Darwin’s abominable mystery: and evolution and diversification of Ficus L.

Sam Bruun-Lund

Darwin’s abominable mystery: and evolution and diversification of Ficus L.

Sam Bruun-Lund^*

^*Corresponding author af dette arbejde

SCIENCE PhD theses

Abstract

Figs (Ficus spp. L.) constitute one of the largest angiosperm lineages with ~800 species distributed in tropical and sub-tropical regions all over the world. Figs may be mostly known for their obligate mutualism with their pollinating fig-wasps (Agaonidae, Chalcidoidea, Hymenoptera). The two linages have codiversified for the last 75 million years. Additionally, figs present a diversity of habits and habitat usage and are considered keystone species in rainforests due to abundant fruit set. Our understanding of the evolutionary history of figs is based on the milestone monographs of Corner and Berg, primarily based on morphology. Meanwhile, the advent of DNA sequencing has unravelled conflicting relationships and questioned all our understanding of the evolution and diversification of figs. However, decades of Sanger sequencing have not provided a comprehensive phylogenetic hypothesis needed to re-test standing hypotheses about the origin and specificity of the mutualism, nor why the figs have been successful in adapting to many environments. In this PhD project, the figs have entered the era of high-throughput sequencing (HTS) plus undergone investigations to why there are so many fig species and the diversification patterns facilitating their diversity. In chapter I, an updated classification is presented with the current largest dataset available with more than 300 species of figs. This proposed new working classification of major lineages and groups is reflecting their evolutionary relationships. However, many relationships between clades are still hindered by lack of resolution in the DNA data. In chapter II, diversification and biogeography in Neotropical figs was investigated. Most diversity is recent, happening within the last 16 million years and diversification during unstable climatic periods seem to have shaped the current diversity. The hemi-epiphytic habit, together with small propagules, seem to lower extinction rates in Neotropical figs. In chapter III, the diversification dynamics of the entire genus was explored. The success and diversity of figs appear to be the product of slow, steady diversification rates with low extinction. No significant bursts of diversification were detected. We hypothesize the success of the genus to be affiliated with hemi-epiphytism, allowing occupation of new niches – and being monoecious with active pollination ensuring reproductive success. In chapter IV, figs entered the era of HTS and the first plastid genome of Ficus religiosa L. was assembled and annotated. Near complete plastid genomes (plastomes) of 65 taxa were used to gain a first ever insight into the evolutionary history of the plastome in fig phylogenetics. We found that cyto-nuclear discordance was present in the genus, possibly as a result of host-shifts and ancient plastome introgression. Thus, chapter V utilizes HTS and targeted sequence capture to focus on nuclear loci for reconstruction the phylogenetic hypothesis. A set of probes that can be used in the entire genus was developed and assessed; our probes can confidently resolve relationships of major lineages. The probes were used on a preliminary taxon set of an Australasian clade of figs and show efficiency to resolve closely related species. The final dataset will be used to test for biomes shifts and linked traits, between wet and dry regions.

Originalsprog	Engelsk

Forlag	Natural History Museum of Denmark, Faculty of Science, University of Copenhagen
Status	Udgivet - 2019

Adgang til dokumentet

PhD-Sam Bruun-Lund ThesisForlagets udgivne version, 38,1 MB

https://rex.kb.dk/permalink/f/h35n6k/KGL01012061259

Andre filer og links

Sign in to request a library copy

Citationsformater

@phdthesis{ddc5a2f5aea246d8b3984879f4f5e4f0,

title = "Darwin{\textquoteright}s abominable mystery: and evolution and diversification of Ficus L.",

abstract = "Figs (Ficus spp. L.) constitute one of the largest angiosperm lineages with ~800 species distributed in tropical and sub-tropical regions all over the world. Figs may be mostly known for their obligate mutualism with their pollinating fig-wasps (Agaonidae, Chalcidoidea, Hymenoptera). The two linages have codiversified for the last 75 million years. Additionally, figs present a diversity of habits and habitat usage and are considered keystone species in rainforests due to abundant fruit set. Our understanding of the evolutionary history of figs is based on the milestone monographs of Corner and Berg, primarily based on morphology. Meanwhile, the advent of DNA sequencing has unravelled conflicting relationships and questioned all our understanding of the evolution and diversification of figs. However, decades of Sanger sequencing have not provided a comprehensive phylogenetic hypothesis needed to re-test standing hypotheses about the origin and specificity of the mutualism, nor why the figs have been successful in adapting to many environments. In this PhD project, the figs have entered the era of high-throughput sequencing (HTS) plus undergone investigations to why there are so many fig species and the diversification patterns facilitating their diversity. In chapter I, an updated classification is presented with the current largest dataset available with more than 300 species of figs. This proposed new working classification of major lineages and groups is reflecting their evolutionary relationships. However, many relationships between clades are still hindered by lack of resolution in the DNA data. In chapter II, diversification and biogeography in Neotropical figs was investigated. Most diversity is recent, happening within the last 16 million years and diversification during unstable climatic periods seem to have shaped the current diversity. The hemi-epiphytic habit, together with small propagules, seem to lower extinction rates in Neotropical figs. In chapter III, the diversification dynamics of the entire genus was explored. The success and diversity of figs appear to be the product of slow, steady diversification rates with low extinction. No significant bursts of diversification were detected. We hypothesize the success of the genus to be affiliated with hemi-epiphytism, allowing occupation of new niches – and being monoecious with active pollination ensuring reproductive success. In chapter IV, figs entered the era of HTS and the first plastid genome of Ficus religiosa L. was assembled and annotated. Near complete plastid genomes (plastomes) of 65 taxa were used to gain a first ever insight into the evolutionary history of the plastome in fig phylogenetics. We found that cyto-nuclear discordance was present in the genus, possibly as a result of host-shifts and ancient plastome introgression. Thus, chapter V utilizes HTS and targeted sequence capture to focus on nuclear loci for reconstruction the phylogenetic hypothesis. A set of probes that can be used in the entire genus was developed and assessed; our probes can confidently resolve relationships of major lineages. The probes were used on a preliminary taxon set of an Australasian clade of figs and show efficiency to resolve closely related species. The final dataset will be used to test for biomes shifts and linked traits, between wet and dry regions.",

author = "Sam Bruun-Lund",

year = "2019",

language = "English",

publisher = "Natural History Museum of Denmark, Faculty of Science, University of Copenhagen",

}

TY - BOOK

T1 - Darwin’s abominable mystery

T2 - and evolution and diversification of Ficus L.

AU - Bruun-Lund, Sam

PY - 2019

Y1 - 2019

N2 - Figs (Ficus spp. L.) constitute one of the largest angiosperm lineages with ~800 species distributed in tropical and sub-tropical regions all over the world. Figs may be mostly known for their obligate mutualism with their pollinating fig-wasps (Agaonidae, Chalcidoidea, Hymenoptera). The two linages have codiversified for the last 75 million years. Additionally, figs present a diversity of habits and habitat usage and are considered keystone species in rainforests due to abundant fruit set. Our understanding of the evolutionary history of figs is based on the milestone monographs of Corner and Berg, primarily based on morphology. Meanwhile, the advent of DNA sequencing has unravelled conflicting relationships and questioned all our understanding of the evolution and diversification of figs. However, decades of Sanger sequencing have not provided a comprehensive phylogenetic hypothesis needed to re-test standing hypotheses about the origin and specificity of the mutualism, nor why the figs have been successful in adapting to many environments. In this PhD project, the figs have entered the era of high-throughput sequencing (HTS) plus undergone investigations to why there are so many fig species and the diversification patterns facilitating their diversity. In chapter I, an updated classification is presented with the current largest dataset available with more than 300 species of figs. This proposed new working classification of major lineages and groups is reflecting their evolutionary relationships. However, many relationships between clades are still hindered by lack of resolution in the DNA data. In chapter II, diversification and biogeography in Neotropical figs was investigated. Most diversity is recent, happening within the last 16 million years and diversification during unstable climatic periods seem to have shaped the current diversity. The hemi-epiphytic habit, together with small propagules, seem to lower extinction rates in Neotropical figs. In chapter III, the diversification dynamics of the entire genus was explored. The success and diversity of figs appear to be the product of slow, steady diversification rates with low extinction. No significant bursts of diversification were detected. We hypothesize the success of the genus to be affiliated with hemi-epiphytism, allowing occupation of new niches – and being monoecious with active pollination ensuring reproductive success. In chapter IV, figs entered the era of HTS and the first plastid genome of Ficus religiosa L. was assembled and annotated. Near complete plastid genomes (plastomes) of 65 taxa were used to gain a first ever insight into the evolutionary history of the plastome in fig phylogenetics. We found that cyto-nuclear discordance was present in the genus, possibly as a result of host-shifts and ancient plastome introgression. Thus, chapter V utilizes HTS and targeted sequence capture to focus on nuclear loci for reconstruction the phylogenetic hypothesis. A set of probes that can be used in the entire genus was developed and assessed; our probes can confidently resolve relationships of major lineages. The probes were used on a preliminary taxon set of an Australasian clade of figs and show efficiency to resolve closely related species. The final dataset will be used to test for biomes shifts and linked traits, between wet and dry regions.

AB - Figs (Ficus spp. L.) constitute one of the largest angiosperm lineages with ~800 species distributed in tropical and sub-tropical regions all over the world. Figs may be mostly known for their obligate mutualism with their pollinating fig-wasps (Agaonidae, Chalcidoidea, Hymenoptera). The two linages have codiversified for the last 75 million years. Additionally, figs present a diversity of habits and habitat usage and are considered keystone species in rainforests due to abundant fruit set. Our understanding of the evolutionary history of figs is based on the milestone monographs of Corner and Berg, primarily based on morphology. Meanwhile, the advent of DNA sequencing has unravelled conflicting relationships and questioned all our understanding of the evolution and diversification of figs. However, decades of Sanger sequencing have not provided a comprehensive phylogenetic hypothesis needed to re-test standing hypotheses about the origin and specificity of the mutualism, nor why the figs have been successful in adapting to many environments. In this PhD project, the figs have entered the era of high-throughput sequencing (HTS) plus undergone investigations to why there are so many fig species and the diversification patterns facilitating their diversity. In chapter I, an updated classification is presented with the current largest dataset available with more than 300 species of figs. This proposed new working classification of major lineages and groups is reflecting their evolutionary relationships. However, many relationships between clades are still hindered by lack of resolution in the DNA data. In chapter II, diversification and biogeography in Neotropical figs was investigated. Most diversity is recent, happening within the last 16 million years and diversification during unstable climatic periods seem to have shaped the current diversity. The hemi-epiphytic habit, together with small propagules, seem to lower extinction rates in Neotropical figs. In chapter III, the diversification dynamics of the entire genus was explored. The success and diversity of figs appear to be the product of slow, steady diversification rates with low extinction. No significant bursts of diversification were detected. We hypothesize the success of the genus to be affiliated with hemi-epiphytism, allowing occupation of new niches – and being monoecious with active pollination ensuring reproductive success. In chapter IV, figs entered the era of HTS and the first plastid genome of Ficus religiosa L. was assembled and annotated. Near complete plastid genomes (plastomes) of 65 taxa were used to gain a first ever insight into the evolutionary history of the plastome in fig phylogenetics. We found that cyto-nuclear discordance was present in the genus, possibly as a result of host-shifts and ancient plastome introgression. Thus, chapter V utilizes HTS and targeted sequence capture to focus on nuclear loci for reconstruction the phylogenetic hypothesis. A set of probes that can be used in the entire genus was developed and assessed; our probes can confidently resolve relationships of major lineages. The probes were used on a preliminary taxon set of an Australasian clade of figs and show efficiency to resolve closely related species. The final dataset will be used to test for biomes shifts and linked traits, between wet and dry regions.

UR - https://rex.kb.dk/permalink/f/h35n6k/KGL01012061259

M3 - Ph.D. thesis

BT - Darwin’s abominable mystery

PB - Natural History Museum of Denmark, Faculty of Science, University of Copenhagen

ER -