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  • 1.
    Aggemyr, Elsa
    et al.
    Stockholm University, Faculty of Science, Department of Physical Geography and Quaternary Geology.
    Cousins, Sara A. O.
    Stockholm University, Faculty of Science, Department of Physical Geography and Quaternary Geology.
    Landscape structure and land use history influence changes in island plant composition after 100 years2012In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 39, no 9, p. 1645-1656Article in journal (Refereed)
    Abstract [en]

    Aim We investigated how current and historical land use and landscape structure affect species richness and the processes of extinction, immigration and species turnover. Location The northern part of the Stockholm archipelago, Baltic Sea, Sweden. We resurveyed 27 islands ranging from 0.3 to 33 ha in area. Methods We compared current plant survey data, cadastral maps and aerial photographs with records obtained from a survey in 1908, using databases and a digital elevation model to examine changes in plant community dynamics in space and time. We examined the effects of local and landscape structure and land use changes on plant species dynamics by using stepwise regression in relation to eight local and three landscape variables. The eight local variables were area, relative age, shape, soil heterogeneity, bedrock ratio, number of houses, forest cover change, and grazing 100 years ago. The three landscape variables were distance to mainland, distance to closest island with a farm 100 years ago, and structural connectivity. Hanskis connectivity measure was modified to incorporate both connectivity and fragmentation. Results The investigated islands have undergone drastic changes, with increasing forest cover, habitation, and abandonment of grassland management. Although the total species richness increased by 31% and mean island area by 23%, we found no significant increase in species richness per unit area. Local variables explain past species richness (100 years ago), whereas both local and landscape variables explain current species richness, extinctions, immigrations and species turnover. Grazing that occurred 100 years ago still influences species richness, even though grazing management was abandoned several decades ago. The evidence clearly shows an increase in nitrophilous plant species, particularly among immigrant species. Main conclusions This study highlights the importance of including land use history when interpreting current patterns of species richness. Furthermore, local environment and landscape patterns affect important ecological processes such as immigration, extinction and species turnover, and hence should be included when assessing the impact of habitat fragmentation and land use change. We suggest that our modified structural connectivity measure can be applied to other types of landscapes to investigate the effects of fragmentation and habitat loss.

  • 2.
    Ahlgren, Hans
    et al.
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Norén, Karin
    Stockholm University, Faculty of Science, Department of Zoology.
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    Lidén, Kerstin
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Multiple prehistoric introductions of the mountain hare (Lepus timidus) on a remote island, as revealed by ancient DNA2016In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 43, no 9, p. 1786-1796Article in journal (Refereed)
    Abstract [en]

    Aim: The majority of the non-volant mammals now present on the island of Gotland, Sweden, have been introduced in modern times. One exception is the mountain hare (Lepus timidus), which was present on the island more than 9000 years ago. This paper investigates the origins of the Gotland hares and temporal changes in their genetic structure, and considers how they may have reached the island.

    Location: The island of Gotland, Sweden (57°30′ N, 18°20′ E).

    Methods: Two fragments of the mitochondrial D-loop 130 + 164 base pairs in length from skeletal remains from 40 ancient mountain hares from Gotland, 38 from the Swedish mainland and five from Lithuania were analysed and compared with 90 modern L. timidus haplotypes from different locations in Eurasia and five haplotypes of the Don-hare (Lepus tanaiticus) morphotype.

    Results: The Mesolithic hares from Gotland (7304 bc–5989 bc) cluster with modern hares from Russia, Scotland, the Alps and Fennoscandia whereas the Gotland hares from the Neolithic and onwards (2848 bc–1641 ad) cluster with Neolithic hares from the Swedish mainland and modern hares from Fennoscandia. The Neolithic haplotypes from Lithuania and the Don-hare haplotypes were dispersed within the network. The level of differentiation (FST) between the Mesolithic and Neolithic hares on Gotland was twice as great as that observed on the mainland.

    Main conclusions: The ancient hares on Gotland fall into two haplogroups separated in time, indicating that the mountain hare became extinct at one point, with subsequent re-colonization events. In view of the isolated location of Gotland, it is probable that the hares were brought there by human means of transport.

  • 3. Appelhans, Marc S.
    et al.
    Kessler, Paul J. A.
    Smets, Erik
    Razafimandimbison, Sylvain G.
    Stockholm University, Faculty of Science, Department of Botany.
    Janssens, Steven B.
    Age and historical biogeography of the pantropically distributed Spathelioideae (Rutaceae, Sapindales)2012In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 39, no 7, p. 1235-1250Article in journal (Refereed)
    Abstract [en]

    Aim The family Rutaceae (rue family) is the largest within the eudicot order Sapindales and is distributed mainly in the tropical and subtropical regions of both the New World and the Old World, with a few genera in temperate zones. The main objective of this study is to present molecular dating and biogeographical analyses of the subfamily Spathelioideae, the earliest branching clade (which includes eight extant genera), to interpret the temporal and spatial origins of this group, ascertaining possible vicariant patterns and dispersal routes and inferring diversification rates through time. Location Pantropics. Methods A dataset comprising a complete taxon sampling at generic level (83.3% at species level) of Spathelioideae was used for a Bayesian molecular dating analysis (beast). Four fossil calibration points and an age constraint for Sapindales were applied. An ancestral area reconstruction analysis utilizing the dispersalextinctioncladogenesis model and diversification rate analyses was conducted. Results Dating analyses indicate that Rutaceae and Spathelioideae are probably of Late Cretaceous origin, after which Spathelioideae split into a Neotropical and a Palaeotropical lineage. The Palaeotropical taxa have their origin inferred in Africa, with postulated dispersal events to the Mediterranean, the Canary Islands, Madagascar and Southeast Asia. The lineages within Spathelioideae evolved at a relatively constant diversification rate. However, abrupt changes in diversification rates are inferred from the beginning of the Miocene and during the Pliocene/Pleistocene. Main conclusions The geographical origin of Spathelioideae probably lies in Africa. The existence of a Neotropical lineage may be the result of a dispersal event at a time in the Late Cretaceous when South America and Africa were still quite close to each other (assuming that our age estimates are close to the actual ages), or by Gondwanan vicariance (assuming that our age estimates provide minimal ages only). Separation of land masses caused by sea level changes during the Pliocene and Pleistocene may have been triggers for speciation in the Caribbean genus Spathelia.

  • 4.
    Audusseau, Hélène
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Paris-Est Créteil University, France.
    Le Vaillant, Maryline
    Stockholm University, Faculty of Science, Department of Zoology.
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Karlsson, Bengt
    Stockholm University, Faculty of Science, Department of Zoology.
    Schmucki, Reto
    Species range expansion constrains the ecological niches of resident butterflies2017In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 44, no 1, p. 28-38Article in journal (Refereed)
    Abstract [en]

    Aim: Changes in community composition resulting from environmental changes modify biotic interactions and affect the distribution and density of local populations. Such changes are currently occurring in nettle-feeding butterflies in Sweden where Araschnia levana has recently expanded its range northward and is now likely to interact with resident species (Aglais urticae and Aglais io). Butterfly occurrence data collected over years and across regions enabled us to investigate how a recent range expansion of A. levana may have affected the environmental niche of resident species.

    Location: We focused on two regions of Sweden (Skane and Norrstrom) where A. levana has and has not established and two time periods (2001-2006 and 2009-2012) during its establishment in Skane.

    Methods: We performed two distinct analyses in each region using the PCA-env and the framework described in Broennimann etal. (2012). First, we described the main sources of variation in the environment. Second, in each time period and region, we characterized the realized niches of our focal species across topographic and land use gradients. Third, we quantified overlaps and differences in realized niches between and within species over time.

    Results: In Skane, A. levana has stabilized its distribution over time, while the distribution of the native species has shifted. These shifts depicted a consistent pattern of avoiding overlap between the native species and the environmental space occupied by A. levana, and it was stronger for A. urticae than for A. io. In both regions, we also found evidence of niche partitioning between native species.

    Main conclusions: Interspecific interactions are likely to affect local species distributions. It appears that the ongoing establishment of A. levana has modified local biotic interactions and induced shifts in resident species distributions. Among the mechanisms that can explain such patterns of niche partitioning, parasitoid-driven apparent competition may play an important role in this community.

  • 5.
    Bengtson, Annika
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Nylinder, Stephan
    Karis, Per Ola
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Anderberg, Arne A.
    Evolution and diversification related to rainfall regimes: diversification patterns in the South African genus Metalasia (Asteraceae-Gnaphalieae)2015In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 42, no 1, p. 121-131Article in journal (Refereed)
    Abstract [en]

    AimThe Cape region is known for its exceptional species richness, although much remains unknown regarding the appearance of the modern Cape flora. One explanation is that floral diversification was influenced by the establishment of winter rainfall/summer arid conditions hypothesized to have occurred towards the end of the Miocene. We studied the evolution and diversification of the plant genus Metalasia (Asteraceae-Gnaphalieae), with the aim of testing whether radiation patterns may have been influenced by the climatic changes. LocationSouth Africa, with emphasis on the south-west. MethodsThe radiation of Metalasia was investigated using two approaches: a species diffusion approach, which estimated the ancestral areas by means of a relaxed random walk while sampling from extant distributions; and a discrete approach, in which distributions were defined according to the phytogeographical centres of the Cape region. Secondarily derived clock rates from an earlier Gnaphalieae study were used for calibration purposes. ResultsOur analyses date Metalasia to approximately 6.9Ma, after the Miocene-Pliocene boundary and the establishment of the winter rainfall/summer arid conditions. Metalasia consists of two sister clades: Clade A and Clade B. Clade B, which is endemic to the winter rainfall area, is estimated to have diversified c. 6.4Ma, whereas Clade A, with a main distribution in the all-year rainfall area, is considerably younger, with a crown group age estimated to 3.3Ma. Diversification rates suggest an early rapid speciation, with rates decreasing through time both for Metalasia and for clades A and B separately. Ancestral area estimations show a possible scenario for the radiation of Metalasia to its current diversity and distribution, with no conflict between results inferred from diffusion or discrete methods. Main conclusionsThe diversification of Metalasia is estimated to have begun after the establishment of the winter rainfall/summer arid conditions, consistent with its radiation having been influenced by changes in the climatic regime.

  • 6. Buerki, Sven
    et al.
    Forest, Felix
    Alvarez, Nadir
    Nylander, Johan A. A.
    Stockholm University, Faculty of Science, Department of Botany.
    Arrigo, Nils
    Sanmartin, Isabel
    An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae2011In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 38, no 3, p. 531-550Article in journal (Refereed)
    Abstract [en]

    Aim Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony-based approaches. Here, we compare a parametric method, dispersal-extinction-cladogenesis (DEC), against a parsimony-based method, dispersal-vicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes-DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study. Location World-wide. Methods Phylogenetic relationships were estimated by Bayesian inference on a large dataset representing generic diversity within Sapindaceae. Lineage divergence times were estimated by penalized likelihood over a sample of trees from the posterior distribution of the phylogeny to account for dating uncertainty in biogeographical reconstructions. We compared biogeographical scenarios between Bayes-DIVA and two different DEC models: one with no geological constraints and another that employed a stratified palaeogeographical model in which dispersal rates were scaled according to area connectivity across four time slices, reflecting the changing continental configuration over the last 110 million years. Results Despite differences in the underlying biogeographical model, Bayes-DIVA and DEC inferred similar biogeographical scenarios. The main differences were: (1) in the timing of dispersal events - which in Bayes-DIVA sometimes conflicts with palaeogeographical information, and (2) in the lower frequency of terminal dispersal events inferred by DEC. Uncertainty in divergence time estimations influenced both the inference of ancestral ranges and the decisiveness with which an area can be assigned to a node. Main conclusions By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence. In contrast, Bayes-DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Care should be taken in defining the palaeogeographical model in DEC because of the possibility of overestimating the frequency of extinction events, or of inferring ancestral ranges that are outside the extant species ranges, owing to dispersal constraints enforced by the model. The wide-spanning spatial and temporal model proposed here could prove useful for testing large-scale biogeographical patterns in plants.

  • 7. Dapporto, Leonardo
    et al.
    Fattorini, Simone
    Voda, Raluca
    Dinca, Vlad
    Stockholm University, Faculty of Science, Department of Zoology. University of Guelph, Canada.
    Vila, Roger
    Biogeography of western Mediterranean butterflies: combining turnover and nestedness components of faunal dissimilarity2014In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 41, no 9, p. 1639-1650Article in journal (Refereed)
    Abstract [en]

    Aim Unpartitioned dissimilarity indices such as the Sorensen index (beta(sor)) tend to categorize areas according to species number. The use of turnover indices, such as the Simpson index (beta(simp)), may lead to the loss of important information represented by the nestedness component (beta(nest)). Recent studies have suggested the importance of integrating nestedness and turnover information. We evaluated this proposition by comparing biogeographical patterns obtained by unpartitioned (beta(sor)) and partitioned indices (beta(simp) and beta(nest)) on presence data of western Mediterranean butterflies. Location Western Mediterranean. Methods We assessed the regionalization of 81 mainland and island faunas according to partitioned and unpartitioned dissimilarity by using cluster analyses with the unweighted pair-group method using arithmetic averages (UPGMA) combined with non-metric multidimensional scaling (NMDS). We also carried out dissimilarity interpolation for beta(sor), beta(simp), beta(nest) and the beta(nest)/beta(sor) ratio, to identify geographical patterns of variation in faunal dissimilarity. Results When the unpartitioned bsor index was used, the clustering of sites allowed a clear distinction between insular and mainland species assemblages. Most islands were grouped together, irrespective of their mainland source, because of the dominant effect of their shared low richness. bsimp was the most effective index for clustering islands with their respective mainland source. bsimp clustered mainland sites into broader regions than clusters obtained using bsor. A comparison of regionalization and interpolation provided complementary information and revealed that, in different regions, the patterns highlighted by bsor could largely be determined either by nestedness or turnover. Main conclusions Partitioned and unpartitioned indices convey complementary information, and are able to reveal the influence of historical and ecological processes in structuring species assemblages. When the effect of nestedness is strong, the exclusive use of turnover indices can generate geographically coherent groupings, but can also result in the loss of important information. Indeed, various factors, such as colonization-extinction events, climatic parameters and the peninsular effect, may determine dissimilarity patterns expressed by the nestedness component.

  • 8.
    Espeland, Marianne
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology.
    Johanson, Kjell Arne
    Swedish Museum of Natural History, Entomology department.
    The effect of environmental diversification on species diversification in New Caledonian caddisflies (Insecta: Trichoptera: Hydropsychidae)2010In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 37, no 5, p. 879-890Article in journal (Refereed)
    Abstract [en]

    Aim To test whether environmental diversification played a role in the diversification of the New Caledonian Hydropsychinae caddisflies.

    Location New Caledonia, south-west Pacific.

    Methods The phylogeny of the New Caledonian Hydropsychinae caddisflies was hypothesized using parsimony and Bayesian methods on molecular characters. The Bayesian analysis was the basis for a comparative analysis of the correlation between phylogeny and three environmental factors: geological substrate (ultrabasic, non-ultrabasic), elevation and precipitation. Phylogenetic divergence times were estimated using a relaxed clock method, and environmental factors were mapped onto a lineage-through-time plot to investigate the timing of environmental diversification in relation to species radiation. The correlation between rainfall and elevation was tested using independent contrasts, and the gamma statistic was calculated to infer the diversification pattern of the group.

    Results The diversification of extant Orthopsyche–Caledopsyche species began in the Middle–Late Oligocene, when much of the island of New Caledonia was covered by ultrabasic substrate and mountain forming was prevalent. Most lineages originated in the Middle–Late Miocene, a period associated with long-term climate oscillation. Optimization of environmental factors on the phylogeny demonstrated that the New Caledonian Hydropsychinae group adapted to ultrabasic substrate early in its evolutionary history. The clade living mostly on ultrabasic substrate was far more species-rich than the clade living mostly on non-ultrabasic substrate. Elevation and rainfall were significantly correlated with each other. The lineage-through-time plot revealed that the main environmental diversification preceded species diversification. A constant speciation through time was rejected, and the negative gamma indicates that most of the diversification occurred early in the history of the clade. According to the inferred phylogeny, the genus Orthopsyche McFarlane is a synonym under Caledopsyche Kimmins, and Abacaria caledona Oláh & Barnard should also be included in Caledopsyche.

    Main conclusions The age of the radiation does not support a vicariance origin of New Caledonian Hydropsychinae caddisflies. Environmental diversification pre-dates lineage diversification, and thus environmental heterogeneity potentially played a role in the diversification of the group, by providing a variety of fragmented habitats to disperse into, promoting speciation. The negative gamma indicates that the speciation rate slowed as niches started to fill.

  • 9. Jonsson, Knud A.
    et al.
    Bowie, Rauri C. K.
    Nylander, Johan A. A.
    Stockholm University, Faculty of Science, Department of Botany.
    Christidis, Les
    Norman, Janette A.
    Fjeldsa, Jon
    Biogeographical history of cuckoo-shrikes (Aves: Passeriformes): transoceanic colonization of Africa from Australo-Papua2010In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 37, no 9, p. 1767-1781Article in journal (Refereed)
    Abstract [en]

    Aim Cuckoo-shrikes and allies (Campephagidae) form a radiation of birds widely distributed in the Indo-Pacific and Africa. Recent studies on the group have been hampered by poor taxon sampling, causing inferences about systematics and biogeography to be rather speculative. With improved taxon sampling and analyses within an explicit spatiotemporal framework, we elucidate biogeographical patterns of dispersal and diversification within this diverse clade of passerine birds. Location Africa, Asia, Australo-Papua, the Pacific, the Philippines and Wallacea. Methods We use model-based phylogenetic methods (MrBayes and garli) to construct a phylogenetic hypothesis of the core Campephagidae (Campephagidae with the exclusion of Pericrocotus). The phylogeny is used to assess the biogeographical history of the group with a newly developed Bayesian approach to dispersal-vicariance analysis (Bayes-diva). We also made use of a partitioned beast analysis, with several calibration points taken from island ages, passerine mitochondrial substitution rates and secondary calibration points for passerine birds, to assess the timing of diversification and dispersal. Results We present a robust molecular phylogeny that includes all genera and 84% of the species within the core Campephagidae. Furthermore, we estimate divergence dates and ancestral area relationships. We demonstrate that Campephagidae originated in Australo-Papua with a single lineage (Pericrocotus) dispersing to Asia early. Later, there was further extensive transoceanic dispersal from Australo-Papua to Africa involving lineages within the core Campephagidae radiation. Main conclusions The phylogenetic relationships, along with the results of the ancestral area analysis and the timing of dispersal events, support a transoceanic dispersal scenario from Australo-Papua to Africa by the core Campephagidae. The sister group to core Campephagidae, Pericrocotus, dispersed to mainland Asia in the late Oligocene. Asia remained uncolonized by the core Campephagidae until the Pliocene. Transoceanic dispersal is by no means an unknown phenomenon, but our results represent a convincing case of colonization over a significant water gap of thousands of kilometres from Australo-Papua to Africa.

  • 10.
    Kainulainen, Kent
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. University of Michigan Herbarium, USA; The Royal Swedish Academy of Sciences, Sweden.
    Razafimandimbison, Sylvain G.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Swedish Museum of Natural History, Sweden; The Royal Swedish Academy of Sciences, Sweden.
    Wikström, Niklas
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. The Royal Swedish Academy of Sciences, Sweden.
    Bremer, Birgitta
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. The Royal Swedish Academy of Sciences, Sweden.
    Island hopping, long-distance dispersal and species radiation in the Western Indian Ocean: historical biogeography of the Coffeeae alliance (Rubiaceae)2017In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 44, no 9, p. 1966-1979Article in journal (Refereed)
    Abstract [en]

    Aim The Western Indian Ocean region (WIOR) is home to a very diverse and largely unique flora that has mainly originated via long-distance dispersals. The aim of this study is to gain insight into the origins of the WIOR biodiversity and to understand the dynamics of colonization events between the islands. We investigate spatial and temporal hypotheses of the routes of dispersal, and compare the dispersal patterns of plants of the Coffeeae alliance (Rubiaceae) and their dispersers. Rubiaceae is the second most species-rich plant family in Madagascar, and includes many endemic genera. The neighbouring archipelagos of the Comoros, Mascarenes and Seychelles also harbour several endemic Rubiaceae.

    Location The islands of the Western Indian Ocean.

    Methods Phylogenetic relationships and divergence times were reconstructed from plastid DNA data of an ingroup sample of 340 species, using Bayesian inference. Ancestral areas and range evolution history were inferred by a maximum likelihood method that takes topological uncertainty into account.

    Results At least 15 arrivals to Madagascar were inferred, the majority of which have taken place within the last 10 Myr. Most dispersal events were supported as being from mainland Africa, but Catunaregam may have dispersed from Asia. Although most Coffeeae alliance lineages are zoochorous, the general pattern of dispersals from Africa is incongruent with the biogeographic origins of the extant Malagasy volant frugivores. Several out-of-Madagascar dispersals were inferred to the neighbouring islands, as well as back-colonizations of Africa.

    Main conclusions The African flora has been of foremost importance as source of dispersal to the islands of the Western Indian Ocean. Following the colonization of Madagascar, rapid radiations appear to have taken place in some clades, and Madagascar has also been an important source area for subsequent dispersal to the Comoros, Mascarenes and Seychelles.

  • 11.
    Kodandaramaiah, Ullasa
    Stockholm University, Faculty of Science, Department of Zoology.
    Use of dispersal–vicariance analysis in biogeography – a critique2010In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 37, p. 3-11Article in journal (Refereed)
    Abstract [en]

    Aim Analytical methods are commonly used to identify historical processes of vicariance and dispersal in the evolution of taxa. Currently, dispersal-vicariance analysis implemented in the software diva is the most widely used method. Despite some recognized shortcomings of the method, it has been treated as error-free in many cases and used extensively as the sole method to reconstruct histories of taxa. In light of this, an evaluation of the limitations of the method is needed, especially in relation to several newer alternatives. Methods In an approach similar to simulation studies in phylogenetics, I use hypothetical taxa evolving in specific geological scenarios and test how well diva reconstructs their histories. Results diva reconstructs histories accurately when evolution has been simple; that is, where speciation is driven mainly by vicariance. Ancestral areas are wrongly identified under several conditions, including complex patterns of dispersals and within-area speciation events. Several potentially serious drawbacks in using diva for inferences in biogeography are discussed. These include the inability to distinguish between contiguous range expansions and across-barrier dispersals, a low probability of invoking extinctions, incorrect constraints set on the maximum number of areas by the user, and analysing the ingroup taxa without sister groups. Main conclusions Most problems with inferences based on diva are linked to the inflexibility and simplicity of the assumptions used in the method. These are frequently invalid, resulting in spurious reconstructions. I argue that it might be dangerous to rely solely on diva optimization to infer the history of a group. I also argue that diva is not ideally suited to distinguishing between dispersal and vicariance because it cannot a priori take into account the age of divergences relative to the timing of barrier formation. I suggest that other alternative methods can be used to corroborate the findings in diva, increasing the robustness of biogeographic hypotheses. I compare some important alternatives and conclude that model-based approaches are promising.

     

  • 12.
    Laenen, Benjamin
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab). University of Liège, Belgium.
    Machac, Antonin
    Gradstein, S. Robbert
    Shaw, Blanka
    Patino, Jairo
    Desamore, Aurelie
    Goffinet, Bernard
    Cox, Cymon J.
    Shaw, Jonathan
    Vanderpoorten, Alain
    Geographical range in liverworts: does sex really matter?2016In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 43, no 3, p. 627-635Article in journal (Refereed)
    Abstract [en]

    AimWhy some species exhibit larger geographical ranges than others remains a fundamental, but largely unanswered, question in ecology and biogeography. In plants, a relationship between range size and mating system was proposed over a century ago and subsequently formalized in Baker's Law. Here, we take advantage of the extensive variation in sexual systems of liverworts to test the hypothesis that dioecious species compensate for limited fertilization by producing vegetative propagules more commonly than monoecious species. As spores are assumed to contribute to random long-distance dispersal, whereas vegetative propagules contribute to colony maintenance and frequent short-distance dispersal, we further test the hypothesis that monoecious species exhibit larger geographical ranges than dioecious ones. LocationWorldwide. MethodsWe used comparative phylogenetic methods to assess the correlation between range size and life history traits related to dispersal, including mating systems, spore size and production of specialized vegetative propagules. ResultsNo significant correlation was found between dioecy and production of vegetative propagules. However, production of vegetative propagules is correlated with the size of geographical ranges across the liverwort tree of life, whereas sexuality and spores size are not. Moreover, variation in sexual systems did not have an influence on the correlation between geographical range and production of asexual propagules. Main conclusionsOur results challenge the long-held notion that spores, and not vegetative propagules, are involved in long-distance dispersal. Asexual reproduction seems to play a major role in shaping the global distribution patterns of liverworts, so that monoecious species do not tend to display, on average, broader distribution ranges than dioecious ones. Our results call for further investigation on the spatial genetic structure of bryophyte populations at different geographical scales depending on their mating systems to assess the dispersal capacities of spores and asexual propagules and determine their contribution in shaping species distribution ranges.

  • 13. Linder, H. Peter
    et al.
    Antonelli, Alexandre
    Humphreys, Aelys M.
    Stockholm University, Faculty of Science, Department of Botany. Imperial College London .
    Pirie, Michael D.
    Wuest, Rafael O.
    What determines biogeographical ranges?: Historical wanderings and ecological constraints in the danthonioid grasses2013In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 40, no 5, p. 821-834Article in journal (Refereed)
    Abstract [en]

    Aim We sought to understand the variables that limit the distribution range of a clade (here the danthonioid grasses). We tested time, area of origin, habitat suitability, disjunction width and nature, and wind direction as possible range determinants. Location Global, but predominantly the Southern Hemisphere. Methods We mapped the range of the subfamily Danthonioideae, and used 39,000 locality records and an ensemble modelling approach to define areas with suitable danthonioid habitat. We used a well-sampled, dated phylogeny to estimate the number and direction of historical dispersal events, based on parsimony optimization. We tested for the impact of wind direction on dispersal rate using a likelihood approach, and for the effects of barrier width with a regression approach. Results We found 17 geographically isolated areas with suitable habitats for danthonioids. All currently suitable Southern Hemisphere areas have been occupied, but three apparently suitable areas in the Northern Hemisphere have not. We infer that southern Africa was first occupied in the Oligocene and that dispersal to the other areas was initiated in the middle Miocene. Inferred dispersal rate was correlated with the width of the disjunctions, up to a distance of 5000km. There was no support for wind direction having influenced differences in dispersal rate. Main conclusions The current range of the Danthonioideae can be predicted ecologically (areas with suitable habitat) and historically (the width of the disjunctions separating the areas with suitable habitat and the area of origin). The direction of dispersal is dictated by the area of origin and by serendipity: there is no evidence for general patterns of dispersal, for example for dispersal occurring more frequently over land than over sea or in an easterly versus a westerly direction around the Southern Hemisphere. Thus the range and range-filling of Danthonioideae can be accounted for by surprisingly few variables: habitat suitability, distance between suitable areas, and area of origin.

  • 14. Lonnell, Niklas
    et al.
    Hylander, Kristoffer
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Calcicolous plants colonize limed mires after long-distance dispersal2018In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 45, no 4, p. 885-894Article in journal (Refereed)
    Abstract [en]

    Aim: Dispersal range is a key factor for understanding species' persistence in dynamic landscapes. However, dispersal, especially over long distances, is inherently difficult to study. Making use of a unique system of anthropogenically disturbed, geographically isolated mires, we assessed dispersal ranges for a group of plants restricted to wet calcareous conditions via empirical studies of colonization patterns. We hypothesized that more species would have colonized the less isolated mires and that colonization frequencies would be related to traits influencing propagule pressure. Location: Sweden. Taxon: Calcicolous vascular plants and bryophytes. Methods: The study system consisted of 52 acidic mires that had acquired a high pH through active liming by the Swedish government during the past two decades. These conditions killed off mat-forming peat mosses, rendering the mires open to colonization by other species. In each mire, we recorded the presence of rich fen plant species typically found in high pH wet soils throughout the country. We used citizen science-collected records of occurrences of obligate-rich fen species surrounding each mire to examine the likely dispersal distances that were involved in creating the colonization patterns. Results: A lower proportion of vascular plants than bryophytes from their respective species pools colonized the limed mires (27% vs. 67%, p = .001). The number of colonized rich fen species per site was 0-6 for vascular plants and 10-31 for bryophytes, and was positively related to potential diaspore sources >20km from the mires (p = .026 and p = .012, respectively). The proportion of colonized mires was positively related to the species' regional frequency, but not with their diaspores' terminal velocity. Main conclusions: Many bryophyte species can effectively disperse over long distances (tens of kilometres) and variation among species in total diaspore production seems to be an important regulator of colonization across landscapes, for both vascular plants and bryophytes, in communities that are open to colonization.

  • 15.
    Manns, Ulrika
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Anderberg, Arne A.
    Biogeography of 'tropical Anagallis' (Myrsinaceae) inferred from nuclear and plastid DNA sequence data2011In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 38, no 5, p. 950-961Article in journal (Refereed)
    Abstract [en]

    Aim 'Tropical Anagallis' corresponds to one of two evolutionary lineages within the genus Anagallis L. Generally, species within this lineage have a limited distribution in (sub-)tropical regions in Africa or Madagascar. Two species, however, are endemic to South America, and exhibit a trans-Atlantic disjunction with the rest of the species within the lineage. To investigate this disjunct distribution, as well as other dispersal events, the distribution of extant taxa was used to hypothesize the ancestral area(s) of distribution. Location Africa, Madagascar, Europe and South America. Methods Dispersal-vicariance analysis (DIVA) was used to optimize distribution areas onto parsimony and Bayesian phylogenies based on sequence data from four chloroplast loci and the nuclear internal transcribed spacers (ITS). Results Parsimony analysis gave one most parsimonious tree while Bayesian analysis resulted in a collapsed node due to alternative placements of Anagallis nummularifolia Baker, endemic to Madagascar. Optimization of the present distribution using DIVA, and the most parsimonious tree and six alternative topologies of the Bayesian analysis, show an origin of the lineage in Europe as most likely, although one topology indicates a broader ancestral distribution area. Dispersal to Africa appears to have been a single event, while two parallel dispersal events seem to have resulted in the American as well as Madagascan distributions. Main conclusions The lineage 'tropical Anagallis' evolved in Europe and may have been present in the Eocene boreotropical forests, although scarcity of fossils makes assessment of age difficult. Dispersal to South America is proposed to have been via the North Atlantic land bridge, or, more likely, through transport by the North Equatorial Current. Dispersal from Europe to Africa represents a single event, while dispersal to Madagascar from mainland Africa has occurred twice.

  • 16.
    Razafimandimbison, Sylvain G.
    et al.
    Stockholm University, Faculty of Science, Department of Botany. Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum.
    McDowell, Timothy D.
    Halford, David A.
    Bremer, Birgitta
    Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum. Stockholm University, Faculty of Science, Department of Botany.
    Origin of the pantropical and nutriceutical Morinda citrifolia L. (Rubiaceae): comments on its distribution range and circumscription2010In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 37, no 3, p. 520-529Article in journal (Refereed)
    Abstract [en]

    Aim Morinda citrifolia L., commercially known as noni or the Indian mulberry plant, is morphologically variable and the only widely distributed member of the pantropical genus Morinda sensu stricto (Rubiaceae). This large distribution has been attributed partly to the ability of the seeds of the large-fruited M. citrifolia L. var. citrifolia L. to be transported by oceanic drifting. This form of M. citrifolia var. citrifolia has been predicted to be the progenitor colonizer of the island endemic Morinda species. Using a phylogenetic approach and large sampling of the widespread, large-fruited M. citrifolia var. citrifolia, we assessed the potential area of origin of M. citrifolia and tested the hypothesis that the large-fruited M. citrifolia var. citrifolia is an ancestral colonizer. Location Tropics. Methods We performed Bayesian analyses of 22 species of the tribe Morindeae (including 11 individuals of the three currently recognized varieties of M. citrifolia) based on combined nrETS, nrITS, rps16 and trnT-F sequence data. Geographic origins of the studied taxa were mapped onto the Bayesian majority rule consensus tree. Results Nine sequenced individuals of M. citrifolia from diverse geographic locations formed a highly supported clade, which was sister to the Australo-Micronesian clade that included M. bracteata var. celebica and M. latibracteata. These sister clades are part of the broader Asian, arborescent Morinda clade. We found no support for the current varietal classification of M. citrifolia. Main conclusions Our analyses suggest a Micronesian origin of M. citrifolia. This implies that the large-fruited M. citrifolia var. citrifolia might well have been present in the Pacific before the arrival of the Micronesian and Polynesian ancestors from Southeast Asia. The wide distribution of this form of M. citrifolia var. citrifolia is attributed partly to the trans-oceanic dispersal of its buoyant seeds, self-pollination and its ability to produce flowers and fruits year-round. The hypothesis that the widespread, large-fruited M. citrifolia var. citrifolia is the progenitor colonizer of the island endemic Morinda species is inconsistent with its derived position within the Asian, arborescent Morinda clade and with the fact that the nine sampled individuals of M. citrifolia form a clade.

  • 17. Sanmartin, Isabel
    et al.
    Wanntorp, Livia
    Stockholm University, Faculty of Science, Department of Botany.
    Winkworth, Richard C.
    West Wind Drift revisited: testing for directional dispersal in the Southern Hemisphere using event-based tree fitting2007In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 34, no 3, p. 398-416Article in journal (Refereed)
    Abstract [en]

    Aim Recent studies suggest that if constrained by prevailing wind or ocean currents dispersal may produce predictable, repeated distribution patterns. Dispersal mediated by the West Wind Drift (WWD) and Antarctic Circumpolar Current (AAC) has often been invoked to explain the floristic similarities of Australia, South America and New Zealand. If these systems have been important dispersal vectors then eastward dispersal - from Australia to New Zealand and the western Pacific to South America - is expected to predominate. We investigate whether phylogenies for Southern Hemisphere plant groups provide evidence of historical dispersal asymmetry and more specifically whether inferred asymmetries are consistent with the direction of the WWD/AAC. Location Southern Hemisphere. Methods We assembled a data set of 23 published phylogenies for plant groups that occur in New Zealand, Australia and/or South America. We used parsimony-based tree fitting to infer the number and direction of dispersals within each group. Observed dispersal asymmetries were tested for significance against a distribution of expected values. Results Our analyses suggest that dispersal has played a major role in establishing present distributions and that there are significant patterns of asymmetry in Southern Hemisphere dispersal. Consistent with the eastward direction of the WWD/ACC, dispersal from Australia to New Zealand was inferred significantly more often than in the reverse direction. No significant patterns of dispersal asymmetry were found between the western Pacific landmasses and South America. However, eastward dispersal was more frequently inferred between Australia and South America, while for New Zealand-South American events westward dispersal was more common. Main Conclusions Our results suggest that eastward circumpolar currents have constrained the dispersal of plants between Australia and New Zealand. However, the WWD/ACC appear to have had less of an influence on dispersal between the western Pacific landmasses and South America. This observation may suggest that differences in dispersal mechanism are important - direct wind or water dispersal vs. stepping-stone dispersal along the Antarctic coast. While our analyses provide useful preliminary insights into dispersal asymmetry in the Southern Hemisphere we will need larger data sets and additional methodological advances in order to test fully these dispersal patterns and infer processes from phylogenetic data.

  • 18.
    Smedmark, Jenny E. E.
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Eriksson, Torsten
    Bremer, Birgitta
    Divergence time uncertainty and historical biogeography reconstruction - an example from Urophylleae (Rubiaceae)2010In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 37, no 12, p. 2260-2274Article in journal (Refereed)
    Abstract [en]

    Aim When hypotheses of historical biogeography are evaluated, age estimates of individual nodes in a phylogeny often have a direct impact on what explanation is concluded to be most likely. Confidence intervals of estimated divergence times obtained in molecular dating analyses are usually very large, but the uncertainty is rarely incorporated in biogeographical analyses. The aim of this study is to use the group Urophylleae, which has a disjunct pantropical distribution, to explore how the uncertainty in estimated divergence times affects conclusions in biogeographical analysis. Two hypotheses are evaluated: (1) long-distance dispersal from Africa to Asia and the Neotropics, and (2) a continuous distribution in the boreotropics, probably involving migration across the North Atlantic Land Bridge, followed by isolation in equatorial refugia. Location Tropical and subtropical Asia, tropical Africa, and central and southern tropical America. Methods This study uses parsimony and Bayesian phylogenetic analyses of chloroplast DNA and nuclear ribosomal DNA data from 56 ingroup species, beast molecular dating and a Bayesian approach to dispersal-vicariance analysis (Bayes-DIVA) to reconstruct the ancestral area of the group, and the dispersal-extinction-cladogenesis method to test biogeographical hypotheses. Results When the two models of geographic range evolution were compared using the maximum likelihood (ML) tree with mean estimates of divergence times, boreotropical migration was indicated to be much more likely than long-distance dispersal. Analyses of a large sample of dated phylogenies did, however, show that this result was not consistent. The age estimate of one specific node had a major impact on likelihood values and on which model performed best. The results show that boreotropical migration provides a slightly better explanation of the geographical distribution patterns of extant Urophylleae than long-distance dispersal. Main conclusions This study shows that results from biogeographical analyses based on single phylogenetic trees, such as a ML or consensus tree, can be misleading, and that it may be very important to take the uncertainty in age estimates into account. Methods that account for the uncertainty in topology, branch lengths and estimated divergence times are not commonly used in biogeographical inference today but should definitely be preferred in order to avoid unwarranted conclusions.

  • 19. Valiranta, Minna
    et al.
    Kaakinen, Anu
    Kuhry, Peter
    Stockholm University, Faculty of Science, Department of Physical Geography and Quaternary Geology.
    Kultti, Seija
    Salonen, J. Sakari
    Seppa, Heikki
    Scattered late-glacial and early Holocene tree populations as dispersal nuclei for forest development in north-eastern European Russia2011In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 38, no 5, p. 922-932Article in journal (Refereed)
    Abstract [en]

    Aim Concepts about patterns and rates of post-glacial tree population migration are changing as a result of the increasing amount of palaeobotanical information being provided by macroscopic plant remains. Here we combine macrofossil, pollen and stomata records from five sites in north-eastern European Russia and summarize the results for the late-glacial-early Holocene transition. The late-glacial-early Holocene transition encompasses the first indications of trees (tree-type Betula, Picea abies, Abies sibirica and Larix sibirica) and subsequent forest development. Considerable time-lags between the first macrobotanical and/or stomata finds of spruce (Picea abies) and the establishment of a closed forest are reconsidered. Location Pechora basin, north-eastern European Russia. Methods We used plant macrofossil, stomata, pollen and radiocarbon analyses to reconstruct late-glacial and early Holocene tree establishment and forest development. The data were derived from lake sediment and peat archives. Results Palaeobotanical data reveal an early Holocene presence (11,500-10,000 cal. yr bp) of arboreal taxa at all five sites. One site presently located in the northernmost taiga zone, shows the presence of spruce and reproducing tree birch during the late-glacial. Given the current view of post-glacial population dynamics and migration rates, it seems likely that the source area of these early tree populations in north-eastern European Russia was not located in southern Europe but that these populations had local origins. Results thus support the emerging view that the first post-glacial population expansions in non-glaciated regions at high latitudes do not reflect migration from the south but were a result of an increase in the size and density of small persisting outlying tree populations. Main conclusions Results suggest that the area east of the margin of the Scandinavian ice sheet to the Ural Mountains had isolated patches of trees during the late-glacial and early Holocene and that these small populations acted as initial nuclei for population expansion and forest development in the early Holocene.

  • 20.
    Wikström, Niklas
    et al.
    Stockholm University, Faculty of Science, Department of Botany. Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum.
    Avino, M.
    Razafimandimbison, S. G.
    Bremer, Birgitta
    Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum.
    Historical biogeography of the coffee family (Rubiaceae, Gentianales) in Madagascar: case studies from the tribes Knoxieae, Naucleeae, Paederieae and Vanguerieae2010In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 37, no 6, p. 1094-1113Article in journal (Refereed)
    Abstract [en]

    Aim In Madagascar the family Rubiaceae includes an estimated 650 species representing 95 genera. As many as 98% of the species and 30% of the genera are endemic. Several factors make the Rubiaceae a model system for developing an understanding of the origins of the Malagasy flora. Ancestral area distributions are explicitly reconstructed for four tribes (Knoxieae, Naucleeae, Paederieae and Vanguerieae) with the aim of understanding how many times, and from where, these groups have originated in Madagascar. Location Indian Ocean Basin, with a focus on Madagascar. Methods Bayesian phylogenetic analyses are conducted on the four tribes. The results are used for reconstructing ancestral areas using dispersal-vicariance analyses. Phylogenetic uncertainties in the reconstructions are accounted for by conducting all analyses on the posterior distribution from the analyses. Results Altogether, 11 arrivals in Madagascar (one in Paederieae, five in Knoxieae, three in Vanguerieae, and two in Naucleeae) are reconstructed. The most common pattern is a dispersal event (followed by vicariance) from Eastern Tropical Africa. The Naucleeae and Paederieae in Madagascar differ and originate from Asia. Numerous out-of-Madagascar dispersals, mainly in the dioecious Vanguerieae, are reconstructed. Main conclusions The four tribes arrived several times in Madagascar via dispersal events from Eastern Tropical Africa, Southern Africa and Tropical Asia. The presence of monophyletic groups that include a number of species only found in Madagascar indicates that much endemism in the tribes results from speciation events occurring well after their arrival in Madagascar. Madagascar is the source of origin for almost all Rubiaceae found on the neighbouring islands of the Comoros, Mascarenes and Seychelles.

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