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2,052 results for “tree species”
Long evolutionary history of an emerging fungal pathogen of diverse tree species in eastern Asia, Australia, and the Pacific Islands
<p>Emerging plant pathogens have been increasing exponentially over the last century. To address this issue, it is critical to determine whether these pathogens are native to ecosystems or have been recently introduced. Understanding the ecological and evolutionary processes fostering emergence can help to manage their spread and predict epidemics/epiphytotics. Using restriction site-associated DNA sequencing data, we studied genetic relationships, pathways of spread, and evolutionary history of <em>Phellinus noxius</em>, an emerging root-rotting fungus of unknown origin, in eastern Asia, Australia, and the Pacific Islands. We analyzed patterns of genetic variation using Bayesian inference, maximum likelihood phylogeny, populations splits and mixtures measuring correlations in allele frequencies and genetic drift, and finally applied coalescent based theory using Approximate Bayesian computation (ABC) with supervised machine learning. Population structure analyses revealed five genetic groups with signatures of complex recent and ancient migration histories. The most probable scenario of ancient pathogen spread is movement from an unsampled population to Malaysia and the Pacific Islands, with subsequent spread to Taiwan and Australia. Furthermore, ABC analyses indicate <em>P. noxius</em> spread occurred thousands of generations ago, contradicting previous assumptions that this pathogen was recently introduced to multiple geographic regions. Our results suggest that recent emergence of <em>P. noxius</em>in eastern Asia, Australia, and the Pacific Islands is likely driven by anthropogenic and natural disturbances, such as deforestation, land-use change, severe weather events, and/or introduction of exotic plants. This study provides a novel example of applying genome-wide allele frequency data to unravel dynamics of pathogen emergence under changing ecosystem conditions.</p>
FIGURE 6 in Mahechadendron puntecascarillo (Vochysiaceae), a new genus and forest tree species from Colombia
FIGURE 6. Distribution map of Mahechadendron puntecascarillo.
Survival and growth data for tree species planted to reforest degraded tropical peat swamp forests and functional trait data for peat swamp forest species across Southeast Asia
<p>Degraded tropical peat swamp forests are harsh environments so difficult to restore. Evidence from past restoration projects can inform selection of species for planting. As part of a systematic review, we collated and synthesised survival and growth monitoring data on trees planted in degraded tropical peat swamp forests across Southeast Asia. A key aim of the systematic review and meta-analysis was to determine which tree species survive best when planted to restore tropical peat swamp forests. We also investigated the impact of seedling and site treatments and climatic conditions (El Niño-Southern Oscillation) on tree seedling survival and growth and the potential to use plant functional traits to predict survival and growth. </p> <p>Full methodological details of the systematic review, including: search strategy, article screening and inclusion criteria, critical appraisal of screened articles, data processing and data analysis can be found in the published article and supporting information stated below.</p> <p>Smith SW, Rahman NEB, Harrison ME, Shiodera S, Giesen W, Lampela M, Wardle DA, Chong KY, Randi A, Wijedasa LS, Teo PY, Fatimah, YA, Teng NT, Joanne YKQ, Alam MJ, Brugues Sintes P, Darusman T, Graham LLB, Katoppo DR, Kojima K, Kusin K, Lestari DP, Metali F, Morrogh-Bernard HC, Nahor MB, Napitupulu RRP, Nasir D, Nath TK, Nilus R, Norisada M, Rachmanadi D, Rachmat HH, Ripoll Capilla B, Salahuddin, Santosa PB, Sukri RS, Tay B, Tuah W, Wedeux, BMM, Yamanoshita T, Yokoyama EY, Yuwati TW, Lee JSH. Tree species that ‘live slow, die older’ enhance tropical peat swamp restoration: evidence from a systematic review. <em>Journal of Applied Ecology. </em>DOI:<a href="https://doi.org/10.1111/1365-2664.14232">10.1111/1365-2664.14232</a></p> <p>In this data repository, we have uploaded the following data used in the meta-analysis to generate the findings presented in the systematic review, specifically:</p> <ul> <li>Screening sheets of eligible articles across languages (English, Indonesian, Japanese and German) read in detailed by multiple authors on the review</li> <li>Survival monitoring data, including predicted half-life (duration until 50% mortality) derived from functional line-fitting</li> <li>Height monitoring data, including standardized relative growth rates (cm × cm<sup>-1 </sup>month<sup>-1</sup>) derived from functional line-fitting</li> <li>Plant functional traits, selected leaf nutrient contents and wood densities for those species used in the functional trait analyses</li> </ul> <p>Each data file has an associated meta-data file explaining the column headers and variables. Please note, data contributors from some studies wished to retain control over access to their monitoring data, but are willing to share this data on request. The relevant study-site code those studies used in the analyses in our systematic review can be found in the meta-data sheets. Details given include study-site code (used in the systematic review), site name and location, author name(s), author contact email(s). All these details have been provided with permission from relevant data contributor co-author(s). </p>
Seed and seedling predation by vertebrates mediates the effects of adult trees in two temperate tree species
<p>This dataset presents the proportion of <em>Fagus sylvatica</em> and <em>Picea abies </em>seeds per plot that transitioned into seedlings within the period of 15 biweekly censuses ("Establishment.csv") and the proportion of surviving <em>Fagus sylvatica</em> and <em>Picea abies </em>seedlings per plot at each seedling census interval ("Survival.csv"). Our experimental design comprised six forest sites, 24 blocks and 192 seedling plots. Because three of the sites were represented by <em>Picea abies</em> monocultures and another three by <em>Fagus sylvatica</em> monocultures, we designed a two-level conspecific vs. heterospecific treatment to test for the effects of conspecific and heterospecific adults. Within each block, we randomly assigned half of the seedling plots to <em>Fagus sylvatica</em> and another half to <em>Picea abies</em>. Plots were then sown with the seeds of a particular species. Conspecific treatment was represented by seeds and seedlings of a species situated in the plots of conspecific monocultures, while heterospecific treatment was characterised by seeds and seedlings of a species situated in the plots of heterospecific monocultures.</p> <p>Given the four seedling plots of each block belonging to either <em>Fagus sylvatica</em> or <em>Picea abies</em>, we randomly assigned one of the four levels of an enemy exclusion treatment to each plot in order to manipulate seed and seedling predation by one or another enemy type. Four levels of this treatment were designed, excluding fungal pathogens by the use of fungicide, herbivorous insects by insecticide and herbivorous vertebrates by cages. The fourth level was used as a control with no enemy exclusion applied.</p> <p>To account for the effects of environmental conditions on seedling establishment and survival, establishment and survival models also included light and soil resource availability parameters.</p> <p>Data contains (1) the proportion of established seedlings (sumEst), adult tree species (Stand), seedling species (Species), enemy exclusion treatment (Treat), block ID , stand ID, plot ID and light and soil resource availability parameters for the analyses of seedling establishment ("Establishment.csv"), and (2) the proportion of established seedlings (sumEst), the proportion of surviving seedlings (Surviving), adult tree species (Stand), seedling species (Species), enemy exclusion treatment (Treat), block ID , stand ID, plot ID, census interval (Week) and light and soil resource availability parameters for the analyses of seedling establishment for the analyses of seedling survival ("Survival.csv").</p>
Leaf miners and gallicolous aphids per tree per species
<p>The source data on leaf miners and gallicolous aphids per tree per species.</p>
Dated tree of 24,000 Angiosperms species incl Canary Island colonisation events
<p><span><span><span><span><span><span><span><span><span><span><span>Insular woodiness (IW), referring to the evolutionary transition from herbaceousness towards woodiness on islands, has arisen more than 30 times on the Canary Islands (Atlantic Ocean). One of the IW hypotheses suggests that drought has been a major driver of wood formation, but we do not know in which palaeoclimatic conditions the insular woody lineages originated. Therefore, we provided an updated review on the presence of IW on the Canaries, reconstructed the palaeoclimate, and estimated the timing of origin of woodiness of 24 insular woody lineages that represent a large majority of the insular woody species diversity on the Canaries. Our single, broad-scale dating analysis shows that woodiness in 60-65% of the insular woody lineages studied originated within the last 3.2 Myr during which Mediterranean seasonality (yearly summer droughts) became established on the Canaries. Consequently, our results are consistent with palaeoclimatic aridification as a potential driver of woodiness in a considerable proportion of the insular woody Canary Island lineages. However, the observed pattern between insular woodiness and palaeodrought during the last couple of million years could potentially have emerged as a result of the typically young age of the native insular flora that is characterised by a high turnover.</span></span></span></span></span></span></span></span></span></span></span></p>
FIGURE. A. Multi-partition plastome tree. B. 35S in Tulipa toktogulica (Liliaceae), a cryptic, endangered new species from the western Tien-Shan, Kyrgyzstan
FIGURE. A. Multi-partition plastome tree. B. 35S rDNA tree. New species shown in red on both trees.
Figure 5. A in Description, biology and conservation of a new species of Australian tree frog (Amphibia: Anura: Hylidae: Litoria) and an assessment of the remaining populations of Litoria genimaculata Horst, 1883: systematic and conservation implications of an unusual speciation event
Figure 5. A representation of the difference in morphology between male Litoria genimaculata and Litoria myola sp. nov. The box plots compare morphology of L. genimaculata from across the Wet Tropics, L. genimaculata from the Kuranda area, and L. myola sp. nov. PC1 accounts for 87.8% of the variation in morphology (SVL, TL, HW, and weight) across L. genimaculata and L. myola sp. nov. PC1 is loaded equally and positively by all four characters (approximately 0.94 for each) and therefore represents body size. The box plots show the median, 25th and 75th quartiles, and minimum and maximum data of PC1.
Figure 4. A in Description, biology and conservation of a new species of Australian tree frog (Amphibia: Anura: Hylidae: Litoria) and an assessment of the remaining populations of Litoria genimaculata Horst, 1883: systematic and conservation implications of an unusual speciation event
Figure 4. A representation of the difference in call between Litoria genimaculata and Litoria myola sp. nov. The box plots compare calls of L. genimaculata from across the Wet Tropics, L. genimaculata from the Kuranda area, and L. myola sp. nov. PC1 accounts for 67.2% of the variation in call (duration, dominant frequency and note rate) across L. genimaculata and L. myola sp. nov. PC1 is loaded heavily by inverse call duration (0.95) and note rate (0.93), and moderately by dominant frequency (0.51). The box plots show the median, 25th and 75th quartiles, and minimum and maximum data of PC1.
Figure 6 in Description, biology and conservation of a new species of Australian tree frog (Amphibia: Anura: Hylidae: Litoria) and an assessment of the remaining populations of Litoria genimaculata Horst, 1883: systematic and conservation implications of an unusual speciation event
Figure 6. The distribution of Litoria myola sp. nov. and Litoria genimaculata in the Kuranda area. The pie charts show the proportion of L. myola sp. nov. (black) and L. genimaculata (grey) individuals on five streams. Nearby sites on the streams are grouped together to provide a consistent scale. Sample size for the pie charts averages 20 individuals. The squares show additional sites where L. myola sp. nov. (black squares) and L. genimaculata (grey squares) have been recorded but relative proportions of each have not been determined. All L. genimaculata are northern lineage individuals. Major stream catchments flowing into the Barron River are marked. The sections of stream without records of either species are either unsuitable habitat or have not yet been surveyed. Sites surrounding this area are occupied by northern lineage L. genimaculata or are unsuitable habitat (Fig. 1).
Supplementary material 1 from: Jagodziński AM, Dyderski MK, Horodecki P, Knight KS, Rawlik K, Szmyt J (2019) Light and propagule pressure affect invasion intensity of Prunus serotina in a 14-tree species forest common garden experiment. NeoBiota 46: 1-21. https://doi.org/10.3897/neobiota.46.30413
: Data type: measurement
Supplementary material 2 from: Jagodziński AM, Dyderski MK, Horodecki P, Knight KS, Rawlik K, Szmyt J (2019) Light and propagule pressure affect invasion intensity of Prunus serotina in a 14-tree species forest common garden experiment. NeoBiota 46: 1-21. https://doi.org/10.3897/neobiota.46.30413
: Data type: measurement
Supplementary material 3 from: Jagodziński AM, Dyderski MK, Horodecki P, Knight KS, Rawlik K, Szmyt J (2019) Light and propagule pressure affect invasion intensity of Prunus serotina in a 14-tree species forest common garden experiment. NeoBiota 46: 1-21. https://doi.org/10.3897/neobiota.46.30413
: Data type: measurement
Supplementary material 4 from: Jagodziński AM, Dyderski MK, Horodecki P, Knight KS, Rawlik K, Szmyt J (2019) Light and propagule pressure affect invasion intensity of Prunus serotina in a 14-tree species forest common garden experiment. NeoBiota 46: 1-21. https://doi.org/10.3897/neobiota.46.30413
: Data type: measurement
Figures 46-51 from: da Silva HAM, Silva-Soares T, de Brito-Gitirana L (2017) Comparative analysis of the integument of different tree frog species from Ololygon and Scinax genera (Anura: Hylidae). Zoologia 34: 1-17. https://doi.org/10.3897/zoologia.34.e20176
Figures 46-51 - Light micrograph of the integument of O. v-signata: (46) Dorsal region (HE-staining); (47) Dorsal region (AB-method); (48) Ventrolateral region (HE-staining); (49) Ventrolateral region (AB-method); (50) Ventral region (HE-staining); (51) Ventral region (AB-method). Melanophores (_) occur in the spongious dermis that is poorly developed in the dorsal region. The EK-layer (Æ) is a continuous layer in all integument regions. Apocrine glands (¬) with heterogeneous content occur in both ventrolateral and ventral regions. Serous glands are visualized in both dorsal and ventrolateral integument. Mixed glands () are observed in the ventral region. E = epidermis; CD = compact dermis.
Figures 41-45 from: da Silva HAM, Silva-Soares T, de Brito-Gitirana L (2017) Comparative analysis of the integument of different tree frog species from Ololygon and Scinax genera (Anura: Hylidae). Zoologia 34: 1-17. https://doi.org/10.3897/zoologia.34.e20176
Figures 41-45 - Light micrograph of the integument of O. trapicheroi: (41) Dorsal region (Mallory´s trichrome staining); (42) Dorsal region (AB-method); (43) Ventrolateral region (AB-method); (44) Ventral region (HE-staining); (45) Ventral region (AB-method). Melanophores (_) occur in the spongious dermis of the dorsal integument, and in the ventrolateral region as isolated groups. They are absent in the ventral integument. In the dorsal region, the EK-layer (Æ) is continuous and well stained by the AB-method. Isolated serous glands (Ø) occur in all integument regions. The apocrine glands with granular content (¬) are visualized in the ventrolateral integument, where they are more developed. In the ventral region, cutaneous elevations (â) are also separated by grooves. The dermis contains several small blood vessels. E= epidermis; CD = compact dermis.
Figures 27-31 from: da Silva HAM, Silva-Soares T, de Brito-Gitirana L (2017) Comparative analysis of the integument of different tree frog species from Ololygon and Scinax genera (Anura: Hylidae). Zoologia 34: 1-17. https://doi.org/10.3897/zoologia.34.e20176
Figures 27-31 - Light micrograph of the integument of O. humilis: (27) Dorsal region (HE-staining); (28) Dorsal region (AB-method); (29) Ventrolateral region (HE-staining) (30) Ventral region (Mallory´s trichrome staining); (31) Ventral region (AB-method). In the dorsal region, the spongious dermis is poorly developed. Melanophores (_) are visualized in all integument regions; however, iridophores (→) are visualized only in both dorsal and ventrolateral integument. Both pigment cells are located just beneath the epidermis. Alcianophilic reaction is observed in cytoplasm of iridophores as well as in the EK-layer (Æ) of the dorsal integument. The EK-layer is absent in the ventral integument. Apocrine glands with heterogeneous content (¬) occur in both ventrolateral and ventral integument. In S. humilis, mixed glands (Ú) are visualized in the ventral region, being formed by serous and mucous cells. Mucous cells exhibit alcianophilic reaction. E = epidermis; CD = compact dermis.
Figures 11-13 from: da Silva HAM, Silva-Soares T, de Brito-Gitirana L (2017) Comparative analysis of the integument of different tree frog species from Ololygon and Scinax genera (Anura: Hylidae). Zoologia 34: 1-17. https://doi.org/10.3897/zoologia.34.e20176
Figures 11-13 - Light micrograph of the integument of O. albicans: (11) Dorsal region (HE-staining); (12) Ventrolateral region (HE-staining); (13) Ventral region (AB-method). In all integument regions, the epidermis (E) rests on the dermis, which is subdivided into the spongious dermis (SD) and the compact dermis (CD). Iridophores (→) occur in the dorsal region; however, they are absent in both ventrolateral and ventral regions. Melanophores (_) in the spongious dermis. Both serous (Ø) and apocrine glands (¬) occur in the spongious dermis. No glandular cell reacts to AB-method, suggesting that secretory units is made up of serous cells. The EK-layer (Æ) exhibits its typical basophilic staining. Note clusters of apocrine glands (¬) with heterogeneous content in the ventrolateral integument. The EK-layer () exhibits typical alcianophilic reaction of its glycoconjugate content. Large blood vessels occur in the hypodermis.
Figures 1-10 from: da Silva HAM, Silva-Soares T, de Brito-Gitirana L (2017) Comparative analysis of the integument of different tree frog species from Ololygon and Scinax genera (Anura: Hylidae). Zoologia 34: 1-17. https://doi.org/10.3897/zoologia.34.e20176
Figures 1-10 - Photograph of the species: (1) O. albicans; (2) O. angrensis; (3) O. flavoguttata; (4) S. hayii; (5) O. humilis; (6) O. perpusilla; (6) S. similis; (8) O. trapicheroi; (9) O. v-signata; (10) S. x-signatus.
Figures 36-40 from: da Silva HAM, Silva-Soares T, de Brito-Gitirana L (2017) Comparative analysis of the integument of different tree frog species from Ololygon and Scinax genera (Anura: Hylidae). Zoologia 34: 1-17. https://doi.org/10.3897/zoologia.34.e20176
Figures 36-40 - Light micrograph of the integument of S. similis: (36) Dorsal region (Mallory´s trichrome staining); (37) Dorsal region (AB-method); (38) Ventrolateral region (HE-staining); (39) Ventral region (Mallory´s trichrome staining); (40) Ventral region (AB-method). Melanophores (_) and iridophores (→) organized as chromatophore units occur in both dorsal and ventrolateral integument. Iridophores exhibit alcianophilic reaction. Note serous glands (Ø) and apocrine glands with granular content (¬) in the spongious dermis. In the ventral region, cutaneous elevations (¬) are separated by prominent grooves (Ú). The EK-layer (Æ) occur in the dorsal integument but not in the ventral integument. Moreover, the epidermis (E) of the ventral region is more developed than other integument regions. E = epidermis; CD = compact dermis; H = hypodermis.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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