Mary M. Peacock

Landscape attributes and life history variability shape genetic structure of trout populations in a stream network

Spatial and temporal landscape patterns have long been recognized to influence biological processes, but these processes often operate at scales that are difficult to study by conventional means. Inferences from genetic markers can overcome some of these limitations. We used a landscape genetics approach to test hypotheses concerning landscape processes influencing the demography of Lahontan cutthroat trout in a complex stream network in the Great Basin desert of the western US. Predictions were tested with population- and individual-based analyses of microsatellite DNA variation, reflecting patterns of dispersal, population stability, and local effective population sizes. Complementary genetic inferences suggested samples from migratory corridors housed a mixture of fish from tributaries, as predicted based on assumed migratory life histories in those habitats. Also as predicted, populations presumed to have greater proportions of migratory fish or from physically connected, large, or high quality habitats had higher genetic variability and reduced genetic differentiation from other populations. Populations thought to contain largely non-migratory individuals generally showed the opposite pattern, suggesting behavioral isolation. Estimated effective sizes were small, and we identified significant and severe genetic bottlenecks in several populations that were isolated, recently founded, or that inhabit streams that desiccate frequently. Overall, this work suggested that Lahontan cutthroat trout populations in stream networks are affected by a combination of landscape and metapopulation processes. Results also demonstrated that genetic patterns can reveal unexpected processes, even within a system that is well studied from a conventional ecological perspective.

Local and Geographic Variability in the Distribution of Stream-Living Lahontan Cutthroat Trout

Abstract We investigated local and geographic variability in the up- and downstream distribution limits of threatened Lahontan cutthroat trout (Oncorhynchus clarki henshawi) in stream habitats of the eastern Lahontan basin in northern Nevada and southeastern Oregon. At a geographic scale, elevations of upstream distribution limits were significantly correlated with latitude and longitude, suggesting a potential influence of climatic gradients. Elevations of upstream distribution limits also were positively correlated with maximum basin elevation, which suggested topographic, rather than climatic constraints may be important. Upstream distribution limits were not significantly affected by local variation in stream size or presumptive dispersal barriers. Stream gradient was related to upstream distribution limits, but this was again confounded by maximum basin elevation. Stream gradients used by Lahontan cutthroat trout at upstream limits were considerably steeper than those observed for other subspecies of...

Assessing the Conservation Value of Hybridized Cutthroat Trout Populations in the Quinn River Drainage, Nevada

Abstract The Lahontan cutthroat trout Oncorhynchus clarki henshawi, an interior basin salmonid, is endemic to the hydrographic Lahontan Basin, which encompasses parts of northern Nevada, northeastern California, and southeastern Oregon. This subspecies is currently listed as threatened under the 1975 U.S. Endangered Species Act. Landscape- and population-level research suggests that this subspecies has survived in a desert environment by living in large, interconnected stream and/or stream-and-lake systems that support a metapopulation dynamic. Threats to the subspecies include habitat fragmentation as well as competition and hybridization with nonnative salmonids. Hybridization with the closely related rainbow trout O. mykiss compromises rangewide recovery efforts by increasing the risk of introgression and subsequent loss of pure populations in restored population networks. Here we use a suite of highly variable genetic markers (microsatellites, simple sequence repeats, and arbitrarily amplified regions...

Assessing Extinction Risk: Integrating Genetic Information

Risks of population extinction have been estimated using a variety of methods incorporating information from different spatial and temporal scales. We briefly consider how several broad classes of extinction risk assessments, including population viability analysis, incidence functions, and ranking methods integrate information on different temporal and spatial scales. In many circumstances, data from surveys of neutral genetic variability within, and among, populations can provide information useful for assessing extinction risk. Patterns of genetic variability resulting from past and present ecological and demographic events, can indicate risks of extinction that are otherwise difficult to infer from ecological and demographic analyses alone. We provide examples of how patterns of neutral genetic variability, both within, and among populations, can be used to corroborate and complement extinction risk assessments.

Strong Founder Effects and Low Genetic Diversity in Introduced Populations of Coqui Frogs

The success of non‐native species may depend on the genetic resources maintained through the invasion process. The Coqui (Eleutherodactylus coqui), a frog endemic to Puerto Rico, was introduced to Hawaii in the late 1980s via the horticulture trade, and has become an aggressive invader. To explore whether genetic diversity and population structure changed with the introduction, we assessed individuals from 15 populations across the Hawaiian Islands and 13 populations across Puerto Rico using six to nine polymorphic microsatellite loci and five dorsolateral colour patterns. Allelic richness (RT) and gene diversity were significantly higher in Puerto Rico than in Hawaii populations. Hawaii also had fewer colour patterns (two versus three to five per population) than Puerto Rico. We found no isolation by distance in the introduced range, even though it exists in the native range. Results suggest extensive mixing among frog populations across Hawaii, and that their spread has been facilitated by humans. Like previous research, our results suggest that Hawaiian Coquis were founded by individuals from sites around San Juan, but unlike previous research the colour pattern and molecular genetic data (nuclear and mtDNA) support two separate introductions, one on the island of Hawaii and one on Maui. Coquis are successful invaders in Hawaii despite the loss of genetic variation. Future introductions may increase genetic variation and potentially its range.

Assessing connectivity in salmonid fishes with DNA microsatellite markers

Connectivity is a key consideration for the management and conservation of any species, but empirical characterizations of connectivity can be extremely challenging. Assessments of connectivity require biologically realistic classifications of landscape structure (Kotliar and Wiens 1990), and an understanding of how landscape structure affects migration, dispersal, and population dynamics (Dunning et al. 1992; Rosenberg et al. 1997; Hanski 1999; Taylor et al. Chapter 2). Empirical assessments of connectivity may be accomplished by studying spatial patterns of habitat occupancy through time (Sjögren-Gulve and Ray 1996; Hanski 1999; Moilanen and Hanski Chapter 3), spatially correlated changes in population demography (Bjornstad et al. 1999; Isaak et al. 2003; Carroll Chapter 15), and individual movements (Millspaugh and Marzluff 2001; Tracey Chapter 14). These approaches have provided important insights for many species, but they can be difficult to implement for species with slow population dynamics or turnover (extinction and recolonization), complex life histories, and long-distance migrations. For species with these characteristics, molecular genetic markers represent a valuable tool for understanding processes that influence connectivity (Avise 1994; Frankham et al. 2004; Frankham Chapter 4). In this chapter, we review applications of molecular genetic markers to assess connectivity in salmonid fishes, a group of relatively well-studied species with

Development of food preferences: social learning by Belding's ground squirrels Spermophilus beldingi

SummaryThe mechanisms by which food selection behavior develops may constrain the evolution of optimal foraging, yet these mechanisms have received relatively little attention in recent optimal foraging studies. We used cafeteria-style feeding trials to examine the role of social learning in the development of food preferences by a generalist mammalian herbivore, Spermophilus beldingi. Naive young spent relatively little time feeding and showed no preferences among five plant species offered in their feeding trials. This random pattern persisted for one set of young during two subsequent trials in the absence of their mother. A second group of young squirrels was tested initially alone, once with their mothers, and then once more alone. These squirrels fed more than those in the control group during their final trials, and showed significant preferences among plant species. These paralleled the preferences of their mothers. These results suggest that social learning may be important in the development of feeding behavior in ground squirrels, and provide a possible mechanism for cultural differences in food preferences among populations.

Differences in population size variability among populations and species of the family Salmonidae

1. How population sizes vary with time is an important ecological question with both practical and theoretical implications. Because population size variability corresponds to the operation of density-dependent mechanisms and the presence of stable states, numerous researchers have attempted to conduct broad taxonomic comparisons of population size variability. 2. Most comparisons of population size variability suggest a general lack of taxonomic differences. However, these comparisons may conflate differences within taxonomic levels with differences among taxonomic levels. Further, the degree to which intraspecific differences may affect broader inferences has generally not been estimated and has largely been ignored. 3. To address this uncertainty, we examined intraspecific differences in population size variability for a total of 131 populations distributed among nine species of the Salmonidae. We extended this comparison to the interspecific level by developing species level estimates of population size variability. 4. We used a jackknife (re-sampling) approach to estimate intra- and interspecific variation in population size variability. We found significant intraspecific differences in how population sizes vary with time in all six species of salmonids where it could be tested as well as clear interspecific differences. Further, despite significant interspecific variation, the majority of variation present was at the intraspecific level. Finally, we found that classic and recently developed measures of population variability lead to concordant inferences. 5. The presence of significant intraspecific differences in all species examined suggests that the ability to detect broad taxonomic patterns in how population sizes change over time may be limited if variance is not properly partitioned among and within taxonomic levels.

Characterization of 13 microsatellites for Lahontan cutthroat trout (Oncorhynchus clarki henshawi) and cross-amplification in six other salmonids.

Thirteen newly developed tri‐ and tetranucleotide repeat microsatellite markers were developed for Lahontan cutthroat trout (Oncorhynchus clarki henshawi), a threatened subspecies endemic to the Lahontan hydrographic basin in the western USA. These loci are highly polymorphic with five to 30 alleles per locus and observed heterozygosities ranging from 0.4 to 0.7. Cross‐species amplification of these markers was most successful in the closely related rainbow trout, Oncorhynchus mykiss, with only three loci amplifying in brown trout, Salmo trutta. Nonoverlapping allelic distributions for many of these loci among the six salmonid species screened suggest these markers may be useful for hybrid determination.

The Evolutionarily Significant Unit Concept and the Role of Translocated Populations in Preserving the Genetic Legacy of Lahontan Cutthroat Trout

Abstract The Lahontan cutthroat trout Oncorhynchus clarkii henshawi, a listed subspecies of cutthroat trout O. clarkii, has been extirpated from over 90% of its historic waters. The 1995 U.S. Fish and Wildlife Service Recovery Plan identified three evolutionarily significant units, or distinct population segments (DPSs), of Lahontan cutthroat trout based upon morphological, genetic, and ecological data. Teams composed of federal and state agency and university biologists were organized to formulate recovery strategies that were specific to each DPS. In this context, fish native to each DPS are considered exclusively for recovery activities. Lahontan cutthroat trout populations in the Willow–Whitehorse drainage of the Coyote Lake basin, Oregon, were initially identified as part of the Northwestern DPS, but recent genetic analyses suggest that these populations may warrant a fourth DPS designation. The Willow–Whitehorse Lahontan cutthroat trout are found in seven within-basin streams and have been transloca...