molecular clock rates around the population-species transition. Nevertheless, appropriate calibration is critical to any inference regarding the absolute timing and scale of demographic changes. Here, we use a mitochondrial cytochrome b gene genealogy, based entirely on modern sequences and calibrated from recent geophysical events, to date the post-glacial expansion of the Eurasian field vole (Microtus agrestis), a widespread temperate mammal species. The phylogeographic structure reflects the subsequent expansion of populations that went through bottlenecks at the time of the Younger Dryas (ca 12,000 years BP) rather than the Last Glacial Maximum (LGM, ca 24,000 years BP), which is usually seen as the time when present-day patterns were determined. The nucleotide substitution rate that was estimated here, ca 4 × 10(-7) substitutions/site/year, remains extremely high throughout the relevant time frame. Calibration with similarly high population-based substitution rates, rather than long-term rates derived from species divergence times, will show that post-LGM climatic events generated current phylogeographic structure in many other organisms from temperate latitudes.
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Affiliation(s)
- Jeremy S Herman
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK.
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45
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Ho SYW, Lanfear R, Phillips MJ, Barnes I, Thomas JA, Kolokotronis SO, Shapiro B. Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Syst Biol 2011; 60:366-75. [PMID: 21296909 DOI: 10.1093/sysbio/syq099] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Simon Y W Ho
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia.
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Horn S, Durka W, Wolf R, Ermala A, Stubbe A, Stubbe M, Hofreiter M. Mitochondrial genomes reveal slow rates of molecular evolution and the timing of speciation in beavers (Castor), one of the largest rodent species. PLoS One 2011; 6:e14622. [PMID: 21307956 PMCID: PMC3030560 DOI: 10.1371/journal.pone.0014622] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 11/10/2010] [Indexed: 11/30/2022] Open
Abstract
Background Beavers are one of the largest and ecologically most distinct rodent species. Little is known about their evolution and even their closest phylogenetic relatives have not yet been identified with certainty. Similarly, little is known about the timing of divergence events within the genus Castor. Methodology/Principal Findings We sequenced complete mitochondrial genomes from both extant beaver species and used these sequences to place beavers in the phylogenetic tree of rodents and date their divergence from other rodents as well as the divergence events within the genus Castor. Our analyses support the phylogenetic position of beavers as a sister lineage to the scaly tailed squirrel Anomalurus within the mouse related clade. Molecular dating places the divergence time of the lineages leading to beavers and Anomalurus as early as around 54 million years ago (mya). The living beaver species, Castor canadensis from North America and Castor fiber from Eurasia, although similar in appearance, appear to have diverged from a common ancestor more than seven mya. This result is consistent with the hypothesis that a migration of Castor from Eurasia to North America as early as 7.5 mya could have initiated their speciation. We date the common ancestor of the extant Eurasian beaver relict populations to around 210,000 years ago, much earlier than previously thought. Finally, the substitution rate of Castor mitochondrial DNA is considerably lower than that of other rodents. We found evidence that this is correlated with the longer life span of beavers compared to other rodents. Conclusions/Significance A phylogenetic analysis of mitochondrial genome sequences suggests a sister-group relationship between Castor and Anomalurus, and allows molecular dating of species divergence in congruence with paleontological data. The implementation of a relaxed molecular clock enabled us to estimate mitochondrial substitution rates and to evaluate the effect of life history traits on it.
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Affiliation(s)
- Susanne Horn
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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Hewitt GM. Quaternary phylogeography: the roots of hybrid zones. Genetica 2011; 139:617-38. [DOI: 10.1007/s10709-011-9547-3] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 01/03/2011] [Indexed: 10/18/2022]
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48
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Domestication of olive fly through a multi-regional host shift to cultivated olives: Comparative dating using complete mitochondrial genomes. Mol Phylogenet Evol 2010; 57:678-86. [DOI: 10.1016/j.ympev.2010.08.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 08/09/2010] [Accepted: 08/10/2010] [Indexed: 11/19/2022]
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49
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Gilbert C, Feschotte C. Genomic fossils calibrate the long-term evolution of hepadnaviruses. PLoS Biol 2010; 8:e1000495. [PMID: 20927357 PMCID: PMC2946954 DOI: 10.1371/journal.pbio.1000495] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 08/16/2010] [Indexed: 11/18/2022] Open
Abstract
Because most extant viruses mutate rapidly and lack a true fossil record, their deep evolution and long-term substitution rates remain poorly understood. In addition to retroviruses, which rely on chromosomal integration for their replication, many other viruses replicate in the nucleus of their host's cells and are therefore prone to endogenization, a process that involves integration of viral DNA into the host's germline genome followed by long-term vertical inheritance. Such endogenous viruses are highly valuable as they provide a molecular fossil record of past viral invasions, which may be used to decipher the origins and long-term evolutionary characteristics of modern pathogenic viruses. Hepadnaviruses (Hepadnaviridae) are a family of small, partially double-stranded DNA viruses that include hepatitis B viruses. Here we report the discovery of endogenous hepadnaviruses in the genome of the zebra finch. We used a combination of cross-species analysis of orthologous insertions, molecular dating, and phylogenetic analyses to demonstrate that hepadnaviruses infiltrated repeatedly the germline genome of passerine birds. We provide evidence that some of the avian hepadnavirus integration events are at least 19 My old, which reveals a much deeper ancestry of Hepadnaviridae than could be inferred based on the coalescence times of modern hepadnaviruses. Furthermore, the remarkable sequence similarity between endogenous and extant avian hepadnaviruses (up to 75% identity) suggests that long-term substitution rates for these viruses are on the order of 10(-8) substitutions per site per year, which is a 1,000-fold slower than short-term rates estimated based on the sequences of circulating hepadnaviruses. Together, these results imply a drastic shift in our understanding of the time scale of hepadnavirus evolution, and suggest that the rapid evolutionary dynamics characterizing modern avian hepadnaviruses do not reflect their mode of evolution on a deep time scale.
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Affiliation(s)
- Clément Gilbert
- Department of Biology, University of Texas, Arlington, Texas, United States of America
| | - Cédric Feschotte
- Department of Biology, University of Texas, Arlington, Texas, United States of America
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de Thoisy B, da Silva AG, Ruiz-García M, Tapia A, Ramirez O, Arana M, Quse V, Paz-y-Miño C, Tobler M, Pedraza C, Lavergne A. Population history, phylogeography, and conservation genetics of the last Neotropical mega-herbivore, the lowland tapir (Tapirus terrestris). BMC Evol Biol 2010; 10:278. [PMID: 20840756 PMCID: PMC2949869 DOI: 10.1186/1471-2148-10-278] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 09/14/2010] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Understanding the forces that shaped Neotropical diversity is central issue to explain tropical biodiversity and inform conservation action; yet few studies have examined large, widespread species. Lowland tapir (Tapirus terrrestris, Perissodactyla, Tapiridae) is the largest Neotropical herbivore whose ancestors arrived in South America during the Great American Biotic Interchange. A Pleistocene diversification is inferred for the genus Tapirus from the fossil record, but only two species survived the Pleistocene megafauna extinction. Here, we investigate the history of lowland tapir as revealed by variation at the mitochondrial gene Cytochrome b, compare it to the fossil data, and explore mechanisms that could have shaped the observed structure of current populations. RESULTS Separate methodological approaches found mutually exclusive divergence times for lowland tapir, either in the late or in the early Pleistocene, although a late Pleistocene divergence is more in tune with the fossil record. Bayesian analysis favored mountain tapir (T. pinchaque) paraphyly in relation to lowland tapir over reciprocal monophyly, corroborating the inferences from the fossil data these species are sister taxa. A coalescent-based analysis rejected a null hypothesis of allopatric divergence, suggesting a complex history. Based on the geographic distribution of haplotypes we propose (i) a central role for western Amazonia in tapir diversification, with a key role of the ecological gradient along the transition between Andean subcloud forests and Amazon lowland forest, and (ii) that the Amazon river acted as an barrier to gene flow. Finally, the branching patterns and estimates based on nucleotide diversity indicate a population expansion after the Last Glacial Maximum. CONCLUSIONS This study is the first examining lowland tapir phylogeography. Climatic events at the end of the Pleistocene, parapatric speciation, divergence along the Andean foothill, and role of the Amazon river, have similarly shaped the history of other taxa. Nevertheless further work with additional samples and loci is needed to improve our initial assessment. From a conservation perspective, we did not find a correspondence between genetic structure in lowland tapir and ecogeographic regions proposed to define conservation priorities in the Neotropics. This discrepancy sheds doubt into this scheme's ability to generate effective conservation planning for vagile species.
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