Amy R. McCune

Morphology of the Semionotus elegans species group from the Early Jurassic part of the Newark Supergroup of eastern North America with comments on the Family Semionotidae (Neopterygii)

ABSTRACT 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...

Reinventing species selection with molecular phylogenies

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.

Ontogeny and Phylogeny in the Northern Swordtail Clade of Xiphophorus

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-

Twenty ways to lose your bladder: common natural mutants in zebrafish and widespread convergence of swim bladder loss among teleost fishes

Summary 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 traits 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.

Biogeographic and stratigraphic evidence for rapid speciation in semionotid fishes

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.

Homology of lungs and gas bladders: Insights from arterial vasculature

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. J. Morphol., 2013.

Evolutionary novelty and atavism in the Semionotus complex : relaxed selection during colonization of an expanding lake

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.

Expression of a lung developmental cassette in the adult and developing zebrafish swimbladder

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.

Using Genetic Networks and Homology to Understand the Evolution of Phenotypic Traits

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.

Lakes as laboratories of evolution; endemic fishes and environmental cyclicity

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.