Mitochondrial Genomes, Phylogenetic Associations, and SNP Recovery for the Key Invasive Ponto-Caspian Amphipods in Europe

The Ponto-Caspian region is the main donor of invasive amphipods to freshwater ecosystems, with at least 13 species successfully established in European inland waters. Dikerogammarus spp. and Pontogammarus robustoides are among the most successful, due to their strong invasive impact on local biota. However, genomic knowledge about these invaders is scarce, while phylogeography and population genetics have been based on short fragments of mitochondrial markers or nuclear microsatellites. In this study, we provide: (i) a reconstruction of six mitogenomes for four invasive gammarids (D. villosus, D. haemobaphes, D. bispinosus, and P. robustoides); (ii) a comparison between the structure of the newly obtained mitogenomes and those from the literature; (iii) SNP calling rates for individual D. villosus and D. haemobaphes from different invasion sites across Europe; and (iv) the first time-calibrated full mitogenome phylogeny reconstruction of several Ponto-Caspian taxa. We found that, in comparison to other gammarids, the mitogenomes of Ponto-Caspian species show a translocation between the tRNA-E and tRNA-R positions. Phylogenetic reconstruction using the mitogenomes identified that Ponto-Caspian gammarids form a well-supported group that originated in the Miocene. Our study supports paraphyly in the family Gammaridae. These provided mitogenomes will serve as vital genetic resources for the development of new markers for PCR-based identification methods and demographic studies

Suunisliigid märgalakoosluste taastamisel

Väitekirja elektrooniline versioon ei sisalda publikatsiooneMärgalakooslused on tuntud oma liigirikkuse ja eripäraste ökosüsteemide poolest. Inimtegevuse tagajärjel on looduslike märgalade pindala maailmas vähenenud 20. sajandist alates enam kui 50%. See on omakorda viinud paljude märgalasid asustavate liikide arvukuse languseni, s.h. niidukahlajad ja kahepaiksed, keda käsitletakse ka antud doktoritöös. Käesolevas töös uuritakse erinevate märgalaelupaikade (tiigid, märjad hooldatud rannaniidud ja metsanduse eesmärgil kuivendatud siirdesoometsad) taastamist Eestis, lähtudes elupaigatundlikest suunisliikidest. Erinevat tüüpi (looduslikud, inimtekkelised, spetsiaalselt kahepaiksetele rajatud) väikeveekogude liigilise koosseisu ja struktuuri uuringust selgus, et kõige liigirikkamad on peamiselt harivesilikule rajatud veekogud. See tähendab, et harivesiliku tarbeks väikeveekogude taastamine ja rajamine loob sobivaid elupaiku ka teistele (pool)veelistele liikidele. Rannaniitude uuringus leiti, et ohustatud kahlajaliikidele (eriti niidurüdile) on sobivaimaks pesitsuspaigaks suurepindalalised ja laiad karjatatavad rannaniidud, kus puuduvad puud ning leidub ajutisi madalaveelisi lompe. Samuti oli neil niitudel arvukamalt kahepaikseid ja mitmekesisem soontaimestik. Tugevalt kuivendatud siirdesoometsade looduslikkuse taastamine osalise metsaraiega näitas, et kraavide varjulisuse vähenemise järgselt kasvas raba- ja rohukonna sigimisaktiivsus drastiliselt. Kraavide sulgemisest tingitud veerežiimi muutuse tagajärjel tekkisid osaliselt üleujutatud alad ja lombid, mis järgnevatel aastatel muutusid pruunide konnade eelistatud sigimispaikadeks. Doktoritöös selgub, et erinevates märgalasüsteemides on suunisliikide esinemise peamised tegurid sarnased: päikesele avatud veekogud või märgade laikudega suured killustamata niidualad. Mõnda neist tingimustest saab kiiresti taastada, näiteks võsa eemaldamise või kraavide sulgemisega. Siiski on tõenäoline, et eriti poollooduslikus keskkonnas (näiteks rannaniitudel või rajatud tiikide ümbruses), on vaja edasist võsastumist vältida pideva karjatamise või niitmisega. Suunisliikide kasutamise kohta märgalakoosluste taastamisel võib seega kokkuvõtvalt öelda, et ohustatud liikidele elupaikade taastamine tagab ka paljude teiste märgaladest ja vee-elupaikadest sõltuvate liikide suurema liigirikkuse.Freshwater ecosystems are long acknowledged by their rich and unique biodiversity. The natural wetland area has declined by more than 50% during the 20th century. Human-caused habitat degradation and loss has resulted in the reduction of wetlands’ biodiversity. Well known is the decline of amphibians and wetland birds, that are also in the focus of the current doctoral thesis. This thesis explores habitat management and restoration of various wetlands (ponds, managed wet grasslands, and peatlands drained for forestry) in Estonia guided by the most habitat-sensitive focal species among amphibians and waders. A study of the species assemblage and structure of different types of small water bodies (natural, man-made, specially created for amphibians) revealed that pond (re)construction specifically for threatened amphibians (particularly for great crested newt) will also provide suitable habitats for other (semi)aquatic species since these ponds supported relatively species-rich assemblages. Extensively grazed large wide and wet coastal grasslands without woody vegetation provide breeding conditions for threatened waders (in particular Baltic dunlin, Black-tailed godwit and Common redshank), larger brown frogs’ populations (common frog and moor frog), and more diverse vascular plant communities. Restoring the heavily engineered ecosystem of ditched forested wetlands toward more natural states by partial forest cutting and ditch blocking may mitigate the overall afforestation-related negative drainage impact to brown frogs. In my study, such restoration rapidly increased the populations of brown frogs typical of natural wetlands. I found that key factors for the presence of focal species in different wetland systems are similar: the area of open habitat (either sun exposed water table or non-fragmented meadow area), with large wet patches. Some of these conditions can be easily restored, for instance by removing brushwood or by ditch blocking. However, it is likely that maintaining these features, especially in semi-natural settings (such as coastal meadows or around constructed ponds) may need sustained grazing or mowing to prevent future overgrowth. My main conclusion is that amphibians and waders can be used as focal species for the restoration of degraded wetlands and brown frogs could supplement the western capercaillie as a focal species to guide sustainable forest management.https://www.ester.ee/record=b535656

Inland Waters

Inland waters, lakes, rivers, and their connected wetlands are the most important and the most vulnerable sources of freshwater on the planet. The ecology of these systems includes biology as well as human populations and civilization. Inland waters and wetlands are highly susceptible to chemical and biological pollutants from natural or human sources, changes in watershed dynamics due to the establishment of dams and reservoirs, and land use changes from agriculture and industry. This book provides a comprehensive review of issues involving inland waters and discusses many worldwide inland water systems. The main topics of this text are water quality investigation, analyses of the ecology of inland water systems, remote sensing observation and numerical modeling methods, and biodiversity investigations

Molecular support for temporal dynamics of induced anti-herbivory defenses in the brown seaweed Fucus Vesiculosus

Grazing by the isopod Idotea baltica induces chemical defenses in the brown seaweed Fucus vesiculosus. A combination of a 33 day induction experiment, feeding choice assays and functional genomic analyses was used to investigate temporal defense patterns and to correlate changes in palatability to changes in gene expression. Despite permanent grazing, seaweed palatability varied over time. Controls were significantly more consumed than grazed pieces only after 18 and 27 days of grazing. Relative to controls, 562/402 genes were up-/down-regulated in seaweed pieces that were grazed for 18 days, i.e. when defense induction was detected. Reprogramming of the regulative expression orchestra (translation, transcription), up-regulation of genes involved in lipid and carbohydrate metabolism, intracellular trafficking, defense and stress response, as well as downregulation of photosynthesis was found in grazed seaweed. These findings indicate short-term temporal variation in defenses and that modified gene expression patterns arise at the same time when grazed seaweed pieces show reduced palatability. Several genes with putative defensive functions and cellular processes potentially involved in defence, such as reallocation of resources from primary to secondary metabolism, were reveale

Successful invaders are better defended: The example of Gracilaria vermiculophylla

To evaluate the importance of anti-herbivore resistance for algal invasion success we compared resistance traits among specimens of the red macroalga Gracilaria vermiculophylla from six native populations in Korea and China and eight invasive populations in Europe and Mexico that were maintained under identical conditions in the laboratory. Herbivorous snails both from the native range (Littorina brevicula) and from the invaded range (Littorina littorea) consumed significantly less of seaweed specimens originating from non-native populations. Metabolome profiling revealed that this preference was correlated with an increased woundactivated production of deterring prostaglandins and hydroxyeicosatetraenoic acids. Thus, invasive populations of G. vermiculophylla are more strongly defended against challenge by herbivores and other biological enemies that cause local tissue or cell disruption and activate oxylipin production. Anthropogenic distribution of genotypes adapted to resist elevated feeding pressure probably contributed to the invasion success of this species

Characterizing freshwater macroinvertebrates of Bangladesh using metagenetic techniques

The degradation of freshwater ecosystems has become a global concern, in particular, the critical conditions of rivers in Bangladesh demand a monitoring programme through the assessment of bioindicator organisms. Macroinvertebrates as prominent bioindicators are widely used for assessing the health of aquatic ecosystems. Recent technological advances have enabled routine assessment with the genomic characterization of macroinvertebrates using different metagenetic techniques such as DNA barcoding for individual specimen identification, metabarcoding for multi-species identification of bulk samples and mitochondrial metagenomics for extraction of mitogenomes from mixed samples. In this thesis, I commence by generating Cytochrome Oxidase subunit (COI) barcodes for Bangladeshi freshwater macroinvertebrates belonging to the Ephemeroptera, Plecoptera, Trichoptera, Coleoptera, Hemiptera, Odonata, Diptera, Gastropoda and Bivalvia. These barcodes can be used as a DNA reference library for species identification in metabarcoding of macroinvertebrates. I also aim for exploring complete mitogenomes from selected macroinvertebrates using a mitochondrial metagenomic pipeline. I carry out phylogenetic analysis with protein-coding genes that reveals the evolutionary relationship of Bangladeshi macroinvertebrate lineages and also support deeper level identification of barcodes placing them into the phylogenetic tree (chapter 2). In chapter 3, I assess some methodological aspects of the metabarcoding pipeline required for diversity estimation from complex bulk samples of macroinvertebrates in large-scale biomonitoring programmes. These include preparation of bulk macroinvertebrate samples, optimization of the procedure of homogenization of samples required for DNA extraction, strategies for DNA pooling from these extracts, choice of robust universal primers, and viable OTU clustering for reliable diversity estimation. The results have implications for the optimization and standardization of these steps in metabarcoding of freshwater macroinvertebrates. In chapter 4, I apply the metabarcoding technique to establish the macroinvertebrate diversity and impact of various types of anthropogenic disturbances on the freshwater macroinvertebrates in highland and lowland rivers. The results document high diversity, local endemicity and pronounced responses to disturbance in largely unexplored but threatened habitats of Bangladesh. My investigations manifest the viability of metagenetic techniques for applied conservation management as a step towards building a biomonitoring system in freshwater ecosystems globally.Open Acces

The invasive tree squirrel Callosciurus erythraeus in Italy: ecology, management and impact on the native squirrel Sciurus vulgaris.

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Metsakuivenduse mõju vee-suurselgrootutele ja kahepaiksetele ning võimalused säästlikuks metsamajandamiseks

Väitekirja elektrooniline versioon ei sisalda publikatsiooneVäikesed ja/või ajuti kuivavad veekogud on erilised elupaigad: olles omadustelt väga heterogeensed, tõstavad need kohalikku liigirikkust ning pakuvad elupaika mitmetele unikaalsetele liikidele. Kuna väikeveekogude arv ja levik maastikus on seotud veehulga muutustega, on need inimtegevusest tugevalt mõjutatud. Oluline väikeveekogude elustiku vaesumist põhjustav tegur on metsakuivendus. Vahetult pärast kraavide rajamist alaneb põhjaveetase, väheneb üleujutuste kestus ning suureneb äravool, kuna liigne vesi juhitakse kraavidega alalt välja. Tulemuseks on ulatuslikud kuivenduskraavide võrgustikud, mida perioodiliselt rekonstrueeritakse, st puhastatakse põhjasetetest ja taimestikust. Käesolevas töös uurisin kuivenduse ja kraavide rekonstrueerimise mõju väikeveekogude elustikule majandusmetsades ja kuivendatud kaitsealadel, keskendudes muuhulgas elustikumõju leevendusvõimalustele tiikide ja kraavilaiendite rajamise näol. Kuivenduse mõju väikeveekogude elustikule ilmneb nii elupaikade kao (lompide kuivamine), kui sellega kaasneva koosluste teisenemise ja üheülbastumise kaudu – väheneb veeselgrootute liigirikkus ning arvukus lompides ning teisenevad kraavide kooslused. Kaitsealadel ei ole kraavide looduslikule suktsessioonile jätmine jätkusuutlik, kuna varjulised kraavid kahepaiksetele väärtuslikke sigimispaiku ei paku, välja arvatud juhul kui kraavidel tegutsevad koprad. Ka majandusmetsades on kahepaiksete elujõuliste populatsioonide säilitamiseks vajalik leevendusmeetmete rakendamine, kuna nende eelistatud veekogud – kraavid ja raiesmikulombid – kipuvad rekonstrueerimisjärgselt suurema tõenäosusega kuivama. Veeselgrootutele ei ole leevendusveekogud n-ö “no net loss” meede, kuna kooslused erinevad loodulike lompide omadest, kuid sellegipoolest soodustavad leevendusveekogud kuivendatud maastikes neis harvemini esinevate liikide esinemist. Kokkuvõttes on leevendusveekogude rajamine üsna tõhus meede väikeveekogudega seotud liikide toetamiseks majandatavates metsadesSmall and/or temporary waterbodies are unique habitats that contribut to regional diversity and support many unique and endemic species. As temporary waterbodies are sensitive to changes in water volumes, their numbers and distribution are strongly affected by human activities. Wetland drainage, including for forestry, could be one of the main reasons why freshwater biodiversity is in decline. Drainage has significant effects on site hydrology by lowering the water table and leading excess water away via ditches. As a consequence, ditch networks constitute a very significant aquatic habitat in drained areas but are subject to periodic ditch network maintenance (DNM). Here I examined the effect of forest drainage and DNM on small waterbodies and their associated fauna in forest and fen landscapes, focusing on the ways to mitigate the loss of biodiversity. The effect of drainage and DNM on macroinvertebrates manifests through habitat loss (desiccation of pools) and subsequent shift and homogenization of assemblages as ditching and DNM substantially decreased the total number and abundance of taxa in remnant pools and changed ditch communities, though mean diversity was unaffected. Leaving drained protected peatlands for natural succession is not a feasible for supporting amphibian populations, as overgrown ditches do not substitute natural floods as breeding habitats presumably because of dense canopy cover. Ditches with beavers on the other hand provide high quality reproduction sites. Special measures are essential to mitigate the effect of DNM to macroinvertebrates and amphibians in drained forests. Remnant pools and newly cleaned ditches, preferred by brown frogs, have higher desiccation risk; therefore their populations in may not be sustainable in the long run without mitigation measures. For macroinvertebrates, construction of mitigation pools cannot be used as a “no net loss” measure, but rather as a means to supplement the species pool as they add species not common in drained forests. Nevertheless, creating mitigation pools alongside DNM seems to be feasible and cost-effective method to increase the diversity and number of available waterbodies in drained forest and thus support biodiversity.https://www.ester.ee/record=b537509