Dennis K. Shiozawa

Contour matching for a fish recognition and migration-monitoring system

Fish migration is being monitored year round to provide valuable information for the study of behavioral responses of fish to environmental variations. However, currently all monitoring is done by human observers. An automatic fish recognition and migration monitoring system is more efficient and can provide more accurate data. Such a system includes automatic fish image acquisition, contour extraction, fish categorization, and data storage. Shape is a very important characteristic and shape analysis and shape matching are studied for fish recognition. Previous work focused on finding critical landmark points on fish shape using curvature function analysis. Fish recognition based on landmark points has shown satisfying results. However, the main difficulty of this approach is that landmark points sometimes cannot be located very accurately. Whole shape matching is used for fish recognition in this paper. Several shape descriptors, such as Fourier descriptors, polygon approximation and line segments, are tested. A power cepstrum technique has been developed in order to improve the categorization speed using contours represented in tangent space with normalized length. Design and integration including image acquisition, contour extraction and fish categorization are discussed in this paper. Fish categorization results based on shape analysis and shape matching are also included.

Empirical tests for ecological exchangeability

The concept of ecological exchangeability, together with genetic exchangeability, is central to both the Cohesion Species Concept as well as to some definitions of Evolutionarily Significant Units. While there are well-established criteria for measuring genetic exchangeability, the concept of ecological exchangeability has generated considerable confusion. We describe a procedure that uses the complementary strengths, while recognising the limitations, of both molecular genetic data and ecological experiments to determine the ecological exchangeability of local populations within a species. This is the first synthesis of a combined approach (experiments and genetics) and the first explicit discussion of testing ecological exchangeability. Although it would be ideal to find functional genes that interact to influence quantitative traits resulting in ecological differences (e.g. growth, size, fecundity), we suggest that our current knowledge of functional markers is too limited for most species to use them to differentiate adaptively different local populations. Thus, we argue that ecological experiments using whole organisms combined with neutral markers that indicate evolutionary divergence, provide the strongest case for detecting adaptive differences among local populations. Both genetic divergence and ecological experiments provide the best information for infering ecological exchangeability. This procedure can be used to decide which local populations should be preserved to maintain intraspecific variation and to determine which populations would enhance captive-breeding programs, augment endangered local populations and could best be used to re-introduce native species into historically occupied areas.

Across the great divide: genetic forensics reveals misidentification of endangered cutthroat trout populations

Accurate assessment of species identity is fundamental for conservation biology. Using molecular markers from the mitochondrial and nuclear genomes, we discovered that many putatively native populations of greenback cutthroat trout (Oncorhynchus clarkii stomias) comprised another subspecies of cutthroat trout, Colorado River cutthroat trout (Oncorhynchus clarkii pleuriticus). The error can be explained by the introduction of Colorado River cutthroat trout throughout the native range of greenback cutthroat trout in the late 19th and early 20th centuries by fish stocking activities. Our results suggest greenback cutthroat trout within its native range is at a higher risk of extinction than ever before despite conservation activities spanning more than two decades.

Genetic Detection of Putative Hybridization between Native and Introduced Rainbow Trout Populations of the Upper Snake River

Abstract Native trout populations throughout western North America have declined because of habitat alteration, introgression with introduced trout, or competitive exclusion by nonnative species. Consequently, identification and preservation of native trout are now the goals of many management programs. We examined allozyme and mitochondrial DNA (mtDNA) variation in seven naturally occurring populations and one hatchery population of rainbow trout Oncorhynchus mykiss from southern Idaho and northern Nevada to determine their genetic origins. Allozyme and mtDNA results were concordant in identifying three populations as genetically pure interior rainbow trout and one population as a hybrid swarm. Results for the remaining four populations were discordant. However, these latter four populations were best classified as hybrid swarms due to the nature of either the allozyme or mtDNA data, which included genetic characteristics of both coastal and interior rainbow trout. Our study demonstrates the utility of m...

Microcrustacea from the Benthos of Nine Minnesota Streams

The occurrence and microdistribution of microcrustaceans in nine low order Minnesota streams were examined. Total densities ranged from 16,652 to 430,863/m2. Eight species of cyclopoid copepods, 13 species of canthocamptid harpacticoid copepods, and one parastenocarid harpacticoid copepod were identified. Nineteen species of cladocerans were collected. Ostracods were quantified but not identified to species. Cyclopoid copepods were most abundant in slow water habitats where the majority lived on the sediment surface; in some cases they occurred in well sorted gravel or pea gravel, and were likely living interstitially. Harpacticoid copepods were most common in coarse sediments with a sand matrix, but occurred in all benthic habitats. Cladocerans included the Daphnidae, Macrothricidae, Bosminidae, and Chydoridae and were most abundant in slow water habitats of the stream; chydorids were the most common, reaching densities of over 25,000/m2.

Influence of introgression and geological processes on phylogenetic relationships of Western North American mountain suckers (Pantosteus, Catostomidae).

Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western USA and into northern Mexico. They are typically found in medium gradient, middle-elevation reaches of rivers over rocky substrates. This study (1) compares molecular data with morphological and paleontological data for proposed species of Pantosteus, (2) tests hypotheses of their monophyly, (3) uses these data for phylogenetic inferences of sister-group relationships, and (4) estimates timing of divergence events of identified lineages. Using 8055 base pairs from mitochondrial DNA protein coding genes, Pantosteus and Catostomus are reciprocally monophyletic, in contrast with morphological data. The only exception to a monophyletic Pantosteus is P. columbianus whose mtDNA is closely aligned with C. tahoensis because of introgression. Within Pantosteus, several species have deep genetic divergences among allopatric sister lineages, several of which are diagnosed and elevated to species, bringing the total diversity in the group to 11 species. Conflicting molecular and morphological data may be resolved when patterns of divergence are shown to be correlated with sympatry and evidence of introgression.

Contour Matching for Fish Species Recognition and Migration Monitoring

A variety of matching and classification techniques have been employed in applications requiring pattern recognition. In this chapter we introduce a simple and accurate real-time contour matching technique specifically for applications involving fish species recognition and migration monitoring. We describe FishID, a prototype vision system that employs a software implementation of our newly developed contour matching algorithms. We discuss the challenges involved in the design of this system, both hardware and software, and we present results from a field test of the system at Prosser Dam in Prosser, Washington. In tests with up to four distinct species, the algorithm correctly determines the species with greater than 90 percent accuracy.

Phylogeographic and nested clade analysis of the stonefly Pteronarcys californica (Plecoptera:Pteronarcyidae) in the western USA

Abstract Long-distance dispersal by aquatic insects can be difficult to detect because direct measurement methods are expensive and inefficient. When dispersal results in gene flow, signs of that dispersal can be detected in the pattern of genetic variation within and between populations. Four hundred seventy-five base pairs of the mitochondrial gene, cytochrome b, were examined to investigate the pattern of genetic variation in populations of the stonefly Pteronarcys californica and to determine if long-distance dispersal could have contributed to this pattern. Sequences were obtained from 235 individuals from 31 different populations in the western United States. Sequences also were obtained for Pteronarcella badia, Pteronarcys dorsata, Pteronarcys princeps, Pteronarcys proteus, and Pteronarcys biloba. Phylogenies were constructed using all of the samples. Nested clade analysis on the P. californica sequence data was used to infer the processes that have generated the observed patterns of genetic variation. An eastern North American origin and 2 distinct genetic lineages of P. californica could be inferred from the analysis. Most of the current population structure in both lineages was explained by a pattern of restricted gene flow with isolation by distance (presumably the result of dispersal via connected streams and rivers), but our analyses also suggested that long-distance, overland dispersal has contributed to the observed pattern of genetic variation.

Phylogenetic relationships of the western North American cyprinid genus Richardsonius, with an overview of phylogeographic structure.

Diversification of many North American taxa, including freshwater fishes, has been heavily influenced by the effects of complex geological and climatic events throughout the Cenozoic that have significantly altered the landscape. Here, we employ an array of phylogenetic analyses using a multiple gene tree approach to address several questions regarding the phylogenetic relationships of the North American cyprinid genus Richardsonius and two other closely related genera, Clinostomus and Iotichthys. We also use divergence time estimates generated using fossil calibrations to qualitatively assess the phylogeographic implications of evolution within the group. Mitochondrial and nuclear DNA sequences show a sister relationship between Iotichthys and Richardsonius, with Clinostomus being sister to an Iotichthys-Richardsonius clade, hence the currently recognized sister relationship between Clinostomus and Richardsonius is not supported. These genera appear to be monophyletic lineages, and sister species within genera appear to be reciprocally monophyletic. The two species within the genus Richardsonius both exhibit phylogeographic structure that is worthy of further investigation. Divergence time estimates between genera and species are Miocene or Pliocene in age, and divergence between phylogroups within species occurred in the late Pliocene to Pleistocene. These splits coincide with documented geological and climatic events.

Inferring dispersal of aquatic invertebrates from genetic variation: a comparative study of an amphipod and mayfly in Great Basin springs

Abstract Whether active or passive, dispersal accompanied by gene flow shapes the genetic makeup of populations and ultimately the evolutionary divergence of species. Our objective was to determine if 2 very different aquatic invertebrates with overlapping distributions show similar dispersal histories in their phylogeographic patterns and genetic uniqueness. Two spring-dwelling invertebrates, Hyalella azteca and Callibaetis americanus, were collected from 6 adjacent closed basins in the Great Basin of western North America. Cytochrome c oxidase subunit I (COI) and the 28S ribosomal subunit were used as genetic markers in Hyalella, and COI with the 16S ribosomal subunit of the mitochondrial genome were examined in Callibaetis. Maximum parsimony (MP) and likelihood (ML) analyses, FST values, analysis of molecular variance (AMOVA), Mantel tests, and nested clade phylogeographical analysis (NCPA) were used to evaluate geographical associations. Hyalella azteca appears to have been in the adjacent basins much longer than has Callibaetis. FST values in H. azteca reached near fixation. Callibaetis americanus FST values were lower suggesting greater gene flow and, consequently, higher dispersal rates. Mantel tests did not detect significant isolation by distance for either species, but NCPA on smaller networks of closely related haplotypes found the genetic structure in C. americanus dominated by restricted gene flow with isolation by distance. Hyalella azteca was characterized more by gradual range expansion followed by fragmentation. These results suggest that these isolated freshwater communities are amalgams of species that entered at different times, with weak dispersers having greater constraints on movement and, thus, reflecting an older geographical story than do species with stronger dispersal capabilities.