From Pima County Sonoran Desert Conservation Plan web site

From the USGS June 28, 2011:

Genetic Analysis Splits Desert Tortoise into Two Species

RIVERSIDE, Calif. – A new study shows that the desert tortoise, thought to be one species for the past 150 years, now includes two separate and distinct species, based on DNA evidence and biological and geographical distinctions.

This genetic evidence confirms previous suspicions, based on life history analysis, that tortoises west and east of the Colorado River are two separate species.

The newly recognized species has been named Morafka’s desert tortoise (Gopherus morafkai) and represents populations naturally found east and south of the Colorado River, from Arizona extending into Mexico.

The originally recognized species, the Agassiz’s desert tortoise (Gopherus agassizii) is listed as threatened under the federal Endangered Species Act. It represents populations naturally found west and north of the Colorado River in Utah, Nevada, northern Arizona and California.

The U.S. Fish and Wildlife Service (FWS), which manages the recovery of threatened and endangered species, had already been treating tortoises on each side of the Colorado River as distinct populations The genetic evidence simply backs up previous observations, such as differences in life history and reproductive strategies.

“The two species have different habitat preferences,” says Kristin Berry, a USGS biologist who has studied desert tortoise biology for more than 40 years and a coauthor on the study. “Morafka’s tortoise prefers to hide and burrow under rock crevices on steep, rocky hillsides, while the Agassiz’s tortoise prefers to dig burrows in valleys.”

Roy Averill-Murray, the desert tortoise recovery coordinator for the Fish and Wildlife Service said, “We appreciate the efforts of USGS and other researchers to increase our scientific knowledge about the taxonomy of the desert tortoise. The study’s finding that the Morafka’s desert tortoise is a new species confirms the Service’s decision to evaluate this population independently from the Agassiz’s desert tortoise, and will not change the status of either species under the Endangered Species Act or change existing recovery plans.”

Distinguishing the two species required some historical detective work by the researchers. Desert tortoises were first described in 1861 by an Army physician, J.G. Cooper. But two of the original specimens were lost, possibly as a result of the San Francisco earthquake and fire of 1906. Fortunately, Cooper had sent a third specimen to the Smithsonian — and its DNA helped researchers in their analysis 150 years later.

The study is published in the journal ZooKeys and authored by Robert Murphy of the Royal Ontario Museum in Canada, Kristin Berry of the USGS, and colleagues from University of Arizona, California Academy of Sciences and Lincoln University (Mo.).

Field research and travel for this study was supported by contracts from University of California Los Angeles, California State University Dominguez Hills, US Army Fort Irwin, USAF Edwards Air Force Base, USMC Air Ground Combat Center Twentynine Palms, California Department of Fish and Game, the Bureau of Land Management and the USGS.

Read a detailed FAQ about the study on the USGS Western Ecological Center webpage.

NOTE: 

Q: Who is the new desert tortoise species named after?

A: The study authors named Gopherus morafkai after Dr. David J. Morafka, the late biologist and professor at California State University Dominguez Hills. Professor Morafka was a renowned desert ecologist who was recognized for his many contributions to the biology and conservation of both bolson and desert tortoises, and his efforts at facilitating collaborative research, even among researchers with very different perspectives.

Wtth all due respect to Morafka it should be the Sonoran Desert Tortoise.

And my commentary from Inside Tucson’s Business February 2011:

Sonoran Desert Tortoise to be next poster child to stop progress

By Hugh Holub, for Inside Tucson Business Inside Tucson Business | 0 comments

The U.S. Fish and Wildlife Service has concluded the Sonoran Desert Tortoise probably deserves to be designated as an endangered species when the feds have sufficient funds to pursue this.

Undoubtedly, radical environmental groups who use the Endangered Species Act to block human development projects will litigate to force the federal government to designate the Sonoran Desert Tortoise and then to adopt a “habitat conservation plan.” This will aim to stop urban growth and infrastructure development in Pima, Pinal and Maricopa counties.

Besides new urban development being threatened by the looming prospect of the tortoise being listed as an endangered species, virtually all of the major infrastructure projects in the region are also threatened.

The Sonoran Desert Tortoise looks to be the best shot for environmental groups to attack any project that might hinder a tortoise from wandering around the countryside.

These days, in the United States — and especially Arizona — protection of endangered species trumps virtually everything else.

As a friend recently joked: If the United States had the Endangered Species Act in the 1930s, we’d still be studying whether or not to build the Hoover Dam.

From the Federal Register:

The following is excerpted from the US Fish and Wildlife decision published in the Federal Register in December 14, 2010: [Federal Register: December 14, 2010 (Volume 75, Number 239)][Page 78093-78146]

Human population growth results in the disturbance or loss of
Sonoran desertscrub or the conversion of land for urban and
agricultural development. Arizona increased its population by 394
percent from 1960 to 2000, and was second only to Nevada as the fastest
growing State during this timeframe (Social Science Data Analysis
Network (SSDAN) 2000, p. 1). Since 1990, Arizona’s population has grown
by 44 percent. From 1960 to 2000, population growth rates in Arizona counties
where the Sonoran desert tortoise occurs have varied by county but are
no less remarkable, and all are increasing: Maricopa (463 percent);
Pima (318 percent); Pinal (54 percent); Santa Cruz (355 percent);
Cochise (214 percent); Yavapai (579 percent); Gila (199 percent);
Graham (238 percent); Yuma (346 percent); LaPaz (142 percent); and
Mohave (2,004 percent) (see SSDAN 2000). The population of Phoenix,
Arizona, grew 67 percent from 1980 to 2000 (Berry et al. 2006, p. 7).

Urban expansion and human population growth trends in Arizona are
expected to continue into the future. Maricopa-Pima-Pinal county areas
of Arizona are expected to grow by as much as 71 percent in the next 15
years, creating rural-urban edge effects across millions of acres of
public lands currently supporting Sonoran desert tortoise populations
(AIDTT 2000, p. 10; BLM files–Lands Livability Initiative). In another
projection, the population in Arizona is expected to more than double
within the next 20 years compared to the 2000 population estimate (U.S.
Census Bureau 2005, p. 1). Many cities and towns within the
distribution of the Sonoran desert tortoise have already experienced
substantial growth during the 8-year time span, 2000-2008: City of
Avondale (118.3 percent); City of Buckeye (392.5 percent); Bullhead
City (20.3 percent), Town of Carefree (30.5 percent); Casa Grande (56
percent); Town of Cave Creek (44.2 percent); City of Chandler (37.5
percent); City of Coolidge (24.9 percent); City of El Mirage (195.6
percent); City of Eloy (22.3 percent); City of Florence (20.3 percent);
Town of Fountain Hills (23.2 percent); City of Gilbert (84.5 percent);
City of Goodyear (203 percent); City of Kingman (32.2 percent); Lake
Havasu City (33.3 percent); City of Litchfield Park (34.2 percent);
City of Mammoth (45 percent); Town of Marana (139.9 percent); City of
Maricopa (2,508 percent); Town of Oro Valley (32.5 percent); Town of
Queen Creek (544.5 percent); Town of Saguarita (507.3 percent); City of
San Luis (58.5 percent); City of Somerton (63.2 percent); City of
Surprise (187.3 percent); City of Tolleson (43.2 percent); and, Town of
Youngtown (62.2 percent) (U.S. Census Bureau 2008, pp. 1-4).

This population growth has spurred a significant increase in
urbanization and development in these areas. Regional development is
predicted to be extreme in certain areas within the distribution of the
Sonoran desert tortoise in Arizona. In particular, a wide swath from
the international border in Nogales, through Tucson, Phoenix, and north
into Yavapai County (called the Sun Corridor “Megapolitan”) is
predicted to have 8 million people by 2030, an 82.5 percent increase
from 2000 (Gammage et al. 2008, pp. 15, 22-23). If build-out occurs as
expected, it will encompass a significant proportion of the Sonoran
desert tortoise distribution in Arizona, and will in effect permanently
isolate Sonoran desert tortoise populations that occur on either side
of the Interstate 19, Interstate 10, and Interstate 17 corridors.

The land area permanently altered by human activities from urban
development and agriculture has grown to 13 percent of all land in the
western United States, Lue et al. (2008, p. 1130). Lue et al. (2008, p.
1133) concluded that in low-productivity habitat, such as desertscrub
habitats, slight human disturbances can have pronounced effects.
Significant urban development occurs within intermountain valleys,
within or adjacent to occupied Sonoran desert tortoise habitat, which
increases the likelihood of effects along the rural-urban interface,
and may also inhibit movement of individuals between populations on
nearby hillsides or mountain ranges. Disturbances to Sonoran desert
tortoise habitat on the landscape can take many forms and cover extreme
distances. Roads, canals, pipelines, and railroad tracks are examples
of linear habitat destruction. We discuss the potential effects of
linear disturbances below in the section titled,

“Development as a Barrier.”

Development pressure across Arizona has slowed due to the recent
economic downturn and decline in the housing market. However,
development will likely continue in the future, although perhaps at a
slower pace than in the earlier part of this century. We also recognize
that economic trends are difficult to predict into the future. The most
recent draft Pinal County Comprehensive Plan (February 2009)
acknowledges that the county is in the middle of the Sun Corridor
Megapolitan and proposes four shorter-term growth areas in defining
where development will likely occur, or be encouraged to develop, over
the next decade, but does not discourage growth outside of these areas
(Pinal County Comprehensive Plan 2009, p. 109). These four growth areas
(Gateway/Superstition Vistas, West Pinal, Red Rock, and Tri-
Communities) fall completely within the range of the Sonoran desert
tortoise. The Gateway/Superstition Vistas growth area alone encompasses
176,000 ac (71,225 ha), or 275 sq mi (712 sq km), of State Trust land,
and it is anticipated that 800,000 to more than 1 million people will
one day live in this development (Pinal County Comprehensive Plan 2009,
p. 115). The loss of 176,000 ac (71,225 ha) constitutes a loss of 0.7
percent of Sonoran desert tortoise habitat in Arizona; rangewide, 0.34
percent. The Pinal County Comprehensive Plan (2009, p. 117) identifies
many miles of new freeways and principal arterials in the analysis area
at build-out, which the plan acknowledges may take over a half century
to realize (Pinal County Comprehensive Plan 2009, p. 115). The effect
of roads on Sonoran desert tortoises is discussed below.
Additionally, the Maricopa County Comprehensive Plan calls for
growth areas to the south and east of Chandler and Mesa, Arizona, which
are within the range of the Sonoran desert tortoise (Maricopa County
Comprehensive Plan 2002 (revised), p. 92). City comprehensive plans
within the range of the Sonoran desert tortoise also call for future
growth areas. For example, the City of Eloy has designated six such
areas encompassing 15,520 ac (6,281 ha), mostly along the Interstate 10
corridor (City of Eloy General Plan 2004, pp. 7-6 through 7-10). The
loss of 15,520 ac (6,281 ha) constitutes a loss of 0.06 percent of
their habitat in Arizona; rangewide, 0.03 percent. While much of this
area has already been impacted by development or irrigated agriculture,
any remaining dispersal habitat for the Sonoran desert tortoise will
likely be negatively affected as development and its associated
infrastructure progress into these areas.

Much of the past and projected development within the range of the
Sonoran desert tortoise in central and southwestern Arizona has
occurred and is expected to continue as a conversion from agricultural
uses to municipal uses. Land traditionally used for agriculture is not
occupied by Sonoran desert tortoises, but has a comparatively minor
effect on adjacent Sonoran desert tortoises. When these lands are
converted to municipal uses, the effect to adjacent Sonoran desert
tortoise populations increases human access, and use of adjacent
undeveloped land increases as a result of development of these former
agricultural areas.

…
Urban development has been identified as a concern for Sonoran
desert tortoise conservation in several areas within Arizona because of
the associated increase in human-based threats to populations in close
proximity. Averill-Murray and Swann (2002, p. 1) stated that urban
development adjacent to the Saguaro National Park in Pima County
threatens the Sonoran desert tortoise via several mechanisms including
harassment and predation by feral or off-leash domestic dogs, illegal
releases of captive Sonoran desert tortoises and exotic species that
may transmit diseases to wild Sonoran desert tortoises, elevated
mortality on roads, and illegal collection for pets. Averill-Murray and
Swann (2002, p. 7) stated that mid- to large-scale development projects
on the bajadas and foothills of the Rincon, Santa Rita, Santa Catalina,
Tortolita, and Tucson Mountains has likely led to area-wide decreases
in Sonoran desert tortoise populations. However, no population
estimates for Sonoran desert tortoises before development of these
areas exist, and, therefore, population responses to development of
these areas cannot be ascertained.

In addition to the Tucson metropolitan area, urban encroachment on
Sonoran desert tortoise habitat occurs adjacent to the greater Phoenix
metropolitan area, in the area around South Mountain and adjacent to
the Superstition Mountains (AGFD 2010, p. 7). Sonoran desert tortoises
are known or suspected to still occur in 12 of the 16 Maricopa County
and City of Phoenix urban mountain parks and reserves. The four parks
where no tortoise sign has been found in recent years are completely
surrounded by urban development (AGFD 2010, p. 7). Urban development
has occurred adjacent to five monitoring plots, but only the Hualapai
Foothills plot is completely surrounded by developed lands (AGFD 2010,
p. 7). A development consisting of 48,000 single family homes, south of
the Colorado River in western Mohave County, is also currently being
planned (THS 2009, p. 4; Mardian 2010, p. 1).

Endangered Species Act —  Critical or Protected  Habitat Designation

The next step in using the Endangered Species Act as a weapon to throttle virtually all human activity in the country is the designation of critical or protected  habitat.

If the species or subspecies or “distinct” population is endangered oe threatened…obviously the plants or animals need a “place” to live without being harmed. That  is the “critical or protected habitat”.

But first one must understand the definition of “harm” that threatens or endangers the plant or animal.

After a convoluted process US Fish and Wildlife will issue a “biological opinion” defining what it believes is threatening or endangered the plant or animal.

This is mostly a non-scientific exercise in speculation….this “may” that “might’ harm the plant or animal.

When you look at petitions for listing in the first place, you will see the alleged “harm” type activities that must be stopped…cattle grazing, global warming, road construction, obstructing natural migratory paths,  wind turbine blades turning, whatever.  If you really want to read some good science fantasy, read this stuff.

Here is just one example from the Sonoran Desert Tortoise decision from US Fish and Wildlife to make the turtle a candidate for listing as an endangered species:

Development as a Barrier

Urban development, canals, and transportation infrastructure, such
as roads and railroads, disrupt ecological processes, increase
mortality in animals, promote the degradation, loss, and isolation of
wildlife habitat, and cause fragmentation of populations (Sonoran desert tortoise populations are island-like in their distribution, meaning they are generally concentrated on the bajadas and hillsides of mountains, and less-
distributed within the valleys between these areas. As a result, they
may be particularly vulnerable to large-scale disturbances that affect
the suitability of intervening habitat.Factors that affect inter-population dynamics in Sonoran desert tortoises include distance between populations, physical size of habitat areas, sizes of source populations, and the ease of which intervening areas can be crossed by dispersing individuals.

The effect of potential barriers to inter-population movements of
Sonoran desert tortoises (discussed above in the Species Information
section) is not equal across their range. The ability for the Sonoran
desert tortoise to move among populations is also important for
allowing shifts in their range in response to climate change, and to
promote recolonization after fire or other regional disturbances. Dispersal of Sonoran desert tortoises between populations through sparse desertscrub is less likely in very hot, dry valleys in the Lower Colorado subdivision of Sonoran desertscrub and populations in mountain ranges, such as the Eagletails, Maricopas, and Sand Tanks, have likely been existing in isolation for a long time.

Genetic analysis of blood samples collected from Sonoran desert
tortoises in Saguaro National Park in Pima County, Arizona, suggest
that intermediate gene flow still occurs, or occurred recently, among
isolated populations at the rate of at least 1 migrant per generation
(12-15 years). However, thousands of acres of tortoise habitat have been recently lost to large residential developments in the foothills of the Santa Catalina, Tortolita, Rincon, and Tucson Mountains in the greater Tucson metropolitan area.

The importance of allowing movement of individual tortoises between
populations is observable by evaluating historical gene flow. Edwards
et al. (2004, p. 485) used seven microsatellite DNA markers to examine
the genetic relationships of tortoises in eight populations in southern
and central Arizona, in the vicinity of Tucson and Phoenix. They also
calculated migration rates among these populations to estimate
historical rates of gene flow, and, therefore, the importance of
individuals moving between populations (Edwards et al. 2004, p. 485).
Edwards et al. (2004, p. 496) found no evidence of recent loss of
genetic diversity that would indicate genetic bottlenecking that could
occur from lack of mixing among Sonoran desert tortoise populations in
southern Arizona. However, the authors acknowledged that a small sample
size and small number of genetic markers (alleles) used in their
analyses would likely not detect this genetic effect. Despite reduced
mixing among populations, Sonoran desert tortoises may be capable of
maintaining small effective population sizes (still viable populations,
despite small size), even with a low degree of genetic diversity
(Edwards et al. 2004, p. 496). However, Edwards et al. (2004, p. 496)
also stated, “Because effective population sizes of Sonoran desert
tortoises are small, dispersal events probably play an important role
in the long-term maintenance of these populations.” This suggests that
while dispersal and movement of tortoises may be rare, they may be
important events. Therefore, barriers that prevent this movement could
result in significant genetic impacts, by preventing mixing of
populations over the long term.

The effect of urban barriers limits inter-population movements of
Sonoran desert tortoises resulting in “closed” populations. Experts
believe that an isolated population of Sonoran desert tortoises that
experiences significant declines in population size could not overcome
losses simply through an increase in reproduction, based on evidence of
past gene flow (Edwards et al. 2004, p. 496). Therefore, if a
population were to experience a catastrophic decline as a result of a
stochastic event such as drought, the immigration of new tortoises from
adjacent populations would be necessary for population recovery
(Edwards et al. 2004, p. 496). Urban barriers effectively prevent this
immigration of new tortoises, resulting in closed, or isolated, Sonoran
desert tortoise populations, which are now evident within the
metropolitan areas of Phoenix and Tucson. Mountains and associated
foothills with Sonoran desertscrub habitat occur in these urban areas,
and although development within this habitat has been restricted by
zoning laws, development is still allowed to virtually surround the
bases of the mountains, isolating tortoise populations. Examples of
this development include the Union Hills, White Tank Mountains,
McDowell Mountains, Black Mountains, and South Mountain Park in the
Phoenix metropolitan area and Tumamoc Hill, Tucson Mountains, and
Saguaro National Park West in the Tucson metropolitan area (Edwards et
al. 2004, p. 496). Zylstra and Swann (2009, pp. 10-11) remarked that
the increasing negative effect of human-made barriers on Sonoran desert
tortoise movements between populations may require translocation
(moving animals out of harm’s way into more secured areas of suitable
habitat), or occasional augmentation of populations with tortoises from
other populations, to remain viable.

Translocation has been considered an option, and implemented to
some degree for Mojave desert tortoise conservation and recovery. In
assessing the viability of translocation as a recovery and conservation
tool for the Mojave population, concern has been expressed for
potentially moving tortoises into areas where threats to desert
tortoise populations remain, which could negate any conservation value
associated with the action. Our (Mojave) Desert Tortoise Recovery
Office stresses that translocation of tortoises should not occur under
such circumstances, emphasizing the need to address threats which
impact all tortoises regardless of origin.

Translocation of desert tortoises has received mixed reviews in the
scientific literature and, as noted, may not be a viable option for the
Sonoran desert tortoise. There are several factors that must be
considered in deciding whether or not to translocate tortoises into new
areas, including temporary or longer-term holding conditions of
tortoises; the propensity for post-release, long-distance movements;
drought; the status of receiving population; and disease screening,
among other factors (Berry 1986a, p. 113; Field et al. 2007, pp. 232,
237, 240, 242; Martel et al. 2009, p. 218). Translocated Mojave desert
tortoises have been shown to settle at release sites, travel in
straight lines for substantial distances, or disperse up to
approximately 4 miles (6.4 km) (Berry 1986a, p. 113). Translocated
desert tortoises may disrupt social hierarchies in receiving
populations by displacing residents or they may be displaced themselves
(Berry 1986a, p. 113). Howland and Rorabaugh (2002, p. 341) suggest
that translocation of Sonoran desert tortoises may not be a viable tool
for conservation because most intact Sonoran desert tortoise
populations in Arizona are currently considered relatively healthy, and
likely occur at or near carrying capacity. Mullen and Ross (1997, pp.
145-146) found that translocated Mojave desert tortoises have a lower
survivorship than resident individuals (especially when moved during
the summer versus during the spring), but that negative effects
commonly associated with translocations are generally short-lived (1-2
years).

A 2004 population viability analysis for the Mojave desert tortoise
recommended that a minimum of 50,000 individuals are required for a 50
percent chance of persistence for 500 years, yet extrapolation of
Sonoran desert tortoise population data from southern Arizona suggest
that most populations number less than 20,000 individuals, with some as
low as several hundred (Edwards et al. 2004, p. 496). Because the
average generation time of a Sonoran desert tortoise is approximately
12-15 years and much of the urban development is relatively recent, the
full effect of developments as barriers to genetic exchange among
Sonoran desert tortoise populations cannot be fully assessed at this
time (Edwards et al. 2004, p. 486). Edwards et al. (2004, p. 495)
further cautioned that their estimates of gene flow are contingent on
what occurred pre-settlement, and should not be taken as evidence that
natural immigration or emigration still occurs.

In conclusion, the literature documents that urban development and
population growth, roads and highways, canals, railroad tracks, and
other types of development threaten the Sonoran desert tortoise by
creating barriers to movement in Arizona and, perhaps to a lesser
extent, in Sonora, Mexico. The creation of barriers affects the
tortoises’ genetic exchange capacity within and between populations,
which in turn affects their ability to recolonize habitat in the event
of population declines or extirpations, and may lead to isolation and
eventual genetic bottlenecking. This threat acts synergistically with
other factors as discussed above.

[Federal Register: December 14, 2010 (Volume 75, Number 239)]
[Proposed Rules]
[Page 78093-78146]

The litanty of threats to plants and animals containined in petitions for endangered species listings and in US Fish and Wildlife decision to list…read like sermons on the evil of huamn activity.

The next step in the process is to throw the net as far and as wide as possible to define where the threatened or endangered plant or animal lives, could live, or once lived.

For prime example, Center for Biological Diversity is pushing for a “critical habitat” designation of most of southern and eastern Arizona for the jaguar.

Not coincidentally all efforts to designate “critical habitat”  or “protected habitat” seem to intersect with proposed projects or existing activities the litigious environmental groups don’t like.

The “critical habitat” of many species pursued for listing and habitat protection cover all the riparian areas of the state, all grazing lands, and so forth.

Right now there is a fight going on about a protected habitat designation for the Chiricahua Leopard Frog, and the Center for Biological Diversity is pushing to have the proposed Rosemont Mine site designated as frog habitat.

Center for Biological Diversity demands Rosemont Mine site be included in protected habitat for frog

Why…because once a “critical habitat” or “proitected habitat” is designated, no one can do anything inside that declared “critical or protected habitat” without permission from US Fish and Wildlife.

You think you own your land or water? Not really if your land and water serves as designated critical or protected habitat for a threatened or endangered species, subspecies or  distinct population.
_________________________________________________
The Endangered Species Act series of articles:

Endangered Species Act…it ain’t what you think it is — Part 1

Endangered Species Act — Part 2– this land is not your land

Endangered Species Act – Part 3 – Never swat a fly

Background info on Endangered Species Act:

Endangered Species Act — an Introduction

Endangered Species Act — Which Animals and Plants are “Threatened” or “Endangered”?

Endangered Species Act — Section 7 Consultation 

Endangered Species Act — USF&W Introduction and Key Sections

Endangered Species Act — Definition of ”Harm” and “Take”

Endangered Species Act–Listing and Critical Habitat

Endangered Species Act–Habitat Conservation Plans

_________________________________________________________

News about litigious environment group activities:

Center for Biological Diversity at war with US Military

Center for Biological Diversity demands Rosemont Mine site be included in protected habitat for frog

Judge puts WildEarth Guardian endangered species agreement on hold

Center for Biological Diversity fights imperiled species deal

Stop The Drilling! A Lizard Is Imperiled

Desert Pupfish Forces Border Agents to Patrol on Foot

New high recorded in frivolous environmental litigation

EPA Doles-Out Taxpayer Dollars to Environmentalist Activist Groups

Legislation to stop huge legal fee payments to environmental litigation factories poised to be introduced

Environmental groups bury feds with Endangered Species petitions