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  • 1. Abrahamczyk, S.
    et al.
    Kessler, M.
    Hanley, D.
    Karger, D. N.
    Mueller, M. P. J.
    Knauer, A. C.
    Keller, F.
    Schwerdtfeger, M.
    Humphreys, Aelys M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Imperial College London, UK.
    Pollinator adaptation and the evolution of floral nectar sugar composition2017Ingår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 30, nr 1, s. 112-127Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A long-standing debate concerns whether nectar sugar composition evolves as an adaptation to pollinator dietary requirements or whether it is 'phylogenetically constrained'. Here, we use a modelling approach to evaluate the hypothesis that nectar sucrose proportion (NSP) is an adaptation to pollinators. We analyse similar to 2100 species of asterids, spanning several plant families and pollinator groups (PGs), and show that the hypothesis of adaptation cannot be rejected: NSP evolves towards two optimal values, high NSP for specialist-pollinated and low NSP for generalist-pollinated plants. However, the inferred adaptive process is weak, suggesting that adaptation to PG only provides a partial explanation for how nectar evolves. Additional factors are therefore needed to fully explain nectar evolution, and we suggest that future studies might incorporate floral shape and size and the abiotic environment into the analytical framework. Further, we show that NSP and PG evolution are correlated - in a manner dictated by pollinator behaviour. This contrasts with the view that a plant necessarily has to adapt its nectar composition to ensure pollination but rather suggests that pollinators adapt their foraging behaviour or dietary requirements to the nectar sugar composition presented by the plants. Finally, we document unexpectedly sucrose-poor nectar in some specialized nectarivorous bird-pollinated plants from the Old World, which might represent an overlooked form of pollinator deception. Thus, our broad study provides several new insights into how nectar evolves and we conclude by discussing why maintaining the conceptual dichotomy between adaptation and constraint might be unhelpful for advancing this field.

  • 2. Barraclough, Timothy G.
    et al.
    Humphreys, Aelys M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Imperial College London, UK.
    The evolutionary reality of species and higher taxa in plants: a survey of post-modern opinion and evidence2015Ingår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 207, nr 2, s. 291-296Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Species are normally considered to be the fundamental unit for understanding the evolution of biodiversity. Yet, in a survey of botanists in 1940, twice as many felt that plant genera were more natural units than plant species. Revisiting the survey, we found more people now regarded species as a more evolutionarily real unit, but a sizeable number still felt that genera were more evolutionarily real than species. Definitions of evolutionarily real' split into those based on shared evolutionary history and those based on shared evolutionary fate via ongoing evolutionary processes. We discuss recent work testing for shared evolutionary fate at the species and higher levels and present preliminary evidence for evolutionarily significant higher taxa in plants.

  • 3.
    Bolinder, Kristina
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Humphreys, Aelys M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Royal Botanic Gardens, UK.
    Ehrlén, Johan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Alexandersson, Ronny
    Ickert-Bond, Stefanie M.
    Rydin, Catarina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    From near extinction to diversification by means of ashift in pollination mechanism in the gymnosperm relict Ephedra (Ephedraceae, Gnetales)2016Ingår i: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 180, nr 4, s. 461-477Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Pollination in gymnosperms is usually accomplished by means of wind, but some groups are insect-pollinated. We show that wind and insect pollination occur in the morphologically uniform genus Ephedra (Gnetales). Based on field experiments over several years, we demonstrate distinct differences between two Ephedra species that grow in sympatry in Greece in pollen dispersal and clump formation, insect visitations and embryo formation when insects are denied access to cones. Ephedra distachya, nested in the core clade of Ephedra, is anemophilous, which is probably the prevailing state in Ephedra. Ephedra foeminea, sister to the remaining species of the genus, is entomophilous and pollinated by a range of diurnal and nocturnal insects. The generalist entomophilous system of E.foeminea, with distinct but infrequent insect visitations, is in many respects similar to that reported for Gnetum and Welwitschia and appears ancestral in Gnetales. The Ephedra lineage is well documented already from the Early Cretaceous, but the diversity declined dramatically during the Late Cretaceous, possibly to near extinction around the Cretaceous-Palaeogene boundary. The clade imbalance between insect- and wind-pollinated lineages is larger than expected by chance and the shift in pollination mode may explain why Ephedra escaped extinction and began to diversify again.

  • 4.
    Bolinder, Kristina
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Norbäck Ivarsson, Lena
    Humphreys, Aelys M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Imperial College London, UK.
    Ickert-Bond, Stefanie M.
    Han, Fang
    Hoorn, Carina
    Rydin, Catarina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Pollen morphology of Ephedra (Gnetales) and its evolutionary implications2016Ingår i: Grana, ISSN 0017-3134, E-ISSN 1651-2049, Vol. 55, nr 1, s. 24-51Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Ephedra lineage can be traced at least to the Early Cretaceous. Its characteristically polyplicate pollen is well-represented in the fossil record and is frequently used as an indicator of paleoclimate. However, despite previous efforts, knowledge about variation and evolution of ephedroid pollen traits is poor. Here, we document pollen morphology of nearly all extant species of Ephedra, using a combination of scanning electron microscopy (SEM) and light microscopy (LM), and reconstruct ancestral states of key pollen traits. Our results indicate that the ancestral Ephedra pollen type has numerous plicae interspaced by unbranched pseudosulci, while the derived pollen type has branched pseudosulci and (generally) fewer plicae. The derived type is inferred to have evolved independently twice, once along the North American stem branch and once along the Asian stem branch. Pollen of the ancestral type is common in Mesozoic fossil records, especially from the Early Cretaceous, but it is less commonly reported from the Cenozoic. The earliest documentation of the derived pollen type is from the latest Cretaceous, after which it increases strongly in abundance during the Paleogene. The results of the present study have implications for the age of crown group Ephedra as well as for understanding evolution of pollination syndromes in the genus.

  • 5. Garwood, Nancy C.
    et al.
    Jordan, Kristina
    Flowers, Nicholas D.
    Humphreys, Aelys M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Russell, Stephen J.
    Neubig, Kurt M.
    Trema domingensis rises like a phoenix from the ashes of Trema integerrima: A reassessment of the entire-leaved species of Neotropical Trema (Cannabaceae)2018Ingår i: Journal of the Botanical Research Institute of Texas, ISSN 1934-5259, Vol. 12, nr 2, s. 555-577Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We resolve three problems concerning the three entire-leaved species of Neotropical Trema. 1) Phylogenetic and morphological results showed that T. integerrima (Beurl.) Standl., T. domingensis Urb., and T. laxiflora Lundell are a single species; therefore, we combine them under a single name. 2) The date of publication gives priority to T. integerrima, as the basionym Sponia integerrima Beurl. was published in 1856. However, the type specimen, Billberg 308 (S), is not a species of Trema but Pouzolzia obliqua (Wedd.) Wedd. (Urticaceae); therefore, Sponia integerrima Beurl. is a new synonym of P. obliqua. The next available name for the entire-leaved species is T. domingensis, published in1912. 3) The type of T. domingensis, Fuertes 312, is a mixed collection. Specimens of Fuertes 312 held at B, NY, U, and USD are T. domingensis, while those at P, G, US, and Z are Celtis trinervia Lam. We provide a historical review to understand how these problems arose and persisted unnoticed for decades.

  • 6.
    Hou, Chen
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Humphreys, Aelys M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Imperial College London, England.
    Thureborn, Olle
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Rydin, Catarina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    New insights into the evolutionary history of Gnetum (Gnetales)2015Ingår i: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 64, nr 2, s. 239-253Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Gnetum (Gnetales: Gnetaceae) constitutes an evolutionarily isolated gymnosperm clade, comprising about 40 species that inhabit tropical areas of the world. While its closest living relative, the monotypic Welwitschia, has a well-documented fossil record from the Early Cretaceous, Gnetum-like fossils are rare and poorly understood. The phylogeny of Gnetum has been studied previously but the distant relationship to outgroups and the difficulty of obtaining plant material mean it is not yet fully resolved. Most species are tropical lianas with an angiospermous vegetative habit that are difficult to find and identify. Here a new phylogeny is presented based on nuclear and chloroplast data from 58 Gnetum accessions, representing 27 putative species, and outgroup information from other seed plants. The results provide support for South American species being sister to the remaining species. The two African species constitute a monophyletic group, sister to an Asian clade, within which the two arborescent species of the genus are the earliest diverging. Estimated divergence times indicate, in contrast with previous results, that the major lineages of Gnetum diverged in the Late Cretaceous. This result is obtained regardless of tree prior used in the BEAST analyses (Yule or birth-death). Together these findings suggest a correlation between early divergence events in extant Gnetum and the breakup of Gondwana in the Cretaceous. Compared to the old stem ages of major subclades of Gnetum, crown nodes date to the Cenozoic: the Asian crown group dates to the Cretaceous-Paleogene (K-Pg) boundary, the African crown group to the mid-Paleogene, and the South American crown group to the Paleogene-Neogene boundary. Although dispersal must have contributed to the current distribution of Gnetum, e.g., within South America and from Southeast Asian islands to the East Asian mainland, dispersal has apparently not occurred across major oceans, at least not during the Cenozoic.

  • 7.
    Humphreys, Aelys M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Imperial College London, England.
    Barraclough, Timothy G.
    The evolutionary reality of higher taxa in mammals2014Ingår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 281, nr 1783Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Species are generally regarded as a fundamental unit of biodiversity. By contrast, higher taxa such as genera and families, while widely used as biodiversity metrics and for classification and communication, are generally not believed to be shaped by shared evolutionary processes in the same way as species. We use simulations to show that processes which are important for emergence of evolutionarily significant units (ESUs) at the species level, namely geographical isolation and ecological divergence, can generate evolutionary independence above the species level and thereby lead to emergence of discrete phylogenetic clusters (higher ESUs). Extending phylogenetic approaches for delimiting evolutionarily significant species to broader phylogenetic scales, we find evidence for the existence of higher ESUs in mammals. In carnivores, euungulates and lagomorphs the hierarchical level of units detected correspond, on average, to the level of family or genus in traditional taxonomy. The units in euungulates are associated with divergent patterns of body mass, consistent with occupation of distinct ecological zones. Our findings demonstrate a new framework for studying biodiversity that unifies approaches at species and higher levels, thus potentially restoring higher taxa to their historical status as natural entities.

  • 8.
    Humphreys, Aelys M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Royal Botanic Gardens, UK.
    Govaerts, Rafaël
    Ficinski, Sarah Z.
    Lughadha, Eimear Nic
    Vorontsova, Maria S.
    Global dataset shows geography and life form predict modern plant extinction and rediscovery2019Ingår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, nr 7, s. 1043-1047Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Most people can name a mammal or bird that has become extinct in recent centuries, but few can name a recently extinct plant. We present a comprehensive, global analysis of modern extinction in plants. Almost 600 species have become extinct, at a higher rate than background extinction, but almost as many have been erroneously declared extinct and then been rediscovered. Reports of extinction on islands, in the tropics and of shrubs, trees or species with narrow ranges are least likely to be refuted by rediscovery. Plant extinctions endanger other organisms, ecosystems and human well-being, and must be understood for effective conservation planning.

  • 9.
    Humphreys, Aelys M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Division of Biology, Imperial College London, Silwood Park Campus, Berkshire, UK.
    Linder, H. Peter
    Evidence for recent evolution of cold tolerance in grasses suggests current distribution is not limited by (low) temperature2013Ingår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 198, nr 4, s. 1261-1273Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Temperature is considered an important determinant of biodiversity distribution patterns. Grasses (Poaceae) occupy among the warmest and coldest environments on earth but the role of cold tolerance evolution in generating this distribution is understudied. We studied cold tolerance of Danthonioideae (c. 280 species), a major constituent of the austral temperate grass flora. We determined differences in cold tolerance among species from different continents grown in a common winter garden and assessed the relationship between measured cold tolerance and that predicted by species ranges. We then used temperatures in current ranges and a phylogeny of 81% of the species to study the timing and mode of cold tolerance evolution across the subfamily. Species ranges generally underestimate cold tolerance but are still a meaningful representation of differences in cold tolerance among species. We infer cold tolerance evolution to have commenced at the onset of danthonioid diversification, subsequently increasing in both pace and extent in certain lineages. Interspecific variation in cold tolerance is better accounted for by spatial than phylogenetic distance. Contrary to expectations, temperature low temperature in particular appears not to limit the distribution of this temperate clade. Competition, time or dispersal limitation could explain its relative absence from northern temperate regions.

  • 10.
    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.

  • 11. Linder, H. Peter
    et al.
    Antonelli, Alexandre
    Humphreys, Aelys M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Botaniska institutionen. Imperial College London .
    Pirie, Michael D.
    Wuest, Rafael O.
    What determines biogeographical ranges?: Historical wanderings and ecological constraints in the danthonioid grasses2013Ingår i: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 40, nr 5, s. 821-834Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 12. Queenborough, Simon A.
    et al.
    Humphreys, Aelys M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Botaniska institutionen.
    Valencia, Renato
    Sex-specific flowering patterns and demography of the understorey rain forest tree Iryanthera hostmannii (Myristicaceae)2013Ingår i: Tropical Conservation Science, ISSN 1940-0829, E-ISSN 1940-0829, Vol. 6, nr 5, s. 637-652Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Sexual dimorphism in dioecious plants is a common phenomenon that has received widespread attention, yet the implications for reproductive function and fitness remain poorly understood. Using data from a long-term study of a population of 839 dioecious Iryanthera hostmannii (Myristicaceae 'nutmeg') trees in a large permanent plot in a lowland tropical rain forest, we examined the effects of greater investment in reproduction by females compared to males for various aspects of life history. Although male trees often produced more inflorescences than females, total dry mass of flowers was roughly equal in two out of three years for both sexes, implying that any investment differential lies in fruit production. There was no difference in the 12-year relative growth rate of males and females, suggesting that females can compensate somehow for their greater reproductive investment, although there were weak suggestions that mortality might have been greater in females. Male flowers opened slightly earlier in the day than female flowers and were short-lived, lasting at most two nights compared to up to four nights in females. Understanding the interacting effects of resource availability (studied here) and pollen movement (currently unknown in Iryanthera) on reproduction is essential in terms of life history theory. Knowledge of reproductive biology is key in considering the ecology and conservation of tropical forest communities.

  • 13. 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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