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Marine metapopulations often exhibit subtle population structure that can be difficult to detect. Given recent advances in high-throughput sequencing, an emerging question is whether various genotyping approaches, in concert with improved sampling designs, will substantially improve our understanding of genetic structure in the sea. To address this question, we explored hierarchical patterns of structure in the coral reef fish Elacatinus lori using a high-resolution approach with respect to both genetic and geographic sampling. Previously, we identified three putative E. lori populations within Belize using traditional genetic markers and sparse geographic sampling: barrier reef and Turneffe Atoll; Glover's Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals at ~10 km intervals throughout these reefs (1,129 individuals from 35 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs; 89 microsatellites; and 57 nonrepetitive nuclear loci. At broad spatial scales, the markers were consistent with each other and with previous findings. At finer spatial scales, there was new evidence of genetic substructure, but our three marker sets differed slightly in their ability to detect these patterns. Specifically, we found subtle structure between the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most effectively. We also documented isolation by distance within the barrier reef. Sensitivity analyses revealed that the number of loci (and alleles) had a strong effect on the detection of structure for all three marker sets, particularly at small spatial scales. Taken together, these results illustrate empirically that high-throughput genotyping data can elucidate subtle genetic structure at previously-undetected scales in a dispersive marine fish.

The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin’s importance for illuminating vertebrate biology and diversity in the genomic era., Analysis of a chromosome-level bowfin genome assembly sheds light into neopterygian fish evolution. Chromatin accessibility and gene expression profiling provides insight into bowfin embryonic development.

The bowfin fish (Amia calva) diverged before the genome duplication in teleost fishes, and its archetypical body plan and slow rate of molecular evolution make it a key species for genomic exploration as a basal representative of the neopterygian fishes. To investigate the evolution and development of ray-finned fishes, we generated a chromosome-level genome assembly for bowfin that enables gene-order analyses which settle its long-debated, phylogenetic relationship with gars. We analyze the genomic underpinnings of the bowfin’s unique combination of derived and ancestral phenotypes involving the immune system as well as scale, respiratory organ, and skeletal development. By detailing chromatin accessibility and gene expression through bowfin development, we connect developmental gene regulatory loci across vertebrates. We illustrate the utility of these genomic resources to connect developmental evolution across bony fishes, showing the importance of bowfin in understanding vertebrate biology and diversity.

Whether phenotypic evolution occurs gradually through time has prompted the search for intermediate forms between the ancestral and derived states of morphological features, especially when there appears to be a discontinuous origin. The gas bladder, a derived character of the Actinopteri, is a modification of lungs, which characterize the common ancestor of bony vertebrates. While gas bladders and lungs are similar in many ways, the key morphological difference between these organs is the direction of budding from the foregut during development; essentially, the gas bladder buds dorsally and the lungs bud ventrally from the foregut. Did the shift from ventral lungs to dorsal gas bladder transition through a lateral-budding stage? To answer this question, the precise location of budding during gas bladder development in bowfin, representing the sister lineage to teleosts, has been debated. In the early 20th-century, it was suggested that the bowfin gas bladder buds laterally from the right wall of the foregut. We used nano-CT scanning to visualize the early development of the bowfin gas bladder to verify the historical studies of gas bladder developmental morphology and determine whether the direction of gas bladder budding in bowfin could be intermediate between ventrally budding lungs and dorsally budding gas bladders. We found that the bowfin gas bladder buds dorsally from the anterior foregut; however, during early development, the posterior gas bladder twists right. As development progresses, the posterior, right-hand twist becomes shallower, and the gas bladder itself shifts toward a mid-dorsal position. The budding site is definitively dorsal, despite the temporary lateral twist of the posterior gas bladder.

How modification of gene expression generates novel traits is key to understanding the evolutionary process. We investigated the genetic basis for the origin of the piscine gas bladder from lungs of ancestral bony vertebrates. Distinguishing these homologous organs is the direction of budding from the foregut during development; lungs bud ventrally and the gas bladder buds dorsally. We investigated whether this morphological inversion is associated with molecular inversion of conserved genes regulating lung and gasbladder development. Using laser-capture microdissection and RNA-seq, we assayed transcript abundance and compared expression patterns between dorsal and ventral foregut tissues at three developmental stages spanning gasbladder development. Our focal taxon, bowfin (Amia calva), representing the sistergroup to teleosts, is an early diverging ray-finned fish with a gas bladder. We discovered a number of genes with unknown function during lung development that are differentially expressed during gas bladder development and annotated to functions relevant for organ budding. We also identified several known lung-regulatory genes exhibiting inverted dorsoventral expression during gasbladder relative to lung development. Specifically, we found Tbx5 is strongly expressed in the dorsal mesoderm surrounding the gas bladder during bowfin development, and several interacting genes are co-expressed dorsally with Tbx5. In contrast, in mouse and bichir (Polypterus senegalus), the only ray-finned fish that have lungs, Tbx5 is expressed in the ventral lung mesoderm during development. Our data demonstrating dorsoventral inversion of conserved genes suggests that these genes may have contributed to the evolutionary transition between ventral lungs and a dorsal gas bladder in ray-finned fishes.

Using multiple taxa to research development is necessary for making general conclusions about developmental patterns and mechanisms. We present a staging series for Cyprinodon variegatus as a basis for further study of the developmental biology of fishes in the genus Cyprinodon and for comparative work on teleost fishes beyond the standard models. Cyprinodon are small, euryhaline fishes, widely distributed in fresh, brackish, and hypersaline waters of southern and eastern North America. Cyprinodontids are closely related to fundulids, providing a comparative reference point to the embryological model, Fundulus heteroclitus. Ecologists and evolutionary biologists commonly study Cyprinodon, and we have been using Cyprinodon to study skull variation and its genetic basis among closely related species. We divided embryonic development of C. variegatus into 34 morphologically identifiable stages. We reference our staging series to that already defined for a related model species, Oryzias latipes (medaka) that is studied by a large community of researchers. We provide a description of the early chondrogenesis and ossification of skull and caudal fin bones during the latter stages of embryonic development. We show that Cyprinodon are tractable for studying development. Eggs can be obtained easily from breeding pairs and our study provides a staging system to facilitate future developmental studies.

Background Understanding the genetic and developmental origins of phenotypic novelty is central to the study of biological diversity. In this study we identify modifications to the expression of genes at four developmental stages that may underlie jaw morphological differences among three closely related species of pupfish (genus Cyprinodon) from San Salvador Island, Bahamas. Pupfishes on San Salvador Island are trophically differentiated and include two endemic species that have evolved jaw morphologies unlike that of any other species in the genus Cyprinodon. Results We find that gene expression differs significantly across recently diverged species of pupfish. Genes such as Bmp4 and calmodulin, previously implicated in jaw diversification in African cichlid fishes and Galapagos finches, were not found to be differentially expressed among species of pupfish. Instead we find multiple growth factors and cytokine/chemokine genes to be differentially expressed among these pupfish taxa. These include both genes and pathways known to affect craniofacial development, such as Wnt signaling, as well as novel genes and pathways not previously implicated in craniofacial development. These data highlight both shared and potentially unique sources of jaw diversity in pupfish and those identified in other evolutionary model systems such as Galapagos finches and African cichlids. Conclusions We identify modifications to the expression of genes involved in Wnt signaling, Igf signaling, and the inflammation response as promising avenues for future research. Our project provides insight into the magnitude of gene expression changes contributing to the evolution of morphological novelties, such as jaw structure, in recently diverged pupfish species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3810-7) contains supplementary material, which is available to authorized users.

Understanding the genetic basis for phenotypic differences is fundamental to the study of macroevolutionary patterns of biological diversity. While technological advances in DNA sequencing have made researching genetic variation in wild taxa routine, fully understanding how these variants affect phenotype requires taking the next step to investigate how genetic changes alter cell and tissue interactions that ultimately produce phenotypes. In this article, we investigate a role for cell proliferation as a developmental source of craniofacial diversity in a radiation of 3 species of Cyprinodon from San Salvador Island, Bahamas. Patterns of cell proliferation in the heads of hatching-age fish differ among species of Cyprinodon, and correlate with differences in allometric growth rate among the jaws of 3 distinct species. Regional patterns of cell proliferation in the head are complex, resulting in an unintuitive result in which lower levels of cell proliferation in the posterior head region are associated with the development of relatively larger jaws in one species. We combine these data with previously published morphological and genomic data to show how studying the mechanisms generating phenotype at the cellular and tissue levels of biological organization can help mechanistically link genomic studies with classic morphological studies.

We propose that insights from the field of evolutionary developmental biology (or ‘evo-devo’) provide a framework for an integrated understanding of the origins of behavioural diversity and its underlying mechanisms. Towards that goal, in this Commentary, we frame key questions in behavioural evolution in terms of molecular, cellular and network-level properties with a focus on the nervous system. In this way, we highlight how mechanistic properties central to evo-devo analyses – such as weak linkage, versatility, exploratory mechanisms, criticality, degeneracy, redundancy and modularity – affect neural circuit function and hence the range of behavioural variation that can be filtered by selection. We outline why comparative studies of molecular and neural systems throughout ontogeny will provide novel insights into diversity in neural circuits and behaviour.

To understand the origins of novelty and the evolution of biological diversity, it is important to investigate the processes that generate phenotypic variation from genotypic variation. A number of path-breaking studies have revealed the genetic basis for phenotypic differences between distantly related taxa, but how qualitative change is produced during the early stages of divergence is largely unexplored. Here, we focus on striking differences in jaw morphology exhibited by three closely related sympatric pupfish species (genus Cyprinodon) from San Salvador Island, Bahamas as a basis for investigating the genetic sources of morphological variation in recently diverged species. San Salvador Island pupfish are trophically diverse and display derived jaw morphologies distinct from any other species in the genus. We illustrate these qualitative morphological differences between species with 3D-reconstructed CT-images and camera lucida drawings of the skulls of wild-caught fish. Quantitative data representing the size of individual bony skull elements in wild fish show how qualitatively novel morphologies arise as a consequence of changes to the size and shape of individual skull elements, particularly the dentary, premaxilla, and maxilla bones associated with the oral jaws. Consistent with these comparative data is that the growth rate of individual bony skull elements, measured on a developmental time series of lab-reared fish, differs between species. Our data provide a critical foundation for future studies developing San Salvador Cyprinodon pupfishes as a model system to understand the evolution and development of novel morphologies at the species level. J. Morphol. 277:935-947, 2016. © 2016 Wiley Periodicals, Inc.

The presence of an air-filled organ (AO), either lungs or a swimbladder, is a defining character of the Osteichthyes (bony vertebrates, including tetrapods). Despite the functional and structural diversity of AOs, it was not previously known whether the same group of developmental regulatory genes are involved in the early development of both lungs and swimbladders. This study demonstrates that a suite of genes (Nkx2.1, FoxA2, Wnt7b, GATA6), previously reported to be co-expressed only in the tetrapod lung, is also co-expressed in the zebrafish swimbladder. We document the expression pattern of these genes in the adult and developing zebrafish swimbladder and compare the expression patterns to those in the mouse lung. Early-acting genes involved in endoderm specification are expressed in the same relative location and stage of AO development in both taxa (FoxA2 and GATA6), but the order of onset and location of expression are not completely conserved for the later acting genes (Nkx2.1 and Wnt7b). Co-expression of this suite of genes in both tetrapod lungs and swimbladders of ray-finned fishes is more likely due to common ancestry than independent co-option, because these genes are not known to be co-expressed anywhere except in the AOs of Osteichthyes. Any conserved gene product interactions may comprise a character identity network (ChIN) for the osteichthyan AO.

Gas bladders of ray-finned fishes serve a variety of vital functions and are thus an important novelty of most living vertebrates. The gas bladder has long been regarded as an evolutionary modification of lungs. Critical evidence for this hypothesized homology is whether pulmonary arteries supply the gas bladder as well as the lungs. Pulmonary arteries, paired branches of the fourth efferent branchial arteries, deliver blood to the lungs in osteichthyans with functional lungs (lungfishes, tetrapods, and the ray-finned polypterid fishes). The fact that pulmonary arteries also supply the respiratory gas bladder of Amia calva (bowfin) has been used to support the homology of lungs and gas bladders, collectively termed air-filled organs (AO). However, the homology of pulmonary arteries in bowfin and lunged osteichthyans has been uncertain, given the apparent lack of pulmonary arteries in critical taxa. To re-evaluate the homology of pulmonary arteries in bowfin and lunged osteichthyans, we studied, using micro-CT technology, the arterial vasculature of Protopterus, Polypterus, Acipenser, Polyodon, Amia, and Lepisosteus, and analyzed these data using a phylogenetic approach. Our data reveal that Acipenser and Polyodon have paired posterior branches of the fourth efferent branchial arteries, which are thus similar in origin to pulmonary arteries. We hypothesize that these arteries are vestigial pulmonary arteries that have been coopted for new functions due to the dorsal shift of the AO and/or the loss of respiration in these taxa. Ancestral state reconstructions support pulmonary arteries as a synapomorphy of the Osteichthyes, provide the first concrete evidence for the retention of pulmonary arteries in Amia, and support thehomology of lungs and gas bladders due to a shared vascular supply. Finally, we use ancestral state reconstructions to show that arterial AO supplies from the celiacomesenteric artery or dorsal aorta appear to be convergent between teleosts and nonteleost actinopterygians.

Lake Tanganyika, Africa's oldest lake, harbours an impressive diversity of cichlid fishes. Although diversification in its radiating groups is thought to have been initially rapid, cichlids from Lake Tanganyika show little evidence for ongoing speciation. In contrast, examples of recent divergence among sympatric colour morphs are well known in haplochromine cichlids from Lakes Malawi and Victoria. Here, we report genetic evidence for recent divergence between two sympatric Tanganyikan cichlid colour morphs. These Petrochromis morphs share mitochondrial haplotypes, yet microsatellite loci reveal that their sympatric populations form distinct genetic groups. Nuclear divergence between the two morphs is equivalent to that which arises geographically within one of the morphs over short distances and is substantially smaller than that among other sympatric species in this genus. These patterns suggest that these morphs diverged only recently, yet that barriers to gene flow exist which prevent extensive admixture despite their sympatric distribution. The morphs studied here provide an unusual example of active diversification in Lake Tanganyika's generally ancient cichlid fauna and enable comparisons of speciation processes between Lake Tanganyika and other African lakes.

Convergence is an important evolutionary phenomenon often attributed solely to natural selection acting in similar environments. The frequency of mutation and number of ways a phenotypic trait can be generated genetically, however, may also affect the probability of convergence. Here we report both a high frequency of loss of gas bladder (swim bladder) mutations in zebrafish and widespread convergent loss of gas bladders among teleost fishes. The phenotypes of 22 of 27 recessive lethal mutations, carried by a sample of 26 wild-caught zebrafish, involve loss or noninflation of the gas bladder. Nine of these bladderless mutations showed no other obvious phenotypic abnormalities other than the lack of an inflated gas bladder. At least 19 of the 22 bladderless mutations are genetically distinct, as shown by unique morphology or complementation. Although we were not able to obtain eggs for all 21 required crosses to demonstrate definitively that the remaining three mutations are different from all other bladderless mutations, all available evidence suggests that these mutants are also distinct. At least 79 of 425 families of extant teleosts include one or more species lacking a gas bladder as adults. Analysis of the trait's phylogenetic distribution shows that the gas bladder has been lost at least 30-32 times independently. Although adaptive explanations for gas bladder loss are convincing, a developmental bias toward bladderless phenotypes may also have contributed to the widespread convergence of this trait among teleosts. If gas bladder development in teleosts is as vulnerable to genetic perturbation as it is in zebrafish, then perhaps a supply of bladderless phenotypes has been readily available to natural selection under conditions for which it is advantageous not to have a gas bladder. In this way, developmental bias and selection can work together to produce widespread convergence.

Danio is a diverse group of small, colourful and easily bred freshwater fishes native to Southern Asia. Biological interest in danios has increased in recent years because the zebrafish, Danio rerio , has become an important model organism, particularly for studies of vertebrate developmental biology and genetics. Though several phylogenetic studies of Danio have been done on a subset of Danio species, the resulting phylogenies conflict in detail. To examine the utility of osteology for systematics of this group at the species level, we studied the axial skeleton for 11 species of Danio. We analyse our morphological data alone and combined with DNA sequence data for five gene sequences generated in earlier phylogenetic studies. The axial skeleton of Danio exhibits 14 characters that prove useful in phylogenetic analysis. Both molecular and morphological data support the monophyly of the danios included in our analysis and both data sets support the monophyly of two subclades: a deep-bodied group and a slender-bodied group. Separate analysis of molecular and morphological data sets show that the molecular data resolves relationships within the slender subclade whereas the topology of the deep-bodied subclade is determined by morphological data. © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 2002, 135 , 529–546.

Despite the importance of selection against deleterious mutations in natural populations, reliable estimates of the genomic numbers of mutant alleles in wild populations are scarce. We found that, in wild-caught bluefin killifish Lucania goodei (Fundulidae) and wild-caught zebrafish Danio rerio (Cyprinidae), the average numbers of recessive lethal alleles per individual are 1.9 (95% confidence limits 1.3 to 2.6) and 1.4 (95% confidence limits 1.0 to 2.0), respectively. These results, together with data on several Drosophila species and on Xenopus laevis , show that phylogenetically distant animals with different genome sizes and numbers of genes carry similar numbers of lethal mutations.

The presence of an air-filled organ (AO), either lungs or a swimbladder, is a defining character of the Osteichthyes (bony vertebrates, including tetrapods). Despite the functional and structural diversity of AOs, it was not previously known whether the same group of developmental regulatory genes are involved in the early development of both lungs and swimbladders. This study demonstrates that a suite of genes (Nkx2.1, FoxA2, Wnt7b, GATA6), previously reported to be co-expressed only in the tetrapod lung, is also co-expressed in the zebrafish swimbladder. We document the expression pattern of these genes in the adult and developing zebrafish swimbladder and compare the expression patterns to those in the mouse lung. Early-acting genes involved in endoderm specification are expressed in the same relative location and stage of AO development in both taxa (FoxA2 and GATA6), but the order of onset and location of expression are not completely conserved for the later acting genes (Nkx2.1 and Wnt7b). Co-expression of this suite of genes in both tetrapod lungs and swimbladders of ray-finned fishes is more likely due to common ancestry than independent co-option, because these genes are not known to be co-expressed anywhere except in the AOs of Osteichthyes. Any conserved gene product interactions may comprise a character identity network (ChIN) for the osteichthyan AO.

It has been hypothesized that morphological diversity within clades can be generated by simple alterations of shared developmental programs. However, few studies have examined changes in heterochrony, the rate and timing of developmentalevents, in an explicitly phylogenetic context. We studied how developmental patterns have changed phylogenetically in the northern swordtail clade of Xiphophorus. We reared individuals of an outgroup and seven of nine species in the clade and followed their development for ~ 300 days. For each individual, we used nonlinear regression toestimatethreegrowth parameters:growth rate,adultbody size,and ageofcessation of growth. Weestimated sword growth rates in males by linear regression. We then used the means of these growth parameters toconstructstandard growth curves for each species and tostudy growth patterns in a phylogenetic context. A combined phylogeny was constructed from both phenotypic and DNAsequencedata.Thephenotypicdataset,compiled fromtheliterature,consistedof86 mor- phological, pigmentation, behavioral, and random amplieed polymorphic DNA characters, many of which had not been used before for phylogenetic analysis. DNA sequence data from three genes for a total of 1284 bases were also obtained from the literature and included in the analysis. Rela- tionships between growth parameters were examined by phylogenetically independent contrasts in relation to seven different phylogenies based on the most-parsimonious trees generated from the phenotypic, DNA sequence, and combined data sets; this allowed us to identify relationships between variables that were not sensitive to ambiguities in Xiphophorus phylogeny. Our analysis revealed statistically signiecant correlations between female body size and male body size, and between femalegrowth rateand malesword growth rate, for allseven phylogenies. Marginally sta- tistically signiecantrelationships werealsoidentieed between female body sizeand femalegrowth rate, and between female growth rate and male body size. We relate these relationships to what is known about the ecology, genetics, and behavior of Xiphophorus to better understand the evolution of growth patterns of both the body as a whole and the sword in particular. The relationship of thesedata totheevolution of swords is discussed. (Development; evolution; growth; heterochrony; independent contrasts; sword; Xiphophorus.) Heterochrony, or changes in the timing of developmental events, has been shown to be a pervasive force in the evolution of mor- phology. Changes in onset, offset, and the rate of development of morphological char- acters have been the basis for much of the observed morphological variation among many types of organisms (Gould, 1977; Al- berchetal.,1979;McKinneyandMcNamara, 1991). However, only when heterochronic changesareexaminedinaphylogeneticcon- text can the evolutionary patterns and pro- cesses of heterochrony be understood (Fink, 1982). The esh genus Xiphophorus (Poeciliidae), comprising 22 described species of sword

In this study I take advantage of an unusual system of fossil lakes in eastern North America to estimate the time for speciation of endemic semionotid fishes. Twenty-one species are all found in sedimentary cycle P4, the deposits of a single Early Jurassic lake, in the Towaco Formation of the Newark Basin in New Jersey. To determine the degree of endemism in the fauna from this fossil lake and estimate time for speciation, I surveyed more than 2000 museum specimens from 45 named localities in the Newark Basin and related basins of the Late Triassic to Early Jurassic Newark Supergroup. Six species not found in deposits equal in age to P4 or older are considered to be endemics, eight species occurring in older deposits presumably colonized Lake P4, and evidence for whether the remaining seven species were endemics or colonists is equivocal. The time for the formation, decline, and evaporation of Lake P4, in which P4 sediments were deposited, has been estimated at 21,000-24,000 years. Because all endemic Semionotus first occur in the first third of lake history, the estimated time for speciation of endemics is six species in 5000-8000 years. This rate is remarkably similar to that estimated for the five cichlids in Lake Nabugabo that diverged from Lake Victoria cichlids in about 4000 years.

Gas bladders of ray-finned fishes serve a variety of vital functions and are thus an important novelty of most living vertebrates. The gas bladder has long been regarded as an evolutionary modification of lungs. Critical evidence for this hypothesized homology is whether pulmonary arteries supply the gas bladder as well as the lungs. Pulmonary arteries, paired branches of the fourth efferent branchial arteries, deliver blood to the lungs in osteichthyans with functional lungs (lungfishes, tetrapods, and the ray-finned polypterid fishes). The fact that pulmonary arteries also supply the respiratory gas bladder of Amia calva (bowfin) has been used to support the homology of lungs and gas bladders, collectively termed air-filled organs (AO). However, the homology of pulmonary arteries in bowfin and lunged osteichthyans has been uncertain, given the apparent lack of pulmonary arteries in critical taxa. To re-evaluate the homology of pulmonary arteries in bowfin and lunged osteichthyans, we studied, using micro-CT technology, the arterial vasculature of Protopterus, Polypterus, Acipenser, Polyodon, Amia, and Lepisosteus, and analyzed these data using a phylogenetic approach. Our data reveal that Acipenser and Polyodon have paired posterior branches of the fourth efferent branchial arteries, which are thus similar in origin to pulmonary arteries. We hypothesize that these arteries are vestigial pulmonary arteries that have been coopted for new functions due to the dorsal shift of the AO and/or the loss of respiration in these taxa. Ancestral state reconstructions support pulmonary arteries as a synapomorphy of the Osteichthyes, provide the first concrete evidence for the retention of pulmonary arteries in Amia, and support thehomology of lungs and gas bladders due to a shared vascular supply. Finally, we use ancestral state reconstructions to show that arterial AO supplies from the celiacomesenteric artery or dorsal aorta appear to be convergent between teleosts and nonteleost actinopterygians.

Lake Tanganyika, Africa's oldest lake, harbours an impressive diversity of cichlid fishes. Although diversification in its radiating groups is thought to have been initially rapid, cichlids from Lake Tanganyika show little evidence for ongoing speciation. In contrast, examples of recent divergence among sympatric colour morphs are well known in haplochromine cichlids from Lakes Malawi and Victoria. Here, we report genetic evidence for recent divergence between two sympatric Tanganyikan cichlid colour morphs. These Petrochromis morphs share mitochondrial haplotypes, yet microsatellite loci reveal that their sympatric populations form distinct genetic groups. Nuclear divergence between the two morphs is equivalent to that which arises geographically within one of the morphs over short distances and is substantially smaller than that among other sympatric species in this genus. These patterns suggest that these morphs diverged only recently, yet that barriers to gene flow exist which prevent extensive admixture despite their sympatric distribution. The morphs studied here provide an unusual example of active diversification in Lake Tanganyika's generally ancient cichlid fauna and enable comparisons of speciation processes between Lake Tanganyika and other African lakes.

Homology can have different meanings for different kinds of biologists. A phylogenetic view holds that homology, defined by common ancestry, is rigorously identified through phylogenetic analysis. Such homologies are taxic homologies (=synapomorphies). A second interpretation, "biological homology" emphasizes common ancestry through the continuity of genetic information underlying phenotypic traits, and is favored by some developmental geneticists. A third kind of homology, deep homology, was recently defined as "the sharing of the genetic regulatory apparatus used to build morphologically and phylogenetically disparate features." Here we explain the commonality among these three versions of homology. We argue that biological homology, as evidenced by a conserved gene regulatory network giving a trait its "essential identity" (a Character Identity Network or "ChIN") must also be a taxic homology. In cases where a phenotypic trait has been modified over the course of evolution such that homology (taxic) is obscured (e.g. jaws are modified gill arches), a shared underlying ChIN provides evidence of this transformation. Deep homologies, where molecular and cellular components of a phenotypic trait precede the trait itself (are phylogenetically deep relative to the trait), are also taxic homologies, undisguised. Deep homologies inspire particular interest for understanding the evolutionary assembly of phenotypic traits. Mapping these deeply homologous building blocks on a phylogeny reveals the sequential steps leading to the origin of phenotypic novelties. Finally, we discuss how new genomic technologies will revolutionize the comparative genomic study of non-model organisms in a phylogenetic context, necessary to understand the evolution of phenotypic traits.

Species selection as a potential driver of macroevolutionary trends has been relegated to a largely philosophical position in modern evolutionary biology. Fundamentally, species selection is the outcome of heritable differences in speciation and extinction rates among lineages when the causal basis of those rate differences can be decoupled from genotypic (within-population) fitnesses. Here, we discuss the rapidly growing literature on variation in species diversification rates as inferred from molecular phylogenies. We argue that modern studies of diversification rates demonstrate that species selection is an important process influencing both the evolution of biological diversity and distributions of phenotypic traits within higher taxa. Explicit recognition of multi-level selection refocuses our attention on the mechanisms by which traits influence speciation and extinction rates.

The cichlid fish of Lake Tanganyika in Eastern Africa are a celebrated example of both ecological and species diversification. Because population subdivision is likely to play an important role in the speciation process, understanding how habitat features interact with species' demographic, behavioral and ecological attributes to influence gene flow and population divergence may help explain the causes of high species richness in this and other systems. Here, we test the roles of isolation-by-habitat and isolation-by-distance in generating fine-scale population genetic structure in three sympatric species of habitat-restricted cichlids in Lake Tanganyika. Using multilocus microsatellite genotypes, we contrast patterns of population differentiation in these habitat specialists along a mosaic coastline of both favorable and unfavorable habitat. Despite their close phylogenetic relationship and shared habitat affinity, these species show striking differences in their pattern of genetic subdivision within the same geographical region, suggesting substantially different patterns of gene flow. In particular, two trophically specialized species exhibit much more restricted gene flow over sandy habitat than a trophically opportunistic species. This result suggests that ecological and behavioral traits have a strong influence on the scale and degree of population subdivision, a finding that has potentially important implications for understanding differential propensities for diversification among lineages and phylogenetic patterns of diversity.

We describe the morphology of Semionotus, focusing on the Semionotus elegans group from the Newark Supergroup of eastern North America. Our description is based largely on specimens from the Boonton Formation (Early Jurassic) of New Jersey because they are particularly well-preserved and include good material of both the dermal skeleton and the endoskeleton. A single anamestic suborbital distinguishes Semionotus from its sister-genus Lepidotes. We restrict the Semionotidae, defined by the presence of dorsal ridge scales between the nape and dorsal fin as well as a large posteriorly directed process on the epiotic, to two genera, Semionotus and Lepidotes. We restrict the Semionotiformes, defined by four characters and five character losses, to the Lepisosteidae, Macrosemiidae, and Semionotidae. Our study of Semionotus and previous work on Watsonulus suggest new interpretations of characters and character polarities. These data support the hypothesis that the Semionotiformes as we define them are m...

The jaw morphology of needlefishes (Beloniformes : Belonidae) passes through distinctive ontogenetic stages. When hatched, larvae have short jaws of equal length. The lower jaw first elongates to produce a halfbeak form, then the upper jaw elongates to produce the adult needlenose morphology. Onset and duration of the halfbeak stage vary among belonid species. We tested the hypothesis that heterochronic evolution produced this diversity in jaw morphology

A latitudinal gradient in biodiversity has existed since before the time of the dinosaurs, yet how and why this gradient arose remains unresolved. Here we review two major hypotheses for the origin of the latitudinal diversity gradient. The time and area hypothesis holds that tropical climates are older and historically larger, allowing more opportunity for diversification. This hypothesis is supported by observations that temperate taxa are often younger than, and nested within, tropical taxa, and that diversity is positively correlated with the age and area of geographical regions. The diversification rate hypothesis holds that tropical regions diversify faster due to higher rates of speciation (caused by increased opportunities for the evolution of reproductive isolation, or faster molecular evolution, or the increased importance of biotic interactions), or due to lower extinction rates. There is phylogenetic evidence for higher rates of diversification in tropical clades, and palaeontological data demonstrate higher rates of origination for tropical taxa, but mixed evidence for latitudinal differences in extinction rates. Studies of latitudinal variation in incipient speciation also suggest faster speciation in the tropics. Distinguishing the roles of history, speciation and extinction in the origin of the latitudinal gradient represents a major challenge to future research.

Natural populations carry deleterious recessive alleles which cause inbreeding depression. We compared mortality and growth of inbred and outbred zebrafish, Danio rerio, between 6 and 48 days of age. Grandparents of the studied fish were caught in the wild. Inbred fish were generated by brother–sister mating. Mortality was 9% in outbred fish, and 42% in inbred fish, which implies at least 3.6 lethal equivalents of deleterious recessive alleles per zygote. There was no significant inbreeding depression in the growth, perhaps because the surviving inbred fish lived under less crowded conditions. In contrast to alleles that cause embryonic and early larval mortality in the same population, alleles responsible for late larval and early juvenile mortality did not result in any gross morphological abnormalities. Thus, deleterious recessive alleles that segregate in a wild zebrafish population belong to two sharply distinct classes: early-acting, morphologically overt, unconditional lethals; and later-acting, morphologically cryptic, and presumably milder alleles.

Introduction Prolific speciation of fishes within lakes has long fascinated evolutionary biologists (e.g., Brooks 1950; Martens 1997), in part because of the difficulty in identifying extrinsic barriers to gene exchange that might permit allopatric speciation of vagile organisms such as fishes in lakes. The cichlid fishes of Lakes Victoria and Malawi (Fryer and Iles 1972; Greenwood 1981b) are the most celebrated examples of intralacustrine speciation, but its generality has been established by many other examples of endemic fishes, both extant (Kornfield and Carpenter 1984; Parenti 1984; Parker and Kornfield 1995; Strecker et al . 1996; Seegers et al . 1999) and fossil (McCune et al . 1984). Whether such intralacustrine speciation could be sympatric has engendered considerable debate (Worthington 1954; Kosswig 1963; Ribbink 1994; Turner 1994), despite previous theoretical arguments that the evolution of reproductive isolation is extremely unlikely without geographic separation (Tregenza and Butlin 1999). Empirical evidence that speciation in some of these fishes occurred in sympatry has been growing, however (Meyer et al . 1990; Schliewen et al . 1994; Johnson et al. 1996a; McCune and Lovejoy 1998), and recent theoretical results suggest that sympatric speciation is more plausible than previously believed (e.g., Dieckmann and Doebeli 1999; Kondrashov and Kondrashov 1999; Chapter 5). According to these latter theoretical studies, nonrandom mating and ecological interactions, like intraspecific competition for resources, can initiate sympatric speciation. In this chapter, intralacustrine radiation of semionotid fishes during the Mesozoic is considered through a paleobiological perspective. While it is impossible to assess nonrandom mating in the fossil record, paleobiological studies do have the potential to illuminate pertinent aspects of ecology over a temporal scale impossible to study in extant organisms. First, some background on semionotid fishes and the ecological setting for their lives and preservation as fossils is given in Sections 18.2 and 18.3. In Section 18.4, parallel radiations of Semionotus in distinct lakes are described. These lacustrine radiations do, indeed, suggest an important role for ecology. Through detailed study of the history of a single lake (Section 18.5), it is shown that both intraspecific variation that subsequently became incorporated into new species and the first appearances of new species are concentrated in early lake history.

To investigate the relationships among the three main groups of extant neopterygian fishes--Amiidae, Lepisosteidae, and Teleostei--we sequenced fragments of three mitochondrial genes from 12 different actinopterygian fishes and translated the nucleotide sequences into amino acid sequences. When all three regions are considered together, Amiidae clusters with Lepisosteidae in the most parsimonious cladograms, but other clades, such as Neopterygii and Teleostei, that are well supported by morphological evidence fail to emerge as monophyletic. When the cytochrome b sequences are analyzed together with previously published sequences for other taxa, the majority-rule consensus tree is consistent with the monophyly of Teleostei and Neopterygii and marginally supports the Amiidae + Lepisosteidae clade. In either analysis, when Neopterygii and Teleostei are constrained to monophyly, all the most-parsimonious cladograms support the Amiidae + Lepisosteidae topology. Where molecules and morphology disagree, provisional morphology-based constraints on the analysis of molecular data offer a practical means of integrating the two types of data.

The Cichlid Fishes Nature's Grand Experiment in Evolution. By George W. Barlow . Perseus, Cambridge, MA, 2000. 351 pp. $28, C$42.50. ISBN 0-7382-0376-9. Although it emphasizes reproductive behavior and parental care over other aspects of cichlid biology, this lively account of an extraordinarily diverse group of fishes will interest evolutionary biologists, ecologists, and aquarium enthusiasts alike.

The living holostean fish Lepisosteus and the closely related Atractosteus offer a unique opportunity to study the development and homology of the ganoine-covered scales typical of early groups of actinopterygian fishes. Unlike the living chondrostean Polypterus, the scales of lepisosteids lack dentine and thus the role of the dentine, epidermis and mesodermal mesenchyme can be compared. Formation of the ‘preganoine’ is shown for the first time in Lepisosteus. Initial results show that in Lepisosteus ganoine is formed on the inner surface of a cell layer, apparently mesenchymal in origin, proliferating deep to the epidermal basement membrane. If this is correct ganoine in Lepisosteus is mesodermal and its formation has changed significantly from the pattern in the closely related fossil Semionotidae where dentine is present and is presumably involved in ganoine formation. The canals of Williamson in early fossil fishes were formed by migrating cells that played a major role in bone morphogenesis. The Lepisosteidae offer a unique opportunity to study these cells in a living vertebrate.

Fishes of the genus Semionotus diversified in the rift lakes of eastern North America during the Mesozoic (Newark Supergroup). Like the well-known cichlid fishes of the African great lakes, diverse complexes of semionotids were apparently endemic to a number of different lakes. Semionotid fishes show considerable morphological diversity in body shape and in a modified row of scales termed "dorsal ridge scales." A number of distinct dorsal-ridge-scale patterns characterize groups of species from the Newark Supergroup. Interestingly, about 5.5% of individuals examined have anomalous scales mixed in with otherwise stereotypic dorsal-ridge-scale patterns. In this study, I take advantage of nearly annual stratigraphic resolution to determine whether dorsal-ridge-scale anomalies are concentrated stratigraphically in the early phase of lake formation and colonization by semionotids. More than 1,700 specimens of semionotid fish were collected from a single lake deposit (cycle P4), representing approximately 21,000 years, in the Early-Jurassic Towaco Formation of the Newark Basin. Dorsal-ridge-scale anomalies are significantly more frequent in older than in younger lake sediments, which I interpret as being the result of relaxed selection during the early colonization of the lake. Anomalous variation parallels variation in dorsal ridge scales between species-groups. Some anomalies are atavisms, while others are unique or foreshadow future evolutionary events. One type of anomaly is incorporated into the dorsal-ridge-scale series of two new species that gave rise to a radiation in a subsequent lake filling the same topographic basin. Because both novelties and atavisms occur in the dorsal-ridge-scale series of single individuals, I argue that the disruptions of the same "developmental program" produced both atavistic and novel traits.

Lacustrine sedimentary sequences have tremendous potential for evolutionary studies because 1) the sedimentary record in lakes provides greater resolution than most other continental or marine sequences and 2) the lake environment seems conducive to speciation, as evidenced by the many examples of lacustrine species flocks. In this paper I present distributional data for 26 species of Semionotus in four temporally distinct lake deposits in the Newark Basin (Late Triassic-Early Jurassic). These data suggest that the effect of environmental cyclicity-the repeated cycles of formation and evaporation of lakes in the same basinis not to accumulate species diversity over the long term. Rather, the effect is to decrease diversity when lakes evaporate and, alternately, to provide ecological opportunity during lake expansion, thus allowing the proliferation of species.