Extinction Risk Models

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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).





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.

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.

Plate 1: Simson Stag BeetleDrawing by Karen Richards

Giant velvet worm (Tasmanipatus barretti )

Plate 2: Giant Velvet WormDrawing by Karen Richards

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).

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

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).

Plate 3: Keeled Snail (Tasmaphena lamproides)Photo by Fred Koolhof



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.

This species has a very complex relationship

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.

Plate 4 Grevillea caleyiPhoto courtesy of D. Keith

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-

driven, principally by volcanism, fire, landslides and wind.

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).

Plate 5: Araucaria araucana:Photo by S. Bekessy

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.

Bedford (Plate 6) is one of approximately 32 species of the

genus Xanthorrhoea, which is also known commonly asthe 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.Plate 6: Xanthorrhoea resinifera Photo courtesy of D. Keith

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 thegenus 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).

Florida scrub jays are endemic to Florida and require well-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.

Plate 7: Florida Scrub-jay.Photo by R. Curry.

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

Yellow-tufted honeyeater ( Lichenostomus

melanops).

Plate 8: Helmeted Honeyeater Photo by P. Menkhorst.

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

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).

Plate 9: Orange-bellied parrot.Photo by D. Watts

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

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.

Plate 10: Sindh IbexPhoto courtesy of Syed Ali Farzoq

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 spotsdown 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

opportunistic hunters and scavengers, with their diet

consisting mostly of small and medium-sized mammals, birds, invertebrates, reptiles, and

sometimes, larger mammals (Belcher 1995).

Plate 11: Spotted-tailed quollPhoto by D. Watts

The Spotted-tailed quoll primarily inhabits thickly vegetated forests in high rainfall areas inTasmania 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,

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

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.

Plate 12: Desert tortoisePhoto from the National Wildlife Foundation

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 km 2)

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 ateither 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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Documents

Extinction Risk Models