AI-based Mapping of the Conservation Status of Orchid Assemblages at Global Scale

Although increasing threats on biodiversity are now widely recognised, there are no accurate global maps showing whether and where species assemblages are at risk. We hereby assess and map at kilometre resolution the conservation status of the iconic orchid family, and discuss the insights conveyed at multiple scales. We introduce a new Deep Species Distribution Model trained on 1M occurrences of 14K orchid species to predict their assemblages at global scale and at kilometre resolution. We propose two main indicators of the conservation status of the assemblages: (i) the proportion of threatened species, and (ii) the status of the most threatened species in the assemblage. We show and analyze the variation of these indicators at World scale and in relation to currently protected areas in Sumatra island. Global and interactive maps available online show the indicators of conservation status of orchid assemblages, with sharp spatial variations at all scales. The highest level of threat is found at Madagascar and the neighbouring islands. In Sumatra, we found good correspondence of protected areas with our indicators, but supplementing current IUCN assessments with status predictions results in alarming levels of species threat across the island. Recent advances in deep learning enable reliable mapping of the conservation status of species assemblages on a global scale. As an umbrella taxon, orchid family provides a reference for identifying vulnerable ecosystems worldwide, and prioritising conservation actions both at international and local levels.Comment: 21 pages, 4 figures. Website URL: https://mapviewer.plantnet.org/?config=apps/store/orchid-status.xml Data and code: https://figshare.com/s/15404886eb3b62363a5

Spatially explicit models for decision-making in animal conservation and restoration

DZ, CK, AKM and GF were supported by the German Science Foundation (DFG) under grant agreement no. ZU 361/1-1. GB was supported by a Royal Society University Research Fellowship (UF160614). We acknowledge the support of the Deutsche Forschungsgemeinschaft and Open Access Publishing Fund of University of Potsdam.Peer reviewedPublisher PD

Invasiivsete liikide roll riimveeliste põhjakoosluste struktuuri ja biomassi muutustes

Väitekirja elektrooniline versioon ei sisalda publikatsiooneVõõrliikide arv Läänemeres kasvab tõusvas tempos. 2015. aastaks oli Läänemeres raporteeritud 130 võõrliiki ja 2022. aastal on võõrliikide arv juba 220. Mitmed võõrliigid on loonud suuri populatsioone ja mõjutavad looduslikke Läänemere ökosüsteeme. Looduslikult on Läänemere põhjakooslused liigivaesed ja esineb palju väheasustatud funktsionaalseid nišše, seega on võõrliikidel palju võimalusi uues elupaigas kanda kinnitada ning oluliselt mõjutada kogu ökosüsteemi funktsioneerimist ja ökosüsteemi teenuseid. Käesolevas doktoritöös käsitletakse olulisi teadmiste lünki võõrliikide (ümarmudil ja harilik rändkrabi) levikus, käitumise eripärades ja mõjudes Läänemeres. Liikide mõju looduslikele ökosüsteemidele uuriti nii eksperimentaalselt kui ka pikkade põhjaloomastiku aegridade uuringutega. Laboratoorsed uuringud näitasid, et mõlemad uued merepõhja kiskjad suudavad süüa suures koguses looduslike põhjakoosluste dominantliike. Põhjaloomastiku pikkade andmeridade analüüs kinnitas, et eksperimentaalselt nähtud intensiivne toitumine toimub ka looduskeskkonnas. Ümarmudil on juba ära söönud suure osa Eesti rannikumere karbipopulatsioonidest, kes toimivad rannikumere loodusliku filtrina ja vähendavad eutrofeerumise ilminguid. Harilik rändkrabi vähendab põhjaloomastiku biomassi ja liigirikkust ning krabi mõju on ulatuslikum, kui kliimamuutustest eeldatavast toiteainekasvust tingitud suurem populatsiooni juurdekasv. Võõrliikide tekitatud muutuste mõju levib ka teistele ökosüsteemi tasemetele ning muutusi mõne piirkonna veesambas on juba täheldatud. Lisaks võivad võõrliigid ökosüsteemi mõjutada ka kui rannikukalade uute toiduobjektidena. Doktoritöö käigus näidati, et ümarmudil on muutunud oluliseks toiduobjektiks ahvenale, kuid hetkel veel ei mõjuta ümarmudila arvukus ahvena üldist toitumust. Seega, suure tõenäosusega ei suuda ahven hetkel ümarmudila arvukust kontrollida ja faktorid, mis hakkavad piirama võõrliikide arvukust, vajavad uurimist tulevikus. Antud doktoritöö näitab selgelt, et võõrliikidel on märkimisväärne roll Läänemere ökosüsteemides ja on oluline, et kõik Läänemere majandamise ja hea keskkonnaseisundi hoidmisega seotud otsused arvestaksid võõrliikide rolliga.Alien species are arriving to the Baltic Sea at high rates. By 2022, already 220 alien species have been recorded in the Baltic Sea. Many of these species have established large populations and are affecting the Baltic Sea ecosystems. Since there are low numbers of native species in the benthic communities of the Baltic Sea, many vacant functional niches are ready to be inhabited by the novel species. Addition of a functionally novel species has the potential to severely effect the Baltic Sea ecosystem functioning and the services they provide. In this thesis large knowledge caps on how these species spread and act in their new environment were addressed. The species long-lasting impact was investigated with both manipulative experiments and long timeseries investigations. Experimental studies showed that the novel benthic predators, the round goby and the Harris mud crab, are able to consume high amounts of all dominant native invertebrates. Field studies showed that the strong impact of alien species observed in experimental communities are also happening in natural communities. The round goby has removed substantial amounts of benthic bivalves from the Estonian coastal sea, who are acting as a natural filter and buffering eutrophication effects. The Harris mud crab reduced benthic invertebrate biomass, even in an elevated nutrient future climate scenario. These impacts are also cascading to other trophic levels with observed increases in phytoplankton biomass. In addition, the alien species directly affect the ecosystem as novel prey objects. The round goby is already a dominant component in the diet of European perch. This thesis shows directly that alien species are playing an important role in the ecosystem and all decisions management and protection of the Baltic Sea ecosystem should consider the role of invasive species.https://www.ester.ee/record=b553329

Riverscape Community Genomics of Ozark Fishes: A Comparative Framework to Infer Ecological and Evolutionary Determinants of Genetic Diversity

Genetic variation is a crucial component of biodiversity and represents the variability and spatial structure of alleles within and among organisms. Evolution modulates this variability over time through mutation, selection, gene flow, and genetic drift. However, our capacity to test foundational theories of population genetics has always been at the mercy of molecular approaches available to quantify patterns of genetic diversity. Initially, techniques for empirical DNA studies were in their infancy and limited by technologies and the price per unit of genetic information. Because of these constraints, our pursuits have generally been limited to investigations of one or a few species simultaneously, hampering our power to draw broadly applicable conclusions. Advances in molecular technologies, e.g., high-throughput sequencing, now provide so much information at so little cost that a multispecies comparative approach to uncovering generalities about evolution is within reach even for applied studies on non-model organisms. Ultimately, genotyping individuals from all species within a community will be feasible and easily replicated across sampling locations and span entire regions. Variability of genetic diversity, within and among species, can be leveraged to explore the relationship between ecology and evolution and between micro- and macroevolution.For my dissertation research, I employed a multispecies framework to link ecological and evolutionary processes driving spatial patterns of biodiversity through comparative analyses of genotypic variability among sympatric species of freshwater fish that inhabit a large sub-basin of the Mississippi River. First, I quantified the extent of admixed ancestry among species within a community by assessing genomic variability among individuals from many species. My analyses uncovered that fish in nature — particularly minnows — have higher than expected hybridization rates. My data even show evidence of hybrid viability and genetic exchange among species (i.e., introgression). I interpret these findings of widespread admixture among distinct species as an indicator that admixture plays a critical role in ecology and evolution – more so than previously considered. Second, I tested for general mechanisms that define spatial genomic variability within species by comparing models of extrinsic drivers of genetic divergence. The river network, or stream hierarchy model, best explained species\u27 genomic variability, as evidenced by the correspondence between genetic divergence and riverine architecture. This general pattern emerged for all species, but the degree of genetic divergence differed widely, indicating that the intrinsic traits of each species may also play an important role. Finally, I further explored how phenotypic traits may modulate species\u27 genetic diversity and ultimately evolutionary trajectories by comparing relationships between traits and metrics of genetic variability among species within a comparative framework. Significant associations between trait values and genetic patterns emerged, allowing me to develop predictive models of genetic diversity using traits alone, without requiring direct genetic assessments. These trait-based models can be applied to prioritize species for conservation and management. My dissertation research demonstrates that modern molecular approaches are uniquely positioned to help unite ecology and evolution, bridging the long-standing dichotomy between these two disciplines. I provide a comparative framework for conservation biology that integrates various temporal and spatial scales and demonstrate with an empirical example how it can be applied to assess thousands of informative genetic markers across entire communities of non-model organisms. My dissertation research elevates population genomics to the community level and outlines how to explore new dimensions in our long-standing inquiry: What drives variation in genetic diversity among species

Genotyping-by-Sequencing and Ecological Niche Modeling Illuminate Phylogeography, Admixture, and Pleistocene Range Dynamics in Quaking Aspen (Populus Tremuloides)

Populus tremuloides is the widest‐ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome‐wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics of P. tremuloides, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal–Cascades (cluster 1), east‐slope Cascades–Sierra Nevadas–Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of the P. tremuloides range, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the “stable‐edge hypothesis” that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited “trailing‐edge” dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the “inland dispersal hypothesis” predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific‐coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable‐edge, refugial locations, and postglacial expansion within P. tremuloides. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific‐coastal genetic lineage of quaking aspen