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Appendix for Authorea preprint DOI: 10.22541/au.161447476.67562312/v1

Inbreeding can have negative effects on survival and reproduction, which may be of conservation concern in small and isolated populations. However, the physiological mechanisms underlying inbreeding depression are not well-known. The length of telomeres, the DNA sequences protecting chromosome ends, has been associated with health or fitness in several species. We investigated effects of inbreeding on early-life telomere length in two small island populations of wild house sparrows (Passer domesticus) known to be affected by inbreeding depression. Using genomic measures of inbreeding we found that inbred nestling house sparrows (n = 371) have significantly shorter telomeres. Using pedigree-based estimates of inbreeding we found a tendency for inbred nestling house sparrows to have shorter telomeres (n = 1195). This negative effect of inbreeding on telomere length may have been complemented by a heterosis effect resulting in longer telomeres in individuals that were less inbred than the population average. Furthermore, we found some evidence of stronger effects of inbreeding on telomere length in males than females. Thus, telomere length may reveal subtle costs of inbreeding in the wild and demonstrate a route by which inbreeding negatively impacts the physiological state of an organism already at early life-history stages.

Flagstad, Ø., Kvalnes, T., Røed, K. H. Våge, J., Strand O., & Sæther B.-E. 2022. Genetisk levedyktig villreinbestand på Hardangervidda. NINA Rapport 2176. Norsk institutt for naturforskning. Villreinbestanden på Hardangervidda, som er Norges største villreinområde, er svært utsatt for habitatfragmentering som følge av utbygging av infrastruktur og annen menneskelig aktivitet. Bestandsstørrelsen er sterkt påvirket av høsting og den årlige bestandsveksten avhenger også av værforholdene. Som et verktøy for CWD-bekjempelse og kartlegging, er høstingsregimet de siste årene endret, med en større andel bukk i uttaket. En endring i høstingsstrategi, enten i form av økte uttak eller en endret kjønns- og aldersstruktur blant de høstede dyra, har ikke bare demografiske effekter, men kan også ha betydelige genetiske konsekvenser. Genetisk variasjon er helt essensielt for en bestands langsiktige overlevelse, og påvirkes av en rekke ulike økologiske og evolusjonære prosesser. Den mest grunnleggende mekanismen - naturlig utvalg eller seleksjon - medfører at de best tilpassede individene under rådende miljøforhold har best mulighet til å videreføre sine gener til etterfølgende generasjoner. Ved en bestandsreduksjon vil naturlig seleksjon bli mindre effektiv, og tilfeldige endringer i genetisk sammensetning, såkalt genetisk drift, får større spillerom. Dette kan føre til økt tap av genetisk variasjon og at dårlige genvarianter (skadelige mutasjoner) øker i frekvens i bestanden. Den helt grunnleggende parameteren som bestemmer omfanget av den genetiske driften, er den effektive bestandsstørrelsen (Ne). Effektiv bestandsstørrelse er bestemt av antall individer av begge kjønn som parer seg og får avkom. Siden ikke alle individer tar del i reproduksjon, er Ne som oftest betydelig lavere enn den faktiske bestandsstørrelsen (N). I denne rapporten redegjør vi for arbeidet med å vurdere den genetiske levedyktigheten til villreinbestanden på Hardangervidda og evaluere de genetiske konsekvensene av bestandsendring som verktøy for CWD-bekjempelse. Våre analyser viser en viss grad av genetisk differensiering mellom stammen på Hardangervidda og nabobestandene, men kun begrenset genetisk særegenhet. De genetiske variantene som finnes på Hardangervidda finnes altså i stor grad også i nabobestandene i Nordfjella og Setesdal, selv om det er forskjeller i deres forekomster. Gitt gjennomsnittlige høstingsrater på Hardangervidda for perioden 2005-2018, estimerte vi Ne til å være i underkant av 2000 dyr. Dette, sammen med noe immigrasjon fra nabobestandene, tilsier svært lave nivåer av genetisk drift i bestanden for denne perioden. Sånn sett framstår bestanden som relativt robust og må kunne betraktes som genetisk levedyktig på lang sikt. Det bør dog understrekes at med inntoget av CWD og det endrede høstingsregimet som ble gjennomført i 2019-2021, er Ne allerede redusert til i underkant av 1000 dyr. Våre simuleringer av til dels betydelige bestandsreduksjoner viser at selv med kort tid (0-5 år) på lavt bestandsnivå (færre enn 2000 dyr i totalbestand), kan man risikere at tapet av genetisk variasjon i form av heterozygositet har oversteget 5% etter 100 år dersom uttaket omfatter en stor andel bukk. I tillegg er det slik at sjeldne alleler ved en plutselig bestandsreduksjon tapes i langt større omfang enn heterozygositet. Slike alleler kan være av betydning for utviklingen av nye tilpasninger til et endret miljø. Konsekvensen av CWD-smitte i bestanden på Hardangervidda og virkningen av ulike tiltak må nøye veies opp mot påvirkningen på bestandens genetiske levedyktighet. Det vurderes som kritisk å ivareta den genetiske variasjonen i bestanden for å sikre dens levedyktighet og tilpasningsevne til nåværende og framtidige miljøbetingelser. Vi vet fremdeles lite om langtidseffektene av endringene som skjer i leveområdet til villreinen og et føre-var prinsipp i forvaltningen av arten anses som viktig. Flagstad, Ø., Kvalnes, T., Røed, K. H. Våge, J., Strand O., & Sæther B.-E. 2022. Genetically viable reindeer population on Hardangervidda. NINA Report 2176. Norwegian Institute for Nature Research. Wild reindeer on Hardangervidda, which is Norway's largest reindeer area, are highly exposed to habitat fragmentation from infrastructure development and other human activity. Population size is strongly influenced by harvesting and annual population growth also depends on weather conditions. As a tool for CWD control and mapping, the harvest regime has been altered in recent years, with a larger proportion of males harvested. An altered harvesting strategy, either as increased harvest or altered sex and age structure among harvested animals, not only has demographic effects, but can also have substantial genetic consequences. Genetic variation is pivotal for long-term population viability and is affected by a number of ecological and evolutionary processes. The most basic mechanism - natural selection - favors the best adapted individuals under prevailing environmental conditions, increasing their probability to pass on their genes to subsequent generations. Upon population reduction, natural selection will become less effective, and random changes in genetic composition, i.e., genetic drift, becomes increasingly important. This can lead to loss of genetic variation at the same time as deleterious mutations may increase in frequency. The basic parameter determining the strength of genetic drift is the effective population size (Ne). Effective population size is determined by the number of individuals of both sexes that mate and produce offspring. Since not all individuals take part in reproduction, Ne is usually considerably lower than the actual population size (N). In this report, we address genetic viability in the population of wild reindeer on Hardangervidda and evaluate the genetic consequences of population reduction as a tool for CWD control. Our analyzes show some genetic differences between the population on Hardangervidda and the neighboring populations, but only limited genetic uniqueness, meaning that virtually all alleles found on Hardangervidda are also found in the neighboring populations in Nordfjella and Setesdal, although their frequencies differ. Given average harvesting rates on Hardangervidda for the period 2005-2018, we estimated Ne to be just below 2,000 animals. This, together with some immigration from neighboring populations, suggests very low levels of genetic drift in the population for this period. From this point of view, the population appears relatively robust and must be considered genetically viable in the long term. However, it should be noted that with the introduction of CWD and the altered harvesting regime implemented in 2019, Ne has already been reduced to less than 1,000 animals. Our simulations of population reduction show that even with a short time (0-5 years) at low population size (fewer than 2000 animals in the total population), there is a risk that the loss of genetic variation (heterozygosity) will exceed 5% after 100 years if the harvest includes a large proportion of males. Moreover, after a sudden population decline, rare alleles are lost to a far greater extent than heterozygosity. Such alleles can be important for the development of new adaptations to environmental change. Indeed, the consequence of CWD infection and the impact of various management actions must be carefully weighed against the impact on the genetic viability of the population. We stress the importance to maintain genetic variation to ensure population viability and adaptability to current and future environmental conditions. We still know little about the long-term effects of the changes that occur in wild reindeer habitats and a precautionary management approach is considered important.

Publisher Copyright: © 2022 selection and editorial matter, Tim Horstkotte, Øystein Holand, Jouko Kumpula and Jon Moen. Traditionally the multipurpose reindeer herd supplied an array of products from both live and slaughtered animals. After the transportation revolution and integration into the market economy in the 1960s and 1970s, however, the focus was directed towards maximizing meat production. Research carried out at the time revealed that the females’ adult body mass was an appropriate proxy for their production potential. Herd composition, selection and slaughter strategies were reformed. A winter herd composed predominantly of productive females with a spring body mass of around 70 kg and herd size not exceeding the available winter resources will yield a high percentage of calves to be slaughtered in autumn. Economic incentives and imposed regulations contributed to this transformation. However, these modern production imperatives were not necessarily compatible with the herders’ traditional values. Indeed, meat productivity varies between and within countries. This chapter discusses abiotic and biotic factors, genetics, as well as management practices that may influence these differences. Herds in good condition are able to withstand and adapt to ongoing climate change and frequent weather extremes. Integrating resilience to environmental variability into reindeer breeding programmes may improve the capacity of the production system.

Supplementary tables and figures for the main results, and supplementary results and derivations.

Genome-wide association studies provide good opportunities for studying the genetic basis of adaptive traits in wild populations. Yet, previous studies often failed to identify major effect genes. In this study, we used high-density single nucleotide polymorphism and individual fitness data from a wild non-model species. Using a whole-genome approach, we identified the MC1R gene as the sole causal gene underlying Arctic fox Vulpes lagopus fur colour. Further, we showed the adaptive importance of fur colour genotypes through measures of fitness that link ecological and evolutionary processes. We found a tendency for blue foxes that are heterozygous at the fur colour locus to have higher fitness than homozygous white foxes. The effect of genotype on fitness was independent of winter duration but varied with prey availability, with the strongest effect in years of increasing rodent populations. MC1R is located in a genomic region with high gene density, and we discuss the potential for indirect selection through linkage and pleiotropy. Our study shows that whole-genome analyses can be successfully applied to wild species and identify major effect genes underlying adaptive traits. Furthermore, we show how this approach can be used to identify knowledge gaps in our understanding of interactions between ecology and evolution.

Knowledge about the underlying genetic architecture of phenotypic traits is needed to understand and predict their evolutionary dynamics. The number of causal loci underlying most phenotypic traits, the magnitude of their effects and their location in the genome is still largely unknown. Here we use genome-wide SNP data from two large-scale datasets on house sparrows and collared flycatchers to examine the genetic architecture of morphological (tarsus length, wing length, body mass, bill depth and bill length) and sexually selected traits (total badge size and visible badge size in house sparrows and white wing patches in collared flycatchers). Heritabilities were estimated using kinship coefficients calculated from the SNP data. The proportion of variance captured by the SNPs (SNP-based heritability) was lower in house sparrows compared to collared flycatchers, as expected given marker density (6,348 SNPs in house sparrows versus 38,689 SNPs in collared flycatchers). Chromosome partitioning analyses demonstrated that the proportion of variance explained by each chromosome was significantly positively related to the chromosome size for most traits. Finally, we only found two genome-wide significant associations with very small effect sizes; one SNP on chromosome 20 associated with bill length in house sparrows and one SNP on chromosome 4 for tarsus length in collared flycatchers. Although we cannot exclude the possibility of undetected large-effect QTL, our results support the hypothesis that variation in morphological and sexually selected traits is typically determined by many loci with small effect. © 2017. This is the authors’ accepted and refereed manuscript to the article. Locked until 14.12.2017 due to copyright restrictions.