BIOGEOGRAPHY AND PHYLOGEOGRAPHY AS LENSES TO STUDY THE EFFECTS OF CLIMATE CHANGE ON COASTAL MARINE COMMUNITIES

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 0211786
• Project Start Date: Jul 1, 2007
• Project End Date: Jun 30, 2013
• Program Code: [(N/A)]- (N/A)

Recipient Organization
CLEMSON UNIVERSITY
(N/A)
CLEMSON,SC 29634

Performing Department
Biological Sciences

Non Technical Summary
Although the debate over the degree to which communities are self-organizing has been illuminating for ecology, this issue has a more practical relevance towards understanding the kinds of changes that can be expected in response to human perturbation of the environment. The aim of this proposal is to reconstruct the late-Quaternary biogeographic history of the rocky-shore fauna of the north Pacific as a means to evaluate the impact that climate change has on community composition, diversity, and cohesiveness.

Animal Health Component

(N/A)

Research Effort Categories

Basic

(N/A)

Applied

(N/A)

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
132	0420	1070	10%
135	0811	1070	60%
136	0811	1070	20%
306	0811	1070	10%

Knowledge Area
135 - Aquatic and Terrestrial Wildlife; 136 - Conservation of Biological Diversity; 132 - Weather and Climate; 306 - Environmental Stress in Animals;

Subject Of Investigation
0420 - Weather; 0811 - Shellfish;

Field Of Science
1070 - Ecology;

Keywords

climate change

geographic range

phylogeography

rocky shore

speciation;

Goals / Objectives
Do natural communities consist of species tightly bound together by strong ecological interactions or do species respond individually to environment? Although the debate over the degree to which communities are self-organizing has been illuminating for ecology, this issue has a more practical relevance towards understanding the kinds of changes that can be expected in response to human perturbation of the environment. Despite uncertainties surrounding the precise scale of change to be expected, there is now a consensus that global temperatures will likely change more in the next century than they have typically changed over recent geologic history. The goal of this research is to develop an understanding of the latitudinal responses of interacting species to Pleistocene climate change. The project will address three basic questions: 1. How was community composition altered during the last glacial maximum? The sampling of species proposed here is focused on groups ofclosely related species that are comprised of species that occupy different vertical positions on rocky shores. Although some of the species differ with respect to other traits that have been implicated in the survival and extinction of high latitude populations during the last glacial maximum (LGM), species have been chosen that differ primarily with respect to shore height, as well other ecological attributes that are associated with this trait to maximize the power of the hypothesis test that species living in more abiotically stressful microhabitats are more likely to respond to climate change. 2. Do range-persistence species show a geographically and temporally concordant genetic break in the Northeastern Pacific? Among the taxa that have been widely surveyed with genetic markers in both British Columbia and Alaska, two show a deep genetic disjunction between populations in southeast Alaska and Northern British Columbia, somewhere between Haida Gwaii, BC and Ketchikan, AK ,indicating the existence of at least one northern glacial refuge in both species. For both species, the molecular-based time of separation between these two regions is approximately 70,000 years, suggesting concordance with respect to the timing of isolation between northern and southern populations. By collecting multilocus data from species exhibiting this break, we will test the hypothesis of temporal concordance in this region. 3. Did Pleistocene climate change cause trans-Pacific speciation? Examples are known in which an ancestral amphi-Pacific taxon gave rise to geographically disjunct and morphologically distinct western and eastern descendants. This vicariant pattern is interpreted as being caused by extinction of populations at high latitudes, resulting in allopatrically distributed populations on eastern and western sides of the north Pacific. Because several of the proposed species for study in #1 above have amphi-Pacific distributions, the research described aboveprovides an opportunity to investigate trans-Pacific patterns of phylogeographic differentiation.

Project Methods
The aim of this proposal is to reconstruct the late-Quaternary biogeographic history of the rocky-shore fauna of the north Pacific as a means to evaluate the impact that climate change has on community composition, diversity, and cohesiveness. To achieve this objective, the research will focus on a multi-species phylogeographic survey of wide taxonomic breadth, highlighting species whose contemporary ecological interactions have been extensively characterized. A. Collections. For most species, except those with small body sizes, we plan to sample non-destructively by clipping small portions of tissue from individuals. Collecting in the western Pacific will be more challenging, but I have obtained the help of several people who can provide logistic support with getting to these sites. B. Overall Strategy for the Molecular Work. The work proposed here involves collecting genetic data from 16-17 species. MtDNA sequences from cytochrome oxidase-1 (CO1) will be collectedfrom all of the species. Despite the difficulty with boosting the statistical power used to estimate summary statistics in coalescent methods, I feel that the collection of additional data from the nuclear genome is absolutely necessary to determine if the general patterns of genetic diversity observed in mtDNA are present in the nuclear genome. Surprisingly, either nuclear introns from protein-coding, single-copy loci or microsatellite loci have been characterized in many of the taxa I am proposing to work on; members of the lab will develop loci for taxa that are currently lacking them. C. DNA Extraction, PCR, and Sequencing. We will first focus on obtaining DNA sequence data from mitochondrial CO1. After obtaining preliminary sequences for each species, we will likely design species- or genus-specific primers. The research here will benefit from the fact that nuclear introns and simple sequence repeat (SSR) loci have been specifically developed for several of the taxa we plan towork on. We think it unlikely that we will be unable to find at least one amplifiable and polymorphic nuclear gene for all of the taxa we are interested. Although members of my lab have used standard enrichment protocols with success in both invertebrates and fishes, we will contract out the library construction and screening to Genetic Identification Services in southern California.

Progress 07/01/07 to 06/30/13

Outputs
Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? No further accomplishments since 2012 CRIS 421 report due to resignation of P.I. from Clemson University.

Publications

Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: Year five of the project was completed, which consisted of data collection for population genetic analysis and manuscript preparation. Three projects have been completed, one in which we assess the amount of genetic data needed to distinguish different biogeographic responses to climate change, a second, which is a meta-analysis of genetic data from species at high latitudes used to infer the responses of species to post-glacial warming of the earth's climate, and a third in which we have conducted a detailed population genetic analysis of a species that shows a rangewide pattern of genetic diversity that is consistent with long-term persistance across glacial-interglacial cycles. PARTICIPANTS: Clemson Participants: Dr. Peter Marko (PI). Collaborators: Dr. Michael Hart, Simon Fraser University (Burnaby, BC, Canada). TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
We have found that assessing genetic variation across the entire genome is essential for unravelling a species' recent demographic history. Our approach has shown that although species may exhibit similar patterns of genetic structure at single loci, a genome-wide survey of spatial patterns of variation can reveal that they may have vastly different biogeographic histories in relation to climate change. Our work with anonymous nuclear loci is unusual given that most studies like ours rely solely on mitochondrial DNA for phylogeography and is one of the first of its kind.

Publications

• Marko, P. B. and M. W. Hart. 2012. Retrospective coalescent methods and the reconstruction of metapopulation histories in the sea. Evolutionary Ecology 26: 291.
• Marko, P. B., Nance, H. A., and K. D. Guynn. 2012. Seafood mislabeling: A response to Mariani. Frontiers in Ecology and the Environment 10: 10.

Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: Year four of the project was completed, which consisted of data collection for population genetic analysis and manuscript preparation. Three projects have been completed, one in which we assess the amount of genetic data needed to distinguish different biogeographic responses to climate change, a second, which is a meta-analysis of genetic data from species at high latitudes used to infer the reponses of species to post-glacial warming of the earth's climate, and a third in which we have conducted a detailed population genetic analysis of a species that shows a rangewide pattern of genetic diversity that is consistent with long-term persistance across glacial-interglacial cycles. PARTICIPANTS: Clemson Participants: Dr. Peter Marko (PI) Dr. Tamara McGovern (Postdoctoral Researcher) Sandra Emme (Technician) Holly Nance (PhD Graduate Student). The project has provided salary and training in molecular biology for a postdoctoral researcher, a lab technician, and one graduate students. Collaborators: Dr. Michael Hart, Simon Fraser University (Burnaby, BC, Canada). TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
We have found that assessing genetic variation across the entire genome is essential for unravelling a species' recent demographic history. Our approach has shown that although species may exhibit similar patterns of genetic structure at single loci, a genome-wide survey of spatial patterns of variation can reveal that they may have vastly different biogeographic histories in relation to climate change. Our work with anonymous nuclear loci is unusual given that most studies like ours rely solely on mitochondrial DNA for phylogeography and is one of the first of its kind.

Publications

• Hart, M. W. & P. B Marko. 2010. Its about time: divergence, demography, and the evolution of developmental modes in marine invertebrates. Integrative and Comparative Biology 50, 643-661.
• Marko, P. B., Hoffman, J. M., Emme, S. A., McGovern, T. M., Keever, C., & L. N. Cox. 2010. The expansion-contraction model of Pleistocene demography: rocky shores suffer a sea change Molecular Ecology 19: 146-169.
• Nance, H. A., Daly-Engle, T. S., & P. B. Marko. 2011. Demographic Processes Underlying Subtle Patterns of Population Structure in the Scalloped Hammerhead Shark, Sphyrna lewini. PLoS One 6: e21459.

Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: Nearly all of the data collection for this project is now complete, primarily surveys of genetic diversity across a diversity of rocky shore species inhabiting the north Pacific. Much of these data have been previously published (with data submitted to NIH-Genbank) but several projects are in an analytical phase, including a large study of genetic differentiation of species distributed between Alaska and Japan. In 2010, results have been presented at national meetings (Society for the Study of Evolution and the Society for Comparative and Integrative Biology). PARTICIPANTS: Research technician: Sandra Emme Graduate student: Nicole Cox TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The largest impact from this work in 2010 is described in a recent publication (McGovern et al. 2010) in which we reconstructed the demographic histories of co-distributed species in the Northeastern Pacific, showing how the geographic and demographic responses of species to climate change during the Pleistocene has been highy varied, with some species showing expected histories of recent colonization. Other new results involve discoveries of unexpectedly high genetic differentiation and high genetic diversity among species inhabiting the northwestern Pacific, including the discovery of novel genetic breakpoints between northern Japan and Sakhalin Island.

Publications

• McGovern, T. M., Keever, C. A., Hart, M. W., Saski, C., & P. B. Marko. 2010. Divergence genetics analysis reveals historical population genetic processes leading to contrasting phylogeographic patterns in co-distributed species. Molecular Ecology 19, 5043-5060.
• Hart, M. W. & P. B Marko. 2010. It's about time: divergence, demography, and the evolution of developmental modes in marine invertebrates. Integrative and Comparative Biology 50:643-661.
• Marko, P. B., Hoffman, J. M., Emme, S. A., McGovern, T. M., Keever, C., & L. N. Cox. 2010. The expansion-contraction model of Pleistocene demography: rocky shores suffer a sea change Molecular Ecology 19:146-169.

Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: Year three of the project was completed, which consisted of data collection for population genetic analysis and manuscript preparation. Three projects have been completed, one in which we assess the amount of genetic data need to distinguish different biogeographic responses to climate change, a second, which is a meta-analysis of genetic data from species at high latitudes used to infer the reponses of species to post-glacial warming of the earth's climate, and a third in which we have conducted a detailed population genetic analysis of a species that shows a rangewide pattern of genetic diversity that is consistent with long-term persistance across glacial-interglacial cycles. PARTICIPANTS: Clemson Participants: Dr. Peter Marko (PI) Dr. Tamara McGovern (Postdoctoral Researcher) Sandra Emme (Technician) Holly Nance (PhD Graduate Student) The project has provided salary and training in molecular biology for a postdoctoral researcher, a lab technician, and one graduate student. Collaborators: Dr. Michael Hart, Simon Fraser University (Burnaby, BC, Canada). TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
Understanding how communities of organisms have responded to past climate change can be used to make predictions about how similar assemblages of species will respond in the future. Using genetic data, we have shown that co-occurring members of marine communities have responded to climate change in a highly variable and unpredictable way, suggesting that predictions about future changes in the abundance and distributions of species will be difficult to predict and therefore mitigate in advance. We have also found that assessing genetic variation across the entire genome is essential for unravelling a species' recent demographic history. Our approach has shown that although species may exhibit similar patterns of genetic structure at single loci, a genome-wide survey of spatial patterns of variation can reveal that they may have vastly different biogeographic histories in relation to climate change. Our work with anonymous nuclear loci is unusual given that most studies like ours rely solely on mitochondrial DNA for phylogeography and is one of the first of its kind.

Publications

• Marko, P. B. & A. L. Moran. 2009. Out of sight, out of mind: High cryptic diversity obscures the identities and histories of geminate species in the marine bivalve subgenus Acar. Journal of Biogeography 36: 1861-1880.
• Nance, H.A., Daly-Engle, T.S., & P. B. Marko. 2009. New microsatellite loci for the endangered scalloped hammerhead shark, Sphyrna lewini. Molecular Ecology Resources 9: 955-957.
• Baldwin, W. S., Marko, P. B. & D. R. Nelson. 2009. The cytochrome P450 (CYP) gene superfamily in Daphnia pulex. BMC Genomics 10:169-182.

Progress 01/01/08 to 12/31/08

Outputs
OUTPUTS: Year two of the project was completed, which consisted of data collection for population genetic analysis and manuscript preparation. Three projects have been completed, one in which we assess the amount of genetic data need to distinguish different biogeographic responses to climate change, a second, which is a meta-analysis of genetic data from species at high latitudes used to infer the reponses of species to post-glacial warming of the earth's climate, and a third in which we have conducted a detailed population genetic analysis of a species that shows a rangewide pattern of genetic diversity that is consistent with long-term persistance across glacial-interglacial cycles. PARTICIPANTS: Clemson Participants: Dr. Peter Marko (PI) Dr. Tamara McGovern (Postdoctoral Researcher) Sandra Emme (Technician) Holly Nance (PhD Graduate Student) The project has provided salary and training in molecular biology for a postdoctoral researcher, a lab technician, and one graduate students. Collaborators: Dr. Michael Hart, Simon Fraser University (Burnaby, BC, Canada) TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
We have found that assessing genetic variation across the entire genome is essential for unravelling a species' recent demographic history. Our approach has shown that although species may exhibit similar patterns of genetic structure at single loci, a genome-wide survey of spatial patterns of variation can reveal that they may have vastly different biogeographic histories in relation to climate change. Our work with anonymous nuclear loci is unusual given that most studies like ours rely solely on mitochondrial DNA for phylogeography and is one of the first of its kind.

Publications

• Baldwin, W. S., Marko, P. B. & D. R. Nelson. 2008. The cytochrome P450 (CYP) gene superfamily in Daphnia pulex. BMC Genomics.
• Marko, P. B. 2008. Allopatry. Pp. 131-138 in The Encyclopedia of Ecology by S. V. Jorgensen (ed.). Elsevier, Oxford, UK.
• Marko, P. B. 2008. Sympatry. Pp. 3450-3458 in The Encyclopedia of Ecology by S. V. Jorgensen (ed.). Elsevier, Oxford, UK.

Progress 01/01/07 to 12/31/07

Outputs
OUTPUTS: Year one of the project was completed, which consisted of specimen collection and development of genomic markers (anonymous nuclear loci: randomly chosen genetic loci) used for population genetic comparisons. We have also completed a first project involving assessing the amount of genetic data that is required to resolve differences in species' recent biogeographic histories. The results from this first project were presented at a national meeting this past January (Society for Integrative and Comparative Biologists) by a postdoctoral researcher funded by my current grant. PARTICIPANTS: Clemson Participants: Dr. Peter Marko (PI) Dr. Tamara McGovern (Postdoctoral Researcher) Sandra Emme (Technician) Holly Nance (PhD Graduate Student) The project has provided salary and training in molecular biology for a postdoctoral researcher, a lab technician, and one graduate students. Collaborators: Dr. Michael Hart, Simon Fraser University (Burnaby, BC, Canada)

Impacts
We have found that assessing genetic variation across the entire genome is essential for unravelling a species' recent demographic history. Our approach has shown that although species may exhibit similar patterns of genetic structure at single loci, a genome-wide survey of spatial patterns of variation can reveal that they may have vastly different biogeographic histories in relation to climate change. Our work with anonymous nuclear loci is unusual given that most studies like ours rely solely on mitochondrial DNA for phylogeography and is one of the first of its kind.

Publications

• Marko, P. B., Rogers-Bennett, L. & A. Dennis. 2007. Population structure and migration of lingcod (Ophiodon elongatus) inferred from mitochondrial DNA: limited dispersal of long-lived pelagic larvae? Marine Biology 150:1301-1311.
• Marko, P.B. & Barr, K.B. 2007. Basin-scale patterns of mtDNA differentiation and gene flow in the bay scallop Argopecten irradians concentricus. Marine Ecology Progress Series 349: 139-150.