Which population are the likely sources of their ancestry or how much ancestry they can trace to each of them.
Left population set: Target/Test populations (whose history of admixture we are investigating) and Reference populations（potential sources of ancestry).
Reight population set: A set of Outgroups.
It requires a set of outgroup populations that contain enough genetic variation to be informative on the relationships between reference and target populations, but to have had no recent gene flow from reference or target populations.
This methodology allows one to model the Target/Test population as an N-way mixture of the Reference populations by exploiting the fact that the Reference populations differ in their relationship to the outgroups.
qpWave/qpAdm was used to model individuals from Northeast Asia (NEs) as mixtures of ancestry related to one, two, or three different sources. This method relies on comparing the relationship each set of target/test and sources share with a set of outgroups, without requiring explicit description of the exact phylogenetic relationship shared between the outgroups.
We first model ancient populations as having ancestry from N=1, 2, 3 other populations.
One-way mixture:
Left = (NE20, Ref)
Ref: Yana1, Yana2, Malta1, UstBelaya_N, Tianyuan, DevilsCave_N, Kolyma, Clovis, USR1, HDYM1, Bbdong, Qihe, Chokhopani, Mebrak, Ikawazu, Oroqen, Han, Ami, Itelman, Aleut, Pima, Mayan, Mixtec, Mixe, Zapotec, Piapoco, Karitiana, Surui, Quechua, Chane, NE56, NE_12K, NE-5, NE-1, NE_10K, NE_9k, NE_9K, NE-45, NE-35, NE-16, NE-49, NE_7K, NE_6K, NE-22, NE_5.5K, NE-59.
Right = (Mota, UstIshim, Kostenki14, GoyetQ116-1, Vestonice16, ElMiron, Villabruna, Stuttgart, Karelia, Loschbour, Satsurblia, Mbuti, French), Melinda A. Yang et.al.,2016.
for i in `cat left_pop`; do echo NE20 $i | tr " " "\n" > $i; sed 's/XX/'${i}'/g' par > par.$i; done
for i in `cat left_pop`; do qsub qpAdm.sh -N $i -F $i ; done &
grep -A 1 "tail prob" *.out |awk '{if ($6>0.05) print }' |grep -v fixed | awk '{print $1}' |cut -f 2,3 -d "." | sed 's/.out-//g' | sort -u
Try more references (NE20 as source):
Left = (NE20, Ref) or (Ref, NE20)
Ref: Malta1, AfontovaGora3, Yana1, Yamnaya, Shamanka_EN, Lokomotiv_EN, UstBelaya_N, UstBelaya_MED, UstBelaya_EBA, Afanasievo, Andronovo, Boisman_MN, DevilsCave_N, Kolyma, Clovis, USR1, Saqqaq, HDYM1, Bbdong, Qihe, Chokhopani, Mebrak, Ikawazu, Altaian, Oroqen, Chukchi, Itelman, Aleut, Koryak, Japanese, Korean, Han, Miao, Ami, Lahu, Onge, Papuan, Pima, Mayan, Mixtec, Mixe, Zapotec, Piapoco, Karitiana, Surui, Quechua, Chane, NE20, NE_12K, NE-5, NE-1, NE_10K, NE_9k, NE_9K, NE-45, NE-35, NE-16, NE-49, NE_7K, NE_6K, NE-22, NE_5.5K, NE-59.
Right = (Mbuti, Yoruba, Mota, Onge, Papuan, Ust’-Ishim, Kostenki14, GoyetQ116-1, Vestonice16, sunghir , Satsurblia), Martin Sikora et.al., Nature, 2019.
for i in `cat left_pop`; do echo $i NE20 | tr " " "\n" > $i; sed 's/XX/'${i}'/g' par > par.$i; done
for i in `cat left_pop`; do qsub qpAdm.sh -N $i -F $i ; done &
grep -A 1 "tail prob" *.out |awk '{if ($6>0.05) print }' |grep -v fixed | awk '{print $1}' |cut -f 2,3 -d "." | sed 's/.out-//g' | sort -u
Try different outgoups
Mota, Ust’-Ishim, Kostenki14, GoyetQ116-1, Vestonice16, ElMiron, Villabruna, Stuttgart, Mbuti, French
Two-way mixture:
Left = (NE20, Ref1, Ref2)
Ref: Malta1, AfontovaGora3, Yana1, Yamnaya, Shamanka_EN, Lokomotiv_EN, UstBelaya_N, UstBelaya_MED, UstBelaya_EBA, Afanasievo, Andronovo, Boisman_MN, DevilsCave_N, Kolyma, Clovis, USR1, Saqqaq, HDYM1, Bbdong, Qihe, Chokhopani, Mebrak, Ikawazu, Altaian, Oroqen, Chukchi, Itelman, Aleut, Koryak, Japanese, Korean, Han, Miao, Ami, Lahu, Onge, Papuan, Pima, Mayan, Mixtec, Mixe, Zapotec, Piapoco, Karitiana, Surui, Quechua, Chane, NE56, NE_12K, NE-5, NE-1, NE_10K, NE_9k, NE_9K, NE-45, NE-35, NE-16, NE-49, NE_7K, NE_6K, NE-22, NE_5.5K, NE-59.
Right = (Mbuti, Yoruba, Mota, Onge, Papuan, Ust’-Ishim, Kostenki14, GoyetQ116-1, Vestonice16, sunghir , Satsurblia), Martin Sikora et.al., Nature, 2019.
for i in `cat left_pop`; do awk -v var=$i '{print var " " $1}' left_pop | grep -v "$i $i" >> 2way_list; done
for i in `cat 2way_list| tr " " "." `;do ( echo $i | tr "." "\n"; echo NE20 ; ) > $i; sed 's/XX/'${i}'/g' par > par.$i; done
for i in `cat 2way_list | tr " " "."`; do qsub qpAdm2.sh -N $i -F $i; done &
grep -A 1 "tail prob" *.out |awk '{if ($6>0.05) print }' |grep -v 'fixed\|infeasible' | awk '{print $1}' |cut -f 2,3 -d "." | sort -u > list.final
One-way mixture:
Left = (NE56, Ref) or (Ref, NE56)
Ref: Malta1, AfontovaGora3, Yana1, Yamnaya, Shamanka_EN, Lokomotiv_EN, UstBelaya_N, UstBelaya_MED, UstBelaya_EBA, Afanasievo, Andronovo, Boisman_MN, DevilsCave_N, Kolyma, Clovis, USR1, Saqqaq, HDYM1, Bbdong, Qihe, Chokhopani, Mebrak, Ikawazu, Altaian, Oroqen, Chukchi, Itelman, Aleut, Koryak, Japanese, Korean, Han, Miao, Ami, Lahu, Onge, Papuan, Pima, Mayan, Mixtec, Mixe, Zapotec, Piapoco, Karitiana, Surui, Quechua, Chane, NE20, NE_12K, NE-5, NE-1, NE_10K, NE_9k, NE_9K, NE-45, NE-35, NE-16, NE-49, NE_7K, NE_6K, NE-22, NE_5.5K, NE-59.
Right = (Mbuti, Yoruba, Mota, Onge, Papuan, Ust’-Ishim, Kostenki14, GoyetQ116-1, Vestonice16, sunghir , Satsurblia), Martin Sikora et.al., Nature, 2019.
for i in `cat left_pop`; do echo $i NE56 | tr " " "\n" > $i; sed 's/XX/'${i}'/g' par > par.$i; done
for i in `cat left_pop`; do qsub qpAdm.sh -N $i -F $i ; done &
grep -A 1 "tail prob" *.out |awk '{if ($6>0.05) print }' |grep -v fixed | awk '{print $1}' |cut -f 2,3 -d "." | sed 's/.out-//g' | sort -u > list.final
Two-way mixture:
Left = (NE56, Ref) or (Ref, NE56)
Ref: Malta1, AfontovaGora3, Yana1, Yamnaya, Shamanka_EN, Lokomotiv_EN, UstBelaya_N, UstBelaya_MED, UstBelaya_EBA, Afanasievo, Andronovo, Boisman_MN, DevilsCave_N, Kolyma, Clovis, USR1, Saqqaq, HDYM1, Bbdong, Qihe, Chokhopani, Mebrak, Ikawazu, Altaian, Oroqen, Chukchi, Itelman, Aleut, Koryak, Japanese, Korean, Han, Miao, Ami, Lahu, Onge, Papuan, Pima, Mayan, Mixtec, Mixe, Zapotec, Piapoco, Karitiana, Surui, Quechua, Chane, NE20, NE_12K, NE-5, NE-1, NE_10K, NE_9k, NE_9K, NE-45, NE-35, NE-16, NE-49, NE_7K, NE_6K, NE-22, NE_5.5K, NE-59.
Right = (Mbuti, Yoruba, Mota, Onge, Papuan, Ust’-Ishim, Kostenki14, GoyetQ116-1, Vestonice16, sunghir , Satsurblia), Martin Sikora et.al., Nature, 2019.
for i in `cat left_pop`; do awk -v var=$i '{print var " " $1}' left_pop | grep -v "$i $i" >> 2way_list; done
for i in `cat 2way_list| tr " " "." `;do ( echo $i | tr "." "\n"; echo NE56 ; ) > $i; sed 's/XX/'${i}'/g' par > par.$i; done
for i in `cat 2way_list | tr " " "."`; do qsub qpAdm2.sh -N $i -F $i; done &
grep -A 1 "tail prob" *.out |awk '{if ($6>0.05) print }' |grep -v 'fixed\|infeasible' | awk '{print $1}' |cut -f 2,3 -d "." | sort -u > list.final
cat ../list.final | while read line; do cp ../../NE56/Two_way/results.2way/par.$line.out .; done
grep "nested" *.out | awk '{if ($11<0.05) print$1}' | cut -f 2,3 -d "." | sort -u > list.final
One-way mixture:
Left = (NE_12K, Ref) or (Ref, NE_12K)
Ref: Malta1, AfontovaGora3, Yana1, Yamnaya, Shamanka_EN, Lokomotiv_EN, UstBelaya_N, UstBelaya_MED, UstBelaya_EBA, Afanasievo, Andronovo, Boisman_MN, DevilsCave_N, Kolyma, Clovis, USR1, Saqqaq, HDYM1, Bbdong, Qihe, Chokhopani, Mebrak, Ikawazu, Altaian, Oroqen, Chukchi, Itelman, Aleut, Koryak, Japanese, Korean, Han, Miao, Ami, Lahu, Onge, Papuan, Pima, Mayan, Mixtec, Mixe, Zapotec, Piapoco, Karitiana, Surui, Quechua, Chane, NE20, NE56, NE-5, NE-1, NE_10K, NE_9k, NE_9K, NE-45, NE-35, NE-16, NE-49, NE_7K, NE_6K, NE-22, NE_5.5K, NE-59.
Right = (Mbuti, Yoruba, Mota, Onge, Papuan, Ust’-Ishim, Kostenki14, GoyetQ116-1, Vestonice16, sunghir , Satsurblia), Martin Sikora et.al., Nature, 2019.
for i in `cat left_pop`; do echo $i NE_12K | tr " " "\n" > $i; sed 's/XX/'${i}'/g' par > par.$i; done
for i in `cat left_pop`; do qsub qpAdm.sh -N $i -F $i ; done &
grep -A 1 "tail prob" *.out |awk '{if ($6>0.05) print }' |grep -v fixed | awk '{print $1}' |cut -f 2,3 -d "." | sed 's/.out-//g' | sort -u
Two-way mixture:
Left = (NE_12K, Ref) or (Ref, NE_12K)
Ref: Malta1, AfontovaGora3, Yana1, Yamnaya, Shamanka_EN, Lokomotiv_EN, UstBelaya_N, UstBelaya_MED, UstBelaya_EBA, Afanasievo, Andronovo, Boisman_MN, DevilsCave_N, Kolyma, Clovis, USR1, Saqqaq, HDYM1, Bbdong, Qihe, Chokhopani, Mebrak, Ikawazu, Altaian, Oroqen, Chukchi, Itelman, Aleut, Koryak, Japanese, Korean, Han, Miao, Ami, Lahu, Onge, Papuan, Pima, Mayan, Mixtec, Mixe, Zapotec, Piapoco, Karitiana, Surui, Quechua, Chane, NE20, NE56, NE-5, NE-1, NE_10K, NE_9k, NE_9K, NE-45, NE-35, NE-16, NE-49, NE_7K, NE_6K, NE-22, NE_5.5K, NE-59.
Right = (Mbuti, Yoruba, Mota, Onge, Papuan, Ust’-Ishim, Kostenki14, GoyetQ116-1, Vestonice16, sunghir , Satsurblia), Martin Sikora et.al., Nature, 2019.
for i in `cat left_pop`; do awk -v var=$i '{print var " " $1}' left_pop | grep -v "$i $i" >> 2way_list; done
for i in `cat 2way_list| tr " " "." `;do ( echo $i | tr "." "\n"; echo NE_12K ; ) > $i; sed 's/XX/'${i}'/g' par > par.$i; done
for i in `cat 2way_list | tr " " "."`; do qsub qpAdm2.sh -N $i -F $i; done &
grep -A 1 "tail prob" *.out |awk '{if ($6>0.05) print }' |grep -v 'fixed\|infeasible' | awk '{print $1}' |cut -f 2,3 -d "." | sort -u > list.final