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Shoal Bass Monitoring in the Chipola River

A man on a boat is holding a large striped fish.

Shoal Bass (Micropterus cataractae) are a unique species of black bass endemic to the Apalachicola-Chattahoochee-Flint River Basin in Florida, Georgia, and Alabama. A recently discovered species that was formally described a little more than two decades ago, Shoal Bass are listed as a species of greatest conservation need by the Florida Fish and Wildlife Conservation Commission (FWC). The Chipola River is a 201-km long tributary to the Apalachicola River that is home to the only naturally reproducing population of Shoal Bass known to exist in the state of Florida. While Shoal Bass have been collected on occasion within the main channel of the Apalachicola River, they are most abundant in a 48-km stretch of the Chipola River between the cities of Marianna, FL and Clarksville, FL.

Shoal Bass are habitat specialists and are typically found within lotic systems (flowing, freshwater environments) with moderate to fast velocities and rocky substrate. Due to being habitat specialists, Shoal Bass tend to have low population density in rivers where suitable habitat is limited, such as the Chipola River (Woodside et al. 2015). This population is recognized to be threatened with population decline and potential extirpation due to habitat degradation (Woodside et al. 2015).

Another potential threat to Shoal Bass conservation is introgressive hybridization with non-native black bass species (Sammons et al. 2015). Spotted Bass M. punctulatus were introduced into the Apalachicola River Basin decades ago and have since become established (Williams and Burgess 1999; Fuller et al. 2020). The Choctaw Bass M. sp. cf. punctulatus is a provisional species found in Choctawhatchee River drainage and systems further west in the Florida Panhandle that is awaiting formal scientific description (Tringali et al. 2015a). Both Spotted Bass and Choctaw Bass have been documented to hybridize with Shoal Bass within the Apalachicola-Chattahoochee-Flint River Basin, including the Chipola River (Alvarez et al. 2015; Tringali et al. 2015b; Taylor et al. 2018). Hybridization between black bass species can lead to loss of fitness and the replacement of native species by non-native species (Alvarez et al. 2015). Genetic introgression can lead to the loss of genetic integrity or complete extirpation of native populations. Estimates suggest that the 88% of the Shoal Bass collected from the Chipola River Shoal Bass population from 2007-2010 had not been impacted by hybridization with any other black bass species. Subsequent sampling found that non-hybrid Shoal Bass made up 89%, 92%, and 95% of the population in 2016, 2017, and 2019, respectively. In comparison, the Flint River Shoal Bass population was estimated to be 62% non-hybrid Shoal Bass from 2005-2015 (Taylor et al. 2018). The Chattahoochee River Shoal Bass population was estimated to be 83% non-hybrid fish from 2009-2013 (Taylor et al. 2018). The Chipola River Shoal Bass population is likely to have been the least impacted by introgression among the populations studied to date.

Effective population size (Ne) is a genetic parameter that is frequently estimated and considered for the conservation and/or management of low-density populations or threatened species. Low Ne indicates that genetic changes can occur rapidly, leading to allele frequency changes, loss of genetic variability, and increased inbreeding. Extremely low Ne suggests an elevated risk of inbreeding and the associated fitness loss known as inbreeding depression. Inbreeding depression is widely considered to be a concern when populations have Ne of 50 or less (Rieman and Allendorf 2001). The most recent estimate of effective population size for the Chipola River Shoal Bass population was from a sample collected in 2017 and suggested that Ne was 134.5 (95% CI 70.3-471.7) at that time.

Hurricane Michael made landfall in the Florida Panhandle on October 10, 2018. With sustained winds of 160 mph, Hurricane Michael was the strongest hurricane to hit the Florida Panhandle since record-keeping began in 1851. The east side of the eyewall swept up through the Chipola River drainage, resulting in the destruction of many small towns along the way. Heavy winds and rain destroyed much of the riparian zone, compromised sewage systems and flushed many, low-oxygen, swamp areas. Subsequently, several fish kills were reported on the Chipola River and Apalachicola River in the days following Hurricane Michael.

Following Hurricane Michael, declines in Shoal Bass relative abundance were observed, creating a need to understand the factors behind this decline. The objectives of this study were 1) to conduct a mark-recapture population estimate to compare the abundance of the Shoal Bass population in 2021 to earlier estimates produced from sampling in 2009-2011, 2) to generate a length frequency graph to identify year class strength, 3) to estimate the effective population size of the Shoal Bass population and 4) to assess the current state of hybridization between Shoal bass and non-native black bass species within the Chipola River.

All Shoal Bass were collected using boat-mounted DC electrofishing in the area from Spring Creek to Johnny Boy Landing. Electrofishing involves briefly stunning fish with an electric current from boats equipped with electrofishing gear. The fish are stunned long enough for biologists to work them up, and then released unharmed back into the river system. A mark-recapture population estimate took place over 9 days in October and November 2021. The river was split into 3 sections and 3 electrofishing passes were conducted on each section on consecutive days (1 pass per day). A total of 372 Shoal Bass were captured and marked. Fifty-five marked Shoal Bass were recaptured. The Schnabel estimate produced from the mark-recapture data suggested that there were 1,039 Shoal Bass (95% CI 660-1,814) from Spring Creek to Johnny Boy Landing in fall 2021. This is 52% lower than the estimate when the same stretch was sampled in 2009 and 42% lower than the 2010-11 estimate. The study suggested that the section with the greatest Shoal Bass population decline was Peacock Landing to Johnny Boy Landing, where the 2021 estimate was 80% lower than 2009 and 79% lower than 2010. Many Shoal Bass (70%) captured during all sampling events in 2021 ranged from 300-380 mm TL. Based on previous data collections and age samples, it is likely that most of the Shoal Bass in this size range are from the year class born in 2019 and were produced after the hurricane. Genetic results indicate that the Chipola River Shoal Bass population currently has very low levels of hybridization with non-native Black Bass. Ninety-eight percent of the Shoal Bass did not show any evidence of hybridization with other species. The results of the hybrid identification analysis suggest that the Chipola River Shoal Bass population currently has very low levels of introgression (>99% Shoal Bass alleles) in comparison to other populations throughout the species range. No pure Choctaw Bass or F₁ hybrids were collected during sampling and it appears that the current introgressive alleles are residuals from past hybridization events between Shoal Bass and Choctaw Bass. However, this does not mean that hybridization will not impact the population in the future. Although hybridization in Shoal Bass is currently low, it will remain a threat to the genetic integrity and conservation of Shoal Bass in the Chipola River if non-native species can move into Shoal Bass habitats.

The effective population size of the Shoal Bass population was estimated to be less than 50. This suggests the population would be vulnerable to introgressive hybridization, genetic diversity loss, and inbreeding depression if the population remains at this level. The effective population size estimates for the 2021 sample are the lowest collected from the Chipola River to date. Prior to Hurricane Michael, the effective population size estimates for the Shoal Bass in the Chipola River were greater than 100. It is likely that this loss in genetic diversity is due to a decline in the abundance of adult Shoal Bass throughout the river. Following the hurricane, the few remaining adults had successful natural reproduction which resulted in a sizeable year class which likely makes up nearly 70% of the current population. FWC biologists will continue to monitor the population and all aspects of abundance and genetic composition in years to come.