井上潤: 系統解析の英語例文

系統解析の英語例文

2012 年 7 月 16 日
井上潤　

タイトル

キャピタライズ
よく単語の先頭が大文字になっているタイトルがあります．それでも and や of などはキャピタライズされていません．オクラホマ出身の MJ 氏によると，大事なものはキャピタライズするそうですが，厳密な決まりはないみたいです．

分岐年代推定

in をつかった例
ある分類群の分岐年代推定，と言いたい場合，前置詞を in にする場合と of にする場合がようです．どうも Native の人たちはある分類群内部の年代推定を言う場合は，in を使うことが多いように思います．

Phylogeny and Divergence Time Estimation in Illicium with Implications
for New World Biogeography (Morris et al. 2007).

Testing the molecular clock: Molecular and paleontological estimates of divergence times in the echinoidea (Echinodermata) (Smith et al. 2006).

Fossil calibrations and molecular divergence time estimates in centrarchid fishes (Teleostei : Centrarchidae)　(Near et al. 2005).

Calibrating molecular estimates of substitution rates and divergence times in birds (Ho et al. 2007).

Time scale を使った例
この場合は，「～の進化に対する時間軸」というように，evolution が必要なようです．
Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution (Hasegawa et al. 2003).

その他
Estimating metazoan divergence times with a molecular clock (Peterson et al. 2004).

結論
Estimation of Fish Divergence Times based on Hole Mitochondrial Genome Sequences (Inoue et al. 2011*)
- MJ 氏によると，「Divergence Times in Fishes」でも間違いではないが，「(現在の)魚の中の年代推定」というイメージがあるので，むしろ，of の方が良いということでした．
- fishes かあるいは fish はよく迷うところです． MJ 氏によると，例えばウナギ目内部でも複数の種を扱っていれば fishes と複数になるそうです．
- Hole Mitochondrial Gnome Sequences の前に「the」はない方が良いそうです．the を付けると，「その (そこにある) 全長 mtGenome 配列」と断定するようになるそうです．ここではより広い意味合いを持たせるために the はいらないそうです．

その他
・～を中心とした
Phylogeny of the basal teleosts, with special reference to the Elopomorpha (Inoue and Miya, 2001).

～にも関わらず

・although ～

・in spite of ～

・while
- While the sequence is a valuable contribution, we are very surprised at the authors' conclusion (Cao et al. 1998).
- Despite more than a century of debate,
the evolutionary position of turtles relative to other amniotes remains uncertain.

・albeit (とは言え)
- Their analysis recovered traditional relationships, albeit with a limited number of taxa.
- Repeated rounds of the cloning trial actually generated clones having a 4.6-kbp insert, albeit in a low efficiency (Kumazawa et al. 1998).

～によらず

Yet, regardless of the phylogenetic method and weighting treatment,
individual mitochondrial genes might potentially produce misleading evolutionary inferences (Zardoya and Meyer, 1997).

ノードやクレード

・～の次に分岐するノード
The next node lower than Archontoglires is the divergence between Metatheria and
Eutheria (Benton et al. 2009).

・より大きなクレード～の一員である — は，
．．．Family Muridae, members of the larger clade of muroid rodents (Benton et al. 2009).

・～につながる枝を～と呼ぶ
Let the branch leading to node k be referred to as branch k (Yang 2006, p231).

クレードに含まれるものの表現
・ contain
- ．．．the clade containing all tetrapods other than amphibians．．．(Benton et al. 2009)
- Both of the duplicated clades (nodes #2 and #3) contained monocot and eudicot genes (Jiao et al. 2011).

・ retain
- The upper clade (node #2) only retaines euditot genes (Jiao et al. 2011).

Paralog
・パラログのうちの一つ
- one of the paralogous clades (Jiao et al. 2011),

遺伝子グループ
・遺伝子グループが～タイプと見なされる．
- This orthogroup was counted once as Type b and once as Type c of Analysis I (Jiao et al. 2011).

外群

・～は — の外群となる．
- Agnatha really do root on the edge leading to amniotes (Cao et al. 1998).

化石記録

・～がーに分類される最も古い化石記録である
Morone sp. is the oldest fossil assigned to moronids (Arfaro et al. 2010).

その後の～で

その後の解析で
These new alignments of sub-clusters were used in subsequent analyses (Anisimova et al. 2007).

解析を行う

系統解析
・解析方法が主語の場合
Analyses with all phylogenetic methods were performed, wntirely excluding third codon positions in each gene (Zardoya and Meyer, 1996).

・データが主語の場合
- Two data sets were subjected to phylogenetic analyses using maximum-likelihood (Zardoya and Meyer, 1996).
- All 13 protein-coding genes combined were subjected to MP analyses (Zardoya and Meyer, 1996).

・系統樹を推定する．
We built molecular phylogenetic trees for 255 selected chicken genes (Kuraku and Kuratani, 2011).

パフォーマンス解析
Cummings, Otto, and Wakeley (1995) conducted a performance analysis of mitochondrial genes (Zarodya and Meyer, 1996).

配列から値を計算する
Each of these peptide seuqneces was subjected to dD and Rin computaion (Kuraku and Kuratani, 2011).

アライメント困難な領域を除外

Ambiguous alignments, mainly at 5' and 3' ends of the protein-coding genes, were excluded from the phylogenetic analyses (Zardoya and Meyer, 1996).

Partition 解析

・set
We set four, five, and 13 partitions depending on the data sets (Inoue et al. 2009).

・partition, assign
Sequences from protein-coding regions (ND1, ND2, and COI genes: 1155 bp) were partitioned by codon position (3 partitions), whereas tRNA regions (535 bp) were assigned to a fourth partition (Brown and Yang, 2009).

3rd ポジション

この結果は，統計的有為さに悪影響を及ぼす高度の飽和を示している．このため，解析から除外する．
This preliminary result indicates
a high degree of saturation that severely affected the statistical significance of the estimates (results not shown) and,
thus, we excluded these sites from the analysis (Schrago and Russo, 2003).

3rd を外して解析を行った．
- A third set of MP analyses were performed in which only third-codon-position transisions were excluded.
- Analyses with all phylogenetic methods were also performed, entirely excluding third codon positions in each gene (Zardoya and Meyer, 1996).

飽和しているが，3rd には系統情報が含まれていることがある．
Third codon positions for both mitochondrial genes,
despite obvious potential saturation problems (Cao et al. 1994),
often contain phylogenetic information, even among distantly related species (Zardoya and Meyer, 1996).

遺伝子別ではなくコドン別に partition を設定する理由

The mitochondrial proteins perform similar functions and are under similar selective constraint, but the 3 codon positions have very different substitution rates because of the strong selective constraint on the protein (see, e.g., Kumar 1996 for rate estimates in vertebrate mitochondrial genes).
We thus partition sites by codon position rather than
by genes (Brown and Yang, 2009).

～によれば

・ according to
According to the results of our analysis (Gardiner et al. 1996),

～の解析では，

・ NJ と ML の解析では，
In the NJ and ML analyses,

・タンパク質の ML の解析では
In the protein ML analyses,

これらのうち

・ Of these
Of these, three are perfect repeats whereas one is imperfect (six nucleotides are different).

～を増加させると，～も増加した．

Even for the less supported sister relationship between the former two species, the bootstrap values were moderately high, increasing from 86 to 91% with increasing transversion weights.

whose の使い方

いくつかの遺伝子の位置が異なっているだけ (whose の使い方)
Mitochondrial genomes of all vertebrate animals analyzed to date have the same 37 genes, whose arrangement in the circular DNA molecule varies in the relative position of a few genes (Mindell et al. 1998).

分布

・分布を検討した．
We then analyzed the distribution of the inferred duplication times using a Bayesina method (Jiao et al. 2011).

・分布の形は～で，X にピークがあった．
The distribution of duplication times was bimodal, with peaks 192±2 and 319±MYA (Jiao et al. 2011).

パフォーマンスを調べる

・遺伝子がよく知られている系統樹を再構築できるか調べた．
We investigated the performance of all mitochondrial protein-coding genes to recocer two expected phylogenies of tetrapods and mammals (Zardoya and Meyer, 1996).

・～がどれほどパフォーマンスと関連があるか，
To address to what extent phylogenetic performance of different genes is related to their particular rates of evolution,
we calculated sequence divergence for each individual gene among the taxa studies (Zardoya and Meyer, 1996).

・パフォーマンスより配列の得やすさで用いられる遺伝子マーカーは決まっていた (San Mauro et al. 2009)．
The favoring of particular genes or genomic regions has reflected the availability of primers, perceived general utility, and the historical legacy of data and alignments that can be expanded,
rather than any special demonstration of their appropriateness for a particular phylogenetic question (Cummings and Meyer, 2005).

～が有用

・ facilitate
The existence and identification of genome-scale single-copy nuclear markers should facilitate the construction of the tree of life (Li et al. 2007).

・ prefer
We suggest that soft bounds are in general preferred to hard bounds for describing fossil uncertainties (Yang and Rannala, 2006).

～の違いを生じさせた原因

原因を指摘
・違いの原因は～であろう．
This discrepancy might be due to an overall higher rate of evolution in mitochondrial genomes．(Benton et al. 2009)

原因が不明
・違いを説明できない．
Simple length differences and rate differences between these genes cannot account for their different phylogenetic performance (Zardoya and Meyer, 1996).

・様々なファクターによって決まっている．
The phylogenetic performance of these mitochondrial genes might depend on various factors that play a role in determining the probability of discovering the correct phylogeny (Zardoya and Meyer, 1996).

結果の比較

・ give
Different programs gave different estimates of node ages (Brown and Yang 2009).

・ obtained
3rd を入れても入れなくても，同じ結果が得られた．
The same phylogenetic relationships were obtained when third codon positions were excluded from the analyses or transitions in third codon positions were not considered (Zardoya and Meyer, 1996).

Figure legend

・ XXX に対して XXX をプロットした．[ここでは X 軸が rate]
The rate of evolution of each gene was plotted against its phylogenetic performance in recovering he expected tree (represented by difference in log-likelihood/bp) (Fig. 4 in Zardoya and Meyer, 1996).

・～は太字で強調している．
Species used in this study are highlighted in bold.

・シンボルとカラーは Fig. X と同じ．
- Symbols and colors same as for Figure 2 (Jiao et al. 2011).

系統樹が解けないときの理由

3rd の TV でも，いくらか飽和があるのは明らか．
It was apparent that some degree of saturation also occurred in 3rd-codons TVs (Yamanoue et al. 2009).

分子データが古い分岐に適していない．
It seems that
these results strongly indicate that
the particular kind of molecular data utilized is not informative for the time period
during which recent teleosts differentiated from remaining actinopterygians (de Pinna 1996).

分岐した時間が短い
その原因　→　サイト間の進化速度が異なるため，分岐した時間が短いため
This is likely doe to
an extensive among -site rate heterogeneity in the rRNA data set and
the narrow window of time in which the three main groups of living amphibians were originated. (Zardoya and Meyer, 2000)

分子データの弱点は，遺伝子ごとの進化速度差異とノイズの蓄積である．分岐した時間が短いとなおさらである (Venkatesh et al. 1999)．
- The pitfalls of molecular sequences include
variations in the rate of evolution of different genes and
the large amounts of phylogenetic "noise" that have accumulated from reversible changes over long evolutionary times .
- In the case of gnathostomes, these problems with sequences are further compounded by the fact that there was a rapid radiation of vertebrates during a very short window of time in the Devonian period (Meyer, 1995).

分岐した時間が短い → 系統樹が解けない
- Such a situation can result from speciation events that have occurred sequentially within a short period of time,
these being well represented by a short internal branch length in the ML tree (Miya and Nishida, 1998)．
- In light of these results, Zardoya and his colleagues suggested that
the difficulty in finding an unequivocal phylogenetic signal could result from the rapid origin of these sarcopterygian lineages,
not the ability of mtDNA to resolve divergences that occurred this far back in time (Curole and Kocher, 1999)

系統樹が解けない → 分岐した時間が短い．
- The lack of resolution at these nodes likely reflects rapid radiation events in the origin of the corresponding lineages (Carroll, 1988). (Zardoya and Meyer, 2000).
- These tentative molecular phylogenetic results point to the inherent difficulty in resolving relationships among lineages which apparently originated in rapid succession during the Devonian. (Zardoya and Meyer, 1997).
- However, a support for a monophyly of Fereuungulate relative to the Chiroptera/Eulipotyphla clade was fragile, and we suggest that the three branchings among Carnivora, Perissodactyla, Cetartiodactyla and Chiroptera/Eulipotyphla occurred successively in a short time period, estimated to be approximately 77 Myr BP.

Taxon sampling
Taxonomic sampling を密にとれば，結果が明瞭になる
- More extensive taxonomic sampling from these groups should indicate clearly which relationship patterns are the most likely (Miya et al. 2001).
- A denser sampling of not only Agnatha, but also Chondrichthyes, Dipnoi, Amphibia, and Reptilia, may improve the phylogenetic estimate from the mitochondrial proteins by helping methods like ML and parsimony to reconstruct likely ancestral states more reliably. (Cao et al. 1998)

Taxonomic sampling が粗であるから，結果がおかしい．
The unorthodox tree had resulted from the effects of "long-branch attraction" (Hendy and Penny, 1989) owing to insufficient taxonomic sampling (Miya and Nishida, 2000).

taxonomic sampling が偏っている
However, the taxonomic sampling within Arthropoda is extremely biased: 7 of 12 sequenced mtDNAs are from the class Insecta, and 5 of those are from a single order (Diptera) (Lavrov et al. 2000)．

Long-branch attraction と粗い taxon sampling
Gene tree estimation may be susceptible to long-branch attraction, particularly with sparse taxon sampling (Jiao etl a. 2011).

Conclusion

核 DNA の新しいマーカーの探索が系統推定に必要．
- Further sequencing of mitochondrial genomes from deliberately chosen teleosts,
along with simultaneous attempts to find new nuclear markers, such as the RAG-1 gene in birds,
will undoubtedly lead to new insights into the higher-level relationships of teleosts (Miya and Nishida, 2000).

- Future studies on this question will require the collection of nuclear protein coding gene sequence data. (Zardoya and Meyer, 1997)

- Future studies on these questions will need to focus on nuclear protein-coding genes and search for phylogenetically informative insertion/deletion events in both coding and noncoding nuclear regions. (Zardoya et al. 1998)

結びの文章

遺伝子配置変動メカニズムの解明に光を当てる
Study of other distantly related chordates may shed light on the sequence of rearrangements by which echinoderm and vertebrate mitochondrial gene orders have arisen (Lee and Kocher 1995).

パフォーマンスの良い遺伝子配列を多く使った方が，系統解析の精度は増すだろう．
It is likely that
the use of combinations of genes with better performance behavior
will lead to increased accuracy in phylogenetic reconstruction (Zarody and Meyer, 1996).

レフリー対応

・下から～行目
"XXXX" is used in line 4 from bottom of p.3.