Periodic Reporting for period 2 - HighThroughFROGS (Reviving ghosts of taxonomy past: Identifying cryptic species using high-throughput sequencing of historical museum specimens for Asian ranids with gastromyzophorous tadpoles)
Période du rapport: 2022-03-01 au 2023-02-28
This study was designed to develop protocols and procedures to obtain genomic DNA data from degraded old museum specimens using High Throughput Sequencing (HTS) using Southeast Asian frogs as focal taxa. Specimens housed in natural history museums are essential raw materials for studies of cryptic speciation that is very common in the tropics. These studies require molecular genetic tools that, to date, could only be applied to freshly collected tissue samples. Because HTS is based on short-fragment sequencing technology, it is more effective at obtaining sequence data from historical specimens than Sanger sequencing, particularly for very old samples collected more than 100 years ago. HTS methods used to assess the phylogenetic and taxonomic position of the Asian ranid frogs with gastromyzophorous tadpoles, a group that has defied taxonomic clarification for decades. The results of this study will be a valuable baseline to assess the feasibility of and to improve exome-capture techniques aimed at retrieving historical DNA from type specimens for future studies. This study will be the first to investigate the evolution of gastromyzophory in Asian ranid frogs. It will also emphasize the need to apply modern techniques in tropical countries with high biodiversity as a critical step in quantifying its diversity and developing conservation actions for cryptic species. Apart from that, this study is an exceptional step towards advancing my career and establish myself as an independent researcher in the field of phylogenetics systematics. Furthermore, I will be able to actively contribute to disseminate my science to broader audience and play an important role as a catalyst for a long term collaborations an opening between the institutions in Germany, USA, and Indonesia in phylogenomic, systematics, and biogeographic studies.
Work performed during the outgoing and incoming phase are as follow:
1. Implementation of WP1-5, which includes hands-on training in genomics methods for phylogenetics and systematics study, protocol testing to optimize DNA yield extracted from historical museum specimens, DNA extraction for a total of 133 samples from both modern and historical samples, and exome capture sequencing for those samples.
2. Implementation of WP6 (include data processing and in depth data analyses).
3. Implementation of WP7 (manuscript writing).
4. Implementation of WP8 (career development), which includes preparation for the next career step after this MSCA program completed.
5. Implementation of other activities: networking, outreach activities, student supervision, etc.
Main results achieved so far are as follow:
1. Extraction protocols that could potentially be used to optimize DNA yield from museum specimens.
2. Raw sequences of modern and historical samples processed in this study.
3. (Preliminary) reconstructions of phylogentic tree for the Asian ranids with gastromyzophorous tadpoles.
4. Rough outline of the manuscripts.
5. Several job/grant applications were submitted, although have not received any positive results thus far.
1. Implementation of WP1-5, which includes hands-on training in genomics methods for phylogenetics and systematics study, protocol testing to optimize DNA yield extracted from historical museum specimens, DNA extraction for a total of 133 samples from both modern and historical samples, and exome capture sequencing for those samples.
2. Implementation of WP6 (include data processing and in depth data analyses).
3. Implementation of WP7 (manuscript writing).
4. Implementation of WP8 (career development), which includes preparation for the next career step after this MSCA program completed.
5. Implementation of other activities: networking, outreach activities, student supervision, etc.
Main results achieved so far are as follow:
1. Extraction protocols that could potentially be used to optimize DNA yield from museum specimens.
2. Raw sequences of modern and historical samples processed in this study.
3. (Preliminary) reconstructions of phylogentic tree for the Asian ranids with gastromyzophorous tadpoles.
4. Rough outline of the manuscripts.
5. Several job/grant applications were submitted, although have not received any positive results thus far.
Progress beyond the state of the art of this project is mainly related to the improvement in the researcher career profile through various trainings obtained during this program.
Expected results of the project are to generate a robust phylogenetic backbone required to establish a proper taxonomy for the Asian ranids group with gastromyzophorous tadpoles as well as elucidate the evolutionary history of the group. Also a protocols/procedures to obtain genomic DNA data from degraded old museum specimens using high throughput sequencing (HTS). The results have not been achieved by the end of the project but I hope to continue the analysis and preparing the manuscript to publish the results in the future.
Potential impacts are as follow:
1. The results from this study will be fundamental resources for any future activities the plan to do for managing biodiversity and designing conservation actions in Indonesia.
2. This study become evidence why we need to apply for modern techniques in tropical countries with high biodiversity as a critical step in quantifying its diversity and developing conservation actions for cryptic species.
3. This study is an exceptional step towards advancing my career and establish myself as an independent researcher in the field of phylogenetics systematics.
Expected results of the project are to generate a robust phylogenetic backbone required to establish a proper taxonomy for the Asian ranids group with gastromyzophorous tadpoles as well as elucidate the evolutionary history of the group. Also a protocols/procedures to obtain genomic DNA data from degraded old museum specimens using high throughput sequencing (HTS). The results have not been achieved by the end of the project but I hope to continue the analysis and preparing the manuscript to publish the results in the future.
Potential impacts are as follow:
1. The results from this study will be fundamental resources for any future activities the plan to do for managing biodiversity and designing conservation actions in Indonesia.
2. This study become evidence why we need to apply for modern techniques in tropical countries with high biodiversity as a critical step in quantifying its diversity and developing conservation actions for cryptic species.
3. This study is an exceptional step towards advancing my career and establish myself as an independent researcher in the field of phylogenetics systematics.