Molecular evolution of the Bovini tribe (Bovidae, Bovinae): Is there evidence of rapid evolution or reduced selective constraint in Domestic cattle?

MacEachern, Sean; McEwan, John C.; McCulloch, Alan; Mather, Andrew; Savin, Keith W.; Goddard, Michael E.

doi:10.1186/1471-2164-10-179

Cited by 38 publications

(32 citation statements)

References 40 publications

(43 reference statements)

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“…The accelerated evolution of genes is often driven by positive selection, relaxed selection or low effective population size (Ne). During cultivation or domestication, both selection pressures for fitness traits important in the wild species and effective population size are reduced (Maceachern et al, 2009). Therefore, reduced selective constraint and reduced Ne could be responsible for the observed elevated evolutionary ratios in cultivated FAN with more elevated interval values (Ka/Ks = 0.5–1.0).…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptomics of Strawberries (Fragaria spp.) Provides Insights into Evolutionary Patterns

et al. 2016

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Multiple closely related species with genomic sequences provide an ideal system for studies on comparative and evolutionary genomics, as well as the mechanism of speciation. The whole genome sequences of six strawberry species (Fragaria spp.) have been released, which provide one of the richest genomic resources of any plant genus. In this study, we first generated seven transcriptome sequences of Fragaria species de novo, with a total of 48,557–82,537 unigenes per species. Combined with 13 other species genomes in Rosales, we reconstructed a phylogenetic tree at the genomic level. The phylogenic tree shows that Fragaria closed grouped with Rubus and the Fragaria clade is divided into three subclades. East Asian species appeared in every subclade, suggesting that the genus originated in this area at ∼7.99 Mya. Four species found in mountains of Southwest China originated at ∼3.98 Mya, suggesting that rapid speciation occurred to adapt to changing environments following the uplift of the Qinghai–Tibet Plateau. Moreover, we identified 510 very significantly positively selected genes in the cultivated species F. × ananassa genome. This set of genes was enriched in functions related to specific agronomic traits, such as carbon metabolism and plant hormone signal transduction processes, which are directly related to fruit quality and flavor. These findings illustrate comprehensive evolutionary patterns in Fragaria and the genetic basis of fruit domestication of cultivated strawberry at the genomic/transcriptomic level.

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Section: Discussionmentioning

confidence: 99%

Comparative Transcriptomics of Strawberries (Fragaria spp.) Provides Insights into Evolutionary Patterns

et al. 2016

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“…The availability of genomic data for domestic animals and plants has stimulated interest in discovering the genetic changes underlying the distinctive characteristics of domestic species (Amaral et al 2011; Andersson 2001; Andersson and Georges 2004; MacEachern et al 2009; Rubin et al 2010). Some such genetic changes presumably involve the loci responsible for traits consciously or inadvertently subjected to artificial selection by humans in the process of domestication (Andersson and Georges 2004).…”

Section: Introductionmentioning

confidence: 99%

“…In addition, certain neutral or even deleterious alleles may be fixed because they are linked to alleles selectively favored in the process of domestication (Fisher 1930). Other genetic changes may involve the relaxation of purifying selection after domestication, as a result of the less stringent selective pressures in the domestic environment (Björnerfeldt et al 2006; Cruz et al 2008; MacEachern et al 2009). Because domestication may involve population bottlenecks, the effectiveness of purifying selection in eliminating slightly deleterious mutations may also be reduced in domesticated populations (Cruz et al 2008).…”

Section: Introductionmentioning

confidence: 99%

“…Comparisons of the ratio of nonsynonymous to synonymous substitutions has been used to test for a relaxation of purifying selection on both mitochondrial and nuclear genes of the domestic dog (Björnerfeldt et al 2006; Cruz et al 2008) and on nuclear genes of domestic cattle (MacEachern et al 2009). Mitochondrial (mt) genomes are expected to particularly prone to the accumulation of slightly deleterious mutations because of their high mutation rate and lack of recombination (Hasegawa et al 1998; Hughes and Hughes 2007; Rand and Kann 1996).…”

Section: Introductionmentioning

confidence: 99%

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Accumulation of slightly deleterious mutations in the mitochondrial genome: A hallmark of animal domestication

Hughes

2013

Gene

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The hypothesis that domestication lead to a relaxation of purifying selection on mitochondrial (mt) genomes was tested by comparative analysis of mt genes from dog, pig, chicken, and silkworm. The three vertebrate species showed mt genome phylogenies in which domestic and wild isolates were intermingled, whereas the domestic silkworm (Bombyx mori) formed a distinct cluster nested within its closest wild relative (B. mandarina). In spite of these differences in phylogenetic pattern, significantly greater proportions of nonsynonymous SNPs than of synonymous SNPs were unique to the domestic populations of all four species. Likewise, in all four species, significantly greater proportions of RNA-encoding SNPs than of synonymous SNPs were unique to the domestic populations. Thus, domestic populations were characterized by an excess of unique polymorphisms in two categories generally subject to purifying selection: nonsynonymous sites and RNA-encoding sites. Many of these unique polymorphisms thus seem likely to be slightly deleterious; the latter hypothesis was supported by the generally lower gene diversities of polymorphisms unique to domestic populations in comparison to those of polymorphisms shared by domestic and wild populations.

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“…From the analysis of ancestral mutations [10], it appears that domesticated cattle populations are able to maintain a high load of unfavorable mutations. This is probably a consequence of the domestication process itself.…”

Section: Genome Biology and Domesticationmentioning

confidence: 99%

The cattle genome reveals its secrets

Burt

2009

J Biol

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MinireviewT Th he e c ca at tt tl le e g ge en no om me e r re ev ve ea al ls s i it ts s s se ec cr re et ts s Cattle belong to an ancient group of mammals, the Cetartiodactyla, that first appeared around 60 million years ago. Domesticated cattle (Bos taurus and Bos taurus indicus) diverged from a common ancestor 250,000 years ago, and have had a long and rich association with human civilization since Neolithic times 8,000-10,000 years ago. All modern cattle breeds originate from large populations of the ancestral aurochs (Bos taurus primigenius; Figure 1) through thousands of years of domestication. During this time, more than 800 cattle breeds have been established, representing an important resource for understanding the genetics of complex traits in ruminants. More than a billion cattle are raised annually worldwide for beef and dairy products, as well as for hides. Cattle therefore represent significant scientific opportunities, as well as an important economic resource.Sequencing of the cattle genome began in December 2003, led by Richard Gibbs and George Weinstock at the Baylor College of Medicine's genome sequencing center in Houston, Texas, USA. The first draft sequence of the bovine genome was based on DNA taken from a Hereford dam, L1 Dominette 01449 (Figure 2), a cattle breed used in beef production. In parallel, a large number of single-nucleotide polymorphisms (SNPs) have also been generated from the partial sequence of six breeds (Holstein, Angus, Jersey, Limousin, Norwegian Red and Brahman). Taken together with the sequence of L1 Dominette 01449 (the reference bovine genome [1]) these represent a valuable resource for marker-assisted selection of genetic traits in commercial breeding programs.The Bovine Genome Project represents a complex collaborative effort between multiple groups and funding from the United States, Canada, France, United Kingdom, New Zealand and Australia.Undoubtedly the current bovine genome sequence will be improved in both its sequence coverage and its annotation, but this draft sequence will form the basis for cattle genetics and genomics for the next 20 years or more. So what have we learned?T Th he e g ge en no om me e a as ss se em mb bl ly y p pr ro ob bl le em m --s st ti il ll l n no ot t s so ol lv ve ed d? ?The technology for generating raw sequence data has advanced rapidly over the past 35 years, starting with Sanger sequencing in the 1970s, automated fluorescent Sanger sequencing in the 1980s and, recently, ultra-high-A Ab bs st tr ra ac ct t throughput methods based on the parallel sequencing platforms produced by 454, Illumina, and ABI. However, the scale of these advances has not been matched by new algorithms and tools for sequence assembly, particularly for large genomes. Common problems associated with large genomes have been repetitive sequences (generally around 50% of a vertebrate genome), gene families and genetic polymorphisms, all of which can cause errors in assembly. Genome assembly is still a problem, requiring a combination of parallel computing...

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Molecular evolution of the Bovini tribe (Bovidae, Bovinae): Is there evidence of rapid evolution or reduced selective constraint in Domestic cattle?

Cited by 38 publications

References 40 publications

Comparative Transcriptomics of Strawberries (Fragaria spp.) Provides Insights into Evolutionary Patterns

Comparative Transcriptomics of Strawberries (Fragaria spp.) Provides Insights into Evolutionary Patterns

Accumulation of slightly deleterious mutations in the mitochondrial genome: A hallmark of animal domestication

The cattle genome reveals its secrets

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