Total= 2+20+36+38

Lit Cited= 6

Investigating Sources of Variance in a Data Set: Hopkins vs. Point Lobos

[2] what sources? make the title more descriptive of the goal of the study

M.H. Schmitt

Long Marine Laboratory, 100 Shaffer Rd, University of California, Santa Cruz, CA 95060

Abstract: [20]

Understanding the different types of variability is a crucial concept in understanding and collecting quality data. To gain a better understanding of sampling issues [???], we compared reef assemblages between two sites (Point Lobos and Hopkins Marine Life Refuge) over two days. We hypothesize that there will be a significant difference between the two sites in overall species assemblages [why??] but that certain taxa may respond to variation in conditions between sampling days yielding an interaction effect between site and sampling day. We found that there is a statistically a significant difference in overall species assemblages between the sites (PERMANOVA: site effect, P=.001). We found a strong effect of site on thesignificant differences in the algael and invertebrate assemblages, but not for the fishes, between at Hopkins and Point Lobos (PERMANOVA: site effect, P=.001). [what about differences between days??] There is was a strong interaction effect between site and day for the composition of fish assemblages for Hopkins and Point Lobos (PERMANOVA: interaction effect, P=.015). [so then what is the conclusion of the study??] We also found that invertebrate assemblages show differences among the sites (PERMANOVA: site effect, .P=.001).

Introduction: [36]

Variability has two aspects - positive or negative. If one is testing to see if two samples are the same, variation would be considered positive since this would indicate that the samples are actually different (Levine, and Stephan 51-52 [Year???] are there no other studies that have considered sources of variation?). However, if the variability is either from a known or unexplained source that interferes with one’s ability to test a hypothesis then it is considered to be negative.

Understanding the different types of variability is a crucial concept in understanding what influences the quality of dataand collecting quality data. [“data quality” is a vague term that you should explain]Variance can come from many known sources such as differences in site/location, period of time (season, time of day) during which data were collected, and conditions under which the data were collected. When sampling for a projectto address a question or hypothesis, it is important to take all possible sources of variation into account to try and identity and limit the ones that hinder the study.

If sampling is conducted over a short period of time, it is generally safe to assume a population is not changing. Factors that influence population change such as birth, death, immigration, and emigration, typically only are seen over longer time frames, rather than a matter of days. However, if sampling occurs over long periods of time (months to years), one has to account for the potential population changes. Theoretically, an observer should get the same results if sampling a population over a short period of time under uniform conditions. [but all this depends on spatial scale of a study and whether organisms are shifting distribution, which would cause differences in population estimates over short periods of time… to motivate why you tested for short-term effects, you need to explain why, in fact, estimates of species abundance might change over short periods of time.]

You may have explained why you are looking at temporal variation above, but what about spatial variation?

Sampling in subtidal systems, such as kelp forests, can be very challenging due to the nature of the system. There are a multitude of factors that can cause unwanted variation in a data set such as weather and light conditions as well as water clarity. It is most likely that not all sampling will be conducted in one day, so it is also apparent that “day” might be a source of variation.

[before laying out such specific questions.. motivate them… why might certain taxa exhibit stronger differences between sites or days??] To gain a better understanding of sampling issues, we compared reef assemblages between two sites (Point Lobos and Hopkins Marine Life Refuge) over two days. We formulated a series of hypotheses to test for the different sources of variance (site and day). We hypothesize that: 1) there is a difference in species composition between Hopkins and Point Lobos 2) there is a difference in species composition between Hopkins and Pt Lobos that varies by taxa 3) a difference in species composition between days overall does not change 4) a difference in species composition between days varies by taxa 5) both site and sampling day affect species composition (interaction effect) 6) the interaction between site and sampling day varies by taxa.

We expect predicted [!! Don’t “expect” to see anything when testing that effect.] to see a significant difference between the two sites in overall species assemblages but that certain taxa may respond to variation in conditions yielding an interaction effect between site and sampling day.

Methods: 38

What was your general approach? To determine the relative spatial and temporal variation in kelp forest communities, we conducted visual underwater surveys on replicate transects to quantify the structure of the algae, invert and fish assemblages at two sites on each of two days.

Study sitessystem 9

To test for variance in reef assemblages, two sites were sampled over a two-day period (October 11th and 13th, 2011) at Stanford’s Hopkins Marine Life Refuge (36o36'N, 121°54'W) located in Pacific Grove on the southern side of Monterey Bay in California, USA. The is a kelp forest at Hopkins growing grows on granitic reefs primarily dominated by Macrocystis pyrifera (McLean 1962, North 1971, Gerard 1976, Watanabe 1984). In shallow areas, large slabs of granite forms high relief outcrops while in deeper areas, shell-fragment rubble covers granite rock reef (Gerard 1976, Watanabe 1984). This reef hosts a variety of species from invertebrates to mammals. This site is one of the most sheltered reefs in central California, giving better protection to the kelp forest and its inhabitants from ocean swell as well as allowing divers to access the reef more easily and often than other areas.

Point Lobos National Monument is comprised of both terrestrial and marine habitats. We used Whaler’s Middle Reef within Whaler’s Cove as our comparative study site (36°31′1.56″N 121°56′33.36″W). From observations, this site is much more exposed to swells and has much higher subtidal relief than Hopkins. We also observed that the predominant species of kelp at Point Lobos are Macrocystis pyrifera, Eisenia arborea, and Pteragophera californica. To access our dive site, we boated to our location and set up our transects.

What species did you sample and why those species??

Survey methods

Comparing algal communities between sites and sampling days

To test for the three sources of variance (site, sampling day, or interaction effect) of algae composition, we followed a predetermined sampling pattern. The sampling method was uniform used similar sampling methods for both Hopkins and Point Lobos, except for the actual position of the initial transect and direction of sampling transects. At Hopkins, there is a permanent cable which is marked in 10 meter increments allowing each buddy pair to find the start of their assigned line transect. Shallow-deep transects were spaced 10 meters apart along the main north-south cable. A total of 14 divers comprised constituted 7 seven buddy pairs (one-half of the total observers) and surveyed the same transects each day. Each buddy pair was responsible for one set of shallow-deep transects (all transects were at depths between 34-40 feet [go metric]) and were 2 meters wide by 30 meters long. Each 60m2 transect was counted as a replicate. [be more explicit about how many transects at each site and day]

At Point Lobos, however, there is no permanent benthic cable. Instead, a transect line was laid out and from this; the observers used this as the starting point for their 30 meter transects. Instead of surveying a “deep” and “shallow” side of the transect line, as was done at Hopkins, observers surveyed two transects in the same direction (there is little depth variation within the area sampled, so it is easiest if transects are done in a uniform direction).

We started from our given mark on the cable (Hopkins) or initial transect line (Point Lobos) and laid out our meter tapes at a 90 degree angle from the main cable/transect for a distance of 30 meters. As we progressed along our transect line, each person in the buddy pair collected data in 10 meter increments. The 30 meter transect was divided into three sections for ease of sampling. A predetermined list of algae was sampled (see table belowTable X). Each buddy was responsible for one meter on either side of the meter tape (left or right). We repeated this same process as we completed our shallow (Hopkins) or second (Point Lobos) transect. Observers that sampled Hopkins the first day, sampled Point Lobos the second sampling day and vise-versa.

Once the dives were completed, we compiled our data as a class and then ran the appropriate statistical analyses. To test for differences in algal communities between Hopkins and Point Lobos we used a PERMANOVA. We used this same analysis to test for differences between algal assemblages over between each sampling day. This test reveals whether the composition (i.e. identity and relative abundance) of algal species compositions are sensitivediffer between to sites, differences in conditions (days) or if there is aare combination combined site by day of effects (i.e. an interaction effect). The relative importance of individual species in contributing to was also examined for the site, day or interactions those effects that were significant (such as site).

In addition, multidimensional scaling (MDS) plots were created using each transect as a replicate. This test reveals whether algal species assemblages differed among the sites or sampling days by comparing the relative distance replicates are to one another on the MDS plot. Replicates closer to one another indicate… whereas replicates further apart indicate… In addition, Mean we caluculated the mean abundance densityof each species across was calculated by summing all values for each species and dividing by the number of replicate transects (n= X)s. This permits us to compare site variance and relative species abundance at each site over both sampling days which can provide information about which species contribute most to overall differences, the relative importance of space and time as sources of variation, and which species might be the best and the poorest candidates for sampling in a range of conditions.

Comparing invertebrate communities

The exact same sampling regime was adopted to compare invertebrate communities between Hopkins and Point Lobos. All the data collected was compiled and analyzed in the same manner as was performed for algae. To test for differences in invertebrate assemblages between Hopkins and Point Lobos, we again used the site effect of a PERMANOVA. To test for differences in invertebrate compositions over the two sampling days we used the day effect also used ain the PERMANOVA. To determine if sites differed in their differences in the invertebrate assemblage between days, we used the PERMANOVA to test for an overall site by day interaction.A PERMANOVA was also used to determine if an interaction effect was present for invertebrate communities.

Comparing fish communities

The same prescribed sampling methods were used for fish surveys, except the observer sampled across a volume of water instead of a meter swath to either side of the transect line as done for the invertebrates and algae. The observer sampled one meter out from the transect, two meters ahead and one meter above the bottom, forming a four m3 volume two meter squared sampling area either side of the transect.

To test for differences in fish assemblages between Hopkins and Point Lobos, we used a PERMANOVA. To test for differences in fish compositions over the two sampling days we also used a PERMANOVA. A PERMANOVA was also used to determine if an interaction effect was present for fish communities.

Results:

To compare reef assemblages, we collected data at both Hopkins and Point Lobos at depths between 34-40 feet with a median depth at both sites around 36.5 feet (Figure 1). The depths of sampling did not differ between the two sites. We found that there is a statistically significant difference in overall species assemblages between the sites (PERMANOVA: site effect, P=.001). Multidimensional scaling (MDS) analyses were performed to produce a spatial model to interpret the data collected. For these figures, each point represents a transect (replicate) displaying how closely related each replicate is. For all species combined, the markers revealed a separation of site (Point Lobos vs. Hopkins) but not sampling day (indicated by a “1” or a “2”) (Figure 2).

Algae

We found a strong effect of site on the algal assemblages at Hopkins and Point Lobos (PERMANOVA: site effect, P=.001). We also found that variance stemmed only from site (Figure 9). Algal abundance is compared over both days and sites in the Multidimensional scaling (MDS) analysis depicting a clear spatial difference indicating a significant difference in algal communities between Hopkins and Point Lobos (Figure 3). Relative abundances across both days for both sites of the specific species counted, reveal this same pattern (Figure 4).