Henry L. Bart

Reconstructing the phylogenetic relationships of the earth's most diverse clade of freshwater fishes—order Cypriniformes (Actinopterygii: Ostariophysi): A case study using multiple nuclear loci and the mitochondrial genome

The order Cypriniformes is the most diverse clade of freshwater fishes and is natively distributed on all continents except South America, Australia, and Antarctica. Despite the diversity of the group and the fundamental importance of these species in both ecosystems and human culture, relatively little has been known about their relationships relative to their diversity. In recent years, with an international effort investigating the systematics of the group, more information as to their genealogical relationships has emerged and species discovery and their descriptions have increased. One of the more interesting aspects of this group has been a traditional lack of understanding of the relationships of the families, subfamilies, and other formally or informally identified groups. Historical studies have largely focused on smaller groups of species or genera. Because of the diversity of this group and previously published whole mitochondrial genome evidence for relationships of major clades in the order, this clade serves as an excellent group to investigate the congruence between relationships reconstructed for major clades with whole mitogenome data and those inferred from a series of nuclear gene sequences. As descent has resulted in only one tree of life, do the phylogenetic relationships of these major clades converge on similar topologies using the large number of available characters through this suite of nuclear genes and previously published mitochondrial genomes? In this study we examine the phylogenetic relationships of major clades of Cypriniformes using previously published mitogenomes and four putative single-copy nuclear genes of the same or closely related species. Combined nuclear gene sequences yielded 3810bp, approximately 26% of the bp found in a single mitogenome; however homoplasy in the nuclear genes was measurably less than that observed in mitochondrial sequences. Relationships of taxa and major clades derived from analyses of nuclear and mitochondrial sequences were nearly identical and both received high support values. While some differences of individual gene trees did exist for species, it is predicted that these differences will be minimized with increased taxon sampling in future analyses.

Outlier Detection with the Kernelized Spatial Depth Function

Statistical depth functions provide from the deepest point a center-outward ordering of multidimensional data. In this sense, depth functions can measure the extremeness or outlyingness of a data point with respect to a given data set. Hence, they can detect outliers observations that appear extreme relative to the rest of the observations. Of the various statistical depths, the spatial depth is especially appealing because of its computational efficiency and mathematical tractability. In this article, we propose a novel statistical depth, the kernelized spatial depth (KSD), which generalizes the spatial depth via positive definite kernels. By choosing a proper kernel, the KSD can capture the local structure of a data set while the spatial depth fails. We demonstrate this by the half-moon data and the ring-shaped data. Based on the KSD, we propose a novel outlier detection algorithm, by which an observation with a depth value less than a threshold is declared as an outlier. The proposed algorithm is simple in structure: the threshold is the only one parameter for a given kernel. It applies to a one-class learning setting, in which normal observations are given as the training data, as well as to a missing label scenario, where the training set consists of a mixture of normal observations and outliers with unknown labels. We give upper bounds on the false alarm probability of a depth-based detector. These upper bounds can be used to determine the threshold. We perform extensive experiments on synthetic data and data sets from real applications. The proposed outlier detector is compared with existing methods. The KSD outlier detector demonstrates a competitive performance.

Inferring the Tree of Life of the order Cypriniformes, the earth's most diverse clade of freshwater fishes: Implications of varied taxon and character sampling

The phylogenetic relationships of species are fundamental to any biological investigation, including all evolutionary studies. Accurate inferences of sister group relationships provide the researcher with an historical framework within which the attributes or geographic origin of species (or supraspecific groups) evolved. Taken out of this phylogenetic context, interpretations of evolutionary processes or origins, geographic distributions, or speciation rates and mechanisms, are subject to nothing less than a biological experiment without controls. Cypriniformes is the most diverse clade of freshwater fishes with estimates of diversity of nearly 3,500 species. These fishes display an amazing array of morphological, ecological, behavioral, and geographic diversity and offer a tremendous opportunity to enhance our understanding of the biotic and abiotic factors associated with diversification and adaptation to environments. Given the nearly global distribution of these fishes, they serve as an important model group for a plethora of biological investigations, including indicator species for future cli- matic changes. The occurrence of the zebrafish, Danio rerio, in this order makes this clade a critical component in understanding and predicting the relationship between mutagenesis and phenotypic expressions in vertebrates, including humans. With the tremendous diversity in Cypriniformes, our understanding of their phylogenetic relationships has not proceeded at an acceptable rate, despite a plethora of morphological and more recent mo- lecular studies. Most studies are pre-Hennigian in origin or include relatively small numbers of taxa. Given that analyses of small numbers of taxa for molecular characters can be compromised by peculiarities of long-branch attraction and nodal-density effect, it is critical that significant progress in our understanding of the relationships of these important fishes occurs with increasing sampling of species to mitigate these potential problems. The recent Cypriniformes Tree of Life initiative is an effort to achieve this goal with morphological and molecular (mitochondrial and nuclear) data. In this early synthesis of our understanding of the phylogenetic relationships of these fishes, all types of data have contributed historically to improving our understanding, but not all analyses are complementary in taxon sampling, thus precluding direct understanding of the impact of taxon sampling on achieving accurate phylogenetic inferences. However, recent molecular studies do provide some insight and in some instances taxon sampling can be implicated as a variable that can influence sister group relationships. Other instances may also exist but without inclusion of more taxa for both mitochondrial and nuclear genes, one cannot distinguish between inferences being dictated by taxon sampling or the origins of the molecular data.

Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae)

The members of the cyprinid subfamily Gobioninae, commonly called gudgeons, form one of the most well-established assemblages in the family Cyprinidae. The subfamily is a species-rich group of fishes, these fishes display diverse life histories, appearances, and behavior. The phylogenetic relationships of Gobioninae are examined using sequence data from four loci: cytochrome b, cytochrome c oxidase I, opsin, and recombination activating gene 1. This investigation produced a data matrix of 4114 bp for 162 taxa that was analyzed using parsimony, maximum likelihood, and Bayesian inference methods. The phylogenies our analyses recovered corroborate recent studies on the group. The subfamily Gobioninae is monophyletic and composed of three major lineages. We find evidence for a Hemibarbus-Squalidus group, and the tribes Gobionini and Sarcocheilichthyini, with the Hemibarbus-Squalidus group sister to a clade of Gobionini-Sarcocheilichthyini. The Hemibarbus-Squalidus group includes those two genera; the tribe Sarcocheilichthyini includes Coreius, Coreoleuciscus, Gnathopogon, Gobiocypris, Ladislavia, Paracanthobrama, Pseudorasbora, Pseudopungtungia, Pungtungia, Rhinogobio, and Sarcocheilichthys; the tribe Gobionini includes Abbottina, Biwia, Gobio, Gobiobotia, Huigobio, Microphysogobio, Platysmacheilus, Pseudogobio, Romanogobio, Saurogobio, and Xenophysogobio. The monotypic Acanthogobio is placed into the synonymy of Gobio. We tentatively assign Belligobio to the Hemibarbus-Squalidus group and Mesogobio to Gobionini; Paraleucogobio and Parasqualidus remain incertae sedis. Based on the topologies presented, the evolution of swim bladder specializations, a distinctive feature among cyprinids, has occurred more than once within the subfamily.

Decline of the Frecklebelly Madtom in the Pearl River Based on Contemporary and Historical Surveys

Abstract The Pearl River has experienced numerous human-caused disturbances since the 1950s, including completion of a navigation channel, reservoir construction, and channel modifications on the main stem of the river. These types of disturbances are known to negatively impact the biotic and abiotic components of riverine ecosystems. Since the 1960s, several fish species in the drainage have declined in abundance or have been extirpated from the drainage. We undertook this study to assess the current conservation status of the frecklebelly madtom Noturus munitus in the Pearl River drainage. A 1999 survey of 53 sites within the historic range of the frecklebelly madtom yielded only 13 specimens from eight localities. We also examined historical population trends for the frecklebelly madtom and other benthic fishes using archived museum material (1950– 1988). After standardizing for variation in collection effort, analysis of long-term collection data indicated that frecklebelly madtom populations have dec...

Morphological Variation of the Palatal Organ and Chewing Pad of Catostomidae (Teleostei: Cypriniformes)

We studied the morphology and shape variation of the palatal organ and chewing pad of sucker fishes, family Catostomidae. The palatal organ is a muscularized structure that forms a large mass on the roof of the posterior part of the buccopharyngeal cavity in cypriniform fishes. It functions in coordination with the branchial arches to separate food items from inorganic debris during feeding. The palatal organ exhibits considerable variability in morphology among catostomids. It is shorter, narrower, and thinner in species of the subfamily Cycleptinae (e.g., Cycleptus elongatus) than in other catostomid subfamilies. The thickest and widest palatal organ is seen in species of the subfamily Ictiobinae (e.g., Ictiobus cyprinellus). The shape and size of the palatal organ generally varies between these extremes in species of subfamily Catostominae (e.g., Catostomus and Moxostoma species). Principal components analysis and analysis of variance has differentiated means of various palatal organ measurements for each monophyletic subfamily and tribe of Catostomidae with statistical significance. These results corroborate previously established typological classification of catostomids based on pharyngeal tooth count, pharyngeal tooth morphology, and diet. A keratinized chewing pad forms on the posterior surface of the palatal organ in catostomids or on a skeletal process in cyprinids and serves as an occlusion surface for pharyngeal teeth. The chewing pad is lunate in catostomids and generally ovoid in cyprinids. It is absent from the species of loaches (e.g., botiids, cobitids, and nemacheilids) and gyrinocheilids examined. A synonymy of terms used in the past to describe the palatal organ and chewing pad of Cypriniformes is provided. J. Morphol., 2011.

Evolutionary Divergence of Duplicate Copies of the Growth Hormone Gene in Suckers (Actinopterygii: Catostomidae)

Catostomid fishes (suckers) have duplicate copies of the growth hormone gene and other nuclear genes, due to a genome duplication event early in the group’s history. Yet, paralogs of GH in suckers are more than 90% conserved in nucleotide (nt) and amino acid (aa) sequence. Within paralogs across species, variation in nt and aa sequence averages 3.33% and 4.46% for GHI, and 3.22% and 2.43% for GHII, respectively. Selection tests suggest that the two GH paralogs are under strong purifying selection. Consensus trees from phylogenetic analysis of GH coding region data for 23 species of suckers, other cypriniform fishes and outgroups resolved cypriniform relationships and relationships among GHI sequences of suckers more or less consistently with analyses based on other molecular data. However, the analysis failed to resolve all sucker GHI and GHII sequences as monophyletic sister groups. This unexpected topology did not differ significantly from topologies constrained to make all GH sequences monophyletic. We attribute this result either to limitations in our GHII data set or convergent adaptive changes in GHII of tribe Catostomini.

A content-based image retrieval system for fish taxonomy

It is estimated that less than ten percent of the worlds species have been discovered and described. The main reason for the slow pace of new species description is that the science of taxonomy, as traditionally practiced, can be very laborious: taxonomists have to manually gather and analyze data from large numbers of specimens, often from broad geographic areas, and identify the smallest subset of external body characters that uniquely diagnoses the new species as distinct from all its known relatives. The pace of data gathering and analysis in taxonomy can be greatly increased by the development of information technology. The Internet is being used to link taxonomists,taxonomic literature and specimen databases in different parts of the globe, and hence enables the development of tools for remote study of specimens archived as digital images. In this paper, we propose a content-based image retrieval system for taxonomic research. The system has a learning component that can identify representative body shape characters of known species based on digitized landmarks. The system can also provide statistical clues for assisting taxonomists to identify new species or subspecies. The experiments on a taxonomic problem involving species of suckers in the genera Carpiodes demonstrate promising results.

Long-term fish community dynamics from a blackwater stream receiving kraft mill effluent between 1973 and 1988

Archived data from a long-term (1973–1988) monitoring study were used to assess the impacts of kraft mill effluents (KME) on fish community dynamics in Elevenmile Creek, a small blackwater stream located in Cantonment, Florida, compared to a neighboring stream, Black Creek, that did not receive KME. The fish community in Elevenmile Creek was generally lower in species richness and diversity than the reference stream. The exception was the mill outfall site, which had similar species richness and diversity to the reference stream. Neither species richness nor diversity changed substantially during the survey period in either stream. Throughout the survey, Elevenmile Creek was numerically dominated by bluegill, Lepomis macrochirus, and eastern mosquitofish, Gambusia affinis. Black Creek had greater abundances of minnows, suckers, and darters. Time series analysis of L. macrochirus for Elevenmile Creek showed that this species was more abundant during winter than summer, but no overall long-term trend was found. Although data used in this study may not be representative of the fish community in Elevenmile Creek as it exists today, results suggest that Elevenmile Creek was highly disturbed during the survey and that species diversity did not increase following mill treatment upgrades.

Geomorphic disturbance and its impact on darter (Teleostomi: Percidae) distribution and abundance in the Pearl River drainage, Mississippi

We examined channel and point bar changes over time in the Pearl River, a meandering, Coastal Plain stream in Mississippi and Louisiana. We interpreted extreme changes in bar area as evidence of channel instability and related this to the diversity and abundance of darters in the river. Darters were less diverse and abundant in more disturbed reaches in comparison with relatively undisturbed reaches. Darter abundance was positively correlated with proximity to extreme bar-area changes. The relationship between channel instability and darter abundance observed here points to the importance of landscape level approaches to in-stream habitat management. The results suggest that river management practices that prevent or mitigate extreme changes in channel or sediment dynamics should be adopted for the benefit of benthic communities.