View source for Present-bacteria speciation

<p><strong>Bacterial Speciation&nbsp;&nbsp;&nbsp;&nbsp; </strong>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</p>

<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 20141215 jihoon moon</p>

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<p><strong>Abstract</strong></p>

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<p>In before lecture, professor say when we speciate specific species, gender isolation is important. But I wonder, when we want to classify some species, how can we classify asexual species (like bacteria)? First I think, bacteria can survive depend on specific circumstance. At that time, in their chromosome, mutation and recombination will occur. &nbsp;But I don&rsquo;t know how much bases are changed to speciate. So I search at google and I found Bacteria Lateral gene transfer and others that determine diversity of the bacteria genome to speciate</p>

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<p><strong>Introduction</strong></p>

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<p>To know bacterial evolution is important for dealing with urgent practical problems. The proper identification and delineation of bacterial species plays critical roles in medical diagnosis, food safety, epidemic, and bioterrorism mitigation</p>

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<p>Microbiologists have been questioning the present species concepts and definitions used in microbiology, namely the morphological species concept for eukaryotic micro-organisms and the species definition for bacteria and archaea based on DNA&ndash;DNA reassociation. There is generally no accepted species concept</p>

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<p>Species are defined by people and separate with standard that made by human. There are old words in bacteria speciation. If genes matches over 70%, they are treated as the same species. But I think it is just old words. Because bacteria have very short DNA comparable to other eukaryotes. And Maybe 70% of them are really small scale in real world. And the variance of the specific portion of the genetic region that decide to specific species is not same with whole genetic variance. So it is very ambiguous.</p>

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<p>In bacteria, the situation is very different from eukaryotes. Bacteria exchange pieces of DNA, not whole genomes. Normally, speciation in eukaryote occur when genetic recombination occur very actively. But, speciation in bacteria occurs when genome-wide genetic recombination events become more limited. Because there is no biological motivation for doing so. In contrast to the eukaryotes, genetic exchange between bacterial species does not hinder adaptive divergence, so the gender isolation is not important. Indeed, bacterial species that exchange genes are free to diverge without bound in all characters.</p>

<p>There are one example that bacteria speciate to new species. At 2008, research by Richard Lenski has even shown new bacterial species evolving in the laboratory. <em>E. coli</em>&nbsp;cells cannot grow on citrate under oxic conditions, and that inability has long been viewed. They then exposed several identical populations of&nbsp;<em>E. coli</em>&nbsp;to an environment high in citrate and low in other energy sources. &quot;For more than around 30,000 generations, One population eventually evolved the Cit+ function that a gene that could metabolize citrate, whereas all of the others remain Cit- and after more than 43,500 generations, the Cit- are extinct. Given that the Cit- trait is a defining feature of&nbsp;<em>E. coli</em>, the population that gained Cit+ could be considered a new species.</p>

<p><img src="file:///C:\Users\문지훈\AppData\Local\Temp\msohtmlclip1\01\clip_image002.jpg" style="height:415px; width:286px" /></p>

<p>Then they make a 3 step model of evolutionary innovation</p>

<ol>
	<li><strong>Potentiation</strong><strong>:</strong> a genetic background evolves in which a trait is mutationally accessible, making the trait&#39;s evolution possible.</li>
	<li><strong>Actualization</strong>: a mutation occurs that produces the trait, making it manifest, albeit likely in a weak form.</li>
	<li><strong>Refinement</strong>: One the trait exists, if it provides selective benefit, mutations will accumulate that improve the trait, making it effective. This phase is open-ended, and will continue so long as refining mutations arise and the trait remains beneficial</li>
</ol>

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<p>There are just hypothesis for the bacterial species concept is that bacteria form coherent genomic clusters that are characterized by distinctive phenotypic properties. The clusters are thought to be created as the effect of two major forces, selection and recombination</p>

<p>But recombination is rare and promiscuous than plants and animals(bacteriophage, plasmid, vector integratoin. homologous recombination is limited by the resistance to intergration of divergent DNA. Restriction endonuclease activity reduce the rate of recombination.). And they are highly localized to a small fraction of genome and recombination sometimes occur in heterologous segment even they are extremely distantly related</p>

<p>How they can recombination? There are important things exchange bacterial genome. Lateral gene transfer of adaptations across species is facilitated by several aspects of bacterial genetic exchange. Not homologous recombination. Across species. Integration of highly divergent DNA can make bacterial genetic exchange. Also important is the localized property of recombination that only a very small fraction of the donor&rsquo;s genome is integrated. This allows for transfer of a generally useful adaptation and make them speciate</p>

<p>But, There are still limitation that we define species. It is not defined by only the Lateral gene transfer. The amount of genomic evidence that can quantify the importance of selection and recombination for the species is currently too limited to allow for robust conclusions. There are many aspects in recombination and many isolated circumstances. We can&rsquo;t set the all of the various circumstances that give us data.</p>

<p>To knowing about bacterial speciation, The key issue is whether closely related isolates of bacteria cluster into discrete groups that can be identified and assigned as species. Then, if species can be identified, the challenge is to identify what processes cause micro-organisms to speciate and the phenomena that generate cohesion within species.</p>

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<p><strong>Result </strong></p>

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<p>Most of the bacteriologists agree to &lsquo;unravelling the puzzle of microbial speciation remains one of the most elusive, important and exciting areas of microbiological research.&rsquo;</p>

<p>Speciation is unlikely to occur by some mechanisms alone, since neutral speciation requires a much steeper reduction in recombination rate by divergence than is suggested by the empirical data. Therefore, we must determine how much the variable recombinations in bacteria impact on our ability to integrated speciation.</p>

<p>The amount of genomic evidence that can quantify the importance of selection and recombination for the species is currently too limited to allow for robust conclusions. So recent developments in sequencing technology and genome analyses are continue to provide the necessary tools for understanding microbial speciation.</p>

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<p><strong>Reference</strong></p>

<p>&nbsp;</p>

<p>Introduction: species and speciation in micro-organisms <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Spratt%20BG%5BAuthor%5D">Brian G Spratt</a>,<sup>1,*</sup> <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Staley%20JT%5BAuthor%5D">James T Staley</a>,<sup>2</sup> and <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Fisher%20MC%5BAuthor%5D">Matthew C Fisher</a><sup>1</sup> (2006)</p>

<p>The bacterial species definition in the genomic era <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Konstantinidis%20KT%5BAuthor%5D&amp;cauthor=true&amp;cauthor_uid=17062412">Konstantinos T Konstantinidis</a>,<sup>*</sup> <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Ramette%20A%5BAuthor%5D&amp;cauthor=true&amp;cauthor_uid=17062412">Alban Ramette</a>,<sup>&dagger;</sup> and <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Tiedje%20JM%5BAuthor%5D&amp;cauthor=true&amp;cauthor_uid=17062412">James M Tiedje</a>(2006)</p>

<p>Bacterial Speciation: Genetic Sweeps in Bacterial Species Frederick&nbsp;M. Cohan(2016)</p>

<p>Genome evolution and adaptation in a long-term experiment with&nbsp;<em>Escherichia coli</em>Jeffrey E. Barrick<a href="http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html#a1" title="affiliated with "><sup>1</sup></a><sup>,</sup><a href="http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html#a7" title="affiliated with "><sup>7</sup></a>,</p>

<p>Dong Su Yu<a href="http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html#a2" title="affiliated with "><sup>2</sup></a><sup>,</sup><a href="http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html#a3" title="affiliated with "><sup>3</sup></a><sup>,</sup><a href="http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html#a7" title="affiliated with "><sup>7</sup></a>, Sung Ho Yoon<a href="http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html#a2" title="affiliated with "><sup>2</sup></a>, Haeyoung Jeong<a href="http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html#a2" title="affiliated with "><sup>2</sup></a>, Tae Kwang Oh<a href="http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html#a2" title="affiliated with "><sup>2</sup></a><sup>,</sup><a href="http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html#a4" title="affiliated with "><sup>4</sup></a>, Dominique Schneider<a href="http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html#a5" title="affiliated with "><sup>5</sup></a>, Richard E. Lenski<a href="http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html#a1" title="affiliated with "><sup>1</sup></a>&nbsp;&amp; Jihyun F. Kim(2009)</p>

<p>http://www.cell.com/current-biology/fulltext/S0960-9822(15)01250-6</p>

<p><a href="https://ncse.com/creationism/analysis/evolving-bacteria">https://ncse.com/creationism/analysis/evolving-bacteria</a></p>

<p>http://blog.naver.com/PostView.nhn?blogId=ohryan77&amp;logNo=60073895598</p>

<p>Bacterial Species and Speciation. FREDERICK M. COHAN(2001)</p>