Molecular Ecology (Modul)
two credit lecture
Kristina Sefc & Steven Weiss
Introduction to the Course
What is Molecular Ecology?
Molecular Ecology is a molecular-based approach to answering evolutionary
and ecological questions. There is no accepted definition of „Molecular
Ecology“, and it was only a few years ago that a textbook appeared devoted to
the subject. There is, however, a peer-reviewed journal Molecular Ecology, and
its description of itself serves as a useful start to understanding what
„Molecular Ecologists“ really do.
An Introduction to Molecular
Ecology
Trevor Beebee
&
Graham Rowe
RC 910 B414
What is Molecular Ecology?
Molecular Ecology publishes papers that utilize molecular genetic techniques
to address consequential questions in ecology, evolution, behaviour and
conservation. We discourage papers that are primarily descriptive and are
relevant only to the taxon being studied. Studies may employ neutral markers
for inference about ecological and evolutionary processes or examine
ecologically important genes and their products directly. Research areas of
interest to the journal include:
•population structure and phylogeography
•reproductive strategies
•relatedness and kin selection
•sex allocation
•population genetic theory
•analytical methods development
•conservation genetics
•speciation genetics
•individual and species identification
•microbial biodiversity
•genetic marker development
•evolutionary dynamics of QTLs
•ecological interactions
•molecular adaptation and environmental genomics
•impact of genetically modified organisms
We can define many of these terms as the course progresses, but the
purpose of this first lecture is to give a background on the ecology of
aquatic organisms (especially fish), and especially those characteristics
that are most important to understand before being able to conduct fruitful
scientific inquiry into evolutionary and ecological processes, using molecular
tools. Our first important lesson here is that regardless
of the technology used, an understanding of the ecology of the organism is a
prerequisite for proper study design and data interpretation.
KNOW YOUR ORGANISM!
Who am I?
We can make a detailed list of what organismal characteristics one should
understand before beginning a molecular based study. In truth, any
characteristic may be important depending on the specific question being asked.
However, let us first consider what is or is not different about aquatic organisms
in general, and especially those traits that will most likely affect their genetic
architecture.
The first obvious factor is the environment (habitats) in which aquatic organisms
live. We can roughly think of two categories (fresh and salt water) and then
further consider flowing (lotic systems) and still (lentic systems) water habitats of
freshwater organisms. Another extremely important characteristic is the thermal
“regime” of the habitat.
freshwater rivers
lakes
oceans
About 70% of the earth‘s surface is covered by oceans, and about 97% of all
water by volume is contained in oceans. This is compared to 1% surface
coverage for freshwater. Only 0.0093% of the earth‘s water by volume is
found in freshwater lakes and streams (the remainder is in the form of ice and
atmospheric gas, etc.). Yet 41% of all modern fish species are found in
freshwater lakes and rivers! Why do you think this is so?
Freshwater habitats are highly fragmented systems compared to oceans.
Organisms in one lake do not easily reach other lakes. River systems are
constrained in a linear fashion, and aquatic organisms can move along a river
channel, but not easily between river channels. This promotes the isolation of
populations.
Reproductive isolation is one of the primary mechanisms promoting speciation.
Indeed, the question of whether or not two populations, or phenotypic variants
within an „apparent“ population are reproductively isolated is posed frequently
in molecular ecological studies. Reproductive isolation is much more easily
achieved by populations of freshwater organisms, as their habitats are
physically isolated from those of other nearby populations. This is the most
basic reason given to explain the high number of freshwater fishes, given the
small areal coverage of freshwater compared to saltwater. Still, there are a
large number of fish species in the ocean, and populations of organisms can
achieve reproductive isolation in other ways that are not strictly related to the
physical separation of habitats. And, freshwater organisms do find ways to
disperse between habitats, or colonize new ones, especially if we consider more
historical, glacial, or geological time scales.
Here is a map of a typical catchment area (Einzugsgebiet)
of a river
A species can often be found throughout one or more catchment areas, or be
limited to only a part of a catchment area. It is always important to ask what is
the distribution area of the organism under study, and for freshwater organisms
this is often most easily understood in terms of catchment areas.
This is a figure from a study on the phylogeography of salmonid fishes in eastern
Siberia. Note that there are 3 catchment areas outlined, corresponding to three
major river systems (Lena, Amur, & Enisey). River basins are physically
separated from each other, at least from the perspective of a fish. However, this
isolation has a temporal dimension. In this study, a few species were distributed
throughout all three catchments, whereas some were limited to one catchment or
the other. How can this occur? How does a
species get from one catchment to another?
The structure of basins can change over
glacial or geological time scales, and when
they do, opportunities are provided for
organisms to disperse from one drainage
system to another. Catchments are
dynamic, and every catchment has a
history. But different species have different
abilities to disperse. Understanding this
dispersal abilitiy is a key element to
understanding an organism‘s evolutionary
history, as well as current demography.
An example of a „river capture“ event
(Flußentzapfung)
Such events normally occur
over geologic or glacial times
scales but can be relevant for
understanding the evolutionary
history of many aquatic
organisms. Many such events
occurred during the Pleistocene
glaciations, and have largely
affected the patterns of
organismal distribution that we
see today, at least in temperate
environments.
the upper region of the
Pugwash river has been
„captured“ by the Philip
river
Dispersal abilities of freshwater organisms
The dispersal ability of various fish species, as well as other aquatic organisms
can differ tremendously, and in ways that are not always apparent to the casual
observer. One may first consider properties of aquatic environments themselves,
such as the frequency and height of floods, the effect of geological events such as
landslides and earthquakes, and the larger-scale dynamic effects of glaciations.
But organisms have intrinsic traits and „abilities“ in the form of their mobility
and tolerance of dynamic changes. Some fish, for example, are good at jumping
over small waterfalls, or swimming up through swift currents.
Other species, such as lampreys, use their suckerformed mouth and dentition to climb vertical rock walls.
river lamprey
(Lampetra planeri)
Bachneunauge
coho salmon
(Oncorhynchus kisutch)
mouth of a sey
lamprey
(Petromyzon
marinus)
When thinking of dispersal ability, it is not only the adult stage of an organism
that is important. Many aquatic organisms have egg or other early life history
stages that play a central role in dispersal. Fish have a wide variety of
breeding behaviours and reproductive strategies, for example. There are both
egg and live-bearing fishes, and among egg layers, some eggs are buried in the
gravel of a stream, some drift with currents, and others are adhesive, clinging
to substrates of various kinds including plants and woody debris. Such eggs
can then be transported by from one waterbody to another, accidentally by
birds or other organisms. Some ocean fishes, such as those living on a coral
reefs, may spend their whole adult life in one small area, but the larvae of such
species can be carried 100‘s or 1000‘s of kms by ocean currents. In general,
dispersal (and thus gene flow) among populations of ocean organisms is very
high, and thus they tend to be more homogeneous than in freshwater
environments. Understanding the life cycle of an organism and especially its
dispersal patter, is of fundamental importance to building hypotheses
concerning its genetic structure. In fact, dispersal is one of the fundamental
characteristics underlying a species‘s ecolgocial potential. While „real-time“
dispersal is studied using such methods as radio-telemetry or simple mark and
recapture, the long term effects of dispersal are understood in genetic terms,
and thus is a task of molecular based research
An organism‘s dispersal ability can be understood in the framework of current
environmental conditions, but the environment is constantly changing. The
most rapid changes are usually those instigated by humans. Presently, several
species of the genus Neogobius, native to the Black and Caspian seas are
expanding their range up the Danube river, and are
appearing in Austrian and Bavarian waters for the
first time in recorded history. This expansion is
believed to be the result of changes in the shipping
industry, that have promoted the use of water as
„ballast“. When a cargo ship is empty it must use a
large quantity of ballast water to obtain the correct
balance and height in the water. When full of cargo,
Round goby
it may need to release ballast water. It is estimated
Neogobius melanostomus
that ballast water can contain up to 3000 species of
aquatic organisms. When this water is discharged, its unknown or unwanted
„passengers“ escape into exotic habitats throughout the world.
The completion of the Danube-Main canal has further promoted the spread of
Neogobius, as well as other aquatic organisms throughout Northern Europe, and
even to North America.
The Danube-Main canal, a project first begun by Charlamagne in 793,
was completed in 1992. This created a 3500 km-long international
waterway connecting
Rotterdam on the North Sea, to the port of
Salina on the Black Sea. Along with the many
economic benefits that such a project has provided,
the canal has also created a number of environmental
problems (as predicted) in providing a colonization
corridor for numerous aquatic organisms.
Another invasive organism, who‘s spread
began long before the construction
of the canal, is the zebra mussel. Zebra mussel
is a temperate freshwater bivalve species
native to the Black and Caspian seas. The
mussels made their way to Western Europe
through canals and inland waterways that
were used for trade during the Industrial
Revolution. Zebra mussels first arrived in the
United States around 1985, when transoceanic
ships released ballast water into Lake St. Clair
of the Great Lakes.
Zebra mussel
Dreissena polymorpha
Zebra mussels
fouling an outboard
moter
1 meter high
accumulation of
Zebra mussel
shells
The European Eel (Anguilla anguilla)
10 mm
leptocephalus
Both the European and American eel
(Anguilla rostrata) spawn in the Sargasso sea, in
100-400 m depths. Their transparent „leptocephalus“ larvae migrate
leptcephalus larval in the Gulf stream for 1-3 years before undergoing metamorphosis
stage of a conger eel and beginning the freshwater stage of the life cycle. This is an
Conger oceanicus example of a catadromous migratory cycle. Anadromous fishes are
those that spawn in fresh water, but live as adults in the ocean.
Potamodromous fishes migrate within freshwater systems. Both an
organism‘s migratory and dispersal patterns have important genetic
consequences.
Since all eels spawn in the same place, and their breeding behaviour is that of a
„mass spawner“ it was assumed that they constitute a „panmictic population“.
Panmixis is the state where all individuals are mating at random. Panmixia across
a whole species is rare in nature. European eels have a very wide geographic
distribution, ranging from the North Atlantic to the Mediterranean Sea, and thus
experience a wide range of habitats. Most freshwater organisms with wide
geographic distributions consist of numerous described phenotypic variants. But
for eels, panmixia was not too difficult an hypothesis to accept. However, this had
never been tested with molecular tools, and several recent molecular based studies
have now launched a controversy as to whether eels are really panmictic or not.
Many pelagic ocean fishes are thought to
have panmictic or nearly panmictic
populations due to their breeding behaviour,
random or chaotic drifting of larvae or eggs,
and more or less physically homogeneous
environoment in which they are found.
However, pelagic fish populations can be
very large, and difficult to sample, so testing
this hypothesis of panmixia is not easy.
A school of herring
Clupea harengus
World Distribution of Brown Trout
The ecology of
individuals or
populations
within their
native range,
can differ greatly
from those in
introduced habitats.
Native range
Introduced
The brown trout (Salmo trutta) has a variable life history
pattern, exhibiting both freshwater resident and
anadromous strategies. Brown trout can, however, carry
out its entire life cycle in a few meters of an alpine moutain
stream. As such habitats exist throughout its range, and
individuals within such populations have little or no
opportunity to migrate to distant habitats, brown trout in
Europe are among the most genetically sub-structured
vertebrates that have been studied thus far. For a species,
this is the contrasting scenario to panmixia.
Fry
Alevin
Smolt
Ocean
phase
Spawning
male
Spawning
female
Life history stages of a pink
salmon (Oncoryhnchus
gorbuscha)
The typical salmon has a 5-stage life
history cycle. Alevins emerge from the
gravel with their yolk-sac still attached.
Fry stage salmon swim freely in small
streams, but in the case of pink salmon
they quickly grow into smolts and
migrate to sea. After 18 months of rapid
growth in the ocean, adult pink salmon
return to their natal stream to spawn,
completing a strict two-year breeding
cycle. Natal site fidelity (or philopatry)
influences genetic relationships among
populations, promoting differentiation
and local adaptation. If salmon
exhibited 100% philopatry, there would
be no dispersal, and no genetic exchange
among populations, and this would not
be advantageous for the long-term
survival of the species.
The pink salmon‘s life history is very special, even among the seven Pacific salmon
species. Its strict two-year cycle results in a interesting phenomena that will help us
introduce an important topic, the population. A population is a very important
concept in evolutionary biology, as it is the unit that evolves. But, what is a
population? If a species of fish lives in a small lake, and all the individuals in that
lake had an equal probability of mating with each other (panmixia), than the lake
would serve as a perfect physical unit describing the population. Another nearby
lake would constitute another population, with no possibility of confusion if, 1) the
lakes were not connected by some stream or river (nearby lakes often are), 2) birds
or other animals do not carry fish or their eggs from one lake to the other (they
sometimes do), and 3) humans are not transporting fish from one lake to another
(given the chance, they will always do this). The same concept can be more or less
suitable in rivers and streams, except it can be much more difficult to define
physical borders as stream systems belong to complex of linear networks that are
all connected to each other (catchment concepts). You should begin to see that the
„physical“ dimension of a population is not the only factor, there is a temporal
dimension that is very important. Given time, individuals of one population will
almost always manage to exchange genes with individuals of another population.
Lets return to the pink salmon. In every stream where there are pink salmon, no
matter how small and isolated, there are always two very distinct populations of
them. Why?
One more important factor in the pink salmon story is that pacific salmon have a
life history strategy that is semelparous. Semelparity means that an organism dies
after its first reproduction, where as iteroparous organisms mate repeatedly over
their life-span. If an organism is semelparous, and confined to a strict two year
cycle, there is an interesting temporal affect on its genetic structure. A pink
salmon born in 2002 will spawn in 2004, and its genes will be passed on to
generations of salmon in 2004, 2006, 2008, etc. But what about the odd years? Are
there no salmon in 2003, 2005, etc.? Some stream populations of pink salmon have
only adults returning to spawn in odd or even years, but many have both. These
odd and even year fish constitute separate populations, because they are
reproductively isolated, even though they live in the same place, and would not
have any „biological“ barrier to interbreeding. Remember again the European
eel. „populations“ (in the physical sense) of eels from the North Sea are a long way
from those in Greece, and these environments are also completely different. But, if
all breeding activity occurs in one place, and if random mating is the rule, then the
entire „species“ may consitute one genetic population. The lesson here is that
populations appear to be quite different from species to species. One must
understand the life-cycle of the organism, its breeding behaviour, its range, and its
pattern of dispersal before trying to define a population. Second, populations are
not discrete inflexible units, but are rather dynamic across both spatial and
temporal scales.
Populations, cohorts, & individuals
In the example of salmon (semelparous), all individuals of a given cohort (yearclass) can be followed as a unit through their entire life-cylce, and thus consist of
a population or genetic „unit“ that is easily defined. There are many benthic
invertebrates, such as stoneflies (Plecoptera), caddisflies (Trichoptera), and
mayflies (Ephemeroptera), that are semelparous, and have discrete life-history
stages, and so each indvidual can easily be assessed in terms of its „year-class“.
Summer stone fly
Claassenia sabulosa
Western March Brown
Rhithrogena morrisoni
American Grannom
Giant red sedge
Brachycentrus americanus
Pycnopsyche scabripennis
Each year class, or life-history stage in such organisms can be considered
as a discrete population unit in genetic terms and such a distinction can become
useful depending on the question being asked (at the very least, samples should be
taken from different stages, to insure that population genetic
estimates are not biased). However, in typical iteroparous organism there is
overlapping generations and sometimes a very complex and/or cryptic age
structure to the population. This is particularly true with long-lived freshwater
fishes. The use of molecular genetic tools to assess the population structure of
marine fish populations, for example, is made more difficult by this complex agestructure, among other cryptic variables. Later in the course, you will here the
term „effective population size“ along with other population genetic principles (e.g
Hardy-Weinberg Equilibrium), most of which have been developed and explored
in model or theoretical systems with a simple structure (such as a randomly
mating, non-overlapping generations). The real world is more complicated,
however, and these complications limit and challenge the tasks of a Molecular
Ecologist. The purpose of this introductory lecture is simply to introduce the
„organism“ and its complexity, and emphasize that a researcher should not loose
site of the organism, while exploring its genome.
Things to ask about your study organism
Who am I?
European grayling
Thymallus thymallus
What is my distribution? Throughout cool water reaches of European rivers
from northernmost Scandinavia, east to the Ural moutains in Russia, south to
former Yugoslavia, including Adriatic drainages of Slovenia and northern
Italy, and west to the upper Loire River basin in southwest France
Repeat spring spawner, primarily in lotic habitats (iteroparous)
Short-distance migrations (to 50 km?), but a poor jumper
Lives in both rivers and lakes
generally salt-intolerant (some populations in the Baltic Sea)
high-population structuring
auto-tetraploid ancestory (see ploidy?)