ECOLOGY OF SMALL MAMMALS IN THE NORTHERN

CHIHUAHUAN DESERT

by

MELINDA L. CLARY, B.S.

A THESIS

IN

BIOLOGY

Submitted to the Graduate Faculty of Texas Tech University in

Partial Fulfillment of the Requirements for

the Degree of

MASTER OF SCIENCE

Approved

Accepted

December, 2000

ACKNOWLEDGEMENTS

Funding for this project was provided by a Department of Defense grant (MIPR

W52EU251606913) administered by William Whitworth at USACERL. I would like to

thank Donna J. Howell and Brian Locke who were Directorates of the Environment at the

Fort Bliss Military Base for their direction and assistance in this study. I would also like

to thank additional personnel at Fort Bliss Military Base (Kelly Fischer, Shane Offut,

Will Roach, and Keith Landreth), as well as the Davis Dome staff for assistance during

this project. I would like to acknowledge the New Mexico Department of Game and Fish

for issuing a scientific collecting permit (# 2865). I also thank Darin Bell, Darin Carroll,

Cody Edwards, Kristina Halcomb, Ted Jolley, Oleksiy Knyazhnitskiy, Nicole Lewis-

Oritt, Stacy Mantooth, Roslyn Martinez, Cole Matson, Anton Nekrutenko, Mark

O'Neill, Lottie Peppers, Dr. Calvin Porter, Heather Roberts, Brenda Rodgers, Irene

Tiemann-Boege, Jeff Wickliffe, and Dr. Frank Yancey II, for assistance in collection and

preparation of specimens. Jody Martin and Nick Parker of the Texas Cooperative Fish

and Wildlife Research Unit, Texas Tech University, provided important administrative

support during this study.

I would like to acknowledge my committee members Drs. Robert D. Bradley,

Robert J. Baker, and Clyde Jones for their direction and encouragement throughout my

graduate career. I would especially like to thank my major advisor Dr. Robert D. Bradley

11

for his patience and guidance throughout the many stages of this project. I am grateful to

Dr. Richard E. Strauss for his everlasting enthusiasm and patience while providing

direction and insight on the statistical analyses generated in this study. I would also like

to express sincere gratitude to President David Schmidly for his constant positive

encouragement in m>' endeavors.

I would like to thank my colleagues Kristina Halcomb, Amy Halter, Nicole Lewis-

Oritt, Francisca Mendez-Harclerode, and Marcia Revelez for their advice and support

through not only the technical aspects of the project, but also through the difficult times

of my career. I would especially like to thank Darin Carroll and Cody Edwards who have

stood by me since the beginning of my degree. I am grateful to them for their professional

assistance in this project, as well as for their constant encouragement always forcing me

to smile. Their presence in my career has been invaluable.

A special thanks to my parents Ron and Carlita Clary and sister Jeana Clary for

their ever-present love and motivation which encouraged me to pursue this degree. I

would never have made it this far without them.

m

TABLE OF CONTENTS

ACKNOWLEDGEMENTS ii

ABSTRACT v

LIST OF TABLES vii

LIST OF FIGURES viii

CHAPTER

I. INTRODUCTION 1

II. A CHECKLIST OF MAMMALS FROM TWELVE HABITAT TYPES AT FORT BLISS MILITARY BASE, 1997-1998 7

III. SMALL MAMMAL COMMUNITIES AND HABITAT ASSOCIATIONS IN THE CHIHUAHUAN DESERT 40

IV. SUMMARY 74

APPENDIX: MATLAB FUNCTIONS 78

IV

ABSTRACT

Fort Bliss Military Base, located in Dona Aiia and Otero counties, New Mexico

and El Paso County, Texas, is within the northern limits of the Chihuahuan Desert. A

small mammal survey was conducted biannually from Spring 1997 to Fall 1998 on twelve

vegetatively distinct habitats. Each habitat contained two duplicate grids constructed

with census and assessments lines as a modification of O'Farrell's method (1977) and

sampled using Sherman live-traps. Sampling generally occurred on two periods of three

consecutive nights (one for census lines and one for assessment lines) for a total of 35,136

trap nights.

The data obtained from this project (number of captures, traps of capture,

species, etc.) will be used to determine the status of rodent communities within the

twelve habitats. Analyses utilizing the obtained data include: relative abundance of each

species; species diversity per habitat and season; species composition per habitat (rodent

community assemblages); rodent density per habitat (number of captured

individuals/hectare); survivability of each species (proportion of individuals recaptured at

a given time); and movement of each species (mean squared deviations from the centroid

of activity).

During the study, 2,091 individuals (19 species) were captured. Diversity was

highest in the sandy arroyo scrub habitat (Simpson's = 0.8859) and lowest in the coppice

dune habitat (Simpson's = 0.4120). On the basis of species composition, all grassland

habitats grouped together with a bootstrap support value of 58% and the acacia hillside

and sand) an'oyo scrub habitats clustered with a value of 85%. Rodent density was

highest in the swale habitat (39.16 individuals/ha) and lowest in the coppice dune habitat

(9.95 individuals/ha). Heterom\ ids displa\ ed the greatest longe\'it>' with six species

surviving through the 18-month stud)' period. Onychomys leucogaster had the highest

a\ erage movement (4.59 mean squared deviations-MSD) and Sigmodon hispidus had the

lowest average movement (2.43 MSD).

Results from this study provide baseline information concerning small mammals

of the Chihuahuan Desert. In addition, these data provide military personnel with the

necessary information to make decisions concerning the possible impact of military

activity on small mammal communities.

VI

LIST OF TABLES

2.1 Description of the 12 habitats sampled in this study 26

2.2 Number of males and females obtained from each census line sampled in the Spring 1997 29

2.3 Number of males and females obtained from each census line sampled in the Fall 1997 31

2.4 Number of males and females obtained from each census line sampled in the Spring 1998 33

2.5 Number of males and females obtained from each census line sampled in the Fall 1998 35

2.6 Number of males and females obtained from each census line sampled during all four trapping seasons 37

3.1 Average rainfall (mm) per season for each of the twelve habitats on Fort Bliss Military Base 59

3.2 The Simpson's diversity index (Simpson, 1949) was used to determine species diversity per season for each of the 12 habitats on Fort Bliss Military Base 61

vu

LIST OF FIGURES

2.1 Map of Fort Bliss Military Base 39

3.1 Photographs of the 12 habitats on Fort Bliss Military Base 62

3.2 Example of the grid system utilized in this study 64

3.3 A grid point-coordinate system was used to determine small mammal movements 65

3.4 Rainfall patterns for each habitat on Fort Bliss Military Base 66

3.5 Species diversity values per habitat and season compared to seasonal rainfall averages 67

3.6 A cluster analysis depicting habitats that grouped together based on similarities of rodent species composition 68

3.7 Rodent density, defined as the number of captures per hectare, for each of the four trapping periods at Fort Bliss Military Base 69

3.8 Survivorship for each species based on percentages of recaptures taken from the total initial captures at 6, 12, and 18 months 70

3.9 Survivorship rate (1 - the exponential rate of decline) of small mammal species 71

3.10 Average species movements depicted as the mean squared deviation from the centroid of activity for each species (p = < 0.001) 72

3.11 Average movements depicted per habitat as the mean squared deviations from the centroid of activity to each trap station of capture (p = 0.002) 73

Vlll

CHAPTER 1

INTRODUCTION

This thesis provides ecological information of small mammals that serves as

baseline data for a large-scale study on Fort Bliss Military Base. In 1996, Dr. Donna J.

Howell, Directorate of the Environment at Fort Bliss Military Base, contacted Drs.

Robert J. Baker and Robert D. Bradley of the Department of Biological Sciences at Texas

Tech University regarding their acceptance as Pi's on Research Work Order (RWO) #25

"Small Mammal and Reptile Abundance, Diversity, and Associations with Habitat on the

McGregor Range, Fort BHss." Dr. Howell served as supervisor of this research project

and the Pi's were to follow her experimental design, which was already in place prior to

the PFs involvement. Eight students were identified to form the core of the research team

and trained in identification of rodent species likely to occur in the Fort Bliss region.

Actual collecting times were scheduled for Spring 1997, Fall 1997, Spring 1998, and Fall

1998. Dr. Brian Locke replaced Dr. Howell in the final stages of the project.

Despite studies previously conducted on Fort Bliss Military Base concerning the

status of small mammals (Jorgensen, 1996; Jorgensen and Demarais, 1996; Root, 1997;

Weeks, 1997), few studies are available for comparing mammal species among and

between different habitat types. Such a study is necessary to provide information about

each habitat for Fort Bliss Military Base personnel to consider when planning military

training activities. Training operations in military areas have the potential to alter floral

and faunal habitats. Such activities have been shown to affect ecosystem stability

(Baumgardner, 1990; Brattstrom and Bondello, 1983; Carroll et al., 1999; Edwards et al.,

1998; Gese et al., 1989; Shaw and Diersing, 1990; and Stephenson et al., 1996) and

therefore should be considered when planning military operations.

Due to the steady increase in human populations and urbanization of surrounding

public lands, it is becoming necessar) for military personnel to ecologically manage the

acres of non-de\'eloped land on their properties in order to preserve areas for existing

wildlife. The information for small mammals pro\ided by this project at Fort Bliss

Military Base (identifying habitats of high diversity, presence of rare species, etc.) will be

used to develop resource management methods (avoiding areas of high rodent diversity,

density, etc.) while incorporating the need for military training activities.

This project's study area was located in the northern regions of the Chihuahuan

Desert within the Tularosa Basin and is typified by lowland valleys, rocky hillsides, and

scattered arroyos (Jorgensen, 1996; Monasmith, 1997). The desert fauna within this

region experience unpredictable fluctuations in climatic conditions and amount of

precipitation. Regardless, many species manage to maintain relatively stable populations

in these adverse conditions (Zeng and Brown, 1987). The Chihuahuan Desert is one of

the most diverse areas for small mammals (Schmidly, 1974; Brown and Zeng, 1989; Zeng

and Brown, 1987; Kotler and Brown, 1988). The region has extraordinarily diverse flora

and fauna. Eight orders, 24 families, 60 genera, and approximately 119 species of

mammals inhabit this desert (Schmidly, 1974).

The second chapter of this thesis represents the following publication:

Clary, M. L., D. M. Bell, C. W. Edwards, T. W. Jolley, O. Knyazhnitskiy, N. Lewis-Oritt, S. J. Mantooth, L. L. Peppers, I. Tiemann-Boege, F. D. Yancey, II, D. J. Howell. B. A. Locke, R. J. Baker, and R. D. Bradley. 1999. Checklist of Mammals from Twelve Habitat Types at Fort Bliss Military Base; 1997-1998. Occasional Papers Museum, Texas Tech University. 192: / + 1-16.

The author line for this publication includes all field crew members who served on the

project for two or more seasons, the project supervisor, and the project Pi's. Included in

this chapter is a descriptive list of small mammal species accounts on Fort Bliss Military

Base in addition to tables presenting the relative abundance of each species. Descriptions

of the 12 distinct habitats are provided.

The third chapter represents the following manuscript being prepared for

publication:

Clary, M. L., R. E. Strauss, R. J. Baker, and R. D. Bradley. Small Mammal Communities and Habitat Associations in the Chihuahuan Desert. In prep.

This chapter includes various ecological analyses of the Fort Bliss Military Base rodent

communities including community diversity, composition, density, species survivorship,

and movement. Each analysis was compared among all habitats and seasons.

The fourth chapter consists of recommendations for future work on Fort Bliss

Military Base. These recommendations were based on the results obtained from the

analyses utilized in Chapter III.

The primary objective for this study was to identify the species of small

mammals present on the base. Once this was achieved, the species density and diversity

of each of the 12 habitats was determined. The results from these ecological parameters

were compared among the habitats to decipher which habitats are the most fragile (i.e.,

low species diversity and density values). These fragile habitats were recognized as areas

of avoidance for military activities. Through this avoidance, the biodiversity of

ecosystems present at Fort Bliss Military Base may be preserved.

Literature Cited

Baumgardner, G. D. 1990. Mammal surveys on land condition trend plots at Fort Hood Texas. Unpublished report for U. S. Army Construction Engineering Research Lab. Department of Wildlife & Fisheries Sciences, Texas A&M University, College Station, TX, 136pp.

Brattstrom, B. H. and M. C. Bondello. 1983. Effects of off-road vehicle noise on desert vertebrates. Pages 167-206 in Enviromiiental effects of off-road vehicles; impacts and management in arid areas (R. H. Webb and H. G. Wilshire, eds.). Springer-Verlag, New York, N.Y.

Brown, J. H. and Z. Zeng. 1989. Comparative population ecology of eleven species of rodents in the Chihuahuan Desert. Ecology. 70:1507-1525.

Carroll, D. S., R. C. Dowler, and C. W. Edwards. 1999. Estimates of relative abundance of the medium-sized mammals of Fort Hood, Texas, using scent-station visitation. Occasional Papers, Museum, Texas Tech University, 188:1-10.

Edwards, C. W., R. C. Dowler, and D. S. Can-oil. 1998. Assessing medium-sized mammal abundance at Fort Hood military installation using live-trapping and spotlight counts. Occasional Papers, Museum, Texas Tech University, 185:1-23.

Gese, E. M., O. J. Rongstad, and W. R. Mytton. 1989. Change in coyote movements due to mihtary activity. Journal of Wildlife Management, 53:334-339.

Jorgensen, E, E. 1996. Small mammal and herpetofauna communities and habitat associations in foothills of the Chihuahuan Desert. Unpublished Ph. D. dissertation, Texas Tech University, Lubbock, TX.

Jorgensen, E. E. and S. Demarais. 1996. Final Report; Small mammal and herpetofauna habitat associations and communities on the McGregor Range, Fort Bliss; Sacramento Mountain foothills. Directorate of Environment, Fort Bliss, El Paso, Texas. 197 pp.

Monasmith, T. J. 1997. Fire effects on small mammals and vegetation of the northern Chihuahuan Desert. Unpublished Master's thesis, Texas Tech University, Lubbock, Texas.

Root, J. J. 1997. Microsite and habitat boundary influences on small mammal capture, diversity, and movements. Master's Thesis, Texas Tech University, Lubbock, Texas.

Schmidly, D. J. 1974. Factors governing the distribution of mammals in the Chihuahuan Desert region. Pp. 163-192 in Transactions of the Symposium on the Biological Resources of the Chihuahuan Desert region United States and Mexico (D. H. Riskind and R. H. Wauer, eds.). Sul Ross State University, Alpine, TX.

Schmidt, R. H. 1986. Chihuahuan climate. Pp. 40-63 in Second Symposium on resources of the Chihuahuan Desert region. (J. C. Barlow, A. M. Powell, B. N. Timmermann, eds.). Chihuahuan Desert Institution, Alpine, TX.

Shaw, R. B. and V. E. Diersing. 1990. Tracked vehicle impacts on vegetation at the Pinon Canyon maneuver site. Colorado. Journal of Environmental Qualit) 19:234-243.

Stephenson, T. R., M. R. Vaughn, and D. E. Andersen. 1996. Mule deer movements in response to military activity in southeast Colorado. Journal of Wildlife Management, 60:777-787.

Weeks, B. E. 1997. Niche partitioning mechanisms of desert heteromyid rodents. Master's Thesis, Texas Tech University, Lubbock, Texas.

Zeng, Z. and J. H. Brown. 1987. Population ecology of a desert rodent: Dipodomys merriami in the Chihuahuan Desert. Ecology, 68:1238-1340.

CHAPTER II

A CHECKLIST OF MAMMALS FROM TWELVE

HABITAT TYPES AT FORT BLISS MILITARY BASE,

1997-1998

The Fort Bliss Military Base is located in Dona Ana and Otero counties. New

Mexico, and El Paso County, Texas. This army base occupies approximately 4,523 km^

(452,279 ha) and is bordered by the Sacramento Mountains to the north, the Organ

Mountains to the west, and the Franklin Mountains to the southwest. Fort Bliss

Military Base is bisected by U.S. Highway 54, resulting in the Dona Ana Range to the

west and the McGregor Range to the east. This region, located within the northern area

of the Chihuahuan Desert (Shreve, 1942), is characterized by a semiarid to arid climate

and is often classified as a desert grassland (Gardner, 1951; Schmidt, 1986).

Geographically, Fort Bliss is located within the Tularosa Basin and is typified by lowland

valleys, rocky hillsides, and scattered arroyos (Jorgensen, 1996; Monasmith, 1997). Two

unusual physiographic features found in this region include coppice sand dunes and Otero

Mesa.

A small mammal survey was conducted using census lines as described in O'Farrell

(1977) in 12 distinct habitat types on McGregor Range in May 1997, September-October

1997, May 1998, and September-October 1998. This study was designed to collect

baseline data concerning small mammal diversity and habitat preference. This paper is an

7

account of species trapped. Analyses and discussion of diversity, seasonal change, and

movements will be addressed in subsequent articles.

Methods and Materials

The research design for this study involved sampling small mammals (rodents) in

12 distinct habitat types with two replicates (census lines) per habitat. Brief descriptions

of the 12 habitat types are provided in Table 2.1. This includes the locality of each

census line given in Universal Transverse Mercater (UTM) coordinates and a list of the

dominant plant species associated with each census line. Habitat selection was done in

conjunction with ongoing floral studies by other Fort Bliss personnel and attempts were

made to utilize the same or nearby areas for both the floral and small mammal studies

(Fig. 2.1). At each census line, two parallel trap lines 30 m apart (240 m in length) were

established with trap stations placed at 10 m intervals along each line resulting in a total

of 50 traps. Each census line was sampled using Sherman (H.B. Sherman Trap Co.,

Tallahassee, FL) live-traps baited with bird seed and rolled oats during two seasonal

periods (Spring and Autumn) for two consecutive years (1997 and 1998). Sampling of

the census lines usually occurred on three consecutive nights during each trapping period,

resulting in 14,400 trap nights. Occasionally, due to full moon phases, weather, and

military operations and schedules, it was not possible to sample particular census lines on

the three consecutive nights. Therefore, we were forced to postpone consecutive night

sampling for periods of one to four days. Individuals captured on census lines were

identified, weighed, sexed, toe-clipped (Animal Care and Use Committee, 1998), assigned

8

a TK number (Texas Tech University Museum identification number), and released at the

site of capture. For simplicity, references to all individuals reported

herein are by season and year rather than by the actual date of capture; likewise, census

lines are used for localities rather than the actual UTM coordinates. These data are

pro\ided in Tables 2.2-2.6.

A reference collection of voucher specimens and tissue samples for at least one

adult male and one adult female, representative of each species, was prepared and

deposited in the Museum, Texas Tech University. In addition, toes obtained during the

toe-clipping procedures were preserved in lysis buffer (Longmire et al. 1997) and serve

as voucher material for specimens obtained during this study. Nomenclature followed

Jones et al. (1997) and specimens were identified using keys and characteristics from

Davis and Schmidly (1994), Findley (1987), and Findley et al. (1975). Additionally, a

few species were observed but not trapped on the Fort Bliss Military Base. These

observations are listed in a separate section (Species Observed in the Results and

Discussion).

Results and Discussion

A description of the 12 habitats and 24 census lines, including UTM coordinates

and dominant plant species, is presented in Table 2.1. During the two years of this study

(1997 and 1998), 2,091 individuals representing 19 species of small mammals were

obtained from the 24 census lines (Tables 2.2-2.6). In the initial year (1997), the greatest

diversity and relative abundance of the 19 species was observed. The two trapping

seasons in 1997 accounted for 72.4% of the individuals (1,513) captured. Most species

(17 of 19) declined in relative abundance from 1997 to 1998 with 578 (28% of the total)

individuals captured in 1998. However, there were two exceptions, Neotoma albigula and

Neotoma micropiis. which increased in relative abundance during 1998. Of the four

trapping periods (Spring 1997, Fall 1997, Spring 1998, and Fall 1998), efforts during

Spring 1997 resulted in the most diversity (19 species) and abundance (44% of the total).

The Spring and Fall 1998 trapping seasons resulted in the lowest number of captures with

only 288 individuals representing 18 species in the Spring and 290 individuals

representing 15 species in the Fall.

During the two-year study, the Chilopsis arroyo habitats (census lines 13 and 8)

accounted for the greatest small mammal diversity with 14 of 19 species. Likewise, one

of the swale sites (census line 10) possessed the highest number of captures (148

individuals) for any individual census line. Trapping efforts from 1997-1998 on one of

the coppice dune sites (census line 21) resulted in the lowest species diversity (5 of the

19 species) and the least number of captures (16 individuals).

Taxa Documented by Live-Trapping

The taxa described below are arranged phylogenetically following Davis and

Schmidly (1994). Actual numbers of captures per taxon, census line, and season are listed

in Tables 2.2-2.6.

10

Spermophilus spilosoma marsinatus Bailev. 1902 Spotted Ground Squirrel

Seven individuals (3 males and 4 females) of Spermophilus spilosoma were

obtained. In all cases, individuals were obtained either in open grasslands or in open areas

associated with dunes. A female was obtained in Spring 1997 in a grama grassland

(census line 15), two females were obtained in Fall 1997 in a coppice dune and a mixed

desert scrub habitat (census lines 21 and 22), and a female was obtained in Spring 1998 in

a grama grassland (census line 11). A male was obtained in Spring 1997 in a creosote

grassland (census line 12) and two males were obtained in Spring 1998, one each in a

nonstabilized dune (census line 1) and grama grassland (census line 11). Individuals of iS.

spilosoma were obtained during every season except Fall 1998. Although this species

appears to be relatively rare, it should be noted that the paucity of individuals obtained

probably was a result of sampling design (traps not open during diurnal hours) and not

indicative of actual abundance.

Perognathus flavescens apache Merriam. 1889 Plains Pocket Mouse

Perognathus flavescens was the least abundant nocturnal species obtained with

seven individuals (5 males and 2 females) captured. This species typically was obtained

in habitats with relatively moderate amounts of vegetation. Two females were obtained in

Fall 1997, one fi-om an acacia hillside (census line 16) and the other from a mixed desert

scrub habitat (census line 22). A male was obtained in Spring 1997 in a sandy arroyo

11

scrub habitat (census line 3), two males were obtained in Fall 1997, one each in a sandy

arroyo scrub habitat (census line 3) and a succulent hillside habitat (census line 7), and

two males were obtained in Spring 1998 on a succulent hillside habitat (census line 7). P.

flavescens was most abundant during Fall 1997 (57% of total captures of this species)

and individuals were obtained every season except Fall 1998.

Perognathus flavus flavus Baird. 1855 Silky Pocket Mouse

Perognathus flavus was the most abundant species obtained during this study

with 388 individuals (215 males and 173 females). This species was captured in all

habitats with the exception of one of the nonstabilized dunes (census line 1) and both

coppice dunes (census lines 19 and 21), and was most abundant in the grama, yucca, and

creosote grasslands. Individuals of P. flavus were obtained in all four trapping seasons,

but were most common in Spring 1997 when 47% of the individuals were captured.

Chaetodipus hispidus paradoxus Merriam. 1889 Hispid Pocket Mouse

Fifteen individuals of Chaetodipus hispidus (9 males and 6 females) were obtained

from three grassland habitats. Five females were obtained in Spring 1997 fi-om grama

(census line 15) and yucca grasslands (census lines 23 and 24), and a female was obtained

in Autumn 1997 in a yucca grassland (census line 23). Six males were obtained in Spring

1997 in creosote (census line 12) and yucca grasslands (census lines 23 and 24), a male

12

was obtained in Fall 1997 in a yucca grassland (census line 23), and two males were

obtained in Spring 1998 in a creosote grassland (census line 12). Our data indicate that

this taxon is restricted to the grama, yucca, and creosote grasslands. Seventy-three

percent of the C. hispidus indi\iduals were obtained in Spring 1997 and no individuals

were captured in Fall 1998. This taxon was the fourth least abundant species (along with

Reithrodontomys montanus) obtained. The low numbers of captures may reflect the fact

that the Fort Bliss study site is located at the periphery of the distributional range of C.

hispidus, where species normally are less abundant.

Chaetodipus intermedius intermedius Merriam. 1889 Rock Pocket Mouse

One hundred forty-eight individuals of Chaetodipus intermedius (67 males and 81

females) were obtained. This species commonly was found throughout the creosote-

tarbush scrub habitats as well as the acacia and succulent hillside habitats. This species

was obtained during all four trapping periods and was most abundant in Spring 1997 with

44%) of the individuals being captured during this period.

Chaetodipus eremicus rMearns. 1898) Chihuahuan Desert Pocket Mouse

Eighty-eight individuals of Chaetodipus eremicus (59 males and 29 females) were

obtained primarily within the mixed desert shrub and acacia hillside habitats. Individuals

13

of C. eremicus were obtained every season and were most abundant during Spring 1997

when 36%) of the total captures was recorded.

Dipodomys merriami ambii^uus Merriam. 1890 Merriam's Kangaroo Rat

Dipodomys merriami was the second most abundant species (349 individuals. 190

males and 159 females). Individuals of this taxon were obtained during all four trapping

periods and from all habitat types. Spring 1997 yielded the most individuals with 38% of

the total captures of this species. During Fall 1997, Spring 1998, and Fall 1998, there

was a slight decrease in trap success for D. merriami.

Dipodomys ordii ordii Woodhouse. 1853 Ord's Kangaroo Rat

One hundred twenty-eight individuals of Dipodomys ordii (77 males and 51

females) were obtained primarily within the coppice (census lines 19 and 21) and

nonstabilized (census lines 1 and 2) sand dune sites. This taxon was obtained in all four

seasons and was most abundant in Spring 1997 (43% of the total captures of this

species).

14

Dipodomys spectabilis baileyi Goldman. 1923 Banner-tailed Kangaroo Rat

Nine individuals of Dipodomys spectabilis (5 males and 4 females) were obtained.

A female was obtained in Spring 1997 on a creosote grassland (census line 12). two

females were obtained in Spring 1998 on a grama grassland (census line 15), and a female

was obtained in Fall 1998 on a creosote grassland (census line 18). A male was obtained

in Spring 1997 on a creosote grassland (census line 18), another male was obtained in

Spring 1998 on a Chilopsis arroyo habitat (census line 13), and three males were obtained

in Fall 1998 on grama (census line 11) and creosote (census line 12) grasslands and a

Chilopsis arroyo (census line 13). No individuals were trapped during Fall 1997.

Typically, individuals of Dipodomys spectabilis were obtained in grassland habitats

(creosote and grama), although two individuals were obtained in a Chilopsis arroyo

habitat. This taxon was the third least abundant species obtained. Although this species

appears to be uncommon throughout the study area, numerous mounds and burrow

systems were observed outside of the designated census lines. The low number of

individuals trapped was probably the result, in part, of the placement of census lines, as

well as the trap size being too small to effectively capture this species.

Reithrodontomys megalotis megalotis rSaird. 1858) Western Harvest Mouse

One hundred seventeen individuals of Reithrodontomys megalotis (77 males and

40 females) were obtained. Our data indicate this species favors tall, thick grassy

15

habitats. Fifty-three percent of the total captures of this species occurred in Spring 1997.

Fall 1997, Spring 1998, and Fall 1998 showed a sharp decline in the number of

Reithrodontomys megalotis captures.

Reithrodontomys montanus monlanus (Baird, 1855) Plains Harvest Mouse

Fifteen individuals of Reithrodontomys montanus (8 male and 7 female) were

obtained; primarily from the grassy areas of the dry Sacramento riverbed. Seven males

were obtained in swale (census line 5) and Chilopsis arroyo (census line 8) habitats and

six females were obtained in Chilopsis arroyo (census line 8) and swale (census line 10)

habitats in Spring 1997. Two individuals (1 male and 1 female) were obtained in a yucca

grassland (census line 24) in Fall 1997. No individuals of R. montanus were captured in

1998. Reithrodontomys montanus was the fourth least abundant species (along with

Chaetodipus hispidus) obtained.

Peromyscus eremicus eremicus fBaird. 1858) Cactus Mouse

One hundred six individuals of Peromyscus eremicus (63 males and 43 females)

were obtained throughout most of the brushy hillside areas including the acacia (census

lines 9 and 16) and succulent (census lines 7 and 20) hillside habitats. Fifty-six percent of

the individuals were captured in Spring 1997.

16

Peromyscus maniculatus blandus Osgood.1904 Deer Mouse

This was the most commonly captured species of Peromyscus with 144

individuals (83 males and 61 females) obtained from a wide variety of habitats. These

habitats ranged from dune sites to grasslands and rocky hillsides. This taxon was

obtained in all four seasons with 59% of the captures for this species occurring in Spring

1997.

Peromyscus leucopus tornillo Mearns. 1896 White-footed Mouse

One hundred forty-nine individuals of Peromyscus leucopus (91 males and 58

females) were obtained in multiple habitats. These ranged from grama grasslands to

succulent hillsides with brush and yucca species generally associated with all habitats.

This species was obtained during all four trapping periods and was most abundant during

the two trapping seasons in 1997, which accounted for 74% of the captures for this

species.

Onychomys arenicola arenicola Mearns. 1896 Mearn's Grasshopper Mouse

Sixty-one individuals of Onychomys arenicola (29 males and 32 females) were

obtained from census lines associated with grama and creosote grasslands as well as

17

swales and creosote-tarbush scrub habitats. This species was obtained during all four

seasons and, unlike most other species, was most abundant in the Fall 1997 trapping

period, which accounted for 66% of the individuals captured.

Onychomys leucogaster ruidosae Stone and Rehn, 1903 Northern Grasshopper Mouse

Eighty individuals of Onychomys leucogaster (46 males and 34 females) were

captured in census lines associated with dune, grassland, and succulent hillside habitats.

This taxon was obtained during all four trapping periods and, like its congener, was most

abundant in Fall 1997 when 51% of the captures of this species occurred.

Sigmodon hispidus berlandieri Baird. 1855 Hispid Cotton Rat

One hundred and thirty-four individuals of Sigmodon hispidus (63 males and 71

females) were obtained primarily in the swale habitats, although a few were captured in

the creosote-tarbush scrub habitats. This species was present during all four trapping

seasons, but was captured predominantly during Spring 1997 when 55% of the total

individuals were obtained.

18

Neotoma albigula albigula Hartlev. 1894 White-throated Woodrat

One hundred sixteen indi\'iduals of Neotoma albigula (52 males and 64 females)

were obtained. This species was common in the nonstabilized dune (census line 1) and

acacia hillside (census lines 9 and 16) habitats, and was captured in all four trapping

periods. In contrast to all other species of rodents, this species, along with Neotoma

micropus, increased in abundance during the final trapping season (Fall 1998) with 32%

of the total captures of this species being recorded.

Neotoma micropus cane seen s J.A.Allen. 1891 Southern Plains Woodrat

Thirty individuals of Neotoma micropus (18 males and 12 females) were obtained

primarily from the sandy arroyo and creosote-tarbush scrub habitats. In Spring 1997,

five males were obtained in sandy arroyo scrub (census line 6), Chilopsis arroyo (census

line 8), creosote-tarbush scrub (census line 14), and creosote grassland (census line 18)

habitats, and six females were obtained in mixed desert scrub (census line 4), sandy arroyo

scrub (census line 6), creosote grassland (census line 12), creosote-tarbush scrub (census

line 14), and acacia hillside (census line 16) habitats. In Fall 1997, two males were

obtained in creosote grassland (census line 12) and creosote-tarbush scrub (census line 14)

habitats . In Spring 1998, four males were obtained in a creosote grassland habitat (census

line 12), and six females were obtained in nonstabilized dune (census line 2), mixed desert

scrub (census line 4), creosote grassland (census line 12), and creosote-tarbush scrub

19

(census line 14) habitats. In Fall 1998, seven males were obtained in nonstabilized dune

(census line 2), mixed desert scrub (census line 4), Chilopsis arroyo (census line 13),

creosote-tarbush scrub (census line 14), succulent hillside (census line 20), and mixed

desert scrub (census line 22) habitats. This species, along with N. albigula, increased in

abundance in Fall 1998.

Species Observed

Many mammal species occurring on the Fort Bliss Military Base were not

trappable with our experimental design and trapping methods. These species were

recorded as observations and are presented below. These observations are not included

with the data presented in Tables 2.2-2.6.

Sylvilagus audubonii goldmani rNelson. 1904) Desert Cottontail

Individuals of Sylvilagus auduboni were observed from succulent hillside and

mixed desert scrub habitats. This species was observed throughout the Fort Bliss

Military Base on each census line and habitat type.

Lepus californicus texianus Waterhouse. 1848 Black-tailed Jack Rabbit

Several individuals of this species were observed during each of the four collecting

periods. This taxon typically occupied the more open grassland areas and roadsides.

20

Cynomys ludovicianus arizonensis Mearns. 1890 Black-tailed Prairie Dog

Several individuals were observed in prairie dog towns located in the open

grassland habitats on Otero Mesa.

Canis latrans texensis Bailev. 1905 Coyote

Evidence of this species (tracks, scat, and dens) was noted throughout all

habitats. Additionally, several individuals were observed along roadsides throughout the

Fort Bliss Military Base.

Urocyon cinereoargenteus scottii Mearns. 1891 Gray fox

Two individuals were observed near census lines 6 and 7 (sandy arroyo scrub and

succulent hillside). The secretive nature of this species created difficulty in estimating the

abundance of this taxon.

21

Taxidea taxus berlanderi Baird. 1858 American Badger

A single specimen was observed in Spring 1997 near census line 8 {Chilopsis

arroyo). In addition, many excavations of rodent burrows were noted and may indicate

that badgers are common.

Lynx rufus bailevi Merriam. 1890 Bobcat

Three individuals were observed during the first two seasons (Spring and Fall

1997) within the riparian habitats below Otero Mesa.

Odocoileus hemionus crooki (Mearns. 1897) Mule Deer

This species was observed throughout most areas of Fort Bliss with the

exception of open grasslands. Most were noted in the early morning near brushy foothills

of Otero Mesa.

Antilocapra americana americana rOrd. 1815) Pronghorn

This species was quite common in the grama and yucca grasslands located on

Otero Mesa. Although little is known about the relative abundance of this species, on

one occasion, at least 70 individuals were observed at a single site.

22

Oryx gazella (Linneaus. 1758) Gemsbok

This introduced species was observed in small groups (2-5 individuals) on

numerous occasions in the swale and nonstabilized dune habitats near the Sacramento

Mountains.

Ammotragus lervia (Pallas, 1977) Barbary Sheep or Aoudad

A single individual of this introduced species was observed on the rocky slopes

just below Otero Mesa.

23

Literature Cited

Animal Care and Use Committee. 1998. Guidelines for the capture, handling, and care of mammals as approved by the American Society of Mammalogists. Journal of Mammalogy, 79: 1416-1431.

Davis, W.B., and D.J. Schmidly. 1994. The Mammals of Texas. Texas Parks and Wildlife Department. Austin, .v + 388 pp.

Findley, J.S., A.H. Harris, D.E. Wilson, and C. Jones. 1975. Mammals of New Mexico. University of New Mexico Press, Albuquerque, x + 360 pp.

Findley, J.S. 1987. The Natural History of New Mexican Mammals. University of New Mexico Press, Albuquerque, x + 150 pp.

Gardner, J. L. 1951. Vegetation of the Creosotebush area of the Rio Grande valley in New Mexico. Ecological Monographs, 21:379-403.

Jones, C , R.S. Hoffman, D.W. Rice, M.D. Engstrom, R.D. Bradley, D.J. Schmidly, C.A. Jones, and R.J. Baker. 1997. Revised Checklist of North American Mammals North of Mexico. Occasional Papers Museum, Texas Tech University, 173:1-18.

Jorgensen, E.E. 1996. Small mammal and herpetofauna communities and habitat associations in foothills of the Chihuahuan Desert. Unpublished Ph.D. dissertation, Texas Tech University, Lubbock, TX.

Longmire, J. L., M. Maltbie, and R. J. Baker. 1997. Use of "lysis buffer" in DNA isolation and its implication for museum collections. Occasional Papers, Museum, Texas Tech University, 163:1-3.

Monasmith, T.J. 1997. Fire effects on small mammals and vegetation of the northern Chihuahuan Desert. Unpublished Master's thesis, Texas Tech University, Lubbock, TX.

24

O'Farrell, M.J., D.W. Kaufman, D.W. Lundahl. 1977. Use of Live-trapping with the Assessment Line Method for Density Estimation. Journal of Mammalogy, 58:575-582.

Schmidt, R.H. 1986. Chihuahuan climate. Pp. 40-63, in Second symposium on resources of the Chihuahuan Desert region. (.l.C. Barlow, A.M. Powell, B.N. Timmermann. eds.). Chihuahuan Desert Institution. Alpine. TX.

Shreve, F. 1942. The desert vegetation of North America. The Botanical Review, 8:195-246.

25

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39

CHAPTER III

SMALL MAMMAL COMMUNITIES AND HABITAT

ASSOCIATIONS IN THE CHIHUAHUAN DESERT

Abstract

From May 1997 to October 1998, a small mammal study was conducted at the

Fort Bliss Military Base to compare the ecology of small mammals among 12 distinct

habitat types. Each habitat type contained two replicate grids for analysis, each examined

for six nights (three for census lines and three for assessment lines) per trapping period

during Spring 1997, Fall 1997, Spring 1998, and Fall 1998. Data recorded from each

capture on the grids included TK number (Texas Tech Museum identification number),

species identification, sex, weight, date of capture, toe-clip number (cross-referenced with

the TK number), and trap station of capture.

The capture data were used in the following analyses: species diversity, density,

and composition per habitat, survivability of species, and movement of each small

mammal species. Species diversity was highest in the sandy arroyo scrub habitat

(Simpson's index value = 0.8859) and lowest in the coppice dune habitat (Simpson's index

value = 0.4120). The swale habitat possessed the highest rodent density value with 39.16

individuals per hectare. Results from a species composition cluster analysis revealed that

habitats with comparable vegetative composition (such as the three grasslands: yucca,

grama, and creosote) formed clusters 50% or more of the time. Species within the family

Heteromyidae were most successful in terms of survivability with six species surviving

40

for at least 18 months. The insectivore Onychomys leucogaster displayed the greatest

average movement of 3.94 MSD among the species and the highest average movement

across all species was found in the moderately vegetated acacia hillside habitat (3.96

MSD).

Introduction

Desert ecosystems are characterized as one of the most unique and diverse areas in

the United States and embody an abundance and diversity of flora and fauna unique to

most habitats. This diversity is in itself phenomenal due to many species maintaining

exceptionally stable populations despite the unpredictable fluctuations in the

environment (Zeng and Brown, 1987). Free-standing water is rarely available in these

dry, arid ecosystems. This lack of available water can be detrimental for species living in

most other environments. Animals residing in deserts have adapted certain morphological

and physiological characteristics which enable them to live and thrive in an environment

that is unsuitable for other species (Ghobrial and Nour, 1975). These characteristics have

resulted in an abundance and diversity of rodent species in desert ecosystems. Despite

this abundance, there appears to be partitioning of resources or some level of coexistence

among desert rodent communities of southwestern North America, resulting in desert

rodents being ideal subjects for studies of coexistence, competition, and community

structure (Heske et al , 1994).

The Chihuahuan Desert is located in the southernmost portion of the Great

American Desert with its region lying in the area bounded by the 90^^ and 108^^

41

meridians and the 2ist and 33^^ parallels (Milstead, 1960). It includes parts of southern

New Mexico, all of Texas west of the Pecos River (except for the Guadalupe Mountains),

the eastern half of Chihuahua, the western portion of Coahuila, and parts of Durango,

Zacatecas, Nuevo Leon, San Luis Potosi, Aguascalietes, and Tamaulipas (Schmidly,

1974). The region has a diverse flora and fauna including eight orders, 24 families, 60

genera, and roughly 119 species of mammals (Sclimidly, 1974).

The Fort Bliss Military Base includes a relatively small portion of the northern

region of the Chihuahuan Desert. It occupies approximately 4, 523 km2 (452,279 ha),

ranging from El Paso County, Texas to Otero County, New Mexico, and is divided by

U.S. Highway 54, with the Dona Aiia Range to the west and the McGregor Range to the

east. It is characterized as a desert grassland with a semiarid to arid climate located within

the Tularosa Basin which is typified by lowland valleys, rocky hillsides, and scattered

arroyos (Gardner, 1951; Schmidt, 1986; Jorgensen, 1996; Monasmith, 1997).

The objectives are: (1) compare small mammal (rodent) composition among the 12

unique habitats in the Chihuahuan Desert to determine which contain relatively high

species diversity values of small mammals and which are "fragile" (those containing

relatively low diversity values), (2) compare small mammal densities per habitat and

determine any influence of vegetative cover, (3) determine if the amount of rainfall

influences density or diversity, (4) determine the survivability of each small mammal

species, and (5) compare the average movement among species and habitats to determine

the influence of vegetative density on rodent activities.

42

Methods

The research design for this study involved sampling small mammals (rodents) in

12 distinct habitat types with each containing two replicate grids. The 12 habitats

analyzed in this study were characterized by range botanists, based on vegetative

composition and density, and labeled as: sandy arroyo scrub, nonstabilized dune, coppice

dune, creosote-tarbush scrub, mixed desert scrub, grama grassland, creosote grassland,

yucca grassland, swale, acacia hillside, Chilopsis arroyo, and succulent hillside habitats

(Figure 3.1). Brief descriptions of the habitats are provided in Table 2.1 including a list of

the dominant plant species associated with each habitat. Each of the habitat types was

ranked on the basis of percent vegetative cover from 1 (0.0-20.0%) to 5 (80.0-100.0%).

Two grids, each with census and assessment lines, were constructed for each

habitat type. The experimental design for this project was described in Clary et al.

(1999). Census lines, including two parallel trap lines 30 m apart (240 m in length)

established with trap stations placed at 10 m intervals along each line resulting in a total

of 50 traps were used for initial captures. The assessment lines, containing 72 traps,

formed a diamond-like configuration about the census lines and were utilized for

estimating recaptures on each grid (Figure 3.2). Each of these lines (census and

assessment) was sampled using Sherman live-traps (H.B. Sherman Trap Co., Tallahassee,

FL) baited with birdseed and rolled oats during two seasonal periods (Spring and Fall) for

two consecutive years (1997 and 1998). Generally, sampling of the grids typically

occurred on three consecutive nights on the census lines followed by sampling for an

additional three consecutive nights on the assessment lines. Total trapping efforts

43

produced 35,136 trap nights. Informative data were recorded for each individual captured

on census lines (TK number -Texas Tech Museum identification number, identification to

species level, weight, sex, toe-clip number -to be cross-referenced with the TK number,

and trap station and date of capture) followed by the individual being released at the site

of capture. Captures on assessment lines were identified from toe-clip patterns and the

date and trap station of capture were recorded. For this study, it was assumed that

animals encountered traps randomly in a particular habitat and neither the sex, age, or

dominance of an animal influenced capture probabilities.

A reference collection of voucher specimens and tissue samples for at least one

adult male and one adult female, representative of each species, was prepared and

deposited in the Museum, Texas Tech University to provide historical and physical

documentation. In addition, toes obtained during the toe-clipping procedures were

preserved in lysis buffer (Longmire et al , 1997) and serve as voucher material for

specimens obtained during this study. Nomenclature followed Jones et al. (1997) and

specimens were identified using keys and characteristics from Davis and Schmidly (1994),

Findley (1987), and Findley and Caire (1974).

To determine monthly precipitation, a rain gauge was attached to a T-post and

placed at the first trap station of each grid. Rainfall was recorded (in millimeters) at the

first of each month from April 1997 to October 1998. In some cases, minor disturbances

on the grids (i.e., cattle) affected the reliability of some of the gauges and monthly

accumulation could not be recorded. These incidences were not included in the

44

accumulation averages of the affected grid. The recorded rainfall for each month was

averaged for each habitat and season (Table 3.1).

All statistical analyses used in this study were generated in the software program

Matlab (Matlab 5.2, 1998). Species diversity was calculated for each rodent species

using the Simpson's diversity index (Simpson, 1949). This index utilizes the number of

species present in a habitat (species ricliness) and the number of individuals within each

species (evenness) to estimate species diversity. Species diversity values were compared

between and among habitats to determine which habitats possessed the highest diversity.

In addition, diversity values were compared to the vegetative density (percent cover) of

each habitat using correlation analyses. Clustering methods similar to those used by

Brown and Heske (1990) were used to determine species composition similarities among

the habitats. Species composition was compared among the habitats by a UPGMA

cluster analysis of species count correlations among habitats. The cluster analysis was

bootstrapped for 1000 iterations and those habitats grouping together at least 50%) of the

time (bootstrap support value = 0.05) were recognized. The average rainfall from each

trapping period was tabulated and compared with each habitat's diversity value through

correlation analyses to determine the influence of rainfall on rodent community diversity.

Rodent density per habitat was defined as the number of individuals captured per

hectare. The results from this analysis were compared among habitats and seasons.

Percent cover (vegetation) per habitat was compared to the results from the rodent

density analysis through correlation analyses to determine if concentrations of vegetation

45

had an effect on small mammal density. In addition, regression analyses were utilized to

determine any influences of rainfall.

Survivability, defined as the proportion of individuals from a given cohort

surviving at a given time (Lincoln et al., 1982), was calculated for each species.

Comparisons were made among species using the proportion of individuals (per species)

recaptured from the total initial captures at six-month intervals (6. 12, and 18 months). In

addition, regression analyses were generated using the number of captures and trapping

period (time) and applied per species to determine the exponential survivorship rate of

decline (r).

The average movement for each species was determined by converting the trap

stations and traps of capture per grid to points on an x,y point-coordinate system. The

centroid (median) of activity for each recaptured individual was generated based on the

assemblage of captures and squared deviations from the centroid to each trap of capture

were averaged (Figure 3.3). The deviations were then averaged per species (mean squared

deviations, MSD) and compared among the species. In addition, the deviations were

averaged per habitat to determine if the differences in vegetative density (percent cover)

among the habitats affected the amount of movement among the residing species. An

analysis of variance (ANOVA) was generated to determine significant differences among

the species and habitat movement averages. Pairwise comparisons were utilized to

determine significant differences within the species and habitat groups.

46

Resuks

Diversity

Nineteen species were obtained from the 12 habitats. Habitat and seasonal

species diversity values are shown in Table 3.2. Estimates of species diversity, for the

four trapping periods, indicated that the sandy arroyo scrub habitat possessed the highest

rodent diversity (Simpson's index = 0.872). Several other habitats possessed similar

diversity values including Chilopsis arroyo (0.828), acacia hillside (0.816), creosote-

tarbush scrub (0.816), succulent hillside (0.803), swale (0.802), yucca grassland (0.796),

creosote grassland (0.742), and mixed desert scrub (0.707) habitats. Species diversity was

lowest in the coppice dune habitat (0.384); whereas nonstabilized dunes (0.645) and

grama grassland (0.472) had low to medium diversity values. Results from correlation

analyses showed a positive correlation (0.56) of habitat species diversity and vegetative

percent cover. However, despite this trend of correlation between the two parameters, it

was not significant (p < 0.05).

Species diversity for most grids remained relatively unchanged between trapping

periods (Spring 1997, Fall 1997, Spring 1998, and Fall 1998) and between years (1997,

1998). However, small mammal diversity increased in the nonstabilized dune habitat

during 1998 (Spring and Fall), decreased in the coppice dune habitat during 1998 (Spring

and Fall), decreased in the mixed desert scrub habitat during Spring 1998, and was lowest

in the yucca grassland habitat during Spring 1997.

All interpretations on community diversity as a function of rainfall were based on

direct observation and correlation analyses. The rainfall in Spring 1998 had the lowest

47

average (5 mm) recorded during the study (Figure 3.4). The recorded seasonal rainfall was

positively correlated with the seasonal diversity values of the mixed desert scrub,

succulent hillside, acacia hillside, creosote-tarbush scrub, and coppice dune habitats with

correlation coefficients of 0.61, 0.72, 0.63, 0.11, 0.36, respectively (Figure 3.5).

However, these positive correlations were not significant (p < 0.05) based on a Student's

/-test.

Results from the UPGMA cluster analysis revealed certain habitats grouping

together by species composition similarities with a bootstrap support value of at least

0.50 at 1000 iterations (Figure 3.6). The coppice dune and mixed desert scrub habitats

clustered with a bootstrap support value of 0.55 and the three grasslands (creosote

grassland, grama grassland, and yucca grassland) clustered with a bootstrap value of 0.58.

In addition, the acacia hillside, sandy arroyo scrub, and succulent hillside habitats

clustered with a bootstrap support value of 0.71 with two of the habitats, acacia hillside

and sandy arroyo scrub, clustering with a bootstrap support value of 0.85.

Density

Rodent densities were determined per habitat by calculating the number of

captured individuals per hectare (Figure 3.7). Results from the swale habitat exhibited the

highest rodent density value of 39.16 individuals/lia. Other habitats having relatively high

values of rodent density were the acacia hillside (38.82 individuals/ha), Chilopsis arroyo

(33.40 individuals/ha), and creosote grassland (30.04 individuals/ha) habitats. The lowest

rodent density (9.95 individuals/ha) was found in the coppice dune habitat. The grama

48

and yucca grassland habitats also contained relati\ely low rodent densities (17.90 and

21.30 individuals/ha, respectively).

Relationships between vegetation and rodent densities for each habitat were

examined by correlation analyses. Percent cover of vegetation and rodent densit> were

positiveh' correlated (0.67) across all habitats and significant at p < 0.05. In addition,

regression analyses were generated to determine the influence of rainfall on rodent

densities per season. Although there appeared to be a decrease in density for some of the

habitats during low accumulation periods, no significant values (p < 0.05) were found in

the analyses.

Survivability

The proportion of individuals recaptured from the total number of initial captures

was calculated at six-month intervals for each species (Figure 3.8). At six months, 16 of

the total 19 captured species were recaptured. Due to deficient sample sizes, the

following species were excluded from the regression analysis: Spermophilus spilosoma,

Perognathus flavescens, Chaetodipus hispidus. and Reithrodontomys montanus. The

percentage of recaptures per species ranged from 3.3% for Neotoma micropus to 26.1%

for Dipodomys merriami. Thirteen species were recaptured at 12 months with the

percentage of recaptures per species ranging from 0.7% for Sigmodon hispidus to 11.1%)

for Dipodomys spectabilis. Six of the thirteen species were from the family Heteromyidae

and possessed the highest recapture percentages (3.4-11.1 %o). Ten species were

recaptured after 18 months with six of the species from the family Heteromyidae. The

49

species percentages ranged from 0.7% for Peromyscus leucopus and P. maniculatus to

11.1%) for Dipodomys spectabilis.

The results from the regression analysis (Figure 3.9) indicated Neotoma micropus

had the highest exponential rate of decline (r = -0.56) from the beginning to the

completion of the study. Other species with high exponential rates of decline were

Onychomys arenicola (r = -0.39), Sigmodon hispidus (r = -0.37), and Reithrodontomys

megalotis (r = -0.35). Dipodomys merriami had the lowest exponential rate of decline (r

= -0.18) followed by Chaetodipus intermedius (r = -0.185), Dipodomys ordii (r = -0.19),

Perognathus flavus (r = -0.21), and Chaetodipus eremicus (r = -0.21).

Movement

When calculating the average movement traveled by each species, six species were

eliminated on the basis of inadequate sample size: P. flavescens, C hispidus, D.

spectabilis, R. montanus, N micropus, and Spermophilus spilosoma. The mean squared

deviations were calculated from the centroid (median) of activity to each trap station of

capture and averaged for each species (Figure 3.10). The averages among the remaining 13

species differed significantly (p = < 0.001). Onychomys leucogaster had the highest

movement average (3.94 MSD) followed by P. maniculatus (3.87 MSD), D. merriami

(3.81 MSD), O. arenicola (3.72 MSD), and D. ordii (3.71 MSD). The lowest average

movement of 2.50 MSD was exhibited by S. hispidus. Other low average values were

found for R. megalotis and P. flavus with averages of 2.65 and 2.74 MSD, respectively.

50

The averaged mean squared deviations across species also were compared among

the twelve habitats (Figure 3.11). These average movements differed significantiy (p =

0.002). Average movements were highest for small mammals from the acacia hillside

habitat (3.96 MSD). Similar results were found for rodents from the grama grassland and

mixed desert scrub habitats with 3.80 and 3.79 MSD, respectively. Results indicated that

the lowest average movement value was for small mammals from the succulent hillside

habitat with 2.66 MSD. Resuhs were similar with the swale and creosote grassland

habitats (3.06 and 3.26 MSD, respectively). Despite the significant differences found

from the ANOVA generated across species and habitat groups, no significant differences

resulted in the pairwise comparisons within each group.

Discussion

With few exceptions, there appeared to be little difference among diversity values

in reference to trapping period or year within the same habitat type. This may be

expected due to the short duration of the study. The low diversity seen in coppice dune

habitats (mainly D. merriami and D. ordii) was possibly a result of kangaroo rats being

more efficient foragers in open habitats when compared to other species. These findings

are similar to those found by Harris (1984), Kotier (1984), and Kotler and Brown (1988).

In terms of overall species diversity, habitats characterized by high percent

vegetative cover (> 60%)) including the swale, Chilopsis arroyo, sandy arroyo scrub, and

acacia hillside habitats were most significant. The more productive a habitat is, the less

frequently competition occurs among species (Brown, 1975). Conversely, the coppice

51

dune habitat (< 20% vegetative cover) consistently demonstrated a paucity of small

mammals. This is probably a result of coppice dunes being inferior habitat for certain

species. There is little cover and seed-producing plants associated with this habitat and

seed production is the key determinant of rodent species diversity in desert ecosystems

Brown (1975). Diverse communities of small mammals have been found to exist more

frequently in densely vegetated habitats than in sparsely vegetated habitats (Jorgensen,

1996; Brown and Zeng, 1989). In a study of desert rodent communities in the Mojave

Desert, species diversity increased with increasing vegetative cover (Hafner, 1977).

Although the results in the correlation analyses were not significant, the decrease

in rodent diversity observed in some of the habitats during Spring 1998 may be due to the

low average precipitation recorded that season. The fiuctuations of rainfall directly affect

water and forage availability. Water accessibility may play a significant role in

coexistence of desert rodents. The effects of available moisture, vegetative density, and

habitat complexity are intricately involved in determining the diversity of rodent

communities (Christian, 1980; Hafner, 1977).

Rodent density results were similar to those found in the species diversity

analysis. Habitats characterized by dense vegetation (> 60% vegetative cover) contained

higher densities of rodents. The swale habitat was characterized as having the highest

percent vegetative cover (80-100%)) and therefore, exhibited the highest rodent density.

Results from the correlation analyses revealed a significantly positive correlation between

rodent density and percent cover of vegetation. These results of high densities of rodents

in densely vegetated habitats may be due to the rodents' preference to a sufficient

52

availability of seed-producing plams. As noted by Thompson (1982), the mean densities

of seeds and the variation in those densities are greater beneath vegetation. In addition,

the ample amount of vegetation may be beneficial as adequate cover to serve as protection

from predators (Kotler and Brown, 1988).

Results from the correlation analysis revealed a significantly positive correlation

between seasonal rodent density and rainfall. The drought period in Spring 1998 seemed

to have an adverse effect on rodent density in most of the habitats. As stated above,

water availability is crucial to most rodent species. Some species of heteromyids are

known to even slow the processes of reproduction during times of low resource

availability.

As shown by the survivorship analyses, only 2.0 % of the total number of initial

captures across species were recaptured after 18 months. The probability of survival

may vary with individual characteristics and also as a function of various environmental

variables (Lebreton et al., 1992). For example, the family Heteromyidae had 6 out of the

10 species recaptured after 18 months (ranging from 1.6% to 11.1 %o of initial captures).

Their success may be due to certain morphological and metabolic adaptations

characteristic of this family. For example, the genus Dipodomys has many attributes,

such as inflated auditory bullae and bipedal ity, which enhance senses and speed for

avoidance of predators in addition to foraging efficiency. Other members of the family

Heteromyidae, including Chaetodipus sp. and Perognathus sp., are known to aestivate

during times of low seed availability.

53

Higher movement averages were present in the habitats characterized by relativel>

sparse vegetative cover (< 40% cover). These sites were primarily dominated by bipedal

species {Dipodomys sp.) while more densely vegetated sites (> 40.0% cover) contained

primarily quadrepedal species. Some microhabitat theories suggest that morphological

adaptations such as locomotion allow species to utilize specific microhabitats (Price,

1978; Price and Brown, 1983; Kotler, 1984). Large, bipedal kangaroo rats {Dipodomys

sp.) are associated with open microhabitats while small, quadrupedal pocket mice

{Perognathus sp.) are associated with shrubby microhabitat (Harris, 1984). For

Dipodomys merriami the presence of open areas is the most important factor affecting its

distribution (Congdon, 1974).

The high average movements found in Onychomys sp. may be the result of their

characteristic guild. Having a diet consisting of primarily insects requires members of this

genus to travel greater lengths in pursuit of food in comparison to coexisting herbivores.

The low average movement found in S. hispidus may be a result of its herbivore feeding

guild as well. This herbivorous species was predominately found within the swale habitat

which contained the lowest average movement across species and is characterized by

abundant, dense vegetation (> 80% vegetative cover).

As shown by the results from the above parameters, stable population dynamics

cannot be attributed to any single combination of traits (Brown and Zeng, 1989). Species

diversity, rodent density, and survivability cannot be defined based on the occurrence of a

single environmental factor. All ecological components of the desert ecosystem are

intricately intertwined. Vegetative composition, density, and rainfall have all proven to

54

be factors affecting rodent community ecology. The organization of a community and its

patterns of temporal change reflect the fluctuations of species populations that comprise

the community (Brown and Heske, 1990).

55

Literature Cited

Brown, J.H. 1975. Geographical ecology of desert rodents. Pp. 315-341, in Ecology And Evolution of Communities (M. L. Cody & J. M Diamond, eds.). The Belknap Press of Harvard University Press, Cambridge, Massachusetts.

Congdon, J. 1974. Effects of habitat quality on distributions of three sympatric species of desert rodents. Journal of Mammalogy, 55:659-662.

Davis, W.B., and D.J.Schmidly. 1994. The Mammals of Texas. Texas Parks and Wildlife Department, Austin, x + 388 pp.

Findley, J.S. 1987. The Natural History of New Mexican Mammals. University of New Mexico Press, Albuquerque, x + 150 pp.

Findley, J.S. and W. Caire. 1974. The status of mammals in the northern region of the Chihuahuan Desert. Pp. 127-140, in Transactions of the Symposium on the Biological Resources of the Chihuahuan Desert region United States and Mexico (D.H. Riskind and R.H.Wauer, eds.). Sul Ross State University.

Gardner, J.L. 1951. Vegetation of the Creosotebush area of the Rio Grande valley in New Mexico. Ecological Monographs, 21:379-403.

Ghobrial, L.I. and T.A. Nour. 1975. The physiological adaptations of desert rodents. Pp. 413-444., in Rodents in Desert Environments (I.Prakash and P.K. Ghosh, eds.). W. Junk, Publishers. The Hague.

Hafner, M.S. 1977. Density and diversity in Mojave Desert rodent and shrub communities. Joumal of Animal Ecology, 46: 925-938.

Harris, J.H. 1984. An experimental analysis of desert foraging ecology. Ecology, 65: 1579-1584.

Heske, E.J., J.H. Brown, and S. Mistry. 1994. Longterm experimental study of a Chihuahuan Desert rodent community: 13 years of competition. Ecology, 75(2): 438-445.

Jones, C , R. S. Hoffmann, D. W. Rice, M. D. Engstrom, R. D. Bradley, D. J. Schmidly, C. A. Jones, R. J. Baker. 1997. Revised checklist of North American mammals north of Mexico, 1997. Occasional Papers, Museum, Texas Tech University, 173:119.

56

Jorgensen, E.E. 1996. Small mammal and herptofauna communities and habitat associations in foothills of the Chihuahuan Desert. Unpublished Ph.D. dissertation, Texas Tech University, Lubbock, TX.

Kotler, B.P. 1984. Risk of predation and the structure of desert rodent communities. Ecology, 65:689-701.

Kotler, B.P. and J.S. Brown. 1988. Environmental heterogeneity and the coexistence of desert rodents. Annual Review of Ecology and Systematics, 19: 281-07.

Krebs. CJ. 1985. Ecology. Third edition. Harper & Row, Publishers, Inc., New York, x + 800 pp.

Lebreton, J., K.P. Burnham. J. Clobert, and D.R. Anderson. 1992. Modeling survival and testing biological hypotheses using marked animals: a unified approach with case studies. Ecological Monographs, 62(1): 67-118.

Lincoln, R.J., G.A. Boxshall, and P.F. Clark. 1982. A Dictionary of Ecology, Evolution, and Systematics. Cambridge University Press, New York, NY, x + 298 pp.

Longmire, J.L., M. Maltbie, and R.J. Baker. 1997. Use of "lysis buffer" in DNA isolation and its implication for museum collections. Occasional Papers, Museum, Texas Tech University. 163:13.

Matlab V. 5.2. 1998. The Math Works, Inc., Upper Saddle River, NJ.

Milstead, W.W. 1960. Rehct species of the Chihuahuan Desert. Southwestern NaturaHst, 5(2):75-88.

Monasmith, T.J. 1997. Fire effects on small mammals and vegetation of the northern Chihuahuan Desert. Unpublished Master's thesis, Texas Tech University, Lubbock.

Price, M. V. 1978. The role of microhabitat in structuring desert rodent communities. Ecology, 60(2): 4-49.

Price, M.V. and J.H. Brown. 1983. Patterns of morphology and resource use in North American desert rodent communities. Great Basin Naturalist Memoirs, 7: 117-134.

57

Schmidly, D.J. 1974. Factors governing the distribution of mammals in the Chihuahuan Desert region Pp. 163-192, in Transactions of the Symposium on the Biological Resources of the Chihuahuan Desert region United States and Mexico (D.H. Riskind and R.H. Wauer, eds.). Sul Ross State University, Alpine, TX.

Schmidt, R.H. 1986. Chihuahuan climate. Pp. 40-63, in Second symposium on Resources of the Chihuahuan Desert region. (.l.C. Barlow, A.M. Powell. B.N. Timmermann, eds.). Chihuahuan Desert Institution. Alpine, Texas.

Simpson, E.H. 1949. Measurement of diversity. Nature, 163 (4148): 688.

Thompson, S.D. 1982. Microhabitat utilization and foraging behavior of bipedal and quadrupedal heteromyid rodents. Ecology, 63(5): 1303-1312.

Zeng, Z. and J.H. Brown. 1987. Population ecology of a desert rodent: Dipodomys merriami in the Chihuahuan Desert. Ecology, 68: 1238-1340.

58

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62

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67

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CHAPTER IV

SUMMARY

Fort Bliss Military Base is a multi-use, highly active military operation in terms of

training activities, which include the use of tank, missile, and terrestrial combat

procedures. Previous studies have demonstrated how these activities can have adverse

effects on the wildlife populations existing on these military areas (Baumgardner, 1990;

Brattstrom and Bondello, 1983; Carroll et al., 1999; Edwards et al, 1998; Gese et al.,

1989; Shaw and Diersing, 1990; Stephenson et al., 1996). The main objective of this

study was to provide baseline information, which is to be used in the development of a

management plan that will allow training operations to be conducted on the base while

avoiding negative impacts on its ecosystems.

Many of the variables examined in this study were constant between trapping

period and year and no distinct patterns in species diversity or rodent density were

detected among or between habitats. In addition, no habitat was found to possess a

unique fauna. Despite the lack of significant findings, there are suggested

recommendations for managing the military landscape in order to prevent future

conditions that may be of threat to Fort Bliss Military Base's faunal communities.

Some of the habitats analyzed in this study should be used cautiously for military

activities due to their high species diversity and rodent density values. The swale,

Chilopsis arroyo, sandy arroyo scrub, and acacia hillside habitats may be important for

maintaining overall diversity of the rodent community based on results of high species

74

diversity and rodent density. Likewise, as some of these habitats are relatively rare on

the Fort Bliss Military Base, special attention should be given in terms of limiting

training and other military activities that may have an adverse effect on these habitats. In

particular, the swale habitat is one of the rarest habitats on the base and therefore should

be given priority.

Alternatively, one could argue that those habitats possessing low species diversity

or rodent density values could be exploited for military activities because little is risked

in terms of biodiversity. However, some of these habitats are rare, such as the coppice

dune habitat. This habitat represents a fragile community and any disturbance may have

a serious impact. Based on this observation, it is advised that military activities in these

particular habitats be minimal.

Water is a vital resource for rodent populations and this was demonstrated by the

notable decline of species diversity and rodent density in most of the habitats during

extensively dry periods (Spring 1998). Although the correlation analysis results were not

significant, it may be necessary to restrict certain activities following prolonged dry

periods, especially in those habitats given priority due to their rich biodiversity or rarity.

Insights into the dynamics of community composition and species populations

must come from long-term studies (Brown and Heske, 1990). The findings reported by

Heske et al. (1994) in their 13-year desert rodent study presented results that were more

representative of possible fluctuations in present populations. An 18-month study such as

this one cannot provide such justifiable interpretations. For instance, both years of the

study received a higher than normal amount of precipitation and consequently, data could

75

not be obtained for drought years akhough Spring 1998 was an exceptionally dry season.

Fluctuations in precipitation may have an impact on vegetation and therefore alter plant

composition within habitat types over the long term. It is difficult to ascertain if the

results presented in this study are refiective of stable Chihuahuan Desert communities or

if they are isolated occurrences. Therefore, to obtain more accurate data concerning the

interaction between rodent communities and habitat preferences, a long-term project is

suggested. The seasonal temporal fluctuations also are difficult to elucidate without

additional comparative years. Although the results found in this study are informative, a

more long-term project is advised to depict the true characteristics and interactions of

rodent communities and their habitats.

76

Literature Cited

Baumgardner, G. D. 1990. Mammal surveys on land condition trend plots at Fort Hood Texas. Unpublished report for U. S. Army Construction Engineering Research Lab. Department of Wildlife & Fisheries Sciences, Texas A&M University, College Station, TX, 136pp.

Brattstrom, B. H. and M. C. Bondello. 1983. Effects of off-road vehicle noise on desert vertebrates. Pages 167-206 in Environmental effects of off-road vehicles; impacts and management in arid areas (R. H. Webb and H. G. Wilshire, eds.). Springer-Verlag, New York, N.Y.

Brown, J.H. and E. J. Heske. 1990. Temporal changes in a Chihuahuan Desert rodent community. Oikos, 59:290-302.

Carroll, D. S., R. C. Dowler, and C. W. Edwards. 1999. Estimates of relative abundance of the medium-sized mammals of Fort Hood, Texas, using scent-station visitation. Occasional Papers, Museum, Texas Tech University, 188:1-10.

Edwards, C. W., R. C. Dowler, and D. S. Carroll. 1998. Assessing medium-sized mammal abundance at Fort Hood military installation using live-trapping and spotUght counts. Occasional Papers, Museum, Texas Tech University, 185:1-23.

Gese, E. M., O. J. Rongstad, and W. R. Mytton. 1989. Change in coyote movements due to military activity. Journal of Wildlife Management, 53:334-339.

Heske, E.J., J.H. Brown, and S. Mistry. 1994. Long-term experimental study of a Chihuahuan Desert rodent community: 13 years of competition. Ecology, 75: 438-445.

Shaw, R. B. and V. E. Diersing. 1990. Tracked vehicle impacts on vegetation at the Pinon Canyon maneuver site, Colorado. Journal of Environmental Quality 19:234-243.

Stephenson, T. R., M. R. Vaughn, and D. E. Andersen. 1996. Mule deer movements in response to military activity in southeast Colorado. Joumal of Wildlife Management, 60:777-787.

77

APPENDIX

MATLAB FUNCTIONS

% Data preparation for Ft Bliss data

load 'rtbliss.txt'; % Load matrix from text file

[genus,species,id,grid,habitat,trap,sex, weight,season,y ear,distance,datej = ... extrcols(ftbliss); % Separate columns

clear ftbliss; % Delete original matrix

save ftbliss;

% ANOVA of abundances among habitats, separately for each species

nspecies = max(species);

for current_species = 1; %:nspecies % Separate anova for each species i = find(species==current_species); habitat = habitat(i); trap = trap(i); grid = grid(i); season = season(i); odd_trap = mod(trap,2);

uh = unique(habitat); for currenthabitat = 1; %:length(uh) J = find(habitat == uh(current_habitat)); htrap = odd_trap(j); hseason = season(j); hgrid = grid(j);

[hseason hgrid htrap]

aseason = zeros(4*24*2,l); acount = zeros(4* 24*2,1);

h = 0; for hs = 1:4 % Season

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for grid = 1:24 for trappos = 0:1 h = h+l; aseason(h) = hs; acount(h) = sum(htrap==trappos & hgrid==grid & hseason==hs);

end; end;

end; [acount aseasonj

[F,pr,df,ss,ms,varcomp,varprop] = anova(acount,aseason) end: end;

% Comparisons of density among habitats and seasons

cover_by_habitat = [ 1 4 2 5 3 4 3 1 2 4 1 2 ] ;

[species,specid,habitat,trap,date 1 ,date2,date3,month,year] = extrcols(surv2);

[uspecid,freqcapture] = uniquef(specid); nspec = length(uspecid);

hab=[]; spec = [ ]; ici=[J; cover = [ ] ; season = [ ];

for is = 1 :nspec i = find(specid=uspecid(is)); leni = length(i);

m = month(i); y = year(i); s = zeros(leni,l); forj = Irleni

if(isin(ma),[4:6])&yG)=97)

sG) = i; elseif (isin(ma),[8:10]) & ya)=97)

79

s(j) = 2; elseif (isin(mG),[4:6]) & yG)==98)

sG) = 3; else (isin(mG),[8:10]) & yG)==98)

sG) = 4; end;

end;

s = uniquef(s,l); lens = length(s); o = ones(lens,l);

hab = [hab; habitat(i(l))*o]; spec = [spec; speciesG(l))*oJ; id = [id;specid(i(l))*o]; cover = [cover; cover_by_habitat(hab(is))*o]; season = [season; s];

end;

save density;

else load density;

end;

hectares_per_habitat = 8.32;

% Mean density (inds/hectare) per habitat, across seasons

if( i) disp('»> Mean density per habitat');

uhab = uniquef(hab); density = zeros(length(uhab),l);

for is = 1 :length(uhab) i = find(hab=uhab(is));

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uid = uniquef(id(i)); n = length(uid); density(is) = n / hectares_per_habitat;

end;

density end;

% Mean density (inds/hectare) per season per habitat

if(l) disp( '»> Mean density per season per habitat');

uhab = uniquef(hab); nhab = length(uhab);

useas = uniquef(season); nseas = length(useas);

density = zeros(nhab,nseas);

for ih = 1 :nhab i = find(hab=uhab(ih));

idh = id(i); seasonh = season(i);

for is = 1 inseas j = find(seasonh = useas(is)); n = length(idhG)); density(ih,is) = n / hectares_per_habitat;

end; end;

density end;

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% Comparisons of diversity among habitats

iter= 1000;

uspec = uniquef(species, 1); % Number and identities of species nspec = length(uspec); uhab = uniquef(habitat,l); nhab = length(uhab) nseas = 4;

% Correlations among habitats, sum across seasons

if(l) counts = zeros(nspec,nhab); % Allocate species x habitat matrix

for curhab = 1 :nhab % Fill in matrix for curspec = 1:nspec i = find(species=curspec & habitat==curhab); counts(curspec,curhab) = length(i);

end; end; counts

kind = 4; % Diversity measure = 1-D (Simpson) [D,Ddiff,Dpr,E,Ediff,Epr] = diverdiff(counts,kind,iter)

end;

% Comparisons of diversity among habitats

clear; close all;

load ftbliss;

iter= 1000; iter = 50

uspec = uniquef(species, 1); % Number and identities of species nspec = length(uspec); uhab = uniquef(habitat,l);

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nliab = length(uhab) nseas = 4;

% Correlations among habitats, sum across seasons

if(0) counts = zeros(nspec,nhab); % Allocate species x habitat matrix

for curhab = 1 :nhab % Fill in matrix for curspec = 1:nspec

i = find(species==curspec & habitat==curhab): counts(curspec,curhab) = length(i);

end; end; counts

kind = 4; % Diversity measure = 1-D (Simpson) [D,Ddiff,Dpr,E,Ediff,Epr] = diverdiff(counts,kind,iter)

end;

% Rarefaction among habitats

if(0) freq = zeros(nspec,l); % Allocate species frequencies

maxind = 0; for curhab = 1 :nhab % For each habitat, habind = 0; for curspec = 1 :nspec % Get species counts i = find(species=curspec & habitat==curhab); habind = habind + length(i);

end; if (habind > maxind) maxind = habind;

end; end;

ES = zeros(maxind,nhab);

for curhab = 1 :nhab % For each habitat,

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for curspec = 1 :nspec % Get species counts i = find(species==curspec & habitat==curhab); freq(curspec) = length(i);

end; figure; cs = rarefact(freq,[ J,[ ], 1); % Rarefaction putxlab('Number of individuals in habitat'); puttitle(sprintf('Habitat %d',curhab)); ES(1 :length(es),curhab) = es:

end; tofile([[l:maxind]' ES],'Rarefact.txf);

ncum= [ ]; ccum = [ ]; figure; hold on; for curhab = 1 :nhab c = ES(:,curhab); i = find(c==0); if (~isempty(i)) c(i) = [ J;

end; lenc = length(c); plot(l:lenc,c,'k'); text(lenc+1 ,c(lenc),tostr(curhab)); ncum = [ncum; [l:lenc]']; ccum= [ccum; c];

end; putbnd(ncum,ccum); putxlab('Number of individuals in habitat*); putylab('Expected number of species'); puttifle('All Habitats'); hold off;

end;

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% Seasonal differences of diversity within habitats

if(0) counts = zeros(nspec,nseas);

for curhab = 1 :nhab % Cycle thru habitats curhab for curseas = 1 :nseas

for curspec = 1 :nspec i = find(species==curspec & habitat==curhab & season==curseas); counts(curspec,curseas) = length(i);

end; end;

rowsum = sum(counts')'; i = find(rowsum==0); counts(i,:) = [ ]; nrows = size(counts,l);

counts

kind = 4; % Diversity measure = 1-D (Simpson) [D,Ddiff,Dpr,E,Ediff,Epr] = diverdiff(counts,kind,iter)

end; end;

% Correlations of diversity with rainfall across seasons, per habitat

if(l) load rainfall.txt; season_per_rainfall=[l;l;NaN;2;2;2;NaN;NaN;NaN;NaN;NaN;NaN;3;3;NaN;4;4;4];

nrainfall = size(rainfall,2);

counts = zeros(nspec,nseas);

for curhab = 1 :nhab % Cycle thru habitats

curhab for curseas = 1: nseas

for curspec = I: nspec

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i = find(species==curspec & habitat==curhab & season==curseas); counts(curspec,curseas) = length(i);

end; end;

rowsum = sum(counts')'; i = find(rowsum==0); counts(i,:) = [ ]; nrows = size(counts,l):

counts

divers = zeros(nseas,l); evenness = zeros(nseas,l); S = zeros(nseas,l); for curseas = 1: nseas

kind = 4; % Diversity measure = 1-D (Simpson) [divers(curseas),evenness(curseas),S(curseas)] = ...

diversity(counts(:,curseas),kind); end;

figure; X = 1 inrainfall; r = rainfall(curhab,:); subplot(2,l,l); plot(x,r,'k'); putbnd(x,r); putylab('Rainfall'); puttitle(sprintf('Habitat%d',curhab));

d = NaN*ones( I,nrainfall); for curseas = I :nseas

i = find(season_per_rainfall == curseas); d(i) = divers(curseas)*ones(l,length(i));

end; i = find(~isfinite(d)); x(i) = [ ] ; dG) = [ ]; r(i) = [ ];

86

subplot(2,l,2); plot(x,d,'k'); putbnd(x,d); putxlab('Month'); putylab('Diversity');

[rankcorr_rainfall_diversity,prob] = rankcoiT(d.r) end;

end;

% Correlations amonjj habitat-composition vectors

load ftbliss;

iter= 1000;

uspec = uniquef(species, 1); % Number and identities of species nspec = length(uspec); uhab = uniquef(habitat,l); nhab = length(uhab) nseas = 4;

% Correlations among habitats, sum across seasons

if(0) counts = zeros(nspec,nhab); % Allocate species x habitat matrix

for curhab = 1 :nhab % Fill in matrix for curspec = 1 :nspec i = find(species=curspec & habitat==curhab); counts(curspec,curhab) = length(i);

end; end; counts

dist = complcor(counts); upgma(dist); putxlabC I -correlation'); puttitle('UPGMA of habitats by species composition');

87

%[dist,topo,support] = cluster(counts,'complcor',iter,l) end;

% Seasonal differences within habitats

i f ( l ) counts = zeros(nspec,nseas);

for curhab = 1 :nhab % Cycle thru habitats curhab

for curseas = 1:nseas for curspec = 1: nspec

i = find(species==curspec & habitat==curhab & season==curseas): counts(curspec,curseas) = length(i);

end; end;

rowsum = sum(counts')'; i = find(rowsum==0); counts(i,:) = [ J; nrows = size(counts,l);

counts

corrseas = corr(counts) % dist = complcor(counts) % Observed

dist = eucl(counts') % Observed pr = zeros(size(dist)); incr = 1/iter;

for it = 1 liter for is = 1 :nseas

counts(:,is) = counts(randperm(nrows),is);

end; % permdist = complcor(counts);

permdist = eucl(counts'); [ij] = fmd(permdist>=dist); if(~isempty(i)) fork= l:length(i)

pr(i(k)o(k)) = pr(i(k)j(k)) + incr;

88

end; end;

end; pr

end; end;

% Comparisons of home range among habitats

clear; close all;

if (0) % Optionally construct database load surv.txt; load trapcrds.txt;

cover_by_habitat = [ 1 4 2 5 3 4 3 1 2 4 1 2 ] ;

[species,specid,habitat,trap] = extrcols(surv);

[uspecid,freqcapture] = uniquef(specid); nspec = length(uspecid);

hab = zeros(nspec,l); spec = zeros(nspec,l); hr = zeros(nspec,l); id = zeros(nspec,l); cover = zeros(nspec,l);

for is = 1 inspec i = find(specid=uspecid(is)); hab(is) = habitat(i(l)); spec(is) = speciesG(l)); idGs) = specid(i(l)); cover(is) = cover_by_habitat(hab(is));

trapid = trap(i); u = uniquef(trapid); if(length(u)>l)

89

crds = trapcrds(trapid,:); hr(is) = homerange(crds,2);

end; end;

save homerange;

else load homerange;

end;

hr = sqrt(hr); % Sqrt of mean squared deviation from centroid

% Mean homerange across species

if(0) disp('»> Mean homerange across species');

mean_by_species = means(hr,spec) [F,pr,df,ss,ms,varcomp,varprop] = anova(hr,spec) %[pr,H,grp_medians,pr_pairs] = kruskwal(hr,spec,1000)

figure; boxplot(spec,hr, 1); putxlab('Species'); putylab('Grid distribution');

uspec = uniquef(spec); for is = 1 :length(uspec)

i = find(spec==uspec(is)); ifGength(i)>l) figure; histgram(hr(i)); putxlab('Grid distribution'); puttitle(sprintf('Species%d',is));

end; end;

end;

90

°/o Mean cover across habitats

if(0) disp( '»> Mean cover across habitats');

mean_by_habitat = means(hr,hab) [F,pr,dfss,ms,varcomp,varprop] = anova(hr.hab) %[pr,H,grp_medians.pr_pairs] = kruskwal(hr,hab, 1000)

figure; boxplot(hab,hr,l); putxlab('Habitat'); putylab('Grid distribution');

uhab = uniquef(hab); for is = l:length(uhab)

i = find(hab==uhab(is)); if(lengthG)>l) figure; histgram(hr(i)); putxlab('Grid distribution'); puttifle(sprintf('Habitat%d',is));

end; end;

end;

% Mean homerange across cover levels

if(0) disp('»> Mean homerange across cover levels');

mean_by_cover = means(hr,cover) [F,pr,df,ss,ms,varcomp,varprop] = anova(hr,cover) %[pr,H,grp_medians,pr_pairs] = kruskwal(hr,cover,1000)

figure; boxplot(cover,hr, I); putxlab('Cover level'); putylab('Grid distribution');

91

ucover = uniquef(cover); for is = 1 :length(ucover)

i = find(cover==ucover(is)); if(lengthG)>l) figure; histgram(hr(i)); put.\lab('Grid distribution'): puttitle(sprintf('Cover level %d'.is)):

end; end;

end;

% Mean homerange across cover levels, bv species

if(l) disp('>» Mean homerange across cover levels, by species');

uspec = uniquef(spec); for is = l:length(uspec)

disp(sprintf(' » Species %d',is)); i = find(spec==uspec(is)); sample_size = length(i) [ucover,ncover] = uniquef(cover(i)); [m,s] = means(hr(i),cover(i)); cover_sampsize_mean_stderr = [ucover ncover m s]

if (length(ucover)> 1) [F,pr,df,ss,ms] = anova(hr(i),cover(i))

end; end;

end;

% Read matrices containing info about recaptures and trap coords, and % % estimate %home-range sizes

[species,specid,habitat,trap] = extrcols(surv); clear surv;

trapcrds = survtraps(:,2:3);

92

[month,year] = extrcols(dates);

season = zeros(size(month)); i = find(year==97 & (month>=5 & month<=7)); season(i) = ones(length(i),l); i = find(year==97 & (month>=8 & month<=l 1)); season(i) = 2*ones(length(i),l); i = find(year==98 & (month>=5 & month<=7)); season(i) = 3*ones(length(i),l); i = find(year==97 & (month>=8 & month<=l 1)); season(i) = 4*ones(length(i),l);

[uspecid,freqspecid] = uniquef(specid); nspec = length(uspecid);

uhrsize = zeros(nspec, 1); % Home-range sizes uhab = zeros(nspec,l); uspecies = zeros(nspec,l); useason = zeros(nspec,l);

for ispec = 1 :nspec i = find(specid==uspecid(ispec)); t = trap(i); uhab(ispec) = habitat(i(l)); uspecies(ispec) = species(i(l)); useason(ispec) = season(i(l)); uhrsize(ispec) = homerange(trapcrds(t,:));

end;

tofile([uspecies uspecid uhab useason uhrsize],'hrsize.txt',4);

% Read matrices containing info about recaptures and trap coords, and % estimate home-range sizes

load 'hrsize.txt';

[species,specid,habitat,season,hrs] = extrcols(hrsize); clear hrsize;

93

uspecies = uniquef(species,l); uhabitat = uniquef(habitat,l); useason = uniquef(season,l);

nspecies = length(uspecies); nhabitats = length(uhabitat); nseasons = length(useason);

% Homerange size per species per habitat

if(0) results = []; for is = 1 :nspecies

for ih = 1:nhabitats i = find(species==uspecies(is) & habitat==uhabitat(ih)); n = length(i); if (~isempty(i))

results = [results; uspecies(is) uhabitat(ih) n mean(hrs(i)) std(hrs(i))]; end;

end; end; tofile(results,'hrspechab.txt',4);

end;

% Homerange size per species per season

if(l) results = []; for is = 1 :nspecies

for it = 1 :nseasons i = find(species==uspecies(is) & season==useason(it)); n = length(i); if (~isempty(i)) results = [results; uspecies(is) useason(it) n mean(hrs(i)) std(hrs(i))];

end; end;

end; tofile(results,'hrspecseas.txt',4);

end;

94

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