Impact of Landscape Management on the Genetic Structure of Red Squirrel Populations M. L. Hale, P. W. W. Lurz, M. D. F. Shirley, S. Rushton, R. M. Fuller, K. Wolff

Supplemental Table 2. Number of S. vulgaris 'populations' and sample size at four woodlot linking distances. The number of populations is the number of woodlot groups containing at least two S. vulgaris individuals. Included individuals are those that were members of a population at that linking distance. Excluded individuals are those that were the sole occupant of a woodlot group.
Woodlot Linking distance	Number of individuals included	Number of individuals excluded	Number of 'populations'	'Population' sample sizes
3.0 km	99	3	3	6,6,87
2.5 km	97	5	5	2,5,6,35,49
2.0 km	93	9	6	2,2,2,3,5,33,46
1.5 km	92	10	11	2,2,2,2,2,2,4,5,10,30,31

Supplemental Table 3. Location and year of collection for all S. vulgaris specimens. 'Population' refers to population determined with a linking distance of 1.5 km. Individuals marked with '-' were used in analyses at greater linking distances, but did not form part of a population at 1.5 km.
Museum ID	Location	Grid Reference	Collection Year	Population
1	Hayton	NY350557	1997	Cumbria
122-1949	Scaleby	NY343563	1949	Cumbria
176/82	Prudhoe, Hospital	NZ410561	1981	Tyne Valley
18-1950	Scaleby	NY343563	1950	Cumbria
1961.141	Wetheral	NY346554	1961	Cumbria
2	High Row, Ulswater	NY322538	1998	Rosthwaite
24-1967	Lazonby	NY354539	1967	Cumbria
26-1957	Whinfell, Westmorland	NY354501	1957	-
29/1972	Stocksfield, Ridley Mill	NZ405561	1971	Tyne Valley
30-1994	Hexham	NY394563	1993	Tyne Valley
38-1998	Patterdale	NY338516	1998	Pooley Bridge
43-1974	South Lambhill	NY342572	1974	Cumbria
49-1967.1	Rosthwaite, Borrowdale	NY324514	1967	Rosthwaite
5	near Croglin	NY357546	1999	Cumbria
50-1936	Gummer's How, Windermere	SD338488	1918	Foulshaw Moss
63/90	Harwood	NY399590	1998	Harwood
65-1970	Floriston Stn, Rockcliffe	NY335564	1970	Cumbria
66-1970	Walton, Woodhead	NY355567	1970	Cumbria
99-1962	Geltside, Brampton	NY351559	1962	Cumbria
4-63	Geltwoods, Brampton	NY352558	1963	Cumbria
C1 (12M54/5/00)	Brampton, Appleby	NY368523	2000	Cumbria
C2 (12M137/7/00)	Broughton, Furness	SD321487	2000	Cumbria
C3 (12M137/7/00)	Broughton, Furness	SD321487	2000	Cumbria
C4 (12M406/10/00)	Appleby	NY368520	2000	Cumbria
C5 (12M129/11/00)	Patterdale, Ulswater	NY339515	2000	Cumbria
C6 (12M137/11/00)	Gosforth, Seascale	NY306503	2000	Cumbria
E1	Sidwood	NY377588	2000	Sidwood
E10 (40-1994)	Warwick Bridge	NY347556	1994	Cumbria
E11 (2-1992)	Coombsland, Longdales Armathwaite	NY351544	1992	Cumbria
E12 (50-1994)	Armathwaite	NY350545	1994	Cumbria
E13 (3-1997)	Gowbarrow Park	NY340520	1997	Cumbria
E14	Renwick	NY361542	1994	Cumbria
E15	Holmwrangle	NY352548	1995	Cumbria
E16	Hutton-in-the-Forest	NY346536	1996	Cumbria
E17	Foulshaw Moss, south of Kendal	SD345483	1995	Foulshaw Moss
E18	Foulshaw Moss	SD345483	1995	Foulshaw Moss
E19	Foulshaw Moss	SD345483	1995	Foulshaw Moss
E2	Hamsterly Forest	NZ404528	1997	Tyne Valley
E20	Foulshaw Moss	SD345483	1995	Foulshaw Moss
E21	Lillyhall, Workington	NY302525	1998	-
E22	Burnbanks, Haweswater	NY351516	1997	Cumbria
E23	Burnbanks, Haweswater	NY351516	2000	Cumbria
E3	Wauchope Forest	NT365604	1997	Wauchope
E4 (10-1999)	Headsnook	NY349555	1999	Wauchope
E5	Lowther Estate office	NY353522	1999	Cumbria
E6	Armathwaite	NY351546	-	Cumbria
E7 (33-1998)	Edenhall	NY356532	1998	Cumbria
E8	Fingland Rigg, Solway	NY327557	1998	Cumbria
E9 (29-1994)	Coombsland Longdales, Armathwaite	NY351544	1994	Cumbria
M0975	Close House, Wylam	NZ412565	1982	Tyne Valley
M0976	West Dipton Wood	NY396560	1981	Tyne Valley
M0993	South Park, Hexham	NY393563	1982	Tyne Valley
M0997	Minsteracres	NZ402556	1966	Tyne Valley
M1101	Dipton Wood	NY396560	1981	Tyne Valley
M1102	Harbottle	NT393604	1982	Harwood
M1103	Hexham	NY394563	1981	Tyne Valley
M1112	Heighley Gate	NZ417589	1983	Rothbury
M1129	Prudhoe	NZ410562	1984	Tyne Valley
M1141	Ovingham	NZ408564	1985	Tyne Valley
M1142	Scots Gap	NZ403586	1985	Rothbury
M1144	Cragside, Rothbury	NU407601	1986	Rothbury
M1147	Chopwell	NZ411558	1985	Tyne Valley
M1153	Morpeth	NZ420586	1989	Morpeth
M1154	Hepscot, Morpeth	NZ422583	1985	Morpeth
M1156	Chathill	NU418627	1986	-
M310	Percy's Cross, Alnwick	NU417614	1962	Ford
M311	Bolam Lake	NZ408581	1975	Rothbury
M313	Scots Gap	NZ404586	1985	Rothbury
M318	Kirkudbright	NX268550	1974	-
M319	Ovingham	NZ408564	1970	Tyne Valley
M322	Hexham	NY394563	1967	Tyne Valley
M323	nr Lauder, Berwickshire	NT363643	1961	-
M331	Belsay	NZ409578	1980	Rothbury
M332	A68 nr Healey, Hexham	NZ402558	1980	Tyne Valley
M333	Ford Castle	NT394637	1981	Ford
M334	Bridges farm, Minsteracres	NZ403550	1978	Tyne Valley
M335	Bywell	NZ405561	1981	Tyne Valley
M336	Whitley Mill, Hexham	NY392558	1981	Tyne Valley
M337	Rothley Cross roads	NZ404590	1979	Rothbury
M338	Darras Hall, Ponteland	NZ414571	1979	Rothbury
M339	Kirkharle Farm	NZ401582	1980	Rothbury
M340	Wylam	NZ411564	1978	Tyne Valley
M346	Ovingham	NZ408564	1985	Tyne Valley
M833	Burnopfield	NZ417556	1978	Tyne Valley
M837	Burnopfield	NZ417556	1978	Tyne Valley
M839	Slaley	NY396555	1978	Tyne Valley
M840	Blanchland, Slaley	NY398554	1979	Tyne Valley
M841	Bywell	NZ404561	1980	Tyne Valley
M842	Bolam	NZ408582	1978	Rothbury
M843	Ford Castle	NT394637	1980	Ford
M844	Stocksfield	NZ405561	1976	Tyne Valley
M846	Hexham to Haltwhistle road	NY388566	1981	Tyne Valley
M847	Glanton	NU407615	1978	Ford
M939	Kelso road, Yetholm	NT381628	1981	-
M940	Black Hedley Farm, Shotley Bridge	NZ405552	1980	Tyne Valley
M969	Whitfield	NY377556	1982	Sidwood
M970	Slayley, Hexham	NY397555	1978	Tyne Valley
M971	Kirkharle	NZ401582	1981	Rothbury
M972	Greenside	NZ413562	1981	Tyne Valley
5-00	Pooley Bridge	NY346524	1998	Pooley Bridge
5-35	Brampton road, Carlisle	NY344556	1935	Cumbria
9-31	Kirkpatrick, Fleming	NY327570	1930	-

Supplemental Table 4. Matrix of pairwise FST values (below diagonal) and Nei's standard distance (DS) (above diagonal) between populations at a linking distance of 1.5km, with Cumbria split into pre-1980 and post-1980. Statistical significance of FST values was tested using a permutation procedure (1000 permutations). FST values significantly greater than zero are indicated in red (P < 0.05).
	Ford	Harwood	Rothbury	Wauchope	Morpeth	Sidwood	Cumbria Pre-1980	Cumbria Post-1980	Tyne Valley	Pooley Bridge	Rosthwaite	Foulshaw Moss
Ford	0.000	0.180	0.229	0.269	0.381	0.255	0.383	0.280	0.357	0.687	0.321	0.450
Harwood	-0.055	0.000	0.233	0.360	0.528	0.180	0.640	0.448	0.335	1.055	0.672	0.458
Rothbury	0.079	0.023	0.000	0.185	0.213	0.243	0.241	0.288	0.085	0.330	0.358	0.476
Wauchope	0.016	-0.008	-0.002	0.000	0.559	0.171	0.353	0.060	0.458	0.392	0.327	0.265
Morpeth	0.092	0.091	0.027	0.121	0.000	0.818	0.228	0.488	0.309	0.266	0.325	0.750
Sidwood	-0.021	-0.162	0.015	-0.158	0.147	0.000	0.662	0.230	0.370	0.923	0.751	0.292
Cumbria pre-1980	0.221	0.293	0.154	0.180	0.101	0.277	0.000	0.258	0.290	0.059	0.079	0.401
Cumbria post-1980	0.123	0.153	0.150	-0.089	0.187	0.030	0.170	0.000	0.580	0.302	0.222	0.213
Tyne Valley	0.177	0.123	0.040	0.188	0.124	0.125	0.199	0.278	0.000	0.478	0.567	0.519
Pooley Bridge	0.387	0.483	0.222	0.294	0.218	0.417	0.000	0.208	0.308	0.000	0.128	0.601
Rosthwaite	0.229	0.397	0.236	0.250	0.269	0.378	0.035	0.156	0.341	0.385	0.000	0.583
Foulshaw Moss	0.148	0.095	0.183	0.013	0.212	-0.001	0.221	0.089	0.235	0.331	0.325	0.000