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Plant phylogenomics: approaches to make phylogenic inference more reliable
Correct phylogenetic inference is especially hard on very shallow and deep taxonomic levels. On intraspecific/intrageneric levels, widely used genetic fingerprinting techniques (AFLP,SSR) tend to yield volatile results, partially because bands of equal size on the gel should not necessarily be orthologous, and absence of a band does not necessarily mean absence of a character, as it might be caused by experimental setup (see Kumar et al., 2009). At the same time, at this taxonomic range commonly used phylogenetic markers such as nuclear ITS regions and chloroplast spacers/genes are only of limited help due to lack of informative characters to resolve tree structure, end even medium-size data sets suffer from lack of resolution. This work demonstrates the benefit of introducing cpDNA-based phylogenomic methodology to shallow level taxonomic research. Well-resolved tree structure allowed for the first time to reveal phylogenetic affinities of the maternal line of domesticated apple sorts. Three distinct chloroplast DNA lineages present in apple cultivars diverged before the origin of agriculture. One line, represented by M. x domestica cv. Granny Smith diverged from Asian apple species, and the other two, comprising the majority of apple cultivars analyzed share sister group relationships to different, unrelated accessions of M. sylvestris from southern and south eastern Europe. The most straightforward explanation for this finding is that apple cultivation has started independently in various regions. The advantages of planting apples close to human dwellings were apparent enough, and people from various places started to grow apple trees taken from locations near about. Lack of the domestication bottleneck and clonal population structure in domesticated apples (Cornille et al., 2012) corroborate their polyphyletic origin. An alternative explanation would be substitution of cpDNA in M. x domestica by hybridisation, through pollination of M. sylvestris by pollen of domesticated apple sorts. In contrast to ...
Plant phylogenomics: approaches to make phylogenic inference more reliable
Correct phylogenetic inference is especially hard on very shallow and deep taxonomic levels. On intraspecific/intrageneric levels, widely used genetic fingerprinting techniques (AFLP,SSR) tend to yield volatile results, partially because bands of equal size on the gel should not necessarily be orthologous, and absence of a band does not necessarily mean absence of a character, as it might be caused by experimental setup (see Kumar et al., 2009). At the same time, at this taxonomic range commonly used phylogenetic markers such as nuclear ITS regions and chloroplast spacers/genes are only of limited help due to lack of informative characters to resolve tree structure, end even medium-size data sets suffer from lack of resolution. This work demonstrates the benefit of introducing cpDNA-based phylogenomic methodology to shallow level taxonomic research. Well-resolved tree structure allowed for the first time to reveal phylogenetic affinities of the maternal line of domesticated apple sorts. Three distinct chloroplast DNA lineages present in apple cultivars diverged before the origin of agriculture. One line, represented by M. x domestica cv. Granny Smith diverged from Asian apple species, and the other two, comprising the majority of apple cultivars analyzed share sister group relationships to different, unrelated accessions of M. sylvestris from southern and south eastern Europe. The most straightforward explanation for this finding is that apple cultivation has started independently in various regions. The advantages of planting apples close to human dwellings were apparent enough, and people from various places started to grow apple trees taken from locations near about. Lack of the domestication bottleneck and clonal population structure in domesticated apples (Cornille et al., 2012) corroborate their polyphyletic origin. An alternative explanation would be substitution of cpDNA in M. x domestica by hybridisation, through pollination of M. sylvestris by pollen of domesticated apple sorts. In contrast to ...
Plant phylogenomics: approaches to make phylogenic inference more reliable
Nikiforova, Svetlana (author) / Hellwig, Frank / Theißen, Günter / Pisani, Davide
2013-01-01
Theses
Electronic Resource
English
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