In the uppermost, highest part of the Indus River basin there are relatively few genera and species: Diptychus, Ptychobarbus, Schizopyge, Schizopygopsis and Schizothorax snowtrout, Triplophysa loaches, and the catfish Glyptosternon reticulatum. Going downstream these are soon joined by the golden mahseer Tor putitora (alternatively T. macrolepis, although it often is regarded as a synonym of T. putitora) and Schistura loaches. Downriver from around Thakot, Tarbela, the Kabul–Indus river confluence, Attock Khurd and Peshawar the diversity rises strongly, including many cyprinids (Amblypharyngodon, Aspidoparia, Barilius, Chela, Cirrhinus, Crossocheilus, Cyprinion, Danio, Devario, Esomus, Garra, Labeo, Naziritor, Osteobrama, Pethia, Puntius, Rasbora, Salmophasia, Securicula and Systomus), true loaches (Botia and Lepidocephalus), stone loaches (Acanthocobitis and Nemacheilus), ailiid catfish (Clupisoma), bagridae catfish (Batasio, Mystus, Rita and Sperata), airsac catfish (Heteropneustes), schilbid catfish (Eutropiichthys), silurid catfish (Ompok and Wallago), sisorid catfish (Bagarius, Gagata, Glyptothorax and Sisor), gouramis (Trichogaster), nandid leaffish (Nandus), snakeheads (Channa), spiny eel (Macrognathus and Mastacembelus), knifefish (Notopterus), glassfish (Chanda and Parambassis), clupeids (Gudusia), needlefish (Xenentodon) and gobies (Glossogobius), as well as a few introduced species. As the altitude further declines the Indus basin becomes overall quite slow-flowing as it passes through the Punjab Plain. Major carp become common, and chameleonfish (Badis), mullet (Sicamugil) and swamp eel (Monopterus) appear. In some upland lakes and tributaries of the Punjab region snow trout and mahseer are still common, but once the Indus basin reaches its lower plain the former group is absent and the latter are rare. Many of the species of the middle sections of the Indus basin are also present in the lower. Notable examples of genera that are present in the lower plain but generally not elsewhere in the Indus River basin are the Aphanius pupfish, Aplocheilus killifish, palla fish (Tenualosa ilisha), catla (Labeo catla), rohu (Labeo rohita) and Cirrhinus mrigala. The lowermost part of the river and its delta are home to freshwater fish, but also several brackish and marine species. This includes pomfret and prawns. The large delta has been recognized by conservationists as an important ecological region. Here, the river turns into many marshes, streams and creeks and meets the sea at shallow levels.

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