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Refugia and post-glacial migration of Nigritella miniata (Orchidaceae): evidence from restriction site-associated DNA sequencing, microsatellite markers, and ecological niche modelling

Jacobsen Ellerstrand, Simon (2020) BION02 20191
Degree Projects in Biology
Abstract
Nigritella miniata is an alpine orchid species disjunctly endemic to the Eastern Alps and the Southeastern Carpathians. It is thought to have arisen only once through a hybridisation event between now extinct ancestors. Questions of interest are whether N. miniata survived in few or many isolated refugia in the Eastern Alps during the Last Glacial Maximum (LGM), and their relationship with the populations in the Carpathians. Further, several segregates have recently been described within the species group, which have received varying support from genetic and morphological studies. Being an allotetraploid species reproducing strictly by asexual agamospermy, bioinformatic considerations must be taken to the evolutionary independent history... (More)
Nigritella miniata is an alpine orchid species disjunctly endemic to the Eastern Alps and the Southeastern Carpathians. It is thought to have arisen only once through a hybridisation event between now extinct ancestors. Questions of interest are whether N. miniata survived in few or many isolated refugia in the Eastern Alps during the Last Glacial Maximum (LGM), and their relationship with the populations in the Carpathians. Further, several segregates have recently been described within the species group, which have received varying support from genetic and morphological studies. Being an allotetraploid species reproducing strictly by asexual agamospermy, bioinformatic considerations must be taken to the evolutionary independent history of paralogous alleles between subgenomes, as well as within subgenomes. A microsatellite dataset from eight effective haploid microsatellite markers from a large database was used to infer population structure and molecular dating through estimated mutation rates of related taxa. A single-digest restriction site-associated DNA (RADtag) library was created, and the resulting RAD sequence (RADseq) data analysed under Maximum Likelihood and Bayesian Coalescence models. Occurrence records from private and public databases were used with ecological niche modelling (ENM) to produce a present-day distribution model, which was projected onto conditions during the LGM to infer possible refugia. The RADtag library preparation and subsequent analyses proved unsuccessful, and possible reasons are thoroughly discussed. Analyses of the microsatellite dataset in conjunction with ENM supports two separate lineages in the Eastern Alps congruent with known biogeographic boundaries and possible refugia. The western lineage probably survived in a large unglaciated valley in western Bayern from where it recolonised the western distributional range with the withdrawal of the ice. The eastern lineage likely survived in many isolated refugia along the periphery of the ice sheet, from the Dolomites in the south to the Northeastern Limestone Alps. Snežnik and the Carpathians were likely colonised through recent long-distance dispersal events from the western and eastern lineages respectively, but a successful RADtag library or a strengthened microsatellite dataset is necessary for better support. Described segregates should not be classified as anything more than varieties. ENM proves to be a useful and inexpensive complement to phylogeographic studies. (Less)
Popular Abstract
The toolkit of the modern time traveller: genetics and mathematical models

Time travel might seem like science fiction, but time travellers have long lived among us. They usually call themselves historians, archaeologists, geologists, astronomers, or like me, biologists. These trades all use their own toolkits for studying the past. Astronomers gaze at the stars through telescopes, historians study archives of texts, while biologists have long compared fossils to present-day wildlife. However, in recent decades science has brought us new tools for studying evolution. We can now apply mathematical models to the information stored in the genetic makeup of today living beings. This allows us to learn something about the history of their... (More)
The toolkit of the modern time traveller: genetics and mathematical models

Time travel might seem like science fiction, but time travellers have long lived among us. They usually call themselves historians, archaeologists, geologists, astronomers, or like me, biologists. These trades all use their own toolkits for studying the past. Astronomers gaze at the stars through telescopes, historians study archives of texts, while biologists have long compared fossils to present-day wildlife. However, in recent decades science has brought us new tools for studying evolution. We can now apply mathematical models to the information stored in the genetic makeup of today living beings. This allows us to learn something about the history of their ancestors, as well as the world in which they resided. We do this, for to understand the present it is necessary to understand the past.

So, what is needed for a biologist to travel back in time? Let us start with the study organism. I used a wild orchid species endemic to the European mountain ranges of the Alps and the Carpathians. The English language calls it the ‘red vanilla orchid’, although a biologist would call it ‘Nigritella miniata’. The genetic makeup of the organism, the DNA, must now be translated and interpreted. I used plant material that had been collected from many plants across the geographic region it occupies. Only small parts of the plants had been taken so that they would survive. In the laboratory I could then go from a piece of a dried flower, to its DNA, to genetic sequences on my computer. But the sequences are only a halfway step in translating the genetic language. Through mathematical models I compared the genetics of several plants to determine which were more or less related to one another. In this way we can learn something about their ancestors. If we also know where the plant material was collected, we can learn something about the world their ancestors resided in.

This is how I was able to reach back in time to the world of the recent ice age, roughly 20,000 thousand years ago. During this time, a vast sheet of ice covered most of the Alps. But not all of it. From discoveries made from previous time travellers including geologist and other biologists, we know that there where places were plants could have not only survived, but thrived. These are called refugia and could have been unglaciated valleys or mountain peaks protruding above the ice. I found that these orchids are descendants of two main lineages that survived the recent ice age in separate refugia. The western lineage likely survived in a large unglaciated valley in the north, today known as the Bavarian Alps. This lineage colonised the uninhabited areas of the west that the withdrawal of the ice left behind as the ice age ended. The eastern lineage is further divided into two sublineages, which survived in several small and isolated refugia in the Northeastern Alps and in the Dolomites. When the ice withdrew, they would both disperse into each other’s areas.

I also discovered something about the population in the Carpathians. Considering the vast distances that separates the Alps and the Carpathians, one might think that they would be farther removed from the populations in the Alps. Remarkably however, I found indications of them being closely related to the eastern lineage. It is known that orchids are one of the few groups of plants bearing seeds so small that they on rare occasions can be carried thousands of kilometres on the whims of the wind. Could it be that the Carpathians were colonised by a few long-distance pioneers from the eastern lineage during the past 20,000 years? That is for another time traveller to find out.

Master’s Degree Project in Biology 45 credits 2020
Department of Biology, Lund University
Main supervisor: Mikael Hedrén, Biodiversity, Department of Biology, Lund University
Co-supervisor: Bengt Hansson, MEMEG, Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Jacobsen Ellerstrand, Simon
supervisor
organization
course
BION02 20191
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
9022416
date added to LUP
2020-06-25 12:13:39
date last changed
2020-06-25 12:13:39
@misc{9022416,
  abstract     = {Nigritella miniata is an alpine orchid species disjunctly endemic to the Eastern Alps and the Southeastern Carpathians. It is thought to have arisen only once through a hybridisation event between now extinct ancestors. Questions of interest are whether N. miniata survived in few or many isolated refugia in the Eastern Alps during the Last Glacial Maximum (LGM), and their relationship with the populations in the Carpathians. Further, several segregates have recently been described within the species group, which have received varying support from genetic and morphological studies. Being an allotetraploid species reproducing strictly by asexual agamospermy, bioinformatic considerations must be taken to the evolutionary independent history of paralogous alleles between subgenomes, as well as within subgenomes. A microsatellite dataset from eight effective haploid microsatellite markers from a large database was used to infer population structure and molecular dating through estimated mutation rates of related taxa. A single-digest restriction site-associated DNA (RADtag) library was created, and the resulting RAD sequence (RADseq) data analysed under Maximum Likelihood and Bayesian Coalescence models. Occurrence records from private and public databases were used with ecological niche modelling (ENM) to produce a present-day distribution model, which was projected onto conditions during the LGM to infer possible refugia. The RADtag library preparation and subsequent analyses proved unsuccessful, and possible reasons are thoroughly discussed. Analyses of the microsatellite dataset in conjunction with ENM supports two separate lineages in the Eastern Alps congruent with known biogeographic boundaries and possible refugia. The western lineage probably survived in a large unglaciated valley in western Bayern from where it recolonised the western distributional range with the withdrawal of the ice. The eastern lineage likely survived in many isolated refugia along the periphery of the ice sheet, from the Dolomites in the south to the Northeastern Limestone Alps. Snežnik and the Carpathians were likely colonised through recent long-distance dispersal events from the western and eastern lineages respectively, but a successful RADtag library or a strengthened microsatellite dataset is necessary for better support. Described segregates should not be classified as anything more than varieties. ENM proves to be a useful and inexpensive complement to phylogeographic studies.},
  author       = {Jacobsen Ellerstrand, Simon},
  language     = {eng},
  note         = {Student Paper},
  title        = {Refugia and post-glacial migration of Nigritella miniata (Orchidaceae): evidence from restriction site-associated DNA sequencing, microsatellite markers, and ecological niche modelling},
  year         = {2020},
}