Microevolutionary processes and taxonomic investigations of the Atacama Desert flora
Microevolutionary processes and taxonomic investigations of the Atacama Desert flora
View/Type of Scholarly Publication
DissertationDate of Exam
09.12.2020Date of Publication
22.12.2020Advisor
Quandt, DietmarCo-Referee
Weigend, MaximilianMetadata
Show full item record
Citable Links 
Abstract
Plant evolutionary processes in the hyper arid Atacama Desert of northern Chile are here investigated using our species/species complexes as case studies based on the following research questions:
(1) Are populations of Tillandsia genetically isolated from each other or do they maintain gene flow across potential barriers such as patches of hyper arid landscape or surface rivers?
(2) Have populations of Huidobria undergone long-term isolation in parallel to the long-lasting aridity of the Atacama Desert?
(3) When did Eulychnia originate, and when and how did it diversify into the Atacama Desert?
(4) Can the considerations regarding of question (3) contribute to produce a taxonomic concept for Eulychnia?
(5) How many species of Ophryosporus are there in Chile?
These research questions are addressed employing a combination of modern population genetic methods (genotyping by sequencing, GBS), molecular phylogenetic methods of Sanger sequencing, as well as traditional alpha taxonomy based on morphological analyses and literature/herbarium review and research.
The dissertation is presented in a cumulative style. It consists of papers that have already been published or accepted for publication, as well as chapters currently in working progress and soon to be submitted to the relevant journals. Each of the five chapters contains its respective introduction and conclusive considerations.
Chapter 1 is a general introduction, which provides an overview of the Atacama Desert, and in which the central research questions of this dissertation are formulated; an overview of the dissertation is provided.
Chapter 2 is a population genomic study of Tillandsia landbeckii (Bromeliaceae). Genetic diversity and gene flow within and between populations was analysed, including a heterozygosity analysis, F-statistics (FST and FIS ), genetic structure, isolation by distance and an interpretation of the data to explain the current distribution of the sampled lomas in the light of landscape evolution in the Atacama. Our results show that founder effects through stepping-stone dispersal are likely responsible for the formation of Tillandsia lomas, and that individuals of different lomas reproduce sexually and/or asexually (clonally). Gene flow between lomas belonging to three geographically and genetically distinct clusters is limited and appears to be impacted by barriers, possibly surface rivers and distance across hyper arid landscape.
Chapter 3 is a population genomic study of Huidobria fruticosa (Loasaceae), an ancient endemic lineage that diverged from its closest known relative between 40–60 Mya. The aim of this chapter was to correlate the evolution of this species to the evolution of aridity in the Atacama Desert. It was expected to find a high genetic differentiation mirroring long-term isolation of populations in aridity. However, our analysis of SNP data employing population genomic methods such as measures of genetic diversity θπ, F-statistics (FST ), genetic structure and measures of time units based on an assumption of mutation rate showed, that the populations of this species are probably of recent origin since the Pleistocene. As in Tillandsia, the populations fell into genetically and geographically distinct clusters, with an estimated divergence age from each other matching geological data which suggests phases of prolonged aridity as the cause of these population cluster-splits. Our results further suggest that effective dispersal and a soil seed bank impact the genetic diversity in Huidobria and probably mitigate extinction risk of sub-populations.
Chapter 4 provides an estimation of the divergence time between two genera of the Cactaceae, Eulychnia and its sister genus Austrocactus. The aim of this study to elucidate the origins of Eulychnia and to reconstruct the diversification of this genus into the Atacama Desert. Phylogenies were produced from two differing data sets based on a complete taxon sampling of the genus Eulychnia. The first phylogeny was based on three plastid markers which were merged into a previously published family-wide phylogeny of the Cactaceae. A second phylogeny was calculated using SNP data obtained from GBS. Both phylogenies were molecular clock dated and a biogeographical analysis was produced. Our results provide an estimated divergence age of Eulychnia from Austrocactus approximately 7 Mya toward the Miocene-Pliocene boundary. Our biogeographic analysis revealed, that Eulychnia has evolved as a coastal taxon, and diversified in response to prolonged phases of aridity during the Pleistocene. Diversification age estimates correlate, as in the previous study on Huidobria, with geological results obtained from cosmogenic nuclide exposure dating and we interpret the current allopatric distribution of Eulychnia taxa as the result of habitat fragmentation through prolonged arid phases. The very recent diversification within this genus in combination with distinct hybrid zones at range limits, points to the preliminary assumption that speciation processes are still underway, with taxa not yet having reached full reproductive isolation. This idea has led to the following chapter.
Chapter 5 provides a taxonomic revision of the genus Eulychnia in the light of the results obtained from the previous chapter and the idea that speciation in Eulychnia has not yet reached reproductive isolation between taxa. The genus has a checkered taxonomic history and posed several issues regarding the type specimens of names provided by Friedrich Ritter. The original names published by Philippi remained untypified until twenty years ago. Several recently published species needed a new taxonomic circumscription. In this synopsis we accept three species and nine subspecies of Eulychnia in line with morphological variation, geographic distribution and phylogenetic results.
Chapter 6 provides a taxonomic revision of the genus Ophryosporus for Chile. There is no recent revision of the genus and confusion existed over names applied to Chilean plants. Some Chilean members of Ophryosporus have only been collected sporadically and a morphological analysis was required to ascertain their taxonomic relationship. Nomenclatural issues were resolved, including some necessary lectotypifications and an epitypification of names, and a key to the Chilean species of Ophryosporus was provided. This work recognises six species of Ophryosporus in Chile and forms the basis for any further studies on the genus.
(1) Are populations of Tillandsia genetically isolated from each other or do they maintain gene flow across potential barriers such as patches of hyper arid landscape or surface rivers?
(2) Have populations of Huidobria undergone long-term isolation in parallel to the long-lasting aridity of the Atacama Desert?
(3) When did Eulychnia originate, and when and how did it diversify into the Atacama Desert?
(4) Can the considerations regarding of question (3) contribute to produce a taxonomic concept for Eulychnia?
(5) How many species of Ophryosporus are there in Chile?
These research questions are addressed employing a combination of modern population genetic methods (genotyping by sequencing, GBS), molecular phylogenetic methods of Sanger sequencing, as well as traditional alpha taxonomy based on morphological analyses and literature/herbarium review and research.
The dissertation is presented in a cumulative style. It consists of papers that have already been published or accepted for publication, as well as chapters currently in working progress and soon to be submitted to the relevant journals. Each of the five chapters contains its respective introduction and conclusive considerations.
Chapter 1 is a general introduction, which provides an overview of the Atacama Desert, and in which the central research questions of this dissertation are formulated; an overview of the dissertation is provided.
Chapter 2 is a population genomic study of Tillandsia landbeckii (Bromeliaceae). Genetic diversity and gene flow within and between populations was analysed, including a heterozygosity analysis, F-statistics (FST and FIS ), genetic structure, isolation by distance and an interpretation of the data to explain the current distribution of the sampled lomas in the light of landscape evolution in the Atacama. Our results show that founder effects through stepping-stone dispersal are likely responsible for the formation of Tillandsia lomas, and that individuals of different lomas reproduce sexually and/or asexually (clonally). Gene flow between lomas belonging to three geographically and genetically distinct clusters is limited and appears to be impacted by barriers, possibly surface rivers and distance across hyper arid landscape.
Chapter 3 is a population genomic study of Huidobria fruticosa (Loasaceae), an ancient endemic lineage that diverged from its closest known relative between 40–60 Mya. The aim of this chapter was to correlate the evolution of this species to the evolution of aridity in the Atacama Desert. It was expected to find a high genetic differentiation mirroring long-term isolation of populations in aridity. However, our analysis of SNP data employing population genomic methods such as measures of genetic diversity θπ, F-statistics (FST ), genetic structure and measures of time units based on an assumption of mutation rate showed, that the populations of this species are probably of recent origin since the Pleistocene. As in Tillandsia, the populations fell into genetically and geographically distinct clusters, with an estimated divergence age from each other matching geological data which suggests phases of prolonged aridity as the cause of these population cluster-splits. Our results further suggest that effective dispersal and a soil seed bank impact the genetic diversity in Huidobria and probably mitigate extinction risk of sub-populations.
Chapter 4 provides an estimation of the divergence time between two genera of the Cactaceae, Eulychnia and its sister genus Austrocactus. The aim of this study to elucidate the origins of Eulychnia and to reconstruct the diversification of this genus into the Atacama Desert. Phylogenies were produced from two differing data sets based on a complete taxon sampling of the genus Eulychnia. The first phylogeny was based on three plastid markers which were merged into a previously published family-wide phylogeny of the Cactaceae. A second phylogeny was calculated using SNP data obtained from GBS. Both phylogenies were molecular clock dated and a biogeographical analysis was produced. Our results provide an estimated divergence age of Eulychnia from Austrocactus approximately 7 Mya toward the Miocene-Pliocene boundary. Our biogeographic analysis revealed, that Eulychnia has evolved as a coastal taxon, and diversified in response to prolonged phases of aridity during the Pleistocene. Diversification age estimates correlate, as in the previous study on Huidobria, with geological results obtained from cosmogenic nuclide exposure dating and we interpret the current allopatric distribution of Eulychnia taxa as the result of habitat fragmentation through prolonged arid phases. The very recent diversification within this genus in combination with distinct hybrid zones at range limits, points to the preliminary assumption that speciation processes are still underway, with taxa not yet having reached full reproductive isolation. This idea has led to the following chapter.
Chapter 5 provides a taxonomic revision of the genus Eulychnia in the light of the results obtained from the previous chapter and the idea that speciation in Eulychnia has not yet reached reproductive isolation between taxa. The genus has a checkered taxonomic history and posed several issues regarding the type specimens of names provided by Friedrich Ritter. The original names published by Philippi remained untypified until twenty years ago. Several recently published species needed a new taxonomic circumscription. In this synopsis we accept three species and nine subspecies of Eulychnia in line with morphological variation, geographic distribution and phylogenetic results.
Chapter 6 provides a taxonomic revision of the genus Ophryosporus for Chile. There is no recent revision of the genus and confusion existed over names applied to Chilean plants. Some Chilean members of Ophryosporus have only been collected sporadically and a morphological analysis was required to ascertain their taxonomic relationship. Nomenclatural issues were resolved, including some necessary lectotypifications and an epitypification of names, and a key to the Chilean species of Ophryosporus was provided. This work recognises six species of Ophryosporus in Chile and forms the basis for any further studies on the genus.
Subjects
Atacama Desert, population genomics, genotyping by sequencing, taxonomy, Asteraceae, Bromeliaceae, Cactaceae, Loasaceae
Classification (DDC)
570 Biowissenschaften, BiologieMerklinger, Felix Franz: Microevolutionary processes and taxonomic investigations of the Atacama Desert flora. - Bonn, 2020. - Dissertation, Rheinische Friedrich-Wilhelms-Universität Bonn.
Online-Ausgabe in bonndoc: https://nbn-resolving.org/urn:nbn:de:hbz:5-60780
Online-Ausgabe in bonndoc: https://nbn-resolving.org/urn:nbn:de:hbz:5-60780
@phdthesis{handle:20.500.11811/8863,
urn: https://nbn-resolving.org/urn:nbn:de:hbz:5-60780,
author = {{Felix Franz Merklinger}},
title = {Microevolutionary processes and taxonomic investigations of the Atacama Desert flora},
school = {Rheinische Friedrich-Wilhelms-Universität Bonn},
year = 2020,
month = dec,
note = {Plant evolutionary processes in the hyper arid Atacama Desert of northern Chile are here investigated using our species/species complexes as case studies based on the following research questions:
(1) Are populations of Tillandsia genetically isolated from each other or do they maintain gene flow across potential barriers such as patches of hyper arid landscape or surface rivers?
(2) Have populations of Huidobria undergone long-term isolation in parallel to the long-lasting aridity of the Atacama Desert?
(3) When did Eulychnia originate, and when and how did it diversify into the Atacama Desert?
(4) Can the considerations regarding of question (3) contribute to produce a taxonomic concept for Eulychnia?
(5) How many species of Ophryosporus are there in Chile?
These research questions are addressed employing a combination of modern population genetic methods (genotyping by sequencing, GBS), molecular phylogenetic methods of Sanger sequencing, as well as traditional alpha taxonomy based on morphological analyses and literature/herbarium review and research.
The dissertation is presented in a cumulative style. It consists of papers that have already been published or accepted for publication, as well as chapters currently in working progress and soon to be submitted to the relevant journals. Each of the five chapters contains its respective introduction and conclusive considerations.
Chapter 1 is a general introduction, which provides an overview of the Atacama Desert, and in which the central research questions of this dissertation are formulated; an overview of the dissertation is provided.
Chapter 2 is a population genomic study of Tillandsia landbeckii (Bromeliaceae). Genetic diversity and gene flow within and between populations was analysed, including a heterozygosity analysis, F-statistics (FST and FIS ), genetic structure, isolation by distance and an interpretation of the data to explain the current distribution of the sampled lomas in the light of landscape evolution in the Atacama. Our results show that founder effects through stepping-stone dispersal are likely responsible for the formation of Tillandsia lomas, and that individuals of different lomas reproduce sexually and/or asexually (clonally). Gene flow between lomas belonging to three geographically and genetically distinct clusters is limited and appears to be impacted by barriers, possibly surface rivers and distance across hyper arid landscape.
Chapter 3 is a population genomic study of Huidobria fruticosa (Loasaceae), an ancient endemic lineage that diverged from its closest known relative between 40–60 Mya. The aim of this chapter was to correlate the evolution of this species to the evolution of aridity in the Atacama Desert. It was expected to find a high genetic differentiation mirroring long-term isolation of populations in aridity. However, our analysis of SNP data employing population genomic methods such as measures of genetic diversity θπ, F-statistics (FST ), genetic structure and measures of time units based on an assumption of mutation rate showed, that the populations of this species are probably of recent origin since the Pleistocene. As in Tillandsia, the populations fell into genetically and geographically distinct clusters, with an estimated divergence age from each other matching geological data which suggests phases of prolonged aridity as the cause of these population cluster-splits. Our results further suggest that effective dispersal and a soil seed bank impact the genetic diversity in Huidobria and probably mitigate extinction risk of sub-populations.
Chapter 4 provides an estimation of the divergence time between two genera of the Cactaceae, Eulychnia and its sister genus Austrocactus. The aim of this study to elucidate the origins of Eulychnia and to reconstruct the diversification of this genus into the Atacama Desert. Phylogenies were produced from two differing data sets based on a complete taxon sampling of the genus Eulychnia. The first phylogeny was based on three plastid markers which were merged into a previously published family-wide phylogeny of the Cactaceae. A second phylogeny was calculated using SNP data obtained from GBS. Both phylogenies were molecular clock dated and a biogeographical analysis was produced. Our results provide an estimated divergence age of Eulychnia from Austrocactus approximately 7 Mya toward the Miocene-Pliocene boundary. Our biogeographic analysis revealed, that Eulychnia has evolved as a coastal taxon, and diversified in response to prolonged phases of aridity during the Pleistocene. Diversification age estimates correlate, as in the previous study on Huidobria, with geological results obtained from cosmogenic nuclide exposure dating and we interpret the current allopatric distribution of Eulychnia taxa as the result of habitat fragmentation through prolonged arid phases. The very recent diversification within this genus in combination with distinct hybrid zones at range limits, points to the preliminary assumption that speciation processes are still underway, with taxa not yet having reached full reproductive isolation. This idea has led to the following chapter.
Chapter 5 provides a taxonomic revision of the genus Eulychnia in the light of the results obtained from the previous chapter and the idea that speciation in Eulychnia has not yet reached reproductive isolation between taxa. The genus has a checkered taxonomic history and posed several issues regarding the type specimens of names provided by Friedrich Ritter. The original names published by Philippi remained untypified until twenty years ago. Several recently published species needed a new taxonomic circumscription. In this synopsis we accept three species and nine subspecies of Eulychnia in line with morphological variation, geographic distribution and phylogenetic results.
Chapter 6 provides a taxonomic revision of the genus Ophryosporus for Chile. There is no recent revision of the genus and confusion existed over names applied to Chilean plants. Some Chilean members of Ophryosporus have only been collected sporadically and a morphological analysis was required to ascertain their taxonomic relationship. Nomenclatural issues were resolved, including some necessary lectotypifications and an epitypification of names, and a key to the Chilean species of Ophryosporus was provided. This work recognises six species of Ophryosporus in Chile and forms the basis for any further studies on the genus.},
url = {https://hdl.handle.net/20.500.11811/8863}
}
urn: https://nbn-resolving.org/urn:nbn:de:hbz:5-60780,
author = {{Felix Franz Merklinger}},
title = {Microevolutionary processes and taxonomic investigations of the Atacama Desert flora},
school = {Rheinische Friedrich-Wilhelms-Universität Bonn},
year = 2020,
month = dec,
note = {Plant evolutionary processes in the hyper arid Atacama Desert of northern Chile are here investigated using our species/species complexes as case studies based on the following research questions:
(1) Are populations of Tillandsia genetically isolated from each other or do they maintain gene flow across potential barriers such as patches of hyper arid landscape or surface rivers?
(2) Have populations of Huidobria undergone long-term isolation in parallel to the long-lasting aridity of the Atacama Desert?
(3) When did Eulychnia originate, and when and how did it diversify into the Atacama Desert?
(4) Can the considerations regarding of question (3) contribute to produce a taxonomic concept for Eulychnia?
(5) How many species of Ophryosporus are there in Chile?
These research questions are addressed employing a combination of modern population genetic methods (genotyping by sequencing, GBS), molecular phylogenetic methods of Sanger sequencing, as well as traditional alpha taxonomy based on morphological analyses and literature/herbarium review and research.
The dissertation is presented in a cumulative style. It consists of papers that have already been published or accepted for publication, as well as chapters currently in working progress and soon to be submitted to the relevant journals. Each of the five chapters contains its respective introduction and conclusive considerations.
Chapter 1 is a general introduction, which provides an overview of the Atacama Desert, and in which the central research questions of this dissertation are formulated; an overview of the dissertation is provided.
Chapter 2 is a population genomic study of Tillandsia landbeckii (Bromeliaceae). Genetic diversity and gene flow within and between populations was analysed, including a heterozygosity analysis, F-statistics (FST and FIS ), genetic structure, isolation by distance and an interpretation of the data to explain the current distribution of the sampled lomas in the light of landscape evolution in the Atacama. Our results show that founder effects through stepping-stone dispersal are likely responsible for the formation of Tillandsia lomas, and that individuals of different lomas reproduce sexually and/or asexually (clonally). Gene flow between lomas belonging to three geographically and genetically distinct clusters is limited and appears to be impacted by barriers, possibly surface rivers and distance across hyper arid landscape.
Chapter 3 is a population genomic study of Huidobria fruticosa (Loasaceae), an ancient endemic lineage that diverged from its closest known relative between 40–60 Mya. The aim of this chapter was to correlate the evolution of this species to the evolution of aridity in the Atacama Desert. It was expected to find a high genetic differentiation mirroring long-term isolation of populations in aridity. However, our analysis of SNP data employing population genomic methods such as measures of genetic diversity θπ, F-statistics (FST ), genetic structure and measures of time units based on an assumption of mutation rate showed, that the populations of this species are probably of recent origin since the Pleistocene. As in Tillandsia, the populations fell into genetically and geographically distinct clusters, with an estimated divergence age from each other matching geological data which suggests phases of prolonged aridity as the cause of these population cluster-splits. Our results further suggest that effective dispersal and a soil seed bank impact the genetic diversity in Huidobria and probably mitigate extinction risk of sub-populations.
Chapter 4 provides an estimation of the divergence time between two genera of the Cactaceae, Eulychnia and its sister genus Austrocactus. The aim of this study to elucidate the origins of Eulychnia and to reconstruct the diversification of this genus into the Atacama Desert. Phylogenies were produced from two differing data sets based on a complete taxon sampling of the genus Eulychnia. The first phylogeny was based on three plastid markers which were merged into a previously published family-wide phylogeny of the Cactaceae. A second phylogeny was calculated using SNP data obtained from GBS. Both phylogenies were molecular clock dated and a biogeographical analysis was produced. Our results provide an estimated divergence age of Eulychnia from Austrocactus approximately 7 Mya toward the Miocene-Pliocene boundary. Our biogeographic analysis revealed, that Eulychnia has evolved as a coastal taxon, and diversified in response to prolonged phases of aridity during the Pleistocene. Diversification age estimates correlate, as in the previous study on Huidobria, with geological results obtained from cosmogenic nuclide exposure dating and we interpret the current allopatric distribution of Eulychnia taxa as the result of habitat fragmentation through prolonged arid phases. The very recent diversification within this genus in combination with distinct hybrid zones at range limits, points to the preliminary assumption that speciation processes are still underway, with taxa not yet having reached full reproductive isolation. This idea has led to the following chapter.
Chapter 5 provides a taxonomic revision of the genus Eulychnia in the light of the results obtained from the previous chapter and the idea that speciation in Eulychnia has not yet reached reproductive isolation between taxa. The genus has a checkered taxonomic history and posed several issues regarding the type specimens of names provided by Friedrich Ritter. The original names published by Philippi remained untypified until twenty years ago. Several recently published species needed a new taxonomic circumscription. In this synopsis we accept three species and nine subspecies of Eulychnia in line with morphological variation, geographic distribution and phylogenetic results.
Chapter 6 provides a taxonomic revision of the genus Ophryosporus for Chile. There is no recent revision of the genus and confusion existed over names applied to Chilean plants. Some Chilean members of Ophryosporus have only been collected sporadically and a morphological analysis was required to ascertain their taxonomic relationship. Nomenclatural issues were resolved, including some necessary lectotypifications and an epitypification of names, and a key to the Chilean species of Ophryosporus was provided. This work recognises six species of Ophryosporus in Chile and forms the basis for any further studies on the genus.},
url = {https://hdl.handle.net/20.500.11811/8863}
}
The following license files are associated with this item:
