ぎょーむ日誌 2007-07-10
2007 年 07 月 10 日 (火)
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0805 起床.
コーヒー.
朝飯.
0905 自宅発.
晴.
0920 研究室着.
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セミナーの予習.
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1030 より
研究室セミナー,
本日は稲葉さんで,
植物が (昆虫とかに) くらった損傷と abortion (種子形成放棄)
の関係とか.
下記 4 論文のうち,
上から 3 論文についての検討.
- Spotswood et al. (2002) Effects of herbivory on the reproductive effort
of 4 prairie perennials. BMC Ecology 2 (2)
Background: Herbivory can affect every aspect of a plant's life.
Damaged individuals may show
decreased survivorship and reproductive output.
Additionally, specific plant species (legumes) and
tissues (flowers) are often selectively targeted by herbivores, like deer.
These types of herbivory influence a plant's growth and abundance.
The objective of this study was to identify the effects of
leaf and meristem removal (simulated herbivory within an exclosure) on fruit and flower
production in four species (Rhus glabra, Rosa arkansana, Lathyrus venosus, and
Phlox pilosa) which are known targets of deer herbivory.
Results: Lathyrus never flowered or went to seed, so we were unable to detect any
treatment effects. Leaf removal did not affect flower number in the other three
species. However, Phlox, Rosa, and Rhus all showed significant negative correlations
between seed mass and leaf removal. Meristem removal had a more negative effect than
leaf removal on flower number in Plhilox and on both flower number and seed mass in Rosa.
Conclusions: Meristem removal caused a greater response than defoliation alone in both
Phlox and Rosa, which suggests that meristem loss has greater effect on reproduction.
The comibation of leaf and meristem removal as well as recruitment limitaion by deer,
which selevtively browse for these species, is likely to be one factor contributing
to their abundance in prairies.
- Marcelis et al. (2004) Flower and fruit abortion in sweet pepper in
relation to source and sink strength. Journal of Experimental Botany
55 (406) 2261-2268
(abstract)
Source strength (assimilate supply) and sink strength
(assimilate demand) of the plant were varied in different
ways to investigate to what extent flower/fruit abortion
in sweet pepper (Capsicum annuum L.) is determined by
the availability of assimilates. Source strength was
varied by changing the light level, plant density, and
leaf pruning. Sink strength was varied by changing the
temperature and the number and position of earlier
formed fruits. Shading as well as heating for short
periods showed that when source strength decreased,
the rate of abortion increased linearly, whether source
strength was decreased by shading, high plant density,
or leaf pruning. That flower and fuit abortion not only
depends on the source strength but also on the sink
strength of competing organs is shown by varying the
number or the position of earlier formed fruits. With the
same source strength, the rate of abortion showed
a close relationship with the growth rate of the earlier
formed competing fruits, suggesting that the induction
of abortion by earlier formed fruits is due to their sink
strength. Most of the variation in abortion could be
related to differences in vegetative growth rate, the latter
being an indicator or the source-sink ratio. However,
with the same vegetative growth rate, the rate of abortion
was lower for the leaf pruning treatments where no
competing fruits were retained than for the fruit load
treatments. This indicates that although most of the
variation in abortion can be related to the source and
sink strength of the plant, some effects of competing
fruits can only be explained by a combination of competition
and dominance.
- Hellstrom et al. (2006) Plasticity of clonal integration in the
perennial herb Linaria vulgaris after damage. Functional Ecology
20 (3) 413-420
1. Clonal integration in plants can improve their ability to cope with heterogeneity.
Integration may increase in response to damage, such as herbivore attack, if
undamaged ramets support damaged ones. To test this, we studied the effect of apex
removal and substantial defoliation on the perfomance of the clonal perennial herb
Linaria vulgaris Mill. in a common-garden growth experiment and 13C-labeling
study.
2. In the growth experiment, contrary to expectations, the target ramet could compensate
for damage better wht the other ramets in the clone were also damaged, indicating
within-clone competition for resource rather than support to damaged ramets.
3. In the 13C-labeling experiment, 5-7% of the lable moved to a neighbor ramet
in controls. Apex removal resulted in a negative net translocation of 13C in
the damged ramet, but defoliation led to zero net translocation.
4. The observed lack of support to damaged ramets in Linaria suggests that plasticity
of clonal integration in this species includes competition between sibling ramets.
Although young ramets may be supported, resources are not directed towards a single
damaged ramet if there are more viable intact ramets in the clone. Our main results
are consistent with the notion that resource allocation among ramets depends on their
relative value in term so fexpected fitness profits in heterogeneous environments.
- Ishikawa et al. (1990) Photosynthetic characteristics and water use
efficiency of three coastal dune plants. Ecological Research 5 (3) 377-391
To clarify the ecophsiological characteristics of plants growing on a coastal dune,
net photosynthetic rate (Pn) and leaf conductance (g1) of three perennial species in
Japanese coastal regions, ...
were compared under controlled environmental conditions and field
conditions at the Kado-ori coast at Ohno Village, Ibaraki. I.anthepheroides achived
photosynthetic CO2 saturation at ca. 100 μl-1 intercellular CO2 concentration (C1),
andits Pn was not light-saturated at a high photosynthetically active photon flux density
(PPFD) of 1000 μmol m-2 s-1. This C4 species showed a high optimal leaf temperature
for Pn (35°C) and a low g1 (0.1 mol H20 m-2 s-1), permitting maintenance of the
highest water use efficiency (WUE, the ratio of Pn to transpirationrate (Tr)) in the field
among the three species.
...
...
ハナシは多年性草本のシュート・ramet における
「今シーズンの繁殖からの撤退を決定づける損傷」
は何か,
といった方向のもので,
葉がやられるのはとうぜん痛いんだけど,
apex だの meristem がヤラれると
(たぶんシグナル分子とかの関連で)
sink 機能低下するようで
「今年はやめた」とあきらめてしまうらしい,
と.
あきらめると隣のシュートに同化物をぶんどられたり
(上から 3 番目の論文),
あるいはもしかしたら地下部にまわして来年用にしてるかも,
と.
-
う,
のんびりと議論やってたらセミナー終了が 1250 になってしまった.
昼飯.
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お茶部屋で亀山さんと
「ある雑種らしき植物個体の遺伝子 (species specific な遺伝子座)
みたときに,その個体が F1, F2,backcross のいずれかを判定する」
統計モデリンングについて検討.
ようするに
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F1 だの何だのという個体ごとの labeling
(もしくは assignment)
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species specific ということになってる遺伝子の頻度
(これは一個体だけでなく標本集団全体で決まる)
のどちらも不確定で,
片方を決めるともう一方が変わる
……
ということで Bayesian とかであつかうべき典型的な問題である.
しかしここでまた新しい階層ベイズモデルなど発明してしまうと
論文一本ぶんの仕事になってしまい
……
(とある事情によってこの問題を安直に解決しなければならぬ現状では)
ちょっと大げさすぎるのである.
-
ということで,
可能なかぎり手ぬきする方法を考えてみた
……
うーむ.
[F2 は遺伝子頻度の影響が少ない]
しかしいっしょに検討してると,
いろいろなことがわかった.
ある「種特異的」対立遺伝子がわりと高めの頻度 p で存在するときに,
F1 におけるその遺伝子のあり・なしは p の影響をもろにうけるけど,
F2 になると dominance の効果で応答性が鈍感になる,
とわかった.
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1600 から農学部の徐さんのデータ解析こんさる.
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1700 ごろからまた亀山さんと雑種問題の検討.
実データをつかって
「F1 であるという尤度」
「F2 であるという尤度」
計算させてみたんだが (くだんの遺伝子頻度をてきとーに与えて),
まあいくつか問題のある個体が.
しかもそれが遺伝子頻度に影響されてて,
すっきりしない.
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とうとうここでも
「めんどうになったらベイズ」
という近ごろのおきまりのパターンが適用されて
……
驚くべきことに
「ある個体が F1 なのか F2 なのかわからん,
ホントの遺伝子頻度もわからん,
それでもともかく個体 i が F2 である確率を求めよ」
という限定的な問題を解決する統計モデルは
ゐんばぐす
で下のごとくごく簡単に記述できる,
とわかった
……
超事前分布すら不要!
# N.sample 個体の遺伝子データ,遺伝子座数は N.loci
# 個体 i の遺伝子座 X[i, j] は 0, 1 のデータをとる (AFLP データ)
# 個体 i が F1 であるとき isF2[i] <- 0,
# F2 であるとき isF2 <- 1 (unknown)
# 遺伝子座 j における種特異的対立遺伝子の存在確率は p[j] (unknown)
model
{
# F1 vs. F2 アサインメント
for (i in 1:N.samples) {
isF2[i] ~ dbern(0.5) # 0, 1: 無情報事前分布
type[i] <- isF2[i] + 1 # 1, 2
for (j in 1:N.loci) {
X[i, j] ~ dbern(prob[type[i], j])
}
}
# 種特異的遺伝子の頻度
for (j in 1:N.loci) {
p[j] ~ dunif(0, 1) # 無情報事前分布
prob[1, j] <- p[j]
prob[2, j] <- 1 - (
p[j] * p[j] / 4 + p[j] * (1 - p[j]) / 2
+ (1 - p[j]) * (1 - p[j])
)
}
}
いつものごとく,
これを
R2WinBUGS
で計算させてみると,
500 MCMC step ぐらいで十分に収束.
個体 i が F2 かどうかをあらわす isF2[i]
の事後分布.
0 と 1 のあいだをいったりきたりしてる.
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そして unknwon な遺伝子頻度
p[j]
の事後分布.
-
……
で問題はいちおうの決着をみた.
しかし作ってみると,
「ハイブリッド問題 (というかアサインメント問題)
に関して Bayesian がこれほど強力な道具であるならば,
だれかがこういう計算プログラムをすで作って公表しているにちがいいない」
という集団遺伝学まわりの分野の良い文化にもとづく推測が成立するので
……
検索してみると,
やはり見つかった.
Eric Christopher Anderson の
NewHybrids,
Anderson, E.C. and Thompson, E.A. (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160: 1217--1229
(上記 URL から PDF file ダウンロード可能).
-
ということで,
亀山さんはこの NewHybrids でもって F1 vs. F2 だけでなく,
バッククロスも含めたより包括的な問題にとりくむことに.
2110 研究室発.
晩飯.
2220 帰宅.
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[今日の運動]
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[今日の食卓]
- 朝 (0820):
米麦 0.5 合.
ダイコンの味噌汁.
キャベツ・ニンジン・タマネギ・キュウリ・レタスのサラダ.
ピーマン・ネギ・ダイコンの皮・ブナピー・ショウガ・
ニンニク・卵の炒めもの.
- 昼 (1310):
研究室お茶部屋.
食パン.
キャベツ・ニンジン・タマネギ・キュウリ・レタスのサラダ.
- 晩 (2140):
北 13 西 3 のピカンティ (スープカレー専門店),
大陸 X スープのベイコン with キャベツ.
集団遺伝学ベイズモデルの
プログラミングばてのカラダにはいいかんぢでした.