David K. Jacobs

Work Address:
Los Angeles, CA 90095

Professor, Ecology and Evolutionary Biology
Research Interests
EVOLUTION & DEVELOPMENT A major focus of investigation in my laboratory is the evolution of the body-plan through the comparative study of developmental genes. The intent of this work is to understand evolutionary events that were fundamental to the generation of the disparate range of invertebrate morphology. We take a number of approaches to the study of development including the phylogenetic analysis of developmental regulatory genes, the recovery of important developmental molecules through PCR and the study of the expression patterns of these molecules with antibody studies and in situ hybridi-zation. As we work on a large number of invertebrate taxa we take a far more comparative approach than other labs that study the evolution of development. We also integrate our results with the fossil record of morphologic evolution. Phylogenetic, “gene tree‿ approach– Mapping the presence of homeodomains on recent phyloge-netic analyses of the eukaryotes indicates that homeodomains are exclusive to a clade that contains all the complex multicellular eukaryotes - plants, slime molds, fungi and Metazoa. In our gene tree analyses, a surprising number of these developmentally important molecules appear to have evolved basal to, or within the base of, the Metazoa, as they are shared between plants and animals or between the Bilateria and more basally branching Metazoa, such as cnidarians and sponges. In addition to general analyses of homeodomains, we have published developmental gene tree analyses assessing the support for homology of eyes and hearts across Metazoa, a comprehensive analysis of Win-gless/Wnt gene, and Nk-2 homeodomain gene families. Rates and Divergence Times- We recently argued that “protein clocks‿ used to infer the time of divergence of major groups, including the divergence of animal groups, are methodologically biased towards early divergence times, and that there is strong evidence for rate heterogeneity correlated with genome size and generation time. Using a simple statistical approach we document that there are strong lineage, rather than gene specific, biases associated with model taxa, and that early molecular dates for the metazoan divergence are a product of this bias. We are currently expanding this work to examine larger numbers of taxa as more sequence data become available. Some of this data is from Flatworms and is based on EST sequencing we have done (see Flatworms below) as well as from data available in genbank. engrailed– Our recently published work on molluscs, combined with observations from other labo-ratories, suggests that this gene delimits regions of skeleton formation across the invertebrate Bilate-ria. This observation may explain the sudden appearance of skeletal elements in the fossil record near the base of the Cambrian. The antecedents of muscle - The homeodomain gene trees discussed above reveal the presence in sponges of homeodomains involved in mesoderm and muscle differentiation in vertebrates and in-sects. To follow up on this evidence we have used PCR to recover from sponges a homologue of a gene, Mef-2, which is an essential component of the regulatory cascade that leads to the differentia-tion of muscles in flies and vertebrates. This result suggests that sponges contain the evolutionary antecedents of muscles. We are now in the process of assessing precisely which cells in sponges express this gene, most likely the elongate contractile cells responsible for closing the oscula. To address this issue we have established a collaboration to study gene expression in sponges with Sally Leys of the University of Alberta. Flatworm neural development - We have an NSF-funded collaboration with Volker Hartenstein fo-cusing on neural development in two groups of flatworms, acoels and macrostomids. This work pro-vides comparative data to interpret the evolution of bilaterian neural development. We are now ex-amining the expression of a range of neural-developmental markers recovered in my lab. In addition, we have generated expressed sequence tag (EST) data from cDNA libraries of these flatworms. These data are proving useful in studies of development, phylogeny and evolutionary rate. Sensory Structures in Basal Metazoa- In NASA-funded research, we have recovered homologues of a number of genes involved in sense organ and sensory cell differe ntiation, e.g. sine oculis , optix, eyes absent , as well as the POU homeodomain containing genes Brain1, Brain3 & Pit, from mol-luscs, flatworms, jellyfish and sponges. In situ hybridization documents that Brain 3 is expressed in the statocyst and eye of the developing medusa of the jellyfish Aurelia suggesting shared ancestry of sense organ development from jellyfish to vertebrates. However, the presence of similar molecules in sponges suggests an even deeper evolutionary antecedent to sense organs - perhaps embodied in the sensory capacity, cellular grouping and interaction of choanocytes, the ciliated collar cells of the sponge. Recovery of a related gene Pit1, previously thought to be specificto vertebrate pituitary de-velopment, in the basal metazoans suggests that the pituitary, a derived sense organ, had a deeper evolutionary origin preceding the evolution of its specific vertebrate function. Thus the recovery of these molecules is forcing the consideration of new interpretations and generating a basis for new theory regarding the evolution of neural and sensory systems HISTORICAL & PHYSICAL PROCESSES CONTROLLING SPECIATION AND DIVERSITY IN THE SEA We examine historical causes of biological patterns, including factors controlling the diversity history of global and regional faunas, such as climatic and oceanographic change. A component of this work is molecular, examining neutral markers as well as markers under selection. These studies are directed at using molecular evidence (e.g. sequence & microsatellite markers) to understand the geographic components of evolutionary process- a discipline referred to as phylogeography. We then integrate multiple studies to undertand the regional evolutionary history of faunas. Much of our work has focussed on the Pacific Coast of Nort h America. We are also interested in the history of how global-scale processes control diversity, including the history of deep-sea and hot-vent faunas. Studies of Estuarine Taxa ?\200\223 My students and I examine the population genetic structure of estuarine restricted taxa. West Coast estuaries provide a linear arr ay of habitat islands that are susceptible to effective phylogeographic analyses. We have work in progress on several species of fish and mol-luscs as well as a detailed study of the trematode parasites of snails. Currently we are expanding our area of research, which has extended south from Alaska along the West Coas t, to include the Gulf of California. Detailed, Phylogeography & Metapopulation Analysis of Endangered Species ?\200\223 Our phylogeographic work has led to studies of, fishes specifically, gobies and stickleback, that are feder-ally listed under the endangered species act. These tax a appear to be ideal for understanding the im-pacts of local extinction and recolonization (metapopulation behavior) on genetic structure. This has direct implications for management of these endangered species, as well as broad implications for assessing the general impacts of metapopulation behavior, an issue of critical scientific, as well as applied interest in conservation.

Evolution/Development of Invertebrate Body Plans, Paleobiology and Marine Speciation Our laboratory brings an evolutionary perspective to the study of developmental genetics. In particular, we are investigating the role played by developmental genes in the early, geologically rapid Cambrian evolution of animal morphology. Comparison of developmental gene expression between morphologically distinct kinds of organisms is the primary focus in the laboratory. To this end, we have retrieved the engrailed gene via PCR from all the major classes of molluscs. We are now in the process of comparing the expression pattern of this gene through in situ hybridization studies in clams, snails, and chitons. In addition, we are reconstructing histories of gene duplication events using phylogenetic methods. The phylogenies produced permit a better understanding of the evolution of the genes, as well as shed light on the sequence of events in the evolution of animal development. Evolutionary hypotheses generated by examination of these developmental gene trees are then tested against the fossil and phylogenetic record of animal evolution. Gene sequences are also useful in reconstructing the relationships between organisms. We are especially motivated to explore such branching histories of organisms when they relate to paleontology, historical aspects of marine biology or climatic process. For example, a new project in the lab involves the use of molecular markers to study gene flow associated with the transport of planktonic larvae in marine organisms. Another molecular study investigates the geologic and climatic isolation of populations of jellyfish in salt water lakes, separated from the sea. In the lab we have ongoing interests in several non-molecular questions in invertebrate paleontology and paleoclimatology. Previous studies have explored the functional morphology of fossil cephalopods. Other studies pertain to the effects of milankovitch-driven climate change on sea level in non-glacial times, mans ongoing contribution to sea-level change, and climatic influences on the evolution of wetland faunas.

Ramachandra, N. B., R. D. Gates, P. D. Ladurner, D. K. Jacobs & V. Hartenstein. Neurogenesis in the Primitive Bilaterian Neochildia fusca I. Normal Development and Isolation of Genes Controlling Neural Fate. . Developmental Genes & Evolution ; .
Jacobs, D. K. & Gates, R. D. Developmental Genes and the Reconstruction of Metazoan Evolution ? Implications of Evolutionary Loss, Limits on Inference of Ancestry and Type 2 Errors. Integrative & Comparative Biology 2003; 43: 619-646.
Lee, SE Gates, RD Jacobs, DK Gene fishing: the use of a simple protocol to isolate multiple homeodomain classes from diverse invertebrate taxa. Journal of molecular evolution. . 2003; 56(4): 509-16.
Holland, ND Venkatesh, TV Holland, LZ Jacobs, DK Bodmer, R AmphiNk2-tin, an amphioxus homeobox gene expressed in myocardial progenitors: insights into evolution of the vertebrate heart. Developmental biology. . 2003; 255(1): 128-37.
Gates, R.D., T. Hadrys, Arenas-Mena, C. & D. K. Jacobs. Determining spatial and temporal patterns of developmental gene expression in vertebrates and invertebrates using in situ hybridization techniques. . In: Methods and Tools in Biosciences and Medicine: Techniques in Molecular Systematics and Evolution. (R. DeSalle ed.) 2002; 365-399.
Dawson, MN Louie, KD Barlow, M Jacobs, DK Swift, CC Comparative phylogeography of sympatric sister species, Clevelandia ios and Eucyclogobius newberryi (Teleostei, Gobiidae), across the California Transition Zone. Molecular ecology. . 2002; 11(6): 1065-75.
Ramachandra, NB Gates, RD Ladurner, P Jacobs, DK Hartenstein, V Embryonic development in the primitive bilaterian Neochildia fusca: normal morphogenesis and isolation of POU genes Brn-1 and Brn-3. Development genes and evolution. . 2002; 212(2): 55-69.
Lee, SE Gates, RD Jacobs, DK The isolation of a Distal-less gene fragment from two molluscs. Development genes and evolution. . 2001; 211(10): 506-8.
Jacobs, D. K. Buoyancy, Hydrodynamics and Structure in Chambered Cephalopods. Paleobiology II 2001; 2: 397-401.
Alroy, J, et al. Effects of sample standardization on estimates of Phanerozoic marine diversification. Proc. Nat. Acad.Sci. USA 2001; 98: 6261-6266.
Dawson, MN Staton, JL Jacobs, DK Phylogeography of the tidewater goby, Eucyclogobius newberryi (Teleostei, Gobiidae), in coastal California. Evolution; international journal of organic evolution. . 2001; 55(6): 1167-79.
Dawson, MN Jacobs, DK Molecular evidence for cryptic species of Aurelia aurita (Cnidaria, Scyphozoa). The Biological bulletin. . 2001; 200(1): 92-6.
Schubert, M Holland, LZ Holland, ND Jacobs, DK A phylogenetic tree of the Wnt genes based on all available full-length sequences, including five from the cephalochordate amphioxus. Molecular biology and evolution. . 2000; 17(12): 1896-903.
Seki, K., K. Tanabe, N. H. Landman, & D. K. Jacobs Hydrodynamic analysis of some Late Cretaceous desmoceratine ammonites. Revue de Paleobiologie, Geneve 2000; 8: 172-179.
Jacobs, DK Wray, CG Wedeen, CJ Kostriken, R DeSalle, R Staton, JL Gates, RD Lindberg, DR Molluscan engrailed expression, serial organization, and shell evolution. Evolution & development. . 2000; 2(6): 340-7.
Lee, SE Jacobs, DK Expression of Distal-less in molluscan eggs, embryos, and larvae. Evolution & development. . 1999; 1(3): 172-9.
Jacobs, DK Lindberg, DR Oxygen and evolutionary patterns in the sea: onshore/offshore trends and recent recruitment of deep-sea faunas. Proceedings of the National Academy of Sciences of the United States of America. . 1998; 95: 9396-401.
Dawson, MN Raskoff, KA Jacobs, DK Field preservation of marine invertebrate tissue for DNA analyses. Molecular marine biology and biotechnology. . 1998; 7(2): 145-52.
Jacobs, David K Chambered, Cephalopod Shells, Buoyancy, Structure and Decoupling: History and Red Herrings. Palaios 1996; 11: 610-614.
Jacobs, D. K. and J. A. Chamberlain, Jr. Hydrostatic and Hydrodynamic Issues in Ammonoid Functional Morphology. Ammonoid Paleobiology 1996; 169-224.
Agosti, D Jacobs, D DeSalle, R On combining protein sequences and nucleic acid sequences in phylogenetic analysis: the homeobox protein case. Cladistics : the international journal of the Willi Hennig Society. . 1996; 12: 65-82.
Jacobs, D. K., & D. L. Sahagian Milankovitch fluctuations in sea level and recent trends in sea level change: Ice may not always be the answer. Sequence Stratigraphy and Sea-Level Change 1995; 329-366 .
Wray, CG Jacobs, DK Kostriken, R Vogler, AP Baker, R DeSalle, R Homologues of the engrailed gene from five molluscan classes. FEBS letters. . 1995; 365(1): 71-4.
Jacobs, D. K, N. H. Landman & J. A. Chamberlain, Jr. Ammmonite shell shape varies with facies and hydrodynamics. Geology 1994; 22: 905-908..
Jacobs, DK Developmental genes and the origin and evolution of Metazoa. EXS. . 1994; 69: 537-49.
Sahagian, D. L., F. W. Schwartz & D. K. Jacobs Direct anthropogenic contributions to 20th century sea level rise. Nature 1994; 367: 54-57..
Jacobs D. K. & N. H. Landman Nautilus - model or muddle. Lethaia 1994; 27: 95-96..
Jacobs, D. K., & D. L. Sahagian. Climate-induced fluctuations in sea level during non-glacial times. Nature 1993; 361: 710-712..
Jacobs, D.K., & N. H. Landman. Is Nautilus a good model for the function and behavior of ammonoids ?. Lethaia 1993; 26: 101-110..
Jones, D. S., & D. K. Jacobs. Photosymbiosis in Clinocardium nuttalli: Implications for tests of photosymbiosis in fossil molluscs. Palaios 1992; 7: 86-95..
Jacobs, D. K. Shape, drag and power, in ammonoid swimming. Paleobiology 1992; 18: 203-220..
Miller, A. I., G. Llewellyn, K. M. Parsons, H. Cummins, B. J. Greenstein, M. R. Boardman, & D. K. Jacobs. The effect of Hurricane Hugo on molluscan skeletal distributions, Salt River Bay, St. Croix, U. S. Virgin Islands. 20 1992; 20: 23-26..
Jacobs, D. K. The support of hydrostatic load in cephalopod shells: A history of adaptive and ontogenetic explanations in morphology and evolution. Evolutionary Biology 1992; 26: 287-349..
Jacobs, D. K. Sutural pattern and shell stress in Baculites with implications for other cephalopod shell morphologies. Paleobiology 1990; 16: 336-348..
Jacobs, DK Selector genes and the Cambrian radiation of Bilateria. Proceedings of the National Academy of Sciences of the United States of America. . 1990; 87(11): 4406-10.