David K. Jacobs

Effects of sampling standardization on estimates of Phanerozoic marine diversification.

Global diversity curves reflect more than just the number of taxa that have existed through time: they also mirror variation in the nature of the fossil record and the way the record is reported. These sampling effects are best quantified by assembling and analyzing large numbers of locality-specific biotic inventories. Here, we introduce a new database of this kind for the Phanerozoic fossil record of marine invertebrates. We apply four substantially distinct analytical methods that estimate taxonomic diversity by quantifying and correcting for variation through time in the number and nature of inventories. Variation introduced by the use of two dramatically different counting protocols also is explored. We present sampling-standardized diversity estimates for two long intervals that sum to 300 Myr (Middle Ordovician-Carboniferous; Late Jurassic-Paleogene). Our new curves differ considerably from traditional, synoptic curves. For example, some of them imply unexpectedly low late Cretaceous and early Tertiary diversity levels. However, such factors as the current emphasis in the database on North America and Europe still obscure our view of the global history of marine biodiversity. These limitations will be addressed as the database and methods are refined.

Molecular evidence for cryptic species of Aurelia aurita (Cnidaria, Scyphozoa)

Morphological taxonomy suggests that marine faunas are species poor compared to terrestrial and freshwater faunas (1). This dichotomy has been attributed to the unique potential of marine plankters for distant dispersal across homogenous oceans with few barriers to gene flow (2). The relative scarcity of opportunities for allopatric divergence has resulted in depauperate marine faunas characterized by a high proportion of widespread or cosmopolitan species. Aurelia aurita (Linnaeus) has been considered a good example of such a cosmopolite (3, 4, 5, 6). However, recent molecular studies have revealed cryptic species in many marine taxa (7), suggesting that marine biodiversity is higher and opportunities for speciation have been more frequent than generally recognized. Here, we present nuclear and mitochondrial DNA sequence evidence of seven sibling species of Aurelia aurita and two additional species, A. limbata Brandt and A. labiata Chamisso & Eysenhardt. These sequence data indicate speciation events as early as the late Cretaceous or early Tertiary, consistent with the formation of well-recognized biogeographic barriers to gene flow in the seas. Traditionally, the genus Aurelia comprises two species: A. limbata, a polar species, and A. aurita, a common inhabitant of nearshore waters circumglobally between about 50 °N and 55 °S (3, 4, 5; Fig. 1). Perhaps due to its ubiquity, A. aurita has become a popular research organism for studies as diverse as protein chemistry, development, ecology, ethology, and hydrodynamics (6). A. aurita also is economically important because worldwide it preys on or competes with larvae of commercial fisheries and because swarms of medusae may impede trawling or block power-plant intakes (8). Furthermore, this “pest” has been introduced at least into San Francisco Bay (9) and possibly many other places (10). A. aurita is also familiar to nonspecialists because it is the most commonly displayed medusa in public aquaria. The systematics of A. aurita therefore is of considerable scientific, economic, and general interest. Aurelia has a typical bipartite scyphozoan life history in which benthic scyphopolyps asexually strobilate ephyrae that grow into sexual medusae, the females of which brood larvae that settle into the shallow coastal benthos within a few days of being released. Of these life stages, the medusa probably is the principal dispersal phase because only the medusa is both long-lived (several months to more than one year; 11) and planktonic (6). The potential of medusae for distant dispersal is consistent with the current classification of A. aurita as a circumglobal, almost cosmopolitan, species (4, 5). However, A. aurita medusae in Saanich Inlet, British Columbia, and perhaps elsewhere, migrate directionally (12), maintaining breeding aggregations within isolated inlets and probably limiting gene flow among populations. Consistent with limited gene flow, allozyme differences have been found between populations of A. aurita in the eastern and western Atlantic Ocean, the Gulf of Mexico, and the eastern and western Pacific Ocean (9, 13). In addition, one species, A. labiata, was recently recognized as native to Pacific North America and distinct from A. aurita (10). Novel DNA sequence data from nuclear internal transcribed spacer one (ITS-1) and mitochondrial cytochrome oxidase c subunit I (COI) reveal highly structured gene genealogies and at least nine distinct clades of Aurelia (Figs. 1, 2). Several lines of argument suggest that these clades warrant recognition as distinct species. First, the length of ITS-1 varies from 240 nucleotides (Charlestown, RI) to 360 nucleotides (Cananeia, Brazil). Such length variation is comparable to that found among congeneric species of Received 7 August 2000; accepted 19 October 2000. * To whom correspondence should be addressed at Coral Reef Research Foundation, Box 1765, Koror, PW 96940, Palau. Reference: Biol. Bull. 200: 92–96. (February 2001)

Extensive population genetic structure in the giraffe.

BackgroundA central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation.ResultsBy analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations.ConclusionSuch extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations.

Comparative phylogeography of sympatric sister species, Clevelandia ios and Eucyclogobius newberryi (Teleostei, Gobiidae), across the California Transition Zone

It is paradigmatic in marine species that greater dispersal ability often, but not always, results in greater gene flow and less population structure. Some of the exceptions may be attributable to studies confounded by comparison of species with dissimilar evolutionary histories, i.e. co‐occurring species that are not closely related or species that are closely related but allopatric. Investigation of sympatric sister species, in contrast, should allow differences in phylogeographic structure to be attributed reliably to recently derived differences in dispersal ability. Here, using mitochondrial DNA control region sequence, we first confirm that Clevelandia ios and Eucyclogobius newberryi are sympatric sister taxa, then demonstrate considerably shallower phylogeographic structure in C. ios than in E. newberryi. This shallower phylogeographic structure is consistent with the higher dispersal ability of C. ios, which most likely results from the interaction of habitat and life‐history differences between the species. We suggest that the paradigm will be investigated most rigorously by similar studies of other sympatric sister species, appended by thorough ecological studies, and by extending this sister‐taxon approach to comparative phylogeographic studies of monophyletic clades of sympatric species.

Molluscan engrailed expression, serial organization, and shell evolution

SUMMARY Whether the serial features found in some molluscs are ancestral or derived is considered controversial. Here, in situ hybridization and antibody studies show iterated engrailed‐gene expression in transverse rows of ectodermal cells bounding plate field development and spicule formation in the chiton, Lepidochitona caverna, as well as in cells surrounding the valves and in the early development of the shell hinge in the clam, Transennella tantilla. Ectodermal expression of engrailed is associated with skeletogenesis across a range of bilaterian phyla, suggesting a single evolutionary origin of invertebrate skeletons. The shared ancestry of bilaterian‐invertebrate skeletons may help explain the sudden appearance of shelly fossils in the Cambrian. Our interpretation departs from the consideration of canonical metameres or segments as units of evolutionary analysis. In this interpretation, the shared ancestry of engrailed‐gene function in the terminal/posterior addition of serially repeated elements during development explains the iterative expression of engrailed genes in a range of metazoan body plans.

Buoyancy and Hydrodynamics in Ammonoids

Information pertaining to the function of ammonoid shells is generated by analogy to living cephalopods, by measurement or experiment designed to elucidate the properties of the ammonoid shell in life situations, and by examination of the distribution and sedimentary environments in which ammonoid fossils are preserved. Virtually all discussions of ammonoid shell function implicitly or explicitly incorporate more than one of these approaches. The combination of analogy with empirical work in the field and laboratory makes the reconstruction of the function of ammonoid shells and interpretation of ammonoid life habits and mode of life particularly intriguing. These interpretations have led to many lively debates among paleobiologists. In this chapter, we examine ammonoid buoyancy and locomotion. We evaluate arguments that have been used to reconstruct the buoyancy and locomotor properties of these extinct cephalopods, discuss recent advances in the understanding of ammonoid locomotion, and suggest directions in which the study of these aspects of ammonoid paleobiology may proceed in the future. Other chapters of this book explore aspects of the structural issues pertaining to the implosion strength of ammonoid shells (Hewitt, Chapter 10, this volume) as well as the environmental information that can be brought to bear on the subject (Westermann, Chapter 16, this volume).

Amphink2-tin, an amphioxus homeobox gene expressed in myocardial progenitors: insights into evolution of the vertebrate heart

We isolated a full-length cDNA clone of amphioxus AmphiNk2-tin, an NK2 gene similar in sequence to vertebrate NK2 cardiac genes, suggesting a potentially similar function to Drosophila tinman and to vertebrate NK2 cardiac genes during heart development. During the neurula stage of amphioxus, AmphiNk2-tin is expressed first within the foregut endoderm, then transiently in muscle precursor cells in the somites, and finally in some mesoderm cells of the visceral peritoneum arranged in an approximately midventral row running beneath the midgut and hindgut. The peritoneal cells that express AmphiNk2-tin are evidently precursors of the myocardium of the heart, which subsequently becomes morphologically detectable ventral to the gut. The amphioxus heart is a rostrocaudally extended tube consisting entirely of myocardial cells (at both the larval and adult stages); there are no chambers, valves, endocardium, epicardium, or other differentiated features of vertebrate hearts. Phylogenetic analysis of the AmphiNk2-tin sequence documents its close relationship to vertebrate NK2 class cardiac genes, and ancillary evidence suggests a relationship with the Drosophila NK2 gene tinman. Apparently, an amphioxus-like heart, and the developmental program directing its development, was the foundation upon which the vertebrate heart evolved by progressive modular innovations at the genetic and morphological levels of organization.

Phylogeography of the tidewater goby, Eucyclogobius newberryi (Teleostei Gobiidae) in coastal California

Abstract.— The tidewater goby, Eucyclogobius newberryi, inhabits discrete, seasonally closed estuaries and lagoons along approximately 1500 km of California coastline. This species is euryhaline but has no explicit marine stage, yet population extirpation and recolonization data suggest tidewater gobies disperse intermittently via the sea. Analyses of mitochondrial control region and cytochrome b sequences demonstrate a deep evolutionary bifurcation in the vicinity of Los Angeles that separates southern California populations from all more northerly populations. Shallower phylogeographic breaks, in the vicinities of Seacliff, Point Buchon, Big Sur, and Point Arena segregate the northerly populations into five groups in three geographic clusters: the Point Conception and Ventura groups between Los Angeles and Point Buchon, a lone Estero Bay group from central California, and San Francisco and Cape Mendocino groups from northern California. The phylogenetic relationships between and patterns of molecular diversity within the six groups are consistent with repeated, and sometimes rapid, northward and southward range expansions out of central California caused by Quaternary climate change. Plio‐Pleistocene tectonism, Quaternary coastal geography and hydrography, and historical human activities probably also influenced the modern geographic and genetic structure of E. newberryi. The phylogeography of E. newberryi is concordant with phylogeographic patterns in several other coastal California taxa, suggesting common extrinsic factors have had similar effects on different species. However, there is no evidence of a phylogeographic break coincident with a biogeographic boundary at Point Conception.

Shape, drag, and power in ammonoid swimming

This study assesses swimming potential in a variety of ammonoid shell shapes on the basis of coefficients of drag (Cd) and the power needed to maintain a constant velocity. Reynolds numbers (Re) relevant to swimming ammonoids, and lower than those previously studied, were examined. Power consumption was scaled to a range of sizes and swimming velocities. Estimates of power available derived from studies of oxygen consumption in modern cephalopods and fish were used to calculate maximum sustainable swimming velocities (MSV). Laterally compressed, small thickness ratio (t. r.) ammonoids, previously assumed to be the most efficient swimmers, do not experience the lowest drag or power consumption at all sizes and velocities. At low values of size and velocity associated with Reynolds numbers below 104, less compressed forms have smaller drag coefficients and reduced power requirements. At hatching a roughly spherical shell shape would have minimized drag in ammonoids; with increasing size, hydrodynamic optima shift toward compressed morphologies. The high energetic cost of ammonoid locomotion may have limited dispersal and excluded ammonoids from high current velocity environments.

sine oculis in basal Metazoa

AbstractWe report the recovery of homologs of Six1/2/sine oculis (so), a homeodomain-containing member of the Six-gene family, from a diverse set of basal Metazoa, including representatives of the poriferan classes Demospongia, Calcarea and Hexactinellida, the cnidarian classes Hydrozoa, Scyphozoa and Anthozoa, as well as a ctenophore. so sequences were also recovered from a platyhelminth, an echiurid and two bivalve molluscs, members of the super-phyletic group Lophotrochozoa. In the case of the platyhelminth, multiple distinct so sequences were recovered, as well as a member of the related group Six4/5/D-Six4. Extended sequences of the so gene were recovered from the demosponge, Haliclona sp., and the scyphozoan Aurelia aurita via PCR, and 3′ RACE. The affinities of all recovered sequences were assessed using a parsimony analysis based on both nucleic and amino acid sequence and using successive character weighting. Our results indicate that so is highly conserved across the animal kingdom. Preliminary expression data for Aurelia reveal that transcripts of the so homolog are present in the manubrium as well as in the rhopalia, which contain the statocyst and eyes, in the free-swimming ephyra and juvenile stages of these jellyfish.