<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Urantowka, A.D.</style></author><author><style face="normal" font="default" size="100%">Kroczak, A.</style></author><author><style face="normal" font="default" size="100%">Mackiewicz, P.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The influence of molecular markers and methods on inferring the phylogenetic relationships between the representatives of the Arini (parrots, Psittaciformes), determined on the basis of their complete mitochondrial genomes</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Evolutionary Biology</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">ATP6</style></keyword><keyword><style  face="normal" font="default" size="100%">ATP8</style></keyword><keyword><style  face="normal" font="default" size="100%">BAYESIAN INFERENCE</style></keyword><keyword><style  face="normal" font="default" size="100%">BIRDS</style></keyword><keyword><style  face="normal" font="default" size="100%">COI</style></keyword><keyword><style  face="normal" font="default" size="100%">COII</style></keyword><keyword><style  face="normal" font="default" size="100%">COIII</style></keyword><keyword><style  face="normal" font="default" size="100%">CONTROL REGION</style></keyword><keyword><style  face="normal" font="default" size="100%">CYTB</style></keyword><keyword><style  face="normal" font="default" size="100%">MAXIMUM LIKELIHOOD</style></keyword><keyword><style  face="normal" font="default" size="100%">METHODOLOGY</style></keyword><keyword><style  face="normal" font="default" size="100%">MITOGENOME</style></keyword><keyword><style  face="normal" font="default" size="100%">ND1</style></keyword><keyword><style  face="normal" font="default" size="100%">ND2</style></keyword><keyword><style  face="normal" font="default" size="100%">ND3</style></keyword><keyword><style  face="normal" font="default" size="100%">ND4</style></keyword><keyword><style  face="normal" font="default" size="100%">ND4L</style></keyword><keyword><style  face="normal" font="default" size="100%">ND5</style></keyword><keyword><style  face="normal" font="default" size="100%">ND6</style></keyword><keyword><style  face="normal" font="default" size="100%">PARROTS</style></keyword><keyword><style  face="normal" font="default" size="100%">PARSIMONY</style></keyword><keyword><style  face="normal" font="default" size="100%">PHYLOGENY</style></keyword><keyword><style  face="normal" font="default" size="100%">TRNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2017</style></year></dates><volume><style face="normal" font="default" size="100%">17</style></volume><pages><style face="normal" font="default" size="100%">166</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&amp;quot;&lt;strong&gt;Background:&lt;/strong&gt; Conures are a morphologically diverse group of Neotropical parrots classified as members of the tribe Arini, which has recently been subjected to a taxonomic revision. The previously broadly defined &lt;em&gt;Aratinga &lt;/em&gt;genus of this tribe has been split into the &amp;lsquo;true&amp;rsquo; Aratinga and three additional genera, &lt;em&gt;Eupsittula&lt;/em&gt;, &lt;em&gt;Psittacara &lt;/em&gt;and &lt;em&gt;Thectocercus&lt;/em&gt;. Popular markers used in the reconstruction of the parrots&amp;rsquo; phylogenies derive from mitochondrial DNA. However, current phylogenetic analyses seem to indicate conflicting relationships between &lt;em&gt;Aratinga &lt;/em&gt;and other conures, and also among other Arini members. Therefore, it is not clear if the mtDNA phylogenies can reliably define the species tree. The inconsistencies may result from the variable evolution rate of the markers used or their weak phylogenetic signal. To resolve these controversies and to assess to what extent the phylogenetic relationships in the tribe Arini can be inferred from mitochondrial genomes, we compared representative Arini mitogenomes as well as examined the usefulness of the individual mitochondrial markers and the efficiency of various phylogenetic methods.&lt;br /&gt;
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	&lt;strong&gt;Results:&lt;/strong&gt; Single molecular markers produced inconsistent tree topologies, while different methods offered various topologies even for the same marker. A significant disagreement in these tree topologies occurred for &lt;em&gt;cytb&lt;/em&gt;, &lt;em&gt;nd2 &lt;/em&gt;and &lt;em&gt;nd6 &lt;/em&gt;genes, which are commonly used in parrot phylogenies. The strongest phylogenetic signal was found in the control region and RNA genes. However, these markers cannot be used alone in inferring Arini phylogenies because they do not provide fully resolved trees. The most reliable phylogeny of the parrots under study is obtained only on the concatenated set of all mitochondrial markers. The analyses established significantly resolved relationships within the former &lt;em&gt;Aratinga &lt;/em&gt;representatives and the main genera of the tribe Arini. Such mtDNA phylogeny can be in agreement with the species tree, owing to its match with synapomorphic features in plumage colouration.&lt;br /&gt;
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	&lt;strong&gt;Conclusions:&lt;/strong&gt; Phylogenetic relationships inferred from single mitochondrial markers can be incorrect and contradictory. Therefore, such phylogenies should be considered with caution. Reliable results can be produced by concatenated sets of all or at least the majority of mitochondrial genes and the control region. The results advance a new view on the relationships among the main genera of Arini and resolve the inconsistencies between the taxa that were previously classified as the broadly defined genus &lt;em&gt;Aratinga&lt;/em&gt;. Although gene and species trees do not always have to be consistent, the mtDNA phylogenies for Arini can reflect the species tree.&lt;/p&gt;
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