Review
Reygondeau G, Dunn D. 2019. - Pelagic Biogeography.- 598.

1. 序論
陸上の生態系は気候や地形により明確に区分されるが、海洋は一見均質に見える。海洋にも生態的な区分が存在するかを探るため、生物地理学の概念が導入された。
5. 生物的区分
海洋生物の分布は、緯度や沿岸からの距離により影響を受ける。
緯度による種の多様性の分布（LDG）は、陸上とは異なり双峰性（両半球の亜熱帯域でピーク）を示す。
温度や大陸棚の広さがこの分布に影響していると考えられている。
6. 種分布と多様性に基づく海洋区分
LonghurstのBGCP (biogeochemical provinces) は、実際の種分布とよく一致している。
Costelloらは、65,000種以上の分布データを用いて、30以上の「海洋領域（oceanic realms）」を定義した。

Costello MJ, Tsai P, Cheung AKL, Basher Z, Chaudhary C. 2018.
Reply to 'Dissimilarity measures affected by richness differences yield biased delimitations of biogeographic realms'. Nat Commun 9:5085.

Castero-Insua et al (2018) へ反論し。Costello etal. (2017) を擁護。Jaccard 係数と Group Average 法は生物地理学でもっとも広く使われる手法。Simpson 係数や Ward 法でも同様の領域パターンが見られたと報告。一つの手法に依存せず、複数の手法を比較すると信頼性の高い結果が得られる。

Castro-Insua A, Gomez-Rodriguez C, Baselga A. 2018.
Dissimilarity measures affected by richness differences yield biased delimitations of biogeographic realms. Nat Commun 9:5084.

Castello et al (2017) は、使用された非類似度指標（Jaccard係数）とクラスタリング手法が偏りを生むと批判。
Costello らのデータを用いて、βsim を使ったクラスタリングを実施。Jaccard 指標は、種の数が少ない地域を「異なる」と見なしてしまい、実際には固有種が存在しないにもかかわらず、独立した領域として誤認される可能性がある。代わりに、**Simpson の非類似度指標（βsim）**のように、種の置換（replacement）にのみ基づく指標を使うべきだと主張。
クラスタリング手法としては、Ward法が最も内部の一貫性が高く、地域区分に適していると判断。

Costello MJ, Tsai P, Wong PS, Cheung AKL, Basher Z, Chaudhary C. 2017.
Marine biogeographic realms and species endemicity. Nat Commun 8:1057.

“Realms contrast with geographic areas defined by communities characterized by their dominant species (i.e. habitats), environment (i.e. ecosystems), and life forms (biomes). These concepts do not consider the endemicity or cosmopolitanism of species.” 1
この記述は、生物地理学的境界（realms）は、優占種や環境ではなく、固有性（endemicity）に基づいて定義されるべきであるという立場を明確に示しています。

なので、
生物地理学的境界は、種の構成ではなく、固有種の分布情報に基づいて定義されるべきである（Costello et al., 2017） と引用して良いとのこと。
英語：
Biogeographic boundaries should be defined not by species composition alone, but by the distribution of endemic species, which better reflects evolutionary history and regional uniqueness (Costello et al., 2017)

Ali, JR, DW Krause. 2011. [GMAP]
Late Cretaceous bioconnections between Indo-Madagascar and Antarctica: refutation of the Gunnerus Ridge causeway hypothesis. Journal of Biogeography.

Costello MJ. 2009.
Distinguishing marine habitat classification concepts for ecological data management. MEPS.

“Because of their size and location, the biota of these regions are likely to reflect their evolutionary history and degree of endemicity, and thus may be considered biogeographic regions.” (p. 257)
上記の文章から、以下のように引用できるかも。と思ったけれど、Castello et al. (2017) の方が、タイトルからして適切。
生物地理学的境界は、種の構成ではなく、固有種の分布情報に基づいて定義されるべきである（Costello, 2009）。
=>英語にすると、Biogeographic boundaries should be defined not by species composition alone, but by the distribution of endemic species, which better reflects evolutionary history and regional uniqueness (Costello, 2009).

Karanth KP. [Out of India Hypothesis]
Out-of-India Gondwanan origin of some tropical Asian biota.
CURRENT SCIENCE 90 (6): 789-792 MAR 25 2006

Waters JM, Craw D
Goodbye Gondwana? New Zealand biogeography, geology, and the problem of circularity
SYSTEMATIC BIOLOGY 55 (2): doi:10.1080/10635150600681659 APR 2006

Sanmartin I, Ronquist F.
Southern Hemisphere biogeography inferred by event-based models: Plant versus animal patterns.
SYSTEMATIC BIOLOGY 53 (2): 216-243 APR 2004

Plant
Rutschmann F, Eriksson T, Schonenberger J, et al. [Out of India Hypothesis]
Did crypteroniaceae really disperse out of india? Molecular dating evidence from rbcL, ndhF, and rpl16 intron sequences.
INTERNATIONAL JOURNAL OF PLANT SCIENCES 165 (4): S69-S83 Suppl. S JUL 2004.

Conti E, Eriksson T, Schonenberger J, et al. [Out of India Hypothesis]
Early tertiary out-of-India dispersal of Crypteroniaceae: Evidence from phylogeny and molecular dating.
EVOLUTION 56 (10): 1931-1942 OCT 2002.

Amphibia
Heinicke, M. P., Duellman, W. E. & Hedges, S. B. 2007
Major Caribbean and Central American frog faunas originated by ancient oceanic dispersal. Proc Natl Acad Sci U S A 104, 10092-7.

Bossuyt F, Brown RM, Hillis DM, et al.
Phylogeny and biogeography of a cosmopolitan frog radiation: Late cretaceous diversification resulted in continent-scale endemism in the family ranidae
SYSTEMATIC BIOLOGY 55 (4): 579-594 AUG 2006

Roelants K, Bossuyt F
Archaeobatrachian paraphyly and pangaean diversification of crown-group frogs
SYSTEMATIC BIOLOGY 54 (1): 111-126 FEB 2005

Roelants, K., Jiang, J., Bossuyt, F., 2004.
Endemic ranid (Amphibia: Anura) genera in southern mountain ranges of the Indian subcontinent represent ancient frog lineages: evidence from molecular data.
Mol. Phylogenet. Evol. 31, 730-740.

Gower DJ, Kupfer A, Oommen OV, et al. [Out of India Hypothesis]
A molecular phylogeny of ichthyophiid caecilians (Amphibia : Gymnophiona : Ichthyophiidae): Out of India or out of South East Asia?
PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES 269 (1500): 1563-1569 AUG 7 2002.

Wilkinson M, Sheps JA, Oommen OV, et al. [Out of India Hypothesis]
Phylogenetic relationships of Indian caecilians (Amphibia : Gymnophiona) inferred from mitochondrial rRNA gene sequences.
MOLECULAR PHYLOGENETICS AND EVOLUTION 23 (3): 401-407 JUN 2002.

Bossuyt, F. & Milinkovitch, M. C. 2001 [Out of India Hypothesis]
Amphibians as indicators of early Tertiary 'out of India' dispersal of vertebrates.
Science 292, 93- 95.

Reptilia
Noonan BP, Chippindale PT
Dispersal and vicariance: The complex evolutionary history of boid snakes
MOLECULAR PHYLOGENETICS AND EVOLUTION 40 (2): 347-358 AUG 2006

Hugall AF, Lee MSY
Molecular claims of Gondwanan age for Australian agamid lizards are untenable
MOLECULAR BIOLOGY AND EVOLUTION 21 (11): 2102-2110 NOV 2004

Macey, J. R., J. A. Schulte II, A. Larson, N. B. Ananjeva, Y. Wang, R. Pethiyagoda, N. Rastegar-Pouyani, and T. J. Papenfuss. 2000. [Out of India Hypothesis]
Evaluating trans-Tethys migration: an example using acrodont lizard phylogenetics.
Syst. Biol. 49:233-256.

Mammalia
Poux C, Chevret P, Huchon D, et al.
Arrival and diversification of caviomorph rodents and platyrrhine primates in South America
SYSTEMATIC BIOLOGY 55 (2): 228-244 APR 2006

Poux, C., O. Madsen, E. Marquard, D. R. Vieites, W. W. de Jong, and M. Vences. 2005.
Asynchronous colonization of Madagascar by the four endemic clades of primates, tenrecs, carnivores and rodents as inferred from nuclear genes.
Syst. Biol. 54:719-730.

Steiper ME, Young NM
Primate molecular divergence dates
MOLECULAR PHYLOGENETICS AND EVOLUTION 41 (2): 384-394 NOV 2006

Murphy WJ, Eizirik E, O'Brien SJ, et al. 2001. [Out of India Hypothesis]
Resolution of the early placental mammal radiation using Bayesian phylogenetics.
SCIENCE 294 (5550): 2348-2351.

Actinopterygii
Ruber L, Britz R, Zardoya R [Out of India Hypothesis ?]
Molecular phylogenetics and evolutionary diversification of labyrinth fishes (Perciformes : Anabantoidei)
SYSTEMATIC BIOLOGY 55 (3): 374-397 JUN 2006

Li X, Musikasinthorn P, Kumazawa Y. 2006. [Out of India Hypothesis]
Molecular phylogenetic analyses of snakeheads (Perciformes: Channidae) using mitochondrial DNA sequences.
Ichthyological Research. 53: 148-159.

Briggs JC.
The biogeography of otophysan fishes (Ostariophysi : Otophysi): a new appraisal
JOURNAL OF BIOGEOGRAPHY 32 (2): 287-294 FEB 2005

Diogo R.
Phylogeny, origin and biogeography of catfishes: support for a Pangean origin of 'modern teleosts' and reexamination of some Mesozoic Pangean connections between the Gondwanan and Laurasian supercontinents.
ANIMAL BIOLOGY 54 (4): 331-351 2004

Kumazawa, Y., and M. Nishida. 2000. [Out of India Hypothesis]
Molecular phylogeny of osteoglossoids: a new model for gondwanian origin and plate tectonic transportation of the Asian arowana.
Mol. Biol. Evol. 17: 1869-1878.