Article

A New Species of Logperch Endemic to Tennessee (Percidae: Etheostomatinae: Percina)

Authors:
To read the full-text of this research, you can request a copy directly from the authors.

Abstract

Percina apina, the Tennessee Logperch, is described as a new species endemic to Tennessee and distributed in the Duck River system and Whiteoak Creek. The earliest collection records for Percina apina date to 1971 and the species was identified as Percina burtoni, the Blotchside Log-perch. A phylogenetic analysis of mitochondrial DNA (mtDNA) published in 2006 showed that populations identified as Percina burtoni in the Duck River system and Whiteoak Creek were a new and undescribed species. In this study, we test the hypothesis that Percina burtoni is composed of multiple species through analyses of mtDNA, nuclear genetic variation, and traditional meristic trait morphology. Our analyses of morphological divergence, nuclear genotypes, mtDNA gene trees, and comparisons with other sister species pairs of logperches confirm the distinctive-ness of Percina apina. Morphologically, Percina apina is distinguished from Percina burtoni through higher average numbers of lateral line scales (93.1 versus 89.9); pored lateral line scales (91.6 versus 88.8); rows of transverse scales (38.1 versus 33.6); and scales around the caudal pe-duncle (36.2 versus 33.5). The two species also differ in patterns of pigmentation; the lateral blotches in Percina apina are typically wider than high, whereas the blotches tend to be higher than wide in Percina burtoni. We recommend that future species descriptions of North American freshwater fishes leverage available genetic resources and include molecular phylogenetic assessments in analyses of taxon distinctiveness. In addition, we advocate the deposition of morphological data used in species descriptions to online data repositories to ensure that other researchers are able to evaluate and modify hypotheses of species delimitations.

No full-text available

Request Full-text Paper PDF

To read the full-text of this research,
you can request a copy directly from the authors.

... Between 1985 and1992, seven new species of Stigmacerca were described: the Blackfin Darter, E. nigripinne, the Fringed Darter, E. crossopterum, the Guardian Darter, E. oophylax, the Relict Darter, E. chienense, the Egg-mimic Darter, E. pseudovulatum, the Barrens Darter, E. forbesi, and the Crown Darter, E. corona (Braasch and Mayden 1985;Page et al. 1992). Starting in 2003, molecular phylogenetic tools became important in the discovery, delimitation, and eventual description of new species of darters (Page et al. 2003;Powers and Mayden 2007;Powers et al. 2012;Keck and Near 2013;Near and Thomas 2015;Near et al. 2017;Near et al. 2021); however, 30 years have passed since the most recent species of Stigmacerca was described (Page et al. 1992). ...
... Together, the first two principal components (PCs) account for 39.6% of the variation (Figure 3). There is overlap in the bivariate PCs, a pattern similar in other closely related species (Layman andMayden 2009, 2012;Kozal et al. 2017;Near et al. 2017;Near et al. 2021). Linear discriminant analysis correctly classified 72.2% (65 of 90) of Etheostoma xanthovum, 95.2% (400 of 420) of E. oophylax, and 95.4% (63 of 66) of E. chienense specimens. ...
... Other tributaries of the Obion River drainage should be surveyed to determine if other populations of E. oophylax are established outside of the Tennessee River basin. The discovery and description of Etheostoma xanthovum embodies the transition from a sole reliance on morphological traits to discover and delimit species of darters to a practice that deploys molecular phylogenetic analyses as a critical tool for species discovery, where a combination of morphological and molecular-based analyses aid in species delimitation (Page et al. 2003;Powers and Mayden 2007;Powers et al. 2012;Keck and Near 2013;Near and Thomas 2015;Near et al. 2017;Near et al. 2021). The agency provided by this protocol is the ability to delineate independently evolving lineages regardless of the magnitude of disparity in morphological traits traditionally used to discover, delimit, and describe species. ...
Article
Etheostoma xanthovum, the Clarks Darter, is described as a new species endemic to the Clarks River drainage in Kentucky and Tennessee, USA. Etheostoma xanthovum was previously recognized as Etheostoma oophylax based on morphological characters. Subsequent to the description of E. oophylax, molecular phylogenetic analyses consistently resolved specimens from the Clarks River drainage and E. chienense as sister species, which together formed a sister clade to all other sampled populations of E. oophylax. Our analyses of morphological trait data, mito-chondrial DNA, and genomic sampling using double digest restriction-site associated DNA sequencing support the distinctiveness of E. xanthovum. Morphologically, E. xanthovum differs slightly from E. oophylax in the modal number of dorsal fin rays (12 versus 11) and in the average number of scale rows around the caudal peduncle (21.8 versus 20.4). Etheostoma xanthovum does not share mitochondrial DNA haplotypes with E. oophylax or E. chienense. Phylogenomic analysis of an average of 28,448 double digest restriction-site associated DNA loci per sampled specimen resolves E. xanthovum and E. chienense as sister species, and assessment of genomic divergence supports the hypothesis that each of these two species represents a distinct and independently evolving lineage. In addition, we report a range extension of E. oophylax in the Obion River drainage, a direct tributary of the Mississippi River.
... Typically, even the most closely related species of darters exhibit appreciable disparity in morphological meristic (i.e., countable) traits, such as differences in the mean number of lateral line scale rows and modal differences in counts of rays and spines in the dorsal, anal, and pectoral fins. 22,[31][32][33][34][35][36] Differences in meristic counts have been the most used form of evidence for the delimitation of darter species since the late nineteenth century. 37 We collected data on 10 meristic traits from 67 Snail Darter and 71 ll Current Biology 35, 1-9, January 20, 2025 ...
... Our reference-based delimitation strategy avoids the over-splitting of taxonomic units that might occur to justify targets of biological conservation, 42,43 facilitating the allocation of resources where they will make the greatest impact in protecting imperiled lineages. It has the equally strong potential to discover unrecognized biodiversity 32,36,41,44 and to draw attention to newly discovered at-risk species needing federal protection. 31,45 Although the ESA prescribes that it should take less than 2 years for a species to move from petition to protection, limited budgets for listing decisions contributed to a median wait time of 9.1 years from 2000 to 2009 and 3.0 years from 2010 to 2020. ...
... The North American darters (subfamily Etheostomatinae) is a taxa-rich (~240 spp.) group of percid fishes for which new species descriptions have abounded in recent years (Williams et al. 2007;Blanton & Jenkins 2008;Near et al. 2011;Kozal et al. 2017;Near et al. 2017;Near et al. 2021). Species descriptions for this group of fishes are usually informed by phylogenetic analyses but often still depend on diagnoseable morphological traits (Keck & Near 2013;Near & Thomas 2015;Kozal et al. 2017;Piller & Bart 2017;Near et al. 2021). ...
Article
Full-text available
In recent years, new species descriptions for the North American darters have proliferated. Most species concepts accepted by contemporary ichthyologists require that a valid species be both monophyletic and diagnoseable, yet many lineages exhibit modal or range differences in morphological characteristics without individuals being diagnosable. Such scenarios present difficulties with regards to proper taxonomic recognition of divergent lineages and often prohibit appropriate conservation action. Following the example of recent authors, we provide meristic, geometric morphometric, and pigmentation data to support the recognition of three subspecies of Etheostoma rupestre, a species endemic to the Mobile Basin. These morphological data cohere with previous genetic work for E. rupestre. The nominate subspecies Etheostoma rupetsre rupestre (Tsai’s Rock Darter) is endemic to the Tombigbee River and Black Warrior River watersheds in Alabama and Mississippi and is characterized by having lower numbers of lateral blotches, lower range and mean of lateral line scales, lower modal number of scales above the lateral line, and lower degrees of nape squamation than other subspecies. Etheostoma rupestre piersoni (Shamrock Darter), ssp. nov., is endemic to the Cahaba and Alabama River Watersheds in Alabama and is characterized by intermediate counts of lateral blotches and higher scale counts and nape squamation than E. r. rupestre. Etheostoma rupestre uphapeense (Jade Darter), ssp. nov., is restricted to several small, disjunct populations in the Coosa and Tallapoosa watersheds in Alabama, Georgia, and Tennessee. Etheostoma r. uphapeense is characterized by having a higher mean number of lateral blotches than both other subspecies and higher scale counts than E. r. rupestre. While E. r. rupestre and E. r. piersoni are widespread and abundant within their respective ranges, E. r. uphapeense has a disjunct range and is often uncommon where it occurs. Etheostoma r. uphapeense should be monitored where it occurs to discern population trends.
... Numbers at nodes are Bayesian posterior probabilities. b Time calibrated DensiTree plot of species tree topologies depicting gene histories support is consistent with their similarity in meristic traits that are often used to discover and delimit closely related species of teleosts (Berendzen et al. 2009;Kozal et al. 2017;Near et al. 2017). Although there is no morphological or genetic data available for B. veneris Sauvage and there is no genetic data available for B. psychrolutes, the high meristics exhibited in the latter provide a viable hypothesis that the species is more closely related to B. chilensis and B. diacanthus. ...
Article
Full-text available
Notothenioids are among the most intensively studied lineages of marine fishes. However, notothenioid research is predominately focused on the approximately 100 species of Antarctic cryonotothenioids. Far less attention is devoted to the non-Antarctic lineages Bovichtidae, Pseudaphritis urvillii, and Eleginops maclovinus, all of which originated prior to the diversification of cryonotothenioid species. Here we utilize DNA sequence data from mitochondrial and nuclear genes, as well as meristic trait morphology to investigate the evolutionary history of Bovichtidae. Bovichtus is the only polytypic lineage of early diverging non-Antarctic notothenioids providing a unique opportunity to contextualize the diversification dynamics of cryonotothenioids with their non-Antarctic relatives. We find strong evidence that species of Bovichtus represent a recent evolutionary radiation with divergence times similar to those estimated among the most closely related species of cryonotothenioids. The divergence in traditional meristic trait morphology among species of Bovichtus is consistent with their phylogenetic relationships. The phylogeny of Bovichtus implies the wide geographic distribution of species in the clade is likely the result of West Wind drift-driven dispersal. The phylogeny and divergence time estimates results reject a hypothesis that species persistence in Bovichtus reflects long periods of evolutionary stasis. Instead, we hypothesize that patterns of extinction and diversification in Bovichtus closely mirror those observed in their Antarctic relatives.
... Both Horton Hobbs Jr. and Raymond Bouchard were aware of Glareocola in the Western Highland Rim (Hobbs 1953;Bouchard & Bouchard 1995). Yet, records of Glareocola species in these systems are exceedingly rare, despite intensive sampling for numerous aquatic organisms, including fishes, crayfishes, mussels, and macroinvertebrates (e.g., Ortmann 1924;Bouchard & Bouchard 1995;Ahlstedt et al. 2017;Near et al. 2017). ...
Article
Cambarus polypilosus sp. nov. is a stream-dwelling crayfish endemic to tributaries in the Buffalo and lower Duck River drainage, and a reach of the lower Tennessee River in the Western Highland Rim of West-Central Tennessee, U.S.A. The new species is closely allied to the three members of the former subgenus Glareocola, but can be differentiated from each by a combination of characters, including body size, coloration, spination, setation, and form I male gonopod morphology. Several meristic measurements and ratios also differentiate C. polypilosus sp. nov. from Cambarus friaufi, to which it is morphologically most similar. Cambarus polypilosus sp. nov. appears to be common in cherty gravel and cobble habitats, where it is typically found in interstices at depths of 0.3 m or more below the substrate surface.
Article
Full-text available
The Stripetail Darter, Etheostoma kennicotti (Putnam), is widely distributed in tributaries of the lower Ohio River, the upper Green River system, the Clarks River system, throughout the Tennessee River system, the Laurel River system, and the upper Cumberland River system. Etheostoma cumberlandicum Jordan and Swain was described in 1883 from a population sampled in the Clear Fork system that drains to the upper Cumberland. A previous morphological analysis led to the placement of E. cumberlandicum into the synonymy of E. kennicotti. Results from molecular phylogenetic and relaxed molecular clock analyses, genetic variation at 25 microsatellite loci, morphological disparity in meristic traits, and variation in pigmentation from specimens sampled throughout the geographic distribution of E. kennicotti (s.l.) indicate E. cumberlandicum is a distinct species and there are multiple undescribed species masquerading as E. kennicotti. We elevate Etheostoma cumberlandicum out of synonymy and propose Moonbow Darter as the common name for the species. The results of the phylogenetic analyses are discussed in the context of the historical biogeography of rivers draining the Eastern Highlands of North America.
Article
Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one of the world’s most popular groups of freshwater sport fish, has a complicated taxonomic history. The results of ddRAD phylogenomic analyses do not provide support for the current taxonomy that recognizes two species, L. megalotis and L. peltastes, in the L. megalotis complex. Instead, evidence from phylogenomics and phenotype warrants recognizing six relatively ancient evolutionary lineages in the complex. The introgressed and hybridizing populations in the L. megalotis complex are localized and appear to be the result of secondary contact or rare hybridization events between non-sister species. Segregating admixed populations from our multispecies coalescent analyses identifies six species with moderate to high genealogical divergence, whereas including admixed populations drives all but one lineage below the species threshold of genealogical divergence. Segregation of admixed individuals also helps reveal phenotypic distinctiveness among the six species in morphological traits used by ichthyologists to discover and delimit species over the last two centuries. Our protocols allow for the identification and accommodation of hybridization and introgression in species delimitation. Genomic-based species delimitation validated with multiple lines of evidence provides a path towards the discovery of new biodiversity and resolving long-standing taxonomic problems.
Article
Percina freemanorum, the Etowah Bridled Darter, is described as a new species endemic to the Etowah River system in Georgia, specifically in Long Swamp Creek, Amicalola Creek, and the upper portion of the Etowah River. The earliest collection records for Percina freemanorum date to 1948 and in 2007 the species was delimited as populations of Percina kusha. Our investigation into the systematics of Percina kusha is motivated by the uncertain status of populations in the Coosawattee River system and observed morphological disparity in several meristic traits between populations in the Conasauga and Etowah River systems. Our analyses of morphological divergence, nuclear genotypes, and mitochondrial DNA (mtDNA) haplotype networks confirm the distinctiveness of Percina freemanorum. Morphologically, Percina freemanorum is distinguished from Percina kusha through lower average numbers of lateral line scales (65.4 vs. 72.3); rows of transverse scales (18.0 vs. 21.4); scales around the caudal peduncle (22.1 vs. 24.9); and modally more pectoral fin rays (14 vs. 13). The two species are not reciprocally monophyletic in phylogenetic analysis of mtDNA sequences, but the two species do not share mtDNA haplo-types. Analysis of up to 158,000 double digest restriction-site associated DNA (ddRAD) sequenc-ing loci resolve each of the two species as reciprocally monophyletic and genomic clustering analysis of single nucleotide polymorphisms identifies two genetic clusters that correspond to the morphologically delimited Percina freemanorum and Percina kusha.
Article
We provide a description of the Blueface Darter, Etheostoma cyanoprosopum, which is distributed in the upper Sipsey Fork of the Mobile Basin and the upper portion of the Bear Creek system in the Tennessee River Drainage. The distinctiveness of Etheostoma cyanoprosopum is assessed through analysis of morphological variation and molecular phylogenetic diversity within the Etheostoma zonistium species complex. In addition to analyzing disparity of morphometric and meristic traits, we present phylogenetic analyses of a mitochondrial gene and two nuclear genes and identify genetic clusters through analysis of 25 microsatellite loci. In the mitochondrial DNA (mtDNA) gene tree, Etheostoma cyanoprosopum is resolved as the sister lineage to a clade containing all other species of the Etheostoma zonistium complex. Etheostoma zonistium is paraphyletic with respect to both Etheostoma pyrrhogaster and Etheostoma cervus, which do not resolve as sister species in the mtDNA gene tree. The two nuclear gene trees are much less resolved, but the S7 ribosomal protein intron 1 (S7) gene tree resolves Etheostoma cyanoprosopum and all sampled populations of Etheostoma zonistium as a clade with strong Bayesian posterior node support. Etheostoma cyanoprosopum is morphologically differentiated from Etheostoma zonistium by a shallower body, a more elongate nape, a higher number of lateral line scales, a higher number of transverse scale rows, and differences in coloration.
Article
Full-text available
It is not known how environmental pressures and sexual selection interact to influence the evolution of extravagant male traits. Sexual and natural selection are often viewed as antagonistic forces shaping the evolution of visual signals, where conspicuousness is favored by sexual selection and crypsis is favored by natural selection. While typically investigated independently, the interaction between natural and sexual selection remains poorly understood. Here, we investigate whether sexual dichromatism evolves stochastically, independent from, or in concert with habitat use in darters, a species-rich lineage of North American freshwater fishes. We find the evolution of sexual dichromatism is coupled to habitat use in darter species. Comparative analyses reveal that mid-water darter lineages exhibit a narrow distribution of dichromatism trait space surrounding a low optimum, suggesting a constraint imposed on the evolution of dichromatism, potentially through predator-mediated selection. Alternatively, the transition to benthic habitats coincides with greater variability in the levels of dichromatism that surround a higher optimum, likely due to relaxation of the predator-mediated selection and heterogeneous microhabitat-dependent selection regimes. These results suggest a complex interaction of sexual selection with potentially two mechanisms of natural selection, predation and sensory drive, that influence the evolution of diverse male nuptial coloration in darters. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
Article
Full-text available
We examined geographic variation within the Ashy Darter, Etheostoma cinereum, of the mitochondrially enconded cyto-chrome b gene (cyt b) and nuclear recombination activation gene 1 (RAG1) as well as pigmentation, 6 meristic variables, and 20 morphometric variables for patterns indicative of speciation within the complex. Four geographically disjunct en-tities were identified by at least one of the datasets corresponding to the Cumberland, Duck, Elk, and upper Tennessee river systems. Monophyly of cyt b and RAG1 sequences, modal meristic differences, moderate morphometric divergence, and unique pigmentation in specimens from the Cumberland River suggest this entity represents an evolutionary species under many different species concepts and is described herein as Etheostoma maydeni. Other populations exhibit varying degrees of divergence in the different datasets and have conflicting relationships in phylogenetic analyses using cyt b and RAG1 sequences, leaving the evolutionary history and taxonomic status of the Duck, Elk and upper Tennessee populations unclear.
Article
Full-text available
As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.
Article
Full-text available
Interspecific divergence along a benthic to pelagic habitat axis is ubiquitous in freshwater fishes inhabiting lentic environments. In this study, we examined the influence of this habitat axis on the macroevolution of a diverse, lotic radiation using mtDNA and nDNA phylogenies for eastern North America's most species-rich freshwater fish clade, the open posterior myodome (OPM) cyprinids. We used ancestral state reconstruction to identify the earliest benthic to pelagic transition in this group and generated fossil-calibrated estimates of when this shift occurred. This transition could have represented evolution into a novel adaptive zone, and therefore, we tested for a period of accelerated lineage accumulation after this historical habitat shift. Ancestral state reconstructions inferred a similar and concordant region of our mtDNA and nDNA based gene trees as representing the shift from benthic to pelagic habitats in the OPM clade. Two independent tests conducted on each gene tree suggested an increased diversification rate after this inferred habitat transition. Furthermore, lineage through time analyses indicated rapid early cladogenesis in the clade arising after the benthic to pelagic shift. A burst of diversification followed the earliest benthic to pelagic transition during the radiation of OPM cyprinids in eastern North America. As such, the benthic/pelagic habitat axis has likely influenced the generation of biodiversity across disparate freshwater ecosystems.
Article
Full-text available
We present STRUCTURE HARVESTER (available at http://taylor0.biology.ucla.edu/structureHarvester/), a web-based program for collating results generated by the program STRUCTURE. The program provides a fast way to assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data. In addition, STRUCTURE HARVESTER will reformat data for use in downstream programs, such as CLUMPP. KeywordsStructure–Population structure–Population genetics–Evanno method–Visualization–Clustering
Article
Full-text available
Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data.Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.Contact: peter@biomatters.com
Article
Full-text available
Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk
Article
Full-text available
Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
Article
Full-text available
Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of North American freshwater fishes. With a near-complete taxon sampling of close to 250 species, we aim to investigate strategies for efficient multilocus data sampling and the estimation of divergence times using relaxed-clock methods when a clade lacks a fossil record. Our phylogenetic data set comprises a single mitochondrial DNA (mtDNA) gene and two nuclear genes sampled from 245 of the 248 darter species. This dense sampling allows us to determine if a modest amount of nuclear DNA sequence data can resolve relationships among closely related animal species. Darters lack a fossil record to provide age calibration priors in relaxed-clock analyses. Therefore, we use a near-complete species-sampled phylogeny of the perciform clade Centrarchidae, which has a rich fossil record, to assess two distinct strategies of external calibration in relaxed-clock divergence time estimates of darters: using ages inferred from the fossil record and molecular evolutionary rate estimates. Comparison of Bayesian phylogenies inferred from mtDNA and nuclear genes reveals that heterospecific mtDNA is present in approximately 12.5% of all darter species. We identify three patterns of mtDNA introgression in darters: proximal mtDNA transfer, which involves the transfer of mtDNA among extant and sympatric darter species, indeterminate introgression, which involves the transfer of mtDNA from a lineage that cannot be confidently identified because the introgressed haplotypes are not clearly referable to mtDNA haplotypes in any recognized species, and deep introgression, which is characterized by species diversification within a recipient clade subsequent to the transfer of heterospecific mtDNA. The results of our analyses indicate that DNA sequences sampled from single-copy nuclear genes can provide appreciable phylogenetic resolution for closely related animal species. A well-resolved near-complete species-sampled phylogeny of darters was estimated with Bayesian methods using a concatenated mtDNA and nuclear gene data set with all identified heterospecific mtDNA haplotypes treated as missing data. The relaxed-clock analyses resulted in very similar posterior age estimates across the three sampled genes and methods of calibration and therefore offer a viable strategy for estimating divergence times for clades that lack a fossil record. In addition, an informative rank-free clade-based classification of darters that preserves the rich history of nomenclature in the group and provides formal taxonomic communication of darter clades was constructed using the mtDNA and nuclear gene phylogeny. On the whole, the appeal of mtDNA for phylogeny inference among closely related animal species is diminished by the observations of extensive mtDNA introgression and by finding appreciable phylogenetic signal in a modest sampling of nuclear genes in our phylogenetic analyses of darters.
Article
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations (“admixture linkage disequilibium”). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.
Article
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
Article
GenBank(®) (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for 370 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or the NCBI Submission Portal. GenBank staff assign accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Nucleotide database, which links to related information such as taxonomy, genomes, protein sequences and structures, and biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. Recent updates include changes to policies regarding sequence identifiers, an improved 16S submission wizard, targeted loci studies, the ability to submit methylation and BioNano mapping files, and a database of anti-microbial resistance genes.
Article
Etheostoma nebra, the Buck Darter, is described as a new species endemic to the Buck Creek system of the Cumberland River drainage in Kentucky, USA. The earliest collection records of Etheostoma nebra date to 1955 and were considered a population of Etheostoma virgatum. Etheostoma nebra is delimited through morphological comparisons with Etheostoma virgatum and phylogenetic analyses using DNA sequences from a mitochondrial gene and five nuclear genes. Etheostoma nebra is distinguished from Etheostoma virgatum by a lower number of total lateral scales, fewer pored lateral scales and modally 13 compared with 12 pectoral fin rays. The two species also differ in patterns of pigmentation and nuptial male coloration. In the molecular phylogenies, Etheostoma nebra is not resolved as the sister species of Etheostoma virgatum. A review of all museum collection records of Etheostoma nebra and extensive field surveys in the Buck Creek system demonstrate a dramatic decline of the species over the past 30 years. Collections made from 1955 to 1981 show that Etheostoma nebra was widespread throughout the Buck Creek system, but the species is currently restricted to a small portion of Flat Lick Creek. Etheostoma nebra is critically imperiled based on its restricted geographic distribution and documented disappearance of populations within the Buck Creek system during the past three decades.
Article
Body size is one of the most important traits influencing an organism's ecology and a major axis of evolutionary change. We examined body size disparification in the highly speciose North American minnows (Cyprinidae), which exhibit diverse body sizes and ecologies, including the giant piscivorous pikeminnows. We estimated a novel phylogeny for 285 species based on a supermatrix alignment of seven mitochondrial and ten nuclear genes, and used this to reconstruct ancestral body sizes (log-total length) and ancestral area. Additionally, given that fishes inhabiting Pacific drainages have historically been subjected to frequent local extinctions due to periodic flooding, droughts, and low drainage connectivity, we also compared body size disparification between the highly speciose Atlantic drainages and comparatively depauperate Pacific drainages. We found that dispersal between Atlantic and Pacific drainages has been infrequent and generally occurred in minnows with southerly distributions, where drainage systems are younger and less stable. The long isolation between Atlantic and Pacific drainages has allowed for divergent patterns of morphological disparification; we found higher rates of body size disparification in minnows from the environmentally harsher Pacific drainages. We propose several possible explanations for the observed patterns of size disparification in the context of habitat stability, niche space, and species diversification. Copyright © 2015. Published by Elsevier Inc.
Article
For many KDD applications, such as detecting criminal activities in E-commerce, finding the rare instances or the outliers, can be more interesting than finding the common patterns. Existing work in outlier detection regards being an outlier as a binary property. In this paper, we contend that for many scenarios, it is more meaningful to assign to each object a degree of being an outlier. This degree is called the local outlier factor (LOF) of an object. It is local in that the degree depends on how isolated the object is with respect to the surrounding neighborhood. We give a detailed formal analysis showing that LOF enjoys many desirable properties. Using real-world datasets, we demonstrate that LOF can be used to find outliers which appear to be meaningful, but can otherwise not be identified with existing approaches. Finally, a careful performance evaluation of our algorithm confirms we show that our approach of finding local outliers can be practical.
Article
We further develop the Bayesian framework for analyzing aligned nucleotide sequence data to reconstruct phylogenies, assess uncertainty in the reconstructions, and perform other statistical inferences. We employ a Markov chain Monte Carlo sampler to sample trees and model parameter values from their joint posterior distribution. All statistical inferences are naturally based on this sample. The sample provides a most-probable tree with posterior probabilities for each clade, information that is qualitatively similar to that for the maximum-likelihood tree with bootstrap proportions and permits further inferences on tree topology, branch lengths, and model parameter values. On moderately large trees, the computational advantage of our method over bootstrapping a maximum-likelihood analysis can be considerable. In an example with 31 taxa, the time expended by our software is orders of magnitude less than that a widely used phylogeny package for bootstrapping maximum likelihood estimation would require to achieve comparable statistical accuracy. While there has been substantial debate over the proper interpretation of bootstrap proportions, Bayesian posterior probabilities clearly and directly quantify uncertainty in questions of biological interest, at least from a Bayesian perspective. Because our tree proposal algorithms are independent of the choice of likelihood function, they could also be used in conjunction with likelihood models more complex than those we have currently implemented.
Article
Conclusons based on a program of numerical taxonomy utilizing 45 characters measured in 32 species of darters resulted in the transfer of Percina crassa and P. roanoka from the subgenus Ericosma to Alvordius, the reduction of Hypohomus to a monotypic subgenus, and the creation of a ninth subgenus (Odontopholis) to contain P. cymatotaenia and an undescribed species. Diagnoses for all nine subgenera of Percina and a phylogeny of the genus are given.
Article
Percina brucethompsoni, the Ouachita Darter, is described as a new species endemic to the Oua-chita River system in the Ouachita Highlands of Arkansas. Bruce Thompson first noted the dis-tinctiveness of the new species from the nominal P. nasuta distributed in the White River and Arkansas River basins in his 1977 doctoral dissertation. The new species is delimited through morphological comparisons with P. nasuta and a phylogenetic analysis of the Percina subclade Swainia using two mitochondrial genes. More than 385 specimens were examined for the mor-phological comparisons, and 54 specimens were sampled for mitochondrial DNA sequencing. Percina brucethompsoni is distinguished from P. nasuta by a shorter snout, a broader and deeper head, six versus seven branchiostegal rays and specific patterns of lateral pigmentation on the side of the body. Phylogenetic analysis of DNA sequences sampled from two regions of the mitochon-drial genome indicate that P. brucethompsoni is the sister species of P. nasuta populations in the White River drainage. Neither P. nasuta nor P. phoxocephala are monophyletic in the mitochon-drial DNA gene tree. Specimens of P. phoxocephala from the Red River drainage are resolved as the sister lineage of a clade containing all other sampled populations of P. phoxocephala, P. brucethompsoni and P. nasuta. Percina nasuta and P. phoxocephala sampled from the Arkansas River drainage form a clade that is the sister lineage of a clade containing P. brucethompsoni and P. nasuta from the White River drainage.
Article
Recent studies determined that darters with specialized breeding strategies can exhibit deep lineage divergence over fine geographic scales without apparent physical barriers to gene flow. However, the extent to which intrinsic characteristics interact with extrinsic factors to influence population divergence and lineage diversification in darters is not well understood. This study employed comparative phylogeographic and population genetic methods to investigate the influence of life-history on gene flow, dispersal ability, and lineage divergence in two sympatric sister darters with differing breeding strategies. Our results revealed highly disparate phylogeographic histories, patterns of genetic structure, and dispersal abilities between the two species suggesting that life-history may contribute to lineage diversification in darters, especially by limiting dispersal among large river courses. Both species also showed striking differences in demographic history, indicating that extrinsic factors differentially affected each species during the Pleistocene. Collectively, our results indicate that intrinsic and extrinsic factors have influenced levels of gene flow among populations within both species examined. However, we suggest that life-history strategy may play a more important role in lineage diversification in darters than previously appreciated, a finding that has potentially important implications for understanding diversification of the rich North American freshwater fish fauna.This article is protected by copyright. All rights reserved.
Article
Phylogenetic relationships among species of Percina are unresolved. Previous sys-tematic studies of Percina have resulted in the recognition of nine subgenera, di-agnosed by external morphological characters. Throughout the history of darter taxonomy characters such as large body size, high meristics, drab coloration, and exploitation of a hyperbenthic habitat have been interpreted as pleisiomorphic. Most species of Percina exhibit these characters, and have been hypothesized to represent the ''primitive'' lineage of darters. The hypotheses that each of the poly-typic subgenera of Percina are monophyletic and that the previously defined primi-tive characters are pleisiomorphic, have not been investigated with cladistic analyses. In this investigation, complete gene sequences of the mitochondrially encoded cy-tochrome b were collected from a total of 79 individual specimens, representing nine of 10 percid genera and all 40 species of Percina. Observed patterns of cyto-chrome b evolution were very similar to those previously reported in other percid fishes. Maximum-parsimony and maximum-likelihood analyses were generally con-gruent. The majority of subgenera (Percina, Imostoma, Cottogaster, Swainia, and Odon-topholis) were recovered as monophyletic in most analyses. The subgenera Alvordius, Hadropterus, and Ericosma were never recovered as monophyletic; however, mono-phyly of Hadropterus and Ericosma could not be rejected in statistical analyses of maximum-likelihood score differences. As a result of these phylogenetic analyses, a novel classification of Percina species is proposed. The use of subgenera in Percina taxonomy is abandoned in favor of the recognition of monophyletic ''species clades.'' Reconstruction of character evolution on the hypothesized phylogenetic relationships suggest that previously identified pleisiomorphic character states in darters may actually be derived within Percina. Hypothesis testing of derived and ancestral traits in darters is complicated by uncertainty in ancestral character state reconstruction. Contributing to the lack of confidence in character optimization are inadequate sampling of Etheostoma species, short internal branches on the phylog-eny, and a high frequency of character change across the entire diversity of darters. W ITH over 180 species, Percidae is the sec-ond largest family of freshwater fishes in North America, and all but three species of North American percids are darters (subfamily Etheostomatinae). Evidence from morphology (Wiley, 1992), behavior (Page, 1985), and mtDNA sequence data (Song et al., 1998) indi-cate that darters are monophyletic. Relation-ships among genera, subgenera, and most spe-cies, however, remain unresolved. Percina is the second largest genus (40 spe-cies) of darters. Phenetic analyses of external morphological characters have been used to classify species of Percina into nine subgenera (Page, 1974, 1981). Most of the characters con-sidered were meristics, morphometric ratios, and pigmentation patterns (Page, 1974, 1981). There is no published cladistic investigation of relationships among species of Percina using dis-cretely coded morphological characters (i.e., os-teology). Percina has been hypothesized to include the plesiomorphic darters (Jordan et al., 1930; Page, 1974; Bailey and Etnier, 1988). Unlike other darter genera, species in Percina exhibit both hypothesized derived and ancestral char-acteristics. For example, Percina lenticula has been regarded as the most ''primitive'' species of Percina (Page, 1974), because it lacks bright breeding colors, has high meristics, and is the largest darter species (Page, 1974; Page and Burr, 1979). On the other hand, Percina roanoka
Article
Etheostoma virgatum has been treated as a species occupying three widely separated regions of the Cumberland River drainage in Kentucky and Tennessee. To test the hypothesis that the three widely disjunct populations of E. virgatum are monophyletic, DNA sequence data from mitochondrial and nuclear loci were gathered on E. virgatum and other species of Catonotus including all species of barcheek darters. Morphological data were analyzed from populations throughout the range of E. virgatum. The three widely separated populations of E. virgatum, although morphologically similar, do not form a monophyletic group in phylogenetic analyses of molecular data. Consistent with this result, two of the populations are described as new species. These three species had been identified as E. virgatum because of the shared presence of bold dark stripes along the side of the body, a feature not found in the other four species of barcheeks. It is unclear whether the presence of bold stripes represents retention of a pleisiomorphic trait (lost in other barcheeks) or whether the condition arose independently in these three species.
Article
Investigations of phylogenetic relationships using comparative morphological characters have led to the hypothesis that Ammocrypta is the sister taxon of the Etheostoma subgenus Ioa. Subsequent molecular analyses have not recovered this proposed relationship. In this investigation, variation in complete cytochrome b sequences sampled from 27 percid species, representing all darter genera and all species of Ammocrypta, is examined in a phylogenetic context. Third codon purine transitions are saturated when all darter species examined are compared; however, saturation is not detected in any character class among species of Ammocrypta. Maximum-parsimony analysis, which excludes potentially homoplasious character classes, and maximum-likelihood analysis of cytochrome b sequences statistically reject the hypothesis that Ammocrypta is the sister taxon of the Etheostoma subgenus Ioa. Etheostoma is not recovered as monophyletic; however, the hypothesis of monophyly cannot be rejected using maximum-parsimony and maximum-likelihood methods. Morphological characters are combined with cytochrome b sequences in a total evidence analysis of relationships within Ammocrypta. A novel hypothesis of relationships is proposed, which includes a sister-taxon relationship between A. clara and A. pellucida. With regard to relationships among species of Ammocrypta, the morphological data do not significantly conflict with the cytochrome b data. Morphological characters provide additional synapomorphies supporting the hypothesis that A. beani and A. bifascia are sister taxa. The biogeographic implications of the total evidence analysis are discussed, and the continued taxonomic placement of Ammocrypta in Etheostoma is discouraged.
Article
We describe a new species of Nothonotus from the Caney Fork River drainage, Tennessee, USA, and assess morphological variation in N. microlepidus and N. sanguifluus with specimens sam-pled from all known populations. We used Linear Discriminant Analysis (LDA) on a meristic dataset from 831 individuals to delimit species of the N. maculatus species group endemic to the Cumberland River drainage. We assigned populations to groups in the LDA on the basis of phy-logenetic lineages identified in previous studies of Nothonotus darters using mitochondrial and nuclear gene DNA sequences. The discriminant functions were able to reasonably differentiate among N. microlepidus, N. sanguifluus and the new species of Nothonotus. The discriminant functions did not reliably differentiate among N. sanguifluus populations sampled from different tributaries in the Cumberland River drainage. Two populations of N. sanguifluus were not in-cluded in the LDA because of limited material and thus could not be assigned to a group; these are tentatively assigned to N. sanguifluus partially on the basis of predictions using the model from the LDA and the estimated phylogeny. Phylogenetic and multivariate analyses of morpho-logical characters allow differentiation of the new species from its closest relatives, N. mi-crolepidus and N. sanguifluus. Additionally, the new species can be differentiated from other species in the N. maculatus species group with a combination of characters, including having red in all median fins of breeding-condition males, the presence of a suborbital bar, extensive red in the pectoral fins, and lower counts of lateral line scales as compared with N. sanguifluus. With the description of this new species of Nothonotus there are now five described endemic darters oc-curring in the Caney Fork above Great Falls.
Article
Percina burtoni (Percidae: subgenus Percina), Blotchside Logperch, historically occupied much of the Tennessee and Cumberland River drainages, but is now restricted to highly fragmented populations where they occur at low densities. Widespread impoundment and subsequent river alteration over the past 60 years has eliminated many populations and reduced the potential for dispersal and gene flow between extant populations. We examined genetic variation at two mitochondrial genes, cytochrome b and ND2, from 74 individuals in ten populations to assess genetic population structure within P. burtoni. These data, as well as the results of recent surveys, were used to assess conservation priorities for this imperiled fish. Phylogenetic analysis recovered two well supported and highly differentiated clades within P. burtoni, one containing individuals from the Duck River drainage and a small tributary to the lower Tennessee River, and the other composed of individuals from the middle and upper Tennessee River drainage. The Duck River clade exhibits lower haplotypic and nucleotide diversity than the Tennessee River clade and shows little geographic partitioning. In contrast, most populations of middle and upper Tennessee River P. burtoni possess unique haplotypes and show strong geographic differentiation. Historical isolation of small populations in tributary systems of the upper Tennessee Basin is hypothesized to be responsible for observed patterns of differentiation within this clade. These results have implications for reintroduction programs and population augmentation with captive-reared individuals. Propagation activities should take fine-scale geographic structure into account prior to any reintroduction activities.
Article
This thesis reports the results of a survey of the fishes of the Big South Fork of the Cumberland River system in Tennessee and Kentucky. This system represents the southeasterly extension of the Cumberland River system. The survey was conducted from June 1968 to September 1969 with the majority of the collecting being made in the summer months of both years. A variety of collecting techniques were employed. A list of the species of fishes collected in the system is presented with notes on their habitat and distribution, both within the system, and in comparison with other systems. Included also is a literature survey and a description of the river system with notes on the current state of pollution in the system. A discussion of the species distribution is included, and possible reasons for the distribution are given. Results of the survey indicate a strong possibility for stream capture between the Big South Fork system and other parts of the Cumberland River system. However, more investigation is needed in this regard.
Article
Introgressive hybridization and incomplete lineage sorting complicate the inference of phylogeny, and available species-tree methods do not simultaneously account for these processes. Both hybridization and ancestral polymorphism have been invoked to explain divergent phylogenies inferred from different datasets for Stigmacerca, a clade of 11 North American darter species. Species of Stigmacerca are characterized by a mating system involving parental care with males guarding nesting territories and fertilized eggs. Males of four species of Stigmacerca develop egg-mimic nuptial structures on their second dorsal fins during the breeding season. Previous phylogenies suggest contrasting scenarios for the evolution of this nuptial trait. Using a combination of coalescent-based methods, we analyzed a dataset comprising a mitochondrial gene and 15 nuclear loci to estimate relationships and simultaneously test for introgressive hybridization. Our analyses identified several instances of interspecific gene flow involving both cytoplamsmic haplotypes and nuclear alleles. The new phylogeny was used to infer a single origin and recent loss of egg-mimic structures in Stigmacerca and led to the discovery of a phylogenetically distinct species. Our results highlight the limited strategies available to account for introgressive hybridization in the inference of species relationships and the likely effects of this process on reconstructing trait evolution.
Article
abstract: This is the third compilation of imperiled (i.e., endangered, threatened, vulnerable) plus extinct freshwater and diadromous fishes of North America prepared by the American Fisheries Society's Endangered Species Committee. Since the last revision in 1989, imperilment of inland fishes has increased substantially. This list includes 700 extant taxa representing 133 genera and 36 families, a 92% increase over the 364 listed in 1989. The increase reflects the addition of distinct populations, previously non-imperiled fishes, and recently described or discovered taxa. Approximately 39% of described fish species of the continent are imperiled. There are 230 vulnerable, 190 threatened, and 280 endangered extant taxa, and 61 taxa presumed extinct or extirpated from nature. Of those that were imperiled in 1989, most (89%) are the same or worse in conservation status; only 6% have improved in status, and 5% were delisted for various reasons. Habitat degradation and nonindigenous species are the main threats to at-risk fishes, many of which are restricted to small ranges. Documenting the diversity and status of rare fishes is a critical step in identifying and implementing appropriate actions necessary for their protection and management.
Article
The greenside darter, Etheostoma blennioides is a small benthic fish found in fast-flowing streams in eastern North America. In Canada, this species is native to three, and introduced into one, Great Lakes tributaries in southwestern Ontario. It is currently listed as a species of Special Concern. To characterize population genetic structure and diversity in the Canadian populations of greenside darter, eight polymorphic microsatellite markers were developed for the species. The polymerase chain reaction primers were tested between 32 and 60 individuals from the Sydenham River and yielded a high number of alleles (four to 42 per locus), and observed heterozygosities ranging from 0.14 to 0.82.
Article
The modified midventral scales on Percina males probably function to induce tactile stimulation of the female during spawning. The midbelly row of modified scales presumably evolved as a result of increased selective advantage of larger and more strongly toothed scales on the midventer; primitive and intermediate conditions in the evolution of the modified scales as well as a distinctly modified row are extant, The morphology of the scales varies seasonally and ontogenetically. The scales are permanent rather than deciduous as described in the literature interspecific variation of the modified scales is pronounced intersubgenerically. less so intrasubgenerically.
Article
Percina nebulosa and Percina bimaculata have been considered synonyms of P. caprodes for over 130 years. The taxonomic history of P. nebulosa is complicated by the fact that the name is preoc-cupied by Perca nebulosa Rafinesque. Percina bimaculata Haldeman is the available and appropri-ate name for this species, and the Chesapeake Logperch is the proposed common name. Recent phylogenetic analyses of mitochondrial DNA gene sequences support the hypothesis that P. bi-maculata is a distinct species; however, a morphological comparison between P. bimaculata and other logperch darter species has never been published. An examination of morphological charac-ters and a new molecular phylogeny of both mitochondrial and nuclear gene sequence data sup-port the recognition of P. bimaculata as a distinct species most closely related to P. kathae and P. austroperca. Historically, P. bimaculata was distributed in the lower Susquehanna River Basin of Pennsylvania and Maryland and the middle to lower Potomac River Basin of Maryland, Virginia and the District of Columbia, USA. The species has not been recorded from the Potomac Basin since the 1930s and is currently found only in the lower Susquehanna River Basin. The restricted geographic distribution and extirpation from the Potomac Basin indicates that P. bimaculata is an imperiled species and may warrant protection under the Endangered Species Act of 1973. The mo-lecular phylogeny also indicates that populations recognized as P. caprodes sampled from the upper Mississippi River Basin in Illinois, Wisconsin and Minnesota are not closely related to P. caprodes populations sampled from the Ohio, Tennessee, White and Hudson river drainages.
Article
We further develop the Bayesian framework for analyzing aligned nucleotide sequence data to reconstruct phylog- enies, assess uncertainty in the reconstructions, and perform other statistical inferences. We employ a Markov chain Monte Carlo sampler to sample trees and model parameter values from their joint posterior distribution. All statistical inferences are naturally based on this sample. The sample provides a most-probable tree with posterior probabilities for each clade, information that is qualitatively similar to that for the maximum-likelihood tree with bootstrap proportions and permits further inferences on tree topology, branch lengths, and model parameter values. On mod- erately large trees, the computational advantage of our method over bootstrapping a maximum-likelihood analysis can be considerable. In an example with 31 taxa, the time expended by our software is orders of magnitude less than that a widely used phylogeny package for bootstrapping maximum likelihood estimation would require to achieve comparable statistical accuracy. While there has been substantial debate over the proper interpretation of bootstrap proportions, Bayesian posterior probabilities clearly and directly quantify uncertainty in questions of biological interest, at least from a Bayesian perspective. Because our tree proposal algorithms are independent of the choice of likelihood function, they could also be used in conjunction with likelihood models more complex than those we have currently implemented.
Article
The number of alleles in a sample (allelic richness) is a fundamental measure of genetic diversity. However, this diversity measure has been difficult to use because large samples are expected to contain more alleles than small samples. The statistical technique of rarefaction compensates for this sampling disparity. Here I introduce a computer program that performs rarefaction on private alleles and hierarchical sampling designs.
Article
Darters are a species-rich radiation of small benthic and benthic-associated stream fishes that comprise approximately 20% of the diversity of the North American freshwater fish fauna. Here, we gather data from 165, or 87%, of described species and use this information to characterize the morphological diversity of the darter radiation. We focus on characters of the oral jaws known to function in prey capture and consumption in other perciform taxa in order to explicitly link morphological diversity to ecological diversity. In addition to a quantitative description of the morphospace occupied by darters, we identify several instances of significant morphological convergence. We also describe three groups of darter species that exhibit unusual jaw morphologies that are used in previously undescribed prey capture behaviours. Despite these new ecomorphs, we find that darters exhibit relatively low variation in trophic morphology when compared with two other radiations of teleost fishes, and that the observed variation is related more to differences in microhabitat use than to differences in prey type. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 30–45.
Article
This paper discusses advantages and shortcomings of the S environment for multivariable geostatistics, in particular when extended with the gstat package, an extension package for the S environments (R, S-Plus). The gstat S package provides multivariable geostatistical modelling, prediction and simulation, as well as several visualisation functions. In particular, it makes the calculation, simultaneous fitting, and visualisation of a large number of direct and cross (residual) variograms very easy. Gstat was started 10 years ago and was released under the GPL in 1996; gstat.org was started in 1998. Gstat was not initially written for teaching purposes, but for research purposes, emphasising flexibility, scalability and portability. It can deal with a large number of practical issues in geostatistics, including change of support (block kriging), simple/ordinary/universal (co)kriging, fast local neighbourhood selection, flexible trend modelling, variables with different sampling configurations, and efficient simulation of large spatially correlated random fields, indicator kriging and simulation, and (directional) variogram and cross variogram modelling. The formula/models interface of the S language is used to define multivariable geostatistical models. This paper introduces the gstat S package, and discusses a number of design and implementation issues. It also draws attention to a number of papers on integration of spatial statistics software, GIS and the S environment that were presented on the spatial statistics workshop and sessions during the conference Distributed Statistical Computing 2003.
Article
In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models. These methods allow millions of partitioning schemes to be compared in realistic time frames and so permit the objective selection of partitioning schemes even for large multilocus DNA data sets. We demonstrate that these methods significantly outperform previous approaches, including both the ad hoc selection of partitioning schemes (e.g., partitioning by gene or codon position) and a recently proposed hierarchical clustering method. We have implemented these methods in an open-source program, PartitionFinder. This program allows users to select partitioning schemes and substitution models using a range of information-theoretic metrics (e.g., the Bayesian information criterion, akaike information criterion [AIC], and corrected AIC). We hope that PartitionFinder will encourage the objective selection of partitioning schemes and thus lead to improvements in phylogenetic analyses. PartitionFinder is written in Python and runs under Mac OSX 10.4 and above. The program, source code, and a detailed manual are freely available from www.robertlanfear.com/partitionfinder.
Article
The rapid accumulation of multilocus data sets has led to dramatic advances in methodologies for estimating evolutionary relationships among closely related species, but relatively less advancement has been made in methods for discriminating between competing species delimitation hypotheses. Multilocus data sets provide an advantage in testing species delimitation scenarios because they offer a direct test of species monophyly and aid in the biological interpretation of such phenomena as allele-sharing and deep coalescent events. Most species tree estimation methods that are designed to analyze multilocus data sets require the a priori assignment of individuals to species categories and therefore do not provide a strategy to directly test competing species delimitation scenarios. An approach was recently proposed that utilizes a coalescent-based species tree estimation method to inform species delimitation decisions by comparing likelihood scores that measure the fit of gene trees within a given species tree. We use a multilocus nuclear and mitochondrial DNA sequence data set to both reexamine a recently proposed species delimitation scenario in the Etheostoma simoterum species complex and test the utility of species tree estimation methods in testing species delimitation hypotheses. Descriptions of species in the E. simoterum species complex of snubnose darters, a group of six teleost freshwater fish species, are based largely on male nuptial coloration. Most of the putative species are nonmonophyletic at every examined locus. Using a novel combination of Bayesian-estimated gene tree topologies, Bayesian phylogenetic species tree inferences, coalescent simulations, and examination of phenotypic variation, we assess the occurrence of shared alleles among species, and we propose that results from our analyses support a three-species rather than a six-species delimitation scenario in the E. simoterum complex. We found that comparing likelihood scores from the species tree estimation approach used across many potential delimitation scenarios resulted in a systematic bias toward over-splitting in the E. simoterum complex and failed to support a species delimitation scenario that was consistent with geography, phenotype, or any previous species delimitation hypothesis. Despite common expectations, we demonstrate that application of molecular approaches to species delimitation can result in the recognition of fewer, instead of a larger number of species. In addition, our analyses highlight the importance of phenotypic character information in providing an independent assessment of alternative species delimitation hypotheses in the E. simoterum species complex.