每一日翻译20190420

xiongrongchuan@126.com

http://blog.sciencenet.cn/u/Bearjazz

(脚注①:编者估摸,核算的正规化为一棵基于数据集营造的最大似然树,核实的面目即为查验被试系统一发布育树与这棵基于最大似然法营造的系统一发布育树的异样,差距富含最大似然值的歧异和p值)

Tadpoles, the premetamorphic life stage of many frogs and toads, play a
key role in anuran biology, and are the focus of various aspects of
anuran research (McDiarmid & Altig 1999). The usually aquatic larval
stage and the corresponding adults are exposed to notably different
selective regimes due to the biphasic life cycle of anurans (e.g., Haas
& Das 2011). Among terrestrial vertebrates, this unique free-living
larval stage is considered a particularly suitable indicator of adaptive
radiation processes in the evolutionary context of lineage
diversification (Bossuyt & Milinkovitch 2000; Roelants et al. 2011).
Under the conditions of current climate change, anuran larvae are of
interest, as numerous effects of varying abiotic factors (e.g.,
temperature, availability of water, ultraviolet radiation) can be
observed in tadpoles and tadpole communities (Reading 2002; Blaustein et
al. 2003; Blaustein et al. 2010). Furthermore, extended amplitudes in
temperature are correlated with chytrid fungus infection in tadpoles
(Hamilton et al. 2012), as the latter host and transport the pathogen on
their external keratinous mouthparts (Marantelli et al. 2004; Wake &
Vredenburg 2008; Venesky et al. 2011). Given that larvae usually occupy
different habitats than the adults, tadpoles are also important to
conservation issues such as the global decline of amphibians that is
attributed to habitat alteration (Becker et al. 2007). Properly
characterising anuran larvae can assist with distinguishing species and
inferring phylogenetic relationships (Eterovick & Sazima 2000; Vences et
al. 2010a).

The Shimodaira–Hasegawa test (SH; [38,39]), which is also based on a
non-parametric bootstrap, was developed to compare multiple topologies.
For this test, the null hypothesis is that all the trees tested are
equally good explanations of the data, and the tested hypothesis is that
one or several trees are better approximations of the data. The SH test
avoids for the violation of a priori tree selection by using a step that
accounts for the contribution of the maximum likelihood tree to the null
distribution. In addition, this test is also one-sided. The SH test can
be very conservative in its rejection of the null hypothesis when the
number of candidate trees is large [40–42]. This bias can be
ameliorated by a weighted SH test [38,42]. Shimodaira [41] has also
suggested the use of a test based on bootstrap replicates of different
sizes to calculate the null distribution called the Approximately
Unbiased test. This test appears to be less biased than the KH and SH
tests. A similar test was proposed by Zarkikh and Li [43] but has been
shown in simulation studies to be less accurate than the AU test [41].
More recently, Susko [44] presented a technique that is appropriate
for maximum likelihood distances, based on a generalized least squares
metric. This technique can use a non-parametric bootstrap or a variance
estimated from the sample average for derivation of the correct, null
distribution. This test should alleviate some of the bias in tree
topology testing as long as the correct substitution model is selected

xiongrongchuan@126.com

Shimodaira–Hasegawa检验(SH;
[38,39])也是依靠非参数自举核实,意在比很多样拓扑结构的争论。在这一检查中,零如若是借使全体被验证的系统一发布育树对数据的解释都以一模一样的,备择纵然是一个或八个树越发贴合数据。SH核算通过采纳三个最大似然树对空遍及的进献度的步骤,进而制止先验树(操作人士自身挑选标准树)选择带来的谬误。其它,这种考察也是单侧的。当候选树的数量极大时,SH核实可以拾分保守地回绝无效倘若[40-42]。这种过错可经过加权SH核实加以改正[38,42]。Shimodaira[41]还提议利用基于不相同尺寸的自举查证重复来计算空布满,称为近似无偏核查。那么些检察如同比KH和SH核准的谬误越来越小。扎尔kikh和Li[43]提出了多少个类似的查看,但在模仿切磋中显示,该检查的正确度低于AU核实[41]。最近,Susko[44]提出了一种基于广义最小二乘矩阵的适用于最大似然距离的本领。此本事可以选择非参数自举核准或从样本均值估摸的方差来演绎正确的零遍布。只要选择准确的替换模型,那些检察就相应缓慢解决树拓扑核准中的一些错事。

蛤蟆是相当的多青蛙和蟾蜍的变态前生命阶段,在无尾类生物学中起着关键作用,是成都百货上千无尾类研商中关心的刀口(McDiarmid
& Altig 1997)。由于无尾两栖动物的双相生命周期(如Haas & Das
二零一一),日常的水生幼体期和相应的成体暴光在接纳机制分明不一样的景况中。在陆生脊椎动物中,这种独特的放肆生活幼体阶段被认为是在谱系多种化的前行背景下适应性辐射进程的贰个特意适宜的标记(Bossuyt
& Milinkovitch 2000; Roelants et al.
2013)。在现阶段天气变化的尺度下,由于在蝌蚪和青蛙群落中能够洞察到无数见仁见智的非生物因素(如温度、水的可利用性、紫外线辐射)的熏陶(阅读二〇〇二;Blaustein
et al. 二零零四; Blaustein et al.
贰零零捌)。另外,温度的宽幅变动与蝌蚪乳糜真菌感染有关(哈密尔敦 et al.
二零一二),前面一个作为宿主,进一步通过其外表角质口器传播病原体(Marantelli et
al. 二零零四; Wake & Vredenburg 2009; Venesky et al.
2011)。思量到蝌蚪平时与成体攻陷差别的栖息地,蝌蚪对部分保障问题也很要紧,举例由于栖息地变化产生两栖动物的海内外衰退(Beckeret al.
二〇〇七)。正确描述蝌蚪的特征有利于区分物种和揣测其系统发育关系(Eterovick
& Sazima 两千; Vences et al. 2009a)。

http://blog.sciencenet.cn/u/Bearjazz

SCHULZE, A., M. JANSEN, G. KÖHLER . Tadpole diversity of Bolivia’s
lowland anuran communities: molecular identification, morphological
characterisation, and ecological assignment. Zootaxa 4016: 1-111.

Planet P J . Tree disagreement: Measuring and testing incongruence in
phylogenies[J]. Journal of Biomedical Informatics, 2006, 39:86-102.

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