| Martha Burford |
| Haibin Zhang |
Cornell Graduate Students
| Laura Eierman |
U. Maryland Graduate Students
| Colin Rose |
| Gang Chen |
| Maria Murray |
| Peter Thompson |
Previous Hare Lab members
Postdocs
| Inken Kruse (currently at IFM-Geomar, Kiel, Germany) |
| Roldan Munoz (currently at NOAA/NFMS Beaufort, NC) |
Undergraduates (U. Maryland)
| Kristina Cammen |
| Olga Peterfalvy |
| Andrew Ascione |
| Ying Yi Zheng |
| Emmanuel Mallam |
| Sarah Beck |
Current Research Topics
Current Research Topics
Diversification at a zoogeographic province boundary
Clustered species range limits in eastern Florida represent a widely recognized boundary between warm-temperate and sub-tropical faunistic provinces. A compression of latitudinal thermoclines along the Florida coast implicates climate as a driving force shaping this community transition, but few studies have directly compared the importance of climate versus hydrographic dispersal barriers or species interactions. The eastern oyster, Crassostrea virginica, is nearly-continuously distributed around Florida, providing an exceptional intraspecific model for distinguishing the relative importance of pre- and postsettlement mechanisms structuring estuarine populations across the province boundary in eastern Florida. A major goal in the Hare lab, funded by NSF, is to understand the biotic and abiotic factors that maintain population differentiation in the oyster, and ultimately to test the generality of these influences on other codistributed species.
Portions of a genetic cline in the oysters, first described as sharply 'stepped' at Cape Canaveral based on 1991 samples, have been stable for the past dozen years (~6 generations; K. Kammen senior thesis). Both dispersal barriers and selection could be maintaining this steep genetic cline. Oysters only occur in the hydrographically semi-closed lagoons behind barrier beaches in eastern Florida, where larval dispersal is predicted to be small-scale, bidirectional and follow a stepping-stone pattern. However, if larvae are flushed out and re-enter lagoons, then coastal currents may generate a leap-frog and directional pattern of dispersal. Dispersal directionality could be a particularly important aspect of this system, and province boundaries in general, because asymmetrical gene flow can steepen clinal variation and truncate species ranges along a selection gradient (Hare et al. 2005). Multilocus assignment tests on newly-settled oysters are being used to measure contemporary dispersal distances and direction without recourse to equilibrium theory. These patterns will be compared with known dispersal constraints and current flow patterns.
The spatial scale of population structure is determined by a balance between dispersal-mediated connectivity and spatially variable selection. Along the eastern Florida ecotone, oyster dispersal patterns are being interpreted in combination with the spatial pattern and magnitude of selection as measured by postsettlement cohort analyses and reciprocal transplants. Hatchery-related studies involving oyster spawning and culture are being conducted in collaboration with John Scarpa at Harbor Branch Oceanographic Institute. Martha Burford is conducting experiments to distinguish three models by which selection may maintain the oyster cline, (1) hybrid unfitness relative to parentals regardless of habitat, (2) habitat-specific hybrid unfitness, and (3) bounded hybrid superiority, with hybrid success constrained to intermediate habitats. She is measuring fitness-related traits including growth rate, survivorship, size-corrected fecundity, and parasite load. Reproductive barriers are also being investigated by Haibin Zhang with in vitro tests of differential cross-fertilization efficiency.
At present, the strongest evidence for divergent selection across the oyster cline comes from a genomic screen of AFLP loci in which locus-specific Fst estimates were used to calculate a genomic mean Fst. A null distribution of Fst was then simulated under neutral drift given the empirical mean Fst ( Murray and Hare 2006). Nonequilibrium and equilibrium simulations were compared to show that the expected neutral variance in Fst around the estimated genomic mean was unaffected by secondary contact history. In a comparison of one population each from the Atlantic and Gulf of Mexico (representing the two tails of the eastern Florida oyster cline), 1.4% of polymorphic AFLP loci had Fst estimates outside the simulated 99th quantile for Fst. A similar test applied to previously-published codominant oyster loci identified only one outlier locus (3.7%). Thus, our genomic screens suggest that a small portion of the genome is shaped by divergent selection. Candidate non-neutral loci will be converted to codominant markers, mapped onto an existing C. virginica genetic map, and used to resolve the genetic basis for relative fitness differences.
Diversification along salinity gradients
Acartia tonsa is a seasonally dominant species of estuarine copepod along the eastern U.S. coast. Enormous populations of this species graze phytoplankton in the water column and provide an important prey item for fish. As with all zooplankton with a high potential for long-distance dispersal mediated by hydrographic currents, allopatric differentiation is only expected at the largest of geographic scales. We have found several deeply divergent mitochondrial DNA lineages within A. tonsa sampled from Chesapeake Bay. While deep mitochondrial lineages were previously reported within A. tonsa, Gang Chen has shown that they represent cryptic, reproductively isolated species based on genealogical concordance across mitochondrial and nuclear loci (Chen and Hare in press). Cryptic species are not novel or surprising in marine invertebrates any more, but in this case ecological speciation is suggested by their parapatric distribution along salinity gradients-one lineage was primarily found at salinities below 11 ppt, while another mostly occurred above that threshold. This habitat specificity could result from speciation in situ along salinity gradients, with each tributary containing sister species of high- and low-salinity copepods. Alternatively, a low-salinity clade might be relatively ancient, with representative populations now occupying most low-salinity habitat patches via colonization. Preliminary phylogeographic results support the latter hypothesis and suggest that the more discontinuous habitat used by the low salinity lineage has promoted allopatric speciation at spatial scales over which the high salinity lineage is only modestly subdivided. Thus, among estuarine species, the apparent propensity for dispersal is far less informative about allopatric diversification than the discreteness of preferred habitat. We will be comparing the phylogeography of each A. tonsa lineage to define the geographic scale at which gene flow is constrained. Direct testing of relative fitness at different salinities is also planned to determine the relative importance of selection and dispersal constraints maintaining population structure across salinity gradients.
Conservation Genetics - Invasive Marine Parasites
Macro- and microparasites in marine systems can have strong effects on community structure and devastating consequences for fisheries. Genetic markers are an under-utilized tool for more thoroughly describing parasite diversity, inferring population structure, and tracing the circumstances that promote changes in geographic range or host spectrum. Work in the Hare lab is focused on these goals with two highly-virulent parasites. Eastern oysters suffer severe mortality from epidemic infections by the protist Perkinsus marinus. This parasite was originally known from the Gulf of Mexico north to Chesapeake Bay, but infections have now become common and severe as far north as New England due to an apparent range expansion. The P. marinus genome is being sequenced as a representative of basal apicomplexans, yet very little is known about its population structure and the relative importance of clonal versus sexual reproduction. Almost all information on this species derives from clonal laboratory cultures. In the Hare lab we use a more direct approach to assay genetic variation in wild strains by using species-specific primers to PCR amplify P. marinus DNA from genomic DNA of infected oysters. We have found evidence for abundant sexual recombination within local populations. Peter Thompson is testing the generality of this result across the range of P. marinus, describing phylogeographic structure at neutral and candidate virulence-related loci, and reconstructing the demographic pattern of range expansion. Our genetic description of population processes and population history will inform efforts to manage the devastating effects of this parasite on oyster fisheries.
Research efforts in the Hare lab are also focused on tracing the invasion history of a rhizocephalan (barnacle) parasite that castrates estuarine mud crabs. Loxothylacus panopaei is endemic to the Gulf of Mexico and southeastern Florida, but was introduced to Chesapeake Bay in 1964. Inken Kruse has found that the invasive Chesapeake population is (1) genetically quite distinct from endemic populations in southeastern Florida, (2) infects a different spectrum of broadly-distributed mud crab species than the parasite in the endemic range, and (3) is expanding its range southward into Florida such that contact with the endemic parasite population is expected over the next few years (Kruse and Hare 2007). We are developing molecular assays to detect early stages of crab infection and Inken has sampled Loxothylacus parasites more broadly within the Gulf of Mexico. Results of these studies will help determine the source population for the Chesapeake invasion, help clarify why this invasion has been successful, and may help determine why a congeneric rhizocephalan parasite infects only southern populations of its commercially valuable host, blue crab.
Conservation Genetics - Eastern Oysters in Chesapeake Bay
The goal of our research on C. virginica in Chesapeake Bay is to test the effectiveness of current restoration efforts and facilitate those efforts by estimating the scale of larval dispersal. This work is collaborative with the Virginia Institute of Marine Science and funded through the NOAA/SeaGrant national Oyster Disease Research Program. Because most Chesapeake oyster restoration after 2000 involved the planting of selectively-bred disease tolerant C. virginica oysters, an additional goal of our research is to evaluate the genetic health of Chesapeake oyster populations and the impact of introgression from restoration plantings.
Spatial scale of dispersal: Using microsatellites to test for temporal and spatial subdivision within Chesapeake Bay, Colin Rose found no evidence for temporal heterogeneity and subtle spatial differentiation consistent with isolation by distance (IBD). This IBD pattern could be an evolutionary equilibrium emerging from stepping-stone dispersal. Alternatively, anthropogenic activities related to fisheries management and restoration may be creating or eroding an IBD pattern. An evolutionary interpretation seems more parsimonious for several reasons (Rose et al. 2006), but more work is needed to distinguish
Restoration efficacy: One such effort includes our direct estimates of oyster dispersal distances based on genetic tags. The 'tagging' is a consequence of genetic drift and selection during breeding of C. virginica for disease tolerance, and further bottlenecks imposed during each hatchery spawn of selected-strain broodstock needed to produce juveniles for restoration plantings (Hare and Rose in prep.). In a tributary where tagged oysters were planted on a single reef, we have traced dispersal of their progeny by using assignment tests on the multilocus genotypes of newly-settled juveniles collected throughout the tributary. In 2002, a year with the high overall recruitment, almost 1600 oyster juveniles were collected and genotyped for eight microsatellite loci and mitochondrial DNA. We estimated that during that year five to ten percent of juveniles originated from parents at the point source (Hare et al. 2006). Sampling is not yet sufficient to characterize average dispersal distances, but this overall level of population enhancement is both good and bad news. On the good side, the glass is half full substantial recruitment enhancement was accomplished and this would not have been discernable without genetic analysis. On the other hand, the enhancement was much lower than anticipated, precipitating critical evaluation of untested assumptions underlying restoration methods.
Genetic health: Restoration efforts in Chesapeake Bay are now focused on targeted supportive breeding using artificially selected, disease tolerant C. virginica to combat high mortalities from parasitic diseases. Supportive breeding reduces early juvenile mortality in the hatchery in order to release millions of seed oysters from relatively few broodstock. This procedure is known to have potential benefits and considerable risks. Recent results from our work have provided the first empirical estimates of population parameters genetic diversity in the wild populations, in the hatchery broodstock, and the annual contribution to recruitment made by restoration seed oysters that determine the magnitude of risk from supportive breeding (Hare et al. 2006; Rose et al. 2006). Theoretical models indicate that overall genetic diversity will be dramatically reduced, and inbreeding depression is expected to result, from a 5-10% supportive breeding contribution to annual recruitment if the hatchery broodstock are extremely inbred. The selectively-bred DEBY strain of oyster previously used to produce restoration seed is highly inbred (Hare and Rose in prep.). Using this oyster strain as restoration broodstock has potential benefits in terms of greater longevity and disease tolerance of seed oysters, but our genetic analyses predict a 50 95% drop in local overall genetic diversity as a result of “successful” supportive breeding. Even while these restoration efforts might be increasing oyster abundance, as currently practiced they will degrade the genetic health of local populations. This will limit the prospects for long-term restoration success. Our recommendation (Hare and Rose in prep.) and that of local experts (url in prep.) is to stop using these strains for restoration except where genetic monitoring is used to test the efficacy of ever-shifting restoration practices. Selectively-bred disease tolerant strains are expected to find continued profitable use for aquaculture
Publications
Chen, G. and M.P. Hare. 2008. Cryptic ecological diversification of a planktonic estuarine copepod, Acartia tonsa. Molecular Ecology in press.
Kruse, I. and M.P. Hare. 2007. Genetic diversity and expanding non-indigenous range of the rhizocephalan Loxothylacus panopaei parasitizing mud crabs in the western North Atlantic. J. Parasitology 93(3):575-582.
Gaines, C.A., M.P. Hare, S.E. Beck and H.C. Rosenbaum. 2005. Nuclear markers confirm taxonomic status and relationships among highly endangered and closely related right whale species. Proceedings of the Royal Society B 272:533-542.
Hare, M.P. and J. Weinberg. 2005. Phylogeography of surf clams, Spisula solidissima, in the western North Atlantic based on mitochondrial and nuclear DNA sequences. Marine Biology 146:707-716.
Robinson T.B., C.L. Griffiths, A. Tonin, P. Bloomer & M.P. Hare. 2005. Naturalized populations of Crassostrea gigas along the South African coast: distribution, abundance and population structure. Journal of Shellfish Research 24(2):443-450.
Hare, M.P. and S.R. Palumbi. 2003. High intron sequence conservation across three mammalian orders suggests functional constraints. Molecular Biology and Evolution 20(6): 969-978.
Hare, M.P., F. Cipriano and S.R. Palumbi. 2002. Genetic evidence on the demography of speciation in allopatric dolphin species. Evolution 56:804-816.
Murray, M. and M.P. Hare. 2006. Genomic evidence for divergent selection between Atlantic and Gulf of Mexico oysters, Crassostrea virginica. Molecular Ecology 15: 42294242.
Hare, M. P., S. K. Allen Jr., P. Bloomer, M. D. Camara, M. D. Carnegie, J. Murfree, M. W. Luckenbach, D. Merritt, C. Morrison, K. T. Paynter, K. S. Reece, and C. G. Rose. 2006. A genetic test for recruitment enhancement in Chesapeake Bay oysters, Crassostrea virginica, after population supplementation with a disease tolerant strain. Conservation Genetics 7: 717734.
Rose, C. G., K. T. Paynter, and M. Hare. 2006. Isolation by distance in the eastern oyster, Crassostrea virginica, in Chesapeake Bay. J. Heredity 97(2): 158-170.
Hare, M.P., C. Guenther and W.F. Fagan. 2005. Nonrandom larval dispersal can steepen marine clines. Evolution 59:2509-2517
Hare, M.P. 2001. Prospects for nuclear gene phylogeography. Trends in Ecology and Evolution 16(12):700-706.
Palumbi, S. R., F. Cipriano and M. P. Hare. 2001. Predicting nuclear gene coalescence from mitochondrial data: The three-times rule. Evolution 55:859-868.
Hare, M.P., S.R. Palumbi and C.A. Butman. 2000. Single-step species identification of bivalve larvae using multiplex polymerase chain reaction. Marine Biology 137:953-961.
Hare, M.P. and S. R. Palumbi. 1999. The accuracy of heterozygous base calling from diploid sequence and resolution of haplotypes using allele-specific sequencing. Molecular Ecology 8:1750-1752.
Hare, M.P. 1998. Using mitochondrial DNA gene trees and nuclear RFLPs to predict genealogical patterns at nuclear loci: examples from the American oyster. Proceedings of the trinational workshop on molecular evolution, M. Uyenoyama and A. von Haeseler, eds. Duke Publications Group, Duke University, Durham, NC.
Hare, M.P. and J.C. Avise. 1998. Population structure in the American oyster as inferred by nuclear gene genealogies. Molecular Biology and Evolution 15:119-128.
Orti, G., M.P. Hare, and J.C. Avise. 1997. Detection and isolation of nuclear haplotypes by PCR-SSCP. Molecular Ecology 6:575-580.
Hare, M.P. and J.C. Avise. 1996. Molecular genetic analysis of a stepped multilocus cline in the American oyster (Crassostrea virginica). Evolution 50:2305-2315.
Hare, M.P., S.A. Karl, and J.C. Avise. 1996. The heterozygote deficiency phenomenon in marine bivalves: Lessons from the refinement of anonymous DNA markers. Molecular Biology and Evolution 13:334-345.