John G. Lundberg

Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity

The Making of Amazonian Diversity The biodiversity of the Amazon Basin is legendary, but the processes by which it has been generated have been debated. In the late 20th century the prevalent view was that the engine of diversity was repeated contraction and expansion of forest refugia during the past 3 million years or so. Hoorn et al. (p. 927) analyze findings from a diverse range of disciplines, including molecular phylogeny, ecology, sedimentology, structural geology, and palaeontology, to offer an overview of the entire history of this region during the Cenozoic era (66 million years ago). The uplift of the Andes was a pivotal event in the evolution of Amazonian landscapes because it continually altered river drainage patterns, which in turn put a variety of pressures on organisms to adapt to changing conditions in a multiplicity of ways. Hence, the diversity of the modern biota of the Amazon has more ancient origins than previously thought. The Amazonian rainforest is arguably the most species-rich terrestrial ecosystem in the world, yet the timing of the origin and evolutionary causes of this diversity are a matter of debate. We review the geologic and phylogenetic evidence from Amazonia and compare it with uplift records from the Andes. This uplift and its effect on regional climate fundamentally changed the Amazonian landscape by reconfiguring drainage patterns and creating a vast influx of sediments into the basin. On this “Andean” substrate, a region-wide edaphic mosaic developed that became extremely rich in species, particularly in Western Amazonia. We show that Andean uplift was crucial for the evolution of Amazonian landscapes and ecosystems, and that current biodiversity patterns are rooted deep in the pre-Quaternary.

Freshwater Ecoregions of the World: A New Map of Biogeographic Units for Freshwater Biodiversity Conservation

ABSTRACT We present a new map depicting the first global biogeographic regionalization of Earths freshwater systems. This map of freshwater ecoregions is based on the distributions and compositions of freshwater fish species and incorporates major ecological and evolutionary patterns. Covering virtually all freshwater habitats on Earth, this ecoregion map, together with associated species data, is a useful tool for underpinning global and regional conservation planning efforts (particularly to identify outstanding and imperiled freshwater systems); for serving as a logical framework for large-scale conservation strategies; and for providing a global-scale knowledge base for increasing freshwater biogeographic literacy. Preliminary data for fish species compiled by ecoregion reveal some previously unrecognized areas of high biodiversity, highlighting the benefit of looking at the worlds freshwaters through a new framework.

Finding Our Way through Phenotypes

Imagine if we could compute across phenotype data as easily as genomic data; this article calls for efforts to realize this vision and discusses the potential benefits.

Taxonomic Impediment or Impediment to Taxonomy? A Commentary on Systematics and the Cybertaxonomic-Automation Paradigm

Marcelo R. de Carvalho AE Flavio A. Bockmann AE Dalton S. Amorim AE Carlos Roberto F. Brandao AE Mario de Vivo AE Jose L. de Figueiredo AE Heraldo A. Britski AE Mario C. C. de Pinna AE Naercio A. Menezes AE Fernando P. L. Marques AE Nelson Papavero AE Eliana M. Cancello AE Jorge V. Crisci AE John D. McEachran AE Robert C. Schelly AE John G. Lundberg AE Anthony C. Gill AE Ralf Britz AE Quentin D. Wheeler AE Melanie L. J. Stiassny AE Lynne R. Parenti AE Larry M. Page AE Ward C. Wheeler AE Julian Faivovich AE Richard P. Vari AE Lance Grande AE Chris J. Humphries AE Rob DeSalle AE Malte C. Ebach AE Gareth J. Nelson

Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature

Background The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. Methodology/Principal Findings We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. Conclusions/Significance The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.

Phenex: ontological annotation of phenotypic diversity.

Background Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. Methodology/Principal Findings Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. Conclusions/Significance Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age

Abstract The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies anatomy ontology with the goal of capturing anatomical data in a systematic and computable manner. An ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies anatomy ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebrafish terms specified as subtypes of teleost terms. We found that the details of ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies anatomy ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways.

Gladioglanis conquistador N. Sp. from Ecuador with Diagnoses of the Subfamilies Rhamdiinae Bleeker and Pseudopimelodinae N. Subf. (Siluriformes: Pimelodidae)

reduced vomer, low number of pectoral-fin rays, ornate pectoral spines, elongate coracoid keel, short but stout dorsal-fin spine, and dorso-ventral asymmetry of caudal-fin ray numbers. Gladioglanis conquistador n. sp., from the Rio Napo basin of Ecuador, is distinguished from its only congener, G. machadoi, by phylogenetically derived features (shorter dorsal-fin spine, anteriormost dorsal-fin pterygiophore in contact with neural spine of vertebra seven, 48-51 vertebrae) and several primitive features. The Rhamdiinae Bleeker is diagnosed by derived conditions of the transverse processes of vertebra four; vertical lamina on the Weberian centra; levator operculi crest on the hyomandibular bone; and quadrate and mesethmoid bones. Tentative subgroups within the Rhamdiinae are suggested based on putative synapomorphies. The Pseudopimelodinae n. subf. is diagnosed by derived conditions of the lateral ethmoid wing; metapterygoid, endopterygoid, and ectopterygoid; proximal radials of the dorsal fin; and hypohyal bones. Within the Pseudopimelodinae, Zungaro is proposed as the sister group of Microglanis, Pseudopimelodus and Lophiosilurus. Derived conditions of oral lip folds and sulci are surveyed across the Siluriformes and it is concluded that, taken alone, the similarity of derived lip structures shared by the Rhamdiinae and most members of Pseudopimelodinae provides only weak evidence for a sister-group relationship between them.

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species. Initial results using a suite of standard methodologies revealed conflicting phylogenetic signal, which supports ten alternative evolutionary histories among early otophysan lineages. By contrast, GGI revealed that the vast majority of gene genealogies supports a single tree topology grounded on morphology that was not obtained by previous molecular studies. We also reanalysed published data sets for exemplary groups with recalcitrant resolution to assess the power of this approach. GGI supports the notion that ctenophores are the earliest-branching animal lineage, and adds insight into relationships within clades of yeasts, birds and mammals. GGI opens up a promising avenue to account for incompatible signals in large data sets and to discern between estimation error and actual biological conflict explaining gene tree discordance.

A Major Food Web Component in the Orinoco River Channel: Evidence from Planktivorous Electric Fishes

Deep-water sampling of the Orinoco River main channel resulted in the collection of an unexpectedly high abundance and diversity of specialized fishes. Twenty-eight of the more than 60 species collected belong to the Gymnotiformes(New World electric or knife fishes). One of the more numerous of these, a recently described species of the genus Rhabdolichops, consumes large numbers of very small planktonic Crustacea and insect larvae. These items are captured in the very swift, turbid, and deep waters of the Orinoco. Although the strong dependence of the river food web on terrestrial and floodplain food sources is well known, the specialized capabilities of Rhabdolichops and of other fishes that occur with it indicate a significant extension of the river food web into the main channel.