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Halvarsson, Peter
Publications (10 of 17) Show all publications
Cortazar-Chinarro, M., Halvarsson, P. & Virgós, E. (2019). Sign surveys for red fox (Vulpes vulpes) censuses: evaluating different sources of variation in scat detectability. Mammal Research, 64(2), 183-190
Open this publication in new window or tab >>Sign surveys for red fox (Vulpes vulpes) censuses: evaluating different sources of variation in scat detectability
2019 (English)In: Mammal Research, ISSN 2199-2401, E-ISSN 2199-241X, Vol. 64, no 2, p. 183-190Article in journal (Refereed) Published
Abstract [en]

Wildlife monitoring is essential for assessing the size of species of conservation or management concern. Wildlife monitoring could be undertaken by selected volunteers when limited resources are available. Here, we study the sources of variation in the detectability of red fox scats and to improve the monitoring of the species by means of volunteers who were briefly trained. We selected nine transects to experimentally evaluate the differences in red fox scat detectability between observers, microsite, and scat abundance. Scats were deposited in five microsites, where we simulate low, medium, and high fox scat abundance. We tested the proposed effects by using GLMM analysis incorporating observer effect as a random factor. Our results indicated effects on scat detectability of observer identity and microsite type. We did not observe the effects of scat abundance on detectability of scats. Detectability was lower for scats located in the middle of the transect and on the rocks. We conclude that large-scale red foxes surveys might be conducted using volunteers, but due to the moderate differences detected among observers should be minimized using a training period.

National Category
Ecology
Identifiers
urn:nbn:se:uu:diva-364960 (URN)10.1007/s13364-018-0404-y (DOI)000461391500004 ()
Available from: 2018-11-07 Created: 2018-11-07 Last updated: 2019-05-06Bibliographically approved
Höglund, J., Wang, B., Sæther, S. A., Blom, M. P., Fiske, P., Halvarsson, P., . . . Ekblom, R. (2017). Blood transcriptomes and de novo identification of candidate loci for mating success in lekking great snipe (Gallinago media). Molecular Ecology, 26(13), 3458-3471
Open this publication in new window or tab >>Blood transcriptomes and de novo identification of candidate loci for mating success in lekking great snipe (Gallinago media)
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2017 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 13, p. 3458-3471Article in journal (Refereed) Published
Abstract [en]

We assembled the great snipe blood transcriptome using data from fourteen lekking males, in order to de novo identify candidate genes related to sexual selection, and determined the expression profiles in relation to mating success. The three most highly transcribed genes were encoding different haemoglobin subunits. All tended to be overexpressed in males with high mating success. We also called single nucleotide polymorphisms (SNPs) from the transcriptome data and found considerable genetic variation for many genes expressed during lekking. Among these, we identified 14 polymorphic candidate SNPs that had a significant genotypic association with mating success (number of females mated with) and/or mating status (mated or not). Four of the candidate SNPs were found in HBAA (encoding the haemoglobin a-chain). Heterozygotes for one of these and one SNP in the gene PABPC1 appeared to enjoy higher mating success compared to males homozygous for either of the alleles. In a larger data set of individuals, we genotyped 38 of the identified SNPs but found low support for consistent selection as only one of the zygosities of previously identified candidate SNPs and none of their genotypes were associated with mating status. However, candidate SNPs generally showed lower levels of spatial genetic structure compared to noncandidate markers. We also scored the prevalence of avian malaria in a subsample of birds. Males infected with avian malaria parasites had lower mating success in the year of sampling than noninfected males. Parasite infection and its interaction with specific genes may thus affect performance on the lek.

National Category
Zoology
Identifiers
urn:nbn:se:uu:diva-300021 (URN)10.1111/mec.14118 (DOI)000403695500012 ()28345264 (PubMedID)
Funder
Carl Tryggers foundation Swedish Research Council
Available from: 2016-08-01 Created: 2016-08-01 Last updated: 2017-09-25Bibliographically approved
Johansson, F., Halvarsson, P., Mikolajewski, D. J. & Höglund, J. (2017). Genetic differentiation in the boreal dragonfly Leucorrhinia dubia in the Palearctic region. Biological Journal of the Linnean Society, 121(2), 294-304
Open this publication in new window or tab >>Genetic differentiation in the boreal dragonfly Leucorrhinia dubia in the Palearctic region
2017 (English)In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 121, no 2, p. 294-304Article in journal (Refereed) Published
Abstract [en]

The last glacial period had a strong influence on the population genetic structure of boreal species in southern and central Europe. In addition, recent and current human impact on the boreal environment has led to habitat loss, which also has a large influence on population genetic structure of species. Here we present the spatial genetic structure of the boreal dragonfly Leucorrhinia dubia using ddRAD sequencing. We sampled individuals from nine locations in Europe, three in Asia (Russia and Japan) and one location of L. intermedia in Japan. Results showed three distinct genetic clusters in Europe. One genetic cluster consisted of individuals sampled from the locations in the Swiss Alps, a second consisted of individuals sampled in the United Kingdom, and a third cluster consisted of individuals from the rest of the seven sampled locations in Europe covering a latitudinal gradient from the French Pyrenees to the north of Finland. There was also a week support that the French Pyrenees and Austrian Alps samples differentiated from the cluster of the five samples from central and north Europe. We suggest that these clusters reflect historical recolonization patterns since the last glaciation. The L. dubia individuals sampled from locations in Asia formed one cluster referring to L. dubia orientalis separated from the individuals sampled in European and from the L. intermedia locality sampled. Our result suggests that aquatic insects in the fragmented boreal landscape in south central Europe and United Kingdom need conservation consideration.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2017
Keywords
boreal, ddRAD, genetic differentiation, Leucorrhinia, population structure, postglacial
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-330736 (URN)10.1093/biolinnean/blw033 (DOI)000405207800006 ()
Available from: 2017-10-10 Created: 2017-10-10 Last updated: 2017-10-10Bibliographically approved
Halvarsson, P. (2016). Host-Parasite Interactions in Natural Populations. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Host-Parasite Interactions in Natural Populations
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Parasitism is one of the most common ways of living and it has arised in many taxa. Parasites feed and live inside or on their hosts resulting in both long and short term consequences for the host. This thesis is exploring the phenotypic and genotypic effects of animals living with parasitic infections. I have been studying three different parasite groups and their associated host species: the great snipe, a lekking freshwater wader bird that migrates between Africa and Northern Europe; the tree sparrow, a stationary passerine found close to human settlements and lastly the water vole, a large rodent living in riparian habitats.

Avian malaria is one of the most commonly studied parasites affecting birds. Atoxoplasma, an intestinal protozoan parasite is less studied but is thought to be endemic in free-ranging birds. Given the freshwater habitat great snipes inhabit, a prevalence of 30% avian malaria infections is not high and that the prevalence fluctuated among years. Sequencing of the avian malaria cytochrome b gene revealed that parasites are similar to avian malaria parasites found in African birds suggesting that they were infected on the wintering grounds in Africa. Tree sparrows had few malaria infected individuals, a result that is consistent with other studies of stationary birds at high latitudes. Atoxoplasma infections were common in tree sparrows and capture-recapture analyses show decreased survival in infected compared to uninfected birds and signs of lower mating success among infected.

Genetic analyses comparing the transcriptome between mated and unmated great snipe males revealed that the genotype is important for mating success and health status for some of the expressed genes. That variations in some of these genes are involved in maintaining a good health status and mating success supports handicap models for sexual selection in this lek mating system.

The major histocompatibility complex (MHC) is a part of the immune system and it contains genes involved in immune response. In water voles, a number of new MHC alleles were identified. Based on their in silico phenotype they were grouped into supertypes to facilitate studies on how helminth infections affect the MHC diversity in the water voles. Some of these MHC supertypes provided resistance to one helminth species, but the same supertype caused the opposite effect for other helminth parasites. Overall, parasites are a driving force for maintaining genetic diversity and parasite infections lowers survival rate, which would lead to a lower lifetime breeding success.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2016. p. 43
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1395
Keywords
Arvicola terrestris, avian malaria, balancing selection, Major histocompatibility complex, parasitetranscriptome
National Category
Zoology
Research subject
Population Biology
Identifiers
urn:nbn:se:uu:diva-300023 (URN)978-91-554-9633-3 (ISBN)
External cooperation:
Public defence
2016-09-20, Zootissalen, Villavägen 9, Uppsala, 13:00 (English)
Opponent
Supervisors
Funder
Carl Tryggers foundation Swedish Research Council FormasSwedish Research Council FormasLars Hierta Memorial Foundation
Available from: 2016-08-26 Created: 2016-08-01 Last updated: 2016-09-05
Griesser, M., Halvarsson, P., Drobniak, S. M. & Vila, C. (2015). Fine-scale kin recognition in the absence of social familiarity in the Siberian jay, a monogamous bird species. Molecular Ecology, 24(22), 5726-5738
Open this publication in new window or tab >>Fine-scale kin recognition in the absence of social familiarity in the Siberian jay, a monogamous bird species
2015 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 22, p. 5726-5738Article in journal (Refereed) Published
Abstract [en]

Kin recognition is a critical element to kin cooperation, and in vertebrates, it is primarily based on associative learning. Recognition of socially unfamiliar kin occurs rarely, and it is reported only in vertebrate species where promiscuity prevents recognition of first-order relatives. However, it is unknown whether the recognition of socially unfamiliar kin can evolve in monogamous species. Here, we investigate whether genetic relatedness modulates aggression among group members in Siberian jays (Perisoreus infaustus). This bird species is genetically and socially monogamous and lives in groups that are formed through the retention of offspring beyond independence, and the immigration of socially unfamiliar nonbreeders. Observations on feeders showed that genetic relatedness modulated aggression of breeders towards immigrants in a graded manner, in that they chased most intensely the immigrant group members that were genetically the least related. However, cross-fostering experiments showed that breeders were equally tolerant towards their own and cross-fostered young swapped as nestlings. Thus, breeders seem to use different mechanisms to recognize socially unfamiliar individuals and own offspring. As Siberian jays show a high degree of nepotism during foraging and predator encounters, inclusive fitness benefits may play a role for the evolution of fine-scale kin recognition. More generally, our results suggest that fine-graded kin recognition can evolve independently of social familiarity, highlighting the evolutionary importance of kin recognition for social species.

Keywords
aggression, cooperation, paternity, self-referent phenotype matching, social evolution, social familiarity
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-271039 (URN)10.1111/mec.13420 (DOI)000365757300016 ()
Available from: 2016-01-05 Created: 2016-01-05 Last updated: 2017-12-01Bibliographically approved
Persson Vinnersten, T. Z., Halvarsson, P. & Lundström, J. O. (2015). Specific detection of the floodwater mosquitoes Aedes sticticus and Aedes vexans DNA in predatory diving beetles. Insect Science, 22(4), 549-559
Open this publication in new window or tab >>Specific detection of the floodwater mosquitoes Aedes sticticus and Aedes vexans DNA in predatory diving beetles
2015 (English)In: Insect Science, ISSN 1672-9609, E-ISSN 1744-7917, Vol. 22, no 4, p. 549-559Article in journal (Refereed) Published
National Category
Ecology Genetics
Identifiers
urn:nbn:se:uu:diva-207839 (URN)10.1111/1744-7917.12146 (DOI)000358380600008 ()24895318 (PubMedID)
Note

Funding: Swedish Environmental Protection Agency

Available from: 2013-09-23 Created: 2013-09-19 Last updated: 2017-12-06Bibliographically approved
Griesser, M., Halvarsson, P., Sahlman, T. & Ekman, J. (2014). What are the strengths and limitations of direct and indirect assessment of dispersal?: Insights from a long-term field study in a group-living bird species. Behavioral Ecology and Sociobiology, 68(3), 485-497
Open this publication in new window or tab >>What are the strengths and limitations of direct and indirect assessment of dispersal?: Insights from a long-term field study in a group-living bird species
2014 (English)In: Behavioral Ecology and Sociobiology, ISSN 0340-5443, E-ISSN 1432-0762, Vol. 68, no 3, p. 485-497Article in journal (Refereed) Published
Abstract [en]

Molecular methods of assessing dispersal have become increasingly powerful and have superseded direct methods of studying dispersal. Although now less popular, direct methods of studying dispersal remain important tools for understanding the evolution of dispersal. Here, we use data from Siberian jays Perisoreus infaustus, a group-living bird species, to compare natal dispersal distances and rates using visual mark-recapture, radio-tracking and microsatellite data. Siberian jays have bimodal natal dispersal timing; socially dominant offspring remain with their parents for up to 5 years (delayed dispersers), while they force their subordinate brood mates to leave the parental territory at independence (early dispersers). Early dispersers moved about 9,000 m (visual mark-recapture, radio-tracking) before settling in a group as a non-breeder. In contrast, delayed dispersers moved about 1,250 m (visual mark-recapture only) and mainly moved to a breeding opening. Dispersal distances were greater in managed habitat compared to natural habitat for both early and delayed dispersers. Molecular estimates based on 23 microsatellite loci and geographical locations supported distance estimates from the direct methods. Our study shows that molecular methods are at least 22 times cheaper than direct methods and match estimates of dispersal distance from direct methods. However, molecular estimates do not give insight into the behavioural mechanisms behind dispersal decisions. Thus, to understand the evolution of dispersal, it is important to combine direct and indirect methods, which will give insights into the behavioural processes affecting dispersal decisions, allowing proximate dispersal decisions to be linked to the ultimate consequences thereof.

Keywords
Natal dispersal, Neighbourhood size, Philopatry, Biased dispersal, Genetic population structure
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-223535 (URN)10.1007/s00265-013-1663-x (DOI)000332980500014 ()
Available from: 2014-04-24 Created: 2014-04-22 Last updated: 2017-12-05Bibliographically approved
Johansson, U. S., Ekman, J., Bowie, R. C. K., Halvarsson, P., Ohlson, J. I., Price, T. D. & Ericson, P. G. P. (2013). A complete multilocus species phylogeny of the tits and chickadees (Aves:Paridae). Molecular Phylogenetics and Evolution, 69(3), 852-860
Open this publication in new window or tab >>A complete multilocus species phylogeny of the tits and chickadees (Aves:Paridae)
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2013 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 69, no 3, p. 852-860Article in journal (Refereed) Published
Abstract [en]

The avian family Paridae (tits and chickadees) contains c. 55 species distributed in the Palearctic, Nearctic, Afrotropics and Indomalaya. The group includes some of the most well-known and extensively studied avian species, and the evolutionary history, in particular the post-glacial colonization of the northern latitudes, has been comparably well-studied for several species. Yet a comprehensive phylogeny of the whole clade is lacking. Here, we present the first complete species phylogeny for the group based on sequence data front two nuclear introns and one mitochondrial gene for 67 taxa of parids. Our results strongly support the inclusion of the Fire-capped Tit (Cephalopyrus flammiceps), currently placed in the Remizidae, as the most basal member of the Paridae. The Yellow-browed Tit (Sylviparus modestus) and the Sultan Tit (Melanochlora sultanea) constitute the next two sequential branches whereas the remaining tits fall into two large clades, one of which contains the seed hoarding and nest excavating species. The indicated clades within these two groups are largely congruent with recent classifications, but with several unforeseen relationships, such as non-monophyly of the Sombre Tit (Poecile lugubris) and the Marsh Tit (Poecile palustris), as well as non-monophyly of both the African gray and the African black tits. Further, our results support a close relationship between the White-fronted Tit (Parus semilarvatus) and the varied Tit (Poecile varius) as well as a close relationship between the White-naped Tit (Parus nuchalis) and the Yellow-cheeked and Black-bred tits (Parus spilonotus and P. xanthogenys). Finally, Hume's Ground-tit (Pseudopodoces humilis) is found to be closely related to the Green-backed Tit (Parus monticolus) and the Great Tit (Parus major). We propose a new classification that is in accordance with this phylogeny. 

Keywords
Molecular phylogeny, Passeriformes, Paridae, Classification
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-212307 (URN)10.1016/j.ympev.2013.06.019 (DOI)000326417600037 ()
Available from: 2013-12-10 Created: 2013-12-09 Last updated: 2017-12-06Bibliographically approved
Liu, Y., Webber, S., Bowgen, K., Schmaltz, L., Bradley, K., Halvarsson, P., . . . Griesser, M. (2013). Environmental factors influence both abundance and genetic diversity in a widespread bird species. Ecology and Evolution, 3(14), 4683-4695
Open this publication in new window or tab >>Environmental factors influence both abundance and genetic diversity in a widespread bird species
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2013 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 14, p. 4683-4695Article in journal (Refereed) Published
Abstract [en]

Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N=12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations.

Keywords
Animals, conservation, molecular ecology, population genetics
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-213821 (URN)10.1002/ece3.856 (DOI)000327304000007 ()
Available from: 2014-01-05 Created: 2014-01-04 Last updated: 2017-12-06Bibliographically approved
Halvarsson, P. (2013). On the Effects of Blood Parasites in Wild Birds. (Licentiate dissertation). Uppsala: Institutionen för ekologi och genetik
Open this publication in new window or tab >>On the Effects of Blood Parasites in Wild Birds
2013 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

Coccidian and haemoatozoan parasites are commonly occurring endo-parasites in wild birds and prevalence can vary among species and populations. In addition to prevalence studies, parasites are often used to investigate effects on life history traits. Findings from these studies are not unambiguous, as correlations with many life history traits are absent, although common findings include negative effects on survival and body condition. In this thesis, coccidian and blood parasite prevalence and their effect on survival were investigated using a PCR approach in eleven popu-lations of great snipes (Gallinago media) and in two populations of tree sparrows (Passer montanus). In great snipes and tree sparrows we investigated the parasites Plasmodium/Haemoproteus (P/H) and Leucocytozoon and in tree sparrows also Atoxoplasma.

In Great snipes the overall adult prevalence was 29.9%. At the main study site, Gåvålia, Norway, a decrease in P/H prevalence with age was found and infected birds had a lower mean age. Two not mutually exclusive alternative explanations are that infected young birds may have a higher mortality and/or that individual birds can purge the infection. There was a variation in prevalence among the sample years in Gåvålia and a difference among populations. Finding fluctuations among year demonstrates the need of long term data to study parasite prevalence variation.  

In tree sparrows the Haematozoan prevalence was 5.9% in adults and 56.5% in Atoxoplasma. By using recapture models to estimate apparent survival rates with the software MARK 4.2, it was suggested that parasite infections may have an impact on the apparent survival rate in one of the populations. Since condition and breeding performance appeared unaffected, it can be hypothesised that this pattern may indicate that chronic infections generally do not appear to impair birds, although subclinical infections may occasionally develop into disease with fatal outcome.

Abstract [sv]

Parasiter är vanliga hos vilda fåglar och de studeras flitigt. Effekten av dem kan vara allt från dödliga till mer eller mindre obefintliga. I den här avhandlingen har jag undersökt förekomst och effekter av två grupper av blodparasiter i två fågelarter med hjälp av molekylära metoder.

Dubbelbeckasinen (Gallinago media) är en lekande migrerande vadare som häckar på fuktiga bergssluttningar i Skandinavien eller i våta flodängar i öster. 30 % av dem är infekterade av någon av parasiterna Plasmodium spp./ Haemproteus spp. eller Leucocytozoon spp som är vektorspridda. Hos fåglar från Gåvålia i Norge minskade förekomsten av parasiter med ålder och fåglar som var infekterade hade en lägre medelålder. Det finns två förklaringar som inte utesluter varandra: (1) Parasiterna leder till en högre dödlighet hos infekterade fåglar, (2) enskilda fåglar kan göra sig av med infektionen. Studien på dubbelbeckasinerna visar på behovet av långa dataserier och många populationer för att upptäcka skillnader i parasitförekomst mellan olika år och populationer.

Pilfinken (Passer montanus) är en stannfågel som häckar i håligheter i träd och den har studerats i två svenska populationer under 5 år. Utöver de parasiter som också studerades hos dubbelbeckasinen, studerades Atoxoplasma spp. som sprids via avföring/födointag. Den här parasitgruppen är dåligt studerad sedan tidigare och effekterna av den är dåligt utredda. Förekomsten av de vektorspridda parasiterna var knappt 6 %, men Atoxoplasma förekom i 56 % av fåglarna. Med hjälp av fångst-återfångstanalys kan det noteras indikationer på parasitinfekterade fåglar hade en lägre årsöverlevnad än oinfekterade en av populationerna. Trots att infektionerna i många fall är kroniska verkar de inte leda till en markant större dödlighet.

Place, publisher, year, edition, pages
Uppsala: Institutionen för ekologi och genetik, 2013. p. 26
Keywords
Atoxoplasma, avian malaria, coccidia, Gallinago media, Haemoproteus, Leucocytozoon, parasite prevalence, Passer montanus, Plasmodium, recapture mod-els, survival
National Category
Zoology Ecology
Research subject
Biology with specialization in Population Biology
Identifiers
urn:nbn:se:uu:diva-206200 (URN)978-91-506-2367-3 (ISBN)
Presentation
2013-09-20, 1003, Norbyvägen 18D, Uppsala, 13:00 (English)
Opponent
Supervisors
Available from: 2013-09-02 Created: 2013-08-29 Last updated: 2013-09-02Bibliographically approved
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