A Comparison of Avian Diversity Metrics in San Joaquin Valley Remnant Riparian Forests

Submitted February 18, 2011

Mark Dettling MS and Christine A. Howell PhD

PRBO Conservation Science

3820 Cypress Drive #11 Petaluma, CA 94954

www.prbo.org

PRBO Contribution # 1798

Suggested citation: M. D. Dettling and C.A. Howell. 2011. A Comparison of Avian Diversity Metrics in San Joaquin

Valley Remnant Riparian Forests. Report to San Joaquin River NWR and Caswell State Park.

PRBO Contribution # 1798.

Introduction

Remnant riparian forest is often used as a benchmark to evaluate riparian restoration efforts. We

surveyed remnant riparian forests throughout the San Joaquin Valley in order to compare metrics

of avian richness and diversity in the region. Vegetation structure and composition were also

quantified in each area. The San Joaquin Valley covers a large area with varied land use history

and with varying types of riparian habitat. Areas included in this regional analysis are the

Cosumnes River Preserve, Mokelumne River, Caswell State Park, San Joaquin River NWR, San

Luis NWR, and along the San Joaquin River below Friant Dam (Figure 1). Data from the latter

two sites were collected in 2004, whereas the other sites were surveyed in 2010. These remnant

forests represent much of the existing riparian forest habitat in the San Joaquin Valley.

Figure 1. Map of areas surveyed for the regional riparian forest analysis.

Study Regions

The regional remnant forest comparison included regions (or rivers) where PRBO has worked in

the past (Cosumnes River Preserve, Mokelumne River, Caswell State Park, San Joaquin River

NWR, San Luis NWR, and along the San Joaquin River below Friant Dam [Figure 1]). All

surveys occurred in riparian forest habitat; the number of points included from each region

varied due to the amount of remnant riparian forest present and the distance between remnant

survey transects (Table 1). Cosumnes surveys occurred at Tall Forest (639117, 4235667 UTM

10S) and Willow Slough (636877, 4235602 UTM 10S). Mokelumne surveys included points east

of the city of Lodi and along the mainstem of the river on private property centered on the

following coordinate (660481, 4226915 UTM 10S). San Joaquin River NWR surveys occurred at

Gardner’s Cove (657741, 4166495 UTM 10S), Hagemann’s Peninsula (659638, 4164954 UTM

10S), and Christman Island (659878, 4165535 UTM 10S). Caswell surveys occurred throughout

the State Park (660499, 4174298 UTM 10S). San Luis NWR surveys occurred in riparian habitat

centered on the following coordinate (697102, 4120580 UTM 10S). Friant surveys occurred at

the DFG’s Willow Unit (255923, 4090261 UTM 11S) and at Cal Mat Cement property (252027,

4087542 UTM 11S). Most bird surveys for the regional analysis occurred during 2010, except

the two southernmost regions (San Luis and Friant) which were surveyed in 2004 (Table 1). Table 1. Number of avian and vegetation survey points and the years data were collected for the regional analyses.

Site

Number of Avian

Survey Points Avian

Survey Year

Number of Vegetation

Survey Points Vegetation Survey Year

Cosumnes 26 2010 15 2010

Mokelumne 27 2010 27 2010

Caswell 15 2010 15 2009

San Joaquin 21 2010 21 2009

San Luis 20 2004 20 2004

Friant 18 2004 18 2003

Methods

Avian Surveys

We compared avian metrics from point count surveys of six remnant forests throughout the San

Joaquin Valley based on data collected in one year. To measure avian performance metrics such

as species richness, diversity, and abundance we used the five-minute, variable circular plot point

count method in which the distance from the observer to each individual detected was estimated.

Detections were estimated within bands of 10m outward to 50m. Three larger bands extended

from 50m to 75m, 75m to 100m, and beyond 100m. We limited analyses to detections within

50m of observers because in some cases the habitat changed outside of the 50m radius (e.g. there

were vineyards or fields beyond 50m). By using the 50m radius we also minimized issues with

observer bias and differences in detectability. We also excluded juveniles and birds flying over

the point that were not directly using the habitat. The type of detection (song, visual, or call) and

any observed breeding behavior (e.g., copulation, material carry, and food carry) was recorded.

Each point was visited twice during the breeding season, at least 10 days apart, between mid-

April and early June according to the protocol outlined in Ralph et al. (1993). Surveys began at

sunrise, in favorable weather conditions (no rain or high winds), and were completed within four

hours.

Transects were surveyed by PRBO biologists with previous experience in songbird field

identification and monitoring methods. In addition, biologists participated in an intensive week-

long training program preceding data collection that included field identification of local bird

species by sight and sound and training in the variable circular plot point count methodology.

Analyses

We calculated abundance, species richness, and diversity for each point. Abundance is simply

the total number of birds detected. Species richness is the total number of species observed

whereas, species diversity measures ecological diversity based on the number of species

detected, weighted by the proportional abundance of each species. A high score generally

indicates high ecological (species) diversity. We calculated the Shannon-Wiener index, which is

symbolized by H' (also called the Shannon-Weaver index or Shannon index; Krebs 1989)

according to the formula below averaged over two visits to each point. pi is the proportion of the

total number of individuals for the i species:

S

1

ii ))(ln( 'Hi

i

pp

We also created species accumulation curves for the regional analysis using the Vegan Package

(Version 1.17-6) in Program R. These curves aid in our understanding of how the species are

distributed throughout a site, as well as if we are capturing the true richness of the site.

We restricted our analyses to landbirds and thus excluded waterbirds, rails, gulls, waterfowl,

introduced species, exotic species, and raptors. From the landbirds we also excluded migratory

species that do not breed in the San Joaquin Valley and Brown-headed Cowbirds (see Appendix

A for scientific names of all species). Because some regions had observations of large

aggregations of various swallow species and Cedar Waxwings, we also excluded these from the

analyses (see Appendix A for complete list of included species).

Vegetation Assessment

The relevé method was used to characterize habitat in terms of plant species composition and

vegetation structure in a 50 meter radius plot surrounding each point count survey station (Ralph

et al. 1993). This method allowed us to relate bird indices with variation in vegetation structure

and composition. General habitat characteristics of the site were recorded, including the percent

cover of each vegetation layer based on plant heights (herb cover = < 0.5 m, shrub cover = 0.5 –

5 m, and tree cover = >5 m). The height of the tallest tree, the height of the lowest live tree

branch (defines bottom of canopy layer), as well as the minimum and maximum tree dbh

(diameter at breast height [1.3m]) were recorded along with the corresponding species. These

characteristics describe the structure of the forest for which certain attributes (closed canopy,

thick understory, etc.) breeding birds cue in on. Means were calculated to compare among sites.

Results

Avian Measures

We observed 100 species across all of the sites of which we included 51 in our analyses. Overall

we see a high degree of agreement in all the measures from the point count data collected at

remnant sites throughout the regions of the San Joaquin Valley (Figures 2-6). The histograms

show the number of survey points (frequency) that had the value of the metric on the x-axis. For

example, in Figure 2 at Cosumnes there were 8 survey points that had between 10-12 birds. The

histograms can then illustrate the approximate mean and the distribution of values at the site.

The distributions of the number of birds detected per point (Figure 2) are very similar across all

of the sites. The majority of survey points had between 10 and 20 birds detected.

Figure 2. Histograms of the total number of birds detected at a point count station for all six remnant riparian

forests.

The number of species detected per point (Figure 3) also show the same patterns with

distributions centered around 4-10 species per point. The Mokelumne region does show a

slightly higher number of species with the majority of points having between 8-12 species per

point. That same pattern occurs when looking at the Shannon-Wiener diversity index (Figure 5).

The mean diversity (Figure 4) is highest at Mokelumne and lowest at San Joaquin River NWR.

Figure 3. Histograms of the number of species detected at a point count station for all six remnant riparian forests

regions.

Figure 4. Patterns in Shannon-Wiener diversity across regions (listed from highest mean Shannon-Wiener diversity

per point to lowest mean Shannon-Wiener diversity per point).

Figure 5. Histograms of the Shannon-Wiener diversity index with the probability density function plot overlaid (red

line) for all six remnant riparian forest regions.

0.0

0.5

1.0

1.5

2.0

2.5

3.0

Div

ers

ity

Max

Mean

Min

The species accumulation curves (Figure 6) show very similar trajectories, indicating that the

species richness is distributed among the survey points of each region in a similar way. By the

time we reach 15 survey points, the rate at which we are detecting new species decreases (the

curve begins to flatten out), reaching the approximate number of species detected in the region.

The one exception is the San Joaquin R. NWR, which appears to continue gaining species as

survey points are added and has not begun to flatten out after 20 points. The Mokelumne region

shows a more rapid increase in the number of species, and a generally higher richness that the

other sites. We ran 500 iterations of each species accumulation curve in order to generate

confidence intervals around each curve; confidence intervals for each region generally

overlapped.

We also show the point at which 25 species have been accumulated. It takes fewer points at

Mokelumne to accumulate 25 species whereas it takes more than twice as many survey points to

accumulate 25 species at San Luis NWR.

Figure 6. Species accumulation curves for all six regions of remnant riparian forest. The dashed line indicates 25

species accumulated

Vegetation Measures

Although each of the regions was selected because they contained remnant forest, the vegetation

analyses show that differences exist in their structure. The amount of tree cover varies from a

low of 13.3% (San Joaquin River NWR) to a high of 80.7% (Caswell). Shrub and herb cover

show a narrower range of values, though still vary. Caswell has the tallest and largest diameter

trees of all the regions, with the shortest at San Luis NWR and the smallest diameter at San

Joaquin River NWR. All of the regions have live tree branches reaching below one meter (low

tree height or bottom of the canopy), meaning the canopy potentially ranges from near the

ground to the tops of the trees.

Within each survey plot the height of the tallest tree was recorded along with the species of that

tree. Similarly, the smallest dbh tree and its species was documented. When interpreting these

results, it is important to keep in mind that only these extreme individuals were measured at a

single vegetation plot. Therefore, we see at Cosumnes (Table 2) the tallest trees were always

Quercus lobata, but at Caswell two thirds of the plots had Quercus lobata as the tallest tree and

the other third had Populus fremontii or Salix gooddingii as the tallest tree. The tallest trees on

each survey plot were dominated by three species (Quercus lobata, Populus fremontii, and Salix

gooddingii) with a few others represented in some regions. There is more species variation in the

youngest (minimum dbh) trees, hinting that the regions are not homogeneous. Quercus lobata is

common at Cosumnes and San Joaquin R. NWR, Acer negundo dominates at Caswell, and at San

Luis NWR Salix gooddingii is very common. The Mokelumne region has a lot of Salix exigua

and the vine Vitis californica, and the Friant region’s small trees are mostly Salix exgua and

Salix gooddingii.

Table 2. Summary of vegetation characteristics for the regional remnant riparian forest analyses. COSU=Cosumnes,

SAJO=San Joaquin R. NWR, CASW=Caswell, MOKE=Mokelumne, FRIA=Friant, and SALU=San Luis.

Characteristic COSU SAJO CASW MOKE FRIA SALU

Mean tree cover (%) 49.7 13.3 80.7 41.5 25.5 33

Mean shrub cover (%) 66 62.4 50.3 50.5 59.7 54.2

Mean herb cover (%) 33.7 29.8 13.7 15.5 39.7 59

Bottom of tree canopy (m) 0.44 0.66 0.03 0.38 0.89 0.35

Mean high tree height (m) 19.9 14.7 38.3 24.4 17.9 11.3

Mean minimum tree dbh (cm) 14.7 9.6 3.3 4.8 9.2 19.1

Mean maximum tree dbh (cm) 73.2 51.7 115.3 88.7 63.6 82.8

Mean top of tree canopy height by species (m; % of survey points)

Quercus lobata 19.9(100%) 20.8(52.4%) 38.5(67%) 20.5(14.8%) 22(27.8%)

Populus fremontii 18.0(14.3%) 38.5(26.6%) 26.9(55.5%) 22.5(22.2%) 13(5%)

Salix gooddingii 12.5(9.5%) 35.0(6.6%) 13(3.7%) 14(16.7%) 11.2(95%)

Fraxinus latifolia 19.2(14.8%)

Juglans californica 28(11.1%)

Platanus racemosa 16(27.8%)

Mean minimum tree dbh by species (m; % of survey points)

Quercus lobata 29.2(33.3%) 24.3(33.3%) 7.8(7.4%) 11(16.7%)

Populus fremontii 10.2(11.1%)

Salix gooddingii 13(13.3%) 3.2(19%) 9.2(27.8%) 19.7(95%)

Fraxinus latifolia 7(26.7%) 3(6.7%) 15(11.1%)

Acer negundo 6(20%) 3.7(46.7%) 6.5(7.4%)

Salix exigua 3.8(23.8%) 3(13.3%) 3.4(22.2%) 7.2(27.8%) 8(5%)

Salix lasiolepis 3(6.7%) 3.4(18.5%)

Juglans californica 4(6.7%)

Platanus racemosa 10(11.1%)

Vitis californica 2.5(26.7%) 1.3(22.2%)

Arundo donax 2.4(3.7%)

Alnus rhombifolia 16(3.7%)

Sambucus nigra 5(3.7%)

Discussion

Avian Measures

We conducted a regional analysis using point count survey data from throughout the San Joaquin

Valley at locations we thought were representative of remnant riparian habitat in the Valley. We

generally found minimal differences among the community metrics in the six regions. Richness

and diversity of birds were similar among the regions, with the Mokelumne region averaging the

highest richness and diversity per point and San Joaquin River NWR averaging the lowest

richness and diversity per point (Figure 4).

We also created species accumulation curves for each region. The trajectories of the curves for

each region shed light onto the differences in species richness among point count locations

within a region. The more unique species each point count location has within a region the more

rapid the slope and acceleration of the curve. The curves for most of the regions follow a similar

trajectory of increase and then begin to flatten out, although they end at a slightly different

species accumulation total (Figure 6). Although Mokelumne had the greatest richness and

diversity per point (Figure 4), the San Joaquin River NWR species accumulation curve shows a

more rapid acceleration (whereas curves for other sites began to level off after 15 points had

been sampled) indicating that with additional sampling, species richness may be highest at the

San Joaquin River NWR (among the regions we sampled).

Overall our results suggest more than 28 points should be sampled of remnant forest in any

region in order to sample enough points for an accumulation curve to level off (and hence to

adequately capture the remnant riparian forest community in the sampling). However, the

amount of remnant riparian habitat (and hence locations to establish points) are often limited in

riparian systems, especially in the San Joaquin Valley. Another factor that could contribute to

the observed differences among the six regions are differences in the surrounding landscape

(Howell et al. 2000, Bernhardt 2005).

Vegetation Measures

The vegetation analyses revealed that although we chose surveys within remnant riparian habitat,

the vegetation structure and composition was variable among regions. Riparian forests in the

Central Valley are characterized by a high degree of canopy cover, created by large trees, with a

thick, lush understory. Our study regions showed a wide range of canopy cover, with the San

Joaquin River NWR and Friant regions (Table 2) being the most sparsely treed. The amount of

shrub cover is much more consistent throughout our study regions. The quality of remnant

habitat accounts for some of the canopy cover variation, but the successional stage and type of

woody vegetation also play a role. Remnant areas affected by river scouring and fires will have

younger, shorter vegetation. Our definition of the tree layer (a woody plant at least 5m tall),

which is really a structural category, means that smaller tree species are accounted for in the

shrub layer.

The largest trees at each survey point tended to be one of three species (Quercus lobata, Populus

fremontii, and Salix gooddingii), which are native and common to riparian areas in the San

Joaquin Valley. The species represented with this measure do not encompass the entire tree

diversity of each region, but rather give us an idea of which species are dominant. More diversity

is captured when reviewing the species of trees with the smallest dbh. These obviously tend to be

the species that are smaller in general, but also we see some of younger dominant species.

Connections between the avian and vegetation metrics in the San Joaquin Valley are difficult to

decipher because of differences among regions. The most consistent difference is that the

Mokelumne region has generally higher values for the avian metrics. The region has an average

amount of canopy cover dominated by Populus fremontii (Table 2), which is typically associated

with high quality riparian habitat. The diversity of dominant trees and small trees in the region

appears to be higher than the other regions as well. These factors may indicate that the remnant

habitat we included in the analysis from the Mokelumne River is high quality, hosting a larger

number and diversity of bird species.

Summary

Our results suggest that there is spatial variation in avian and vegetation measures of remnant

riparian forest in the San Joaquin Valley. When using avian metrics to evaluate riparian forest

restorations, it is important to compare them to a remnant site which shares characteristics

(location and vegetation structure) of the expected restoration outcome. Alternately there may

also be annual variation in the avian metrics, requiring additional years of data collection to draw

accurate conclusions. We also found that to capture the true richness of an area, about 28 sites

need to be surveyed. Future studies should consider this in their design.

Acknowledgements

We would like to thank the staffs of Caswell State Park and San Joaquin River NWR for

allowing us to conduct surveys on their lands, especially Joanne Karlton, Eric Hopson, Bob

Parris, and Kim Forrest. Thanks to the PRBO staff and interns for help with the field work,

including Amber Wingert, Matt Rogers, Ryan DiGaudio, and Andy Pfeffer. Thanks to San

Joaquin County Resource Conservation District for facilitating our surveys along the

Mokelumne River.

Literature Cited

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Clayton, C. Dahm, J. Follstad-Shah, D. Galat, S. Gloss, P. Goodwin, D. Hart, B. Hassett,

R. Jenkinson, S. Katz, G. M. Kondolf, P. S. Lake, R. Lave, J. L. Meyer, T. K. O'Donnell,

L. Pagano, B. Powell, and E. Sudduth. 2005. Synthesizing U.S. river restoration efforts.

Science 308: 636-637.

Howell, C. A., S. C. Latta, T. M. Donovan, P. A. Porneluzi, G. R. Parks, and J. Faaborg. 2000.

Landscape effects mediate breeding bird abundance in Midwestern forests. Landscape

Ecology 15: 547-562.

Krebs, C.J. 1989. Ecological Methodology. Harper and Row Publishers, New York, New York:

654 pp.

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methods for monitoring landbirds. Gen. Tech. Rep. PSW-GTR-144. Albany, CA.

Appendix A. Common and scientific names of all birds observed in the San Joaquin Valley

as part of the regional analyses. An X in the Regional Analysis column indicates that it was

included in our analyses.

Common Name Scientific Name Regional analysis Acorn Woodpecker Melanerpes formicivorus X

American Bittern Botaurus lentiginosus

American Coot Fulica americana

American Crow Corvus brachyrhynchos X

American Goldfinch Carduelis tristis X

American Kestrel Falco sparverius

American Robin Turdus migratorius X

American White Pelican Pelecanus erythrorhynchos

Anna's Hummingbird Calypte anna X

Ash-throated Flycatcher Myiarchus cinerascens X

Barn Swallow Hirundo rustica

Belted Kingfisher Ceryle alcyon

Bewick's Wren Thryomanes bewickii X

Black-chinned Hummingbird Archilochus alexandri X

Black-headed Grosbeak Pheucticus melanocephalus X

Black Phoebe Sayornis nigricans X

Black-throated Gray Warbler Dendroica nigrescens X

Blue Grosbeak Passerina caerulea X

Brewer's Blackbird Euphagus cyanocephalus X

Brown-headed Cowbird Molothrus ater

Bullock's Oriole Icterus bullockii X

Bushtit Psaltriparus minimus X

California Quail Callipepla californica X

California Thrasher Toxostoma redivivum X

California Towhee Pipilo crissalis X

Canada Goose Branta canadensis

Cassin's Vireo Vireo cassinii

Cedar Waxwing Bombycilla cedrorum

Cliff Swallow Petrochelidon pyrrhonota

Common Yellowthroat Geothlypis trichas X

Cooper's Hawk Accipiter cooperii

Double-crested Cormorant Phalacrocorax auritus

Downy Woodpecker Picoides pubescens X

European Starling Sturnus vulgaris

Gadwall Anas strepera

Golden-crowned Sparrow Zonotrichia atricapilla

Great Blue Heron Ardea herodias

Great Egret Ardea alba

Common Name Scientific Name Regional analysis

Green Heron Butorides virescens

Hermit Warbler Dendroica occidentalis

Horned Lark Eremophila alpestris

House Finch Carpodacus mexicanus X

House Wren Troglodytes aedon X

Hutton's Vireo Vireo huttoni X

Killdeer Charadrius vociferus

Lark Sparrow Chondestes grammacus X

Lazuli Bunting Passerina amoena X

Lesser Goldfinch Carduelis psaltria X

Loggerhead Shrike Lanius ludovicianus

MacGillivray's Warbler Oporornis tolmiei

Mallard Anas platyrhynchos

Marsh Wren Cistothorus palustris X

Mourning Dove Zenaida macroura X

Nashville Warbler Vermivora ruficapilla

Northern Flicker Colaptes auratus X

Northern Harrier Circus cyaneus

Northern Mockingbird Mimus polyglottos X

Northern Rough-winged Swallow Stelgidopteryx serripennis

Nuttall's Woodpecker Picoides nuttallii X

Oak Titmouse Baeolophus inornatus X

Orange-crowned Warbler Vermivora celata

Oregon Junco Junco hyemalis

Osprey Pandion haliaetus

Pacific-slope Flycatcher Empidonax difficilis X

Phainopepla Phainopepla nitens

Pied-billed Grebe Podilymbus podiceps

Red-shouldered Hawk Buteo lineatus

Red-tailed Hawk Buteo jamaicensis

Red-winged Blackbird Agelaius phoeniceus X

Ring-necked Pheasant Phasianus colchicus

Ruby-crowned Kinglet Regulus calendula

Song Sparrow Melospiza melodia X

Spotted Towhee Pipilo maculatus X

Swainson's Hawk Buteo swainsoni

Swainson's Thrush Catharus ustulatus X

Townsend's Warbler Dendroica townsendi

Tree Swallow Tachycineta bicolor

Tricolored Blackbird Agelaius tricolor X

Turkey Vulture Cathartes aura

Unidentified Blackbird Agelaius spp.

Common Name Scientific Name Regional analysis

Unidentified Hummingbird

Unidentified Woodpecker

Virginia Rail Rallus limicola

Warbling Vireo Vireo gilvus X

Western Bluebird Sialia mexicana X

Western Kingbird Tyrannus verticalis X

Western Meadowlark Sturnella neglecta X

Western Scrub-Jay Aphelocoma californica X

Western Tanager Piranga ludoviciana X

Western Wood-Pewee Contopus sordidulus X

White-breasted Nuthatch Sitta carolinensis X

White-crowned Sparrow Zonotrichia leucophrys

White-faced Ibis Plegadis chihi

White-tailed Kite Elanus leucurus

Wild Turkey Meleagris gallopavo

Willow Flycatcher Empidonax traillii X

Wilson's Warbler Wilsonia pusilla

Wood Duck Aix sponsa

Wrentit Chamaea fasciata X

Yellow-billed Magpie Pica nuttalli X

Yellow-breasted Chat Icteria virens X

Yellow-rumped Warbler Dendroica coronata

Yellow Warbler Dendroica petechia X