Population genetic structure and phylogeography of invasive aquatic weed, Elodea canadensis (Hydrocharitaceae) and comparative analyses with E. nuttallii

The introductions of invasive species are one of the most important threats to global biodiversity and ecosystem function. In addition, invasive species often cause large economical and social consequences. Genetic characteristics of introduced populations have an impact on their capacity of range expansion in the non-native areas. Therefore, understanding the evolutionary consequences of invasions will provide knowledge for the design of appropriate methods for managing introduced populations. In addition, detailed genetic data enables the design of molecular genetic markers useful in monitoring risky species and in early detection of new invasions. In this thesis, I developed novel genetic markers to investigate population genetic structure and phylogeography of two invasive aquatic weeds, Elodea canadensis Michx and E. nuttallii (Planch.) St. John (Hydrocharitaceae). I investigated the genetic population structure of introduced Finnish E. canadensis populations using microsatellite markers. The results revealed a moderate level of variation within and among Finnish populations analysed. Despite of the genetic variation detected, the possibility of only one introduction followed by post-establishment evolution cannot be rejected based on the results in this thesis. Furthermore, I surveyed the geographical distribution of the chloroplast (cp) DNA haplotypes within the native and introduced ranges of E. canadensis and E. nuttallii in order to reconstruct the spreading histories of these species. Only a single haplotype was found in the introduced range in both species and these haplotypes were widespread also in the native range. Therefore, I was not able to identify the geographic origin of the introduced populations or test the hypothesis of single versus multiple introductions. I sequenced the complete cp genome sequence and characterized the cp genome organization of E. canadensis. The results showed that the cp genome of E. canadensis has gone through less rearrangements or gene losses when compared to assumed ancestral species than have the other monocots studied. The inverted repeat region (IR) of E. canadensis has a unique structure among the monocot species studied so far. Only few cp genomes representing early lineages of monocots have been sequenced and, therefore, this thesis provides valuable information about the course of evolution in the divergence of monocot lineages. This thesis addresses key issues in the biology of invasive species and gives novel information on the genetic patterns at native and introduced populations of E. canadensis and E. nuttallii. It also provides a source of genetic markers for future investigations of the population genetics of invasive species. The results highlight the need for further investigation of the Elodea species, as well as studies on other invasive plant species. Future research should focus on predictive analyses of potential future invaders and other preventive methods to minimize new introductions.Haitalliset vieraslajit ovat maailmanlaajuisesti yksi suurimmista uhkatekijöistä luonnon monimuotoisuudelle. Vieraslajeilla on usein lisäksi taloudellisia, terveydellisiä ja sosiaalisia vaikutuksia. Molekyylimenetelmien avulla voidaan kerätä tärkeää tietoa vieraslajien populaatioiden geneettisestä rakenteesta. Menetelmillä voidaan myös tutkia vieraslajien leviämisreittejä ja leviämisen alkuperää. Molekyylimenetelmät voivat toimia myös lajintunnistuksen apuvälineinä, joilla voidaan tehokkaasti tarkkailla potentiaalisten vieraslajien populaatioita ja havaita ajoissa uudet invaasiot. Näitä tietoja voidaan hyödyntää, kun pohditaan menetelmiä vieraslajipopulaatioiden hallintaan ja pyritään estämään uusia invaasioita. Tämän väitöstutkimuksen kohteena olivat kanadanvesirutto (Elodea canadensis) ja kiehkuravesirutto (E. nuttallii), jotka ovat Pohjois-Amerikasta kotoisin olevia vesikasvilajeja. Kumpikin vesiruttolaji on levinnyt alkuperäisalueiltaan Eurooppaan ja muille mantereille ja muodostaa uusilla kasvupaikoillaan massakasvustoja. Kasvustot voivat syrjäyttää alkuperäislajeja sekä aiheuttaa muutoksia vesistön happamuus- ja ravinnetasossa. Lisäksi massakasvustot vaikeuttavat vesistöjen virkistyskäyttöä. Kanadanvesirutto aiheuttaa ongelmia myös monissa Suomen vesistöissä. Kiehkuravesirutto on levinnyt suureen osaan Eurooppaa ja sen arvellaan leviävän lähivuosina myös Suomeen. Kehitin väitöstutkimuksessani tuman DNA:n molekyylimerkkejä, joiden avulla tutkin kanadanvesiruton geneettistä populaatiorakennetta Suomen tulokaspopulaatioissa ja selvitin lajin leviämishistoriaa Suomessa. Lisäksi selvitin kanadanvesiruton kloroplastigenomin DNA:n emäsjärjestyksen ja kehitin kloroplastin DNA:n molekyylimerkkejä, joiden avulla tutkin kanadanvesiruton ja kiehkuravesiruton populaatioita laajasti alkuperäis- ja tulokasalueilla. Tarkoituksenani oli selvittää geneettisen muuntelun maantieteellistä jakautumista ja lajien tulokaspopulaatioiden mahdollista alkuperää. Tutkimustulokset osoittavat, että Suomen kanadanvesiruttopopulaatioissa esiintyy kohtuullinen määrä muuntelua. Näiden tulosten perusteella ei kuitenkaan voida päätellä, onko laji levinnyt Suomeen useita kertoja. On mahdollista, että geneettinen muuntelu on seurausta yhden invaasion jälkeen seuranneesta nopeasta evolutiivisesta muutoksesta tulokaspopulaatioissa. Tutkittaessa geneettisen muuntelun maantieteellistä jakautumista löydettiin yhteensä kolme kanadanvesiruton ja neljä kiehkuravesiruton haplotyyppiä. Molemmilla lajeilla havaittiin yksi valtahaplotyyppi, joka kattaa suurimman osan alkuperäisalueesta ja kaikki populaatiot uusilla kasvupaikoilla. Euroopan tulokaspopulaatiot saattavat olla peräisin yhdestä tai useammasta invaasiosta, jotka edustavat samaa haplotyyppiä. Tulokset osoittavat lisäksi, että kanadanvesiruton kloroplastigenomin rakenne on hyvin samankaltainen kuin alkukantaisilla putkilokasveilla ja eroaa kaikista tähän mennessä tutkituista yksisirkkaisista kasvilajeista. Siten tutkimus tuo uutta tietoa yksisirkkaisten evoluutiosta. Osa tutkimuksessa kehitetyistä molekyylimerkeistä toimii tehokkaina työkaluina vesiruttolajien välisessä lajintunnistuksessa ja on siten apuna uusien invaasioiden varhaisessa havainnoinnissa. Tämä väitöstutkimus tuo lisätietoa vieraslajien biologian keskeisistä tutkimuskysymyksistä. Tulokset kuitenkin osoittavat, että lisäselvitykset ovat tarpeen. Lisäksi tarvitaan käytännön toimia, sillä biologisen tutkimuksen avulla ei voida ratkaista kaikkia vieraslajeihin liittyviä ongelmia. Tulevaisuudessa tutkimuksen tulisi keskittyä erityisesti vieraslajien leviämisen ennaltaehkäisevään torjuntaan ja uusien invaasioiden mahdollisimman varhaisen havaitsemisen tehostamiseen

Comparative analyses of plastid sequences between native and introduced populations of aquatic weeds Elodea canadensis and E. nuttallii.

Peer reviewe

Patterns of genetic variation in leading-edge populations of Quercus robur : genetic patchiness due to family clusters

The genetic structure of populations at the edge of species distribution is important for species adaptation to environmental changes. Small populations may experience non-random mating and differentiation due to genetic drift but larger populations, too, may have low effective size, e.g., due to the within-population structure. We studied spatial population structure of pedunculate oak,Quercus robur, at the northern edge of the species' global distribution, where oak populations are experiencing rapid climatic and anthropogenic changes. Using 12 microsatellite markers, we analyzed genetic differentiation of seven small to medium size populations (census sizes 57-305 reproducing trees) and four populations for within-population genetic structures. Genetic differentiation among seven populations was low (Fst = 0.07). We found a strong spatial genetic structure in each of the four populations. Spatial autocorrelation was significant in all populations and its intensity (Sp) was higher than those reported in more southern oak populations. Significant genetic patchiness was revealed by Bayesian structuring and a high amount of spatially aggregated full and half sibs was detected by sibship reconstruction. Meta-analysis of isoenzyme and SSR data extracted from the (GD)(2)database suggested northwards decreasing trend in the expected heterozygosity and an effective number of alleles, thus supporting the central-marginal hypothesis in oak populations. We suggest that the fragmented distribution and location of Finnish pedunculate oak populations at the species' northern margin facilitate the formation of within-population genetic structures. Information on the existence of spatial genetic structures can help conservation managers to design gene conservation activities and to avoid too strong family structures in the sampling of seeds and cuttings for afforestation and tree improvement purposes.Peer reviewe

Accounting for species interactions is necessary for predicting how arctic arthropod communities respond to climate change

Species interactions are known to structure ecological communities. Still, the influence of climate change on biodiversity has primarily been evaluated by correlating individual species distributions with local climatic descriptors, then extrapolating into future climate scenarios. We ask whether predictions on arctic arthropod response to climate change can be improved by accounting for species interactions. For this, we use a 14-year-long, weekly time series from Greenland, resolved to the species level by mitogenome mapping. During the study period, temperature increased by 2 degrees C and arthropod species richness halved. We show that with abiotic variables alone, we are essentially unable to predict species responses, but with species interactions included, the predictive power of the models improves considerably. Cascading trophic effects thereby emerge as important in structuring biodiversity response to climate change. Given the need to scale up from species-level to community-level projections of biodiversity change, these results represent a major step forward for predictive ecology.Peer reviewe

Higher host-plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient

How community-level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root-associated fungi for plant species, asking whether the level of specialization varies with elevation. For this, we applied DNA barcoding based on the ITS region to root samples of five plant species equivalently sampled along an elevational gradient at a high arctic site. To assess whether the level of specialization changed with elevation and whether the observed patterns varied between mycorrhizal and endophytic fungi, we applied a joint species distribution modeling approach. Our results show that host plant specialization is not environmentally constrained in arctic root-associated fungal communities, since there was no evidence for changing specialization with elevation, even if the composition of root-associated fungal communities changed substantially. However, the level of specialization for particular plant species differed among fungal groups, root-associated endophytic fungal communities being highly specialized on particular host species, and mycorrhizal fungi showing almost no signs of specialization. Our results suggest that plant identity affects associated mycorrhizal and endophytic fungi differently, highlighting the need of considering both endophytic and mycorrhizal fungi when studying specialization in root-associated fungal communities.Peer reviewe

Higher host-plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient

How community-level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root-associated fungi for plant species, asking whether the level of specialization varies with elevation. For this, we applied DNA barcoding based on the ITS region to root samples of five plant species equivalently sampled along an elevational gradient at a high arctic site. To assess whether the level of specialization changed with elevation and whether the observed patterns varied between mycorrhizal and endophytic fungi, we applied a joint species distribution modeling approach. Our results show that host plant specialization is not environmentally constrained in arctic root-associated fungal communities, since there was no evidence for changing specialization with elevation, even if the composition of root-associated fungal communities changed substantially. However, the level of specialization for particular plant species differed among fungal groups, root-associated endophytic fungal communities being highly specialized on particular host species, and mycorrhizal fungi showing almost no signs of specialization. Our results suggest that plant identity affects associated mycorrhizal and endophytic fungi differently, highlighting the need of considering both endophytic and mycorrhizal fungi when studying specialization in root-associated fungal communities.Peer reviewe

Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic

Knowledge about the distribution and local diversity patterns of arbuscular mycorrhizal (AM) fungi are limited for extreme environments such as the Arctic, where most studies have focused on spore morphology or root colonization. We here studied the joint effects of plant species identity and elevation on AM fungal distribution and diversity. We sampled roots of 19 plant species in 18 locations in Northeast Greenland, using next generation sequencing to identify AM fungi. We studied the joint effect of plant species, elevation and selected abiotic conditions on AM fungal presence, richness and composition. We identified 29 AM fungal virtual taxa (VT), of which six represent putatively new VT. Arbuscular mycorrhizal fungal presence increased with elevation, and as vegetation cover and the active soil layer decreased. Arbuscular mycorrhizal fungal composition was shaped jointly by elevation and plant species identity. We demonstrate that the Arctic harbours a relatively species-rich and nonrandomly distributed diversity of AM fungi. Given the high diversity and general lack of knowledge exposed herein, we encourage further research into the diversity, drivers and functional role of AM fungi in the Arctic. Such insight is urgently needed for an area with some of the globally highest rates of climate change

Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic

Knowledge about the distribution and local diversity patterns of arbuscular mycorrhizal (AM) fungi are limited for extreme environments such as the Arctic, where most studies have focused on spore morphology or root colonization. We here studied the joint effects of plant species identity and elevation on AM fungal distribution and diversity. We sampled roots of 19 plant species in 18 locations in Northeast Greenland, using next generation sequencing to identify AM fungi. We studied the joint effect of plant species, elevation and selected abiotic conditions on AM fungal presence, richness and composition. We identified 29 AM fungal virtual taxa (VT), of which six represent putatively new VT. Arbuscular mycorrhizal fungal presence increased with elevation, and as vegetation cover and the active soil layer decreased. Arbuscular mycorrhizal fungal composition was shaped jointly by elevation and plant species identity. We demonstrate that the Arctic harbours a relatively species-rich and nonrandomly distributed diversity of AM fungi. Given the high diversity and general lack of knowledge exposed herein, we encourage further research into the diversity, drivers and functional role of AM fungi in the Arctic. Such insight is urgently needed for an area with some of the globally highest rates of climate change.Peer reviewe

Protax-fungi : a web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences

Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed Protax-fungi, a general tool for taxonomic placement of fungal internal transcribed spacer (ITS) sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. With empirical data on root- and wood-associated fungi, Protax-fungi reliably identified (with at least 90% identification probability) the majority of sequences to the order level but only around one-fifth of them to the species level, reflecting the current limited coverage of the databases. Protax-fungi outperformed the Sintax and Rdb classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence database coverage. We applied Protax-fungi to examine the internal consistencies of the Index Fungorum and UNITE databases. This revealed inconsistencies in the taxonomy database as well as mislabelling and sequence quality problems in the reference database. The according improvements were implemented in both databases. Protax-fungi provides a robust tool for performing statistically reliable identifications of fungi in spite of the incompleteness of extant reference sequence databases and unresolved taxonomic relationships.Peer reviewe

SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes

The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent-coverage threshold to filter out false positives, (b) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R2 = .93, mitogenomes R2 = .95) and a high repeatability across environmental-sample replicates (barcodes R2 = .94, mitogenomes R2 = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species-specific abundances, and phenology. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities