Final Report Summary - DOLPHIN ECOLOGY (Testing for “porous” genomic boundaries between habitat specialist populations of the spinner dolphin)
Project objectives
Our project aims to increase understanding of the evolutionary mechanisms driving adaptation in the marine environment. To accomplish this, we are examining the relationships between morphological, behavioral, ecological, and genetic variation among populations of the spinner dolphin (Stenella longirostris) to identify parts of the genome under different adaptive pressures between dolphins occurring in ecologically different habitats. We are using a cutting-edge DNA sequencing method to explore thousands of regions across the spinner dolphin genome. We then identify parts of the genome that show unusually high levels of divergence between populations of dolphins (“outlier loci”), and we target these genomic regions as candidates for being influenced by divergent adaptive pressures driven by ecological habitat differences. We map these outlier loci onto the publicly available sequenced genome of the bottlenose dolphin (Tursiops truncatus) to identify associations with functional portions of the genome. By comparing groups of dolphins with different morphological, behavioral, and habitat characteristics at these functional parts of the genome, we expect to develop a better understanding of the mechanisms promoting adaptive evolution in the spinner dolphin.
Work Performed
The fellow developed a laboratory protocol for preparing genomic DNA samples for Restriction-Associated-DNA sequencing (“RADseq”) on an Illumina DNA sequencer. To aid in the development of this protocol, she traveled to the University of Liverpool to receive training from staff members at the Centre for Genomic Research for one week. She also undertook an extensive literature search regarding the different RADseq library prep protocols. She then designed a protocol tailored to the research project. The fellow used this protocol to prepare genomic DNA libraries for 252 spinner dolphin specimens for sequencing on an Illumina HiSeq DNA sequencer.
The fellow received training in bioinformatics analyses by attending two workshops: ConGen 2013 Population Genomic Data Analysis Course (University of Montana Flathead Lake Biological Field Station, USA, 3-8 September 2013), and Workshop on Genomics (Cesky Krumlov, Czech Republic, 12-24 January 2014). She worked with Information Technology staff at the host institution to compile population genomics analytical software onto a Linux server. She then conducted bioinformatics analyses on the Illumina DNA sequence data generated from this project. These analyses included sorting the DNA sequences by barcode (a unique DNA sequence added to each sample), discarding low quality sequence reads, aligning sequence reads against the publicly available bottlenose dolphin genome, genotype calling using a Maximum-Likelihood framework, estimating genetic divergence at each variable genetic site, identifying “outlier loci” that exhibit unusually high levels of genetic divergence, and identifying genes located close to outlier loci on the bottlenose dolphin genome.
Main Results & Conclusions
Illumina sequencing has been completed for 174 specimens, and sequencing will be conducted for an additional 78 specimens in March 2015. Bioinformatic analyses of sequence data from 174 specimens resulted in genotypes from 5,801 independent variable sites (“genetic loci”) across the genome. This number of variable sites exceeded our target goal of 4,600 variable sites. Genomic analyses using all 5,801 loci indicated that spinner dolphins form genetically distinct populations at each geographic location sampled (Figure 1). Analyses to detect outlier loci revealed 213 candidate loci under the influence of divergent adaptive pressures across geographic locations. Population genomic analyses restricted to these outlier loci revealed elevated genetic divergence for just one group of dolphins occurring along the east coast of Australia (Figure 1). Dolphins in this region differ from other spinner dolphins both morphologically and ecologically, with a smaller body size, different body coloration, and a coral reef habitat unique to this group. Our results provide evidence that these ecologically and morphologically divergent features have a genomic basis. Identification of genes linked to these loci provided a list of 76 genes potentially under unique adaptive pressures for this group. Ongoing work initiated during this project (with sequencing to be completed in March 2015) will compare additional morphologically distinct populations in the Eastern Tropical Pacific that so far have shown low levels of genetic differentiation. Some of the differences in body shape and color are quite striking, even though the populations are geographically next to each other. We will test the expectation that outlier loci will show strong patterns of differentiation among these populations compared to that seen at loci not under the influence of natural selection.
Impact
The data generated from this study provide valuable insight into the evolutionary mechanisms driving ecological and morphological divergence in the spinner dolphin. We found evidence that dolphins along the east coast of Australia experience different adaptive pressures than spinner dolphins at nearby locations, perhaps resulting from the unique coral reef habitat in this region. Furthermore, this study provided insight into levels of genetic isolation and diversity at different geographic locations for the spinner dolphin. This information is critical for assessing the impact of human activities on the health of spinner dolphin populations. Many spinner dolphin populations across the world are negatively impacted by fisheries and habitat destruction, and there are growing concerns that dolphin ecotourism may also have a negative impact on populations. Results from our work will help managers define and assess the vulnerability of management units for conservation of this species.
We also expect the laboratory and bioinformatics protocols developed by the fellow to benefit the research community (see Andrews et al. 2014; further details to be published in the methods sections of planned papers). The establishment of these methods for generating and analyzing next-generation sequencing data has already benefited other researchers in the host lab working on population genomics and phylogenomics.
Finally, we expect the review papers, workshops, and website (http://kimberlyandrews.net/research/(s’ouvre dans une nouvelle fenêtre)) generated through this project to increase awareness and understanding within the scientific community and the general public regarding the use of cutting-edge DNA sequencing technologies in population genomics and other biological disciplines.
Literature Cited
Andrews KR, Hohenlohe PA, Miller MR, et al. (2014) Trade-offs and utility of alternative RADseq methods: Reply to Puritz et al. 2014. Molecular Ecology 23, 5943-5946.
Our project aims to increase understanding of the evolutionary mechanisms driving adaptation in the marine environment. To accomplish this, we are examining the relationships between morphological, behavioral, ecological, and genetic variation among populations of the spinner dolphin (Stenella longirostris) to identify parts of the genome under different adaptive pressures between dolphins occurring in ecologically different habitats. We are using a cutting-edge DNA sequencing method to explore thousands of regions across the spinner dolphin genome. We then identify parts of the genome that show unusually high levels of divergence between populations of dolphins (“outlier loci”), and we target these genomic regions as candidates for being influenced by divergent adaptive pressures driven by ecological habitat differences. We map these outlier loci onto the publicly available sequenced genome of the bottlenose dolphin (Tursiops truncatus) to identify associations with functional portions of the genome. By comparing groups of dolphins with different morphological, behavioral, and habitat characteristics at these functional parts of the genome, we expect to develop a better understanding of the mechanisms promoting adaptive evolution in the spinner dolphin.
Work Performed
The fellow developed a laboratory protocol for preparing genomic DNA samples for Restriction-Associated-DNA sequencing (“RADseq”) on an Illumina DNA sequencer. To aid in the development of this protocol, she traveled to the University of Liverpool to receive training from staff members at the Centre for Genomic Research for one week. She also undertook an extensive literature search regarding the different RADseq library prep protocols. She then designed a protocol tailored to the research project. The fellow used this protocol to prepare genomic DNA libraries for 252 spinner dolphin specimens for sequencing on an Illumina HiSeq DNA sequencer.
The fellow received training in bioinformatics analyses by attending two workshops: ConGen 2013 Population Genomic Data Analysis Course (University of Montana Flathead Lake Biological Field Station, USA, 3-8 September 2013), and Workshop on Genomics (Cesky Krumlov, Czech Republic, 12-24 January 2014). She worked with Information Technology staff at the host institution to compile population genomics analytical software onto a Linux server. She then conducted bioinformatics analyses on the Illumina DNA sequence data generated from this project. These analyses included sorting the DNA sequences by barcode (a unique DNA sequence added to each sample), discarding low quality sequence reads, aligning sequence reads against the publicly available bottlenose dolphin genome, genotype calling using a Maximum-Likelihood framework, estimating genetic divergence at each variable genetic site, identifying “outlier loci” that exhibit unusually high levels of genetic divergence, and identifying genes located close to outlier loci on the bottlenose dolphin genome.
Main Results & Conclusions
Illumina sequencing has been completed for 174 specimens, and sequencing will be conducted for an additional 78 specimens in March 2015. Bioinformatic analyses of sequence data from 174 specimens resulted in genotypes from 5,801 independent variable sites (“genetic loci”) across the genome. This number of variable sites exceeded our target goal of 4,600 variable sites. Genomic analyses using all 5,801 loci indicated that spinner dolphins form genetically distinct populations at each geographic location sampled (Figure 1). Analyses to detect outlier loci revealed 213 candidate loci under the influence of divergent adaptive pressures across geographic locations. Population genomic analyses restricted to these outlier loci revealed elevated genetic divergence for just one group of dolphins occurring along the east coast of Australia (Figure 1). Dolphins in this region differ from other spinner dolphins both morphologically and ecologically, with a smaller body size, different body coloration, and a coral reef habitat unique to this group. Our results provide evidence that these ecologically and morphologically divergent features have a genomic basis. Identification of genes linked to these loci provided a list of 76 genes potentially under unique adaptive pressures for this group. Ongoing work initiated during this project (with sequencing to be completed in March 2015) will compare additional morphologically distinct populations in the Eastern Tropical Pacific that so far have shown low levels of genetic differentiation. Some of the differences in body shape and color are quite striking, even though the populations are geographically next to each other. We will test the expectation that outlier loci will show strong patterns of differentiation among these populations compared to that seen at loci not under the influence of natural selection.
Impact
The data generated from this study provide valuable insight into the evolutionary mechanisms driving ecological and morphological divergence in the spinner dolphin. We found evidence that dolphins along the east coast of Australia experience different adaptive pressures than spinner dolphins at nearby locations, perhaps resulting from the unique coral reef habitat in this region. Furthermore, this study provided insight into levels of genetic isolation and diversity at different geographic locations for the spinner dolphin. This information is critical for assessing the impact of human activities on the health of spinner dolphin populations. Many spinner dolphin populations across the world are negatively impacted by fisheries and habitat destruction, and there are growing concerns that dolphin ecotourism may also have a negative impact on populations. Results from our work will help managers define and assess the vulnerability of management units for conservation of this species.
We also expect the laboratory and bioinformatics protocols developed by the fellow to benefit the research community (see Andrews et al. 2014; further details to be published in the methods sections of planned papers). The establishment of these methods for generating and analyzing next-generation sequencing data has already benefited other researchers in the host lab working on population genomics and phylogenomics.
Finally, we expect the review papers, workshops, and website (http://kimberlyandrews.net/research/(s’ouvre dans une nouvelle fenêtre)) generated through this project to increase awareness and understanding within the scientific community and the general public regarding the use of cutting-edge DNA sequencing technologies in population genomics and other biological disciplines.
Literature Cited
Andrews KR, Hohenlohe PA, Miller MR, et al. (2014) Trade-offs and utility of alternative RADseq methods: Reply to Puritz et al. 2014. Molecular Ecology 23, 5943-5946.
