Tools & technologies
Faculty Contacts
Background
Species respond to rapid environmental change by (i) altering timing of life history events (phenology) or other forms of ecological and evolutionary adjustment (eg. changes in diet or phenotype), (ii) shifting their geographic distribution to maintain viable populations, or (iii) extinction. From the fossil record of responses to rapid change in the past, we know that there is considerable variation among species in how these processes play out, making prediction of future trajectories a major challenge. Nonetheless, the historical record of change, over millenial to decadal time scales is the best evidence we have from which to forecast future responses.
Museum collections, complemented by long-term ecological studies at field stations, provide a uniquely rich and, thus far, largely untapped information bank that can be mined for this purpose. At the core is the specimens and associatedd information (field notes, images, tissues), providing gold standard data on what was where and when. But, with new technologies, we can take this much further. As explained below, we can quantify ecological and evolutionary responses through analyses of diet (isotopes), phenotype and genomes over time, all in the context of geographic range and environmental change within that range. This can be achieved over deep time using fossils and through the 20th C using our historical collections. Only by putting the whole picture together, initially for exemplar systems, will we be able to generate secure predictions on which components of biodiversity are sensitive vs robust to ongoing, human-driven, environmental change.
Distribution shifts
As museum collections are digitized and precisely georeferenced (ie. latitude and longitude assigned), we can use GIS methods to map and/or model species distributions across the landscape, and thereby measure changes in geographic and enviromental range over time. Recent advances in biodiversity informatics, many developed at Berkeley, enable species records from museums across the world to be extracted on-line. When combined with rich, spatially explicit information on environmental change, as obtained from climate data/models or remote sensing, we can identify which species are expanding, declining or shifting ranges in response to changes in climate or land use. Such studies at Berkeley have revealed substantial change in the birds and small mammals of Yosemite and other other western National Parks and contractions of neotropical salamanders. Much more is possible. Combined with statistical modeling, we are then in a position to identify taxa that are most threatened by future change.
Phenotypes
Evolutionary response to rapid environmental change manifests as change in species phenotypes – ecologically relevant morphological, physiological and phenological traits. Museum collections can provide information on all three, but most obviously eco-morphology. By comparing historical (including fossil) with modern specimens, we can measure changes in size or shape of skulls, in color and, in plants, growth form. By combining this information with knowledge of inheritance of traits, we can estimate the strength of selection necessary to produce the observed change in phenotypes. For example, comparisons of skulls from early 20th C vs modern specimens of Sierrran chipmunks and ground squirrels have demonstrated significant change in size and shape, reflecting strong selection, in geographically declining, but not stable species. For both fauna and flora, changes in the timing of reproduction can be inferred from the temporal distribution of breeding/flowering individuals before and after rapid change.
STable Isotopes
In the past twenty-five years or so the development and application of stable isotope tools in the life and environmental sciences and revolutionized our ability to address unanswered and unanswerable questions like never before. Just like the ways in which modern genetic and genomic tools have allowed biologists to deepen our ecological and evolutionary understanding of the processes that have lead to genetic changes in response to novel selection pressures like human-induced environmental change, isotope methods have permitted biologists to interpret both the patterns and the processes that have lead to changes in the chemical (isotope) composition of microbial, animal, plant and soil samples. For example, the analysis of the both the carbon (C) and nitrogen (N) stable isotope composition of hair from mammals collected at different times in the same location has revealed how their diet and range of food sources may have shifted. Also, the analyses of insects like bees and other herbivorous species (e.g., grasshoppers, beetles) over time and space has show us how each species has changed, uniquely, in the types of plants they consume in response to a change in the plant community brought about by human-related disturbances like urbanization. What is most exciting is that when additional information on the C and N isotope composition of food plants is also known we can reconstruct how the apparent diet or range shifts were brought about by ecological or climatic changes such as increased community disturbance or drought and how entire communities have responded (or not). Such analyses were never possible until biologists began to use stable isotope tools.
More recently, work on changes in the oxygen (O) stable isotope composition of plant cellulose in leaf or tree ring samples as well as in the bone of birds, mammals and even indigenous human’s have shown how their habitat preferences have shifted as the climate has become warmer and/or drier in Mediterranean regions of the world like California (as well as in South Africa, SW Australia, Italy, Portugal, Spain and Chile). Simultaneous analysis of the C, N and O isotope composition of insect, plant, animal and soil samples have just recently provided incredible new insights into the diverse responses global biodiversity have in different biome types (tropical forests, grasslands, woodlands, shrub lands) in response to recent human-induced climatic change. When coupled with geographically-based information scientists are able to create novel maps or “Isocapes” that show a spatially explicit and time-resolved picture of how regions have or have not responded to the sorts of environmental changes these organisms have never experienced before in their history. A great deal of this type of research has been or is being done by the faculty and students on the UC Berkeley campus; they are some of the most creative leaders and innovators in the emerging fields of stable isotope ecology, biogeochemistry and forensic science anywhere in the world.
These techniques allow us to understand the the past and contemporary responses e.g. mining genomic and stable isotopic signatures of past (decadal or millenial) responsed from specimens using new high-throughput technologies, connecting where appropriate to the paleorecord and spatial models of species or habitat change. Target organisms have been selected that would serve as initial “proof of concept” systems for investigation of organismal responses to recent environmental change in California. The requirements of choosing a study group or organism is that we can obtain some type of historical data about it and this it is amenable to modern genetic/genomic and stable isotope analyses. The model systems selected for the concept document are: Honey Bees (native, solitary, ‘honey’), Ground squirrels (Grinnell resurvey, elevation indicator), Mureletts, and Tree rings and fog.
Genomics
The genomes of all organisms contain a wealth of information about the past, present and future. Historical patterns of selection and demographic changes can be gleaned from genome-wide analyses. The number, composition, and networking of genes provide insights into myriad contemporary biological processes, including physiology, behavior, metabolism, and development. Future evolutionary trajectories can be predicted from functional genetic studies, often in experimental contexts. These types of genetic and genomic analyses are particularly powerful and informative when they include a historical dimension (such as the analysis of preserved museum specimens) and when higher levels of structuring (populations, ranges, species) can be analyzed and compared.
Unique opportunities to apply these approaches to studies of global biological change have proliferated with the advent of whole genome sequencing projects, “next-generation” DNA sequencing technologies, and high-throughput platforms for genotyping and variant detection. For example, we recently obtained 1x coverage of the entire genome of a 60 year old rodent skin, using a single toe bone, with just a single lane of Illumina sequencing. Through genome-scale comparisons of historical (eg. skins, pinned insects or pressed plants) vs recent specimens, we have an unparalleled opportunity to measure genetic change over time in the context of change in phenotype and distribution. Combined with advanced statistical genomics, another strength at Berkeley, we can then identify genes under selection because of rapid environmental change and infer changes in population size and connectivity.
Experimental manipulation
Analyzing genomes provides incredible information about such broad-ranging issues as historical patterns of selection, demographic changes, and insights into physiology, behavior, metabolism, and development. Opportunities to apply new approaches to global change biology have proliferated with the advent of whole genome sequencing projects, “next-generation” DNA sequencing technologies, and high-throughput platforms for genotyping. By comparing historical (e.g. skins or pressed plants) and recent specimens, BIGCB will measure species' genetic, phenotype, and distribution changes over time with unparalleled resolution. Combined with advanced statistical genomics, another UC Berkeley strength, we can identify genes and pathways under selection because of rapid environmental change. Coupling genomic dynamics with measured changes in traits — e.g. shifts in morphology and timing of life history events — will deepen our knowledge of key processes and identify robust predictors of population collapse.”
The analysis of genetic/genomic, phenotypic, and distribution changes over time can give us hypotheses about the molecular changes that occur as organisms face altered environmental conditions and either adapt, or fail to adapt, to these changes. Certainly advanced statistical methods can point to correlative changes, but experimental analyses must be carried out to go beyond correlation. For example, genomic analyses may identify a number of candidate genes whose expression changes in correlation with environmental changes. But to prove a functional relationship, and more importantly to understand the mechanistic basis of how these changes alter the physiology, phenotypic plasticity, and adaptability of an organism, it is imperative to experimentally test these ideas by manipulating the expression of these candidate genes in experimentally tractable species. This could mean using well-established techniques to alter gene expression in model species such as Drosophila or mice. However, it is becoming increasing possible to carry out similar manipulations in all manner of species (using RNAi, morpholinos, transient transgenesis, etc.), making it possible to test these hypotheses in animals that are key species or sentinels within specific environments.
Furthermore, particularly species face extreme fluctuations in environmental condition on a daily basis. For example marine organisms that reside in intertidal regions experience drastic changes in temperature and salinity with each tidal change. Molecular analyses of how these organisms respond on both the short term (daily) and the long term (decades of global environmental alterations) may help us define the genetic variation that allows some organisms to adapt readily to global change, and thus could help us both predict and ameliorate the effects of environmental degradation.
Such studies could take advantage of intertidal organisms native to California coastal environments, as well as well previously studied species that inhabit the tropical waters in Hawaii and Moorea. These analyses could take advantage of the expertise provided by Berkeley faculty who are part of the Center for Integrative Genomics.
Model systems
HONEY BEES:
European honeybees (Apis mellifera) occupy a unique place in human society. Their actions as pollinators influence our food supply more than any other animal, they provide products such as honey, beeswax and propolis, yet reactions to their venomous sting cause more than 100 deaths in the U.S. each year.
Honeybees are also ecologically unique. Enormous populations are managed for agricultural purposes, but even larger populations of feral honeybees exist in sympatry with managed bees. With the recent and mysterious collapse of honeybee populations in the U.S., it has become clear that we know far too little about the ecological and evolutionary forces that act on wild and managed honeybees, and the interactions between these populations.
The UC-Berkeley Essig Museum of Entomology currently houses 1,781 honeybee specimens from California, including bees collected during every decade since the 1890s, and from 54 of 58 counties. Amazingly, many of these specimens have retained the pollen that was collected by the living bee. We are beginning to use these specimens to 1) perform whole-genome sequencing to identify genetic changes during the past 120 years, 2) screen these honeybees for diseases using an insect microbe microarray, 3) identify pollen collected to document how plant-pollinator interactions have changed through time, and 4) use stable isotope analysis to examine responses of bees to global change.
The extensive insect collections held at the Essig Museum of Entomology and other natural history collections offer tremendous opportunities to extend this model of historical genomic analyses to other species, including native insects (bees, butterflies, ant) and damaging invasive species.
CALIFORNIA VERTEBRATES:
Through the MVZ's Grinnell Resurvey Project (GRP), we are re-examining diversity of small mammals and birds at 100's of sites in California, especially the Sierra Nevada, for which we have large collections and extensive field notes and images from the early 20th C. This has demonstrated substantial changes in species distributions, but also variability in response, with many high elevation species contracting upwards, formerly low elevation species expansind upwards, and other related species not changing at all. A corrollary is substantial changes in local community composition. On the positive side, large protected landscapes, such as Yosemite National Park, have retained overall species richness. Using these collections, we are now testing different approaches to spatial prediction of specices' responses to environmental change, analysing change in diet via stable isotope analysis and changes in phenotypic and genomic diversity. This study demonstrates how rich historical collections combined with modern resurveys and new technologies can elucidate the various dynamics of biodiversity in the face of rapid change. Proposed expansions of the GRP are to expand surveys into the sky islands of the Great Basin and Mohave, to develop and apply methods for historical genomics, and to extend the analyses to the rich fossil record of the region.
Faculty contacts
Group Leaders: Todd Dawson, Neil Tsutsui, and Craig Moritz
Participating Faculty & Staff: