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Due to several factors populations of the American paddlefish have been greatly endangered and genetic diversity within their populations has been decreased. Destruction of habitat, caused by dam building has impeded the ability of this migratory species to reproduce. This species is also very long lived and does not reproduce until it is very old. Over harvest of paddlefish has also lead to their demise and inability to reproduce, as they have often been killed before they have a chance to spawn. Due to their very low numbers in some areas, the individuals that do exist most likely have originated from some of the same parents, thus resulting in very low diversity of genes and reduced fitness.

The American paddlefish has been decreasing in numbers due to various reasons, one of which is habitat fragmentation. The ecology of this species is that they live in riverine waterways that have been through many tears been dammed up by human interactions. Where damming has occurred these river areas have become reservoirs. The American paddle fish has been found to live and survive in this new habitat, but their habits and ecology has changed due to the habitat change. American paddlefish populations living in lentic and lotic systems have different population characteristics, the most important being growth, mortality, and reproduction rates. The importance of non-impounded riverine habitat for this species is mainly for the use of spawning habitat. Creating impoundments increases mortality rates, reduces spawning habitat, and impedes the ability of this fish to migrate as it would in a natural river system. (Paukert 2001)

Paddlefish are a highly migratory species and the different habitats have different effects on migration. Paddlefish were found to move to different areas of the reservoir when seasons changed. Both sexes had similar behavior, but males generally hung around upstream spawning grounds for longer than females. Dams that block migration routes are figured to lower fitness and reduce the chance that the blocked area will be repopulated if the area experiences a local extinction. (Stancill)

Conservation issues have gone to using genetics as a tool to help increase and repopulate areas where they were once sustainably populated. There is not much genetic diversity within paddlefish populations, and most individuals in a population are most likely derived from the same parents, or the same few parents. Microsatellite loci are being utilized to study the diversity of genes within broodstocks used for aquaculture purposes. The goal is to maximize genetic diversity within aquaculture to ensure healthiness of the individual fish. Several Methods are utilized, such as DNA extraction, PCR amplification, and Genotyping. (Kaczmarczyk)

A study conducted concluded that paddlefish populations have low levels of genetic diversity. DNA sequencing was used on 10 different paddlefish from Nebraska, Montana, and Louisiana to determine this. Mitochondrial genotypes were observed, and 9 were found in the 10 individuals that were tested. Six haplotypes were recorded along with the 93 fish analyzed by PCR-RFLP analysis.(Szalanski)

Kaczmarczyk D, Kohlmann K, Kersten P, Luczynski M (2007) Polymorphism of microsatellite loci – a tool in studying biodiversity of paddlefish aquaculture broodstock. Environmental Biotechnology, 3(2), 44-48

Paukert CP, Fisher WL (2001) Characteristics of Paddlefish in a Southwestern U.S. Reservoir, with Comparisons of Lentic and Lotic Populations. Transactions of the American Fisheries Society, 130, 634-643

Stancill W, Jordan GR, Paukert CP (2002) Seasonal Migration Patterns and Site Fidelity of Adult Paddlefish in Lake Francis Case, Missouri River. North American Journal of Fisheries Management, 22, 815-824.

Szalanski AL, Bischof R, Mestl G (2000) Population Genetic Structure of Nebraska Paddlefish Based on Mitochondrial DNA Variation. Transactions of the American Fisheries Society, 129, 1060-1065.