Table 1.

Desert Tortoise sample locality information

Site ID	n	Taxa	Biotic community	Location	Site
UT	2	Goag‐ Northern	Mojave Desertscrub	Utah, USA	Near St. George
TC*	2	Goag‐ Northern	Mojave Desertscrub	Nevada, USA	Trout Canyon
SV	2	Goag‐ Northern	Mojave Desertscrub	California, USA	Shadow Valley
IV	2	Goag‐ Northern	Mojave Desertscrub	California, USA	Ivanpah
KH	1	Goag‐ Western	Mojave Desertscrub	California, USA	Kramer Hills
FIC	2	Goag‐ Western	Mojave Desertscrub	California, USA	Fort Irwin
ORC	1	Goag‐ Western	Mojave Desertscrub	California, USA	Ord‐Rodman
MCSH	1	Goag‐ Western	Mojave Desertscrub	California, USA	Marine Corps Air Ground Combat Center
MCB	1	Goag‐ Western	Mojave Desertscrub	California, USA	Marine Corps Air Ground Combat Center
CM	1	Goag‐ Western	Lower Colorado River Valley	California, USA	Chocolate Mountain Aerial Gunnery Range
FEN	1	Goag‐ Western	Mojave Desertscrub	California, USA	Fenner
G	1	Goag‐ Western	Mojave Desertscrub	California, USA	Goffs
CH	1	Goag‐ Western	Mojave Desertscrub	California, USA	Chemehuevi
UWV	2	Goag‐ Western	Mojave Desertscrub	California, USA	Upper Ward Valley
GS	2	Goag‐ Western	Ecotone: SDS/MDS	Arizona, USA	Southwest side of Black Mtns.
WBM	4	Admixed ‐ MOJ/SON	Ecotone: SDS/MDS	Arizona, USA	West side of Black Mtns.
EB	4	Admixed ‐ MOJ/SON	Ecotone: SDS/MDS	Arizona, USA	East Bajada Long Term Monitoring Plot
HSC	1	Admixed ‐ MOJ/SON	Ecotone: SDS/MDS	Arizona, USA	Hualapai Mtns.
HAR	2	Gomo ‐ SON	SDS: Arizona Upland	Arizona, USA	Harcuvar Mtns.
WM	4	Gomo ‐ SON	SDS: Arizona Upland	Arizona, USA	Wickenburg Mtns.
NW	1	Gomo ‐ SON	Ecotone: SDS/Lower Colorado River Valley	Arizona, USA	New Water Mtns.
EAG	2	Gomo ‐ SON	Ecotone: SDS/Lower Colorado River Valley	Arizona, USA	Eagletail Mtns.
SAU	2	Gomo ‐ SON	Ecotone: SDS/Lower Colorado River Valley	Arizona, USA	Sauceda Mtns. region
SL	3	Gomo ‐ SON	SDS: Arizona Upland	Arizona, USA	Sugarloaf, Mazatzal Mtns.
GRH	2	Gomo ‐ SON	SDS: Arizona Upland	Arizona, USA	Granite Hills
RK	2	Gomo ‐ SON	SDS: Arizona Upland	Arizona, USA	Saguaro National Park and adjacent land
SP	2	Gomo ‐ SON	SDS: Arizona Upland	Arizona, USA	San Pedro Valley
CAN	2	Gomo ‐ SON	Ecotone: SDS/Lower Colorado River Valley	Sonora, Mexico	La Candelaria
BAM	2	Gomo ‐ SON	Ecotone: SDS/Lower Colorado River Valley	Sonora, Mexico	Bamuri
TIB	4	Gomo ‐ SON	SDS: Central Gulf Coast	Sonora, Mexico	Tiburon Island
SER	2	Gomo ‐ SON	SDS: Central Gulf Coast	Sonora, Mexico	Seri region
RSJ*	2	Gomo ‐ SON	SDS: Plains of Sonora	Sonora, Mexico	San Judas
RM	3	Admixed ‐ SON/SIN	Ecotone: STS/SDS	Sonora, Mexico	Moscobampo
RAS	3	Admixed ‐ SON/SIN	Sinaloan Thornscrub	Sonora, Mexico	Arroyo Seco
OPO	4	Admixed ‐ SON/SIN	Sinaloan Thornscrub	Sonora, Mexico	Opodepe‐Las Milpas region
REA	3	Gomo ‐ SIN	Ecotone: TDF/STS	Sonora, Mexico	El Alamo
RLN	2	Gomo ‐ SIN	Ecotone: TDF/STS	Sonora, Mexico	La Noria
ALC	2	Gomo ‐ SIN	Tropical Deciduous Forest	Sonora, Mexico	Alamos‐Las Cabras
ALS*	2/2	Gomo ‐ SIN	Tropical Deciduous Forest	Sonora, Mexico	Alamos‐La Sierrita
FUE	4	Gomo ‐ SIN	Tropical Deciduous Forest	Sinaloa, Mexico	Rio Fuerte

Site ID corresponds with Figure 1; n = number of individuals sampled. Biotic community descriptions: TDF = Tropical Deciduous Forest, STS = Sinaloan Thornscrub, SDS = Sonoran Desertscrub and MDS = Mojave Desertscrub. Asterisk (*) indicates sites sampled for RNA‐seq (ALS samples used in both DNA and RNA analyses).