Compiled by EISI participants

**Accommodation** - adjustments made by either a species or the environment to allow interaction between them.

**ACDP** - Acoustic Current Doppler Profiler, used to visualize flow fields in 3 dimensions

Dial- having to do with or dealing with a time scale of a day

**Advection model/Advection**: the transport mechanisms of a substance, or a conserved property, by a fluid, due to a fluid’s bulk motion in a particular direction. (ex: transport of pollutants of silt in a river)

- can be described mathematically as a vector field, where the material is transported as a scalar concentration of a substance contained in a fluid
- advection equation is a partial differential equation that governs the motion of a conserved scalar as it is advected by a known velocity field

**Alevin **- a salmonid hatchling which cannot feed on its own. It relies on an external sack of egg yolk for food. It lives in a gravel bed.

**Alluvium/colluvium** (n) – In geology, alluvium refers to sediment or rock that has been transported downslope, and thus eroded and reshaped, by water. In contrast, colluvium describes loose sediment transported downslope by gravity alone. understanding the distinction helps one better understand the surrounding environment as a whole–alluvium tends to be younger, smoother, and more porous than colluvium, which tends to be older and rougher.

**Anadromy **- life history of pacific salmonid species, which is characterized by fish that spawn in freshwater, migrate to a marine habitat to grow, return to freshwater to spawn.

**Attenuate** (v) – The gradual loss of intensity of any flux through a medium. In my research project, this word is used to describe the effects of vegetation and sediment on incoming coastal waves. The waves are “attenuated”–their amplitudes tend to decrease, reflection is minimized, and their periods become less regular. The specifics of this particular type of attenuation are the subject of the research.

**Auto Regressive model **- (A) a type of random process which is often used to model and predict various types of natural and social phenomena

(B) a model that projects points based on some number of previous ones plus some noise

**BACI (Before After Control Impact)** – A classic method of design where measured affects can be analyzed by gauging conditions *before* a planned activity and then comparing the findings to those conditions measured *after*—an approach that is applicable for comparing the affects of anticipated future activities. In the cases where it may not be possible to measure the *before* conditions, studies often make use of an unaffected or *control* reach and use those data for comparisons to an affected or *impacted* reach.

**Basal** - At or near the bottom

**Basal area** - in forest management, the area of a given section of land that is occupied by the cross-section of tree trunks and stems at their base. (diameter of tree at 1-1.5 m of ground (breast height))

Basal Area = (3.1416 x (DBH/2)2)/(4 x 144)

Add all basal areas of trees in area and divide by the area of land measured

**Bayesian theorem and networks** - a theorem describing how the conditional probability of each of a set of possible causes for a given observed outcome can be computed from knowledge of the probability of each cause and the conditional probability of the outcome of each. The Bayesian Network is a probabilistic graphical model that represents a set of random variables and their conditional independencies via a directed acyclic graph.

**Biome** - A major regional or global biotic community, such as a grassland or desert, characterized chiefly by the dominant forms of plant life and the prevailing climate.

**Bryophyta** - Mosses

**Calcareous** – containing calcium or limestone, chalky

**Catadromy** - life history of fish where the fish spawns in a marine environment and migrates to freshwater to grow; effectively the opposite of anadromy.

**Colluvial** - fallen by gravity

**Commensalism** - a relation between two kinds of organisms in which one obtains food or other benefits from the other without damaging or benefiting it

**Communities** - Communities are composed of individual organisms integrated to such an extent that the processes holding the parts of the community together cannot be readily isolated

**Confluent** - Flowing together; blended into one; merging or running together so as to form a mass

**Connate** - Having bases of opposite leaves fused around the stem.

**Connate fusion** - With like parts or organs integrally fused to one another with histological continuity.

**Costa** - A prominent rib or vein; in ferns, the midrib of a pinna or pinnule

Depth Sounder- device used to determine water levels in piezometer. Device works by beeping when it comes in contact with water. Also called a water tape.

**Cuspate** - geographical features found on coastlines and created by long shore drift.

**Diapause** - ahormonally inducedstate of lowmetabolic activity,thereby increasingthe resistance tounfavorableenvironmentalconditions

**Diel** (adj) – Having a 24-hour period regardless of day or night. I heard this word used in the context of “diel fluctuations,” which means changes in some measured quantity over the course of a day. This is a valuable word when dealing with scale – it implies the temporal scale of a day.

**Discharge** (n) – In hydrology, the volume of river that passes through a cross-section of the river in one unit of time. Overall units are L^3/T. A valuable measure of a river that seems to tell a lot about its other characteristics, like the amount of biodiversity it can support.

**Deterministic** - means that, if x’(t)=f(t,x(t)) is a system and x(t0)= y0 is an initial condition that describe the primary state of the system, then the future state of the system is unique and at time t is x(t). More, generally a system is said to be deterministic if from the initial state of the system is and knowledge of the behavior of the system, then from these data a forecast of the future state system can be drawn. A deterministic process is in contrast to a stochastic process; a process in which some form of randomness is involved in the eventual outcome, or states of the system.

**Deterministic model** - one in which every set of variable states is uniquely determined by parameters in the model and by sets of previous states of these variables.

**Dichotomy** - any splitting of a whole into exactly two non-overlapping parts, meaning it is a procedure in which a whole is divided into two parts, or in half.

**Digital elevation model (DEM)** - a digital representation of ground surface topography and terrain. It can be represented by a raster (grid of squares) or a triangular irregular network. These are commonly build using remote sensing techniques, but also done from land surveying. (Used in digital relief maps and GIS).

**Empirical mode decomposition** – A method to break down a complicated signal into component signals. It is a relatively new technique which is simpler than Fourier transforms and is considered especially useful for looking at signals from natural systems.

**Empirical orthogonal function** - the decomposition of a signal or data set in terms of orthogonal basis functions determined from the data. Performing a principle component analysis on data but this method finds both time series and spatial patterns

**Endemic** (adj) – Only occurring in a specific area. For example, certain vegetation is “endemic” to Oregon, while the moth species, being found elsewhere, are not. Brings up interesting philosophical points about preservation of biodiversity – should endemic species require special consideration, as affecting their populations in a single place could potentially render them extinct.

**Ergodic** – (A) The study of dynamical systems. Ergodic theory is specifically interested in the trajectory of a system of a long period of time.

(B) When the temporal average of a dynamical system equals its analytic solution

**Eulerian flow** - an ideal fluid flow model, one matching Navier-Stokes equations with "zero viscosity and heat conduction".

**Evapo-transpiration** - the sum of the evaporation and plants transpiration from the Earth’s land surface and atmosphere. Evaporation accounts for movement of water to air from soil, canopy interception and waterbodies. Transpiration accounts for movement of water within a plant and loss through stomata in leaves.

**Fractals** - a rough or fragmented geometric shape that can be split into parts, each of which is (at least approximately) a reduced-size copy of the whole

**Fluvial salmon **- a life history in which salmon rear for a time in their natal stream, migrate to larger rivers to grow, and return to the smaller stream to spawn

**Frequency domain** - a term used to describe the analysis of mathematical functions or signals with respect to frequency rather than time

**Fourier transform** - an operation that transforms one complex-valued function of a real variable into another

**Fry** - young salmon; once the alevin has used up the external egg sac, it wriggles out of the gravel bed and emgerges into the stream. At this stage the salmon can feed on its own.

**Glabrous** – (A) Smooth, bald

(B) a leaf that is hairless

** Glaucous** - (from the Latin

**Gymnosperm** - Ok, basic, basic ecology, I know - But I clarified the classification in my mind, as gymnosperms (including conifers) having exposed seeds/ovules, as compared to angiosperms, flowering plants.

**Head** - combination of potential and pressure energy

**Herbaceous** – (A) having little or no woody tissue and persisting usually for a single growing season

(B) having the texture, color, or appearance of a leaf

**Heteroscedasticity** - In statistics, a sequence of random variables is heteroscedastic, or heteroskedastic, if the random variables have different variances. The term means "differing variance" and comes from the Greek "hetero" ('different') and "skedasis" ('dispersion'). In contrast, a sequence of random variables is called homoscedastic if it has constant variance.

**Hilbert transform** – A linear operator which takes a function and produces a function with the same domain. It is a concept used in Fourier transforms.

**Hyaline **- Thin and transparent or translucent

**Hydraulic lift** - the process by which some deep-rooted plants take in water from lower soil layers and exude that water into upper, drier soil layers.

**Hydraulic radius** (n) – In hydrology, this is the cross sectional area of channel flow divided by the wetted perimeter, or for a river, two times its height plus its width. There was some confusion about this figure, and I wanted to ensure I knew what it meant. I believe the hydraulic radius is often used to normalize discharge between different rivers for a better comparison.

**Hydrograph** - graph showing the changes in the discharge of a river over a period of time.

**Hydrology** - is the science that treats of the Aqueous Kingdom: its properties, behavior, and distribution over the stony realm.

correlation coefficient.

**Hyporheic zone** – (A) lateral area beneath ground adjacent to stream where groundwater and stream water mix (ex: under gravel bars)

(B) An area or ecosystem beneath the bed of a river or stream that is saturated with water and that supports invertebrate fauna which play a role in the larger ecosystem.

i-button- temperature sensing device that can be installed inside fish

**Induration** (geology): The process of becoming hard

**Indusium** - An epidermal outgrowth or reflexed and modified leaf margin which covers the sori of many ferns

**Infiltration** - (A) The process by which the water on the ground surface enters the soil

(B) indicates the penetration of particles. For example the infiltration of sea-water through lava, or sea water traveling up through arctic ice. In the context of hydrology, infiltration refers to the sum of water that enters the top layer of hill-slope soil as precipitation. In the forest during a storm, precipitation is first

**Intercepted** - by the high canopy layer and lower lying understory, precipitation which falls through these layers and reaches the forest floor percolates down into topsoil.

**Interflow** - generally indicates a flowing into each other; an intermingling. In the context of hydrology, interflow is the aggregate of water that enters a stream channel directly from the subsurface as groundwater.

**Iteoparity** - life-history pattern which pacific trout generally follow; of survival after spawning.

**Latosols** - Soil that is rich in iron, alumina, or silica and formed in tropical woodlands under very humid climate with relatively high temperature.

**Leaf area index** the ration of the total upper leaf surface of vegetation divided by the surface area of the land on which the vegetation grows

-used to predict photosynthetic primary production

-inverse exponential relation between LAI and light interception (linearly proportional to primary production rate)

**Loam** - is soil composed of sand, silt, and clay in relatively even concentration (about 40-40-20% concentration respectively).

**Manifold** - a surface of any dimension

**Markov Chain** - a stochastic process that has the Markov property (next state depends on current state)

**Markov process** - means that P{Xn=in | X0= i0 , X1= i1,…, Xn-1= in-1} = P{ Xn= in | Xn-1= in-1}. What the previous statement says in plain language is that predictions about the future state of the system can be made from the present state of the system, regardless of the system’s past history. In other words, it is not important how things came to be the way they are; that they are that way, is what will determine the future.

**Mathematical modeling **- the use of mathematical functions and relationships to predict or understand a real-world process.

**Matric potential** – (A) The pressure required to suck liquid out of different kinds of soil

(B) The force required to overcome surface tension and pull water out of soils

**Meta analysis** - a statistical technique that combines the results of several studies that address a set of related research hypotheses

**Mesophytic** - Mesophytes are terrestrial plants which are adapted to neither a particularly dry nor particularly wet environment

**Metapopulation theory** - In classical metapopulation theory, each population cycles in relative independence of the other populations and eventually goes extinct as a consequence of demographic stochasticity (fluctuations in population size due to random demographic events); the smaller the population, the more prone it is to extinction.

**Model Validation** – The comparison of a model with a preexisting calibrated model (i.e. tight vs. loose predictions).

**Monoecious** - an individual that has both male and female reproductive units (flowers, conifer cones, or functionally equivalent structures) on the same plant; from Greek for "one household". Individuals bearing separate flowers of both sexes at the same time are called simultaneously or synchronously monoecious. Individuals that bear flowers of one sex at one time are called consecutively monoecious; plants may first have single sexed flowers and then later have flowers of the other sex.

**Monte Carlo Method** – (A) A method that solves a problem by generating suitable random numbers and observing that fraction of the numbers obeying some property or properties. This method is useful for obtaining numerical solutions to problems that may be too complicated to solve analytically. Essentially, a class of computational algorithms that rely on repeated random sampling to compute their results.

(B) a method which uses many random predictions and statistics on a random simulation to predict processes which have too many or poorly understood inputs.

**Nurse Log** – A decaying log that becomes a host and food source for insects, fungi, and young plants.

**Ordination** – a statistical technique in which data from a large number of sites or populations are represented as points in a two- or three-dimensional coordinate frame.

**Ovate** - a leaf that is egg shaped, with the thicker end closer to the stem

**Parametric** – Assuming the continuous value of a statistical parameter for the purpose of analysis.

**Parr marks** - green-brown bars on the side of non-migrating, young salmon residing in streams probably used for camouflage. Having these marks distinguish parr from fry.

**Peak Flow** - the level that a stream rises to as a result of a rain event

**Permeability** - The ability of a substance to allow another substance to pass through it, especially the ability of a porous rock, sediment, or soil to transmit fluid through pores and cracks

**Petiole** -the stalk of a leaf, attaching the blade to the stem

**Phenology** - the timing of natural events.

**Phenotypicplasticity** - the samegenotype produces adifferent phenotypeunder differentenvironmentalconditions

**Photoperiodicity** - Photoperiodicity is the physiological reaction of organisms to the length of day or night. It occurs in plants and animals.

**Phototactic** – locomotory movement or organisms responding to light stimulous

**Phototaxy** - the movement of an entire organism in response to light

**Physiognomy** – general appearance without reference to implied characteristic

**Phytophagous** – feeding on plants

**Piezometer** - a small-diameter observation used to measure the hydraulic head of groundwater in aquifers. It can also be used to measure the pressure of fluid at a speicifc location in a column.

**Pinnate** - Having two rows of lateral branches or appendages, or parts along an axis, like barbs on a feather

**Porosity** - The measure of ‘empty space’ in a material often used to determine how much water a particular material can store per unit volume.

**Principal components** (n) – If there are multiple, possibly correlated variables in a problem, they can be consolidated into principal components that are uncorrelated. The first principal component deals with as much variance as possible, and the second deals with as much of the remaining variance as possible, etc. If one wants to show relationships between data points using a plot, but there are too many variables to cleanly represent, the variables can be perhaps broken down into three principal components that are easy to plot and reveal the same relationships between the data points as a more complex plot.

**Provincial** (as used in the context of the paper): within the appropriate sphere

**Rachis** - A main axis, such as that of a compound leaf

**Random variable** - means that X has a value for each associated outcome. Suppose Xn, n=0,1,2,… is a collection of random variables describing a system, and the probabilities for each state the system are given as P{ X0= i0 , X1= i1,…, Xn= in}.

**Reynold’s number** (n) – A dimensionless number representing the ratio of inertial forces to viscous forces present. It thus quantifies the relative importance of these two types of forces for given flow conditions. More generally, this describes the behavior of a substance as it moves through another. Two situations with the same Re will have the same flow properties, so this is useful when making small-scale models to design and test more expensive things.

**Riparian vegetation** - vegetation that grows at the interface between the land and a river of stream

**Rhizome** - Horizontal stem of a plant that is usually found underground, often sending out roots and shoots from its nodes

**Saltation** - the movement of particles when they are picked up by river flow then deposited later on the bed.

**Sapflux density** - Sapflux density or xylem sapflow velocities are measured by injecting a small pulse of heat into the conducting wood of the tree. The sapflow velocity is determined from the rate of ascent of this pulse within the conducting wood of the tree. Sapflow velocity multiplied by the cross sectional conducting wood area gives the volume flow per unit time.

**Semelparity** - life-history pattern of imminent death after spawning. Pacific Salmon follow this pattern (save for a few individual exceptions)

**Sessile** - (A) stationary, not motile

(B) Organs are those that are in immediate contact to the structure to which they are attached, and thus having no footstalk or peduncle.

(C) attached directly by the base : not raised upon a stalk or peduncle. Ex: a sessile leaf

(D) permanently attached or established : not free to move about. Ex: sessile sponges and coral polyps

**Smolt** - transitional stage between freshwater fry/parr and adult, marine salmon. Smolts are found preparing for migration or migrating in freshwater, and in the nearshore marine environment. Does not apply to salmon which have been feeding at sea for an extended period of time

**Sorus** (sori) - A cluster of sporangia (dots on the underside of ferns)

**Stage** - the height of river water from a chosen reference point.

**Stream Order** - A number used to classify the size of a stream in a watershed, the highest streams are of order 1, when streams meet the order increases only when they are of the same size. IE 2 order 2 streams converging results in an order 3 stream, but an order 2 stream flowing into an order 3 stream does not increase the order.

**Stochastic** (adj) – (A) Non-deterministic, or something that can be described in terms of predictable and random elements. Stochastic models incorporate a random variable that is specially designed to account for random variation that cannot be quantified.

(B) - In probability theory, a stochastic process, or sometimes random process, is the counterpart to a deterministic process (or deterministic system). Instead of dealing with only one possible reality of how the process might evolve under time (as is the case, for example, for solutions of an ordinary differential equation), in a stochastic or random process there is some indeterminacy in its future evolution described by probability distributions. This means that even if the initial condition (or starting point) is known, there are many possibilities the process might go to, but some paths may be more probable and others less.

**Stochastic process** is a collection of random variables, Xt indexed by time.

**Synchrony** – simultaneous emergence and/or development of herbivore and host plant

**Tensor** (adj) – (A) An extension of a vector to a higher order to provide more information about a system than a vector alone could. Tensors are often produced by including gradients or stress values for the system.

(B) a mathematical object analogous to but more general than a vector, represented by an array of components that are functions of the coordinates of a space.

(C) multidimensional vector

**Ternate** - In groups of 3

**Topology** - the study of geometric properties and spatial relations unaffected by the continuous change of shape or size of figures.

**Tortuosity **– the arc-chord ratio, defined by a ratio of the length of the curve to top channel width. Generally, when tortuosity is below 3, cross-stream flows become generate additional forces along the outside of the meander banks, in addition to the spiraling (helicoidal) flows of meanders.

**Tractable** – capable of being handled/touched

**Transpiration** - loss of water vapor from parts of the plant (leaves, stem, flowers, roots). Transpiration cools plants and enables a flow of mineral nutrients and water from the roots to the shoots caused by the decrease in hydrostatic(water) pressure in the upper part of plants due to diffusion

**T-test** - a statistical hypothesis test used 1) one sample location test on whether the mean on a normally distributed population has a value specified in a null hypothesis

2) a test of a null hypothesis that the difference between two responses measured on the same statistical unit has a mean value of zero

3) a test of whether the slope of a regression line differs significantly from zero

**Vagile** - (A) motile (B) free to move about. Ex: vagile organisms

**Vagility** - the attribute or ability to disperse or be dispersed in a given environment. The less vagile a species is, the less likely it is that the species will be able to overcome barriers.

**Villous** - Pubescent with long, soft, often bent or curved, but not matted hairs

**V-notch weir** - a discharge measuring device (flow rate measurement). A weir is a structure consisting of an obstruction such as a dam or bulkhead placed across an open channel (V-notch)

- For a triangular or v-notch weir the flow rate can be expressed as:*q = 8/15 cd (2 g)1/2 tan(θ/2) h5/2 where θ = v-notch angle*

**Wave attenuation** - the process by which waves lose their energy and intensity when traveling through a medium