Patterns of Polymorphism and Demographic History in Natural Populations of Arabidopsis lyrata

Many of the processes affecting genetic diversity act on local populations. However, studies of plant nucleotide diversity have largely ignored local sampling, making it difficult to infer the demographic history of populations and to assess the importance of local adaptation. Arabidopsis lyrata, a self-incompatible, perennial species with a circumpolar distribution, is an excellent model system in which to study the roles of demographic history and local adaptation in patterning genetic variation.We studied nucleotide diversity in six natural populations of Arabidopsis lyrata, using 77 loci sampled from 140 chromosomes. The six populations were highly differentiated, with a median FST of 0.52, and structure analysis revealed no evidence of admixed individuals. Average within-population diversity varied among populations, with the highest diversity found in a German population; this population harbors 3-fold higher levels of silent diversity than worldwide samples of A. thaliana. All A. lyrata populations also yielded positive values of Tajima's D. We estimated a demographic model for these populations, finding evidence of population divergence over the past 19,000 to 47,000 years involving non-equilibrium demographic events that reduced the effective size of most populations. Finally, we used the inferred demographic model to perform an initial test for local adaptation and identified several genes, including the flowering time gene FCA and a disease resistance locus, as candidates for local adaptation events.Our results underscore the importance of population-specific, non-equilibrium demographic processes in patterning diversity within A. lyrata. Moreover, our extensive dataset provides an important resource for future molecular population genetic studies of local adaptation in A. lyrata

A Note on Liveness in Generalized Petri Nets

We introduce the notions of homogeneity of generalized Petri nets and of sufficiently marked place sets which are basic for our generalization of COMMONERs liveness theorem to a subclass of all generalized Petri nots. We show that a corresponding decision problem (the nonsufficiency problem) is equivalent with the reachabllity problem.</jats:p

Glacial history affected phenotypic differentiation in the Alpine plant Campanula thyrsoides

Numerous widespread Alpine plant species show molecular differentiation among populations from distinct regions. This has been explained as the result of genetic drift during glacial survival in isolated refugia along the border of the European Alps. Since genetic drift may affect molecular markers and phenotypic traits alike, we asked whether phenotypic differentiation mirrors molecular patterns among Alpine plant populations from different regions. Phenotypic traits can be under selection, so we additionally investigated whether part of the phenotypic differentiation can be explained by past selection and/or current adaptation. Using the monocarpic Campanula thyrsoides as our study species, a common garden experiment with plants from 21 populations from four phylogeographic groups located in regions across the Alps and the Jura Mountains was performed to test for differentiation in morphological and phenological traits. Past selection was investigated by comparing phenotypic differentiation among and within regions with molecular differentiation among and within regions. The common garden results indicated regional differentiation among populations for all investigated phenotypic traits, particularly in phenology. Delayed flowering in plants from the South-eastern Alps suggested adaptation to long sub-mediterranean summers and contrasted with earlier flowering of plants experiencing shorter growing seasons in regions with higher elevation to the West. Comparisons between molecular and phenotypic differentiation revealed diversifying selection among regions in height and biomass, which is consistent with adaptation to environmental conditions in glacial refugia. Within regions, past selection acted against strong diversification for most phenotypic traits, causing restricted postglacial adaptation. Evidence consistent with post-glacial adaptation was also given by negative correlation coefficients between several phenotypic traits and elevation of the population's origin. In conclusion, our study suggests that, irrespective of adaptation of plants to their current environment, glacial history can have a strong and long-lasting influence on the phenotypic evolution of Alpine plants

Differentiation in morphology and flowering phenology between two Campanula thyrsoides L. subspecies

Subspecies are usually characterized by sets of morphological discontinuities. By means of common garden experiments, we investigated genetic differentiation in morphological and phenological traits in two geographically disjunct subspecies of Campanula thyrsoides L., i.e. subsp. thyrsoides (= C.* thyrsoides) occurring in the European Alps and Jura Mountains, and subsp. carniolica (= C.* carniolica) occurring in the Southeastern Alps and the Dinaric Arc. Nine out of 16 investigated traits were significantly different between C.* thyrsoides and C.* carniolica. For C.* carniolica inflorescence length was 1.4×, and above-ground biomass 2.7× higher, while flower density was significantly lower. Campanula* carniolica also showed delayed flowering and flower development from bottom to top compared to C.* thyrsoides which flowered from top to bottom. The inflorescence growth was indeterminate and flowering took several weeks in C.* carniolica, whereas C.* thyrsoides showed determinate flowering, rapidly opening all flowers within a few days. This differentiation in flowering phenology is likely to be adaptive. The submediterranean climate favours indeterminate flowering in C.* carniolica, allowing ongoing growth of the inflorescence throughout the long summer until environmental conditions worsen, whereas determinate and early flowering in C.* thyrsoides is favourable in the short growing season in the high Alps where seed production must be secured before temperature drops. Glacial survival in refugia with different climates (alpine vs. submediterranean) may have caused this regional differentiation

Oppdatert tiltaksanalyse for elvemusling i Ualandsåna (Varhaugåna)

Magerøy, J.H., Wacker, S., Saksgård, R., Tjensvoll, A.E., Eriksen, K.S & Sandring, S. 2024. Oppdatert tiltaksanalyse for elvemusling i Ualandsåna (Varhaugåna). Revidert utgave. NINA Rapport 2328b. Norsk institutt for naturforskning. Elvemuslingbestanden i Ualandsåna er klassifisert som ikke livskraftig, pga. svært lav rekruttering av ungmuslinger. Det er derfor svært viktig å identifisere og gjennomføre tiltak for å forbedre miljøforholdene og øke rekrutteringen i bestanden. Det har blitt pekt på tre potensielle årsaker til den lave rekrutteringen av elvemusling i Ualandsåna: 1. Eutrofiering og partikkeltilførsel. 2. Forsuring. 3. Mangel på egnet vertsfisk. Innsamlingen av nye data tilsier at eutrofiering og partikkeltilførsel er den viktigste årsaken til den lave rekrutteringen av ungmuslinger i elven, men at mangel på tilgang på egnet vertsfisk også er en viktig årsak. Forsuring er en mindre viktig årsak, men kan påvirke muslingen negativt i øvre deler av utbredelsesområdet. Det viktigste tiltaket for å redusere eutrofiering og partikkeltilførsel til Ualandsåna er inngjerding av elven og etablering av kantsoner. Dette vil bidra til redusert erosjon av elvebredden og redusert avrenning av næringsstoffer og partikler i forbindelse med beite og gjødsling. Kantsonen til vassdrag har et spesielt vern i vannressursloven, men det er viktig å opprette og opprettholde enda bredere kantsoner langs Ualandsåna. I den foreslåtte tiltaksplanen for vassdraget er det anbefalt en kantsone på 6 m, men en kantsone opp mot 10 m vil være enda mer effektiv. Det er også andre tiltak som kan redusere eutrofiering og partikkeltilførsel til Ualandsåna. Man bør utbedre traktorveier og kjørespor. Nydyrking, dreneringsarbeid og bekkelukking bør forhindres, og vedlikehold av dreneringsgrøfter må gjennomføres på en skånsom måte. Det er også viktig at hogst av plantefeltene langs elven gjennomføres på en skånsom måte. Restaurering av myr i nedbørfeltet kan bidra til å redusere avrenningen. Tiltak for å redusere eutrofiering og partikkeltilførsel til Ualandsåna er også viktige for å øke tilgangen på vertsfisken (ørret) for elvemuslingen. I tillegg vil fjerning av vandringshindre bidra til økt oppgang av anadrom fisk, men om dette vil øke tettheten av ørret eller kun laks er usikkert. Det som er sikkert at det er viktig å hindre negativ påvirkning på og gjennomføre habitatforbedrende tiltak i sidebekkene til elven, da disse utgjør viktig gyte- og oppveksthabitat for ørret. Kalking kan være aktuelt i øvre del av Ualandsåna. Det er likevel usikkert om kalking vil påvirke elvemuslingen positivt, da det vil kunne favorisere laks over ørret. Derfor er det usikkert om det bør kalkes. Videre vannkvalitetsovervåking kan bidra til å avgjøre om det er nødvendig. Innsamlingen av de nye dataene førte også til at enkelte andre tiltak er ansett som viktige. Restaurering av myr kan bidra til høyere vannføring i tørkeperioder. Man bør også forhindre uttak av vann av samme grunn. En høyere vannføring vil ha en positiv effekt både på elvemusling og fisk. Kultivering av elvemusling fra Ualandsåna ansees i dag ikke som et aktuelt tiltak. Grunnen til dette er at bestander med svært lavt antall muslinger ikke tas inn til kultiveringsanlegget, pga. problemer med dødelighet blant stammuslingene ved anlegget i tidligere år. Hvis overlevelsen av stammusling er god i årene fremover, kan det bli aktuelt å kultivere muslinger fra elven. For å gjennomføre tiltakene på en god måte er det viktig å følge opp regelverk, vurdere incentivordninger for grunneierne og involvere lokale interessenter.Magerøy, J.H., Wacker, S., Saksgård, R., Tjensvoll, A.E., Eriksen, K.S & Sandring, S. 2024. Updated management action plan for the freshwater pearl mussel in the Ualandsåna River. Revised edition. NINA Report 2328b. Norwegian Institute for Nature Research. The freshwater pearl mussel population in the Ualandsåna River is classified as non-viable, due to low recruitment of juveniles. Thus, it is very important to identify and undertake management actions to improve environmental conditions and increase the recruitment in the population. Previously, three potential causes of the low recruitment of mussels in Ualandsåna has been pointed out: Eutrophication and particle runoff. 2. Acidification. 3. Lack of suitable host fish. The collection of new data indicates that eutrophication and particle runoff is the most important cause of the low recruitment of juveniles in the river. However, the lack of host fish is also an important cause. Acidification is less important, although it can impact the mussel negatively in the upper reaches of the distribution area. The most important action to reduce eutrophication and particle runoff to Ualandsåna, is fencing the river off and establishing riparian vegetation zones. This will reduce erosion of the riverbanks and runoff of nutrients and particles due to grazing and the spreading of manure. Riparian vegetation zones are protected under Norwegian law, but it is important to maintain even wider vegetation zones along Ualandsåna. In the proposed management plan for the watercourse, a 6 m wide zone is recommended. However, a zone up to 10 m wide will be more effective. There are other actions that can reduce eutrophication and particle runoff to Ualandsåna. One should improve agricultural roads and tracks. Cultivation of new land, drainage works and closing of streams should be prevented, and the maintenance of drainage ditches should be undertaken while minimizing runoff. It is also important to minimize runoff during logging of spruce plantations. Restoring wetlands in the catchment can also reduce runoff. Actions to reduce eutrophication and particle runoff to Ualandsåna are also important to increase the access to the host fish (trout) for the mussel. In addition, removing migration barriers can increase the migration of anadromous fish, but it is unknown whether this will primarily benefit trout or salmon. It is certain that it is important to prevent negative impacts and undertake habitat improvement in the tributaries, as they are important spawning and rearing habitat for trout. Liming can be undertaken in the upper reaches of Ualandsåna, However, it is uncertain if liming will benefit the mussel, as it could favor salmon over trout. Thus, it is uncertain if liming should be undertaken. Further water quality analyses could help decide if it is necessary. New data collection also resulted in recommendation of additional actions. Restoration of wetlands can also contribute to higher water flow during draughts. One should also prevent water withdrawal for the same reason. Higher water flow will be positive for both mussels and fish. Currently, cultivation of the mussels from Ualandsåna is currently not a plausible action. This is because populations with very low mussel numbers are not collected for cultivation, due to problems with mortality among brood stock at the cultivation facility in recent years. If the survival of brood stock is good in the years to come, one could consider cultivating mussels from the river. To successfully undertake the recommended actions, it is important to enforce rules, consider incentives for landowners and involve local stakeholders

Local adaptation in European populations of <em>Arabidopsis lyrata</em> (Brassicaceae)

We studied local adaptation to contrasting environments usingan organism that is emerging as a model for evolutionary plantbiology—the outcrossing, perennial herb Arabidopsis lyratasubsp. petraea (Brassicaceae). With reciprocal transplant experiments,we found variation in cumulative fitness, indicating adaptivedifferentiation among populations. Nonlocal populations didnot have significantly higher fitness than the local population.Experimental sites were located in Norway (alpine), Sweden (coastal),and Germany (continental). At all sites after one year, thelocal population had higher cumulative fitness, as quantifiedby survival combined with rosette area, than at least one ofthe nonlocal populations. At the Norwegian site, measurementswere done for two additional years, and fitness differencespersisted. The fitness components that contributed most to differencesin cumulative fitness varied among sites. Relatively small rosettearea combined with a large number of inflorescences producedby German plants may reflect differentiation in life history.The results of the current study demonstrate adaptive populationdifferentiation in A. lyrata along a climatic gradient in Europe.The studied populations harbor considerable variation in severalcharacters contributing to adaptive population differentiation.The wealth of genetic information available makes A. lyrataa highly attractive system also for examining the functionaland genetic basis of local adaptation in plants.</p