Method for detecting mutations in a mitochondrial DNA (mtDNA), chloroplastic DNA (cpDNA), or plasmid DNA target sequence, comprising a) providing: i) a bulk sample comprising more than 100 copies of said mtDNA, cpDNA, or plasmid DNA target sequence, and ii) a sample comprising 10 or fewer copies of said mtDNA, cpDNA, or plasmid DNA target sequence, and iii) detection reagents comprising at least one detectably distinguishable probe set of two hybridization probes which hybridize to adjacent sequences in said target sequence, each probe set comprising: A) a quencher probe labeled with a non-fluorescent quencher, and B) a signaling probe labeled with a fluorescence-emitting dye and a non-fluorescent quencher, wherein said signal probe does not emit fluorescence above background when not hybridized to its target sequence, but emits a fluorescence signal above background upon hybridization to its target sequence in the absence of bound quencher probe, wherein, if both signaling and quencher probes are hybridized to their adjacent target nucleic acid sequences, the non-fluorescent quencher of the quencher probe quenches the signal from the signaling probe; b) generating a temperature-dependent fluorescence signature for each probe set with said sample comprising 10 or fewer copies at a range of temperatures; c) generating a temperature-dependent fluorescence signature for each probe set with said bulk sample at a range of temperatures; and d) comparing said temperature-dependent fluorescence signature of said sample comprising 10 or fewer copies with said temperature-dependent fluorescence signature of said bulk sample to detect mutations in said mtDNA, cpDNA or plasmid DNA. a) providing: i) a bulk sample comprising more than 100 copies of said mtDNA, cpDNA, or plasmid DNA target sequence, and ii) a sample comprising 10 or fewer copies of said mtDNA, cpDNA, or plasmid DNA target sequence, and iii) detection reagents comprising at least one detectably distinguishable probe set of two hybridization probes which hybridize to adjacent sequences in said target sequence, each probe set comprising: A) a quencher probe labeled with a non-fluorescent quencher, and B) a signaling probe labeled with a fluorescence-emitting dye and a non-fluorescent quencher, wherein said signal probe does not emit fluorescence above background when not hybridized to its target sequence, but emits a fluorescence signal above background upon hybridization to its target sequence in the absence of bound quencher probe, wherein, if both signaling and quencher probes are hybridized to their adjacent target nucleic acid sequences, the non-fluorescent quencher of the quencher probe quenches the signal from the signaling probe; i) a bulk sample comprising more than 100 copies of said mtDNA, cpDNA, or plasmid DNA target sequence, and ii) a sample comprising 10 or fewer copies of said mtDNA, cpDNA, or plasmid DNA target sequence, and iii) detection reagents comprising at least one detectably distinguishable probe set of two hybridization probes which hybridize to adjacent sequences in said target sequence, each probe set comprising: A) a quencher probe labeled with a non-fluorescent quencher, and B) a signaling probe labeled with a fluorescence-emitting dye and a non-fluorescent quencher, wherein said signal probe does not emit fluorescence above background when not hybridized to its target sequence, but emits a fluorescence signal above background upon hybridization to its target sequence in the absence of bound quencher probe, wherein, if both signaling and quencher probes are hybridized to their adjacent target nucleic acid sequences, the non-fluorescent quencher of the quencher probe quenches the signal from the signaling probe; A) a quencher probe labeled with a non-fluorescent quencher, and B) a signaling probe labeled with a fluorescence-emitting dye and a non-fluorescent quencher, wherein said signal probe does not emit fluorescence above background when not hybridized to its target sequence, but emits a fluorescence signal above background upon hybridization to its target sequence in the absence of bound quencher probe, wherein, if both signaling and quencher probes are hybridized to their adjacent target nucleic acid sequences, the non-fluorescent quencher of the quencher probe quenches the signal from the signaling probe; b) generating a temperature-dependent fluorescence signature for each probe set with said sample comprising 10 or fewer copies at a range of temperatures; c) generating a temperature-dependent fluorescence signature for each probe set with said bulk sample at a range of temperatures; and d) comparing said temperature-dependent fluorescence signature of said sample comprising 10 or fewer copies with said temperature-dependent fluorescence signature of said bulk sample to detect mutations in said mtDNA, cpDNA or plasmid DNA.