Extinction risk models

Prepared by:
Tracey J. Regan

For

Southwest Fisheries Science Center

January 2006
Introduction
In June 2004 NOAA Fisheries established a Steering Committee and a Quantitative Working
Group (QWG) to work toward developing quantitative procedures that will make listing decisions
under the Endangered Species Act (1973) more transparent, consistent, and scientifically and
legally defensible. A recommendation from the QWG was that final decisions regarding listing
criteria and decision metrics be made in the context of performance testing. Performance testing
involves an assessment of alternative listing criteria and decision metrics for a given listing
criterion. It involves utilizing the outcomes of a set of population models for hypothetical but
realistic representations of species dynamics in order to assess how alternative quantitative listing
criteria and decision metrics perform.

This document outlines some existing population models that could be utilized in the
performance testing phase of the project. The existing models represent a large variety of species
with different life history traits and population dynamics, habitat preferences, ecological
specialization, distribution, threats and the occurrence and response to disturbance or
catastrophes. The existing models are made up of a set of real species and a set of hypothetical
species with realistic representations of species population dynamics. The remainder of this
document describes all the available models for the real species and the hypothetical species. In
addition, descriptions of all the real species, including life history traits, habitat requirements,
response to disturbance and threats are provided.

Existing models
Twenty models in total are available that either simulate real species or hypothetical species
(Table 1). For the real species, 12 population models exist. These models were developed in
independent studies and for various reasons, often to determine the outcome of management
strategies and to perform sensitivity analysis. All models have been peer reviewed and either
published in international journals, as book chapters, PhD theses, or as government reports. The
majority of the models for the real species use RAMAS GIS (Akcakaya 2001) or RAMAS
Metapop (Akcakaya & Root 2002), part of the suite of RAMAS software development tools for
building stochastic metapopulation models and habitat suitability models. The population for
Grevillea caleyi is an individual based model written in Fortran (Regan et al. 2003) while the
model developed for the Orange-bellied parrot uses Turbo Pascal (McCarthy 1996; Drechsler
1998).
Various aspects are common to all the models for the real species. All are structured models,
including demographic information on the age or stage classes of the species. Each model is
stochastic and includes both demographic and environmental stochasticity. All the models include
density dependence functions that are thought to be appropriate for the species, as either
scramble, contest or ceiling competition. Two plant models (Grass Tree and the Monkey-puzzle
Tree) have stage specific density dependence to incorporate shading of smaller plants by larger
individuals. Competition in the Grevillea model was a reduction in growth due to shading of
nearby plants.

Perceived threats and catastrophes are included in the models for the real species where
appropriate. The invertebrates and the Spotted-tailed quoll are subject to future land clearing
which will destroy their habitat. This is modeled as deterministic change in habitat quality (i.e.
change in carrying capacity) over time. The Giant velvet worm is also threatened by wildfires
that destroy the microhabitat. The plant species inhabit fire prone areas and the Sindh ibex is
subject to monsoons. These factors have been modeled as probabilistic occurrences that impact
each species differently but appropriately. While fire promotes germination for the Grass tree and
the Grevillea, it also increased mortality in standing plants. Fire increased mortality of immature
Monkey Puzzle tree individuals. Disease is thought to be an important factor for both the Grass
tree and the Florida scrub jay and have been incorporated into the population models. Disease is
subsumed into the vital rates for the Grass tree model while for the Florida scrub-jay, disease is
modeled as a probabilistic event that affects the abundances of different stage classes of the
species. The Monkey puzzle tree is also subject to seed harvest that is modeled as a portion of the
available seeds harvested each year.

The population models for all the real species are spatially explicit and function as
metapopulations unless movement and spatial correlations were considered unimportant or
negligible for the species (i.e. plants with very low seed dispersal) or there only exists one
population. The metapopulation structure for many of the population models were based on
habitat models for the species that identified suitable habitat patches within the study area. These
suitable patches were then delineated as separate sub-populations within a metapopulation
structure connected by dispersal events appropriate for each species (Akcakaya 2001). The
models for the real species that included specific habitat models for patch identification were: the
Stag beetle, Giant velvet worm, Monkey puzzle tree, Florida scrub-jay, Sindh ibex, Spotted-tailed
quoll and the Desert Tortoise. The Helmeted honeyeater and the Orange-bellied parrot each have
only a single breeding population. A habitat model is not necessary in these cases. However, the
Helmeted honeyeater lives in territories and these have been modeled explicitly.

Eight models exists for hypothetical species that had sufficient detail such that they could be
considered as being representative of real species. Very detailed population models with various
life history attributes and characteristics were written for each of the hypothetical species. The
characteristics considered were inbreeding depression, deterministic trends in abundance, trophic
dynamics, and dynamics in response to weather, although not all features were included in all the
models (Table 1). This is partly to ensure that there was some diversity in the combination of the
attributes. All hypothetical species were developed by Michael McCarthy either in C or in
RAMAS Metapop and published in (McCarthy et al. 2004).
 Table 1: Summary of existing models for the real and hypothetical species

Age or stage based Spatially Density

Real species: common name Model Platform Threats Reference
explicit dependence
Stag beetle RAMAS GIS2 Yes Yes Scramble Habitat destruction (Fox et al. 2004)
Giant velvet worm RAMAS GIS Yes Yes Scramble Habitat destruction and fire (Fox et al. 2004)
Keeled snail RAMAS GIS Yes Yes Scramble Habitat destruction (Regan & Bonham 2004)
Caley’s grevillea Fortran Individual based Yes Individual based Fire, seed predation (Regan et al. 2003)
Monkey puzzle tree RAMAS GIS Yes Yes Stage specific Fire and seed harvest (Bekessy et al. 2004)
Grass tree RAMAS Metapop Yes No Stage specific Fire/disease (Regan 2004)
Florida scrub-jay RAMAS Metapop Yes Yes Contest Disease (Root 1998)
Helmeted honeyeater RAMAS Metapop Yes Yes Contest - (McCarthy 1996)
Orange-bellied parrot OBPRA Yes No Contest Wind farms (Drechsler 1993, 1998, 1999)
Sindh ibex RAMAS GIS Yes Yes Scramble Monsoons (Yamada et al. 2003)
Spotted-tailed quoll RAMAS GIS Yes Yes Contest Habitat destruction, inbreeding depression (Fox et al. 2004)
Desert tortoise RAMAS Metapop Yes Yes Ceiling - (Root 1999)
Spatially Density
Hypothetical species Model Platform Threats Reference
explicit dependence
Butterfly C Yes Yes Scramble - (McCarthy et al. 2004)
Snail C Yes Yes Scramble (McCarthy et al. 2004)
Shrub C Yes Yes Scramble Fire (McCarthy et al. 2004)
Herb C Yes No Scramble - (McCarthy et al. 2004)
Owl RAMAS Metapop Yes Yes Contest Habitat destruction (McCarthy et al. 2004)
Small mammal C Yes No Contest - (McCarthy et al. 2004)
Salmon RAMAS Metapop Yes Yes Contest Harvesting (McCarthy et al. 2004)
Frog C Yes No Scramble - (McCarthy et al. 2004)
Descriptions of Real Species
Invertebrates

Simson stag beetle (Hoplogonus simsoni)

Simsons stag beetle (Hoplogonus simsoni) (Plate 1) is a flightless

black beetle endemic to north-east Tasmania, Australia. Stag
beetles have two life stages, larval and adult. The larvae are
edaphic (soil dwelling), feeding on organic matter within the soil.
Adult stag beetles do not feed but spend their time wandering
amongst leaf litter in search of mates. The longevity of the larval
stage is approximately 2 years and adults live for about 1-2 years.

Plate 1: Simson Stag Beetle

Drawing by Karen Richards H. simsoni appears to be confined to wet sandy clay soils in a cool
moist stable microclimate with the absence of recent wildfire.
Optimal habitat for the beetle has been defined as wet eucalypt forest below 300m elevations with
a deep leaf litter at a slope of <5 degrees. Since European settlement, there has been gradual
reduction in the area occupied by H. simsoni. The main current threat to the H. simsoni is habitat
destruction through anthropogenic disturbance in the form of either plantation conversion or
clearfelling and regeneration burning. Plantation is unsuitable habitat for H. simsoni and will
result in local extinctions. However, native regeneration is likely to support beetle populations
once niche attributes have developed.

Giant velvet worm (Tasmanipatus barretti)

The Giant velvet worm (Tasmanipatus barretti)

(Plate 2) is a member of the Phylum Onychophora. It
was first discovered approximately 60 years ago
(Barrett 1938). Species of this Phylum are of
exceptional evolutionary interest because they are
considered intermediates or “missing links” between
two major invertebrate groups, the arthropods
(jointed invertebrates) and annelids (worms).
Plate 2: Giant Velvet Worm
Drawing by Karen Richards

Velvet worms are carnivorous and predatory, feeding

on insects and other litter-dwelling invertebrates such as termites, crickets and amphipods. Giant
velvet worms live in colonies and are largely restricted to moist habitats. Their ideal
microhabitats are deep within large decaying eucalypt logs (Mesibov 1988). They are known to
disperse and recolonize although this is very slow (Mesibov, pers. comms.).

T. barretti is endemic to northeast Tasmania, Australia and is currently restricted to an area of

about 610 km2. It occurs from near sea level to about 500 m elevation in wet and dry forest types.
Densities of T. barretti are highly uncertain but it is estimated that, across its range, the average
overall density is around 80 individuals per hectare but could be as low as zero and as high as 400
individuals per hectare in some areas (Mesibov, pers comm.).

The main threat to T. barretti is habitat destruction. The area occupied by T. barretti is managed
by Forestry Tasmania and is within timber production forest. Conversion of native forest to
plantation (eucalypt tree farm or pine plantation) destroys the rotting log micro-climate and
eliminates Giant velvet worm populations. Clearing of forest for agriculture will also result in
loss of log and litter layers. Other potential threats to Giant velvet worms are frequent fires and
high intensity fires, which also eliminate the decaying log habitat. Giant velvet worms can,
however, survive selective logging as well as low intensity regeneration fires because the rotting
log environment is generally undisturbed by these activities (Mesibov 1988; Horner 1998).

Keeled snail (Tasmaphena lamproides)

Tasmaphena lamproides (Plate 3) is a carnivorous

land snail that occurs predominantly in northwest
Tasmania (Bonham & Taylor 1997) and is one of
at least two species in the genus Tasmaphena. It is
found in wet forest and requires deep leaf litter to
survive. It is usually found under logs or in the
Plate 3: Keeled Snail (Tasmaphena lamproides)
Photo by Fred Koolhof litter at the base of trees, or in leaf litter in ditches
and depressions. T. lamproides requires food
supplies including calcium for shell growth (usually obtained from the shells of dead snail species
or from the soil), moisture, shelter from predators and protection from adverse weather (Bonham
& Taylor 1997).
The extent of habitat for the species covers an area of approximately 290 km2 with an occupied
area of roughly 140 km2. Densities range between 12-25 individuals per hectare depending on
habitat quality. Prior to European settlement, the major source of disturbance to T. lamproides
was fire. Recently, an additional source of disturbance to populations of T. lamproides has been
logging and conversion of native forest to plantations. Logging and fires are likely to kill
individuals that experience direct disturbance. However, snails probably survive in streamside
reserves and 100 m wide wildlife habitat strips that are present between logging areas in some
locations. T. lamproides tends not to occur in young native forest regrowth, probably due to
inadequate levels of litter and associated absence of invertebrates. Older regrowth, however, is
just as supportive as old growth and the species is known to recolonise areas following
disturbance, once the necessary niche attributes have developed.

Plants

Caley’s grevillea (Grevillea caleyi)

Grevillea caleyi (R. Br.) (Plate 4) is an

understorey shrub of eucalypt forest from fire-
prone habitats in northern Sydney, Australia.
It is a bushy shrub up to 5 × 5 m requiring
unique laterite soils. The life span ranges
between 16-30 years with plants producing
seeds in the first 2-4 years.

Plate 4 Grevillea caleyi

This species has a very complex relationship
Photo courtesy of D. Keith
with fire. Standing plants of G. caleyi are
killed by fire, which also promotes the breaking of dormancy in seeds in the soil seed bank.
Successful establishment of seedlings is very rare in the absence of fire, unless there has been
some other disturbance, such as clearing. Populations of G. caleyi may be eliminated if fires
occur when seed availability is low. Populations are also eliminated (including seeds in the seed
bank) if there are three successive years with fire.

Grevillea caleyi is endemic to New South Wales, Australia with a highly restricted geographic
area (approximately 6 km × 6 km) and area of occupancy (less 5 km2). There are approximately
21 known patches that are remnants of former populations. The patches result from fragmentation
of the landscape by major roads and urbanization (Scott & Auld 1998; NSW NPWS 1999).
The number of individuals is highly variable, fluctuating widely over a short period of time in
response to fire. The species will persist as seed in the soil and after a future fire there may be a
significant recruitment of seedlings (NSW NPWS 1999).

Habitat loss is still continuing and threatens the survival of many of the remaining patches of G.
caleyi. These existing remnant patches of G. caleyi are subject to a number of threats, including
inappropriate fire regimes, weed encroachment and disturbance by rubbish dumping and clearing
(Auld & Scott 1996). Only one and part of another subpopulation are within the boundaries of the
National Park system. The remainder are threatened by clearing (Keith & Ilowski 1999). All
subpopulations are exposed to adverse fire regimes and seed predation. An isolated fire event
usually burns a whole population or part there of. Some remnant patches are burnt in major
wildfires or in hazard reduction burns to protect life and property, while others, isolated from
nearby large patches of remnant vegetation by urban areas, are rarely burnt.

Monkey puzzle tree (Araucaria araucana)

Commonly known as the Monkey puzzle tree, Araucaria

araucana (Molina.) K. Koch (Plate 5) is an impressively
large and long-lived conifer, attaining 50 m in height, 2.5
m in girth and reaching ages of at least 1,500 years
(Montaldo 1974). Originating around 60 million years ago
Araucaria araucana is one of two members of the genus
Araucaria occurring in South America and one of 19
species world-wide.

The ecology of the Monkey puzzle tree is disturbance-

Plate 5: Araucaria araucana: driven, principally by volcanism, fire, landslides and wind.
Photo by S. Bekessy
The species has developed effective adaptations, such as
thick bark and epicormic buds, to survive such disturbances (Veblen 1982), although only large
trees (> 30 cm diameter at breast height) tend to survive major disturbances (Burns 1993).

A. araucana occurs over a very wide ecological range across Chile and Argentina (Veblen 1982).
It grows on a wide range of soils, from well-developed soils derived from metamorphic or
sedimentary rocks to incipient soils on recent volcanic ash deposits (Armesto et al. 1996).
Populations range in size from small fragmented groups of only several trees to dedicated
national parks of tens of thousands of hectares. Highly fragmented populations exist outside
National Parks in both Chile and Argentina, but are most common in the Argentinian steppe.

Monkey-puzzle is generally dioecious, but may occasionally be monoecious with predominantly

gravity dispersed seed and wind dispersed pollen. Both seed and pollen are relatively heavy and
generally do not disperse over large distances (Munoz 1984). Seeds generally fall between 2 to
13 m from the mother tree and are heavily preyed upon by parakeets, rodents, people, goats and
cattle. The seed are viable for 1 year only; hence there is no seed bank. The sex ratio of
Monkey-puzzle is approximately 1:1 and trees reach reproductive maturity as young as 30 years
(Armesto et al. 1996), but usually take much longer (>200yrs) if suppressed as seedlings.
Maximum ages estimated at over the 1500 years recorded in tree ring studies. Between 30 to
100% of sexually mature females produce seed each year and the number of cones per tree varies
between 1 to 30. Cones contain between 30 to 300 seeds, but trees only have an abundant seed
crop once every 2 to 5 years (Munoz 1984).

Although a number of Monkey Puzzle populations are protected within National Parks or
reserves, human impact is very evident, including the effects of cattle grazing, introduced species,
human-lit fires, intensive tourism and harvesting of seeds and occasionally timber (Aagesen
1998). Levels of regeneration are low for most stands and the increased frequency of fires has
resulted in few representatives of middle size classes. There are also natural demographic factors,
such as a slow life cycle, variation in annual seed production and the short period of seed
viability, that could also threaten the species. Additionally, restriction to small isolated reserves
can jeopardise survival in the event of catastrophic events, such as volcanic eruptions (Farjon &
Page 1999).
Grass tree (Xanthorrhoea resinifera)

Xanthorrhoea resinifera (Sol ex Kite) E. C. Nelson & D. J.

Plate 6: Xanthorrhoea resinifera
Photo courtesy of D. Keith
Bedford (Plate 6) is one of approximately 32 species of the
genus Xanthorrhoea, which is also known commonly as
the Grass tree. It is a long-lived perennial (≈ 300 years),
which grows to approximately 2 m in height and when it
matures, develops a trunk that can exist either above or
below the ground. It has frond-like leaves and produces a
tall flowering spike that grows from the top of the grassy
head of the plant. It inhabits heathland areas around
Sydney and in particular the Royal National Park just south
of Sydney, Australia.

Fire plays a dual role in the population dynamics of the species. It causes some mortality of
seedlings and mature plants with above ground stems, and triggers flowering and seed production
in mature plants (Keith & Tozer in review). It appears that X. resinifera only flowers after a fire
event with individuals first producing flowers at around 50-70 years of age. Rain is also a key
factor in the survival of the species, especially for germinants. For a germinant to survive, the
rainfall needs to be greater than the average rainfall of 1000 mm for the year in which the seed
germinates (Tootell 1998).

There are several threats to Xanthorrhoea resinifera. Phytophthora cinnamomi, a pathogen that
reduces survivorship of established plants, is a potential threat as it is known to kill other
Xanthorrhoea species. Recently Phytophthora cinnamomi was isolated from the roots of dying
plants at several sites within the National Park. The disease seems to be causing slow attrition
especially in plants that have an above ground trunk. Inappropriate fire regimes and seed
predation are also threats that can reduce survival and recruitment of the species although fire is
essential for flowering. A further threat may be posed by commercial harvesting driven by the
cultural and economic value of Xanthorrhoea as ornamental plants.
 Birds

Florida scrub jay

The Florida scrub jay (Bosc, 1795) (Plate 7) is a 30 cm-long

blue and grey crestless jay. It is one of three species in the
genus Aphelcoma (Woolfenden & Fitzpatrick 1984) with the
Florida scrub jay being one of approximately 11 subspecies of
Scrub Jay. It is thought that senescence occurs after age 16
years making the Florida scrub jay the longest-lived passerine
species for which extensive data (approximately 30 years) are
available (Woolfenden & Fitzpatrick 1984).

Plate 7: Florida Scrub-jay. Florida scrub jays are endemic to Florida and require well-
Photo by R. Curry.
drained oak scrub habitat that has little or no canopy with bare
open patches of sand. Scrub Jays usually nest near the ground and prefer less cover for better
visibility of predators and ease of movement (Woolfenden & Fitzpatrick 1984). Scrub jays are
omnivores, feeding principally on insects, small vertebrates and acorns (Woolfenden &
Fitzpatrick 1984). Florida Scrub Jays are territorial and cooperative breeders. They always reside
in territories with well-defined boundaries defended year around, often occupying the same
territory for their whole life. Most young delay breeding for 1-4 years and remain as non-breeding
“helpers” in their natal territories. This is primarily due to all suitable breeding habitat within a
population being occupied and defended by other jays.

The total population in Brevard County (a subset of the total population) makes up approximately
355 families. The subpopulation in neighbouring Indian River County comprises an additional 48
families. Records show that the Brevard Scrub Jay population declined steeply in the 1950’s due
to habitat destruction and fire suppression. The population declined by at least 50% (Cox 1987)
and perhaps as great as 80% (J. Fitzpatrick pers. comm.). Most remaining populations are
vulnerable to extinction due to low population size, habitat fragmentation, and degradation
(Fitzpatrick et al. 1991).

The main threats to the Florida scrub jay are habitat destruction due to urban development and
habitat degradation due to fire suppression. Declining habitat quality is a direct consequence of
fire suppression. Epidemics are an additional threat to Florida scrub jays. There have been two
severe epidemics recorded during 30 years of study at the Archbold Biological Station.
Hurricanes are another potential threat. Hurricane strike probabilities are greatest in southernmost
Florida and decrease northward along the Atlantic coast (Dunn & Miller 1960). Hurricanes can be
catastrophic to scrub jays. However, destruction of scrub habitat is unlikely as scrub vegetation is
resilient to high winds and sea spray (Myers 1990).

The future of the Florida scrub jay depends on the continued existence of its scrub habitat. Most
scrublands are in areas that have high real estate value. Much of the coastal scrub has been
cleared (i.e., forest clearing) for beachfront hotels, houses, and condominiums. Scrub habitats in
the interior of the Florida peninsular are subject to development for citrus groves and housing
developments.

Helmeted honeyeater (Lichenostomus melanops cassidix)

The Helmeted honeyeater (Lichenostomus

melanops cassidix, Gould, 1867) (Plate 8) is
a songbird, black, yellow and olive-brown in
colour. Honeyeaters are found
predominantly in Australasia and around
170 species have been recorded in the genus
Lichenostomus. It is the largest and most
colourful of the four subspecies of the
Plate 8: Helmeted Honeyeater
Photo by P. Menkhorst. Yellow-tufted honeyeater (Lichenostomus
melanops).

The Helmeted honeyeater is endemic to south-central Victoria in Australia. It is confined to

streamside and swamp forests of low altitude (20-120 m) and high rainfall (800-1200 mm per
annum). All current sites are dominated by Mountain Swamp Gum (Eucalypt camphora). The
understorey consists of shrubs, tussock grasses and sedges, with shrubs providing nest sites
(Menkhorst et al. 1999).

The Helmeted honeyeater has never been a highly abundant bird. It was thought that in the late
1800s there were approximately 1000 birds. The numbers then steadily declined. In 1967 there
were 167 birds. By 1987 this number dropped to a low of 50 individuals. This prompted an
extensive conservation effort in 1989 (Menkhorst & Middleton 1991) to restore previous numbers
and suitable habitat. Consequently, there has been a steady increase in numbers since 1990. In
the 1998/1999 breeding season, the total population of Helmeted honeyeaters was 103 individuals
with 20 breeding pairs (Menkhorst et al. 1999).

The Helmeted honeyeater is restricted to about 5 km of remnant streamside vegetation along two
streams within the Yellingbo Nature Reserve, 50 km east of Melbourne in the State of Victoria
(Menkhorst et al. 1999). Wildfires and dieback of eucalypts presents the highest potential
environmental threats (Menkhorst et al. 1999). The continuing spread of the bell miner
(Manorina melanophrys), a competitor for similar habitat and food supplies, is also a significant
limiting factor for the Helmeted Honeyeater, lowering breeding successes and reducing the
availability of high quality breeding habitat.

Orange-bellied Parrot (Neophema chrysogaster)

The Orange-bellied parrot (Neophema

Plate 9: Orange-bellied parrot.
Photo by D. Watts
chrysogaster, Latham 1790) (Plate 9) is a small
brightly colored bird with bright green plumage
above royal blue leading edges to the wings and
light green to bright yellow feathering on the
underside and a distinctive orange patch on the
belly. The Orange-bellied parrot is one of six
species in the genus Neophema (Christidis &
Bolres 1994).

The Orange-bellied parrot is a migratory bird that breeds only in coastal southwest Tasmania in
the summer months and spends the winter in coastal Victoria and South Australia. It nests in
hollows in eucalypt trees that grow adjacent to its feeding plains. The birds arrive in southwest
Tasmania in early October, and depart after the breeding season usually in March and April
(Starks 1988).

The Orange-bellied Parrot has a single breeding population containing less than 200 mature
adults in the wild (Starks 1988). The species has declined in abundance and range this century.
However, it is likely that apart from periodic fluctuations the population has always been
relatively small and numbers are unlikely to have exceeded one thousand since the 1940’s
(Brown et al. 1985).

When breeding in southwest Tasmania, the Orange-bellied parrot occupies an area of

approximately 1600 km2, but during winter migration the species is otherwise dispersed widely
along the coastline of southeastern Australia, mainly in Victoria but extending into South
Australia. While the breeding areas in southwestern Tasmania have remained largely unaffected
by Europeans, the wintering habitat has been greatly fragmented and reduced in extent and
quality over the last 100 years (Menkhorst et al. 1989). Urbanization and industrial development
on the winter saltmarsh feeding grounds is thought to have contributed to the decline and
alteration of the species' habitat. Other threats include the potential impact of proposed wind
farms in coastal areas along the migratory pathway of the bird. Many predators inhabit the areas
used by Orange-bellied parrots. On mainland Australia, both foxes and feral cats are a threat. In
addition, the small population size may make the Orange-bellied parrot more sensitive to disease
and sudden catastrophes such as storms during migrations.

Since 1978 there has been a major effort to save the Orange-bellied parrot from extinction with
support from the State Governments of South Australia, Tasmania and Victoria, the
Commonwealth Government, Royal Australasian Ornithologists Union (RAOU – now called
Birds Australia) and World Wildlife Fund (Australia). A team of specialists was established to
coordinate the recovery of the Orange-bellied Parrot by implementing a Recovery Plan (Brown &
Wilson 1984; Orange-bellied Parrot Recovery Team 1999). A captive breeding program for the
Orange-bellied parrot began in 1985. Since 1991, 72 captive-bred birds were released into the
wild population. Monitoring of the breeding population indicates that the released birds remained
in the breeding ground, paired with other released birds or wild birds, with many successfully
raising young. At least some captive-bred birds have migrated successfully, with several being
sighted in Victoria in the winter and Tasmania in the summer for up to three consecutive years
(Orange-bellied Parrot Recovery Team 1999).
 Mammals

Sindh ibex (Capra aegagrus)

The Sindh ibex (Capra aegagrus Hume, 1875

ssp. Blythi) (Plate 10) is a wild mountain goat,
restricted to high and relatively extensive arid-
zone mountain ranges within the Kirthar
National Park (KNP) in Pakistan. Capra
aegagrus blythi is one of two subspecies of
Plate 10: Sindh Ibex
Photo courtesy of Syed Ali Farzoq Capra aegagrus. The main habitat requirements
of the Ibex seem to be precipitous crags at high elevation (up to 3350m), which are safe from
direct disturbance from shepherds and domestic goats. Ibex tend to remain in the high ground
only venturing into lowland areas when moving between ranges.

The Kirthar National Park has a total area of 308,733 ha or 3087 km2. The estimated habitat for
Sindh ibex is 1,200 km2 and the population was estimated in 2001 to be between 10,890 and
14,510 individuals (Yamada et al. 2003). Ibex have experienced pressures from hunting, human
encroachment on habitat and overgrazing of habitat by domestic livestock. Prior to 1967, when
legal protection of the Ibex was introduced, the population is thought to have decreased to a low
of around 200 individuals. Since that time there has been an increase in densities. In 1972/3
Schaller estimated densities to be between 3.3 and 4.1/km2 (Edge & Olson-Edge 1990). In
1970-71 Holloway and Khan (1971) reported 1200 ibex from the Kirthar National Park and the
Sumbak Game reserve, with the Karchat subpopulation having around 500 individuals (Mirza &
Asghar 1980). A census in 1977 by Mirza and Asghar (1980) estimated approximately 1,480
individuals in KNP and approximately 880 individuals within the Game reserve. The significant
increase in the population is thought to be due to protecting the animals from hunting activities
(Mirza & Asghar 1980).
Spotted-tailed quoll (Dasyurus maculatus maculatus)

The Tasmanian spotted-tailed quoll (Dasyurus

maculatus maculatus) (Plate 11) is a carnivorous
marsupial with dark brown fur with white spots
down to its tail (Strahan 1995). It is the largest
subspecies with males weighing on average 3.5kg,
and a female average weight of 1.8kg. Quolls are
Plate 11: Spotted-tailed quoll
Photo by D. Watts opportunistic hunters and scavengers, with their diet
consisting mostly of small and medium-sized mammals, birds, invertebrates, reptiles, and
sometimes, larger mammals (Belcher 1995).

The Spotted-tailed quoll primarily inhabits thickly vegetated forests in high rainfall areas in
Tasmania and along the east coast of mainland Australia. Major habitat requirements are adequate
populations of suitable prey species (medium-sized mammals, such as possums and gliders and
bandicoots), habitat in which they can hunt effectively, and suitable refugia for denning. There is
evidence that significant competition for food may occur among the Tasmanian guild of
marsupial carnivores. Dietary overlap between spotted-tailed quolls, Tasmanian devils
(Sarcophilus harrisii), and eastern quolls (Dasyurus viverrinus) may result in suppression of
population size and may partially explain the low density across its range (Jones 1997; Jones &
Barmuta 1998).

The quoll is likely to have a polygynous breeding system. Females do not breed until their second
year. Males have a size/age based dominance hierarchy, and are unlikely to mate until their
second or third years (Belcher 2000). On average, females rear 4-5 young in a year but may not
breed every year. They may have as many as 6 in one year. Quolls are predated on by Tasmanian
devils. This results in high juvenile mortality in the first year up to approximately 0.5. Males
suffer higher mortality rates than females; nearly all roadkills are males (95%) and most quolls
killed on farms are also males. The annual mortality rate for males could be as high as 50%, and
for females approximately 35%.

Contest competition density dependence was assumed. It is appropriate for quolls as they tend to
be territorial, possibly having exclusive home ranges. Vital rates are sampled from the lognormal
distribution. An Allee effect occurs when populations become small, and the ability of the
population to survive is impaired due to factors such as difficulties in finding mates, disruption of
social structure and inbreeding. It seems reasonable to postulate the existence of Allee effects in
this species because of its territorial behaviour, the limited dispersal ability of females, and the
potential for the development of relatively small, isolated subpopulations. Dispersal dynamics
were assumed to consist predominantly of short range female dispersal events (a modest average
annual dispersal of 2km with a majority of events being less than 10km). However, some long-
range male dispersal events were also included, with infrequent events occurring over distances
of 10 to 100km. A distance-decay function was derived that characterized these dispersal
dynamics.

Threats include introduced species such as foxes, feral cats, domestic cats and dogs (Strahan
1995). This species also competes with Tasmanian devils for food (Jones & Barmuta 1998). The
quoll is also threatened by habitat destruction in the form of logging and plantation conversion.
After disturbance it appears likely that regenerating forest is unsuitable until approximately 40
years of age, after which it gradually recovers, and approaches its original habitat value at 100
years of age. Areas converted to plantation do not provide suitable habitat for quolls.

Reptiles

Desert tortoise (Gopherus agassizii)

The Desert tortoise (Gopherus agassizii,

Plate 12: Desert tortoise
Photo from the National Wildlife Foundation
of four species in the genus Gopherus. The Desert tortoise typically lives for an average of 60 to
80 years, but may live to 100 years of age.
Cooper 1863) (Plate 12) is a large,
herbivorous reptile found in portions of the
California, Arizona, Nevada and Utah
deserts. It is the only naturally occurring
tortoise in the Mojave Region. According
to the fossil record, the Desert tortoise has
lived in the arid southwestern US for the
last ten to twelve thousand years and is one

Desert tortoises are restricted to arid areas. They live in a variety of habitats from sandy flats to
rocky foothills where suitable soils for den construction are found. Other habitat requirements
include sufficient plants for forage and cover, and suitable substrates for burrow and nest sites.
Optimal habitat for the Desert tortoise has been characterized as areas with creosote bush scrub.
Their diet consists of native and introduced grasses, spring and summer annual wildflowers and
any available edible plants, cactus fruit and forbs (Jennings 1997).

The distribution of the Desert tortoise covers a large geographic area encompassing four U.S.
states. Within this range are six distinct population units, which have been identified according to
habitat suitability, genetic variability, morphology and behavioural patterns. Within these units
are several reserves or Desert Wildlife Management Areas (DWMA). These range from 415 to
3,367 km2. In total, the population units make up approximately 26,087 km2 of Desert tortoise
habitat. Additional habitat for the tortoise is within the Joshua Tree National Park (2,574 km2)
and within the boundaries of the Desert Tortoise Research Natural Area (100 km2).

There are numerous threats that affect the Desert tortoise and associated wildlife, and all are
primarily caused by human activities. Individual tortoises are killed due to poaching, collection
for pets, military activities, vehicular impact, livestock trampling, disease and attacks by ravens.
Habitat degradation and fragmentation occurs mainly through urban development and livestock
grazing. Efforts to protect the declining Desert tortoise population and its habitat have spanned
more than 20 years. In February 1994, the U.S. Fish and Wildlife Service (USFWS) designated
2.6 million hectares of critical habitat for the tortoise. In a recent meeting of the Fort Irwin
Tortoise panel, there was a consensus that the current status of the tortoise is thought to be further
from recovery than when first listed.

Description of models for hypothetical species

All population models for the seven hypothetical species were developed by Michael McCarthy
and published in (McCarthy et al. 2004). Below is an exert from the appendices of the paper
describing each of the models.
Invertebrates

Butterfly

The population dynamics of the butterfly were influenced by weather, density dependence,
parasitism and movement of individuals among breeding populations. The dynamics of a
specialist parasitoid was controlled by its attack rate on the butterfly larvae and rate of spread
among the 52 habitat patches. After metamorphosis, female butterflies searched for mates, laid
eggs and possibly moved between habitat patches on a daily basis. Dispersal rates depended on
the size of the current patch and the proximity and size of potential target patches. The daily
survival rate (and hence the annual fecundity) depended on weather conditions. The survival rates
of caterpillars depended on population density and the amount of rainfall. Impacts of generalist
parasitoids was embedded within the density dependent function.

Snail

Rainfall, age structure, density dependence in survival, and cannibalism of eggs influenced the
population dynamics of the snail. Recruitment and survival rates increased with rainfall. Younger
individuals had lower fecundity rates. Survival rates declined and cannibalism rates of eggs
increased with population density.
Plants

Shrub

The population dynamics of the shrub were influenced by weather, age structure, density
dependence in reproductive opportunities, random fires, and the spatial structure of the available
habitat. Habitat occurred continuously throughout a network of gullies, and was represented by an
array of cells on a square grid. Germination only occurred following fires, when all burnt
individuals died. Occurrence of fires within grid cells was spatially correlated. There was no soil-
stored seed bank. The amount of seed on each plant was maximized at 40 years of age. The
probability of fire increased with time since the last fire and as the amount of rainfall in the
previous year decreased. Flower production decreased with increases in the density of adult
plants, and germination rates declined with increases in the density of germinants. The
germination rate and survival rate of adults increased with rainfall. A small number of seeds
dispersed to adjacent cells.

Herb

The population dynamics of the herb were influenced by rainfall, age structure, inbreeding
depression, a soil seed bank, density dependence in survival, seed-production rates and selfing
rates (proportion of a plant’s seeds that are self-pollinated). Rainfall was modeled as a correlated
process in a manner similar to that used for the small mammal. Most plants died after one year,
although some lived into a second year. Inbreeding depression was modeled for each individual
by assigning alleles to 10 genes for each individual. Genes were passed from adult plants to seeds
by randomly assigning one allele for each gene from each parent. The selfing rate increased as
population sizes declined. For non-selfed seeds, the source of the pollen was determined by
choosing a plant randomly from the population. The level of heterozygosity in individuals
(proportion of genes with the same two alleles) influenced their survival as seeds in the soil, their
survival as adults, and their production of seeds. Germination rates and survival rates of adults to
their second year were enhanced by annual rainfall. Seed-production and survival rates declined
as population size increased.
Birds

Owl

The population dynamics of the owl were influenced by age structure, density dependence in
reproductive opportunities, and logging of habitat. Suitable habitat was distributed among 16
patches. The owl was relatively long-lived with low reproductive output. Juveniles were more
likely to disperse to nearby rather than more distant habitat patches, but the majority stayed in
their natal patch. Once a breeding territory was established, adults did not move from that patch.
The number of breeding territories within each patch was limited by the amount of suitable
breeding habitat. Logging at various rates in different patches reduced the amount of habitat
available.

Mammals

Small mammal

A model was developed to simulate the population of a small mammal closely resembling a
pygmy possum (McCarthy & Broome 2000). The population dynamics of the small mammal
were influenced by weather conditions, the availability of prey, age structure and mate-finding
ability. Weather was modeled by drawing standard normal deviates for rainfall and temperature
for 6-month periods (“winter” and “summer”). Temperatures in each 6-month period were
positively correlated, and precipitation was negatively correlated with temperature in winter and
summer. Prey (nominally thought of as insects) were modeled using a stochastic Ricker density-
dependence function. Stochasticity in the prey dynamics entered through the influence of the
temperature over the winter and the rainfall of the current summer. The quality of the
environment for the small mammal in summer was influenced by the abundance of prey and by
an extra source of stochasticity. This influenced their survival and reproduction over summer.
Survival of adults and newborns over winter was influenced by a combination of winter rainfall,
winter temperatures and the quality of the preceding summer. Intermediate temperatures and
rainfall lead to the highest survival rates. The rate of pregnancy of females declined with the
density of males (McCarthy 1997).
 Fish

Salmon

The population dynamics of the salmon were influenced by age structure, density dependence,
fishing rates and movement of individuals among breeding populations. Fish returned to breed at
either 3 years (half of the surviving fish), 4 years (80% of the surviving fish) or 5 years (all the
surviving fish) of age. Most returned to spawning in their natal stream, but a small proportion (<5
%) returned to other breeding sites. In 13 areas, spawning occurred in spring (headwater streams),
while spawning occurred in autumn in two areas. Dispersal between these breeding areas was
limited but did occur. The number of offspring produced depended on the availability of suitable
spawning sites, and their subsequent survival was also density dependent. All individuals died
after spawning. Fishing removed spawning individuals from the population. In the future, a dam
was to be removed and the quality of that stream as breeding habitat increased.

Amphibians

Frog

Rainfall, age structure, density dependence in reproductive opportunities, and inbreeding

depression influenced the population dynamics of the frog. Recruitment rates were maximized at
intermediate levels of rainfall. Low levels limited tadpole development and high levels led to loss
of eggs and tadpoles that were washed into a downstream dam. Younger individuals had lower
fecundity rates. Survival rates were greatest for frogs of an intermediate age. Females had higher
survival rates than males. Inbreeding was simulated in the same way as for the small plant.
Inbreeding depression acted only on survival of tadpoles.

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