spp.

菌種

関

bacterial strain、sp.、species

WordNet

1. (biology) taxonomic group whose members can interbreed
2. a specific kind of something; "a species of molecule"; "a species of villainy"

PrepTutorEJDIC

1. 〈C〉(生物分類上の)『種』(しゅ),種族(「属」(genus)の下の単位) / 〈C〉(…の)種類《+『of』+『名』》 / 《the ~》人類(mankind)
2. special / species / specimen / spelling / spirit

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2015/03/06 12:23:02」(JST)

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生物 ドメイン 界（かい） 門（もん） 綱（こう） 目（もく） 科（か） 属（ぞく） 種（しゅ）

種（しゅ）とは、生物分類上の基本単位である。2004年現在、命名済みの種だけで200万種あり、実際はその数倍から十数倍以上の種の存在が推定される。新しい種が形成される現象、メカニズムを種分化という。

ラテン語の species より、単数の場合は省略形 sp. 、複数の場合は省略形 spp. で書き表す。「イヌ属のある種」であれば「Canis sp.」、「ネコ属のいくつかの種」であれば、「Felis spp.」と表現する。

基本理念

生物は、無数の個体からなるが、それらが非常に多様な形質を持つと同時に、一定の類型に分けられることを人は古くから経験的に知っており、それらに名前を付けていた。たとえば虫、魚、鳥、草、苔などである。更にそれらの大まかの分類の中にも多様な形質を観察することができ、より細かい不連続な集団に分けられることに気がつく。つまり、形質のかなり細部までが共通する集団が見分けられ、それらの集団の間には不連続性が見られる。たとえばミカンの木につく青虫を育てれば、そこから出てくるチョウは、黄色のまだらのものか、真っ黒の羽根のものかである。前者はアゲハチョウで、後者はクロアゲハであるが、それらは色だけでなく、羽根の形や幼虫の姿でも少し異なっている。また、このような形質は世代を越えて維持される。そのような集団を種という。博物学や生物学の知識の蓄積に伴って、すべての生物がこのような集団に区分できることが明らかとなっていった。それぞれの種に体系的に名を付け、分類体系を築こうとしたのがリンネである。その100年後にはダーウィンが進化と種分化の理論を提唱し、リンネの「形態に基づく分類体系」が何故そのようになっているか、理論的説明を与えた。

しかし、リンネの時代には生物は現在言うところのEukaryote（真核生物）しか知られていなかった。現在それ以外にもMonera（モネラ、真正細菌、いわゆる狭義の細菌）、Archaea（アーキア、古細菌）、そして生物かどうかの異論もある、Virus（ウイルス）やViroid（ウイロイド）といった存在があることが知られている。そしていわゆる真核生物とはMonera とArchaea、見方によっては Virusが複数共生した複合生命体であることが定説になっている（細胞内共生説、ミトコンドリア、葉緑体、レトロウイルス等を参照）。このため、リンネの考えた種の概念は真核生物では比較的よく適合するが、それ以外のMonera 、Archaea 、Virus、Viroidといったものには適合性が良くない。Monera、Archaea はリンネの唱えた2名法による種名が付いているが、その概念と範囲は真核生物における物とは全く異なることに留意すべきである。Virus、Viroidではそもそも2名法による種名は付けられていない。

有性生殖の役割

個体間で生殖が可能かどうかは種の判断で重視される。これは、種の特徴が世代を越えて維持されるものであること、古くは同種であれば子供を残せるはず、との素朴な判断があったためである。しかし、現在では有性生殖の理解が変化している。つまり有性生殖は、それぞれの個体の属する系統の間で互いの遺伝子を交換し合う行為であり、互いに交配可能であれば、いつかは実際にその遺伝子が交換される可能性がある。そのような関係で結びついた個体の集団は、同じ遺伝子プールを形成する。同一範囲の遺伝子集団を所有する限りは、形態的にもその同一性が保証されるはずと考えることができる。

しかし種における重要な概念の「有性生殖（による遺伝子交換）」そのものが真核生物に特有の概念である。例えば真正細菌では、有性生殖にあたる接合だけではなく、プラスミドの交換などを通して相当に遠縁でも遺伝情報の交換ができる。接合が知られていないものも極めて多く、相当遠縁の同士でも接合が起こることがある。また、外形は極めて変化に乏しいが、遺伝的には極めて多様なことが知られている。つまり、リンネの定義では、種を非常に細かく分けることも、非常におおざっぱに分けることもできてしまう。現在の細菌の種の定義は真核生物の分類と比較すると非常に大きい集団を指しているものと思われる。例えば細菌の種分類の基準として用いられることの多いDNA - DNA分子交雑法で再結合率が70%以上であることや、核酸塩基配列の相同性が90%程度などを用いた場合、動植物では目レベルの分類群が全て同一の種に属することになるであろう。種の定義・概念は、現在、22以上あり、研究が進むほどに増加している。

種の定義

昆虫の種の分類は多様である

以下にはよりなじみの深い真核生物の分類、より厳密に言えば動物を中心に成り立つ種分類上の留意点について記述する。ここには真核生物でも植物 (Plant)、菌類 (Fungi)、原生生物 (Protista) などでは成立しない定義も多く含まれている。上述した「有性生殖の役割」も植物、菌類、原生生物では成立しないケースがある。これらでは有性生殖がほとんど認められなかったり、交配できない不和合接合型（クローンや親子兄弟など同じもしくは近い型の間では有性生殖が成立しない）が認められたりする例が多数ある。このため「交配可能かどうか」は種の分類に使いにくい場面が多い。専門家の間で完全に同意を得られるような種の定義はない。つまり、生物の集団をどうとらえるかは、研究者・分類群・研究の目的によって異なり、全ての生物の分類に適用可能な種の概念は存在しないということである。

形態的種の概念

様々な生物を分類するにあたって、外観や解剖学的特徴によって区別することは最も古くから行われてきた。生物の形態によって種を区別することを形態的種の概念と言う。形態的な差を種の同定の基準に用いることは分類が主観的になりすぎる問題がある。特に視覚的な基準を用いるのは人間の視覚が発達しているためでしかない。生物個体のどのような特徴を判断の基準とするかがあいまいである。また性的二型のような多型を別種と誤解する可能性がある。しかし、現在記載されている種のほとんどは形態的種で、特に化石生物は全て形態的種である。なお、このような分類では生殖器の構造、特に交接器の構造が重視される。これは生殖器の物理的な差異が配偶を困難にし、生殖的隔離をもたらす可能性が高いと推定できるためで、生物学的種の同定の基準となりうるからである。

北アメリカでは複数種の同属のホタルがおり、それらは外見上は区別が困難であるが、それぞれの発光パターンが異なる。このパターンによる雌雄のやりとりで交尾が行われるので、種間の生殖隔離は成立している。このような生物は隠蔽種（英：cryptic species）と呼ばれ、形態によって区別することはできないから、他の概念を適用することでその存在が知られる。その場合でも、そこに種の違いが存在することを知った上で研究が行われれば、わずかの形態の違いで区別が可能となる場合もある。

生物学的種の概念

ヤナギムシクイは輪状種を証明する種の一つ

マイヤーによって1942年に提案された、生物学では最も一般に用いられている種の概念。この定義では、同地域に分布する生物集団が自然条件下で交配し、子孫を残すならば、それは同一の種とみなす。しかし、同地域に分布しても、遺伝子の交流がなされず、子孫を残さない（＝生殖的隔離が完了している）ならば、異なる種とされる。たとえば、ヒョウとライオンを強制的に交雑することによってレオポンと呼ばれる雑種が生まれるが、レオポンはほとんど繁殖力を持たない。よって、ヒョウとライオンは同一の種ではない。ラバ（ロバとウマ）についても同様である。

それぞれの生物集団が異なる地域に属していたり、違う時代に属している場合、生殖的隔離の検証が出来ないため、その生物の形態の比較、集団レベルでの交配および受精の可能性の検証、雑種の妊性（稔性）の確認を通じて、同一の種であるかが検討される。

ただし雑種が全て生殖能力に劣るわけではない。特に、植物では従来の見解では異種であった個体群を交配させて園芸品種を作ることは頻繁に行われている。このようなときは、この定義を厳密に当てはめた場合種ではなく亜種として分類しなおすことになる。野生下での交配可能性のみを問題にする立場からしても、イヌ属やカモ属、キジ属などの場合は亜種として扱うことになる。

生物学的種を普遍的なものとして扱いたい場合に最も根本的な問題となるのは交配せず無性生殖のみを行う生物である。この定義を適用すれば全ての個体の系統が異なる種に分類されることになり、現実的ではない。はるか昔に絶滅した種を扱う古生物学にも適用できない。また実際的な問題として、無数の生物の組み合わせ全てで実際に交配が行われるかどうかを確認するのは不可能である。

さらに輪状種の存在は生物学的種に困難をもたらす。輪状種とは近接して生息する個体群AとB、BとCが交配可能であるが、離れて生息する個体群AとCの間に生殖的隔離が存在する亜種の混合個体群のことである。この場合AとCは生物学的に別種であるが、AとB、BとCは定義上、同種である。全ての種は時間的には連続した存在だが、輪状種はそれを空間的に見ていると言うことができる。

生態学的種

生物をその生活している場またはニッチ（生態的地位）で分かれているかどうかを判断する立場。実験室内では交雑可能であっても、その生息域や行動から、交配の可能性がなく、別個体群としてふるまっていれば、別種とみなす。たとえば、ニホンザルとタイワンザルは交配可能であり、その子孫も繁殖力があるが、地域的に完全に隔離されており、その限りでは形態的差にも差があり、別種と見なして良いと判断する。また、イヌとオオカミはしばしば同じ地域に生息し交配も可能であるが、繁殖サイクル、行動、学習パターン、主な食料などの点で全く異なるニッチに属しているため生態学的には別種といえる。

地理学的種

地理的に隔離されている物を別種と見なす。種の分化はどんな形であれ、最初に地理的隔離が起きたのだと考える説が有力であるが、それに基づけば、「地理的な種」は生物学的には未分化であっても、いくらかの遺伝子の差異が存在し、いずれは完全に異なる種になりうる。一般的にこの地理学的種の定義が用いられるのは生物の地域的変異（の保護など）に言及する場合が多い。しかしこの定義では（他の定義以上に）亜種と種の区別が困難であり、恣意的に用いることになる。上述のニホンザルとタイワンザルも厳密には地理学的種である。

進化学(系統学)的種

単系統に属し、他の系統と異なる特徴、進化的傾向を持つ生物群や系統を種とする。この場合、進化的傾向は恣意的であること、個体群と真の種の間の区別ができない事などが問題となる。

時間的種

時間的種は種の誕生と終焉によって定義される。種の誕生は種分化あるいは単系統の漸進的な変遷であり、終焉とは絶滅あるいは漸進的な変遷である。この定義は形態的種や生物学的種が進化的時間を考慮していないことから提案されたが、種の分類には形態が用いられるという点で同様の欠点がある。特に親種からの漸進的な変遷、孫種への漸進的な変遷が起きた場合、どこで種の区別をするかが恣意的にならざるを得ない。

それ以外の種概念

Maydenによる分類からいくつか引用する

• 無性種概念
• 分岐学的種概念
• 認識種概念
• 系統発生種概念
• 生態学的種概念
• 進化的に重要な単位
• 遺伝的種概念
• 繁殖競争概念
• 遺伝子型クラスター定義
• ヘニッヒ的種概念

種の下位分類

研究の積み上げが進んだ中から、現実的には種に分けてことが済まない場合が多々見つかる。たとえば同種内とは考えられるものの、はっきりと差のある群が発見され、種以下の分類を考える必要が生じ、亜種や変種、品種などの階級が作られた。例えば異なる地域に分布する集団からなる種では、種の内部で異なる形態的特徴を持つ地域集団が存在することがある。これを亜種と呼ぶ。 日本列島に棲息する大型哺乳類の多くは、大陸産の同種とは異なる亜種として分類されている。ただし、亜種と認定される基準は必ずしも客観的でない場合がある。

品種は作物や家畜などの人間が飼育した生物の中で、他の生物集団より区別できる生物集団を指す。ハイブリッド品種など、ある品種の子孫が親と同じ品種とされないことも多い。

なお、人種は形態学的な特徴の中でも毛髪、目、皮膚の色、骨格など外部から容易に観察できる形質によってヒトという種を下位分類する概念である。現生する全ての人種を含む現生人類はヒト科ヒト亜科ヒト属のホモ･サピエンスただ一種である。ただし古人類学は化石人類にホモ・サピエンス以外の種をいくつか認めている。異人種間での生殖隔離が見られないこと、異人種間にみられる遺伝情報の多様性よりも人種内の遺伝情報の多様性の方が高いこと、また人種差別への懸念から、生物学的な文脈では人種の有効性は極めて限定的だとされている。

種の問題

種の定義や実在性に関わる議論を種の問題という。

種の実在性

進化学の立場から、時間的と空間的距離などにより種は変化したり別の複数種に分かれたりするものであることはもはや定説である。リンネの時代には全て、あるいは多くの種は別個に創造され、変種は生み出すが別種は生みだなさいと考えられていた。しかしそのような種の不変性という立場を取ることはもはやできない。現在の所、種の概念そのものはおおよそ認められてはいる。しかしながら、それを全く認めない立場も含め、さまざまな議論がある。この論争は13世紀の普遍論争にまで遡ることができる。

種の本質主義

ある生物が「その生物たらしめているなんらかの”本質”を親から受け継いでいるからその種なのだ」という概念を種の本質主義と呼ぶ。ダーウィン以前の分類の定義（それは主に形態学的種概念であるが）は本質主義に含められる。本質主義では種は種内変異や人工的な品種を生み出すが、異なる種に変化することはないと仮定する。本質主義は厳密には正しくないが、形態学的種概念を含めて現在のいくつかの種概念も異なる程度に本質主義を仮定している。

種の問題の原因

種の問題の原因は次のようにまとめられている

1. 観察される生物のパターンは、人間の認識と判断能力の産物である。人間の認識能力は別の用途のために進化したので、自然の全てを精巧に関知できるわけではない。
2. 生物の集団は明確に分かれているとは限らない。重複したり、内部に別の構造が存在することもある。
3. 人間が認識できる生物のパターンはそれぞれの生物の進化的過去に起きた進化の産物であるが、進化のプロセスは現在も継続中である。

関連項目

• 生物の分類
• 学名
• タイプ (分類学)：種の判断の基礎となる標本など
• Encyclopedia of Life - 分類学上の種すべてについて記載することを目指すオンラインの百科事典プロジェクト

参考文献

関連文献

日本語のオープンアクセス文献

• 網谷祐一 「E・マイヤーの生物学的種概念」 科学基礎論研究 Vol.29, No.2 (2002) pp.75-80 PDF

一般書籍

• 日本生物科学者協会編集「特集：種についての終わりなき論争」『生物科学』Volume 59 Number 4（2008年5月号）2008年、農山漁村文化協会。

外部リンク

• 「Species」 - スタンフォード哲学百科事典にある「種」についての項目（英語）

wiki en

[Wiki en表示]

For other uses, see Species (disambiguation).

The hierarchy of biological classification's eight major taxonomic ranks. A genus contains one or more species. Intermediate minor rankings are not shown.

In biology, a species (abbreviated sp., with the plural form species abbreviated spp.) is one of the basic units of biological classification and a taxonomic rank. A species is often defined as the largest group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, the difficulty of defining species is known as the species problem. Differing measures are often used, such as similarity of DNA, morphology, or ecological niche. Presence of specific locally adapted traits may further subdivide species into "infraspecific taxa" such as subspecies (and in botany other taxa are used, such as varieties, subvarieties, and formae).

Species hypothesized to have the same ancestors are placed in one genus, based on similarities. The similarity of species is judged based on comparison of physical attributes, and where available, their DNA sequences. All species are given a two-part name, a "binomial name", or just "binomial". The first part of a binomial is the generic name, the genus to which the species belongs. The second part is either called the specific name (a term used only in zoology) or the specific epithet (the term used in botany, which can also be used in zoology). For example, Boa constrictor is one of four species of the Boa genus. While the genus gets capitalized, the species name does not. The binomial is written in italics when printed and underlined when handwritten.

A usable definition of the word "species" and reliable methods of identifying particular species are essential for stating and testing biological theories and for measuring biodiversity, though other taxonomic levels such as families may be considered in broad-scale studies. Extinct species known only from fossils are generally difficult to assign precise taxonomic rankings, which is why higher taxonomic levels such as families are often used for fossil-based studies.

The total number of non-bacterial and non-archaeal species in the world has been estimated at 8.7 million, with previous estimates ranging from two million to 100 million.

§History and development of the concept

John Ray

Carl Linnaeus believed in the fixity of species.

In the earliest works of science, a species was simply an individual organism that represented a group of similar or nearly identical organisms. No other relationships beyond that group were implied. Aristotle used the words genus and species to mean generic and specific categories. Aristotle and other pre-Darwinian scientists took the species to be distinct and unchanging, with an "essence", like the chemical elements. When early observers began to develop systems of organization for living things, they began to place formerly isolated species into a context. Many of these early delineation schemes would now be considered whimsical and these included consanguinity based on color (all plants with yellow flowers) or behavior (snakes, scorpions and certain biting ants).

John Ray (1686), an English naturalist, was the first to give a biological definition of the term species.

In the 18th century Swedish scientist Carl Linnaeus classified organisms according to shared physical characteristics, and not simply based upon differences. He is also established the idea of a taxonomic hierarchy of classification based upon observable characteristics and intended to reflect natural relationships. At the time, however, it was still widely believed that there was no organic connection between species, no matter how similar they appeared. This view was influenced by European scholarly and religious education at the time, which held that the categories of life are dictated by God, in a hierarchical scheme. Although there are always differences (although sometimes minute) between individual organisms, Linnaeus strove to identify individual organisms that were exemplary of the species, and considered other non-exemplary organisms to be deviant and imperfect.

By the 19th century most naturalists understood that species could change form over time, and that the history of the planet provided enough time for major changes. Jean-Baptiste Lamarck, in his 1809 Zoological Philosophy, offered one of the first logical arguments against creationism. The new emphasis was on determining how a species could change over time. Lamarck suggested that an organism could pass on an acquired trait to its offspring (i.e. he attributed the giraffe's long neck to generations of giraffes stretching to reach the leaves of higher treetops). With the acceptance of the natural selection idea of Charles Darwin in the 1860s, however, Lamarck's view of goal-oriented evolution, also known as a teleological process, was eclipsed. Recent interest in inheritance of acquired characteristics centers around epigenetic processes (e.g. methylation) that do not affect DNA sequences, but instead alter expression in an inheritable manner. Thus, Neo-Lamarckism, as it is sometimes termed, is not a challenge to the theory of evolution by natural selection.

Charles Darwin and Alfred Wallace provided what scientists now consider as the most powerful and compelling theory of evolution. Darwin argued that it was populations that evolved, not individuals. His argument relied on a radical shift in perspective from that of Linnaeus: rather than defining species in ideal terms (and searching for an ideal representative and rejecting deviations), Darwin considered variation among individuals to be natural. He further argued that variation, far from being problematic, actually provides the explanation for the existence of distinct species.

Darwin's work drew on Thomas Malthus' insight that the rate of growth of a biological population will always outpace the rate of growth of the resources in the environment, such as the food supply. As a result, Darwin argued, not all the members of a population will be able to survive and reproduce. Those that did will, on average, be the ones possessing variations—however slight—that make them slightly better adapted to the environment. If these variable traits are heritable, then the offspring of the survivors will also possess them. Thus, over many generations, adaptive variations will accumulate in the population, while counter-adaptive traits will tend to be eliminated.

Whether a variation is adaptive or non-adaptive depends on the environment: different environments favor different traits. Since the environment effectively selects which organisms live to reproduce, it is the environment (the "fight for existence") that selects the traits to be passed on. This is the theory of evolution by natural selection. In this model, the length of a giraffe's neck would be explained by positing that proto-giraffes with longer necks would have had a significant reproductive advantage to those with shorter necks. Over many generations, the entire population would be a species of long-necked animals.

In 1859, when Darwin published his theory of natural selection, the mechanism behind the inheritance of individual traits was unknown. Although Darwin made some speculations on how traits are inherited (pangenesis), his theory relies only on the fact that inheritable traits exist, and are variable (which makes his accomplishment even more remarkable.) Although Gregor Mendel's paper on genetics was published in 1866, its significance was not recognized. It was not until 1900 that his work was rediscovered by Hugo de Vries, Carl Correns and Erich von Tschermak, who realised that the "inheritable traits" in Darwin's theory are genes.

The theory of the evolution of species through natural selection has two important implications for discussions of species—consequences that fundamentally challenge the assumptions behind Linnaeus' taxonomy. First, it suggests that species are not just similar, they may actually be related. Some students of Darwin argue that all species are descended from a common ancestor. Second, it supposes that "species" are not homogeneous, fixed, permanent things; members of a species are all different, and over time species change. This suggests that species do not have any clear boundaries but are rather momentary statistical effects of constantly changing gene-frequencies. One may still use Linnaeus' taxonomy to identify individual plants and animals, but one can no longer think of species as independent and immutable.

The rise of a new species from a parental line is called speciation. There is no clear line demarcating the ancestral species from the descendant species.

Although the current scientific understanding of species suggests that there is no rigorous and comprehensive way to distinguish between different species in all cases, biologists continue to seek concrete ways to operationalize the idea. One of the most popular biological definitions of species is in terms of reproductive isolation; if two creatures cannot reproduce to produce fertile offspring of both sexes, then they are in different species. This definition captures a number of intuitive species boundaries, but it remains imperfect. It has nothing to say about species that reproduce asexually, for example, and it is very difficult to apply to extinct species. Moreover, boundaries between species are often fuzzy: there are examples where members of one population can produce fertile offspring of both sexes with a second population, and members of the second population can produce fertile offspring of both sexes with members of a third population, but members of the first and third population cannot produce fertile offspring, or can only produce fertile offspring of the homozygous sex. Consequently, some people reject this definition of a species.

Richard Dawkins defines two organisms as conspecific if and only if they have the same number of chromosomes and, for each chromosome, both organisms have the same number of nucleotides (The Blind Watchmaker, p. 118). However, most taxonomists would disagree. For example, in many amphibians, most notably in New Zealand's Leiopelma frogs, the genome consists of "core" chromosomes that are mostly invariable and accessory chromosomes, of which exist a number of possible combinations. Even though the chromosome numbers are highly variable between populations, these can interbreed successfully and form a single evolutionary unit. In plants, polyploidy is extremely commonplace with few restrictions on interbreeding; as individuals with an odd number of chromosome sets are usually sterile, depending on the actual number of chromosome sets present, this results in the odd situation where some individuals of the same evolutionary unit can interbreed with certain others and some cannot, with all populations being eventually linked as to form a common gene pool.

The classification of species has been profoundly affected by technological advances that have allowed researchers to determine relatedness based on molecular markers, starting with the comparatively crude blood plasma precipitation assays in the mid-20th century to Charles Sibley's DNA-DNA hybridization studies in the 1970s leading to DNA sequencing techniques. The results of these techniques caused revolutionary changes in the higher taxonomic categories (such as phyla and classes), resulting in the reordering of many branches of the phylogenetic tree (see also: molecular phylogeny). For taxonomic categories below genera, the results have been mixed so far; the pace of evolutionary change on the molecular level is rather slow, yielding clear differences only after considerable periods of reproductive separation. DNA-DNA hybridization results have led to misleading conclusions, the Pomarine Skua – Great Skua phenomenon being a famous example. Turtles have been determined to evolve with just one-eighth of the speed of other reptiles on the molecular level, and the rate of molecular evolution in albatrosses is half of what is found in the rather closely related storm-petrels. The hybridization technique is now obsolete and is replaced by more reliable computational approaches for sequence comparison. Molecular taxonomy is not directly based on the evolutionary processes, but rather on the overall change brought upon by these processes. The processes that lead to the generation and maintenance of variation such as mutation, crossover and selection are not uniform (see also molecular clock). DNA is only extremely rarely a direct target of natural selection rather than changes in the DNA sequence enduring over generations being a result of the latter; for example, silent transition-transversion combinations would alter the melting point of the DNA sequence, but not the sequence of the encoded proteins and thus are a possible example where, for example in microorganisms, a mutation confers a change in fitness all by itself.

§Biologists' working definition

A usable definition of the word "species" and reliable methods of identifying particular species is essential for stating and testing biological theories and for measuring biodiversity. Traditionally, multiple examples of a proposed species must be studied for unifying characters before it can be regarded as a species. It is generally difficult to give precise taxonomic rankings to extinct species known only from fossils.

Some biologists may view species as statistical phenomena, as opposed to the traditional idea, with a species seen as a class of organisms. In that case, a species is defined as a separately evolving lineage that forms a single gene pool. Although properties such as DNA-sequences and morphology are used to help separate closely related lineages, this definition has fuzzy boundaries. However, the exact definition of the term "species" is still controversial, particularly in prokaryotes, and this is called the species problem. Biologists have proposed a range of more precise definitions, but the definition used is a pragmatic choice that depends on the particularities of the species of concern.

§Common names and species

The commonly used names for plant and animal taxa sometimes correspond to species: for example, "lion", "walrus", and "Camphor tree" – each refers to a species. In other cases common names do not: for example, "deer" refers to a family of 34 species, including Eld's Deer, Red Deer and Elk (as the use in American English meaning Wapiti, not the use in British English meaning moose). The last two species were once considered a single species, illustrating how species boundaries may change with increased scientific knowledge.

§Placement within genera

Ideally, a species is given a formal, scientific name, although in practice there are very many unnamed species (which have only been described, not named). When a species is named, it is placed within a genus. From a scientific point of view this can be regarded as a hypothesis that the species is more closely related to other species within its genus (if any) than to species of other genera. Species and genus are usually defined as part of a larger taxonomic hierarchy. The best-known taxonomic ranks are, in order: life, domain, kingdom, phylum, class, order, family, genus, and species. This assignment to a genus is not immutable; later a different (or the same) taxonomist may assign it to a different genus, in which case the name will also change.

In biological nomenclature, the name for a species is a two-part name (a binomial name), treated as Latin, although roots from any language can be used as well as names of locales or individuals. The generic name is listed first (with its leading letter capitalized), followed by a second term. The terminology used for the second term differs between zoological and botanical nomenclature.

• In zoological nomenclature, the second part of the name can be called the specific name or the specific epithet. For example, gray wolves belong to the species Canis lupus, coyotes to Canis latrans, golden jackals to Canis aureus, etc., and all of those belong to the genus Canis (which also contains many other species). For the gray wolf, the genus name is Canis, the specific name or specific epithet is lupus, and the binomen, the name of the species, is Canis lupus.
• In botanical nomenclature, the second part of the name can only be called the specific epithet. The 'specific name' in botany is always the combination of genus name and specific epithet. For example, the species commonly known as the longleaf pine is Pinus palustris; the genus name is Pinus, the specific epithet is palustris, the specific name is Pinus palustris.

This binomial naming convention, later formalized in the biological codes of nomenclature, was first used by Leonhart Fuchs and introduced as the standard by Carolus Linnaeus in his 1753 Species Plantarum (followed by his 1758 Systema Naturae, 10th edition).

§Abbreviated names

Books and articles sometimes intentionally do not identify species fully and use the abbreviation "sp." in the singular or "spp." (Species pluralis, Latin abbreviation for multiple species) in the plural in place of the specific epithet (e.g. Canis sp.) This commonly occurs in the following situations:

• The authors are confident that some individuals belong to a particular genus but are not sure to which exact species they belong. This is particularly common in paleontology.
• The authors use "spp." as a short way of saying that something applies to many species within a genus, but do not wish to say that it applies to all species within that genus. If scientists mean that something applies to all species within a genus, they use the genus name without the specific epithet.

Sometimes, the aforementioned plural is rendered as "sps.", which may lead to confusion with "ssp.", this one standing for subspecies instead. In books and articles, genus and species names are usually printed in italics. Abbreviations such as "sp.", "spp.", "sps.", "ssp.", "subsp.", etc. should not be italicized.

§Identification codes

Various codes have been devised for identifying particular species. For example:

• National Center for Biotechnology Information (NCBI) employs a numeric 'taxid' or Taxonomy identifier, a "stable unique identifier", e.g. the taxid of H. sapiens is 9606.
• Kyoto Encyclopedia of Genes and Genomes (KEGG) employs a three- or four-letter code for a limited number of organisms; in this code, for example, H. sapiens is simply hsa.
• UniProt employs an "organism mnemonic" of not more than five alphanumeric characters, e.g. HUMAN for H. sapiens.
• Integrated Taxonomic Information System (ITIS) provides a unique number for each species.

§Difficulty defining or identifying species

Main article: Species problem

It is surprisingly difficult to define the word "species" in a way that applies to all naturally occurring organisms, and the debate among biologists about how to define "species" and how to identify actual species is called the species problem. Over two dozen distinct definitions of "species" are in use amongst biologists.

This problem dates as early as to the writings of Charles Darwin. While Darwin wrote the following in On the Origin of Species, Chapter II:

No one definition has satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species. Generally the term includes the unknown element of a distinct act of creation.

He readdressed the question in The Descent of Man, specifically discussing the "question whether mankind consists of one or several species," where he revised his opinion, writing:

it is a hopeless endeavour to decide this point on sound grounds, until some definition of the term "species" is generally accepted; and the definition must not include an element that cannot possibly be ascertained, such as an act of creation.

Most modern textbooks follow Ernst Mayr's definition, known as the Biological Species Concept (BSC) of a species as "groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups". It has been argued that this definition of species is not only a useful formulation, but is also a natural consequence of the effect of sexual reproduction on the dynamics of natural selection. (Also see Speciation.)

Various parts of this definition serve to exclude some unusual or artificial matings:

• Those that as a result of deliberate human action, or occur only in captivity (when the animal's normal mating partners may not be available)
• Those that involve animals that may be physically and physiologically capable of mating but, for various reasons, do not normally do so in the wild

The typical textbook definition above works well for most multi-celled organisms, but there are several types of situations in which it breaks down:

• By definition it applies only to organisms that reproduce sexually. So it does not work for asexually reproducing single-celled organisms and for the relatively few parthenogenetic or apomictic multi-celled organisms. The term "phylotype" is often applied to such organisms.
• Biologists frequently do not know whether two morphologically similar groups of organisms are "potentially" capable of interbreeding.
• There is considerable variation in the degree to which hybridization may succeed under natural conditions, or even in the degree to which some organisms use sexual reproduction between individuals to breed.
• In ring species, members of adjacent populations interbreed successfully but members of some non-adjacent populations do not.

Among microorganisms, in particular, the problem of species identification is made difficult by discordance between molecular and morphological investigations; these can be categorized as two types: (i) one morphology, multiple lineages (e.g. morphological convergence, cryptic species) and (ii) one lineage, multiple morphologies (e.g. phenotypic plasticity, multiple life-cycle stages). In addition, in these and other organisms, horizontal gene transfer (HGT) makes it difficult to define the term species. All species definitions assume that an organism acquires its genes from one or two parents very like the "daughter" organism, but HGT makes that assumption false. There is strong evidence of HGT between very dissimilar groups of prokaryotes, and at least occasionally between dissimilar groups of eukaryotes. Williamson argues that there is also evidence for HGT in some crustaceans and echinoderms.

§Definitions of species

Prior to Darwin, naturalists viewed species as ideal or general types, which could be exemplified by an ideal specimen bearing all the traits general to the species. Darwin's theories shifted attention from uniformity to variation and from the general to the particular. According to intellectual historian Louis Menand,

Once our attention is redirected to the individual, we need another way of making generalizations. We are no longer interested in the conformity of an individual to an ideal type; we are now interested in the relation of an individual to the other individuals with which it interacts. To generalize about groups of interacting individuals, we need to drop the language of types and essences, which is prescriptive (telling us what finches should be), and adopt the language of statistics and probability, which is predictive (telling us what the average finch, under specified conditions, is likely to do). Relations will be more important than categories; functions, which are variable, will be more important than purposes; transitions will be more important than boundaries; sequences will be more important than hierarchies.

This shift results in a new approach to "species"; Darwin concluded that species are what they appear to be: ideas, which are provisionally useful for naming groups of interacting individuals. "I look at the term species", he wrote, "as one arbitrarily given for the sake of convenience to a set of individuals closely resembling each other ... It does not essentially differ from the word variety, which is given to less distinct and more fluctuating forms. The term variety, again, in comparison with mere individual differences, is also applied arbitrarily, and for convenience sake."

Practically, biologists define species as populations of organisms that have a high level of genetic similarity. This may reflect an adaptation to the same niche, and the transfer of genetic material from one individual to others, through a variety of possible means. The exact level of similarity used in such a definition is arbitrary, but this is the most common definition used for organisms that reproduce asexually (asexual reproduction), such as some plants and microorganisms.

This lack of any clear species concept in microbiology has led to some authors arguing that the term "species" is not useful when studying bacterial evolution. Instead they see genes as moving freely between even distantly related bacteria, with the entire bacterial domain being a single gene pool. Nevertheless, a kind of rule of thumb has been established, saying that species of Bacteria or Archaea with 16S rRNA gene sequences more similar than 97% to each other need to be checked by DNA-DNA Hybridization if they belong to the same species or not. This concept has been updated recently, saying that the border of 97% was too low and can be raised to 98.7%.

In the study of sexually reproducing organisms, where genetic material is shared through the process of reproduction, the ability of two organisms to interbreed and produce fertile offspring of both sexes is generally accepted as a simple indicator that the organisms share enough genes to be considered members of the same species. Thus a "species" is a group of interbreeding organisms.

This definition can be extended to say that a species is a group of organisms that could potentially interbreed—fish could still be classed as the same species even if they live in different lakes, as long as they could still interbreed were they ever to come into contact with each other. On the other hand, there are many examples of series of three or more distinct populations, where individuals of the population in the middle can interbreed with the populations to either side, but individuals of the populations on either side cannot interbreed. Thus, one could argue that these populations constitute a single species, or two distinct species. This is not a paradox; it is evidence that species are defined by gene frequencies, and thus have fuzzy boundaries.

Consequently, any single, universal definition of "species" is necessarily arbitrary. Instead, biologists have proposed a range of definitions; which definition a biologists uses is a pragmatic choice, depending on the particularities of that biologist's research.

In practice, these definitions often coincide, and the differences between them are more a matter of emphasis than of outright contradiction. Nevertheless, no species concept yet proposed is entirely objective, or can be applied in all cases without resorting to judgment.

For most vertebrates, this is the biological species concept (BSC), and to a lesser extent (or for different purposes) the phylogenetic species concept (PSC). Many BSC subspecies are considered species under the PSC; the difference between the BSC and the PSC can be summed up insofar as that the BSC defines a species as a consequence of manifest evolutionary history, while the PSC defines a species as a consequence of manifest evolutionary potential. Thus, a PSC species is "made" as soon as an evolutionary lineage has started to separate, while a BSC species starts to exist only when the lineage separation is complete. Accordingly, there can be considerable conflict between alternative classifications based upon the PSC versus BSC, as they differ completely in their treatment of taxa that would be considered subspecies under the latter model (e.g. the numerous subspecies of honey bees).

§Typological species

A group of organisms in which individuals are members of the species if they sufficiently conform to certain fixed properties. The clusters of variations or phenotypes within specimens (i.e. longer or shorter tails) would differentiate the species. This method was used as a "classical" method of determining species, such as with Linnaeus early in evolutionary theory. However, we now know that different phenotypes do not always constitute different species (e.g. a four-winged Drosophila born to a 2-winged mother is not a different species). Species named in this manner are called morphospecies.

§Evolutionary species

A single evolutionary lineage of organisms within which genes can be shared, and that maintains its integrity with respect to other lineages through both time and space. At some point in the evolution of such a group, some members may diverge from the main population and evolve into a subspecies, a process that may eventually lead to the formation of a new species if isolation (geographical or ecological) is maintained. The process through which species are formed by evolution is called speciation. A species that gives rise to another species is a paraphyletic species, or paraspecies.

§Phylogenetic (cladistic) species

A phylogenetic or cladistic species is a group of organisms that shares an ancestor—a lineage that maintains its hereditary integrity with respect to other lineages through both time and space. At some point in the evolution of such a group, members may diverge from one another: when such a divergence becomes sufficiently clear, the two populations are regarded as separate species. This category of species definition differs from evolutionary species in that the parent of the phylogenetic species goes extinct taxonomically when a new species evolves; the mother and daughter populations now forming two new species. Subspecies as such are not recognized under this definition; either a population is a phylogenetic species or it is not taxonomically distinguishable.

It has been argued, that operation of the phylogenetic species concept (PSC) will lead to taxonomic inflation, since smaller and smaller units of its population can be distinguished—even down to individuals. Species of bovine (i.e., cattle) for example, could be split up into any number of species based on this concept.

§Other species concepts

Ecological species

A set of organisms adapted to a particular set of resources, called a niche, in the environment. According to this concept, populations form the discrete phenetic clusters that we recognize as species because the ecological and evolutionary processes controlling how resources are divided up tend to produce those clusters.

Reproductive species

Two organisms that are able to reproduce naturally to produce fertile offspring of both sexes. Organisms that can reproduce but almost always make infertile hybrids of at least one sex, such as a mule, hinny or F1 male cattalo are not considered to be the same species.

Isolation species

A set of actually or potentially interbreeding populations. This is generally a useful formulation for scientists working with living examples of the higher taxa like mammals, fish, and birds, but more problematic for organisms that do not reproduce sexually. The results of breeding experiments done in artificial conditions may or may not reflect what would happen if the same organisms encountered each other in the wild, making it difficult to gauge whether or not the results of such experiments are meaningful in reference to natural populations.

Genetic species

Based on similarity of DNA of individuals or populations. Techniques to compare similarity of DNA include DNA-DNA hybridization, and genetic fingerprinting (or DNA barcoding).

Cohesion species

Most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion mechanisms. This is an expansion of the mate-recognition species concept to allow for post-mating isolation mechanisms; no matter whether populations can hybridize successfully, they are still distinct cohesion species if the amount of hybridization is insufficient to completely mix their respective gene pools.

Evolutionarily significant unit (ESU)

An evolutionarily significant unit is a population of organisms that is considered distinct for purposes of conservation. Often referred to as a species or a wildlife species, an ESU also has several possible definitions, which coincide with definitions of species.

Phenetic species

Based on phenetics.

Microspecies

A species with very little genetic variability, usually one that reproduces by apomixis.

Recognition species

Based on shared reproductive systems, including mating behavior. The Recognition concept of species has been introduced by Hugh E. H. Paterson, after earlier work by Wilhelm Petersen.

Mate-recognition species

A group of organisms that are known to recognize one another as potential mates. Like the isolation species concept above, it applies only to organisms that reproduce sexually. Unlike the isolation species concept, it focuses specifically on pre-mating reproductive isolation.

§Numbers of species

Main article: Global biodiversity

An estimate of the number of some undiscovered and discovered eukaryotic species.

Bearing in mind the aforementioned problems with categorizing species, the following numbers are only a guide. Based on various discussions from the first decade of the new millennium, counts can roughly be broken down as follows:

§Number of prokaryotic species, domain Bacteria

This number is very difficult to assess, but the discussed range varies from tens of thousands to billions; most recent approaches and studies appear to favor the larger magnitude number. Smaller numbers arise from assumptions based on a plateauing of identification of new species (which has technical explanations other than that fewer species remain to be identified). Larger numbers address the fact that success in culturing bacteria has only been achieved in half of identified Bacterial phyla (where lack of success in attempts to culture a bacterial isolate limits abilities to study and delineate new species), and address the difficulty of applying traditional botanic and zoologic definitions of species to asexually reproducing bacteria (where more modern sequencing and molecular approaches support higher species tallies).

§Number of prokaryotic species, domain Archaea

As a further microbial domain, the issues and difficulties of domain Bacteria also pertain to any counting of species of Archaea, all the more given their various extreme habitats. The classification of archaea into species is also controversial, as they also reproduce asexually (likewise eliminating applicability of species definitions based on interbreeding), and face the same difficulties associated with organism isolation and culturing (see citations for Bacteria, above). Archaebacteria have been shown to exhibit high rates of horizontal gene transfer (resulting from a bacterial cognate of sex), including between organisms quite separate based on genomic analysis. As the Archaea article notes, "[c]urrent knowledge on genetic diversity is fragmentary and the total number of archaean species cannot be estimated with any accuracy" ... though like domain Bacteria, the number of cultured and studied phyla relative to the total is low (as of 2005, less than 50% of known phyla cultured). Taken together, very high numbers of unique archaebacterial types are likely, as in the case of domain Bacteria.

§Number of eukaryotic species

This number has historically varied from a few million to about 100 millions. However these higher numbers, which were based on the potential deep marine and arthropod diversity, are now considered unlikely. The total number of eukaryotic species is likely to be 5 ± 3 million of which about 1.5 million have been already named. Some older estimates for various eukaryote phyla are:

• As many as 1.5 million fungi
• 3,067 brown algae
• 17,000 lichens
• 321,212 plants, including:
  • 10,134 red and green algae
  • 16,236 mosses
  • 12,000 ferns and horsetails
  • 1,021 gymnosperms
  • 281,821 angiosperms
• 1,367,555 non-insect animals, including:
  • 1,305,250 invertebrates
    • 2,175 corals
    • 85,000 mollusks
    • As many as 1.1 million arachnids, including ~1 million mites and ~100,000 other arachnids
    • 47,000 crustaceans
    • 68,827 other invertebrates
  • 63,649 vertebrates
    • 31,300 fish
    • 7,093 amphibians
    • 9,768 reptiles
    • 9,998 birds
    • 5,490 mammals
• As many as 10–30 million insects

At present, organisations such as the Global Taxonomy Initiative, the European Distributed Institute of Taxonomy and the Census of Marine Life (the last of these only for marine organisms) are trying to improve taxonomy and add previously undiscovered species to the taxonomy system. Current knowledge covers only a portion of the organisms in the biosphere and thus does not enable a complete understanding of the workings of the environment. Humankind is also currently wiping out undiscovered species at an unprecedented rate, which means that even before a new species has had the chance of being studied and classified, it may already be extinct.

§Lumping and splitting of taxa

Main article: Lumpers and splitters

The naming of a particular species may be regarded as a hypothesis about the evolutionary relationships and distinguishability of that group of organisms. As further information comes to hand, the hypothesis may be confirmed or refuted. Sometimes, especially in the past when communication was more difficult, taxonomists working in isolation have given two distinct names to individual organisms later identified as the same species. When two named species are discovered to be of the same species, the older species name is usually retained, and the newer species name dropped, a process called synonymization, or colloquially, as lumping. Dividing a taxon into multiple, often new, taxons is called splitting. Taxonomists are often referred to as "lumpers" or "splitters" by their colleagues, depending on their personal approach to recognizing differences or commonalities between organisms.

Traditionally, researchers relied on observations of anatomical differences, and on observations of whether different populations were able to interbreed successfully, to distinguish species; both anatomy and breeding behavior are still important to assigning species status. As a result of the revolutionary (and still ongoing) advance in microbiological research techniques, including DNA analysis, in the last few decades, a great deal of additional knowledge about the differences and similarities between species has become available. Many populations formerly regarded as separate species are now considered a single taxon, and many formerly grouped populations have been split. Any taxonomic level (species, genus, family, etc.) can be synonymized or split, and at higher taxonomic levels, these revisions have been still more profound.

From a taxonomical point of view, groups within a species can be defined as being of a taxon hierarchically lower than a species. In zoology only the subspecies is used, while in botany the variety, subvariety, and form are used as well. In conservation biology, the concept of evolutionary significant units (ESU) is used, which may define either species or smaller distinct population segments. Identifying and naming species is the providence of alpha taxonomy.

§See also

• Cline
• Cryptic species complex
• Encyclopedia of Life
• Endangered species
• Global biodiversity
• Koinophilia
• Ring species
• Speciation
• Species description
• Species naming
• Species problem
• Systematics

§References

§Further reading

• Other Species Concepts – U.C. Berkeley
• 2003-12-31, ScienceDaily: Working On The 'Porsche Of Its Time': New Model For Species Determination Offered
• 2003-08-08, ScienceDaily: Cross-species Mating May Be Evolutionarily Important And Lead To Rapid Change
• 2004-01-09 ScienceDaily: Mayo Researchers Observe Genetic Fusion Of Human, Animal Cells; May Help Explain Origin Of AIDS
• 2000-09-18, ScienceDaily: Scientists Unravel Ancient Evolutionary History Of Photosynthesis

§External links

• Barcoding of species
• Catalogue of Life
• European Species Names in Linnaean, Czech, English, German and French
• Speciation
• Stanford Encyclopedia of Philosophy entry: Species
• VisualTaxa
• Wikispecies – The free species directory that anyone can edit from the Wikimedia Foundation

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English Journal

• Determination of some minerals and β-carotene contents in aromatic indica rice (Oryza sativa L.) germplasm.

• Renuka N1, Mathure SV1, Zanan RL1, Thengane RJ1, Nadaf AB2.
• Food chemistry.Food Chem.2016 Jan 15;191:2-6. doi: 10.1016/j.foodchem.2015.05.045. Epub 2015 May 19.
• 39 aromatic indica rice (Oryza sativa L.) cultivars were characterized for Iron, Zinc, Calcium, Magnesium, Copper and β-carotene contents. The β-carotene contents were ranging from 1.23 to 9.9μg/g in brown and 0.08 to 1.99μg/g in milled rice. Among the mineral contents, Magnesium was found rangi
• PMID 26258694

• Canine ehrlichiosis: prevalence and epidemiology in northeast Brazil.

• Guedes PE1, Oliveira TN1, Carvalho FS2, Carlos RS3, Albuquerque GR3, Munhoz AD3, Wenceslau AA3, Silva FL3.
• Revista brasileira de parasitologia veterinaria = Brazilian journal of veterinary parasitology : Orgao Oficial do Colegio Brasileiro de Parasitologia Veterinaria.Rev Bras Parasitol Vet.2015 12/06;24(2):115-121. Epub 2015 Jun 12.
• Ehrlichiosis is a zoonotic disease that is caused by bacteria of the genus Ehrlichia. The aims of this study were to detect the presence of Ehrlichia spp. in the blood of dogs in Ituberá, Bahia, and to compare the sensitivities and specificities of blood smear, serological, and molecular examinatio
• PMID 26083691

• Community of thermoacidophilic and arsenic resistant microorganisms isolated from a deep profile of mine heaps.

• Casas-Flores S1, Gómez-Rodríguez EY, García-Meza JV.
• AMB Express.AMB Express.2015 Dec;5(1):132. doi: 10.1186/s13568-015-0132-5. Epub 2015 Aug 19.
• Soluble arsenic (As) in acidic feed solution may inhibit the copper (Cu) bioleaching process within mine heaps. To clarify the effect of soluble arsenic on the live biomass and bioxidative activity in heaps, toxicological assays were performed using a synthetic feed solution given by a mine company.
• PMID 26283066

Japanese Journal

• Nestedness patterns of sand fly (Diptera: Psychodidae) species in a neotropical semi-arid environment

• Acta Tropica 153, 7-13, 2016-01
• NAID 120005665863

• Ultra-thin and polarization-independent phase gradient metasurface for high-efficiency spoof surface-plasmon-polariton coupling

• Appl. Phys. Express 8(12), 122001, 2015-11-02
• NAID 150000111474

• 食肉製品の成分規格に規定されるサルモネラ属菌について

• 食品衛生研究 = Food sanitation research 65(10), 17-19, 2015-10
• NAID 40020614071

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★リンクテーブル★

リンク元	「sp.」「bacterial strain」
拡張検索	「Leptotrichia spp.」「Enterobacter spp.」「Porphyromonas spp.」
関連記事	「SPP」

「sp.」

　　[★]

菌種

関

bacterial strain、species、spp.

　

「bacterial strain」

　　[★]

• 菌種

関

sp.、species、spp.

「Leptotrichia spp.」

　　[★] レプトトリキア属菌種

関

レプトトリキア属

「Enterobacter spp.」

　　[★] エンテロバクター属

「Porphyromonas spp.」

　　[★] ポルフィロモナス属

「SPP」

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• sphingosine 1-phosphate？