Recently it was brought to my attention that it would be engaging to discuss topics where actual data collection takes place and hypothesis are put forth. I am all for this. Considering I mainly rely on data that others have collected, it seems apt to discuss someone else’s data, and fortunate for us, one of our members recently returned from collecting data. I do not intend to put anybody on the spot here, but since some people seem to be bored with my topics of interest, I would like to shift gears and go in the direction of somebody else’s interest. I decided to go with FreedomHater’s because it is something that I am very interested in, yet I feel like I know very little about.

If you wouldn’t mind telling us a little about what you are doing and what you have done, I would enjoy engaging in some sort of productive discourse here. If you don’t feel like giving a summary, feel free to post or upload some of your previous writings. I have a great interest in biology and I have considerable statistical training and I would love to get involved and offer a helping hand. Or, at the very least, offer a listening ear.

Here are some documents written recently, one is a grant proposal and the other is an informal letter describing some of the field season. If there is questions about these I will certainly elaborate further. Skyhook if there is a better way to put these on the board please tell me. Sorry for the super long post.

1)the grant proposal
Ecological Variation in Sonoran Mud Turtle (Kinosternon sonoriense) Populations of the Peloncillo Mountains

Temporary and permanent aquatic habitats vary in resources, permanence, and relative importance of abiotic and biotic factors (Skelly 1995, Wellborn et al. 1996). A survival tradeoff suggests organisms inhabiting permanent aquatic habitats may experience increased predation and competition (biotic factors) but also experience a stable and predictable habitat (abiotic factors). On the other hand, organisms inhabiting temporary aquatic habitats may experience periodic resource depletion due to an unpredictable environment (abitoic factors), but conversely, experience decreased predation and competition (biotic factors). I will investigate this dichotomy in the form of two hypotheses derived from the literature, the biotic limitation hypothesis and the abiotic limitation hypothesis. Specifically, my research focuses on variation in body size, growth rate, population density, and juvenile recruitment of Sonoran mud turtles, Kinosternon sonoriense, in permanent and temporary aquatic habitats. I will test predictions of the biotic limitation hypothesis, which states that negative biotic interactions (i.e. competition and predation) in permanent aquatic habitats will cause decreased body size, growth rate, population density, and juvenile recruitment. Similarly, the abiotic limitation hypothesis predicts that resource reduction in temporary aquatic habitats will cause decreased body size, growth rate, population density, and juvenile recruitment.

The Sonoran Mud Turtle is a freshwater turtle with a geographic distribution across central Arizona, southwest New Mexico, and north Sonora (Ernst et al. 1994). I will study turtles that occur in the Peloncillo Mountains, Hidalgo Co., New Mexico and Cochise Co., Arizona. The Peloncillo Mountains are nestled between the Animas and Chiricahuan Mountains and the Sonoran and Chihuahuan deserts, making this semi-arid region a hotspot for ecological diversity. K. sonoriense occur in aquatic habitats that span the permanence gradient including slow moving rivers, creeks and streams, stock tanks, canals, cienegas, ephemeral ponds and seasonal pools (Ernst et. al 1994). Therefore, K. sonoriense are likely to be impacted by various environmental and ecological factors related to the permanence of aquatic habitats. K. sonoriense is a prime candidate for study because of its unique locality, its previously reported variation (Rosen 1987, Van Loben Sels et al. 1997, Ligon and Peterson 2002, Stone 2001), and its co-occurrence with vertebrate competitors (mainly introduced fish).

I used intensive sampling to investigate variation in body size, growth rate, and juvenile recruitment. Midline carapace length (MCL) was used to measure body size and will be analyzed with an ANOVA. Growth rates are estimated using techniques described in Ernst et al. (1973), and will be analyzed using an ANCOVA with MCL and year as covariates. Juvenile recruitment was determined by comparing the number of hatchlings present in aquatic habitats and a t-test will be used for this analysis. I will use mark-recapture techniques and program MARK to generate estimates of population density and boundaries. Multiple samples with significant recapture rates are required to use program MARK and t-tests will be used for this analysis.

Last field season we sampled the study area from 1 July to 13 October, 2007 in 12 stock tanks and 12 canyons with dissimilar permanence regimes, with varying intensity and success. We caught a total of 1266 turtles with nearly 400 new adult and juvenile captures, and batch marked over 140 hatchlings. At this time no official statistical analyses have been conducted on the 2007 data. Preliminary data suggest body size is largest in permanent aquatic habitats, population density is lowest in permanent aquatic habitats and temporary aquatic habitats with short hydroperiods, and recruitment is highest in temporary aquatic habitats with longer hydroperiods. These data support predictions made by the biotic and abiotic limitation hypotheses but more data are necessary to ensure a stronger data set.

Next field season, I will continue to sample populations established last year. Several populations still require adequate sampling because they were discovered late in the field season. Additionally, data on growth and survivorship of hatchling turtles are avenues which still require investigation and therefore merit more research trips to the study area. I am applying for this grant to help fund a two-week long trip to the study area. Money from this grant will be used for all travel costs (i.e. gas and lodging). Travel costs quickly accumulate and are by far the most expensive portion of conducting research in this region. Additionally, this money would indirectly support volunteer field assistants; mostly undergraduates from the Department of Biology at UCO. The aim of this study is to investigate interpopulational variation of the Sonoran mud turtle, K. sonoriense, in permanent and temporary aquatic habitats of the Peloncillo Mountains. The proposed study will enhance knowledge of biological and ecological patterns in this species, as well as identify potential population threats and limitations.


2)the letter

Dear All,

As many of you know, Ken Locey and I camped and conducted research in the Peloncillo Mountains for nearly 3 1/2 months (1 July through 13 October). Data were collected for my Master’s Thesis, which focuses on interpopulation variation among Sonoran mud turtles (Kinosternon sonoriense) in permanent and temporary aquatic habitats. We collected loads of data on nearly everything we could get our hands on including invertebrates, aquatic vegetation, water availability, water chemistry, canyon flow (after monsoon rains), blood for genetic studies, terrestrial activity, and diet via feces, not to mention data directly associated with the thesis hypotheses. Many days in the field were fantastic, while others were not; I guess that comes with camping in the field for an extended period. We tried to collect data from as many areas that were logistically possible. Below is table of all the sites we visited and observations on water and silt (Table 1). Overall the trip was a complete success. DID NOT INCLUDE TABLE ON THIS POST

Here are some basic “numbers” and/or observations during our field season:
-sampled several canyons and stock tanks of varying permanence
-caught over 1266 turtles (recaptures included)
-marked 400 new adult and juvenile turtles
-caught over 190 hatchlings (recaptures included)
-had 437 trap nights and an estimated 795 man hours each
-witnessed the flooding of all major canyons
-observed many species of reptile, bird, and mammal (see Animals section)
-replaced a tent, cooler, air mattress, and truck tires

Sonoran mud turtles in the Peloncillo Mountains appear to be patchily distributed, which suggests that not all canyons and tanks provide adequate habitat. Some canyons and tanks support large populations, while others support little or no turtles. Particular tanks were clearly more permanent than others and harbored fish populations and emergent aquatic vegetation. Conversely, some tanks and canyons filled only after the onset of monsoon rains. Interestingly, there are tanks and canyons that have high amounts of silt, while others do not have nearly as much silt. In some cases, tanks are completely filled in with silt (ex. Prospect Tank, Cedar Tank), while others look like they might fill soon (ex. Blackwater Hole), still others seem to have no threat of filling (ex. Cloverdale Spring). It is unclear if silt is having negative impacts on Sonoran mud turtle populations in the Peloncillo Mountains.

The focus of my investigation was on body size, population density, juvenile recruitment, and growth rates of Sonoran mud turtles in varying aquatic habitats. The general trend appears to be that in permanent aquatic habitats turtles are larger, grow faster, but have lower population densities and fewer hatchling recruits. On the other hand, in temporary aquatic habitats turtles are smaller, grow slower, but have higher population densities and more hatchling recruits.

During our field season we observed many species of animals. Below is a brief summary of some interesting animal observations.

Amphibians: (
We saw the endangered Chiricahaun Leopard Frog (Rana chiricahaunensis) in two locations: (i) Stateline Tank – a tank with enough permanence that it appears to support an actively reproducing population (we observed egg masses and half metamorphosed frogs) and (ii) Estes Canyon – a canyon that harbors very few deep pools and a lot of silt. At this location we saw a single adult R. chiricahaunensis (N 31°27.664’ W 109°04.441’)
Several canyons contained both Bufonid and Hylid tadpoles.

Aves:
On several occasions we saw rafters of Gould’s turkeys (both adults and juveniles). Most were seen in the fields near the campgrounds close to the edge of the National Forest and in the fields after the turnoff to Black CCC from Geronimo Trail.
Several species of hawk were identified including Zone-tails, Red-tails, Gray, and Swainson’s. Also, several species of waterfowl including Mexican mallards, American Coots, and Great Blue Herons were seen at several tanks.

Mammals:
We saw two black bear cubs, one was in our camp and the other was near the Geronimo Trail. Unfortunately, there was an incident where we returned to our camp to find it completely trashed. We suspect that a black bear was the culprit because of the nice surprise it left us. Mule deer and whitetail deer where commonly observed while pronghorn were not seen as often. Foxes, coyotes, coatimundis, ringtails, striped skunks, and javelinas were all observed throughout the field season but were not common.

Reptiles:
Blacktail rattlesnakes, Western Diamonback rattlesnakes, Gopher snakes, Black-necked garter snakes were commonly seen throughout the field season. Banded Rock rattlesnakes, Western rattlesnakes, Sonoran whipsnakes, Coachwhips, Striped whipsnakes, and a Big Bend Patchnose were all observed but were not common. We did observe and photograph a green rat snake (N 31°30.561’ W 109°02.676’) on the Geronimo Trail approx. 350 m beyond Mormon Pass near the New Mexico/Arizona monument border. Species of Sceloperis, Cnemidophorous, and Urosaurus were commonly seen throughout the mountain range. We also observed two Gila Monsters on the Geronimo Trail between the edge of the national forest and Douglas, AZ. One juvenile Short Horned lizard was identified near Clanton Tank, and Ornate Box turtles were commonly seen on Highway 338 between the Geronimo Trail and Animas, NM. We also had an interesting observation where S. jarrovii displayed an aquatic escape behavior. This lizard attached itself to the wall at BW Hole underwater and stayed there for at least 70 seconds, it only moved when we tried to grab it. Additionally, we saw a turtle foraging on a bird that was floating in a canyon pool. This is the second time we observed this type of opportunistic foraging behavior.

how many years will you continue your research?

Current research on this species in this area (Paul's previous work) has been going on for 14 years. I am planning on making a few more trips to the study area next summer (of which you are all invited) to tie up some loose ends and get some growth rate data on this years hatchling cohorts. But I imagine that I will be loosely involved in research on this species in the peloncillos for as long as my academic and research career lasts. That is not to say that I will go there each year but will go there every now and again. It is a place I really enjoy and I could see myself taking a vacation there to collect data and further the ongoing research that is beyond what my thesis focus is (i.e. genetic population structure, terrestrial movement, reproduction life-history studies, movements due to water availability, behavior, foraging ecology, etc, etc.).

Very nice. Thanks for sharing with us. Reading this has got my mind running in several directions. I will start with a couple of questions. Feel free to respond or to tell me to bug off.

What methods are being used to determine the relative permanence / impermanence of habitats? Obviously one of the key variables in this studious venture revolves around some measure of habitat permanence. Are you approaching the permanent / temporary dichotomy as strictly two categories? Do you have any plans in include other categories such as “semi-permanent” or, for example, describing habitats that exist for hours, days, weeks, months, years… As far as operational defining habitat permanence goes, I assume some measure of time (duration of permanence) will be used. Perhaps physical measures relating to the properties of water, calculating times of evaporation, factoring depth of pools/tanks, permeability of ground, slopes of surrounding landscape, vegetation, etc…. might lead to a decent way to describe permanence. But this sounds very difficult and complicated. Maybe you have a much easier way.

I will leave the questions at that for now. It seems like there is some interesting stuff here, but I still have a way to go before I completely understand the ins and outs.

We will measure permanence 4 ways
1)presence of adult fish- obvious fish cannot live without water
2)presence of bulrushes- these plants cannot survive w/o adequate and persistent water
3)yearly and site visit observations- 15 years of previous data
4)historical records- both the national forest and the diamond a ranch have extensive historical records on water permanence. In addition, I will talk with local ranchers about there private land. This is ranching country and water is very vital to their success.

permanence scale (still in works) least --> greatest
1)canyon w/o stock tank
2)canyon with silt filled stock tank
3)farm pond
4)canyon w/ stock tank
5)Natural springs
6)Natural springs reinforced by dams

We did measure some physical parameters (depth, area, pH, turbidity, DO, temp) but I think very few of these will help with categorizing permanence but might tell us more about species living in the aquatic habitat.

Assuming you are able to reject the null hypothesis and determine that biotic interactions act to decrease your proposed measures in permanent aquatic habitats while abiotic factors act to increase your proposed measures in temporary aquatic habitats, how will this information serve to identify potential population threats and limitations? Are there any proposed interventions that require this information?

I mean, aside from the common sense notions that reduced resource availability in temporary habitats and increased competition in permanent habitats will have an effect on the size and population of an organism, what information or actions are you trying to support in this relatively difficult effort of study?

It's interesting because despite all our data that suggests sonoran mud turtles can live quite well in temporary aquatic habitats. It is an idea that is not really accepted by most persons in state game and fish communities. Very few people recognize this turtles ability to survive in harsh environments. Early reports of this species (70-80's) described this species as totally aquatic and it is a paradigm that seems to have taken hold. Even today research from Arizona suggests that these turtles are highly aquatic yet in our study area (New Mexico) they seem to to reach high numbers in relatively drought ridden areas. So there is something ecologically interesting about a species that seems to limited by the aquatic habitat in some areas but not in others. So one goal is to provide even more awareness to state game and fish people about where this turtle could possibly live (maybe extending its range).

Another goal..... despite the common sense application you spoke of it has never been tested in turtles. This is probably because there are not many locations where you can isolate one turtle and few fish. I mean, usually if there is aquatic habitat you will find assemblages of turtles (at least a few species) and if the habitat is permanent you may find several types of fish. In our study area there is only the sonoran mud turtle, this allows us to isolate its interactions directly with fish. (Which have been introduced and there is huge amount of literature describing the impacts that introduced exotic species has on an environment). Despite the current paradigm that is in our society of how turtles hurt fish populations, it has never been tested (i am not testing this). In fact, we kind of think the opposite that fish can hurt turtle populations (i am trying to test this). So describing the biotic interactions between a specific turtle and fish have ecological importance (has only been done once that I know of). However, there is a ton of literature dealing with temporary and permanent aquatic habitats and how it affects anurans and salamanders. I don't feel the turtle should be left out.

But in my readings of the literature, there are many instances when a author will report differences in populations that are in the same area but separated by some gradient. Many times the author (in his conclusions) will report that the differences seen were likely due to habitat but they rarely test this and suggest further research is needed. I am starting where they are leaving off, so this research will assist many researchers studying animals in similar situations.

I may have lost you in the incoherent ramblings above so if this does not answer what you want, please tell me and i will try to be more clear and concise.

I was just thinking...

Since turtles have environmental sex determination, how might increasing global temperatures affect those little Sonoran guys? For those who are not turtologists, environmental sex determination refers to the observation that, in most species, turtle eggs that are in relatively warmer environments during their first trimester will yield female turtles, while colder eggs will yield male turtles.

As I understand it, there are studies out there demonstrating that average temperature increases by as little as 2-5 degrees Celsius can drastically change the sex ratio of a species. How might having an increased number of females affect the population FreedomHater is studying? At what temperature does the extinction of males (and therefore the females after one generation) become a real threat? Are there any known biological safe-guards against this threat?

Turtles are not the only animal that uses the temperature to determine sex. I wonder if the effects of global warming on these types of animals is potentially disastrous.

Increasing Global temperatures are considered a potential danger for many species exhibiting environmental sex determination (ESD). However, I am relatively uninformed about the exact consequences, and I am not certain that much research has been directed at mud turtles (genera I study) in this regard.

In general, ESD has been found in many turtles but not all. Of turtles that have been karyotyped, some have sex chromosomes and some don't. To make mattes worse, some that have sex chromosomes have shown patterns of ESD. And just to clarify ESD can be broken down into temperature sex determination(TSD) and moisture dependent sex determination.

If I remember correctly, mud turtles (Kinosternon spp.) have temperature dependent sex determination (TSD). There seem to be two patterns for TSD; (1) the one that Hook described and (2) where females develop at both high and low temperatures and males develop at intermediate temperatures. It should be noted that mortality is more common at high and low temperatures. Also, two species of Kinosternon have sex chromosomes and most have been unstudied in this regard.

Which brings us to Kinosternon sonoriense (Sonoran Mud Turtle).
There is no empirical data on K. sonoriense sex determination (temperature or moisture). It is assumed to be pattern 2. I am unsure about the karyotype.

So for the sake of discussion, I will assume that K. sonoriense has TSD pattern 2 and no sex chromosome influence. This turtle is distributed across the southwest deserts, and I imagine that if precip levels remain constant and temperatures increase, it would probably have profound effects on the developmental biology of K.sonoriense, thus affecting population size, and possibly resulting in the species decline. On the other hand, TSD pattern 2 predicts females at low temperatures also. So there may be some type of balancing act of sex-ratio. None of this takes into account the increase or decrease of moisture. So to answer your question, I feel that it would probably negatively impact them but to what degree, I am unsure. I make this conclusion because the area is already hot and dry, and increasing these factors may exacerbate the situation. This probably represents a good research project.

Also this is a good review of of threats to Reptiles and mentions global climate changehttp://www.bioone.org/perlserv/?request=...2.0.CO%3B2

I was going to let everyone know that my first Natural history note was published in the newest volume of Herpetological Review. Yay me.

YAY YOU! thats great, man.

Congratulations!

Can you post it here so we can read it? (or a link to it)

Congrats Man!

It's a natural history note, so they don't have links to them. You would have to get the Herp Review issue. Sorry.
You could probably go to some type of UCO library search engine and find it.

Do you have a copy of the draft you submitted?

If it is too much trouble, don't worry about it.

Yeah, I have reprints. I will get one to you next time we kick it.

Were the calculations done on an abacus?

The data is clearly copyrighted by the author, and Nilla isn't prepared to infringe on himself.

BiodiversityR: GUI for biodiversity and community ecology analysis

This package provides a GUI (Graphical User Interface, via the R-Commander) and some utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website.

http://cran.r-project.org/web/packages/B...index.html

adehabitat: Analysis of habitat selection by animals

A collection of tools for the analysis of habitat selection by animals

http://cran.r-project.org/web/packages/a...index.html


A big list of packages for R can be found here.

It's funny that you posted that. I am actually at the school working through all the labs to teach myself how to run a DCA for my thesis. R is a fucking amazing tool and its free. You guys know how much I like free things.