Abstract:
:Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in a pedigree of seven wolves. Putative de novo mutations were discovered by whole-genome sequencing and were verified by Sanger sequencing of parents and offspring. Using stringent filters and an estimate of the false negative rate in the remaining observable genome, we obtain an estimate of ∼4.5 x 10-9 per base pair per generation and provide conservative bounds from 2.6 x 10-9 and 7.1 x 10-9. Although our estimate is consistent with recent mutation rate estimates from ancient DNA (4.0 x 10-9 and 3.0-4.5 x 10-9), it implies a wider possible range. We also examined the consequences of our rate and the accompanying interval for dating several critical events in canid demographic history. For example, applying our full range of rates to coalescent models of dog and wolf demographic history implies a wide set of possible divergence times between the ancestral populations of dogs and extant Eurasian wolves (16,000 - 64,000 years ago) although our point estimate indicates a date between 25,000 and 33,000 years ago. Aside from one study in mice, ours provides the only direct mammalian mutation rate outside of primates, and is likely to be vital to future investigations of mutation rate evolution.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Koch E,Schweizer RM,Schweizer TM,Stahler DR,Smith DW,Wayne RK,Novembre Jdoi
10.1093/molbev/msz159subject
Has Abstractpub_date
2019-07-12 00:00:00eissn
0737-4038issn
1537-1719pii
5531468pub_type
杂志文章abstract::There are many examples of groups (such as birds, bees, mammals, multicellular animals, and flowering plants) that have undergone a rapid radiation. In such cases, where there is a combination of short internal and long external branches, correctly estimating and rooting phylogenetic trees is known to be a difficult p...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm178
更新日期:2007-11-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004141
更新日期:2002-06-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss188
更新日期:2012-12-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr005
更新日期:2011-06-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu131
更新日期:2014-06-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq355
更新日期:2011-05-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx161
更新日期:2017-08-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026364
更新日期:2000-06-01 00:00:00
abstract::Seminal fluid proteins (SFPs) mediate an array of postmating reproductive processes that influence fertilization and fertility. As such, it is widely held that SFPs may contribute to postmating, prezygotic reproductive barriers between closely related taxa. We investigated seminal fluid (SF) diversification in a recen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz235
更新日期:2020-02-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss161
更新日期:2012-11-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss058
更新日期:2012-07-01 00:00:00
abstract::The evolutionary transition from invertebrates to vertebrates involved extensive gene duplication, but understanding precisely how such duplications contributed to this transition requires more detailed knowledge of specific cases of genes and gene families. Myogenic differentiation (MyoD) has long been recognized as ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa147
更新日期:2020-10-01 00:00:00
abstract::Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa194
更新日期:2020-12-16 00:00:00
abstract::Although there is substantial evidence that, in animals, male-inherited neutral DNA evolves at a higher rate than female-inherited DNA, the relative evolutionary rate of male- versus female-inherited DNA has not been investigated in plants. We compared the substitution rates at neutral sites of maternally and paternal...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004151
更新日期:2002-06-01 00:00:00
abstract::This study establishes a phylogenetic framework for the natural geographic isolates of the widely studied nematode species Caenorhabditis elegans. Virtually complete mitochondrial genomes are sequenced from 27 C. elegans natural isolates to characterize mitochondrial divergence patterns and to investigate the evolutio...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg044
更新日期:2003-03-01 00:00:00
abstract::Baleen whales (suborder Mysticeti) comprise 11 extant species that are classified into four families. Although several phylogenetic hypotheses about these taxa have been proposed, their phylogenetic relationships remain confused. We addressed this problem using short interspersed repetitive element (SINE) insertion da...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj071
更新日期:2006-05-01 00:00:00
abstract::Multipartite genomes, containing at least two large replicons, are found in diverse bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to gain insights into the role and emergence of multipar...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy248
更新日期:2019-03-01 00:00:00
abstract::The grass family (Poaceae), the fourth largest family of flowering plants, encompasses the most economically important cereal, forage, and energy crops, and exhibits a unique gametophytic self-incompatibility (SI) mechanism that is controlled by at least two multiallelic and independent loci, S and Z. Despite intense ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv335
更新日期:2016-04-01 00:00:00
abstract::Selenocysteine (Sec) is the 21st amino acid in the genetic code, inserted in response to UGA codons with the help of RNA structures, the SEC Insertion Sequence (SECIS) elements. The three domains of life feature distinct strategies for Sec insertion in proteins and its utilization. While bacteria and archaea possess s...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw122
更新日期:2016-09-01 00:00:00
abstract::There is increasing evidence that X chromosomes have an unusual complement of genes, especially genes that have sex-specific expression. However, whereas in worm and fly the X chromosome has a dearth of male-specific genes, in mice genes that are uniquely expressed in spermatogonia are especially abundant on the X chr...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg131
更新日期:2003-07-01 00:00:00
abstract::Because of the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being "synonymous," these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is typically attributed to mutation...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz124
更新日期:2019-10-01 00:00:00
abstract::The AID/APOBEC family (comprising AID, APOBEC1, APOBEC2, and APOBEC3 subgroups) contains members that can deaminate cytidine in RNA and/or DNA and exhibit diverse physiological functions (AID and APOBEC3 deaminating DNA to trigger pathways in adaptive and innate immunity; APOBEC1 mediating apolipoprotein B RNA editing...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi026
更新日期:2005-02-01 00:00:00
abstract::The selective constraints influencing mRNA editing in plant organelles are largely unknown. To investigate these, we compared patterns of editing between monocot and dicot mitochondrial mRNA. On average, 24% of sites that are edited form C to U in one species have been substituted during evolution by a genomic T in th...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025768
更新日期:1997-03-01 00:00:00
abstract::Gene expression changes contribute to complex trait variations in both individuals and populations. However, the evolution of gene expression underlying complex traits over macroevolutionary timescales remains poorly understood. Snake venoms are proteinaceous cocktails where the expression of each toxin can be quantif...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz125
更新日期:2019-09-01 00:00:00
abstract::Sherpa population is an ethnic group living in south mountainside of Himalayas for hundreds of years. They are famous as extraordinary mountaineers and guides, considered as a good example for successful adaptation to low oxygen environment in Tibetan highlands. Mitochondrial DNA (mtDNA) variations might be important ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst147
更新日期:2013-12-01 00:00:00
abstract::Successful fertilization in free-spawning marine organisms depends on the interactions between genes expressed on the surfaces of eggs and sperm. Positive selection frequently characterizes the molecular evolution of such genes, raising the possibility that some common deterministic process drives the evolution of gam...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl062
更新日期:2006-10-01 00:00:00
abstract::Male sexual behavior in the fruit fly Drosophila melanogaster is regulated by fruitless (fru), a sex-determination gene specifying the synthesis of BTB-Zn finger proteins that likely function as male-specific transcriptional regulators. Expression of fru in the nervous system specifies male sexual behavior and the mus...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj070
更新日期:2006-03-01 00:00:00
abstract::Purifying selection can substantially alter patterns of molecular evolution. Its main effect is to reduce overall levels of genetic variation, leading to a reduced effective population size. However, it also distorts genealogies relative to neutral expectations. A structured coalescent method has been used to describe...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss170
更新日期:2012-11-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg139
更新日期:2003-08-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu343
更新日期:2015-03-01 00:00:00