Browsing by Subject "biogeography"

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  • Fondi, Marco; Karkman, Antti; Tamminen, Manu V.; Bosi, Emanuele; Virta, Marko; Fani, Renato; Alm, Eric; McInerney, James O. (2016)
    The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as everything is everywhere but the environment selects." While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge.
  • Guo, Baocheng; Fang, Bohao; Shikano, Takahito; Momigliano, Paolo; Wang, Cui; Kravchenko, Alexandra; Merilä, Juha (2019)
    Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study the prevalence and extent of introgression among recognized species, genomic data sets of both reference genome-anchored single nucleotide polymorphisms and de novo assembled RAD-tag loci were constructed with RAD-seq data. Both data sets yielded topologically identical and well-supported species trees. Incongruence between nuclear and mitochondrial DNA-based trees was found and suggested possibly frequent hybridization and mitogenome capture during the evolution of Pungitius sticklebacks. Further analyses revealed evidence for frequent nuclear genetic introgression among Pungitius species, although the estimated proportions of autosomal introgression were low. Apart from providing evidence for frequent hybridization, the results challenge earlier mitochondrial and morphology-based hypotheses regarding the number of species and their affinities in this genus: at least seven extant species can be recognized on the basis of genetic data. The results also shed new light on the biogeographical history of the Pungitius-complex, including suggestion of several trans-Arctic invasions of Europe from the Northern Pacific. The well-resolved phylogeny should facilitate the utility of this genus as a model system for future comparative evolutionary studies.
  • Woolley, Skipton; Bax, Nicolas; Currie, Jock; Dunn, Daniel; Hansen, Cecilie; Hill, Nicole; O'Hara, Timothy; Ovaskainen, Otso; Sayre, Roger; Vanhatalo, Jarno; Dunstan, Piers (2020)
    Bioregions are important tools for understanding and managing natural resources. Bioregions should describe locations of relatively homogenous assemblages of species occur, enabling managers to better regulate activities that might affect these assemblages. Many existing bioregionalization approaches, which rely on expert-derived, Delphic comparisons or environmental surrogates, do not explicitly include observed biological data in such analyses. We highlight that, for bioregionalizations to be useful and reliable for systems scientists and managers, the bioregionalizations need to be based on biological data; to include an easily understood assessment of uncertainty, preferably in a spatial format matching the bioregions; and to be scientifically transparent and reproducible. Statistical models provide a scientifically robust, transparent, and interpretable approach for ensuring that bioregions are formed on the basis of observed biological and physical data. Using statistically derived bioregions provides a repeatable framework for the spatial representation of biodiversity at multiple spatial scales. This results in better-informed management decisions and biodiversity conservation outcomes.
  • Farstad, Miia (Helsingin yliopisto, 2021)
    Due to the harsh conditions in high latitude alpine and arctic regions, climate or land use changes make them very vulnerable. Thus, it is vital to study the habitats of these regions and increase our understanding of what factors impact species distributions. Species distribution modelling can be used to predict possible habitats for species and further inspect the relationships between different environmental variables and species. Generally, these species distribution models have been created using variables describing the topographical and climatic conditions of the study area. Recently there has been more evidence supporting the inclusion of biotic variables to species distribution models at all scales. Including biotic variables can be difficult, as these relationships can be challenging to quantify. This study uses the Normalized Difference Vegetation Index (NDVI) as a surrogate for plant biomass, thus representing biotic interactions. This study aims to answer what are the relationships between environmental variables and the predicted distributions and will including a biotic variable improve the species distribution models. The study data includes observational data from 683 arctic and alpine plant species from Norway, Sweden, and Finland. The observation data were collected from the three national databanks of Norway, Sweden and Finland and completed with observations from the Global Biodiversity Information Facility and observation data collected by the BioGeoClimate Modelling Lab. The cohesive study area was outlined with the biogeographical regions defined by the European Environment Agency. Overall, six environmental variables are used in this study: annual mean temperature, the maximum temperature of the warmest month, annual precipitation, elevation difference in a cell, bedrock class, and NDVI. The NDVI data was gathered by NASA’s MODIS sensors. The observations and the environmental variables were projected into a grid consisting of 1 x 1 km cells covering the whole study area. This study uses the ensemble modelling technique with four individual modelling methods: generalized linear models (GLM), generalized additive models (GAM), generalized boosted models (GBM) and random forests (RF). The modelling process consisted of two modelling rounds so that the impact of NDVI could be evaluated. The first modelling round included all the environmental variables except NDVI (the topoclimate model) and the second modelling round included all the environmental variables (the full model). The two temperature variables, annual mean temperature and the maximum temperature of the warmest month, had the highest mean variable importance values. With the topoclimate model, annual precipitation ranked third with the rest of the climate variables, but when NDVI was added to the models, it rose above annual precipitation. Overall, among the studied arctic and alpine species, the variable importance values of both the edaphic and topographical variables were low. In general, both the topoclimate models and full models performed very well. The mean AUC- and TSS-values were all higher for the full models, indicating that including a biotic variable improved the models. When the binary predictions of both modelling rounds were compared, it was clear that NDVI refined the projected distributions for most species. The results from this study confirm the discovery that including a biotic variable, such as NDVI, has the potential to increase the predictive power of species distribution models. One of the main problems with including biotic variables in species distribution models has been the difficulty of quantifying biotic interactions. NDVI can thus be a promising tool to overcome these difficulties, as it is one of the most direct variables to describe ecosystem productivity, can be acquired at various scales, and as remotely sensed data, it can also cover areas that are difficult to access.
  • Kunttu, Panu; Helo, Teppo; Kulju, Matti; Julkunen, Jari; Kotiranta, Heikki (Finnish Mycological Society, 2020)
    Karstenia Mycological Journal 58, 1 (2020)
    We contribute to the knowledge on the occurrences and distributions of both aphyllophoroid and heterobasidioid fungi in Finland. We present four species new to Finland, i.e. Helicogloea sebacea, Phanerochaete cremeo-ochracea, Steccherinum cremeoalbum, and Uncobasidium luteolum, as well as 46 new records (locations) of 34 rare or rarely collected species. Additionally, we report on 40 species considered new to a certain subzone of the boreal forest vegetation zone in Finland. These records contain notes on their substrata, and the ecology and distribution of nationally new species are briefly discussed.
  • Ribas, Camila C.; Aleixo, Alexandre (2019)
    Amazonia has been a focus of interest since the early days of biogeography as an intrinsically complex and extremely diverse region. This region comprises an intricate mosaic that includes diverse types of forest formations, flooded environments and open vegetation. Increased knowledge about the distribution of species in Amazonia has led to the recognition of complex biogeographic patterns. The confrontation of these biogeographic patterns with information on the geological and climatic history of the region has generated several hypotheses dedicated to explain the origin of the biological diversity. Genomic information, coupled with knowledge of Earth's history, especially the evolution of the Amazonian landscape. presents fascinating possibilities for understanding the mechanisms that govern the origin and maintenance of diversity patterns in one of the most diverse regions of the world. For this we will increasingly need more intense and coordinated interactions between researchers studying biotic diversification and the evolution of landscapes. From the interaction between these two fields of knowledge that are in full development, an increasingly detailed understanding of the historical mechanisms related to the origin of the species will surely arise.
  • Moura, Carina Carneiro de Melo; Fernandes, Alexandre M.; Aleixo, Alexandre; Pereira de Araujo, Helder Farias; Mariano, Erich de Freitas; Wink, Michael (2020)
    We focus on reconstructing a spatiotemporal scenario of diversification of a widespread South American species, the Pectoral Sparrow Arremon taciturnus (Aves: Passerellidae). This species is widely distributed in both the humid and the dry forests of South America and therefore provides an interesting model for understanding the connection between different biomes of South America. We examined nucleotide sequences of the mitochondrial genes Cytochrome b (cyt-b) and NADH subunit 2 (ND2) from 107 specimens, and one nuclear marker (intron 7 of the beta-fibrinogen gene) from a subset of samples collected across the distribution ranges of A. t. taciturnus and A. t. nigrirostris. Six major lineages were recovered in the phylogenies that displayed high levels of variance of allele frequencies and corresponded to distinct geographical locations. The estimation of divergence times provided evidence that diversification of the six lineages of the Pectoral Sparrow occurred throughout the Late Pleistocene across major cis-Andean biomes and Amazonian interfluves. Our dataset for A. taciturnus provides further evidence that rivers in Amazonia constitute barriers promoting allopatric speciation, with occasional sharing of alleles among lineages, particularly those with adjacent distributions.
  • Buechley, Evan R.; Santangeli, Andrea; Girardello, Marco; Neate-Clegg, Montague H.C.; Oleyar, Dave; McClure, Christopher J.W.; Şekercioğlu, Çagan H. (2019)
    Abstract Aim Raptors serve critical ecological functions, are particularly extinction-prone and are often used as environmental indicators and flagship species. Yet, there is no global framework to prioritize research and conservation actions on them. We identify for the first time the factors driving extinction risk and scientific attention on raptors and develop a novel research and conservation priority index (RCPI) to identify global research and conservation priorities. Location Global. Methods We use random forest models based on ecological traits and extrinsic data to identify the drivers of risk and scientific attention in all raptors. We then map global research and conservation priorities. Lastly, we model where priorities fall relative to country-level human social indicators. Results Raptors with small geographic ranges, scavengers, forest-dependent species and those with slow life histories are particularly extinction-prone. Research is extremely biased towards a small fraction of raptor species: 10 species (1.8% of all raptors) account for one-third of all research, while one-fifth of species have no publications. Species with small geographic ranges and those inhabiting less developed countries are greatly understudied. Regions of Latin America, Africa and Southeast Asia are identified as particularly high priority for raptor research and conservation. These priorities are highly concentrated in developing countries, indicating a global mismatch between priorities and capacity for research and conservation. Main conclusions A redistribution of scientific attention and conservation efforts towards developing tropical countries and the least-studied, extinction-prone species is critical to conserve raptors and their ecological functions worldwide. We identify clear taxonomic and geographic research and conservation priorities for all raptors, and our methodology can be applied across other taxa to prioritize scientific investment.
  • Teittinen, Anette; Wang, Jianjun; Stromgard, Simon; Soininen, Janne (2017)
    Aim: Elevational biodiversity patterns are understudied in high-latitude aquatic systems, even though these systems are important for detecting very early impacts of climatic changes on Earth. The aim of this study was to examine the elevational trends in species richness and local contribution to beta diversity (LCBD) of three biofilm microbial groups in freshwater ponds and to identify the key mechanisms underlying these patterns. Location: One hundred and forty-six ponds in subarctic Finland and Norway distributed across the tree line along an elevational gradient of 10-1,038 m a.s.l., spanning from forested landscape to barren boulder fields. Time period: July-August 2015. Major taxa studied: Diatoms, cyanobacteria and non-cyanobacteria. Methods: Generalized linear models were used to identify the most important pond variables explaining richness and LCBD. Structural equation models were used to explore the direct and indirect effects of multiscale drivers on richness and LCBD. Results: Diatom and cyanobacteria richness showed unimodal elevational patterns, whereas non-cyanobacteria richness decreased with increasing elevation. The LCBD-elevation relationship was U-shaped for all three microbial groups. Diatom and cyanobacteria richness and LCBD were best explained by local pond variables, especially by pH. Non-cyanobacteria richness and LCBD were related to pond variables, elevation as a proxy for climatic conditions, and normalized difference vegetation index as a proxy for terrestrial productivity. Main conclusions: Aquatic autotrophs were primarily controlled by environmental filtering, whereas heterotrophic bacteria were also affected by terrestrial productivity and elevation. All studied aspects of microbial diversity were directly or indirectly linked to elevation; therefore, climatic changes may greatly alter aquatic microbial assemblages.
  • Alahuhta, Janne; Lindholm, Marja; Baastrup-Spohr, Lars; García-Girón, Jorge; Toivanen, Maija; Heino, Jani; Murphy, Kevin (Elsevier, 2021)
    Aquatic Botany 168: 103325
    Broad-scale studies of species distributions and diversity have contributed to the emergence of general macroecological rules. These rules are typically founded on research using well-known terrestrial taxa as models and it is thus uncertain whether aquatic macrophytes follow these macroecological rules. Our purpose is to draw together available information from broad-scale research on aquatic macrophytes growing in lakes, ponds, wetlands, rivers and streams. We summarize how different macroecological rules fit the patterns shown by freshwater plants at various spatial scales. Finally, we outline future actions which should be taken to advance macroecological research on freshwater plants. Our review suggested that some macroecological patterns are relatively well-evidenced for aquatic macrophytes, whereas little information exists for others. We found, for example, that the species richness-latitude relationship follows a unimodal pattern, and species turnover prevails over species nestedness, whereas higher nestedness-related richness differences are found in low beta diversity regions. Contrary to terrestrial plants, climate or history seem not to be dominant determinants explaining these broad-scale patterns; instead local explanatory variables (e.g., water quality, such as alkalinity and nutrients, and hydromorphology) are often important for freshwater plants. We identified several knowledge gaps related, for example, to a smaller number of studies in lotic habitats, compared with lentic habitats, lack of spatially-adequate aquatic plant studies, deficiency of comprehensive species traits databases for aquatic macrophytes, and absence of a true phylogeny comprising most freshwater plant lineages. We hope this review will encourage the undertaking of additional macroecological investigations on freshwater plants across broad spatial and temporal scales.
  • Jousimo, Jussi (Helsingfors universitet, 2011)
    Markov random fields (MRF) are popular in image processing applications to describe spatial dependencies between image units. Here, we take a look at the theory and the models of MRFs with an application to improve forest inventory estimates. Typically, autocorrelation between study units is a nuisance in statistical inference, but we take an advantage of the dependencies to smooth noisy measurements by borrowing information from the neighbouring units. We build a stochastic spatial model, which we estimate with a Markov chain Monte Carlo simulation method. The smooth values are validated against another data set increasing our confidence that the estimates are more accurate than the originals.
  • Davydov, E. A.; Yakovchenko, L. S.; Galanina, I. A.; Paukov, A. G.; Frolov, I. V.; Ahti, T. (2021)
    Aspicilia subepiglypta, Buellia subdisciformis, Calogaya arnoldii, Flavoplaca flavocitrina, Lecanora swartzii, and Lecidella scabra are reported as new records for the Russian Far East. Rinodina gennarii and Lecidella asema are newly recorded for the mainland of the Russian Far East. Rare lichens Cladonia subconistea and Leptotrema litophila are newly found in coastal habitats; Caloplaca atroflava is new for Sakhalin Island, and Umbilicaria vellea is new for Kuril Islands.
  • Rocha, A. V.; Cabanne, G. S.; Aleixo, A.; Silveira, L. F.; Tubaro, P.; Caparroz, R. (2020)
    Based on phylogeographic and niche model analyses of the narrow-billed woodcreeperLepidocolaptes angustirostris, we evaluated the predictions of two diversification hypotheses related to the dry diagonal of South America: (I) isolation by distance (IBD) and (II) landscape heterogeneity. We also investigated the influence of the Pleistocene climatic oscillations on the diversification and population dynamic of this species, and discussed the implications of our findings for the taxonomy of this woodcreeper. We sampled 63 individuals including all subspecies described forL. angustirostris, and compared them using a mitochondrial (ND2) and a nuclear (FIB5) fragments. We performed a Mantel test and spatial autocorrelation analysis, reconstructed the phylogenetic relationships among haplotypes, investigated changes in population size and estimated divergence time among the genetic lineages. We refuted the hypothesis that bird species associated with open environments have shallow geographic differentiation and showed that strong genetic structure observed inL. angustirostriscan not be explained by IBD. Paleo-modeling showed strong association between climatic stable areas and the genetic lineages, suggesting that Pleistocene climatic oscillations have primarily driven the intraspecific diversification of this species. In addition, the association between genetic lineages and the dry diagonal biomes supports that landscape heterogeneity may be acting as a secondary barrier restricting gene flow among the lineages. The genetic lineages found inL. angustirostrisdo not correspond to the subspecies described, indicating that this species can be considered as a single species with strong genetic structure. In conclusion, our data corroborate other studies indicating that Pleistocene climatic oscillations may have had a strong influence in the intraspecific divergence of dry diagonal fauna and that biomes of the dry diagonal should be considered as independent units in further biogeographic studies.
  • Aubriot, Xavier; Knapp, Sandra; Syfert, Mindy; Poczai, Péter; Buerki, Sven (2018)
    • While brinjal eggplant (Solanum melongena L.) is the second most important solanaceaous vegetable crop, we lack firm knowledge of its evolutionary relationships. This in turn limits efficient use of crop wild relatives in eggplant improvement. Here, we examine the hypothesis of linear step-wise expansion of the eggplant group from Africa to Asia. • We use museum collections to generate nuclear and full-plastome data for all species of the eggplant clade. We combine a phylogenomic approach with distribution data to infer a biogeographic scenario for the clade. • The eggplant clade has Pleistocene origins in northern Africa. Dispersions to tropical Asia gave rise to Solanum insanum, the wild progenitor of the eggplant, and to Africa distinct lineages of widespread and southern-African species. Results suggest that spread of species to southern Africa is recent and was likely facilitated by large mammal herbivores feeding on Solanum fruits (African elephant, impala). • Rather than a linear ‘Out Of Africa’ sequence, our results are more consistent with an initial event into Asia, and subsequent wide dispersion and differentiation across Africa driven by large mammalian herbivores. Our evolutionary results will impact future work on eggplant domestication and use of wild relatives in breeding of this increasingly important solanaceous crop.
  • Jorissen, Michiel W. P.; Pariselle, Antoine; Huyse, Tine; Vreven, Emmanuel J.; Snoeks, Jos; Decru, Eva; Kusters, Thomas; Lunkayilakio, Soleil Wamuini; Bukinga, Fidel Muterezi; Artois, Tom; Vanhove, Maarten P. M. (2018)
    The Lower Congo Basin is characterized by a mangrove-lined estuary at its mouth and, further upstream, by many hydrogeographical barriers such as rapids and narrow gorges. Five localities in the mangroves and four from (upstream) left bank tributaries or pools were sampled. On the gills of Coptodon tholloni, Coptodon rendalli, Hemichromis elongatus, Hemichromis stellifer and Tylochromis praecox, 17 species of parasites (Dactylogyridae & Gyrodactylidae, Monogenea) were found, eight of which are new to science. Six of these are herein described: Cichlidogyrus bixlerzavalai n. sp. and Cichlidogyrus omari n. sp. from T praecox, Cichlidogyrus calycinus n. sp. and Cichlidogyrus polyenso n. sp. from H. elongatus, Cichlidogyrus kmentovae n. sp. from H. stellifer and Onchob-della ximenae n. sp. from both species of Hemichromis. On Cichlidogyrus reversati a ridge on the accessory piece was discovered that connects to the basal bulb of the penis. We report a putative spillback effect of the native parasites Cichlidogyrus berradae, Cichlidogyrus cubitus and Cichlidogyrus flexicolpos from C. tholloni to the introduced C. rendalli. From our results, we note that the parasite fauna of Lower Congo has a higher affinity with the fauna of West African and nearby freshwater ecoregions than it has with fauna of other regions of the Congo Basin and Central Africa.
  • Kiljunen, Niina; Pajunen, Timo; Fukushima, Caroline; Soukainen, Arttu; Kuurne, Jaakko; Korhonen, Tuuli; Saarinen, Joni; Falck, Ilari; Laine, Erkka; Mammola, Stefano; Urbano, Fernando; Macias-Hernandez, Nuria; Cardoso, Pedro (2020)
    Background A spider taxonomy and ecology field course was organised in Kilpisjarvi Biological Station, northern Finland, in July 2019. During the course, four 50 x 50 m plots in mountain birch forest habitat were sampled following a standardised protocol. In addition to teaching and learning about spider identification, behaviour, ecology and sampling, the main aim of the course was to collect comparable data from the Kilpisjarvi area as part of a global project, with the purpose of uncovering global spider diversity patterns. New information A total of 2613 spiders were collected, of which 892 (34%) were adults. Due to uncertainty of juvenile identification, only adults are included in the data presented in this paper. The observed adult spiders belong to 51 species, 40 genera and 11 families, of which the Linyphiidae were the most rich and abundant with 28 (55%) species and 461 (52%) individuals. Lycosidae had six species and 286 individuals, Gnaphosidae five species and 19 individuals, Thomisidae four species and 24 individuals, Theridiidae two species and 23 individuals. All other six families had one species and less than 40 individuals. The most abundant species were the linyphiid Agnyphantes expunctus (204) and the lycosids Pardosa eiseni (164) and Pardosa hyperborea (107).
  • Venn, Stephen (2016)
    This review considers factors affecting the flight capacity of carabid beetles and the implications of flight for carabids. Studies from the Dutch polders in particular show that young populations of carabids consist predominantly of macropterous species and macropterous individuals of wing-dimorphic species. Also populations of wing-dimorphic carabid species at the periphery of their geographical range contain high proportions of macropterous individuals. However, studies from Baltic archipelagos show that older populations of even highly isolated island habitats contain considerable proportions of brachypterous species and individuals. This suggests that macroptery is primarily an adaptation for dispersal and that there exists a mechanism for subsequently reducing the ratio of macropterous to brachypterous species under stable conditions, due to the competitive advantage of brachyptery. Populations in isolated habitats, such as islands and mountains, have high proportions of brachypterous species. Many macropterous species do not possess functional flight muscles. Species of unstable habitats, such as tree canopies and wet habitats, are mostly macropterous. Brachypterous species tend to disappear from disturbed habitats. There is uncertainty regarding the extent to which carabid dispersal is directed and how much passive. Both Den Boer and Lindroth recognized that mostly macropterous individuals of macropterous and wing-dimorphic species disperse and found new populations, after which brachyptery tends to rapidly appear and proliferate in the newly founded population. It is most likely that the allele for brachyptery would arrive via the dispersal of gravid females which had mated with brachypterous males prior to emigration. Whilst many studies consider wing morphology traits of carabid beetles to be species-specific and permanent, a number of studies have shown that the oogenesis flight syndrome, whereby females undertake migration and subsequently lose their flight muscles by histolysis before eventually regenerating them after reproducing, has been reported for a growing number of carabid species. Wing morphology of carabid beetles clearly offers strong potential for the study of population dynamics. This field of study flourished during the 1940's to the late 1980's. Whilst a considerable amount of valuable research has been performed and published, the topic clearly holds considerable potential for future study.