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Genetic variation and inference of demographic histories in non-model species
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.ORCID iD: 0000-0001-7777-4133
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Both long-term environmental changes such as those driven by the glacial cycles and more recent anthropogenic impacts have had major effects on the past demography in wild organisms. Within species, these changes are reflected in the amount and distribution of neutral genetic variation. In this thesis, mitochondrial and microsatellite DNA was analysed to investigate how environmental and anthropogenic factors have affected genetic diversity and structure in four ecologically different animal species. Paper I describes the post-glacial recolonisation history of the speckled-wood butterfly (Pararge aegeria) in Northern Europe. A decrease in genetic diversity with latitude and a marked population structure were uncovered, consistent with a hypothesis of repeated founder events during the postglacial recolonisation. Moreover, Approximate Bayesian Computation analyses indicate that the univoltine populations in Scandinavia and Finland originate from recolonisations along two routes, one on each side of the Baltic. Paper II aimed to investigate how past sea-level rises affected the population history of the convict surgeonfish (Acanthurus triostegus) in the Indo-Pacific. Assessment of the species’ demographic history suggested a population expansion that occurred approximately at the end of the last glaciation. Moreover, the results demonstrated an overall lack of phylogeographic structure, probably due to the high dispersal rates associated with the species’ pelagic larval stage. Populations at the species’ eastern range margin were significantly differentiated from other populations, which likely is a consequence of their geographic isolation. In Paper III, we assessed the effect of human impact on the genetic variation of European moose (Alces alces) in Sweden. Genetic analyses revealed a spatial structure with two genetic clusters, one in northern and one in southern Sweden, which were separated by a narrow transition zone. Moreover, demographic inference suggested a recent population bottleneck. The inferred timing of this bottleneck coincided with a known reduction in population size in the 19th and early 20th century due to high hunting pressure. In Paper IV, we examined the effect of an indirect but well-described human impact, via environmental toxic chemicals (PCBs), on the genetic variation of Eurasian otters (Lutra lutra) in Sweden. Genetic clustering assignment revealed differentiation between otters in northern and southern Sweden, but also in the Stockholm region. ABC analyses indicated a decrease in effective population size in both northern and southern Sweden. Moreover, comparative analyses of historical and contemporary samples demonstrated a more severe decline in genetic diversity in southern Sweden compared to northern Sweden, in agreement with the levels of PCBs found.

Place, publisher, year, edition, pages
Stockholm: Department of Molecular Biosciences, The Wenner-Gren Institute Stockholm University , 2014. , 33 p.
National Category
Biological Sciences
Research subject
Molecular Genetics
Identifiers
URN: urn:nbn:se:su:diva-109896ISBN: 9789176490563 (print)OAI: oai:DiVA.org:su-109896DiVA: diva2:767558
Public defence
2015-01-14, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 14:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript.

Available from: 2014-12-18 Created: 2014-12-01 Last updated: 2016-12-14Bibliographically approved
List of papers
1. Signature of post-glacial expansion and genetic structure at the northern range limit of the speckled wood butterfly
Open this publication in new window or tab >>Signature of post-glacial expansion and genetic structure at the northern range limit of the speckled wood butterfly
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2014 (English)In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 113, no 1, 136-148 p.Article in journal (Refereed) Published
Abstract [en]

The post-glacial recolonisation of northern Europe has left distinct signatures in the genomes of many organisms, both due to random demographic processes and divergent natural selection. However, information on differences in genetic variation in conjunction with patterns of local adaptations along latitudinal gradients is often lacking. In this study, we examine genetic diversity and population structure in the speckled wood butterfly Pararge aegeria in northern Europe to investigate the species post-glacial recolonisation history and discuss how this may have affected its life-history evolution. We collected 209 samples and analysed genetic variation in nine microsatellite loci. The results demonstrated a more pronounced population structure in northern Europe compared with populations further south, as well as an overall decrease in genetic diversity with latitude, likely due to founder effects during the recolonisation process. Coalescent simulations coupled with approximate Bayesian computation suggested that central Scandinavia was colonised from the south, rather than from the east. In contrast to further south, populations at the northern range margin are univoltine expressing only one generation per year. This suggests either that univoltinism evolved independently on each side of the Baltic Sea, or that bivoltinism evolved in the south after northern Europe was recolonised.

Keyword
Bayesian analyses, coalescent simulations, demographic inference, microsatellites, Pararge aegeria, population structure, post-glacial recolonisation
National Category
Developmental Biology
Identifiers
urn:nbn:se:su:diva-107607 (URN)10.1111/bij.12327 (DOI)000340585700011 ()
Note

AuthorCount:8;

Available from: 2014-09-26 Created: 2014-09-22 Last updated: 2017-12-05Bibliographically approved
2. Indo-Pacific population genetic  structure and demographic history of a highly abundant and widespread coral reef fish, Acanthurus triostegus
Open this publication in new window or tab >>Indo-Pacific population genetic  structure and demographic history of a highly abundant and widespread coral reef fish, Acanthurus triostegus
(English)Manuscript (preprint) (Other academic)
National Category
Biological Sciences
Research subject
Molecular Genetics
Identifiers
urn:nbn:se:su:diva-109907 (URN)
Available from: 2014-12-01 Created: 2014-12-01 Last updated: 2016-12-14Bibliographically approved
3. Genetic landscape with sharp discontinuities shaped by complex demographic history in moose (Alces alces)
Open this publication in new window or tab >>Genetic landscape with sharp discontinuities shaped by complex demographic history in moose (Alces alces)
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2016 (English)In: Journal of Mammalogy, ISSN 0022-2372, E-ISSN 1545-1542, Vol. 97, no 1, 1-13 p.Article in journal (Refereed) Published
Abstract [en]

The moose (Alces alces) is the most intensely managed game species in Fennoscandia; approximately one-third of the population, ca. 160,000 animals, is harvested annually. Despite the species' biological and socioeconomic importance, there are knowledge gaps with respect to its intraspecific diversity and genetic structure. Recent studies of moose in neighboring countries report 2 genetic groups in Finland, 3 in Norway with one of them suggested to be of ancient origin, and no indications of bottlenecks. To delineate the spatial genetic landscape of the Swedish moose, we used allozyme variability from over 20,000 georeferenced moose collected all over Sweden in combination with 12 microsatellites (n = 1,200) and mitochondrial DNA (mtDNA) sequences (n = 44). We combined individual-based and traditional statistical approaches with coalescence-based simulations. The results indicate a complex history with bottlenecks and recent expansions that is consistent with historical records. Swedish moose are separated into 2 major genetic groups, a northern and a southern one, where the southern group is further divided into 3 subgroups. The 2 main subpopulations are moderately differentiated (F-ST = 0.1; R-ST = 0.07) and separated by sharp genetic discontinuities occurring over a relatively narrow transition zone in central Sweden that coincides with a similar, previously reported transition zone in Norway. This differentiation is not reflected in mtDNA variation, where no significant divergence was observed. Together with the F-ST andR(ST) similarities, this suggests that the 2 major subpopulations in Sweden reflect divergence shaped after the postglacial recolonization of Scandinavia. Neighborhood size assessments indicate that gene flow is relatively restricted with an estimated average dispersal distance of 3.5-11.1 km, and spatial autocorrelograms suggest that genetic similarity decreases almost linearly over space resulting in continuous genetic clines within major subgroups. Management areas largely coincide with genetic clusters, simplifying the integration of genetic information into management.

Keyword
approximate Bayesian computation, population genetic structure, spatial autocorrelation, wildlife management
National Category
Biological Sciences
Research subject
Population Genetics; Molecular Genetics
Identifiers
urn:nbn:se:su:diva-127869 (URN)10.1093/jmammal/gyv146 (DOI)000369232600001 ()
Available from: 2016-05-16 Created: 2016-03-14 Last updated: 2017-11-30Bibliographically approved
4. Population structure and recent temporal changes in genetic variation in Eurasian otters from Sweden
Open this publication in new window or tab >>Population structure and recent temporal changes in genetic variation in Eurasian otters from Sweden
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2015 (English)In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 16, no 2, 371-384 p.Article in journal (Refereed) Published
Abstract [en]

The Eurasian otter (Lutra lutra) population in Sweden went through a drastic decline in population size between the 1950s and 1980s, caused mostly by anthropogenic factors such as high hunting pressure and the introduction of environmental toxic chemicals into the otter's habitats. However, after the bans of PCBs and DDT in the 1970s, the population began to recover in the 1990s. This study compares microsatellite data across twelve loci from historical and contemporary otter samples to investigate whether there has been a change in population structure and genetic diversity across time in various locations throughout Sweden. The results suggest that otters in the south were more severely affected by the bottleneck, demonstrated by a decline in genetic diversity and a shift in genetic composition. In contrast, the genetic composition in otters from northern Sweden remained mostly unchanged, both in terms of population structure and diversity. This suggests that the decline was not uniform across the country. Moreover, our analyses of historical samples provide an overview of the level of genetic variation and population structure that existed prior to the bottleneck, which may be helpful for the future management and conservation of the species.

Keyword
Lutra lutra, Microsatellites, Population structure, Bottleneck, Coalescent simulations
National Category
Biological Sciences
Research subject
Molecular Genetics
Identifiers
urn:nbn:se:su:diva-116758 (URN)10.1007/s10592-014-0664-2 (DOI)000351287400010 ()
Note

AuthorCount:6;

Available from: 2015-05-12 Created: 2015-04-27 Last updated: 2017-12-04Bibliographically approved

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