Michael E Alfaro

University of California, Los Angeles | UCLA · Ecolo

Across the Tree of Life, most studies of phenotypic disparity and diversification have been restricted to adult organisms. However, many lineages have distinct ontogenetic phases that differ from their adult forms in morphology and ecology. Focusing disproportionately on the evolution of adult forms unnecessarily hinders our understanding of the pr...

Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and account for more than a quarter of all living vertebrate species. Previous time-calibrated phylogenies and patterns from the fossil record explain this dominance by correlating the origin of major acanthomorph lineages with the Cretaceous–Palaeogene mass extinction. Here we infe...

Boxfish (Ostraciidae) have peculiar body shapes, with conspicuous keels formed by their bony carapaces. Previous studies have proposed various hydrodynamic roles for these keels, including reducing drag during swimming, contributing to passive stabilization of the swimming course, or providing resistance against roll rotations. Here, we tested thes...

Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and comprise more than a quarter of all living vertebrate species1-3. It is believed that this dominance resulted from explosive lineage and phenotypic diversification coincident with the Cretaceous-Paleogene (K-Pg) mass-extinction event4. It remains unclear, however, if living acan...

The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradl...

During the Last Glacial Maximum (LGM), global sea levels were 120‐130 m lower than today, resulting in the emergence of most continental shelves and extirpation of subtidal organisms from these areas. During the interglacial periods, rapid inundation of shelf regions created a dynamic environment for coastal organisms, such as the charismatic leafy...

Gobies, sleepers, and cardinalfishes represent major clades of a species rich radiation of small bodied, ecologically diverse percomorphs (Gobiaria). Molecular phylogenetics has been crucial to resolving broad relationships of sleepers and gobies (Gobioidei), but the phylogenetic placements of cardinalfishes and nurseryfishes, as reciprocal or sequ...

Questions about the evolution of material culture are widespread in the humanities and social sciences. Statistical modeling of long-term changes in material culture is less common due to a lack of appropriate frameworks. Our goal is to close this gap and provide robust statistical methods for examining changes in the diversity of material culture....

Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased r...

The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early diverg...

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncert...

Comprehensive, time‐scaled phylogenies provide a critical resource for many questions in ecology, evolution and biodiversity. Methodological advances have increased the breadth of taxonomic coverage in phylogenetic data; however, accessing and reusing these data remain challenging. We introduce the Fish Tree of Life website and associated r package...

Understanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or the intrinsic capacity of lineages for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have...

Complexity in how mechanistic variation translates into ecological novelty could be critical to organismal diversification. For instance, when multiple distinct morphologies can generate the same mechanical or functional phenotype, this could mitigate trade-offs and/or provide alternative ways to meet the same ecological challenge. To investigate h...

Neotropical freshwaters host more than 6000 fish species, of which 983 are suckermouth armored catfishes of the family Loricariidae – the most-diverse catfish family and fifth most species-rich vertebrate family on Earth. Given their diversity and ubiquitous distribution across many habitat types, loricariids are an excellent system in which to inv...

Resolving patterns of ancient and rapid diversifications is one of the most challenging tasks in evolutionary biology. These difficulties arise from confusing phylogenetic signals that are associated with the interplay of incomplete lineage sorting and homoplasy. Phylogenomic analyses of hundreds, or even thousands, of loci offer the potential to r...

Background Phylogenies provide critical information about convergence during adaptive radiation. To test whether there have been multiple origins of a distinctive trophic phenotype in one of the most rapidly radiating groups known, we used ultra-conserved elements (UCEs) to examine the evolutionary affinities of Lake Malawi cichlids lineages exhibi...

For tropical marine species, hotspots of endemism occur in peripheral areas furthest from the center of diversity, but the evolutionary processes that lead to their origin remain elusive. We test several hypotheses related to the evolution of peripheral endemics by sequencing ultraconserved element (UCE) loci to produce a genome-scale phylogeny of...

Target enrichment of conserved nuclear loci has helped reconstruct evolutionary relationships among a wide variety of species. While there are preexisting bait sets to enrich a few hundred loci across all fishes or a thousand loci from acanthomorph fishes, no bait set exists to enrich large numbers (>1000 loci) of ultraconserved nuclear loci from o...

Far more species of organisms are found in the tropics than in temperate and polar regions, but the evolutionary and ecological causes of this pattern remain controversial1,2. Tropical marine fish communities are much more diverse than cold-water fish communities found at higher latitudes3,4, and several explanations for this latitudinal diversity...

The fossil record shows that the vast majority of all species that ever existed are extinct and that most lineages go through an expansion and decline in diversity. However, macroevolutionary analyses based upon molecular phylogenies have difficulty inferring extinction dynamics, raising questions about whether the neontological record can contribu...

The Cretaceous-Palaeogene (K-Pg) mass extinction is linked to the rapid emergence of ecologically divergent higher taxa (for example, families and orders) across terrestrial vertebrates, but its impact on the diversification of marine vertebrates is less clear. Spiny-rayed fishes (Acanthomorpha) provide an ideal system for exploring the effects of...

Despite genome scale analyses, high-level relationships among Neoaves birds remain contentious. The placements of the Neoaves superorders are notoriously difficult to resolve because they involve deep splits followed by short internodes. Using our approach, we investigate whether filtering UCE loci on their phylogenetic signal to noise ratio helps...

The New World Halichoeres comprises about 30 small to medium sized wrasse species that are prominent members of reef communities throughout the tropical Western Atlantic and Eastern Pacific. We conducted a phylogenetic analysis of this group and related lineages using new and previously published sequence data. We estimated divergence times, evalua...

Convergent evolution of small body size occurs across many vertebrate clades and may reflect an evolutionary response to shared selective pressures. However it remains unclear if other aspects of phenotype undergo convergent evolution in miniaturized lineages. Here we present a comparative analysis of body size and shape evolution in marine angelfi...

Adaptive radiations could often occur in discrete stages. For instance, the species flock of ∼1000 species of Lake Malawi cichlid fishes might have only diverged once between rocky and sandy environments during the initial stage of their diversification. All further diversification within the rock-dwelling (mbuna) or sand-dwelling (utaka) cichlids...

Ostariophysi is a superorder of bony fishes including more than 10,300 species in 1100 genera and 70 families. This superorder is traditionally divided into five major groups (orders): Gonorynchiformes (milkfishes and sandfishes), Cypriniformes (carps and minnows), Characiformes (tetras and their allies), Siluriformes (catfishes), and Gymnotiformes...

Aim Our aim was to examine gracile capuchin ( Cebus ) and robust capuchin monkey ( Sapajus ) diversification, with a focus on recent Sapajus expansion within Amazonia. We wanted to reconstruct the biogeographical history of the clade using statistical methods that model lineages’ occupation of different regions over time in order to evaluate recent...

Background Flatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increas...

Decoupling of the upper jaw bones-jaw kinesis-is a distinctive feature of the ray-finned fishes, but it is not clear how the innovation is related to the extraordinary diversity of feeding behaviours and feeding ecology in this group. We address this issue in a lineage of ray-finned fishes that is well known for its ecological and functional divers...

Although diet is believed to be a major factor underlying the evolution of venom, few comparative studies examine both venom composition and diet across a radiation of venomous species. Cone snails within the family, Conidae, comprise more than 700 species of carnivorous marine snails that capture their prey by using a cocktail of venomous neurotox...

We were delighted to read Madias' reply [1] to our comparative analysis [2], and we are excited that others see the value of making clinical predictions from a comparative life history study. We agree that further research on non-humans specifically aimed at identifying the mechanism(s) underlying capture myopathy would be valuable. The suggestions...

Advances in genomics and informatics have enabled the production of large phylogenetic trees. However, the ability to collect large phenotypic data sets has not kept pace. Here, we present a method to quickly and accurately gather morphometric data using crowdsourced image‐based landmarking. We find that crowdsourced workers perform similarly to ex...

1. Advances in genomics and informatics have enabled the production of large phylogenetic trees. However, the ability to collect large phenotypic datasets has not kept pace. 2. Here, we present a method to quickly and accurately gather morphometric data using crowdsourced image-based landmarking. 3. We find that crowdsourced workers perform similar...

Capture myopathy (CM) syndromes in wildlife may be a model for human stress cardiomyopathy, including Takotsubo cardiomyopathy. Emotional stress or grief may trigger heart attack-like symptoms, and occasionally, sudden death in some humans. Similarly, wildlife exposed to predatory stresses, chase, or capture occasionally results in sudden death. To...

Ultraconserved elements (UCEs) have become popular markers in phylogenetic studies because of their cost effectiveness in phylogenomic analyses and because of their potential to resolve problematic phylogenetic questions such as interspecific relationships within the ray-finned fishes. Although UCE datasets typically contain a much larger number of...

Several hypotheses have been proposed to explain the limitation of brain size in vertebrates. Here we test three hypotheses of brain size evolution using marine teleost fishes: the direct metabolic constraints hypothesis, the expensive tissue hypothesis, and the temperature-dependent hypothesis. Our analyses indicate that there is a robust positive...

The shape of the carapace protecting the body of boxfishes has been attributed an important hydrodynamic role in drag reduction and in providing automatic, flow-direction realignment and is therefore used in bioinspired design of cars. However, tight swimming-course stabilization is paradoxical given the frequent, high-performance manoeuvring that...

The demand that anatomical structures work together to perform biological functions is thought to impose strong limits on morphological evolution. Breakthroughs in diversification can occur, however, when functional integration among structures is relaxed. Although such transitions are expected to generate variation in morphological diversification...

The squirrel monkey, Saimiri, is a pan-Amazonian Pleistocene radiation. We use statistical phylogeographic methods to create a mitochondrial DNA-based timetree for 118 squirrel monkey samples across 68 localities spanning all Amazonian centers of endemism, with the aim of better understanding (1) the effects of rivers as barriers to dispersal and d...

Trait decoupling, wherein evolutionary release of constraints permits specialization of formerly integrated structures, represents a major conceptual framework for interpreting patterns of organismal diversity. However, few empirical tests of this hypothesis exist. A central prediction, that the tempo of morphological evolution and ecological diver...

Abstract Convergence is central to the study of evolution because it demonstrates the power of natural selection to deterministically shape phenotypic diversity. However, the conditions under which a common morphology repeatedly evolves may be restrictive. Many factors, such as differing genetic and environmental backgrounds and many-to-one mapping...

Sharks occupy marine habitats ranging from shallow, inshore environments to pelagic, and deepwaters, and thus provide a model system for testing how gross habitat differences have shaped vertebrate macroevolution. Palaeontological studies have shown that onshore lineages diversify more quickly than offshore taxa. Among onshore habitats, coral reef-...

Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data has increased dramatically in the last few years. Many existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger...

The faces of Old World monkeys and apes (Catarrhini) exhibit every possible hue in the spectrum of mammal colours. Animal colouration experiences selection for communication, physiology and ecology; however, the relative importance of these factors in producing facial diversity in catarrhines is not known. Here we adopt a comparative approach to te...

The ability to sustain high swimming speeds is believed to be an important factor affecting resource acquisition in fishes. While we have gained insights into how fin morphology and motion influences swimming performance in coral reef fishes, the role of other traits, such as body shape, remains poorly understood. We explore the ability of two mech...

Anguilliformes are an ecologically diverse group of predominantly marine fishes whose members are easily recognized by their extremely elongate bodies, and universal lack of pelvic fins. Recent studies based on mitochondrial loci, including full mitogenomes, have called into question the monophyly of both the Anguilliformes, which appear to be para...

Ray-finned fishes constitute the dominant radiation of vertebrates with over 32,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the en...

Species tree based upon STAR analysis. Topology based upon analysis of all loci 50 base pairs that contained both Polypterus and Acipenser (N = 136). Node values indicate bootstrap proportion based upon 1000 replicates. We collapsed nodes having 50% bootstrap support. (EPS)

Some of the more valuable contributions of a standardized DNA sequence database (the DNA barcode) are matching specimens of different life stages and confirming the species identity of individuals from distant locations. These applications can facilitate the detective work required to solve difficult taxonomic problems. In this case, a match was ma...

Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found littl...

Tetraodontiform fishes represent one of the most peculiar radiations of teleost fishes. In spite of this, we do not currently have a consensus on the phylogenetic relationships among the major tetraodontiform lineages, with different morphological and molecular datasets all supporting contrasting relationships. In this paper we present the results...

Balistoid fishes (triggerfishes, filefishes, leatherjackets) represent one of the most successful radiations of tetraodontiform fishes across the world's oceans. Balistids (triggerfishes) are largely circumtropical in coral reef environments while most monacanthids (filefishes, leatherjackets) are distributed across reef and non-reef habitats in th...

Background Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great “Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generaliz...

Habitat shifts are implicated as the cause of many vertebrate radiations, yet relatively few empirical studies quantify patterns of diversification following colonization of new habitats in fishes. The pufferfishes (family Tetraodon-tidae) occur in several habitats, including coral reefs and freshwater, which are thought to provide ecological oppor...