Population Genetics of Marine Organisms

by Dennis Hedgecock

From its inception, U.S. GLOBEC has been concerned with resolving the systematics and population genetic structures of organisms targeted for long-term field study. This concern reflects a growing interest on the part of biological oceanographers and fisheries scientists in the theory and practice of population genetics, particularly as enhanced by molecular biological methods. Recent expressions of this interest, among others, have been the National Science Foundation Fellowships in Marine Biotechnology, the National Research Council's Ocean Studies Board planning meeting, "Marine Biodiversity and the Ocean Environment," held at the University of California, Irvine, in April 1993, and the recent symposium at the 1993 CalCOFI Conference, "Genetics of the Fauna of the California Current." This article is a personal view of exciting new developments in marine population genetics research and their application to U.S. GLOBEC.

Major scientific questions being addressed by population geneticists working on marine animals can be grouped under five headings: (1) identification of morphologically cryptic, sibling species; (2) amount and spatial structure of genetic diversity within species; (3) temporal genetic change; (4) retrospective analyses of historical oceanographic collections; (5) phylogenetic and phylogeographic analyses; and (6) development of theory and statistics to aid in the analysis and interpretation of rapidly accumulating, molecular data.

Sibling Species

A major contribution of population genetic studies to marine biology has been the identification of biological species within morphologically defined taxa, including some that are well studied such as Mytilus, Capitella, and Calanus (reviewed by Knowlton 1993). These discoveries, which are often serendipitous by-products of research directed at other questions, could eventually increase marine biodiversity at the species level by an order of magnitude. A systematic investigation of the frequency of sibling species in various taxa appears warranted. Prudence dictates that the taxonomy of all U.S. GLOBEC target organisms be confirmed by both traditional and molecular methods and that voucher specimens be kept.

Amount and Spatial Structure of Genetic Diversity within Species

The amount of genetic variation maintained in species is perhaps the most thoroughly studied aspect of marine population genetics. Early studies of protein polymorphism documented widely varying levels of genetic diversity among marine taxa, but causes of this variation are not entirely clear. Comparative studies of taxa differing in life-history or ecological traits have provided few compelling general explanations for the maintenance of different levels of genetic diversity in different taxonomic groups (Ward et al. 1992). Certainly, the amount of diversity measured for a particular taxon depends to a great extent on the particular type and set of genetic markers studied. Spatial structure of genetic diversity or population subdivision is the topic of most interest to oceanographers and the U.S. GLOBEC community, because it is tied to the hope that the geographic sources of recruitment to marine animal populations might be identified by their genetic makeup. Indeed, "biotechnology" has in part been sold to this community as the solution to this important, mass transport problem. For most species of interest, those that comprise the zooplankton broadly speaking, this hope is not well founded in logic or fact. Population genetic theory tells us that dispersal among geographic populations, even very low levels of dispersal on the order of a few migrants per generation, can eliminate the very genetic differences among geographic populations that are supposed to permit identification of provenance. Early studies of proteins established that species with dispersing, planktotrophic larvae had, as expected, much less geographic variation or population subdivision than species with poorly dispersing, lecithotrophic larvae (Burton 1983). The many genetic studies that have now been made of fish and invertebrate marine species with planktonically dispersing larvae have clearly shown them to be genetically quite homogeneous over very large regions, though not often over their entire geographic ranges. A common measure of population genetic differences is FST, the ratio of the variance of allelic frequencies among localities to the maximum variance that would obtain if each locality were fixed for one of the alternative alleles without change in mean allelic frequency. FST is generally much less than 0.05 for marine species with planktonic larvae.

The oceanographer's problem is to detect if a sample of zooplankton is a genetic mixture and if so, to determine the contributions of different geographic populations to the mix. This problem has been solved for certain mixed-stock fisheries, particularly for anadromous species; sophisticated statistical analysis of genetic data can identify source populations and their relative contributions to ocean salmon catches (Utter and Ryman 1993). These methods work well for salmon because anadramous source populations are identifiable in space and are genetically distinct, with FST values ranging up to 0.5; these same methods are not likely to work for the many marine species that lack obvious spatial genetic structure (Fig. 1).

Identification of sources and sinks of zooplanktonic populations is critical to understanding their distribution and abundance. It remains to be seen, however, whether the promise of greater resolution of individual and population genetic differences afforded by DNA analyses will make such identifications tractable. The fundamental limitation may be the dispersal biology of such species, which homogenizes the frequencies of alleles at all loci, be they DNA sequences or allozymes.

Nevertheless, studies of spatial genetic variation should be made for all U.S. GLOBEC target species as a part of a baseline population genetic description. Such studies may reveal exceptions to the general rule or they may reveal a previously unrecognized barrier to dispersal that has resulted in a major genetic subdivision. As a rule, however, we should not expect such studies to yield conclusive information about the sources of recruits or the water masses bearing them.

Temporal Genetic Change

Despite the generalization that marine species with planktonic dispersal are genetically homogeneous over large geographic regions, statistical comparisons of allelic frequencies among samples taken sometimes on scales of meters often indicate significant, "chaotic," microspatial heterogeneity embedded within the basin-scale similarity of allelic frequencies. Recent work on this paradox has focused attention on temporal genetic change in marine populations, which in the few studies conducted thus far appears to be as large or larger than geographic variation on basin scales (reviewed by Hedgecock 1994).

Microspatial heterogeneity and temporal change may be jointly explained by the hypothesis that a large variance in individual reproductive success results from a sweepstakes-chance matching of reproductive effort with spatio-temporal windows of oceanographic conditions conducive to spawning, fertilization, larval survival, and recruitment (Hedgecock 1994). According to this hypothesis, only small fractions (from 1/100 to 1/100,000) of spawning adults effectively reproduce and replace standing adult populations each generation, so that random genetic drift of allelic frequencies should be measurable in some populations. This prediction has been borne out by temporal studies of semi-isolated natural oyster populations. Amounts of genetic drift imply effective population sizes that are many orders of magnitude less than the simple abundance of adults. More detailed studies of larval populations are needed to test a second prediction that specific cohorts of larvae should show genetic evidence of having been produced by only a segment of the potential parental pool.

This hypothesis establishes a connection between oceanography and population genetics in the study of recruitment and may explain how local adaptations and speciation can occur in seemingly large, well-mixed marine populations. Temporal genetic studies are therefore germane to U.S. GLOBEC field studies.

Retrospective Analyses of Historical Collections

An exciting new technology for enzymatically amplifying specific DNA sequences from small and preserved biological samples, the polymerase chain reaction or PCR (Saiki et al 1988) can potentially be applied to the study of preserved material in large historical oceanographic collections such as those maintained at Woods Hole Oceanographic Institute and Scripps Institution of Oceanography. Molecular methods could aid in a more rapid systematic treatment of these collections and be used to establish genetic histories for particular species of interest. Geneticists urge that future collections be stored in alcohol rather than formalin, which can chemically degrade nucleic acids.

Phylogenetics, Phylogeography, and Paleo-oceanography

Molecular genetic analyses are being used to reconstruct genetic phylogenies at all taxonomic levels and for many phyla. The application of phylogenetic methods to molecular as well as organismal traits such as morphology, life history and behavior, will undoubtedly shed new light on the evolution and systematics of marine organisms. Comparisons of genetic divergence within and between closely related species across paleo-oceanographic barriers of known age, such as the arctic land barrier or the Isthmus of Panama, are useful for calibrating rates of molecular evolution and reconstructing the history of faunal exchanges. Ultimately such studies may provide the basis for development of biotechnological tools for rapid, automated classification of oceanographic samples and collections.

Within the past decade, the application of phylogenetic approaches to molecular variation within species has yielded new insights into population histories and a new conceptual framework for uniting the traditionally separate disciplines of systematics and population genetics (Avise et al. 1987). Studies of mitochondrial DNA in several species living along the Gulf of Mexico and Atlantic coasts of the U.S. have revealed concordant patterns of major genetic subdivisions. In all of these species, Gulf haplotypes give way to Atlantic haplotypes across a previously recognized biogeographical boundary in southeastern Florida. Gulf and Atlantic haplotypes represent clades that separated over a million years ago. Thus, "phylogeographic" patterns reflect the persistence of historical events in the gene pools of organisms. Such information is relevant to management and conservation efforts and begs for inter-disciplinary, paleo-oceanographic explanation. U.S. GLOBEC studies of species in the California Current may well encounter similar intraspecific, phylogeographic patterns of variation across the biogeographic boundary at Point Conception.

Data Analysis, Interpretation, and Archiving

Molecular methods are beginning to generate more information than can be presently handled by theory and statistical methods developed for the analysis of allozyme or early DNA-RFLP data. As the potential for resolving genetic individuality at the level of DNA sequences is realized, identification of relatedness and clustering of individuals into biologically meaningful groups become challenging problems. Given the density of population genetic information in the future, such computations will likely require routine use of supercomputers. There is need also to develop new theory for gene phylogenies at the intraspecific level so that the causes of discordant phylogeographic patterns among different classes of molecular markers can be interpreted. Finally, genetic and organismal information from U.S. GLOBEC studies should be entered into perpetual data sets that can serve as the basis for detecting long-term trends or shifts in biodiversity. (Dennis Hedgecock is with the Bodega Marine Laboratory, University of California, Davis, and is a former member of the U.S. GLOBEC Scientific Steering Committee.)


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