| 1. |
- Bokma, Folmer, et al.
(författare)
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50 years of inordinate fondness
- 2014
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Ingår i: Systematic Biology. - : Oxford University Press. - 1063-5157 .- 1076-836X. ; 63:2, s. 251-256
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Tidskriftsartikel (refereegranskat)
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| 2. |
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| 3. |
- Bokma, Folmer
(författare)
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Detection of "punctuated equilibrium" by Bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny
- 2008
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 62:11, s. 2718-26
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Tidskriftsartikel (refereegranskat)abstract
- Speciation and extinction probabilities can be estimated from molecular phylogenies of extant species that are complete at the species level. Because only a fraction of published phylogenies is complete at the species level, methods have been developed to estimate speciation and extinction probabilities also from incomplete phylogenies. However, due to different estimation techniques, estimates from complete and incomplete phylogenies are difficult to compare statistically. Here I show with some examples how existing likelihood functions can be used to obtain Bayesian estimates of speciation and extinction probabilities, and how this approach is applied to both complete and incomplete phylogenies.
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| 4. |
- Bokma, Folmer
(författare)
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Evolution as a Largely Autonomous Process
- 2015
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Ingår i: Macroevolution. - Cham : Springer. - 9783319150444 - 9783319150451 ; , s. 87-112
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Bokkapitel (refereegranskat)abstract
- 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.
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| 5. |
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| 6. |
- Bokma, Folmer
(författare)
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Speciation and Patterns of Diversity
- 2010
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Ingår i: Systematic Biology. - : Oxford University Press. - 1063-5157 .- 1076-836X. ; 59:3, s. 365-367
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Recension (refereegranskat)
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| 7. |
- Bokma, Folmer, et al.
(författare)
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Testing for Deperet's Rule (Body Size Increase) in Mammals using Combined Extinct and Extant Data
- 2016
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 65:1, s. 98-108
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 8. |
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| 9. |
- Bokma, Folmer, et al.
(författare)
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Unexpectedly many extinct hominins
- 2012
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Ingår i: Evolution. - Hoboken, NJ : Wiley-Blackwell. - 0014-3820 .- 1558-5646. ; 66:9, s. 2969-2974
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies indicate that Neanderthal and Denisova hominins may have been separate species, while debate continues on the status of Homo floresiensis. The decade-long debate between splitters, who recognize over 20 hominin species, and lumpers, who maintain that all these fossils belong to just a few lineages, illustrates that we do not know how many extinct hominin species to expect. Here, we present probability distributions for the number of speciation events and the number of contemporary species along a branch of a phylogeny. With estimates of hominin speciation and extincton rates, we then show that the expected total number of extinct hominin species is 8, but may be as high as 27. We also show that it is highly unlikely that three very recent species disappeared due to natural, background extinction. This may indicate that human-like remains are too easily considered distinct species. Otherwise, the evidence suggesting that Neanderthal and the Denisova hominin represent distinct species implies a recent wave of extinctions, ostensibly driven by the only survivor, H. sapiens.
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| 10. |
- Bokma, Folmer
(författare)
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Why do species go extinct?
- 2014
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Ingår i: Thule. - Umeå : Kungl. Skytteanska samfundet. - 9789186438470 ; , s. 61-74
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 11. |
- Hedström, Per, 1974-, et al.
(författare)
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Brownification increases winter mortality in fish
- 2017
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Ingår i: Oecologia. - : Springer Science and Business Media LLC. - 0029-8549 .- 1432-1939. ; 183:2, s. 587-595
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 12. |
- Hortal, Joaquin, et al.
(författare)
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Perspectives on the use of lakes and ponds as model systems for macroecological research
- 2014
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Ingår i: Journal of limnology. - : Pagepress. - 1129-5767 .- 1723-8633. ; 73:Suppl. 1, s. 46-60
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 13. |
- Johansson, Frank, et al.
(författare)
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Evolution of the G-matrix in life history traits in the common frog during a recent colonisation of an island system
- 2012
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Ingår i: Evolutionary Ecology. - : Springer Science and Business Media LLC. - 0269-7653 .- 1573-8477. ; 26:4, s. 863-878
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Tidskriftsartikel (refereegranskat)abstract
- Studies of genetic correlations between traits that ostensibly channel the path of evolution away from the direction of natural selection require information on key aspects such as ancestral phenotypes, the duration of adaptive evolution, the direction of natural selection, and genetic covariances. In this study we provide such information in a frog population system. We studied adaptation in life history traits to pool drying in frog populations on islands of known age, which have been colonized from a mainland population. The island populations show strong local adaptation in development time and size. We found that the first eigenvector of the variance-covariance matrix (g (max)) had changed between ancestral mainland populations and newly established island populations. Interestingly, there was no divergence in g (max) among island populations that differed in their local adaptation in development time and size. Thus, a major change in the genetic covariance of life-history traits occurred in the colonization of the island system, but subsequent local adaptation in development time took place despite the constraints imposed by the genetic covariance structure.
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| 14. |
- Johansson, Frank, et al.
(författare)
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Insect wing shape evolution: independent effects of migratory and mate guarding flight on dragonfly
- 2009
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Ingår i: Biological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4066 .- 1095-8312. ; 97, s. 362-372
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Tidskriftsartikel (refereegranskat)abstract
- Although, in some insect taxa, wing shape is remarkably invariant, the wings of Anisopteran dragonflies show considerable variation among genera. Because wing shape largely determines the high energetic costs of flight, it may be expected that interspecific differences are partly due to selection. In the present study, we examined the roles of long-distance migration and high-manoeuvrability mate guarding in shaping dragonfly wings, using a phylogeny-based comparative method, and geometric morphometrics to quantify wing shape. The results obtained show that migration affects the shape of both front and hind wings, and suggest that mate guarding behaviour may also have an effect, especially on the front wing. These effects on front wing shape are at least partly independent. Our findings are interesting when compared with the geographically widespread and ecologically diverse dipterans Acalyptratae (including the genus Drosophila). The wings in that group are similar in function and structure, but show strikingly low levels of interspecific variation.
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| 15. |
- Leppälä, Johanna, et al.
(författare)
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Investigating incipient speciation in Arabidopsis lyrata from patterns of transmission ratio distortion
- 2013
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 194:3, s. 697-708
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Tidskriftsartikel (refereegranskat)abstract
- Our understanding of the development of intrinsic reproductive isolation is still largely based on theoretical models and thorough empirical studies on a small number of species. Theory suggests that reproductive isolation develops through accumulation of epistatic genic incompatibilities, also known as Bateson-Dobzhansky-Muller (BDM) incompatibilities. We can detect these from marker transmission ratio distortion (TRD) in hybrid progenies of crosses between species or populations, where TRD is expected to result from selection against heterospecific allele combinations in hybrids. TRD may also manifest itself because of intragenomic conflicts or competition between gametes or zygotes. We studied early stage speciation in Arabidopsis lyrata by investigating patterns of TRD across the genome in F-2 progenies of three reciprocal crosses between four natural populations. We found that the degree of TRD increases with genetic distance between crossed populations, but also that reciprocal progenies may differ substantially in their degree of TRD. Chromosomes AL6 and especially AL1 appear to be involved in many single- and two-locus distortions, but the location and source of TRD vary between crosses and between reciprocal progenies. We also found that the majority of single- and two-locus TRD appears to have a gametic, as opposed to zygotic, origin. Thus, while theory on BDM incompatibilities is typically illustrated with derived nuclear alleles proving incompatible in hybrid zygotes, our results suggest a prominent role for distortions emerging before zygote formation.
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| 16. |
- Mattila, Tiina M, et al.
(författare)
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Extant mammal body masses suggest punctuated equilibrium.
- 2008
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Ingår i: Proc Biol Sci. - : The Royal Society. - 0962-8452. ; 275:1648, s. 2195-9
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Tidskriftsartikel (refereegranskat)abstract
- Is gradual microevolutionary change within species simultaneously the source of macroevolutionary differentiation between species? Since its first publication, Darwin's original idea that phenotypic differences between species develop gradually over time, as the accumulation of small selection-induced changes in successive generations has been challenged by palaeontologists claiming that, instead, new species quickly acquire their phenotypes to remain virtually unchanged until going extinct again. This controversy, widely known as the 'punctuated equilibrium' debate, remained unresolved, largely owing to the difficulty of distinguishing biological species from fossil remains. We analysed body masses of 2143 existing mammal species on a phylogeny comprising 4510 (i.e. nearly all) extant species to estimate rates of gradual (anagenetic) and speciational (cladogenetic) evolution. Our Bayesian estimates from mammals as well as separate sub-clades such as primates and carnivores suggest that gradual evolution is responsible for only a small part of body size variation between mammal species.
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| 17. |
- Mobley, Kenyon B., et al.
(författare)
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Morphological and genetic divergence in Swedish postglacial stickleback (Pungitius pungitius) populations
- 2011
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Ingår i: BMC Evolutionary Biology. - London : BioMed Central. - 1471-2148. ; 11, s. 287-
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Tidskriftsartikel (refereegranskat)abstract
- Background: An important objective of evolutionary biology is to understand the processes that govern phenotypic variation in natural populations. We assessed patterns of morphological and genetic divergence among coastal and inland lake populations of nine-spined stickleback in northern Sweden. Coastal populations are either from the Baltic coast (n = 5) or from nearby coastal lakes (n = 3) that became isolated from the Baltic Sea (< 100 years before present, ybp). Inland populations are from freshwater lakes that became isolated from the Baltic approximately 10,000 ybp; either single species lakes without predators (n = 5), or lakes with a recent history of predation (n = 5) from stocking of salmonid predators (~50 ybp).Results: Coastal populations showed little variation in 11 morphological traits and had longer spines per unit of body length than inland populations. Inland populations were larger, on average, and showed greater morphological variation than coastal populations. A principal component analysis (PCA) across all populations revealed two major morphological axes related to spine length (PC1, 47.7% variation) and body size (PC2, 32.9% variation). Analysis of PCA scores showed marked similarity in coastal (Baltic coast and coastal lake) populations. PCA scores indicate that inland populations with predators have higher within-group variance in spine length and lower within-group variance in body size than inland populations without predators. Estimates of within-group PST (a proxy for QST) from PCA scores are similar to estimates of FST for coastal lake populations but PST > FST for Baltic coast populations. PST > FST for PC1 and PC2 for inland predator and inland no predator populations, with the exception that PST < FST for body size in inland populations lacking predators.Conclusions: Baltic coast and coastal lake populations show little morphological and genetic variation within and between groups suggesting that these populations experience similar ecological conditions and that time since isolation of coastal lakes has been insufficient to demonstrate divergent morphology in coastal lake populations. Inland populations, on the other hand, showed much greater morphological and genetic variation characteristic of long periods of isolation. Inland populations from lakes without predators generally have larger body size, and smaller spine length relative to body size, suggesting systematic reduction in spine length. In contrast, inland populations with predators exhibit a wider range of spine lengths relative to body size suggesting that this trait is responding to local predation pressure differently among these populations. Taken together the results suggest that predation plays a role in shaping morphological variation among isolated inland populations. However, we cannot rule out that a causal relationship between predation versus other genetic and environmental influences on phenotypic variation not measured in this study exists, and this warrants further investigation.
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| 18. |
- Mobley, Kenyon B., et al.
(författare)
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No evidence that stickleback spines directly increase risk of predation by an invertebrate predator
- 2013
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Ingår i: Evolutionary Ecology Research. - 1522-0613 .- 1937-3791. ; 15:2, s. 189-198
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Tidskriftsartikel (refereegranskat)abstract
- Background: Some populations of stickleback have a reduced number and/or relative size of spines. Hypothesis: Macroinvertebrate predators such as dragonfly larvae cause selective pressure against spines by capturing more stickleback with pelvic spines than stickleback that are spineless. Organisms: Ninespine stickleback (Pungitius pungitius) and dragonfly larvae (Aeshna grandis). Methods: We used 10 stickleback, five with pelvic spines and five with their pelvic spines removed. We put them in containers with two dragonfly larvae. Every day for 4 days we monitored how many stickleback were captured by the larvae. We repeated this experiment ten times at two different densities of fish and predators. We also developed a model to determine whether selection for spinelessness can be distinguished from drift. Results: Dragonfly larvae caught as many stickleback with spines as without. The absence of spines was not associated with a decrease in predation risk. We substituted Bayesian estimates of the selection coefficient into quantitative genetic models of allele frequency change, and the results of the models suggest that the selective advantage of spine loss is so small that its effects cannot be distinguished from drift.
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| 19. |
- Monroe, Melanie J., 1982-, et al.
(författare)
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Do speciation rates drive rates of body size evolution in mammals?
- 2009
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Ingår i: American Naturalist. - : University of Chicago Press. - 0003-0147 .- 1537-5323. ; 174:6, s. 912-918
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Tidskriftsartikel (refereegranskat)abstract
- Recently, it has been shown with large data sets of extinct mammals that large‐bodied lineages experienced higher speciation and extinction rates; with extant mammals, it has been shown that body size evolution is accelerated during speciation. Therefore, it is interesting to investigate whether mammalian body size evolution is faster in large‐bodied lineages. Phylogenetic analysis assuming size‐independent speciation rates suggested that the rate of body size evolution increases with body size, whereas size differences in recent sister species (that are little affected by species turnover) appear to be independent of size. This supports the hypothesis that high rates of species turnover increase the rate at which interspecific differences accumulate in large‐bodied clades, whereas rates of evolution in single lineages are approximately size invariant. Similarly, these findings support the notion that mammalian body size evolution is indeed concentrated in speciation events.
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| 20. |
- Monroe, Melanie J., et al.
(författare)
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Does density-dependent diversification mirror ecological competitive exclusion?
- 2017
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Ingår i: PLOS ONE. - : Public Library Science. - 1932-6203. ; 12:10
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 21. |
- Monroe, Melanie J., 1982-, et al.
(författare)
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Little evidence for Cope’s rule from Bayesian phylogenetic analysis of extant mammals
- 2010
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Ingår i: Journal of Evolutionary Biology. - : Wiley. - 1010-061X .- 1420-9101. ; 23:9, s. 2017-2021
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Tidskriftsartikel (refereegranskat)abstract
- According to Cope’s rule, lineages tend to evolve towards larger body size, possibly because of selective advantages of being large. The status of Cope’s ‘rule’ remains controversial as it is supported in some but not all large-scale fossil studies. Here, we test for Cope’s rule by Bayesian analyses of average body masses of 3253 extant mammal species on a dated phylogenetic tree. The data favour a model that does not assume Cope’s rule. When Cope’s rule is assumed, the best estimate of its strength is an average ancestor-descendant increase in body size of only 0.4%, which sharply contrasts with the 9% bias estimated from fossil mammals. Thus, we find no evidence for Cope’s rule from extant mammals, in agreement with earlier analyses of existing species, which also did not find support for Cope’s rule.
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| 22. |
- Monroe, Melanie J., 1982-, et al.
(författare)
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Mass extinctions do not explain skew in interspecific body size distributions
- 2013
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Ingår i: Journal of Zoological Systematics and Evolutionary Research. - : Hindawi Limited. - 0947-5745 .- 1439-0469. ; 51:1, s. 13-18
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- In several higher animal taxa, such as mammals and birds, the distribution of species’ body sizes is heavily skewed towards small size. Previous studies have suggested that small-bodied organisms are less prone to extinction than large-bodied species. If small body size is favorable during mass extinction events, a post mass extinction excess of small-bodied species may proliferate and maintain skewed body size distributions afterwards. Here, we modeled mass extinctions, and found that even unrealistically strong body mass selection has little effect on the skew of interspecific body size distributions. Counter intuitively, selection against large body size may skew size distributions towards large body size. Subsequent evolutionary diversification rapidly erases the rather small effects mass extinctions may have on size distributions. Next, we tested whether skewed body size distributions in mammals and birds can be due to mass extinctions at the transition from Cretaceous to Paleogene, approximately 65 million years ago. Body size distributions of clades that originated during the Cretaceous are on average more skewed than their subclades that originated during the Paleogene, but the difference is only minor in mammals, and in birds it can be explained by a positive relationship between species richness and skewness that is also present in clades that originated after the transition. Hence, we cannot infer from extant species whether the K-Pg mass extinctions were size-selective, but they are not the reason why most extant bird and mammal species are small-bodied.
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| 23. |
- Monroe, Melanie J., 1982-, et al.
(författare)
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Punctuated equilibrium in a neontological context
- 2010
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Ingår i: Theory in biosciences. - : Springer. - 1431-7613 .- 1611-7530. ; 129:2-3, s. 103-111
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Tidskriftsartikel (refereegranskat)abstract
- The theory of punctuated equilibrium, which proposes that biological species evolve rapidly when they originate rather than gradually over time, has sparked intense debate between palaeontologists and evolutionary biologists about the mode of character evolution and the importance of natural selection. Difficulty in interpreting the fossil record prevented consensus, and it remains disputed as to what extent gradual change in established species is responsible for phenotypic differences between species. Against the historical background of the concept of evolution concentrated in speciation events, we review attempts to investigate tempo and mode of evolution using present-day species since the introduction of the theory of punctuated equilibrium in 1972. We discuss advantages, disadvantages, and prospects of using neontological data, methodological advances, and the findings of some recent studies.
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| 24. |
- Monroe, Melanie J., 1982-, et al.
(författare)
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The dynamics underlying avian extinction trajectories forecast a wave of extinctions
- 2019
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Ingår i: Biology Letters. - : Royal Society Publishing. - 1744-9561 .- 1744-957X. ; 15:12
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 25. |
- Monroe, Melanie, 1982-
(författare)
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The tempo and mode of evolution : a neontological reappraisal
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The theory of “punctuated equilibrium” suggests that species evolve rapidly during or immediately upon speciation, “punctuating” long periods of little or no morphological evolution. Here I confirm that body size differences within clades of birds and mammals are best explained using a model of punctuated evolution. This allows me to suggest that rates of speciation and extinction are responsible for why there are more small mammals than large, as large mammals likely speciate and go extinct at a higher rate than small mammals, and hence undergo cladogenetic change more often. Likewise, mammals appear to evolve at a higher rate than birds, because mammals, as a whole, speciate and go extinct at a higher rate than birds. Furthermore I show that mass extinctions and competition, i.e. forms of natural selection, do not seem to explain differences in body size between species on a macroevolutionary scale. Taken together, these findings not only contradict the idea that apparently different rates of evolution are due to differential selection intensities, and emphasize the importance of the speciation process in evolution, but raise the intriguing question as to what limits evolution in established species. Here I suggest that phenotypic traits, dependent on one another for development and/or function may constrain evolution by exerting stabilizing selection from within the organism, as opposed to external environmental selection, which has been the main focus of evolutionary studies thus far.
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| 26. |
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| 27. |
- Olajos, Fredrik, et al.
(författare)
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Estimating species colonization dates using DNA in lake sediment
- 2018
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Ingår i: Methods in Ecology and Evolution. - : British Ecological Society. - 2041-210X. ; 9:3, s. 535-543
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Tidskriftsartikel (refereegranskat)abstract
- 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.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.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.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.
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| 28. |
- Olajos, Fredrik, 1987-
(författare)
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Using environmental DNA to unravel aquatic ecosystem dynamics
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Human-induced climate change has led to unprecedented declines in Earth's biodiversity and significant habitat loss. Aquatic ecosystems areespecially at risk, facing pollution, overexploitation, and destruction. Consequently, monitoring biodiversity is critical. Traditional monitoring methods are often low in detection rates, time-consuming, invasive, and harmful to species, which hampers comprehensive biodiversity assessments. Environmental DNA (eDNA) offers a rapid alternative fortaxonomic identification, extracting genetic material from soil, sediments, or water without capturing living organisms, proving useful where traditional methods fall short. However, its integration into aquatic ecology is hampered by unresolved methodological issues.This thesis demonstrates how eDNA can help reconstruct fish colonization histories in lakes post-glacial retreat. I employed species-specific primers with digital droplet PCR and metagenomic shotgun sequencing on ancient DNA from Holocene lake sediments. My findings show the detectability of DNA from ancient fish populations. However, each method exhibited technical limitations that led to varying degrees offalse negatives and false positive results. Additionally, I examined how Northern pike (Esox Lucius) affects ecological speciation in Europeanwhitefish (Coregonus lavaretus), promoting a shift from insectivorous to piscivorous states, enhancing predator biodiversity and biomass. Dietan alyses of piscivorous birds through digital droplet PCR revealed that smaller whitefish support a larger, more diverse bird community. Finally, I compared two molecular techniques for quantifying bird diets from fecal DNA, finding that metabarcoding with a universal fish primer and digital droplet PCR yielded similar results. This research enhances ourunderstanding of the potential and limitations of molecular tools forspecies identification and aids the integration of eDNA into aquatic ecology.
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| 29. |
- Outomuro, David, et al.
(författare)
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Hind wing shape evolves faster than front wing shape in Calopteryx damselflies
- 2012
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Ingår i: Evolutionary biology. - : Springer Science and Business Media LLC. - 0071-3260 .- 1934-2845. ; 39:1, s. 116-125
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Tidskriftsartikel (refereegranskat)abstract
- Wing shape has been shown in a variety of species to be influenced by natural and sexual selection. In damselflies, front- and hind wings can beat independently, and functional differentiation may occur. Males of Calopteryx damselflies show species-specific nuptial flights that differ in colour signalling with the hind wings. Therefore, hind wing shape and colour may evolve in concert to improve colour display, independent of the front wings. We predicted that male hind wing shape evolves faster than front wing shape, due to sexual selection. Females do not engage in sexual displays, so we predicted that females do not show differences in divergence between front- and hind wing shape. We analysed the nonallometric component of wing shape of five European Calopteryx taxa using geometric morphometrics. We found a higher evolutionary divergence of hind wing shape in both sexes. Indeed, we found no significant differences in rate of evolution between the sexes, despite clear sexspecific differences in wing shape. We suggest that evolution of hind wing shape in males is accelerated by sexual selection on pre-copulatory displays and that this acceleration is reflected in females due to genetic correlations that somehow link the rates of wing shape evolution in the two sexes, but not the wing shapes themselves.
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| 30. |
- Savolainen, Outi, et al.
(författare)
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Adaptation of forest trees to climate change
- 2007
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Ingår i: Climate change and forest genetic diversity. - Rome : Bioversity International. - 9789290437499 ; , s. 19-30
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Konferensbidrag (refereegranskat)
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| 31. |
- Stadler, Tanja, et al.
(författare)
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Estimating Speciation and Extinction Rates for Phylogenies of Higher Taxa
- 2013
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Ingår i: Systematic Biology. - : Oxford University Press. - 1063-5157 .- 1076-836X. ; 62:2, s. 220-230
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Tidskriftsartikel (refereegranskat)abstract
- Speciation and extinction rates can be estimated from molecular phylogenies. Recently, a number of methods have been published showing that these rates can be estimated even if the phylogeny is incomplete, that is, if not all extant species are included. We show that the accuracy of such methods strongly depends on making the correct assumptions about how the sampling process was performed. We focus on phylogenies that are incomplete because some subclades (e.g., genera and families) are each represented as a single lineage. We show that previous methods implicitly assumed that such subclades are defined by randomly (or in an extreme deterministic way) choosing the edges that define the subclades from the complete species phylogeny. We show that these methods produce biased results if higher taxa are defined in a different manner. We introduce strict higher level phylogenies where subclades are defined so that the phylogeny is fully resolved from its origin to time x(cut), and fully unresolved thereafter, so that for all subclades, stem age > x(cut) > crown age. We present estimates of speciation and extinction rates from a phylogeny of birds in which this subclade definition was applied. However, for most higher level phylogenies in the literature, it is unclear how higher taxa were defined, but often such phylogenies can be easily transformed into strict higher level phylogenies, as we illustrate by estimating speciation and extinction rates from a near-complete but only partly resolved species-level phylogeny of mammals. The accuracy of our methods is verified using simulations.
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| 32. |
- Stadler, Tanja, et al.
(författare)
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On age and species richness of higher taxa
- 2014
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Ingår i: American Naturalist. - : University of Chicago Press. - 0003-0147 .- 1537-5323. ; 184:4, s. 447-455
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 33. |
- van den Brink, Valentijn, et al.
(författare)
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Estimating population differentiation between isolated root vole (Microtus oeconomus) populations in the Netherlands using geometric morphometrics
- 2011
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Ingår i: Lutra. - : Zoogdiervereniging. - 0024-7634. ; 54:2, s. 111-121
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- We investigated morphological differentiation in threatened populations of the root vole subspecies Microtus oeconomus arenicola, measured by using geometric morphometrics on skulls recovered from owl pellets. Using populations from Finland as a reference, we compared measures of morphological differentiation to levels of genetic differentiation reported in literature for the same populations. We found that the degree of morphometric population differentiation was generally lower than the degree of genetic differentiation, yet it revealed broadly similar patterns of geographic isolation. This suggests that skull shape is conserved in isolated root vole populations, and that geometric morphometric measurements from skeletal parts recovered from owl pellets may provide a cost-effective method to monitor population subdivision.
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| 34. |
- van den Brink, Valentijn, et al.
(författare)
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Morphometric shape analysis using learning vector quantization neural networks : an example distinguishing two microtine vole species
- 2011
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Ingår i: Annales Zoologici Fennici. - 0003-455X .- 1797-2450. ; 48:6, s. 359-364
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Tidskriftsartikel (refereegranskat)abstract
- Closely related species may be very difficult to distinguish morphologically, yet sometimes morphology is the only reasonable possibility for taxonomic classification. Here we present learning-vector-quantization artificial neural networks as a powerful tool to classify specimens on the basis of geometric morphometric shape measurements. As an example, we trained a neural network to distinguish between field and root voles from Procrustes transformed landmark coordinates on the dorsal side of the skull, which is so similar in these two species that the human eye cannot make this distinction. Properly trained neural networks misclassified only 3% of specimens. Therefore, we conclude that the capacity of learning vector quantization neural networks to analyse spatial coordinates is a powerful tool among the range of pattern recognition procedures that is available to employ the information content of geometric morphometrics.
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