Breeding System 3 mtdna 4 Latitude Longitude. C 1 ON lake FF CP PCe Ghabooli. C 2 ME lake FF CP PCe Lynch

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1 Additional File 1. Table.1. Isolates from the Daphnia pulex species complex analyzed for this study. 1. C = D. pulicaria, = D. pulex, C = pulicaria/pulex hybrid, ARE = D. arenata, EPC = European D. pulicaria, EP = European D. pulex, MEL = D. melanica, MID = D. middendorfiana, TEN = D. tenebrosa, SAPC = South American D. pulicaria, OBT = D. obtusa 2. Canadian provinces and USA states have 2-letter codes. Countries have 3-letter UN codes. 3. CP = cyclic parthenogenesis; OP = obligate parthenogenesis; U = unknown 4. D. pulicaria is subdivided into eastern (Pce) and western (PCw) lineages. The remaining codes refer to species as in column 1. Species 1 no. Prov/St Country 2 Habitat LDHA genotype Breeding System 3 mtdna 4 Latitude Longitude Source Lab C 1 ON lake FF CP PCe Ghabooli C 2 ME lake FF CP PCe Lynch C 3 MI lake FF CP PCw Lynch C 4 PA lake FF CP PCw Lynch C 5 SK lake FF CP PCw Crease C 6 WY lake FF CP PCw Crease C 7 IL lake FF CP P Caceres C 8 ID lake FF CP P Lynch C 9 IL lake FF CP P Caceres C 10 IL lake FF CP P Caceres C 11 WA lake FF CP P Hebert C 12 QC pond FF OP PCw Dufresne C 13 SK prairie pothole FF U PCw Crease C 14 SK prairie pothole FF U PCw Crease C 15 MB prairie pothole FF U P Crease C 16 MB prairie pothole FF U P Crease C 17 SK prairie pothole FF U P Crease C 1 ISL pond SF OP PCe Weider C 2 QC pond SF OP PCe Dufresne C 3 MI pond SF OP P Crease C 4 ME pond SF OP P Herrish/Hairston C 5 NB pond SF OP P Lynch C 6 NB pond SF OP P Lynch C 7 IN pond SF OP P Dudycha C 8 ON pond SF OP P Cristescu C 9 ON pond SF OP P Cristescu C 10 ME pond SF OP P Lynch C 11 MI pond SF OP P Innes C 12 NB pond SF OP P Lynch C 13 NT pond SF OP P Crease C 14 ON pond SF U P Crease C 15 MB pond SF U P Crease C 16 MB pond SF U P Crease C 17 SK pond SF U P Crease C 18 SK pond SF U P Crease 1 MI pond SS CP P Crease 2 IL pond SS CP P Caceres 3 WI pond SS CP P Lynch 4 IL pond SS CP P Crease

2 Species 1 no. Prov/St Country 2 Habitat LDHA genotype Breeding System 3 mtdna 4 Latitude Longitude Source Lab 5 ON pond SS CP P Innes 6 MN pond SS CP P Lynch 7 ON pond SS CP P Crease 8 IL pond SS CP P Lynch 9 ON pond SS CP P Crease 10 IN pond SS CP P Lynch 11 IN pond SS CP P Crease 12 MI pond SS CP P Lynch 13 MI pond SS CP P Lynch 14 QC pond SS OP P Crease 15 QC pond SS OP P Crease 16 MI pond SS OP P Crease 17 ON pond SS OP P Crease 18 NY pond SS OP P Lynch 19 MI pond SS OP P Lynch 20 WI pond SS OP P Lynch 21 OR pond SS OP P Pfrender 22 QC pond SS OP P Lynch 23 QC pond SS OP P Lynch 24 MI pond SS OP P Lynch 25 MN pond SS OP P Lynch 26 ME pond SS OP P Lynch 27 NY pond SS OP P Lynch 28 ON pond SS OP P Lynch 29 ME pond SS OP P Lynch 30 OH pond SS OP P Lynch 31 ON pond SS U P Crease 32 SK pond SS U P Crease 33 SK pond SS U P Crease 34 SK pond SS U P Crease 35 IL pond SS U P Geedey ARE 1 OR pond SS CP AR Lynch ARE 2 OR pond SS CP AR Lynch ARE 3 OR pond SS CP AR Lynch MEL OR pond FF CP ME Lynch MID 1 MB pond SF OP MI Dufresne MID 2 NUN pond SS OP MI Weider EPC 1 CZE lake SS CP EC Dufresne EPC 2 ESP lake SS CP EC Dufresne EPC 3 CZE lake SS CP EC Adam TEN NT pond SS OP TE Weider SAPC 1 BOL lake SF OP SA-C Mergeay SAPC 2 PER lake SF U SA-C Adamowicz SAPC 3 BOL lake SF U SA-C Adamowicz EP CZE pond SS CP E Adam OBT IL pond SS CP OB Lynch

3 Additional File 1. Table 2. List of LdhA and LdhB allele groups used in the nt diversity analysis of D. pulex and D. pulicaria NOTE Alleles from hybrids involving species other than North American D. pulex or D. pulicaria were not included in the diversity analyses. LDHA group LDHA group C LDHB group LDHB group C 01A_MI C 01_ON 01A_MI C 01A_ON 01B_MI C 02_ME 01B_MI C 01B_ON 02A_IL C 03_MI 02A_IL C 02A_ME 02B_IL C 04_PA 02B_IL C 02B_ME 03A_WI C 05A_SK 03A_WI C 03A_MI 03B_WI C 05B_SK 03B_WI C 03B_MI 04A_IL C 06A_WY 04A_IL C 04A_PA 04B_IL C 06B_WY 04B_IL C 04B_PA 05_ON C 07_IL 05A_ON C 05A_SK 06A_MN C 08A_ID 05B_ON C 05B_SK 06B_MN C 08B_ID 06A_MN C 06A_WY 07_ON C 09_IL 06B_MN C 06B_WY 08A_IL C 10_IL 07A_ON C 07A_IL 08B_IL C 11_WA 07B_ON C 07B_IL 09_ON C 12A_QC 08_IL C 08A_ID 10_IN C 12B_QC 09A_ON C 08B_ID 11A_IN C 13_SK 09B_ON C 09A_IL 11B_IN C 14A_SK 10A_IN C 09B_IL 12A_MI C 14B_SK 10B_IN C 10A_IL 12B_MI C 15A_MB 11_IN C 10B_IL 13A_MI C 15B_MB 12A_MI C 11A_WA 13B_MI C 16A_MB 12B_MI C 11B_WA 014A_QC C 16B_MB 13A_MI C 12A_QC 014B_QC C 17_SK 13B_MI C 12B_QC 015A_QC C 01A_ICE 14A_QC C 13A_SK 15B_QC C 02A_QC 14B_QC C 13B_SK 16A_MI C 03A_MI 15A_QC C 14A_SK 16B_MI C 04A_ME 15B_QC C 14B_SK 17_ON C 05A_NB 16A_MI C 15A_MB 18A_NY C 06A_NB 16B_MI C 15B_MB 18B_NY C 07B_IN 17_ON C 16A_MB 19A_MI C 08A_ON 18A_NY C 16B_MB 19B_MI C 09A_ON 18B_NY C 17A_SK 20A_WI C 10A_ME 19A_MI C 17B_SK 20B_WI C 11A_MI 19B_MI C 01A_ICE 21_OR C 12A_NB 20_WI C 02B_QC 22_QC C 13A_NT 21_OR C 03B_MI 23A_QC C 14A_ON 22_QC C 04A_ME 23B_QC C 15A_MB 23A_QC C 06B_NB 24_MI C 16A_MB 23B_QC C 07A_IN 25A_MN C 17A_SK 24A_MI C 08A_ON 25B_MN C 18A_SK 24B_MI C 09A_ON 26_ME N=42 25A_MN C 10A_ME 27_NY 25B_MN C 11B_MI 28A_ON 26_ME C 12A_NB 28B_ON 27A_NY C 13B_NT 29A_ME 27B_NY C 14B_ON 29B_ME 28A_ON C 15A_MB 30A_OH 28B_ON C 16A_MB

4 30B_OH 29A_ME C 16B_MB 31_ON 29B_ME C 17A_SK 32A_SK 30B_OH C 17B_SK 32B_SK 31A_ON C 18A_SK 33A_SK 31B_ON C 18B_SK 33B_SK 32A_SK 30A_OH 34A_SK 33A_SK 32B_SK 34B_SK 35B_IL 33B_SK 35A_IL C 02A_QC 34_SK 35B_IL C 03A_MI 35A_IL C 02B_QC C 04B_ME N=59 C 04B_ME C 05_NB C 05B_NB C 06A_NB C 06B_NB C 07B_IN C 07A_IN C 08B_ON C 08B_ON C 09B_ON C 09B_ON C 10B_ME C 10B_ME C 11A_MI C 11B_MI C 12B_NB C 12B_NB C 13A_NT C 13B_NT C 14A_ON C 14B_ON C 15B_MB C 15B_MB N=71 C 16B_MB C 17B_SK NOTES C 18B_SK LDHA-C-03B_MI is an MI allele and is omitted N=75 LDHA-C-01B_ICE is an EC allele and is omitted LDHB-C-01B_ICE is an EC allele and is omitted

5 Additional File 1. Table 3. Results of the recombination analysis among alleles of Ldh A in D. pulicaria and D. pulex. Population 1: LDHA_pulex Number of sequences: 75 Population 2: LDHA_pulicaria Number of sequences: 42 Number of Gene Conversion tracts identified: 30 group Line: LDHA-C-02b_QC (population 1). Tract located between sites: Line: LDHA-C-02b_QC (population 1). Tract located between sites: Line: LDHA-C-07a_IN (population 1). Tract located between sites: C Line: LDHA-C-07a_IN (population 1). Tract located between sites: Line: LDHA-C-13b_NT (population 1). Tract located between sites: Line: LDHA-C-13b_NT (population 1). Tract located between sites: Line: LDHA-C-14b_ON (population 1). Tract located between sites: Line: LDHA-C-15b_MB (population 1). Tract located between sites: Line: LDHA-C-15b_MB (population 1). Tract located between sites: Line: LDHA-C-16b_MB (population 1). Tract located between sites: Line: LDHA-C-16b_MB (population 1). Tract located between sites: Line: LDHA-C-17b_SK (population 1). Tract located between sites: Line: LDHA-C-17b_SK (population 1). Tract located between sites: Line: LDHA-C-18b_SK (population 1). Tract located between sites: Line: LDHA-C-18b_SK (population 1). Tract located between sites: Line: LDHA--06b_MN (population 1). Tract located between sites: Line: LDHA--06b_MN (population 1). Tract located between sites: Line: LDHA--02a_SK (population 1). Tract located between sites: Line: LDHA--32b_SK (population 1). Tract located between sites: Line: LDHA--32b_SK (population 1). Tract located between sites: Line: LDHA--33a_SK (population 1). Tract located between sites: Line: LDHA--33a_SK (population 1). Tract located between sites: Line: LDHA--33b_SK (population 1). Tract located between sites: Line: LDHA--33b_SK (population 1). Tract located between sites: Line: LDHA--34a_SK (population 1). Tract located between sites: Line: LDHA--34a_SK (population 1). Tract located between sites: Line: LDHA--34b_SK (population 1). Tract located between sites: Line: LDHA--34b_SK (population 1). Tract located between sites: Line: LDHA--35b_IL (population 1). Tract located between sites: Line: LDHA-C-07b_IN (population 2). Tract located between sites: Nucleotide distance (excluding gaps): 127 C

6 Additional File 1. Table 4. Results of the recombination analysis among alleles of Ldh B in D. pulicaria and D. pulex. Population 1: LDHB_pulex Number of sequences: 71 Population 2: LDHB_pulicaria Number of sequences: 59 Number of Gene Conversion tracts identified: 15 group Line: 'LDHB-C-03b_MI' (population 1). Tract located between sites: Nucleotide distance (excluding gaps): 76 C Line: 'LDHB-C-02a_QC' (population 2). Tract located between sites: Line: 'LDHB-C-03a_MI' (population 2). Tract located between sites: Line: 'LDHB-C-04b_ME' (population 2). Tract located between sites: Nucleotide distance (excluding gaps): 2 Line: 'LDHB-C-04b_ME' (population 2). Tract located between sites: Line: 'LDHB-C-13a_NT' (population 2). Tract located between sites: Line: 'LDHB--04a_IL' (population 2). Tract located between sites: Line: 'LDHB--05b_ON' (population 2). Tract located between sites: Line: 'LDHB--27a_NY' (population 2). Tract located between sites: Line: 'LDHB--29b_ME' (population 2). Tract located between sites: Line: 'LDHB--30b_OH' (population 2). Tract located between sites: Nucleotide distance (excluding gaps): 76 Line: 'LDHB--32a_SK' (population 2). Tract located between sites: Nucleotide distance (excluding gaps): 501 Line: 'LDHB--33a_SK' (population 2). Tract located between sites: Nucleotide distance (excluding gaps): 2 Line: 'LDHB--35b_IL' (population 2). Tract located between sites: Nucleotide distance (excluding gaps): 2 Line: 'LDHB--35b_IL' (population 2). Tract located between sites:

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