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Bokma, Folmer
Alternative names
Publications (10 of 35) Show all publications
Monroe, M. J., Butchart, S. H. M., Mooers, A. O. & Bokma, F. (2019). The dynamics underlying avian extinction trajectories forecast a wave of extinctions. Biology Letters, 15(12), Article ID 20190633.
Open this publication in new window or tab >>The dynamics underlying avian extinction trajectories forecast a wave of extinctions
2019 (English)In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 15, no 12, article id 20190633Article in journal (Refereed) Published
Abstract [en]

Population decline is a process, yet estimates of current extinction rates often consider just the final step of that process by counting numbers of species lost in historical times. This neglects the increased extinction risk that affects a large proportion of species, and consequently underestimates the effective extinction rate. Here, we model observed trajectories through IUCN Red List extinction risk categories for all bird species globally over 28 years, and estimate an overall effective extinction rate of 2.17 x 10(-4)/species/year. This is six times higher than the rate of outright extinction since 1500, as a consequence of the large number of species whose status is deteriorating. We very conservatively estimate that global conservation efforts have reduced the effective extinction rate by 40%, but mostly through preventing critically endangered species from going extinct rather than by preventing species at low risk from moving into higher-risk categories. Our findings suggest that extinction risk in birds is accumulating much more than previously appreciated, but would be even greater without conservation efforts.

Place, publisher, year, edition, pages
Royal Society Publishing, 2019
Keywords
biodiversity, birds, mass extinction, endangered species, conservation, population decline
National Category
Ecology Ecology
Identifiers
urn:nbn:se:umu:diva-166892 (URN)10.1098/rsbl.2019.0633 (DOI)000503237800003 ()31847745 (PubMedID)2-s2.0-85076835489 (Scopus ID)
Funder
Swedish Research Council, 637-2013-274
Available from: 2020-01-07 Created: 2020-01-07 Last updated: 2021-10-18Bibliographically approved
Olajos, F., Bokma, F., Bartels, P., Myrstener, E., Rydberg, J., Öhlund, G., . . . Englund, G. (2018). Estimating species colonization dates using DNA in lake sediment. Methods in Ecology and Evolution, 9(3), 535-543
Open this publication in new window or tab >>Estimating species colonization dates using DNA in lake sediment
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2018 (English)In: Methods in Ecology and Evolution, E-ISSN 2041-210X, Vol. 9, no 3, p. 535-543Article in journal (Refereed) Published
Abstract [en]
  1. Detection of DNA in lake sediments holds promise as a tool to study processes like extinction, colonization, adaptation and evolutionary divergence. However, low concentrations make sediment DNA difficult to detect, leading to high false negative rates. Additionally, contamination could potentially lead to high false positive rates. Careful laboratory procedures can reduce false positive and negative rates, but should not be assumed to completely eliminate them. Therefore, methods are needed that identify potential false positive and negative results, and use this information to judge the plausibility of different interpretations of DNA data from natural archives.
  2. We developed a Bayesian algorithm to infer the colonization history of a species using records of DNA from lake-sediment cores, explicitly labelling some observations as false positive or false negative. We illustrate the method by analysing DNA of whitefish (Coregonus lavaretus L.) from sediment cores covering the past 10,000 years from two central Swedish lakes. We provide the algorithm as an R-script, and the data from this study as example input files.
  3. In one lake, Stora Lögdasjön, where connectivity with the proto-Baltic Sea and the degree of whitefish ecotype differentiation suggested colonization immediately after deglaciation, DNA was indeed successfully recovered and amplified throughout the post-glacial sediment. For this lake, we found no loss of detection probability over time, but a high false negative rate. In the other lake, Hotagen, where connectivity and ecotype differentiation suggested colonization long after deglaciation, DNA was amplified only in the upper part of the sediment, and colonization was estimated at 2,200 bp based on the assumption that successful amplicons represent whitefish presence. Here the earliest amplification represents a false positive with a posterior probability of 41%, which increases the uncertainty in the estimated time of colonization.
  4. Complementing careful laboratory procedures aimed at preventing contamination, our method estimates contamination rates from the data. By combining these results with estimates of false negative rates, our models facilitate unbiased interpretation of data from natural DNA archives.
Place, publisher, year, edition, pages
British Ecological Society, 2018
Keywords
ancient DNA, colonization, Coregonus lavaretus, detection probability, divergence, environmental DNA, lake sediment, population age
National Category
Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-143248 (URN)10.1111/2041-210X.12890 (DOI)000426867600010 ()2-s2.0-85030156606 (Scopus ID)
Funder
Swedish Research Council, 2013-5110
Available from: 2017-12-19 Created: 2017-12-19 Last updated: 2024-01-17Bibliographically approved
Hedström, P., Bystedt, D., Karlsson, J., Bokma, F. & Byström, P. (2017). Brownification increases winter mortality in fish. Oecologia, 183(2), 587-595
Open this publication in new window or tab >>Brownification increases winter mortality in fish
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2017 (English)In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 183, no 2, p. 587-595Article in journal (Refereed) Published
Abstract [en]

In northernclimateswinter is a bottleneck for many organisms. Low light and resource availability constrain individual foraging rates,potentially leading tostarvation and increasedmortality.Increasinginput of humic substances to aquatic ecosystems causesbrownification of water and hence a further decreaseof light availability,which may lead tofurther decreased foraging ratesand starvation mortality during winter.To test this hypothesis, we measured the effectsof experimentally increased humicwaterinput on consumption and survival of young-of-the-year (YOY) three-spined stickleback (Gasterosteus aculeatus) over winterin largeoutdoor enclosures. Population densitieswereestimated in autumn andthefollowing springand food availabilityand consumptionwere monitoredoverwinter. As hypothesized,mortality washigher underhumic(76%)as compared to ambientconditions (64%).Also, body condition and ingested prey biomass werelower under humic conditionseven thoughresource availability wasnotlower under humic conditions. Light conditions were significantly poorer under humic conditions. This suggeststhat increased mortality and decreased body condition and ingested prey biomasswasnot due to decreased resource availability but due todecreasedsearch efficiencyin this visual feeding consumer. Increased future brownification of aquatic systems may therefore negatively affect both recruitment and densities of fish.

Keywords
Brownification, winter mortality, light limitation, feeding efficiency, metabolism
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-127940 (URN)10.1007/s00442-016-3779-y (DOI)000394254500023 ()2-s2.0-85001099564 (Scopus ID)
Funder
The Kempe FoundationsSwedish Research Council for Environment, Agricultural Sciences and Spatial Planning, 621-2011-3908Ecosystem dynamics in the Baltic Sea in a changing climate perspective - ECOCHANGE
Note

Originally published in manuscript form.

Available from: 2016-11-21 Created: 2016-11-21 Last updated: 2023-03-24Bibliographically approved
Monroe, M. J. & Bokma, F. (2017). Does density-dependent diversification mirror ecological competitive exclusion?. PLOS ONE, 12(10), Article ID e0184814.
Open this publication in new window or tab >>Does density-dependent diversification mirror ecological competitive exclusion?
2017 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 12, no 10, article id e0184814Article in journal (Refereed) Published
Abstract [en]

Density-dependence is a term used in ecology to describe processes such as birth and death rates that are regulated by the number of individuals in a population. Evolutionary biologists have borrowed the term to describe decreasing rates of species accumulation, suggesting that speciation and extinction rates depend on the total number of species in a clade. If this analogy with ecological density-dependence holds, diversification of clades is restricted because species compete for limited resources. We hypothesize that such competition should not only affect numbers of species, but also prevent species from being phenotypically similar. Here, we present a method to detect whether competitive interactions between species have ordered phenotypic traits on a phylogeny, assuming that competition prevents related species from having identical trait values. We use the method to analyze clades of birds and mammals, with body size as the phenotypic trait. We find no sign that competition has prevented species from having the same body size. Thus, since body size is a key ecological trait and competition does not seem to be responsible for differences in body size between species, we conclude that the diversification slowdown that is prevalent in these clades is unlikely due to the ecological interference implied by the term density dependence.

Place, publisher, year, edition, pages
Public Library Science, 2017
National Category
Evolutionary Biology Ecology
Identifiers
urn:nbn:se:umu:diva-141482 (URN)10.1371/journal.pone.0184814 (DOI)000412845100009 ()2-s2.0-85031106326 (Scopus ID)
Funder
Swedish Research Council, 90382001Swedish Research Council, 637-2013-274Swedish Research Council Formas, 215-2012-1372
Available from: 2017-11-20 Created: 2017-11-20 Last updated: 2023-03-24Bibliographically approved
Bokma, F., Godinot, M., Maridet, O., Ladeveze, S., Costeur, L., Sole, F., . . . Laurin, M. (2016). Testing for Deperet's Rule (Body Size Increase) in Mammals using Combined Extinct and Extant Data. Systematic Biology, 65(1), 98-108
Open this publication in new window or tab >>Testing for Deperet's Rule (Body Size Increase) in Mammals using Combined Extinct and Extant Data
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2016 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 98-108Article in journal (Refereed) Published
Abstract [en]

Whether or not evolutionary lineages in general show a tendency to increase in body size has often been discussed. This tendency has been dubbed "Cope's rule" but because Cope never hypothesized it, we suggest renaming it after Deperet, who formulated it clearly in 1907. Deperet's rule has traditionally been studied using fossil data, but more recently a number of studies have used present-day species. While several paleontological studies of Cenozoic placental mammals have found support for increasing body size, most studies of extant placentals have failed to detect such a trend. Here, we present a method to combine information from present-day species with fossil data in a Bayesian phylogenetic framework. We apply the method to body mass estimates of a large number of extant and extinct mammal species, and find strong support for Deperet's rule. The tendency for size increase appears to be driven not by evolution toward larger size in established species, but by processes related to the emergence of new species. Our analysis shows that complementary data from extant and extinct species can greatly improve inference of macroevolutionary processes.

Keywords
Body size, Cope's rule, macroevolution, paleontology, phylogenetics
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-117854 (URN)10.1093/sysbio/syv075 (DOI)000369955500007 ()26508768 (PubMedID)2-s2.0-84960464659 (Scopus ID)
Funder
Swedish Research Council Formas, 215-2012-1372
Available from: 2016-03-16 Created: 2016-03-04 Last updated: 2023-03-23Bibliographically approved
Bokma, F. (2015). Evolution as a Largely Autonomous Process. In: Emanuele Serrelli och Nathalie Gontier (Ed.), Macroevolution: Explanation, Interpretation and Evidence (pp. 87-112). Cham: Springer
Open this publication in new window or tab >>Evolution as a Largely Autonomous Process
2015 (English)In: Macroevolution: Explanation, Interpretation and Evidence / [ed] Emanuele Serrelli och Nathalie Gontier, Cham: Springer, 2015, p. 87-112Chapter in book (Refereed)
Abstract [en]

Evolutionary theory has proven generally successful in predicting phenotypic changes over one or a few generations of natural or artificial selection, but fails to predict evolutionary dynamics over longer periods of time, which is a major shortcoming: At longer timescales, existing theory is largely concerned with a posteriori explanations and cannot even predict whether a population or species will adapt to environmental change, or go extinct. Based on a review of key literature from before Darwin to today, I argue that the reason for this shortcoming is that in the Modern Synthesis fitness is regarded as determined exclusively by how well traits are suited to the biotic and abiotic environment. I argue that much can be gained by explicitly considering that fitness has a significant intrinsic component, determined by how well different traits are adapted to each other. Due to adaptation of traits to each other, those traits that are important for the functioning of many other traits can vary only within narrow tolerance limits. Short-term selection experiments and year-to-year fluctuations in natural populations taking place within these tolerance limits give the appearance of rapid evolution. Yet the tolerance limits will prevent changes to accumulate over time, and hence, these traits evolve in a million years no more than they do in a decade. Only traits like coloration that have little influence on other traits can evolve freely, but that will rarely be sufficient to prevent extinction. Significant evolutionary departures require a reshuffling of the interactions between traits and will often coincide with speciation. Emerging from a complex system of interacting traits, the magnitude and direction of these changes will be largely independent of the factors that triggered them, rendering macroevolution a largely autonomous process.

Place, publisher, year, edition, pages
Cham: Springer, 2015
Series
Interdisciplinary Evolution Research, ISSN 2199-3068 ; 2
Keywords
Extinction, Macroevolution, Microevolution, Natural selection, Speciation
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-112476 (URN)10.1007/978-3-319-15045-1_3 (DOI)978-3-319-15044-4 (ISBN)978-3-319-15045-1 (ISBN)
Available from: 2015-12-08 Created: 2015-12-08 Last updated: 2018-06-07Bibliographically approved
Bokma, F., Baek, S. K. & Minnhagen, P. (2014). 50 years of inordinate fondness. Systematic Biology, 63(2), 251-256
Open this publication in new window or tab >>50 years of inordinate fondness
2014 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, no 2, p. 251-256Article in journal (Refereed) Published
Place, publisher, year, edition, pages
Oxford University Press, 2014
Keywords
Taxa, species, distributions, maximum entropy, random group formation
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-81886 (URN)10.1093/sysbio/syt067 (DOI)000332044900010 ()2-s2.0-84894573926 (Scopus ID)
Available from: 2013-10-22 Created: 2013-10-22 Last updated: 2023-03-24Bibliographically approved
Stadler, T., Rabosky, D. L., Ricklefs, R. E. & Bokma, F. (2014). On age and species richness of higher taxa. American Naturalist, 184(4), 447-455
Open this publication in new window or tab >>On age and species richness of higher taxa
2014 (English)In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 184, no 4, p. 447-455Article in journal (Refereed) Published
Abstract [en]

Many studies have tried to identify factors that explain differences in numbers of species between clades against the background assumption that older clades contain more species because they have had more time for diversity to accumulate. The finding in several recent studies that species richness of clades is decoupled from stem age has been interpreted as evidence for ecological limits to species richness. Here we demonstrate that the absence of a positive age-diversity relationship, or even a negative relationship, may also occur when taxa are defined based on time or some correlate of time such as genetic distance or perhaps morphological distinctness. Thus, inferring underlying processes from distributions of species across higher taxa requires caution concerning the way in which higher taxa are defined. When this definition is unclear, crown age is superior to stem age as a measure of clade age.

Place, publisher, year, edition, pages
University of Chicago Press, 2014
Keywords
birth-death process, diversification, macroevolution, phylogenetics, speciation
National Category
Ecology Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-95261 (URN)10.1086/677676 (DOI)000342281100005 ()25226180 (PubMedID)2-s2.0-84907144273 (Scopus ID)
Available from: 2014-11-04 Created: 2014-10-27 Last updated: 2023-03-24Bibliographically approved
Hortal, J., Nabout, J. C., Calatayud, J., Carneiro, F. M., Padial, A., Santos, A. M. C., . . . Ventura, M. (2014). Perspectives on the use of lakes and ponds as model systems for macroecological research. Journal of limnology, 73(Suppl. 1), 46-60
Open this publication in new window or tab >>Perspectives on the use of lakes and ponds as model systems for macroecological research
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2014 (English)In: Journal of limnology, ISSN 1129-5767, E-ISSN 1723-8633, Vol. 73, no Suppl. 1, p. 46-60Article in journal (Refereed) Published
Abstract [en]

Macroecology studies large-scale patterns aiming to identify the effects of general ecological processes. Although lakes (and ponds) are particularly suited for macroecological research due to their discrete nature and non geographically-structured variability, the development of this discipline in lentic habitats is comparatively much smaller than for terrestrial environments. This is despite the interest of limnologists for large-scale phenomena, which results in the high level of development of some disciplines such as predictive limnology. Here we discuss how current state-of-the-art in macroecology may benefit from research in lentic habitats at five topics. First, by including an island biogeography analytical framework to incorporate the effects of lake origin and history on lentic biodiversity. Second, by studying local and regional effects on the latitudinal gradients of species richness. Third, by considering lakes and ponds altogether for the study of beta diversity and metacommunity structure, which is already common ground in limnological research. Fourth, by relating species traits with ecosystem structure and functioning; here we consider in particular the potential effects of body size-determined dispersal and competitive exclusion processes on lake-wide trophic organization. And fifth, by incorporating current research in functional (i.e., trait) and phylogenetic diversity to the study of community structure. We finally conclude that lentic habitats can be particularly important for the development of the most functional aspects of macroecology, due to the relative ease of studying the different biotic and abiotic components of the system separately, compared to most terrestrial systems. This can allow teasing apart many of the confounding factors that are characteristic of macroecological research, thus helping the development of future theoretical syntheses.

Place, publisher, year, edition, pages
Pagepress, 2014
Keywords
biodiversity gradients, body size, dispersal, ecosystem functioning, ecosystem structure, metacommunity
National Category
Biological Sciences
Research subject
Limnology
Identifiers
urn:nbn:se:umu:diva-91871 (URN)10.4081/jlimnol.2014.887 (DOI)000338929200005 ()2-s2.0-84904252524 (Scopus ID)
Available from: 2014-08-18 Created: 2014-08-18 Last updated: 2023-03-24Bibliographically approved
Bokma, F. (2014). Why do species go extinct?. In: Roger Jacobsson (Ed.), Thule: Kungl. Skytteanska samfundets årsbok 2014 (pp. 61-74). Umeå: Kungl. Skytteanska samfundet
Open this publication in new window or tab >>Why do species go extinct?
2014 (English)In: Thule: Kungl. Skytteanska samfundets årsbok 2014 / [ed] Roger Jacobsson, Umeå: Kungl. Skytteanska samfundet , 2014, p. 61-74Chapter in book (Other academic)
Place, publisher, year, edition, pages
Umeå: Kungl. Skytteanska samfundet, 2014
Series
Thule, ISSN 0280-8692 ; Årg. 27
National Category
Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-112473 (URN)9789186438470 (ISBN)
Available from: 2015-12-08 Created: 2015-12-08 Last updated: 2018-06-07Bibliographically approved
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