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  • 1.
    Auffret, Alistair G.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi. University of York, UK.
    Kimberley, Adam
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    Plue, Jan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    Skånes, Helle
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    Jakobsson, Simon
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    Waldén, Emelie
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    Wennbom, Marika
    Wood, Heather
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    Bullock, James M.
    Cousins, Sara A. O.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    Gartz, Mira
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    Hooftman, Danny A. P.
    Tränk, Louise
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    HistMapR: Rapid digitization of historical land-use maps in R2017Ingår i: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 8, nr 11, s. 1453-1457Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Habitat destruction and degradation represent serious threats to biodiversity, and quantification of land-use change over time is important for understanding the consequences of these changes to organisms and ecosystem service provision. Comparing land use between maps from different time periods allows estimation of the magnitude of habitat change in an area. However, digitizing historical maps manually is time-consuming and analyses of change are usually carried out at small spatial extents or at low resolutions. HistMapR contains a number of functions that can be used to semi-automatically digitize historical land use according to a map's colours, as defined by the RGB bands of the raster image. We test the method on different historical land-use map series and compare results to manual digitizations. Digitization is fast, and agreement with manually digitized maps of around 80-90% meets common targets for image classification. We hope that the ability to quickly classify large areas of historical land use will promote the inclusion of land-use change into analyses of biodiversity, species distributions and ecosystem services.

  • 2. Baeten, Lander
    et al.
    Warton, David I.
    Van Calster, Hans
    De Frenne, Pieter
    Verstraeten, Gorik
    Bonte, Dries
    Bernhardt-Roemermann, Markus
    Cornelis, Johnny
    Decocq, Guillaume
    Eriksson, Ove
    Stockholms universitet, Naturvetenskapliga fakulteten, Botaniska institutionen.
    Hedl, Radim
    Heinken, Thilo
    Hermy, Martin
    Hommel, Patrick
    Kirby, Keith
    Naaf, Tobias
    Petrik, Petr
    Walther, Gian-Reto
    Wulf, Monica
    Verheyen, Kris
    A model-based approach to studying changes in compositional heterogeneity2014Ingår i: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 5, nr 2, s. 156-164Artikel i tidskrift (Refereegranskat)
  • 3. Dapporto, Leonardo
    et al.
    Voda, Raluca
    Dinca, Vlad
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Pompeu Fabra University, Spain; Autonomous University of Barcelona, Spain.
    Vila, Roger
    Comparing population patterns for genetic and morphological markers with uneven sample sizes. An example for the butterfly Maniola jurtina2014Ingår i: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 5, nr 8, s. 834-843Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    1. Integrating genetic and/or phenotypic traits at population level is considered a fundamental approach in the study of evolutionary processes, systematics, biogeography and conservation. But combining the two types of data remain a complex task, mostly due to the high, and sometimes different, sample sizes required for reliable assessments of community traits. Data availability has been increasing in recent years, thanks to online resources, but it is uncommon that different types of markers are available for any given specimen. 2. We provide new R functions aimed at directly correlating traits at population level, even if data sets only overlap partially. The new functions are based on a modified Procrustes algorithm that minimizes differences between bidimensional ordinations of two different markers, based on a subsample of specimens for which both characters are known. To test the new functions, we used a molecular and morphological data set comprising Mediterranean specimens of the butterfly Maniola jurtina. 3. By using this method, we have been able to maximize similarities between genotypic and phenotypic configurations obtained after principal coordinate analysis for the model species and evaluated their degree of correlation at both individual and population level. The new recluster. procrustes function retained the information of the relative importance of different morphological variables in determining the observed ordinations and preserved it in the transformed configurations. This allowed calculating the best combination of morphological variables mirroring genetic relationships among specimens and populations. Finally, it was possible to analyse the modality and variance of the phenotypic characters correlated with the genetic structure among populations. 4. The genetic and phenotypic markers displayed high overall correlation in the study area except in the contact zone, where discrepancies for particular populations were detected. Interestingly, such discrepancies were spatially structured, with southern populations displaying typical western morphotype and eastern haplotypes, while the opposite occurred in the northern populations. The methodology here described can be applied to any number and type of traits for which bidimensional configurations can be obtained, and opens new possibilities for datamining and formeta-analyses combining existing data sets in biogeography, systematics and ecology.

  • 4.
    Gorokhova, Elena
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Individual growth as a non-dietary determinant of the isotopic niche metrics2018Ingår i: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 9, nr 2, s. 269-277Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    1. Quantitative analytical approaches for isotopic niche analysis in the trophic diversity studies are proliferating rapidly; however, the assumptions behind the isotopic niche applications are rarely tested. One of the main assumptions is independence of the niche metrics and physiological status of the animals. The aim of this experimental study was to test the relationship between growth and Layman's metrics of isotopic niche in consumers eating the same food but in different quantities and growing at different rates.

    2. Based on research indicating that individual variability in isotopic fractionation increases under suboptimal conditions, I hypothesized that a group of consumers originating from the same population and exposed to food limitation would have greater estimates of the niche breadth and diversity as a result of higher inter-individual variability in growth rate and stable isotope signatures than in non-limiting feeding conditions. This hypothesis was tested using Baltic mysids Neomysis integer fed isotopically uniform diet under laboratory conditions and analysing individual growth and stable isotope signature in concert.

    3. As hypothesized, mysid growth rate was a significant negative predictor of most niche metrics. These effects were related to both increased inter-individual variability and higher trophic fractionation in malnourished animals, whereas in actively growing mysids, lower fractionation was observed together with lower values for niche size, isotopic range and trophic diversity.

    4. These findings challenge how we interpret the intrapopulation isotopic variance and evaluate isotopic evidence of individual specialization and call for integrated approaches for isotopic niche and growth assessment.

  • 5.
    Humphreys, Aelys M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Imperial College London, UK.
    Rydin, Catarina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Jonsson, Knud A.
    Alsop, David
    Callender-Crowe, Leah M.
    Barraclough, Timothy G.
    Detecting evolutionarily significant units above the species level using the generalised mixed Yule coalescent method2016Ingår i: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 7, nr 11, s. 1366-1375Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    There is renewed interest in inferring evolutionary history by modelling diversification rates using phylogenies. Understanding the performance of the methods used under different scenarios is essential for assessing empirical results. Recently, we introduced a new approach for analysing broadscale diversity patterns, using the generalised mixed Yule coalescent (GMYC) method to test for the existence of evolutionarily significant units above the species (higher ESUs). This approach focuses on identifying clades as well as estimating rates, and we refer to it as clade-dependent. However, the ability of the GMYC to detect the phylogenetic signature of higher ESUs has not been fully explored, nor has it been placed in the context of other, clade-independent approaches. We simulated >32000 trees under two clade-independent models: constant-rate birth-death (CRBD) and variable-rate birth-death (VRBD), using parameter estimates from nine empirical trees and more general parameter values. The simulated trees were used to evaluate scenarios under which GMYC might incorrectly detect the presence of higher ESUs. The GMYC null model was rejected at a high rate on CRBD-simulated trees. This would lead to spurious inference of higher ESUs. However, the support for the GMYC model was significantly greater in most of the empirical clades than expected under a CRBD process. Simulations with empirically derived parameter values could therefore be used to exclude CRBD as an explanation for diversification patterns. In contrast, a VRBD process could not be ruled out as an alternative explanation for the apparent signature of hESUs in the empirical clades, based on the GMYC method alone. Other metrics of tree shape, however, differed notably between the empirical and VRBD-simulated trees. These metrics could be used in future to distinguish clade-dependent and clade-independent models. In conclusion, detection of higher ESUs using the GMYC is robust against some clade-independent models, as long as simulations are used to evaluate these alternatives, but not against others. The differences between clade-dependent and clade-independent processes are biologically interesting, but most current models focus on the latter. We advocate more research into clade-dependent models for broad diversity patterns.

  • 6. May, Michael R.
    et al.
    Höhna, Sebastian
    Stockholms universitet, Naturvetenskapliga fakulteten, Matematiska institutionen. University of California, USA.
    Moore, Brian R.
    A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary2016Ingår i: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 7, nr 8, s. 947-959Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible-jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree-wide diversification-rate variation and mass-extinction events by specifying a biologically informed prior on the magnitude of mass-extinction events and empirical hyperpriors on the diversification-rate parameters. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events and provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e. <5%) false-discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction approximate to 23Ma. This new approach - the CPP on Mass-Extinction Times (CoMET) model - provides an effective tool for detecting the impact of mass-extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.

  • 7. Merow, Cory
    et al.
    Dahlgren, Johan P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. University of Southern Denmark, Denmark.
    Metcalf, C. Jessica E.
    Childs, Dylan Z.
    Evans, Margaret E. K.
    Jongejans, Eelke
    Record, Sydne
    Rees, Mark
    Salguero-Gomez, Roberto
    McMahon, Sean M.
    Advancing population ecology with integral projection models: a practical guide2014Ingår i: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 5, nr 2, s. 99-110Artikel, forskningsöversikt (Refereegranskat)
  • 8. Shafer, Aaron B. A.
    et al.
    Peart, Claire R.
    Tusso, Sergio
    Maayan, Inbar
    Brelsford, Alan
    Wheat, Christopher W.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Wolf, Jochen B. W.
    Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference2017Ingår i: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 8, nr 8, s. 907-917Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    1. Restriction site-associated DNA sequencing (RAD-seq) provides high-resolution population genomic data at low cost, and has become an important component in ecological and evolutionary studies. As with all high-throughput technologies, analytic strategies require critical validation to ensure precise and unbiased interpretation. 2. To test the impact of bioinformatic data processing on downstream population genetic inferences, we analysed mammalian RAD-seq data (>100 individuals) with 312 combinations of methodology (de novo vs. mapping to references of increasing divergence) and filtering criteria (missing data, HWE, F-IS, coverage, mapping and genotype quality). In an effort to identify commonalities and biases in all pipelines, we computed summary statistics (nr. loci, nr. SNP, pi, Het(obs), F-IS, F-ST, N-e and m) and compared the results to independent null expectations (isolation-by-distance correlation, expected transition-to-transversion ratio T-s/T-v and Mendelian mismatch rates of known parent-offspring trios). 3. We observed large differences between reference-based and de novo approaches, the former generally calling more SNPs and reducing F-IS and T-s/T-v. Data completion levels showed little impact on most summary statistics, and FST estimates were robust across all pipelines. The site frequency spectrum was highly sensitive to the chosen approach as reflected in large variance of parameter estimates across demographic scenarios (single-population bottlenecks and isolation-with-migration model). Null expectations were best met by reference-based approaches, although contingent on the specific criteria. 4. We recommend that RAD-seq studies employ reference-based approaches to a closely related genome, and due to the high stochasticity associated with the pipeline advocate the use of multiple pipelines to ensure robust population genetic and demographic inferences.

  • 9. Spens, Johan
    et al.
    Evans, Alice R.
    Halfmaerten, David
    Knudsen, Steen W.
    Sengupta, Mita E.
    Mak, Sarah S. T.
    Sigsgaard, Eva E.
    Hellström, Micaela
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Natural History Museum of Denmark, Denmark.
    Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol: advantage of enclosed filter2017Ingår i: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 8, nr 5, s. 635-645Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Aqueous environmental DNA (eDNA) is an emerging efficient non-invasive tool for species inventory studies. To maximize performance of downstream quantitative PCR (qPCR) and next-generation sequencing (NGS) applications, quality and quantity of the starting material is crucial, calling for optimized capture, storage and extraction techniques of eDNA. Previous comparative studies for eDNA capture/storage have tested precipitation and open' filters. However, practical enclosed' filters which reduce unnecessary handling have not been included. Here, we fill this gap by comparing a filter capsule (Sterivex-GP polyethersulfone, pore size 022m, hereafter called SX) with commonly used methods. Our experimental set-up, covering altogether 41 treatments combining capture by precipitation or filtration with different preservation techniques and storage times, sampled one single lake (and a fish-free control pond). We selected documented capture methods that have successfully targeted a wide range of fauna. The eDNA was extracted using an optimized protocol modified from the DNeasy((R)) Blood & Tissue kit (Qiagen). We measured total eDNA concentrations and Cq-values (cycles used for DNA quantification by qPCR) to target specific mtDNA cytochrome b (cyt b) sequences in two local keystone fish species. SX yielded higher amounts of total eDNA along with lower Cq-values than polycarbonate track-etched filters (PCTE), glass fibre filters (GF) or ethanol precipitation (EP). SX also generated lower Cq-values than cellulose nitrate filters (CN) for one of the target species. DNA integrity of SX samples did not decrease significantly after 2weeks of storage in contrast to GF and PCTE. Adding preservative before storage improved SX results. In conclusion, we recommend SX filters (originally designed for filtering micro-organisms) as an efficient capture method for sampling macrobial eDNA. Ethanol or Longmire's buffer preservation of SX immediately after filtration is recommended. Preserved SX capsules may be stored at room temperature for at least 2weeks without significant degradation. Reduced handling and less exposure to outside stress compared with other filters may contribute to better eDNA results. SX capsules are easily transported and enable eDNA sampling in remote and harsh field conditions as samples can be filtered/preserved on site.

  • 10. Szorkovszky, Alex
    et al.
    Kotrschal, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Read, James E. Herbert
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Sumpter, David J. T.
    Kolm, Niclas
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Pelckmans, Kristiaan
    An efficient method for sorting and quantifying individual social traits based on group-level behaviour2017Ingår i: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 8, nr 12, s. 1735-1744Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    1. In social contexts, animal behaviour is often studied in terms of group-level characteristics. One clear example of this is the collective motion of animals in decentralized structures, such as bird flocks and fish schools. A major goal of research is to identify how group-level behaviours are shaped by the traits of individuals within them. Few methods exist to make these connections. Individual assessment is often limited, forcing alternatives such as fitting agent-based models to experimental data. 2. We provide a systematic experimental method for sorting animals according to socially relevant traits, without assaying them or even tagging them individually. Instead, they are repeatedly subjected to behavioural assays in groups, between which the group memberships are rearranged, in order to test the effect of many different combinations of individuals on a group-level property or feature. We analyse this method using a general model for the group feature, and simulate a variety of specific cases to track how individuals are sorted in each case. 3. We find that in the case where the members of a group contribute equally to the group feature, the sorting procedure increases the between-group behavioural variation well above what is expected for groups randomly sampled from a population. For a wide class of group feature models, the individual phenotypes are efficiently sorted across the groups and thus become available for further analysis on how individual properties affect group behaviour. We also show that the experimental data can be used to estimate the individual-level repeatability of the underlying traits. 4. Our method allows experimenters to find repeatable variation in social behaviours that cannot be assessed in solitary individuals. Furthermore, experiments in animal behaviour often focus on comparisons between groups randomly sampled from a population. Increasing the behavioural variation between groups increases statistical power for testing whether a group feature is related to other properties of groups or to their phenotypic composition. Sorting according to socially relevant traits is also beneficial in artificial selection experiments, and for testing correlations with other traits. Overall, the method provides a useful tool to study how individual properties influence social behaviour.

  • 11. Talavera, Gerard
    et al.
    Dinca, Vlad
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Pompeu Fabra University, Spain.
    Vila, Roger
    Factors affecting species delimitations with the GMYC model: insights from a butterfly survey2013Ingår i: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 4, nr 12, s. 1101-1110Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The generalized mixed Yule-coalescent (GMYC) model has become one of the most popular approaches for species delimitation based on single-locus data, and it is widely used in biodiversity assessments and phylogenetic community ecology. We here examine an array of factors affecting GMYC resolution (tree reconstruction method, taxon sampling coverage/taxon richness and geographic sampling intensity/geographic scale). We test GMYC performance based on empirical data (DNA barcoding of the Romanian butterflies) on a solid taxonomic framework (i.e. all species are thought to be described and can be determined with independent sources of evidence). The data set is comprehensive (176 species), and intensely and homogeneously sampled (1303 samples representing the main populations of butterflies in this country). Taxonomy was assessed based on morphology, including linear and geometric morphometry when needed. The number of GMYC entities obtained constantly exceeds the total number of morphospecies in the data set. We show that c.80% of the species studied are recognized as entities by GMYC. Interestingly, we show that this percentage is practically the maximum that a single-threshold method can provide for this data set. Thus, the c.20% of failures are attributable to intrinsic properties of the COI polymorphism: overlap in inter- and intraspecific divergences and non-monophyly of the species likely because of introgression or lack of independent lineage sorting. Our results demonstrate that this method is remarkably stable under a wide array of circumstances, including most phylogenetic reconstruction methods, high singleton presence (up to 95%), taxon richness (above five species) and the presence of gaps in intraspecific sampling coverage (removal of intermediate haplotypes). Hence, the method is useful to designate an optimal divergence threshold in an objective manner and to pinpoint potential cryptic species that are worth being studied in detail. However, the existence of a substantial percentage of species wrongly delimited indicates that GMYC cannot be used as sufficient evidence for evaluating the specific status of particular cases without additional data. Finally, we provide a set of guidelines to maximize efficiency in GMYC analyses and discuss the range of studies that can take advantage of the method.

  • 12. Tang, Cuong Q.
    et al.
    Humphreys, Aelys M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Imperial College London, United Kingdom.
    Fontaneto, Diego
    Barraclough, Timothy G.
    Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data2014Ingår i: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 5, nr 10, s. 1086-1094Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses.

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