Table 4.
A summary of phylogenetic analyses performed on various data subsets. Inclusion of data from each marker is denoted by the shaded boxes at left. The partitioning strategy with markers is indicated within the box. Combination of all characters of a marker is denoted by “+”. Coding sequence partitioning based on codon positions is denoted by “1/2/3”, etc. Additional random partitioning within codon position partitions is denoted “11/22/33”. Partitioning by stem-loop structure is denoted “S/L”. Doublet modeling in stem regions is denoted “Sd/L”. Tree scores for maximum likelihood (ML) analyses represent the log likelihood of the best tree according to the model. For Bayesian inference (BI) analyses, tree scores are given as the harmonic mean of the log likelihood. Tree scores from maximum parsimony (MP) analyses are given in the number of tree steps. For Bayesian analyses topologies reflect majority consensus trees. Topologies listed for ML analyses are from 50% bootstrap consensus trees. For MP analyses the most parsimonious tree or strict consensus of equally most parsimonious trees is shown. Tree topologies are described by abbreviating species and species groups as follows: CST, castaneum species group with internal topology as in Fig. 1; CNF, confusum species group; cnf, T. confusum; ana, T. anaphe; dst, T. destructor; brv, T. brevicornis; Lth, Latheticus oryzae; Gnt, Gnathocerus cornutus; Ten, Tenebrio molitor.
| dataset |
method | tree score | 2(lnL0−lnL1) | topology | Fig. | ||||
|---|---|---|---|---|---|---|---|---|---|
| cox1 | 16S | wg | 28S | H3 | |||||
| 1/2/3 | Sd/L | 12/3 | Sd/L | 1/2/3 | BI | 12332.8 | 2799.0 | ((((CST,CNF),Lth),Gnt),brv),Ten | 1 |
| + | + | + | + | + | BI | 13348.3 | 767.8 | ((CST,CNF),(Gnt,Lth)),brv),Ten | |
| 12 random partitions of set length | BI | 13749.0 | −33.4 | ((((CST,CNF),Lth),Gnt),brv),Ten | |||||
| 5 random partitions of set length | BI | 13728.8 | 6.9 | ((CST,CNF),(Gnt,Lth)),brv),Ten | |||||
| 5 random partitions of random length | BI | 13729.9 | 4.6 | ((CST,CNF),(Gnt,Lth)),brv),Ten | |||||
| combined | BI | 13732.2 | (L0) | (CST,CNF),brv,(Gnt,Lth),Ten | |||||
| combined | ML | 13705.2 | (CST,CNF),brv,(Gnt,Lth),Ten | ||||||
| combined | MP | 2272 | (((CST,(CNF,Lth)),brv),Gnt),Ten | ||||||
| 1/2/3 | Sd/L | 12 | Sd/L | 1/2/3 | BI | 11154.2 | ((((CST,CNF),Lth),Gnt),brv),Ten | ||
| 1/2/3 | Sd/L | 12 | Sd/L | 1/2 | BI | 10260.7 | ((((CST,CNF),Lth),Gnt),brv),Ten | (1) | |
| combined (w/o wg&H3 3rd pos) | MP | 1726 | ((((CST,CNF),Lth),brv),Gnt),Ten | 2 | |||||
| 1/2 | Sd/L | 12 | Sd/L | 1/2 | BI | 7700.3 | ((((CST,CNF),Lth),Gnt),brv),Ten | ||
| combined (only 3rd positions) | BI | 4284.8 | (((CST,(cnf,Lth)),brv),Gnt),Ten | ||||||
| 1/2/3 | Sd/L | BI | 6390.4 | 1055.2 | ((((CST,Lth),CNF),Gnt),brv),Ten | ||||
| combined | BI | 6918.0 | (L0) | (((CST,Lth),CNF,Gnt),brv),Ten | |||||
| combined | ML | 7699.1 | ((Lth w/in CST),(CNF,brv),Gnt),Ten | ||||||
| combined | MP | 1321 | ((CST,Lth),Gnt),(CNF,brv),Ten | ||||||
| 12/3 | Sd/L | 1/2/3 | BI | 5902.7 | 1318.1 | (CST,cnf),brv,(Gnt,Lth),Ten | |||
| combined | BI | 6561.8 | (L0) | ((CST,cnf),brv),(Gnt,Lth),Ten | |||||
| combined | ML | 6542.1 | (CST,cnf),brv,(Gnt,Lth),Ten | ||||||
| combined | MP | 937 | (((CST,(cnf,Lth)),brv),Gnt),Ten | ||||||
| 12 | Sd/L | 1/2/3 | BI | 4724.7 | 939.1 | resolves only (CST,cnf) | |||
| combined (w/o wg pos3) | BI | 5194.3 | (L0) | ((CST,cnf),brv),(Gnt,Lth),Ten | |||||
| 12 | Sd/L | 1/2 | BI | 3765.6 | 751.0 | ((CST,cnf),brv),Gnt,Lth,Ten | |||
| combined (no pos3) | BI | 4141.1 | (L0) | ((CST,cnf),brv),(Gnt,Lth),Ten | |||||
| combined (no pos3) | MP | 390 | ((((CST,cnf),Lth),Gnt),brv),Ten | ||||||
| 11/22/33 | BI | 4193.4 | 540.0 | ((CST,CNF,Lth,Gnt),brv),Ten | |||||
| 1/2/3 | BI | 4192.2 | 542.4 | ((CST,CNF,Lth,Gnt),brv),Ten | 4A | ||||
| 12/3 | BI | 4235.7 | 455.5 | resolves only CST | |||||
| rand (3) | BI | 4472.5 | −18.0 | resolves only CST and (cnf,dst) | |||||
| + | BI | 4463.4 | (L0) | ((CST,Lth,Gnt),(cnf,dest),ana,brv),Ten | |||||
| + | ML | 4431.1 | (((CST,Lth),Gnt),CNF),brv),Ten | ||||||
| + | MP | 897 | (((((Lth w/in CST),cnf),ana),(brv,Gnt)),dst),Ten | 4F | |||||
| Sd/L | BI | 2187.5 | 213.4 | ((CST,Lth),CNF,Gnt),brv),Ten | 4B | ||||
| S/L | BI | 2275.7 | 36.8 | ((CST,Lth),CNF,Gnt),brv),Ten | |||||
| rand | BI | 2292.0 | 4.3 | ((CST,Lth),CNF,Gnt),brv),Ten | |||||
| + | BI | 2294.2 | (L0) | ((CST,Lth),CNF,Gnt),brv),Ten | |||||
| + | ML | 2265.7 | (((CST,Lth)(CNF,Gnt)),brv),Ten | ||||||
| + | MP | 421 | ((((Lth w/in CST),Gnt),CNF),brv),Ten | 4G | |||||
| 1/2/3 | BI | 1985.4 | 214.1 | (((Gnt,Lth),cnf),brv),(Ten w/in CST) | |||||
| 12/3 | BI | 1971.0 | 242.8 | (((Gnt,Lth),brv),cnf),(Ten w/in CST) | 4C | ||||
| rand | BI | 2089.4 | 6.0 | (((Gnt,Lth),cnf),brv),(Ten w/in CST) | |||||
| + | BI | 2092.4 | (L0) | (((Gnt,Lth),brv),cnf),(Ten w/in CST) | |||||
| + | ML | 2074.4 | resolves only (Gnt,Lth) and (cst,Ten) | ||||||
| + | MP | 361 | (((Lth,Gnt),brv),cnf),mad,fre,cst,Ten | 4H | |||||
| 1/2 | BI | 752.0 | 3.0 | (((CST,brv),cnf),(Gnt,Lth)),Ten | |||||
| 12 | BI | 753.5 | (L0) | (((CST,cnf),brv),(Gnt,Lth)),Ten | 4C' | ||||
| 12 | MP | 57 | resolves only CST | ||||||
| Sd/L | BI | 2614.5 | 681.9 | ((CST,cnf),brv),Lth,Gnt,Ten | 4D | ||||
| S/L | BI | 2899.0 | 112.9 | ((CST,cnf),brv),Lth,Gnt,Ten | |||||
| rand | BI | 2953.5 | 3.9 | ((CST,cnf),brv),Lth,Gnt,Ten | |||||
| + | BI | 2955.5 | (L0) | ((CST,cnf),brv),Lth,Gnt,Ten | |||||
| + | ML | 2932.4 | ((CST,cnf),brv),Lth,Gnt,Ten | ||||||
| + | MP | 312 | ((((CST,cnf),Lth),Gnt),brv),Ten | 4I | |||||
| 1/2/3 | BI | 1294.2 | 317.9 | (CST,cnf,Lth),brv,Gnt,Ten | 4E | ||||
| 12/3 | BI | 1317.4 | 271.6 | (CST,cnf,Lth),brv,Gnt,Ten | |||||
| rand | BI | 1446.2 | 13.9 | (CST,cnf),Lth),brv),Gnt),Ten | |||||
| + | BI | 1453.1 | (L0) | (CST,cnf),brv,Lth,Gnt,Ten | |||||
| + | ML | 1426.0 | ((((CST,cnf),Lth),brv),Gnt),Ten | ||||||
| + | MP | 247 | (((CST,(cnf,Lth)),Gnt),brv),Ten | 4J | |||||
| 1/2 | BI | 407.8 | 25.1 | ((CST,cnf),brv,Gnt),Lth,Ten | |||||
| 12 | BI | 420.4 | (L0) | resolves only (cst,fre,mad,cnf) | |||||
| 12 | MP | 17 | (((cst,mad),fre,(cnf,brv),Gnt),Lth),Ten | ||||||