Genetic monitoring in California
State Parks: Potential for including genetic sampling as part
of the IMAP and for consequently improving genetic management
of native species
Rogers, D.L., R.A. Woodward, P.E. McGuire, S.K. Brown,
D.R. Elam, H.B. Ernest, E.R. Heeg, J.M. Hull, L.S. Kimsey, K.J.
Rice, H.B. Shaffer, B.N. Sacks, R.S. Schwartz, and J.A. Well
Prepared with funding from the California Department
of Parks and Recreation through Interagency Agreement # C0218001
with the Genetic Resources Conservation Program, University of
Summary and recommendations
On February 16, 2005 the California Department of Parks and
Recreation (DPR) sponsored and co-organized, with the Genetic
Resources Conservation Program of the University of California,
a workshop on genetic monitoring. Attended by mainly UCD researchers
who conduct genetic studies on California native plants and animals,
together with individuals from agencies and organizations that
manage or contribute to the conservation of these taxa, the objective
was to discuss the opportunity for including genetic monitoring
as part of the Inventory, Monitoring & Assessment Program
(IMAP) of the DPR. Presentations illustrated the various kinds
of information that could be gained from genetic monitoring,
how monitoring methods and timeframes would vary according to
general taxonomic groups, the different kinds of genetic information
and what they reflect, and how contextual information (species
characteristics, spatial and temporal environmental information)
is critical for appropriately interpreting genetic information.
Although formal recommendations were not put forward by the group,
several points emerged from discussions that can be framed as
- It is neither reasonable nor feasible to collect biological
samples towards a goal of genetically monitoring all taxaor
even all plant and animal taxain State Parks. However,
in some situations, genetic monitoring is well recommended for
the information that it can provide towards identifying potential
problems or more effective conservation. Priorities could include:
listed species; species that have recently undergone severe habitat
reduction, habitat fragmentation, or loss of census size; populations
suspected of possible hybridization with introduced conspecific
populations or sexually compatible species; or species that may
reflect environmental quality or contamination.
- Prior to collecting samples for genetic monitoring, it is
advisable to contact a researcher who conducts (or has conducted)
genetic studies on the species of interest or a related species.
This can serve three purposes: i) Provide information on sampling
protocol, including season, timeframe, and methods for sampling
(Genetic monitoring is difficult to reduce into a standard protocol.
It varies according to both objective and the species under consideration);
ii) Ensure there is an interested researcher to receive, store,
analyse, and interpret the samples; and iii) Ensure the information
(research results, DNA sequence information, etc.) is shared
and stored appropriately (e.g., Genbank, Natural Diversity Database,
USGSs Biological Information Observation System (BIOS),
- For genetic monitoring, it is just as essential to collect
environmental information (e.g., sample location, site description)
as it is the biological sample itself. This is critical for meaningful
interpretation of the genetic data.
- Insects are a special case: although for most insect species
there is probably not enough basic information to support genetic
monitoring, monitoring on a species (or higher taxonomic level)
is very important. There are major blackholes in our knowledge
of California insects and yet they play critical ecological (and
agricultural) roles. Considerable taxonomic expertise is required
for monitoring insect species. It is recommended that this expertise
be incorporated, where possible, into training for IMAP so that
the diversity and health of insect populations (as well as potential
threats from invasives) can be better monitored.
- There is a need for coordinated efforts for seed collections,
inventories, and biological collections to support effective
genetic monitoring. A directed workshop (and suitable actions
following from that) is recommended.
- In addition to determining more information about the populations
and species of interest, genetic monitoring can be used, in specific
cases, to indicate changes in environmental condition or quality.
For this reason, priorities for genetic monitoring should also
consider environmental areas of concern or interest, in addition
to the species themselves.
The California Department of Parks and Recreation (hereafter
called Cal Parks) has recently expanded and revised
their monitoring program for plant and animal taxa in State Parks:
the Inventory, Monitoring & Assessment Program (IMAP). A
workshop (Genetic monitoring in California State Parks:
Improving connections between species management and genetic
research) was conducted on February 16, 2005 to provide
an opportunity to explore the idea of including some genetic
aspects to IMAP activities-making additional observations or
collections as part of IMAP field activities that would contribute
to genetic research; providing information on the genetic nature
of species that would have implications for the monitoring program;
or any other ideas that would contribute to increasing the information
gained through IMAP, particularly about the genetic diversity
of species. The objectives were to provide Cal Parks (and other
interested and participating agencies and organizations) with
some ideas about the utility/application of genetic monitoring
for various taxa, to provide selected genetic researchers with
information about the State Parks monitoring program, and to
discuss ideas for how the Cal Parks inventory/monitoring program
might include genetic monitoring and enhance research. The workshop
was initiated, funded, and co-organized by Cal Parks (Dr. Roy
Woodward) and was co-organized and hosted by the Genetic Resources
Conservation Program of the University of California (Drs. Deborah
Rogers and Patrick McGuire).
Genetic monitoring refers to assessment of genetic diversity
over time. Other types of genetic studies may investigate genetic
relationships among species or subspecies or the relationship
between the genetic diversity of a species and the way it is
structured spatially across the species range. Genetic
monitoring implies a temporal component to the study. The appropriate
timeframe for sampling genetic diversity to detect meaningful
changes will vary according to species (for example, the length
of their individual lifespans: in general, the longer lived the
species and the longer the time to reproductive maturity, the
longer it will take in absolute time to detect genetic changes)
and to the environment (for example, how quickly the environment
is changing or the presence and severity of human influences
such as habitat loss or environmental degradation). Biologically
meaningful changes in the genetic diversity of a species occur
over generations of that species, rather than within the lifetimes
What genetic monitoring can potentially
Within the context of natural areas management, there are
two main uses of genetic monitoring: to determine genetic responses
of species to severe environmental contamination (e.g., increased
mutation rate in response to a major pollution event; for example,
see Lavie and Nevo 1987) and to detect genetic
changes over time in native populations that may be in response
to more gradual or cumulative changes in the environmenteither
natural or human-influenced. The interest here is on the latter
Monitoring the genetic diversity of populations of native
species over time can be useful in detecting situations or trends
that may confirm normal levels of diversity or alert managers
to potential problems. Examples of situations that can be detected
with genetic monitoring include the following:
- Loss of genetic diversity: Monitoring can detect biologically
significant changes in genetic diversity over time. Large losses
in diversity could have negative effects on fitness and survival
in the long term, and ability to adapt to changing environmental
- Genetic structure (or loss of genetically differentiated
populations): In addition to the spatial pattern of genetic diversity
in a species (e.g., how well differentiated or similar are the
various populations or regions of a species), monitoring can
track changes in this structure over time, indicate a metapopulation
structure, or detect a trend towards loss of a population (prior
to actual decrease in census number).
- New hybridizations: Hybridizations between subspecies or
species, such as those between reintroduced populations or between
native and exotic species, can be detected.
- Effects of fragmentation: Genetic impacts can result from
fragmentation of habitat. In outbreeding plants, for example,
major fragmentation of habitat can lead to an increase in inbreeding
and possibly inbreeding depression.
- Has population undergone a bottleneck: Genetic monitoring
can determine whether the population has gone through a severe
reduction in census size in the usually distant past, regardless
of current size. This history can have implications for the genetic
diversity and viability of the population.
- Susceptibility to disease: In some cases, genetic diversity
can indicate susceptibility to disease. For example, there may
be genetic resistance that can be determined; certain genetic
conditions (e.g., inbreeding depression) may make a population
more susceptible to contracting or suffering the effects of introduced
- Gender ratio (in absence of sexual dimorphism): Sexual identity
and gender ratios can be determined by genetic analysis, even
when this is not apparent from morphological traits.
- Clones, family structure/relationships: The genetic relationship
among individuals can be determined from genetic studies. This
can be particularly important in small populations where inbreeding
depression could be a concern.
- Genetic contamination: If nonlocal plant materials or animals
are introduced to an area, breeding with the native population(s)
could potentially undermine local adaptations in the long term.
- Domestic - wild populations (interbreeding, assimilation):
The degree to which domesticated individuals (e.g., landscaping
plants, hatchery fish, farm animals) are interbreeding with native
wild populations can be determined by genetic studies.
Comments on collecting biological samples
for genetic assessment
Various kinds of tissues can be used to obtain DNA for genetic
analysis. This can be done nondestructively in most casesthat
is, without harm or discomfort (in the case of animals). Depending
on the species and situation, road-killed animals may be valuable
sources of genetic information. However, the type of tissue most
useful, the amount of tissue needed, and even storage conditions
may vary from species to species or at least among major taxonomic
groups. For example, seeds of conifer species (e.g., pines) contain
different kinds of genetic information than do seeds of angiosperms
(e.g., poppies or poplars). Consequently, before making a collection
it is important to connect with a researcher who is familiar
with the species and interested in doing a genetic study or at
least in maintaining a collection of tissues or extracted DNA,
so that specific sampling and transport/storage information can
be obtained. Some generalizations include:
- Formalin is not recommended for storing tissue samples.
- Depending on tissue type, the stability of the protein or
DNA may be affected by certain temperature or moisture conditions.
The sensitivity of samples to changes in moisture (either too
much humidity or desiccation) and temperature extremes should
be determined. In addition, the optimum transport time (from
field collection to reception by researcher) should be known.
- Environmental information should be collected in concert
- The identity of the sample should be maintained at all times
and full records should be kept (redundancy is desirable).
Interpreting genetic information
Because of the different types of genetic diversity and the
various statistical and mathematical methods to analyse them,
genetic information requires considerable context and expertise
for appropriate interpretation. In general:
- Genetic information needs biological context for meaningful
interpretation (e.g., implications of sample size; limitations
of method/data type; environmental influences; management effects;
genome context (different implications of mtDNA, cpDNA, nuclear
DNA); controls or baseline data).
- One type of genetic data or genetic method of analysis is
not necessarily better than others: however, each has appropriate
uses and also limitations.
- In some cases (especially where the outcome of a genetic
monitoring project could have serious economic or political outcomes)
peer review of the genetic information (i.e., interpretation
by various, appropriate researchers) may be needed to ensure
that the appropriate biological context has been provided and
to approach objectivity in interpretation.
- If a genetic monitoring study does not provide evidence of
genetic differentiation (e.g., among populations), this result
may be related to methods.
- Ubiquitous distribution and high mobility does not necessarily
mean there will be no spatial genetic structure in a species
(e.g., coyotes: see the presentation abstract by Holly
Ernest and colleagues, below).
- Patterns revealed by genetic monitoring require careful interpretation
in their relation to historical versus current or ongoing influences.
There can be a significant lag effect in genetic information
reflecting event (e.g., cessation of gene flow; see Slatkin
and Barton 1989).
- Neutral genetic variation does not mean unimportant
genetic variation. Rather, it means genetic variation that is
not under the influence of natural selection.
Opportunities and priorities for genetic
monitoring in Cal Parks
It is not realistic (or reasonable) to monitor genetic diversity
in all taxa in California State Parks. But there are some taxa
or situations that would greatly benefit from the information
provided by genetic monitoring. Also, there are some good research
opportunities/situations where genetic monitoring might provide
some valuable insights, including:
- Wild populationse.g., populations at periphery of natural
ranges (could be small populations at risk, locally adapted populations,
populations with valuable genetic diversity in responding to
climate change, etc.); species or populations that have experienced
recent and rapid decreases in size; species or populations that
have experienced rapid habitat loss or fragmentation; listed
- Restored populationswhere genetic monitoring is critical
to predict the success of the restoration.
- Species or populations that are in particular areas where
there is concern about responses to particular environmental
events or influences.
- Research opportunitiese.g., long-term studies with
one sampling event (overlapping generationse.g., coast
redwood, giant sequoia; soil or canopy seed banks).
Abstracts of presentations
monitoring in California State Parks: Improving connections between
species management and genetic researchDeborah
Rogers (Genetic Resources Conservation Program, University
Questions that relate to genetic monitoring with the California
State Parks system and are within the scope of this workshop
- How to make biological collections and monitoring more biologically
- How to incorporate genetic information into monitoring activities?
- How to collect genetic information?
- Which taxa might be most appropriate for genetic monitoring?
- What can genetic monitoring tell us?
- How to share and coordinate biological collections?
Genetic monitoring is difficult to reduce into a standard
protocol. It varies according to both objective and the species
under consideration. For each objective and species, the following
questions can then be raised to help determine an appropriate
- What is the appropriate time-scale to detect significant
- What genetic measures are appropriate?
- What is the appropriate (spatial, seasonal, etc.) sampling
- What genetic attribute (derived from the genetic data) is
the most effective to capture the potential genetic change (Effective
population size? Diversity? Genetic structure?)?
It is reasonable to consider monitoring genetic diversity
in some cases, because of the importance of genetic diversity
to species fitness, evolutionary potential, ability to
occupy new ecological niches, and potential to respond to environmental
change. See Reed and Frankham (2003) for evidence
of a significant and positive relationship between genetic diversity
and fitness across a broad range of taxa.
Genetic diversity is dynamic, constantly being influenced
by natural processes. These processes include natural selection,
random genetic drift, and gene flow. Consequently, genetic monitoring
studies or programs are best designed with the timeframe, direction,
and general influence of these processes in mind, so as to allow
detection of genetic changes that are from other sources (e.g.,
habitat loss or direct species loss, unnatural hybridizations
or genetic contamination from nonlocal introduced or planted
populations, etc.). A proper background of genetic variation
is important to establish to enable detection of unusual or undesirable
Genetic monitoring can provide information that normal census
data may not, for example:
- In some species (lacking sexual dimorphism), sex identification;
gender ratio in a population
- Clone identification in species that reproduce asexually
- Family relationships among individuals
- Dramatic changes in population size over time (that have
occurred historically, and for which there is still a record
in the genetic diversity of the populations)
- Population dynamics (gene flow/migration among populations,
evidence of local adaptations, etc.)
- Hybridizations among subspecies or species
Use of genetics
and monitoring in FWS Recovery Plans: Observations and case studiesDiane
Elam (US Fish and Wildlife Service, Sacramento, CA)
A search (using the California Natural Diversity Database and the
Department of Parks and Recreation (R.A. Woodward, pers. com.))
revealed that approximately 24 plant taxa and 21 animal taxa
that occur on California State Parks are federally listed. Among
the listed plant taxa, recovery plans for 12 recommended preserving
genetic material ex situ (seed collections, greenhouse populations)
and 10 recommended genetic studies (patterns of genetic diversity,
limiting genetic factors, systematics, clonality, hybridization).
For example, the endangered Eriodictyon altissimum is
known from six locations, two of them in Montaña de Oro
State Park. Both this species, and the endangered Lompoc yerba
santa (Eriodictyon capitatum), can reproduce vegetatively,
so genetic studies would be useful in determining the extent
of genetic diversity and size/number of clones. Genetic research
has been recommended for the endangered Cupressus abramsiana
to determine whether, or to what extent, hybridization with native
cypresses has occurred. For six plant taxa, FWS recovery plans
indicated introductions or supplementations of native material.
Genetic studies could help determine the most appropriate sources
of plant material and help determine any impacts on the native
populations. For only one of the listed plant species was genetic
monitoring recommendedthe Otay tarplant (Deinandra conjugens).
This threatened species, present at Anza-Borrego Desert State
Park, is self-incompatible. Incompatibility is controlled by
the S-locus and individual plants are only sexually
compatible if they have different alleles at this locus. The
recommended study involves determination of the S-allele variation,
identification of isolated populations that may need augmentation,
identification of genetic augmentation techniques, monitoring
genetic variability, and research to identify limiting genetic
Of the 21 listed animal species in State Parks, recovery plans
for seven indicated preserving genetic material ex situ (captive
propagation). Examples include the California condor and the
riparian brush rabbit. For 14 of the listed animal taxa, recovery
actions included recommendations for genetic research to determine
patterns of genetic diversity, relationship with other species/taxa,
or hybridization issues. For some speciesincluding peninsular
bighorn sheep and desert pupfishgenetic monitoring was
Can we link
ecological monitoring with evolutionary processes? or Genetics
on the cheapKevin Rice (Department
of Plant Sciences and Center for Population Biology, UCD)
Genetic differences among or between populations of a species
may represent differences in local adaptations. There is also
genetic diversity within each of the populationsthat diversity
represents potential to adapt to new environmental conditions
in the future.
There are various kinds of genetic diversity and many ways
to measure it. Some genetic diversity represents adaptation;
some is neutral-meaning that it is (or assumed to
be) not influenced by natural selection. However, neutral
genetic variation should not be misconstrued as unimportant.
It simply is not currently and apparently influenced by selection.
These different types of genetic diversity are not necessarily
correlated with one another. Consequently, it is important to
interpret genetic diversity measures carefully, as each may tell
us a different part of the story, and one is not necessarily
better than the other, but simply more appropriate for answering
different types of questions. Furthermore, there is a lag between
the influence on genetic diversity (e.g., cessation of gene flow
between two populations, or the beginning of a new type or degree
of natural selection) and its reflection in the DNA or other
The different natural processes that influence the amount
and pattern of genetic diversity in native populations include
mutation, natural selection, genetic drift, and migration (gene
flow). Natural selection and genetic drift tend to increase the
genetic differentiation among populations; gene flow among populations
tends to homogenize differences.
Inbreeding depression can result when previously outcrossing
individuals are restricted in their breeding activities and mate
with relatives. At the genetic level, this means that alleles
(i.e., one copy of a gene) that previously were deleterious but
recessive (i.e., cloaked by being paired with a beneficial
or neutral allele that was dominant) are now more likely to co-occur.
When that happens (i.e., two recessive deleterious alleles are
paired), the deleterious effect is expressed. Collectively, this
can lead to lower viability and fitness in the long term. This
chain of events happens more quickly in small populations.
The census size of a population (the total number of individuals)
and its effective population size (the number of
individuals involved in reproduction) are often not the same.
Unequal gender ratios (in animal species and dioecious plant
species), fluctuating population sizes from one generation to
another, and other influences can cause the effective size to
be much smaller than the census size.
Good, bad, & uglyShould we care?Lynn
Kimsey (Department of Entomology and the Bohart Museum of
Insects are small but they dominate habitats. E.O. Wilson
estimated that in the US there are 400 lbs of insects relative
to 14 lbs of humans per acre! There are many different insect
species or taxa: in fact, there are more kinds of insects than
any other group of animals or plants (see Purvis
and Hector 2000). However, many insects have not yet been
documented or, if named, they still remain largely unknown. The
number of insects with common names is less than 0.001% of the
total species. Insects also have major impacts on other species
and on ecosystem functioning. Every insect species has at least
one species of insect parasite. Among the vast number of insect
species, there is an amazing variety of biologies: mosquitoes
and houseflies can have a new generation every two weeks during
warm weather; jewel beetles spend 1 to 10 years in a larval stage;
mayflies live one year as a larva and three days as an adult;
monarch butterflies live two to three years as adults and three
months as larvae; aphids are born pregnant. There is also immense
diversity in reproductive potential: one aphid can produce 10108
descendents in her lifetime; monarch butterflies produce only
about 20 offspring. This diversity of life histories also illustrates
the potential complexity of any monitoring program. For example,
the frequency of monitoring would vary greatly depending on the
generation times of the species studied, and what would be monitored
would depend on the life stages and time spent in each stage.
In California, there are an estimated 100,000 species of insects.
Of these, 12% are endemic, 9% are new to science, and in some
habitats up to 70% may be exotic. California is particularly
rich in insect species, with 500 insect families occurring here,
with only 600 families in all of North America. In South America,
there are about 900 families of insects known. There are various
distribution patterns for California insects; some are based
on geography or environmental conditions (e.g., a west-east gradient,
with the number of families of insects increasing as you move
inland from the coast), others are based on research foci (that
is, there are distributions that reflect the work from particular
research programs or researchers), and others are related to
the location of programs that monitor for insects. There are
large blackholes in our knowledge of insects, and entire counties
or habitat types in California for which we know little about
the insect species.
Insect species play a diversity of important ecosystem roles-as
food, pollinators (i.e., most plants need insect pollinators;
endangered plants may have only one insect pollinator), disease
vectors, and recyclers (i.e., as wood feeders, detrivores, carrion
feeders, and scavengers). They can also be bioindicators of environmental
quality as they are fine-tuned to the environment. For example,
shifts in insect populations or species can indicate acid mine
run-off (e.g., as indicators of changes in pH), contamination
from such sources as livestock or sewage, or even activities
such as marijuana plantations (related to sharp changes in certain
nutrients). In particular, aquatic insects can be excellent bioindicators
as they have very specific water quality requirements (and thus
changes in species would reflect changes in conditions) and they
are easy to sample. However, taxonomic expertise is required
for such monitoring.
Monitoring insect populations, consequently, can not only
provide more information directly on these species, but provide
information on indirect impacts on other species, environmental
quality, and new exotics that might become invasive and problematic.
To make insect monitoring feasible and useful, additional taxonomic
expertise (more entomologists) and training of field staff are
monitoring of wildlife: Mammals and birdsHolly
Ernest, Ben Sacks, Joshua Hull, Sarah Brown, Elizabeth Heeg,
and Jay Well (Wildlife & Ecology Unit, Veterinary Genetics
Genetic monitoring of wildlife populations in California can
contribute information useful to protecting their health, conserving
their long-term viability, and providing management options.
As most species studied by the Wildlife & Ecology Unit are
wide ranging, the studies cross multiple states and sometimes
country borders. Genetic monitoring of the yellow-billed magpie
(Pica nutalli) is focused on determining the current level
of genetic diversity, population genetic structure, and the relationshipif
anybetween genetic diversity and structure and the observed
decline in the numbers of birds. Similarly, genetic studies of
the Swainson's hawk (Buteo swansoni), red-tailed hawk
(Buteo jamaicensis), and the great gray owl (Strix
nebulosa) seek information on the genetic relationship among
populations-whether certain populations are distinct and the
level and direction of gene flow among them. A genetic study
of coyote populations in California revealed a diverse pattern
of population relationships: some genetically distinct populations
in the south and central coast areas of California, continuous
(i.e., high gene flow) populations in northern and eastern California,
and moderate gene flow (moderate genetic similarity) between
east-west populations in the northern and southern regions of
the Central Valley. In general, although coyotes have been previously
described as ubiquitous in California and assumed to be fairly
wide ranging (and consequently expected to have mid- to high
levels of gene flow), genetic studies suggest there are habitat-specific
genetic subdivisions statewide. Additional samples are currently
being collected from southern California. Ongoing studies for
the red fox and black bear are seeking information on population
genetic structure and historical patterns of gene flow (migration).
Feral pigs in Californiaoriginating from free-range
domestic pigs in the coastal region in the 1700s and from wild
boars introduced into Monterey County in 1925 and the 1950shave
caused much damage to natural environments (such as oak woodlands)
and to livestock (direct predator activity and transmitting diseases
such as cholera, swine brucellosis, foot and mouth disease, and
African swine fever). Statewide genetic studies are helping to
determine genetic structure and relationship with landscape influences
and how populations change over time.
Genetic analysis is also used in forensic studies of wildlife
to help determine illegal activities (such as harvesting of protected
species) or wildlife behavior that may impact public health or
welfare (e.g., wildlife attacks, impacts to food supply). For
example, genetic analysis can be useful in discriminating closely
related species-a decision that is important when one of the
species is endangered and protected. Genetic studies were used
to determine whether a diesel fuel spill into Suisun Marsh killed,
among other mammals, an endangered mouse (Reithrodontomys
raviventris) or a common harvest mouse (Reithrodontomys
monitoring in selected California fish and amphibiansRachel
Schwartz and Bernie May (Department of Animal Science, UCD)
Sampling fish for genetic studies can be done nondestructively
and fairly easily. After catching the fish, a small sample from
a fin is removed and stored (dry) in a coin envelope or in a
small plastic tube in 95% ethanol (quickly returning the fish
to the water after sampling). For fish species, genetic monitoring
is most commonly used to help delineate management units (by
determining patterns of genetic differentiation), determine hybridization,
improve restoration activities, and suggest potential health/population
viability problems. For most fish species, the life expectancies
of individuals and life history stages are such that sampling
for genetic information would logically occur either annually
(to detect changes in genetic diversity over time; over perhaps
over longer periods) or twice or more per year (to detect genetically
significant differences in offspring survival or differences
in genetic contributions among parents). Because of the large
impact of commercial salmon fishing and hatcheries, genetic studies
for native salmon and trout species often focus on the genetic
effects on native populations of hatchery-raised fish, hybridization
between domestic and wild fish, and genetic impacts from habitat
fragmentation. For example, a genetic study of California golden
trout investigated the degree of hybridization between this species
and rainbow trout that were released in their native habitat
in Golden Trout Creek and in the lower South Fork Kern River.
Genetic monitoring of the Sacramento perchreintroduced
to Suisun Marsh after becoming locally extinctwill help
determine the health (e.g., genetic diversity, number of parents
participating in reproduction) of the reintroduced population
and whether this population is interbreeding with other native
monitoring in some California amphibians and reptilesH.
Bradley Shaffer (Section of Evolution and Ecology, College
of Biological Sciences, UCD)
A genetic study of 84 populations of the tiger salamander
(Ambystoma californiense), encompassing its entire range in California,
revealed six genetically differentiated regions. Populations
from Santa Barbara and Sonoma Counties are particularly well
differentiated and geographically isolated from all others. These
two populations are defensible as genealogical species. The geological
history of California, together with the genetic evidence, suggest
that the Santa Barbara population has been isolated for at least
0.74 to 0.92 million years and the Sonoma clade is equally ancient.
The remaining units in the Southern San Joaquin Valley, Central
Coast Range, Central Valley, and San Francisco Bay Area are separated
by geological features, ecological zone boundaries, or both.
In combination with previous and ongoing landscape ecological
studies, this work suggests that, within units, California tiger
salamanders are not particularly philopatric, but there is a
deep genetic differentiation among major geographical regions
(Trenham et al. 2001; Shaffer
et al. 2004b; Trenham and Shaffer 2005).
Genetic studies of nuclear and mitochondrial DNA have also
elucidated patterns of interspecific hybridization among native
and introduced tiger salamander species. The barred tiger salamander
(Ambystoma tigrinum mavortium) was introduced
by bait dealers into the native range of the California tiger
salamander (A. californiense). Hybridization and backcrossing
have been occurring in central California for 50 to 60 years,
or an estimated 15 to 30 generations. Hybridization was studied
by analyzing the relative frequencies of hybrid genotypes in
three kinds of breeding habitats: natural vernal pools, ephemeral
man-made cattle ponds, and perennial man-made ponds. Perennial
man-made ponds tended to have higher frequencies of nonnative
alleles than either type of seasonal pond. This was true even
in cases where perennial and seasonal ponds were within a few
hundred meters of one another. This is most likely the result
of differing types of natural selection between the two pond
types. Thus, for these species, the hybrid zone has a mosaic
structure that depends on pond hydrology or ecology (Riley
et al. 2003; Fitzpatrick and Shaffer 2004).
The red-legged frog, Rana aurora, is currently recognized
as one species with two subspecies, aurora and draytonii.
R.a. draytonii is protected under the US Endangered Species
Act. A recent genetic survey (using mitochondrial DNA) of 50
populations of red-legged frogs from across their range provided
several major results. (1) Consistent with several other lines
of independent evidence, aurora and draytonii are
each distinct, evolutionary lineages; the mtDNA data indicate
that they do not constitute a monophyletic group, but rather
that aurora and R. cascadae from the Pacific northwest
are sister taxa; (2) the range of the draytonii mtDNA
clade extends about 100 km further north in coastal California
than was previously suspected, and corresponds closely with the
range limits or phylogeographical breaks of several codistributed
taxa; (3) a narrow zone of overlap exists in southern Mendocino
County between aurora and draytonii haplotypes,
rather than a broad intergradation zone; and (4) the critically
endangered population of draytonii in Riverside County,
CA forms a distinct clade with frogs from Baja California, Mexico.
The currently available evidence favors recognition of aurora
and draytonii as separate species with a narrow zone of
overlap in northern California (Shaffer
et al. 2004a).
The western pond turtle, Emys marinorata, is declining
throughout its range, primarily because of loss of habitat via
urbanization, conversion to agriculture, and interactions with
invasive turtles. Recent genetic studies across this species
native range (Washington state to northern Baja California) have
identified four distinctive groups within this species: a large
northern group that includes those populations in Washington,
Oregon, and northern California; a southern group (roughly, east
of Santa Barbara, CA and south); a San Joaquin Valley group;
and a small localized group near Santa Barbara. The identity
of, and relationships among, these groups and the two recognized
subspecies, E.m. marmorata and E.m. pallida, provides
a more detailed framework for appropriate management strategies
for conservation and restoration (Spinks et
al. 2003; Spinks and Shaffer 2005).
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US Fish & Wildlife Service
US Geological Survey
California Department of Fish & Game
Mary Ann Showers
California Department of Parks and Recreation
California Native Plant Society
Misa Ward (alternate
UC Davis Department of Plant Sciences, CAES
UC Davis Department of Animal Science, CAES
UC Davis Department of Entomology, CAES
UC Davis Section of Evolution and Ecology, CBS
UC Davis Wildlife and Ecology Unit, Veterinary Genetics
Genetic Resources Conservation Program, University of California
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