Opening the Museum's Vault: Historical Field Records Preserve Reliable Ecological Data.

AbstractMuseum specimens have long served as foundational data sources for ecological, evolutionary, and environmental research. Continued reimagining of museum collections is now also generating new types of data associated with but beyond physical specimens, a concept known as "extended specimens." Field notes penned by generations of naturalists contain firsthand ecological observations associated with museum collections and comprise a form of extended specimens with the potential to provide novel ecological data spanning broad geographic and temporal scales. Despite their data-yielding potential, however, field notes remain underutilized in research because of their heterogeneous, unstandardized, and qualitative nature. We introduce an approach for transforming descriptive ecological notes into quantitative data suitable for statistical analysis. Tests with simulated and real-world published data show that field notes and our transformation approach retain reliable quantitative ecological information under a range of sample sizes and evolutionary scenarios. Unlocking the wealth of data contained within field records could facilitate investigations into the ecology of clades whose diversity, distribution, or other demographic features present challenges to traditional ecological studies, improve our understanding of long-term environmental and evolutionary change, and enhance predictions of future change.

Organismal form constrains the evolution of complex lever systems in Neotropical cichlid four-bar linkages.

The diversification of functional traits may be limited by the intrinsic constraints of organismal form (i.e., constructional constraints), owing to the differential investment in different anatomical structures. In this study, we test whether overall organismal form impacts the evolution of shape and function in complex lever systems. We examined the relationship between four-bar shape and overall head shape in two four-bar linkage systems: the oral-jaw and hyoid-neurocranium systems in Neotropical cichlids. We also investigated the strength of form-function mapping in these four-bar linkages and the impact of constraining head shape on these correlations. We quantified the shape of the head and two four-bar linkages using geometric morphometrics and compared these with the kinematic transmission coefficient of each linkage system. The shapes of both linkages were strongly correlated with their mechanical properties, and head shape appears to constrain the shape of both four-bar linkages. Head shape induced greater integration between the two linkages, was associated with stronger form-function correlations and higher rates of evolution in biomechanically important features. Head shape constraints may also contribute to a weak but significant trade-off in linkage kinematics. Elongation of the head and body, in particular, appears to minimize the impact of this trade-off, possibly through maximizing anterior-posterior space availability. However, the strength of relationships between shape and function, and the impact of head shape differed between the two linkages, with the hyoid four-bar in general showing stronger form-function relationships despite being more independent from head shape constraints.

Long-term ecological research in freshwaters enabled by regional biodiversity collections, stable isotope analysis, and environmental informatics.

Biodiversity collections are experiencing a renaissance fueled by the intersection of informatics, emerging technologies, and the extended use and interpretation of specimens and archived databases. In this article, we explore the potential for transformative research in ecology integrating biodiversity collections, stable isotope analysis (SIA), and environmental informatics. Like genomic DNA, SIA provides a common currency interpreted in the context of biogeochemical principles. Integration of SIA data across collections allows for evaluation of long-term ecological change at local to continental scales. Challenges including the analysis of sparse samples, a lack of information about baseline isotopic composition, and the effects of preservation remain, but none of these challenges is insurmountable. The proposed research framework interfaces with existing databases and observatories to provide benchmarks for retrospective studies and ecological forecasting. Collections and SIA add historical context to fundamental questions in freshwater ecological research, reference points for ecosystem monitoring, and a means of quantitative assessment for ecosystem restoration.

Ecology and the Origin of Nonephemeral Species.

AbstractResearch over the past three decades has shown that ecology-based extrinsic reproductive barriers can rapidly arise to generate incipient species-but such barriers can also rapidly dissolve when environments change, resulting in incipient species collapse. Understanding the evolution of unconditional, "intrinsic" reproductive barriers is therefore important for understanding the longer-term buildup of biodiversity. In this article, we consider ecology's role in the evolution of intrinsic reproductive isolation. We suggest that this topic has fallen into a gap between disciplines: while evolutionary ecologists have traditionally focused on the rapid evolution of extrinsic isolation between co-occurring ecotypes, speciation geneticists studying intrinsic isolation in other taxa have devoted little attention to the ecological context in which it evolves. We argue that for evolutionary ecology to close this gap, the field will have to expand its focus beyond rapid adaptation and its traditional model systems. Synthesizing data from several subfields, we present circumstantial evidence for and against different forms of ecological adaptation as promoters of intrinsic isolation and discuss alternative forces that may be significant. We conclude by outlining complementary approaches that can better address the role of ecology in the evolution of nonephemeral reproductive barriers and, by extension, less ephemeral species.

DiceCT for fishes: recommendations for pairing iodine contrast agents with µCT to visualize soft tissues in fishes.

Computed tomography (CT) scanning and other high-throughput three-dimensional (3D) visualization tools are transforming the ways we study morphology, ecology and evolutionary biology research beyond generating vast digital repositories of anatomical data. Contrast-enhanced chemical staining methods, which render soft tissues radio-opaque when coupled with CT scanning, encompass several approaches that are growing in popularity and versatility. Of these, the various diceCT techniques that use an iodine-based solution like Lugol's have provided access to an array of morphological data sets spanning extant vertebrate lineages. This contribution outlines straightforward means for applying diceCT techniques to preserved museum specimens of cartilaginous and bony fishes, collectively representing half of vertebrate species diversity. This study contrasts the benefits of using either aqueous or ethylic Lugol's solutions and reports few differences between these methods with respect to the time required to achieve optimal tissue contrast. It also explores differences in minimum stain duration required for different body sizes and shapes and provides recommendations for staining specimens individually or in small batches. As reported by earlier studies, the authors note a decrease in pH during staining with either aqueous or ethylic Lugol's. Nonetheless, they could not replicate the drastic declines in pH reported elsewhere. They provide recommendations for researchers and collections staff on how to incorporate diceCT into existing curatorial practices, while offsetting risk to specimens. Finally, they outline how diceCT with Lugol's can aid ichthyologists of all kinds in visualizing anatomical structures of interest: from brains and gizzards to gas bladders and pharyngeal jaw muscles.

Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations.

African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate the relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as the sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system. [African cichlids; Blenniiformes; Gene tree heterogeneity; Hybrid assembly; Phylogenetic network; Pseudocrenilabrinae; Species tree.].

Relaxed Feeding Constraints Facilitate the Evolution of Mouthbrooding in Neotropical Cichlids.

AbstractMultifunctionality is often framed as a core constraint of evolution, yet many evolutionary transitions involve traits taking on additional functions. Mouthbrooding, a form of parental care where offspring develop inside a parent's mouth, increases multifunctionality by adding a major function (reproduction) to a structure already serving other vital functions (feeding and respiration). Despite increasing multifunctionality, mouthbrooding has evolved repeatedly from other forms of parental care in at least seven fish families. We hypothesized that mouthbrooding is more likely to evolve in lineages with feeding adaptations that are already advantageous for mouthbrooding. We tested this hypothesis in Neotropical cichlids, where mouthbrooding has evolved four or five times, largely within winnowing clades, providing several pairwise comparisons between substrate-brooding and mouthbrooding sister taxa. We found that the mouthbrooding transition rate was 15 times higher in winnowing than in nonwinnowing clades and that mouthbrooders and winnowers overlapped substantially in their buccal cavity morphologies, which is where offspring are incubated. Species that exhibit one or both of these behaviors had larger, more curved buccal cavities, while species that exhibit neither behavior had narrow, cylindrical buccal cavities. Given the results we present here, we propose a new conceptual model for the evolution of mouthbrooding, integrating the roles of multifunctional morphology and the environment. We suggest that functional transitions like mouthbrooding offer a different perspective on multifunctionality: increasing constraints in one trait may release them for another, generating new evolutionary opportunities.

Evolution, inactivation and loss of short wavelength-sensitive opsin genes during the diversification of Neotropical cichlids.

Natural variation in the number, expression and function of sensory genes in an organism's genome is often tightly linked to different ecological and evolutionary forces. Opsin genes, which code for the first step in visual transduction, are ideal models for testing how ecological factors such as light environment may influence visual system adaptation. Neotropical cichlid fishes are a highly ecologically diverse group that evolved in a variety of aquatic habitats, including black (stained), white (opaque) and clear waters. We used cross-species exon capture to sequence Neotropical cichlid short wavelength-sensitive (SWS) opsins, which mediate ultraviolet (UV) to blue visual sensitivity. Neotropical cichlid SWS1 opsin (UV-sensitive) underwent a relaxation of selective constraint during the early phases of cichlid diversification in South America, leading to pseudogenization and loss. Conversely, SWS2a (blue-sensitive) experienced a burst of episodic positive selection at the base of the South American cichlid radiation. This burst coincides with SWS1 relaxation and loss, and is consistent with findings in ecomorphological studies characterizing a period of extensive ecological divergence in Neotropical cichlids. We use ancestral sequence reconstruction and protein modelling to investigate mutations along this ancestral branch that probably modified SWS2a function. Together, our results suggest that variable light environments played a prominent early role in shaping SWS opsin diversity during the Neotropical cichlid radiation. Our results also illustrate that long-term evolution under light-limited conditions in South America may have reduced visual system plasticity; specifically, early losses of UV sensitivity may have constrained the evolutionary trajectory of Neotropical cichlid vision.

Unraveling the systematics and evolution of the 'Geophagus' brasiliensis (Cichliformes: Cichlidae) species complex.

The 'Geophagus' brasiliensis complex is one of the most abundant groups of cichlids from eastern coastal basins in South America. Traditionally, this fish group has been recognized as incertae sedis because of phylogenetic uncertainties and unclear taxonomy. In addition, the remarkable morphological, chromosomal, and DNA variation reported over recent years in several populations of these cichlids has increased the debate about their species richness and their distributional range. Here, we tested the presence of independent evolutionary lineages within the 'G.' brasiliensis complex, addressing their taxonomic status and evolutionary relationships, including a comparative analysis of genetic and morphological patterns, based on an extensive dataset, comprising 172 sampling sites along most of their known range using a mitochondrial marker, RADseq data and geometric morphometrics. The number of putative species in the present study varied from 9 to 11 depending on the molecular species delimitation methods used. Our results revealed at least two putative new taxa ('Geophagus' sp. Doce and 'Geophagus' sp. Upper Contas). Morphometric analyses, particularly those based on Canonical Variate Analysis (CVA), revealed significant morphological differentiation between species within the main clades. On the other hand, analyses of morphological phylogenetic signal and phylomorphospace provided no evidence of adaptive differentiation among these species. Thus, diversification in the 'G.' brasiliensis complex seems to have been influenced by hydrogeological events that promoted allopatry, such as the presence of paleodrainages and distributional reconfiguration through river captures. We propose major changes in the known distribution of some species within the complex and conservatively suggest the recognition of 10 species within the 'Geophagus' brasiliensis complex, with the potential for further dividing 'G.' rufomarginatus after additional taxonomic evaluation.

When Does Form Reflect Function? Acknowledging and Supporting Ecomorphological Assumptions.

Ecomorphology is the study of relationships between organismal morphology and ecology. As such, it is the only way to determine if morphometric data can be used as an informative proxy for ecological variables of interest. To achieve this goal, ecomorphology often depends on, or directly tests, assumptions about the nature of the relationships among morphology, performance, and ecology. We discuss three approaches to the study of ecomorphology: morphometry-driven, function-driven, and ecology-driven and study design choices inherent to each approach. We also identify 10 assumptions that underlie ecomorphological research: 4 of these are central to all ecomorphological studies and the remaining 6 are variably applicable to some of the specific approaches described above. We discuss how these assumptions may impact ecomorphological studies and affect the interpretation of their findings. We also point out some limitations of ecomorphological studies, and highlight some ways by which we can strengthen, validate, or eliminate systematic assumptions.

New Myloplus from Essequibo River basin, Guyana, with discussion on the taxonomic status of Myleus pacu (Characiformes: Serrasalmidae)

A new species in the serrasalmid genus Myloplus is described from the middle Mazaruni River, Essequibo River basin, Guyana. The new species is similar to Myleus pacu and Myloplus planquettei in its silver to purplish black coloration and its overall morphology, and has a putative syntopic distribution with those species. The new species is, however, readily distinguishable from the other two by meristic counts of the unpaired fins and by differences in color pattern, primarily in males. Additionally, we provide comments on Myleus pacu and other species that have been confounded under that name.(AU)

Uma nova espécie de serrasalmídeo do gênero Myloplus é descrita do médio rio Mazaruni, bacia do rio Essequibo, Guyana. A nova espécie é similar a Myleus pacu e Myloplus planquettei pela sua coloração prateada a preto arroxeado e pela morfologia geral do corpo, e por ter suposta distribuição sintópica com essas espécies. No entanto, a nova espécie é prontamente distinguida dessas duas últimas espécies por contagens das nadadeiras não pares, e por diferenças no padrão de coloração, principalmente nos machos. Adicionalmente, fornecemos comentários sobre Myleus pacu e outras espécies que têm sido confundidas sob esse nome.(AU)

Intrinsic Constraints on the Diversification of Neotropical Cichlid Adductor Mandibulae Size.

The diversification of functional traits may be constrained by intrinsic factors, such as structural, mechanical, developmental, or physiological limitations. We explored the biomechanical and constructional constraints on the size of the major jaw closing muscles, the adductor mandibulae complex (AM), in a diverse clade of freshwater fish - the Neotropical cichlids. Using phylogenetic comparative methods, we contrasted patterns of size variation and diversification rates of three AM divisions with variables describing head size and biomechanical coefficients describing force and velocity transmission. We found that all three AM muscles examined were impacted by constructional constraints, namely, (1) the space available in the head (head length and width-all AMs), (2) competition with the eye (AM1 and AM2), (3) competition for space among the three major AM divisions (e.g., AM1 vs. AM3), and (4) potentially the shape of the lower jaw (AM2). Only AM2 size was significantly associated with lower jaw biomechanical coefficients, but opposite predictions based on force transmission (i.e., no compensation for low mechanical advantage). Diversification rates of the mass of the divisions of the AM were also not connected to the diversification rates of their biomechanical coefficients. Previously suggested compensation in AM mass for reduced force transmission among ram-feeding predators appears to be driven by overall body plan changes (lengthening of the head in elongate bodies) and only indirectly to biomechanical trade-offs. Strong constructional constraints on AM size likely limit potentially functional morphospace occupation, and highlight the highly integrated nature of ram-suction feeding functional adaptations in Neotropical cichlids. Anat Rec, 301:216-226, 2018. © 2018 Wiley Periodicals, Inc.

Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and identifies remaining conflicting clades (Cichliformes: Cichlidae: Cichlinae).

The phenotypic, geographic, and species diversity of cichlid fishes have made them a group of great interest for studying evolutionary processes. Here we present a targeted-exon next-generation sequencing approach for investigating the evolutionary relationships of cichlid fishes (Cichlidae), with focus on the Neotropical subfamily Cichlinae using a set of 923 primarily single-copy exons designed through mining of the Nile tilapia (Oreochromis niloticus) genome. Sequence capture and assembly were robust, leading to a complete dataset of 415 exons for 139 species (147 terminals) that consisted of 128 Neotropical species, six African taxa, and five Indo-Malagasy cichlids. Gene and species trees were calculated using alternative partitioning schemes and reconstruction methods. In general, all methods yielded similar topologies to previously hypothesized relationships within the Cichlinae and clarified several relationships that were previously poorly supported or in conflict. Additional work will be needed to fully resolve all aspects of Cichlinae phylogeny. Overall, this approach yielded a well-resolved phylogeny of Neotropical cichlids that will be of utility for future assessments of the evolutionary and ecological processes within this diverse group of fishes. Furthermore, the general methodology employed here of exon targeting and capture should be applicable to any group of organisms with the availability of a reference genome.

Accelerated Evolution and Functional Divergence of the Dim Light Visual Pigment Accompanies Cichlid Colonization of Central America.

Cichlids encompass one of the most diverse groups of fishes in South and Central America, and show extensive variation in life history, morphology, and colouration. While studies of visual system evolution in cichlids have focussed largely on the African rift lake species flocks, Neotropical cichlids offer a unique opportunity to investigate visual system evolution at broader temporal and geographic scales. South American cichlid colonization of Central America has likely promoted accelerated rates of morphological evolution in Central American lineages as they encountered reduced competition, renewed ecological opportunity, and novel aquatic habitats. To investigate whether such transitions have influenced molecular evolution of vision in Central American cichlids, we sequenced the dim-light rhodopsin gene in 101 Neotropical cichlid species, spanning the diversity of the clade. We find strong evidence for increased rates of evolution in Central American cichlid rhodopsin relative to South American lineages, and identify several sites under positive selection in rhodopsin that likely contribute to adaptation to different photic environments. We expressed a Neotropical cichlid rhodopsin protein invitro for the first time, and found that while its spectral tuning properties were characteristic of typical vertebrate rhodopsin pigments, the rate of decay of its active signalling form was much slower, consistent with dim light adaptation in other vertebrate rhodopsins. Using site-directed mutagenesis combined with spectroscopic assays, we found that a key amino acid substitution present in some Central American cichlids accelerates the rate of decay of active rhodopsin, which may mediate adaptation to clear water habitats.

Multilocus molecular phylogeny of the ornamental wood-eating catfishes (Siluriformes, Loricariidae, Panaqolus and Panaque) reveals undescribed diversity and parapatric clades.

Approximately two-dozen species in three genera of the Neotropical suckermouth armored catfish family Loricariidae are the only described fishes known to specialize on diets consisting largely of wood. We conducted a molecular phylogenetic analysis of 10 described species and 14 undescribed species or morphotypes assigned to the wood-eating catfish genus Panaqolus, and four described species and three undescribed species or morphotypes assigned to the distantly related wood-eating catfish genus Panaque. Our analyses included individuals and species from both genera that are broadly distributed throughout tropical South America east of the Andes Mountains and 13 additional genera hypothesized to have also descended from the most recent common ancestor of Panaqolus and Panaque. Bayesian and maximum likelihood analyses of two mitochondrial and three nuclear loci totaling 4293bp confirmed respective monophyly of Panaqolus, exclusive of the putative congener 'Panaqolus' koko, and Panaque. Members of Panaqolus sensu stricto were distributed across three strongly monophyletic clades: a clade of 10 generally darkly colored, lyretail species distributed across western headwaters of the Amazon Basin, a clade of three irregularly and narrowly banded species from the western Orinoco Basin, and a clade of 11 generally brown, broadly banded species that are widely distributed throughout the Amazon Basin. We erect new subgenera for each of these clades and a new genus for the morphologically, biogeographically and ecologically distinct species 'Panaqolus' koko. Our finding that perhaps half of the species-level diversity in the widespread genus Panaqolus remains undescribed illustrates the extent to which total taxonomic diversity of small and philopatric, yet apparently widely distributed, Amazonian fishes may remain underestimated. Ranges for two Panaqolus subgenera and the genus Panaque overlap with the wood-eating genus Cochliodon in central Andean tributaries of the upper Amazon Basin, which appear to be a global epicenter of wood-eating catfish diversity.

Continental cichlid radiations: functional diversity reveals the role of changing ecological opportunity in the Neotropics.

Adaptive radiations have been hypothesized to contribute broadly to the diversity of organisms. Models of adaptive radiation predict that ecological opportunity and ecological release, the availability of empty ecological niches and the response by adapting lineages to occupy them, respectively, drive patterns of phenotypic and lineage diversification. Adaptive radiations driven by 'ecological opportunity' are well established in island systems; it is less clear if ecological opportunity influences continent-wide diversification. We use Neotropical cichlid fishes to test if variation in rates of functional evolution is consistent with changing ecological opportunity. Across a functional morphological axis associated with ram-suction feeding traits, evolutionary rates declined through time as lineages diversified in South America. Evolutionary rates of ram-suction functional morphology also appear to have accelerated as cichlids colonized Central America and encountered renewed opportunity. Our results suggest that ecological opportunity may play an important role in shaping patterns of morphological diversity of even broadly distributed lineages like Neotropical cichlids.

Selection towards different adaptive optima drove the early diversification of locomotor phenotypes in the radiation of Neotropical geophagine cichlids.

BACKGROUND: Simpson envisaged a conceptual model of adaptive radiation in which lineages diversify into "adaptive zones" within a macroevolutionary adaptive landscape. However, only a handful of studies have empirically investigated this adaptive landscape and its consequences for our interpretation of the underlying mechanisms of phenotypic evolution. In fish radiations the evolution of locomotor phenotypes may represent an important dimension of ecomorphological diversification given the implications of locomotion for feeding and habitat use. Neotropical geophagine cichlids represent a newly identified adaptive radiation and provide a useful system for studying patterns of locomotor diversification and the implications of selective constraints on phenotypic divergence in general. RESULTS: We use multivariate ordination, models of phenotypic evolution and posterior predictive approaches to investigate the macroevolutionary adaptive landscape and test for evidence of early divergence of locomotor phenotypes in Geophagini. The evolution of locomotor phenotypes was characterized by selection towards at least two distinct adaptive peaks and the early divergence of modern morphological disparity. One adaptive peak included the benthic and epibenthic invertivores and was characterized by fishes with deep, laterally compressed bodies that optimize precise, slow-swimming manoeuvres. The second adaptive peak resulted from a shift in adaptive optima in the species-rich ram-feeding/rheophilic Crenicichla-Teleocichla clade and was characterized by species with streamlined bodies that optimize fast starts and rapid manoeuvres. Evolutionary models and posterior predictive approaches favoured an early shift to a new adaptive peak over decreasing rates of evolution as the underlying process driving the early divergence of locomotor phenotypes. CONCLUSIONS: The influence of multiple adaptive peaks on the divergence of locomotor phenotypes in Geophagini is compatible with the expectations of an ecologically driven adaptive radiation. This study confirms that the diversification of locomotor phenotypes represents an important dimension of phenotypic evolution in the geophagine adaptive radiation. It also suggests that the commonly observed early burst of phenotypic evolution during adaptive radiations may be better explained by the concentration of shifts to new adaptive peaks deep in the phylogeny rather than overall decreasing rates of evolution.

Multilocus molecular phylogeny of the suckermouth armored catfishes (Siluriformes: Loricariidae) with a focus on subfamily Hypostominae.

The Neotropical catfish family Loricariidae is the fifth most species-rich vertebrate family on Earth, with over 800 valid species. The Hypostominae is its most species-rich, geographically widespread, and ecomorphologically diverse subfamily. Here, we provide a comprehensive molecular phylogenetic reappraisal of genus-level relationships in the Hypostominae based on our sequencing and analysis of two mitochondrial and three nuclear loci (4293bp total). Our most striking large-scale systematic discovery was that the tribe Hypostomini, which has traditionally been recognized as sister to tribe Ancistrini based on morphological data, was nested within Ancistrini. This required recognition of seven additional tribe-level clades: the Chaetostoma Clade, the Pseudancistrus Clade, the Lithoxus Clade, the 'Pseudancistrus' Clade, the Acanthicus Clade, the Hemiancistrus Clade, and the Peckoltia Clade. Results of our analysis, which included type- and non-type species for every valid genus in Hypostominae, support the reevaluation and restriction of several historically problematic genera, including Baryancistrus, Cordylancistrus, Hemiancistrus, and Peckoltia. Much of the deep lineage diversity in Hypostominae is restricted to Guiana Shield and northern Andean drainages, with three tribe-level clades still largely restricted to the Guiana Shield. Of the six geographically widespread clades, a paraphyletic assemblage of three contain lineages restricted to drainages west of the Andes Mountains, suggesting that early diversification of the Hypostominae predated the late Miocene surge in Andean uplift. Our results also highlight examples of trophic ecological diversification and convergence in the Loricariidae, including support for three independent origins of highly similar and globally unique morphological specializations for eating wood.

A time-calibrated, multi-locus phylogeny of piranhas and pacus (Characiformes: Serrasalmidae) and a comparison of species tree methods.

The phylogeny of piranhas, pacus, and relatives (family Serrasalmidae) was inferred on the basis of DNA sequences from eleven gene fragments that include the mitochondrial control region plus 10 nuclear genes (two exons and eight introns). The new data were obtained for a representative sampling of 53 specimens, collected from all major South American rivers, accounting for over 40% of the valid species and all genera excluding Utiaritichthys. Two fossil calibration points and relaxed-clock Bayesian analyses were used to estimate the timing of diversification. The new multilocus dataset also is used to compare several species-tree approaches against the results obtained using the concatenated alignment analyzed under maximum likelihood and Bayesian inference. Individual gene trees showed substantial topological discordance, but analyses based on concatenation and Bayesian and maximum likelihood-based species trees approaches converged onto a single phylogeny. The resulting phylogenetic hypothesis is robust and supports a division of the family into three major clades, consistent with previous results based on mitochondrial DNA alone. The earliest branching event separated a "pacu" clade (Colossoma, Mylossoma and Piaractus) from the rest of the family in the Late Cretaceous (over 68 Ma). The other two clades, that contain most of the diversity, are formed by the "true piranhas" (Metynnis, Pygopristis, Pygocentrus, Pristobrycon, Catoprion, and Serrasalmus) and the Myleus-like pacus (the Myleus clade). The "true" piranha clade originated during the Eocene (∼53 Ma) but the most recent diversification of flesh-eating piranhas within the genera Serrasalmus and Pygocentrus did not start until the Miocene (∼17 Ma). A comparison of species tree approaches indicates that most methods tested are consistent with results obtained by concatenation, suggesting that the gene-tree incongruence observed is mild and will not produce misleading results under simple concatenation analysis. Non-monophyly of several genera (Pristobrycon, Tometes, Myloplus, Mylesinus) and putative species (Serrasalmus rhombeus) was obtained, suggesting that further study of this family is necessary.

Body size diversity and frequency distributions of Neotropical cichlid fishes (Cichliformes: Cichlidae: Cichlinae).

Body size is an important correlate of life history, ecology and distribution of species. Despite this, very little is known about body size evolution in fishes, particularly freshwater fishes of the Neotropics where species and body size diversity are relatively high. Phylogenetic history and body size data were used to explore body size frequency distributions in Neotropical cichlids, a broadly distributed and ecologically diverse group of fishes that is highly representative of body size diversity in Neotropical freshwater fishes. We test for divergence, phylogenetic autocorrelation and among-clade partitioning of body size space. Neotropical cichlids show low phylogenetic autocorrelation and divergence within and among taxonomic levels. Three distinct regions of body size space were identified from body size frequency distributions at various taxonomic levels corresponding to subclades of the most diverse tribe, Geophagini. These regions suggest that lineages may be evolving towards particular size optima that may be tied to specific ecological roles. The diversification of Geophagini appears to constrain the evolution of body size among other Neotropical cichlid lineages; non-Geophagini clades show lower species-richness in body size regions shared with Geophagini. Neotropical cichlid genera show less divergence and extreme body size than expected within and among tribes. Body size divergence among species may instead be present or linked to ecology at the community assembly scale.