Fishes, the principal group of vertebrates found in running waters, are of great human interest because of their commercial and recreational value. Approximately 41% (about 8500 species) of the world's fishes live in freshwater. Of these, almost all have representatives that occur in running waters, although with varying degrees of river dependency and saltwater tolerance. Groups with little or no tolerance for saltwater (e.g., Cyprinidae, Centrarchidae, and Characidae) are considered to be primary freshwater fishes, and have dispersed through freshwater routes or evolved in place from distant marine ancestors. Secondary freshwater fishes (e.g., Cichlidae and Poeciliidae) are usually restricted to freshwater but have some tolerance to saltwater. Diadromous fishes migrate between freshwater and saltwater. Anadromous fishes, including many salmonids, lampreys, shad, and sturgeon, spend most of their lives in the sea and migrate to freshwater to reproduce. American and European eels are catadromous fishes, which spend most of their lives in freshwater and migrate to the sea to reproduce. Catadromy appears to be more prevalent in the tropics, and anadromy more common at higher latitudes.

Longitudinal gradients of fish assemblages are common within river systems, and have resulted in several attempts to classify stream zones by the dominant fish species or assemblage found. Because fish faunas vary considerably among geographic and climatic regions, zonation schemes can usually be applied only locally except in Europe. Longitudinal gradients arise as the result of species addition and/or replacement, and reflect adaptations to the type and volume of habitat and available food along the river continuum. Upstream fishes, typified by salmonids and sculpins, have high metabolic rates and consequent high demands for oxygen. Salmonids are active, streamlined fishes with strong powers of locomotion that can maintain position in swift water to feed upon drifting invertebrates. Sculpins, with depressed heads and large pectoral fins, hold close to the streambed and forage for invertebrates among stones on the bottom. Upstream fishes are usually solitary in habit and may exhibit territoriality associated with both breeding and spatial resources. They may extend downstream where oxygen and temperatures are suitable, to join deeper-bodied fishes more tolerant of warmer temperatures and reduced oxygen. Species richness is usually greatest in the mid-order segments, in association with increased pool development and overall habitat heterogeneity. The Cyprinidae, one of the largest and most widespread of primary fish families, is characteristic of moderate gradient streams. Shoaling behavior is common within this group. In high-order reaches, fish assemblages include larger, deep-bodied fishes such as suckers and catfishes that feed on bottom deposits, invertivorous sun-fishes, and predatory pike.

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