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Afromontane Forest Diversity and the Role of Grassland-Forest Transition in Tree Species DistributionAbiem, IverenArellano, GabrielKenfack, DavidChapman, Hazel2020DOI: info:10.3390/d12010030Diversityv. 12No. 11191–191424-2818
Abiem, Iveren, Arellano, Gabriel, Kenfack, David, and Chapman, Hazel. 2020. "Afromontane Forest Diversity and the Role of Grassland-Forest Transition in Tree Species Distribution." Diversity 12 (1):1–19.
ID: 154309
Type: article
Authors: Abiem, Iveren; Arellano, Gabriel; Kenfack, David; Chapman, Hazel
Keywords: STRI
Abstract: Local factors can play an important role in defining tree species distributions in species rich tropical forests. To what extent the same applies to relatively small, species poor West African montane forests is unknown. Here, forests survive in a grassland matrix and fire has played a key role in their spatial and temporal dynamics since the Miocene. To what extent these dynamics influence local species distributions, as compared with other environmental variables such as altitude and moisture remain unknown. Here, we use data from the 20.28 ha montane forest plot in Ngel Nyaki Forest Reserve, South-East Nigeria to explore these questions. The plot features a gradient from grassland to core forest, with significant edges. Within the plot, we determined tree stand structure and species diversity and identified all trees ≥1 cm in diameter. We recorded species guild (pioneer vs. shade tolerant), seed size, and dispersal mode. We analyzed and identified to what extent species showed a preference for forest edges/grasslands or core forest. Similarly, we looked for associations with elevation, distance to streams and forest versus grassland. We recorded 41,031 individuals belonging to 105 morphospecies in 87 genera and 47 families. Around 40% of all tree species, and 50% of the abundant species, showed a clear preference for either the edge/grassland habitat or the forest core. However, we found no obvious association between species guild, seed size or dispersal mode, and distance to edge, so what leads to this sorting remains unclear. Few species distributions were influenced by distance to streams or altitude.
Palaeontological framework from Pirabas Formation (North Brazil) used as potential model for equatorial carbonate platform - ScienceDirectAguilera, OrangelOliveira de Araújo, Olga M.Hendy, AustinNogueira, Anna A. E.Nogueira, Afonso C. R.Wagner Maurity, ClovisTavares Kutter, ViniciusAlves Martins, Maria VirginiaColetti, GiovanniBorba Dias, BrunaSilva-Caminha, SilaneJaramillo, CarlosBencomo, KarenLopes, Ricardo Tadeu2020DOI: info:10.1016/j.marmicro.2019.101813Marine Micropaleontologyv. 1541231–230377-8398
Aguilera, Orangel, Oliveira de Araújo, Olga M., Hendy, Austin, Nogueira, Anna A. E., Nogueira, Afonso C. R., Wagner Maurity, Clovis, Tavares Kutter, Vinicius, Alves Martins, Maria Virginia, Coletti, Giovanni, Borba Dias, Bruna, Silva-Caminha, Silane, Jaramillo, Carlos, Bencomo, Karen, and Lopes, Ricardo Tadeu. 2020. "Palaeontological framework from Pirabas Formation (North Brazil) used as potential model for equatorial carbonate platform - ScienceDirect." Marine Micropaleontology 154:1–23.
ID: 154319
Type: article
Authors: Aguilera, Orangel; Oliveira de Araújo, Olga M.; Hendy, Austin; Nogueira, Anna A. E.; Nogueira, Afonso C. R.; Wagner Maurity, Clovis; Tavares Kutter, Vinicius; Alves Martins, Maria Virginia; Coletti, Giovanni; Borba Dias, Bruna; Silva-Caminha, Silane; Jaramillo, Carlos; Bencomo, Karen; Lopes, Ricardo Tadeu
Keywords: STRI
Defensive fruit metabolites obstruct seed dispersal by altering bat behavior and physiology at multiple temporal scalesBaldwin, Justin W.Dechmann, Dina K. N.Thies, WibkeWhitehead, Susan R.2020DOI: info:10.1002/ecy.2937Ecologyv. 101No. 2e02937e029371939-9170
Baldwin, Justin W., Dechmann, Dina K. N., Thies, Wibke, and Whitehead, Susan R. 2020. "Defensive fruit metabolites obstruct seed dispersal by altering bat behavior and physiology at multiple temporal scales." Ecology 101 (2):e02937.
ID: 153430
Type: article
Authors: Baldwin, Justin W.; Dechmann, Dina K. N.; Thies, Wibke; Whitehead, Susan R.
Keywords: STRI
Abstract: The paradoxical presence of toxic chemical compounds in ripe fruits represents a balance between plant enemies and allies: chemical traits can defend seeds against antagonistic herbivores, seed predators or fungal pathogens, but also can impose costs by repelling mutualistic seed dispersers, although the costs are often difficult to quantify. Seeds gain fitness benefits from travelling far from the parent plant, as they can escape from parental competition and elude specialized herbivores as well as pathogens that accumulate on adult plants. However, seeds are difficult to follow from their parent plant to their final destination. Thus, little is known about the factors that determine seed dispersal distance. We investigated this potential cost of fruit secondary compounds – reduced seed dispersal distance - by combining two datasets from previous work on a Neotropical bat-plant dispersal system (bats in the genus Carollia and plants in the genus Piper). We used data from captive behavioral experiments, which show how amides in ripe fruits of Piper decrease the retention time of seeds and alter food choices. With new analyses, we show that these defensive secondary compounds also delay the time of fruit removal. Next, with a behaviorally annotated bat telemetry dataset, we quantified post-feeding movements (i.e. seed dispersal distances). Using generalized additive mixed models we found that seed dispersal distances varied nonlinearly with gut retention times as well as with the time of fruit removal. By interrogating the model predictions, we identified two novel mechanisms by which fruit secondary compounds can impose costs in terms of decreased seed dispersal distances: 1) small scale reductions in gut retention time and 2) causing fruits to forgo advantageous bat activity peaks that confer high seed dispersal distances.
A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness IndexBarco, R. A.Garrity, G. M.Scott, J. J.Amend, J. P.Nealson, K. H.Emerson, D.2020DOI: info:10.1128/mBio.02475-19mBiov. 11No. 1Article e02475-19American Society for MicrobiologyArticle e02475-192150-7511
Barco, R. A., Garrity, G. M., Scott, J. J., Amend, J. P., Nealson, K. H., and Emerson, D. 2020. "A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index." mBio 11 (1):Article e02475-19.
ID: 154064
Type: article
Authors: Barco, R. A.; Garrity, G. M.; Scott, J. J.; Amend, J. P.; Nealson, K. H.; Emerson, D.
Keywords: STRI
Abstract: Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of taxa, increasing the proportion of directly impacted genera to at least 43% and pointing at inaccuracies on the use of the 16S rRNA gene as a taxonomic marker, despite its precision. Altogether, these results suggest that genomic coherence is an emergent property of genera in Bacteria and ArchaeaIMPORTANCE In recent decades, the taxonomy of Bacteria and Archaea, and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the average nucleotide identity. Our findings are of importance to the microbiology community because the emergent properties of Bacteria and Archaea that are identified in this study will help assign genera with higher taxonomic resolution.
Specialized bacteriome uncovered in the coralloid roots of the epiphytic gymnosperm, Zamia pseudoparasiticaBell-Doyon, PhilipLaroche, JérômeSaltonstall, KristinVillareal Aguilar, Juan Carlos2020DOI: info:10.1002/edn3.66Environmental DNAHoboken, New JerseyWiley2637-4943
Bell-Doyon, Philip, Laroche, Jérôme, Saltonstall, Kristin, and Villareal Aguilar, Juan Carlos. 2020. "Specialized bacteriome uncovered in the coralloid roots of the epiphytic gymnosperm, Zamia pseudoparasitica." Environmental DNA
ID: 154061
Type: article
Authors: Bell-Doyon, Philip; Laroche, Jérôme; Saltonstall, Kristin; Villareal Aguilar, Juan Carlos
Keywords: STRI
Abstract: Epiphytes face several constraints regarding nutrient acquisition: They are disconnected from soil minerals and they have to mainly rely on nutrients leached by precipitation and microbes. The cycad, Zamia pseudoparasitica Yates, is the only known strictly epiphytic gymnosperm, and it is endemic to Panamanian rainforests. Cycads have evolved specialized coralloid roots that host endophytic cyanobacteria specialized in nitrogen fixation. We collected coralloid roots from plants in the Omar Torrijos National Park, Provincia de Coclé. DNA was extracted from fresh inner coralloid roots, and the bacteriome was described using two molecular markers: rbcL-rbcX (targeting cyanobacteria) and 16S (all bacteria). Sixteen samples were sequenced for rbcL-rbcX yielding sequences belonging to a monophyletic group within the order Nostocales. One hundred and sixty-five amplicon sequence variants (ASVs) were found in at least two of our 27 samples amplified for 16S. Nostocales, Rhizobiales, and Acetobacterales were the three most diverse and abundant orders of bacteria found within the coralloid roots, and the candidate phylum WPS-2 was also found in many samples. We performed a de novo assembly from a single culture of the endophytic cyanobacteria. A phylogenomic analysis of the isolate places the cyanobacterium in a sister clade to mostly symbiotic taxa from mosses, liverworts, and lichens. Additionally, the isolate has genes putatively involved in symbiotic signaling, hormogonium differentiation, ammonium transport, nitrogen fixation, heterocyst differentiation, sulfate transport, and secondary metabolites. Although dominated by organisms with the capacity to fix nitrogen, coralloid roots are also inhabited by a diverse community of other taxa which may also play biologically important roles.
A new species of the genus Psammogorgia (Cnidaria: Anthozoa: Octocorallia) from the Hannibal Bank in Pacific PanamaBreedy, OdaliscaGuzmán, Héctor M.Murillo, CatalinaVargas, Sergio2020DOI: info:10.5343/bms.2019.0072Bulletin of Marine Sciencev. 96No. 1169180169–1800007-4977
Breedy, Odalisca, Guzmán, Héctor M., Murillo, Catalina, and Vargas, Sergio. 2020. "A new species of the genus Psammogorgia (Cnidaria: Anthozoa: Octocorallia) from the Hannibal Bank in Pacific Panama." Bulletin of Marine Science 96 (1):169–180.
ID: 152760
Type: article
Authors: Breedy, Odalisca; Guzmán, Héctor M.; Murillo, Catalina; Vargas, Sergio
Keywords: STRI
Abstract: The octocoral fauna occurring at mesophotic depths (from 40 to 150 m) has been relatively unexplored. Recent expeditions to Hannibal Bank, a guyot seamount off Pacific Panama have yielded new octocoral species and new records for the tropical eastern Pacific. Herein, we describe a new species for the genus Psammogorgia , Psammogorgia pax sp. nov., characterised by having a whitish flabellate colony with orange polyp apertures, slightly raised and sparse calyces, and colourless coenenchymal sclerites, which are mostly spindles and large wart-clubs. A preliminary molecular phylogenetic analysis supports the differences between the new species with other congener and other related taxa.
Host Records for Tortricidae (Lepidoptera) Reared from Seeds and Fruits in PanamaBrown, John W.Gripenberg, SofiaBasset, YvesCalderón, OsvaldoSimon, IndiraFernandez, CatalinaCedeno, MarjorieRivera, Marleny2020DOI: info:10.4289/0013-8797.122.1.12Proceedings of the Entomological Society of Washingtonv. 122No. 11224Washington, DCEntomological Society of Washington12–240013-8797
Brown, John W., Gripenberg, Sofia, Basset, Yves, Calderón, Osvaldo, Simon, Indira, Fernandez, Catalina, Cedeno, Marjorie, and Rivera, Marleny. 2020. "Host Records for Tortricidae (Lepidoptera) Reared from Seeds and Fruits in Panama." Proceedings of the Entomological Society of Washington 122 (1):12–24.
ID: 154782
Type: article
Authors: Brown, John W.; Gripenberg, Sofia; Basset, Yves; Calderón, Osvaldo; Simon, Indira; Fernandez, Catalina; Cedeno, Marjorie; Rivera, Marleny
Keywords: NMNH; NH-Entomology; STRI
Abstract: A survey of Lepidoptera reared from seeds and fruits primarily on Barro Colorado Island, Panama, yielded 444 specimens of Tortricidae representing 20 species. Nearly 90% of reared tortricids and 65% of the species are members of the tribe Grapholitini, a group that includes numerous economically important pests of fruit worldwide. We present host records for the following species: Histura panamana Brown, Platynota obliqua Walsingham complex, Platynota subargentea Walsingham, Spinipogon triangularis Brown, Cryptaspasma perseana Gilligan and Brown, Steblopotamia streblopa (Meyrick), Cydia pyraspis (Meyrick) complex, Eriosocia guttifera (Meyrick), Riculorampha ancyloides Rota and Brown, Grapholita mabea Razowski, Ricula croceus Brown, Ricula lacistema Brown, Ricula sp. 1, Ricula sp. 2, Talponia sp. 1, Talponia sp. 2, and four unidentified Grapholitini. In a comparison of studies focused on fruit- and seed-feeding insects in Thailand, Panama, and Kenya, Grapholitini represented 73% (in Thailand) to 90% (in Panama) of the total number of reared specimens of Tortricidae, and 45% (in Kenya) to 65% (in Panama) of the total number of tortricid species. However, a similar survey in Papua New Guinea produced considerably different results, with Grapholitini representing 46% of the tortricid specimens and only 20% of the species.
A major locus controls a biologically active pheromone component in Heliconius melpomeneByers, Kelsey J. R. P.Darragh, KathyMusgrove, JamieAlmeida, Diana AbondanoGarza, Sylvia FernandaWarren, Ian A.Rastas, Pasi M.Kucka, MarekChan, Yingguang FrankMerrill, Richard M.Schulz, StefanMcMillan, W. O.Jiggins, Chris D.2020DOI: info:10.1111/evo.13922Evolution; international journal of organic evolutionv. 74No. 2349364349–3641558-5646
Byers, Kelsey J. R. P., Darragh, Kathy, Musgrove, Jamie, Almeida, Diana Abondano, Garza, Sylvia Fernanda, Warren, Ian A., Rastas, Pasi M., Kucka, Marek, Chan, Yingguang Frank, Merrill, Richard M., Schulz, Stefan, McMillan, W. O., and Jiggins, Chris D. 2020. "A major locus controls a biologically active pheromone component in Heliconius melpomene." Evolution; international journal of organic evolution 74 (2):349–364.
ID: 154060
Type: article
Authors: Byers, Kelsey J. R. P.; Darragh, Kathy; Musgrove, Jamie; Almeida, Diana Abondano; Garza, Sylvia Fernanda; Warren, Ian A.; Rastas, Pasi M.; Kucka, Marek; Chan, Yingguang Frank; Merrill, Richard M.; Schulz, Stefan; McMillan, W. O.; Jiggins, Chris D.
Keywords: STRI
Abstract: Understanding the production, response, and genetics of signals used in mate choice can inform our understanding of the evolution of both intraspecific mate choice and reproductive isolation. Sex pheromones are important for courtship and mate choice in many insects, but we know relatively little of their role in butterflies. The butterfly Heliconius melpomene uses a complex blend of wing androconial compounds during courtship. Electroantennography in H. melpomene and its close relative H. cydno showed that responses to androconial extracts were not species-specific. Females of both species responded equally strongly to extracts of both species, suggesting conservation of peripheral nervous system elements across the two species. Individual blend components provoked little to no response, with the exception of octadecanal, a major component of the H. melpomene blend. Supplementing octadecanal on the wings of octadecanal-rich H. melpomene males led to an increase in the time until mating, demonstrating the bioactivity of octadecanal in Heliconius. Using quantitative trait locus (QTL) mapping, we identified a single locus on chromosome 20 responsible for 41% of the parental species' difference in octadecanal production. This QTL does not overlap with any of the major wing color or mate choice loci, nor does it overlap with known regions of elevated or reduced FST . A set of 16 candidate fatty acid biosynthesis genes lies underneath the QTL. Pheromones in Heliconius carry information relevant for mate choice and are under simple genetic control, suggesting they could be important during speciation. This article is protected by copyright. All rights reserved.
A new Miocene turtle from Colombia sheds light on the evolutionary history of the extant genus Mesoclemmys Gray, 1873Cadena, Edwin-AlbertoVanegas, AndrésJaramillo, CarlosCottle, John M.Johnson, Thomas A.2020DOI: info:10.1080/02724634.2019.1716777Journal of Vertebrate Paleontology1111–110272-4634
Cadena, Edwin-Alberto, Vanegas, Andrés, Jaramillo, Carlos, Cottle, John M., and Johnson, Thomas A. 2020. "A new Miocene turtle from Colombia sheds light on the evolutionary history of the extant genus Mesoclemmys Gray, 1873." Journal of Vertebrate Paleontology 1–11.
ID: 154852
Type: article
Authors: Cadena, Edwin-Alberto; Vanegas, Andrés; Jaramillo, Carlos; Cottle, John M.; Johnson, Thomas A.
Keywords: STRI
Abstract: Mesoclemmys is the most diverse extant genus of South American pleurodires or side-necked turtles, with at least 10 species inhabiting fluvial to littoral environments. Despite this high extant diversity and extensive geographic distribution, the evolutionary history and fossil record of this genus are completely unknown. Here, we describe the first fossil record of this genus, which supports a previous molecular-based hypothesis that indicates a minimum split time of 13.5 Ma between this and other genera of South American chelids. Mesoclemmys vanegasorum, sp. nov., is represented by a nearly complete shell (carapace and plastron) and some postcranial bones found in the middle Miocene (13.6 ± 0.2 Ma), La Victoria Formation, Tatacoa Desert, Colombia, increasing the turtle paleodiversity of La Venta Fauna. It differs from all extant species of Mesoclemmys by vertebral scute 1 reaching the sutural boundary between peripherals 1 and 2; shorter cervical and marginal scutes 1 to 3; pleurals 1 very advanced over the peripherals; pygal bone with a posteromedial shallow notch; vertebral 5 covering half of the pygal bone; small extragulars reaching only half of the epiplastra length; and a fine microvermiculation of the shell. Our phylogenetic results show a close relationship between M. vanegasorum, sp. nov., and the extant M. hogei. The overall morphology and size of Mesoclemmys genus have remained relatively constant for at least the last 13.6 million years. However, its geographic distribution has decreased drastically in northwestern South America, being restricted today to the lower region of the Magdalena River Basin.
Soil abiotic and biotic properties constrain the establishment of a dominant temperate tree into boreal forestsCarteron, AlexisParasquive, VladBlanchard, FlorenceGuilbeault-Mayers, XavierTurner, Benjamin L.Vellend, MarkLaliberté, Etienne2020DOI: info:10.1111/1365-2745.13326Journal of Ecology1141–141365-2745
Carteron, Alexis, Parasquive, Vlad, Blanchard, Florence, Guilbeault-Mayers, Xavier, Turner, Benjamin L., Vellend, Mark, and Laliberté, Etienne. 2020. "Soil abiotic and biotic properties constrain the establishment of a dominant temperate tree into boreal forests." Journal of Ecology 1–14.
ID: 154310
Type: article
Authors: Carteron, Alexis; Parasquive, Vlad; Blanchard, Florence; Guilbeault-Mayers, Xavier; Turner, Benjamin L.; Vellend, Mark; Laliberté, Etienne
Keywords: STRI
Abstract: Climate warming is expected to cause the poleward and upward elevational expansion of temperate plant species, but non-climatic factors such as soils could constrain this range expansion. However, the extent to which edaphic constraints on range expansion have an abiotic (e.g. soil chemistry) or biotic (e.g. micro-organisms) origin remains undetermined. We conducted greenhouse experiments to test if the survival and growth of a major North American temperate tree species, Acer saccharum (sugar maple), is independently or jointly constrained by abiotic and biotic properties of field-collected soils from within and beyond the species' elevational range. Abiotic factors, particularly low base cation concentrations, were major constraints to seedling establishment in boreal forest soils (beyond the range edge), but insufficient arbuscular mycorrhizal fungal inoculum (biotic factor) also strongly reduced seedling performance in these soils. Synthesis. Our results suggest that forecasting future changes in forest composition under climate warming requires consideration of soil properties as well as the mycorrhizal status of tree species.
Host affinity of endophytic fungi and the potential for reciprocal interactions involving host secondary chemistryChristian, NatalieSedio, Brian E.Florez-Buitrago, XimenaRamírez-Camejo, Luis A.Rojas, Enith I.Mejía, Luis C.Palmedo, SageRose, AutumnSchroeder, John W.Herre, Edward Allen2020DOI: info:10.1002/ajb2.1436American Journal of Botanyv. 107No. 2219228219–2281537-2197
Christian, Natalie, Sedio, Brian E., Florez-Buitrago, Ximena, Ramírez-Camejo, Luis A., Rojas, Enith I., Mejía, Luis C., Palmedo, Sage, Rose, Autumn, Schroeder, John W., and Herre, Edward Allen. 2020. "Host affinity of endophytic fungi and the potential for reciprocal interactions involving host secondary chemistry." American Journal of Botany 107 (2):219–228.
ID: 154731
Type: article
Authors: Christian, Natalie; Sedio, Brian E.; Florez-Buitrago, Ximena; Ramírez-Camejo, Luis A.; Rojas, Enith I.; Mejía, Luis C.; Palmedo, Sage; Rose, Autumn; Schroeder, John W.; Herre, Edward Allen
Keywords: STRI
Abstract: PREMISE: Interactions between fungal endophytes and their host plants present useful systems for identifying important factors affecting assembly of host-associated microbiomes. Here we investigated the role of secondary chemistry in mediating host affinity of asymptomatic foliar endophytic fungi using Psychotria spp. and Theobroma cacao (cacao) as hosts. METHODS: First, we surveyed endophytic communities in Psychotria species in a natural common garden using culture-based methods. Then we compared differences in endophytic community composition with differences in foliar secondary chemistry in the same host species, determined by liquid chromatography-tandem mass spectrometry. Finally, we tested how inoculation with live and heat-killed endophytes affected the cacao chemical profile. RESULTS: Despite sharing a common environment and source pool for endophyte spores, different Psychotria host species harbored strikingly different endophytic communities that reflected intrinsic differences in their leaf chemical profiles. In T. cacao, inoculation with live and heat-killed endophytes produced distinct cacao chemical profiles not found in uninoculated plants or pure fungal cultures, suggesting that endophytes, like pathogens, induce changes in secondary chemical profiles of their host plant. CONCLUSIONS: Collectively our results suggest at least two potential processes: (1) Plant secondary chemistry influences assembly and composition of fungal endophytic communities, and (2) host colonization by endophytes subsequently induces changes in the host chemical landscape. We propose a series of testable predictions based on the possibility that reciprocal chemical interactions are a general property of plant-endophyte interactions.
Millennial-scale change in the structure of a Caribbean reef ecosystem and the role of human and natural disturbanceCramer, Katie L.O'Dea, AaronLeonard-Pingel, Jill S.Norris, Richard D.2020DOI: info:10.1111/ecog.04722Ecographyv. 43No. 2283293Hoboken, New JerseyWiley283–2930906-7590
Cramer, Katie L., O'Dea, Aaron, Leonard-Pingel, Jill S., and Norris, Richard D. 2020. "Millennial-scale change in the structure of a Caribbean reef ecosystem and the role of human and natural disturbance." Ecography 43 (2):283–293.
ID: 153282
Type: article
Authors: Cramer, Katie L.; O'Dea, Aaron; Leonard-Pingel, Jill S.; Norris, Richard D.
Keywords: STRI
Abstract: Caribbean coral reefs have transformed into algal-dominated habitats over the past half-century, but the role of specific anthropogenic drivers is unresolved due to the lack of ecosystem-level data predating human disturbance. To better understand the extent and causes of long-term Caribbean reef declines, we produced a continuous 3000-yr record of the ecosystem state of three reefs in Bocas del Toro, Caribbean Panama. From fossils and sediments obtained from reef matrix cores, we tracked changes in reef accretion rates and the taxonomic and functional group composition of fish, coral, urchin, bivalve and benthic foraminifera. This dataset provided a comprehensive picture of reef community and environmental change. At all sites, reefs shifted from systems with greater relative abundance of herbivorous fish, epifaunal suspension feeding bivalves and Diadema urchins to systems with greater relative abundance of micropredator fish, infaunal bivalves and Echinometra urchins. These transitions were initiated a millennium ago at two less-degraded reefs fringing offshore islands and 250 yr ago at a degraded patch reef near the continental coast. Ecosystem shifts were accompanied by a decline in reef accretion rates, and at the patch reef, a decline in water quality since the 18th century. Within all cores, synchronous increases in infaunal bivalves and declines in herbivorous fish regardless of water quality suggest a loss of hard substrate and increasingly hypoxic sediment conditions related to herbivore loss. While the early timing of ecosystem transitions at the fringing reefs implicates large-scale hydrological change, the more recent timing of change and loss of water quality at the patch reef implicates terrigenous runoff from land-clearing. Our whole-ecosystem reconstruction reveals that reef ecosystem deterioration appears to follow a predictable trajectory whether driven by natural or anthropogenic disturbances and that historical local human activities have quickly unraveled reefs at a scale similar to longer-term natural environmental change.
Using Nutritional Geometry to Explore How Social Insects Navigate Nutritional LandscapesCrumière, Antonin J. J.Stephenson, Calum J.Nagel, ManuelShik, Jonathan Z.2020DOI: info:10.3390/insects11010053Insectsv. 11No. 11141–142075-4450
Crumière, Antonin J. J., Stephenson, Calum J., Nagel, Manuel, and Shik, Jonathan Z. 2020. "Using Nutritional Geometry to Explore How Social Insects Navigate Nutritional Landscapes." Insects 11 (1):1–14.
ID: 154291
Type: article
Authors: Crumière, Antonin J. J.; Stephenson, Calum J.; Nagel, Manuel; Shik, Jonathan Z.
Keywords: STRI
Abstract: Insects face many cognitive challenges as they navigate nutritional landscapes that comprise their foraging environments with potential food items. The emerging field of nutritional geometry (NG) can help visualize these challenges, as well as the foraging solutions exhibited by insects. Social insect species must also make these decisions while integrating social information (e.g., provisioning kin) and/or offsetting nutrients provisioned to, or received from unrelated mutualists. In this review, we extend the logic of NG to make predictions about how cognitive challenges ramify across these social dimensions. Focusing on ants, we outline NG predictions in terms of fundamental and realized nutritional niches, considering when ants interact with related nestmates and unrelated bacterial, fungal, plant, and insect mutualists. The nutritional landscape framework we propose provides new avenues for hypothesis testing and for integrating cognition research with broader eco-evolutionary principles.
Counting niches: Abundance-by-trait patterns reveal niche partitioning in a Neotropical forestD'Andrea, RafaelGuittar, JohnO'Dwyer, James P.Figueroa, HectorWright, S. JosephCondit, Richard S.Ostling, Annette2020DOI: info:10.1002/ecy.3019EcologyArticle e03019Ecological Society of AmericaArticle e030191939-9170
D'Andrea, Rafael, Guittar, John, O'Dwyer, James P., Figueroa, Hector, Wright, S. Joseph, Condit, Richard S., and Ostling, Annette. 2020. "Counting niches: Abundance-by-trait patterns reveal niche partitioning in a Neotropical forest." Ecology Article e03019.
ID: 154738
Type: article
Authors: D'Andrea, Rafael; Guittar, John; O'Dwyer, James P.; Figueroa, Hector; Wright, S. Joseph; Condit, Richard S.; Ostling, Annette
Keywords: STRI
Abstract: Tropical forests challenge us to understand biodiversity, as numerous seemingly similar species persist on only a handful of shared resources. Recent ecological theory posits that biodiversity is sustained by a combination of species differences reducing interspecific competition and species similarities increasing time to competitive exclusion. Together, these mechanisms counterintuitively predict that competing species should cluster by traits, in contrast with traditional expectations of trait overdispersion. Here, we show for the first time that trees in a tropical forest exhibit a clustering pattern. In a 50 ha. plot on Barro Colorado Island in Panama, species abundances exhibit clusters in two traits connected to light capture strategy, suggesting that competition for light structures community composition. Notably, we find four clusters by maximum height, quantitatively supporting the classical grouping of Neotropical woody plants into shrubs, understory, midstory, and canopy layers.
Silicon Dynamics During 2 Million Years of Soil Development in a Coastal Dune Chronosequence Under a Mediterranean Climatede Tombeur, FelixTurner, Benjamin L.Laliberté, EtienneLambers, HansCornelis, Jean-Thomas2020DOI: info:10.1007/s10021-020-00493-9Ecosystems1171–171435-0629
de Tombeur, Felix, Turner, Benjamin L., Laliberté, Etienne, Lambers, Hans, and Cornelis, Jean-Thomas. 2020. "Silicon Dynamics During 2 Million Years of Soil Development in a Coastal Dune Chronosequence Under a Mediterranean Climate." Ecosystems 1–17.
ID: 154745
Type: article
Authors: de Tombeur, Felix; Turner, Benjamin L.; Laliberté, Etienne; Lambers, Hans; Cornelis, Jean-Thomas
Keywords: STRI
Abstract: Silicon (Si) in plants confers a number of benefits, including resistance to herbivores and water or nutrient stress. However, the dynamics of Si during long-term ecosystem development remain poorly documented, especially the changes in soils in terms of plant availability. We studied a 2-million-year soil chronosequence to examine how long-term changes in soil properties influence soil Si pools. The chronosequence exhibits extreme mineralogical changes-from carbonate-rich to quartz-rich soils-where a carbonate weathering domain is succeeded by a silicate weathering domain. Plant-available Si concentrations were lowest in young soils (Holocene, < 6.5 ka), increased in intermediate soils (Middle Pleistocene, 120 ka), and finally decreased toward the oldest, quartz-rich soil (Early Pleistocene, 2 Ma). Silicon availability is likely low and relatively constant in the young soils because (1) carbonate weathering consumes protons and therefore reduces weathering of silicate minerals and (2) Si adsorption by secondary minerals is high in alkaline soils. In the middle-aged sites, Si availability rises with the loss of carbonates and the formation of kaolinite that appears to drive its concentration, and then falls in the oldest sites with quartz enrichment. The increasing accumulation of biogenic silica following carbonate depletion indicates stronger soil–plant Si cycling as ecosystem development proceeds. A literature analysis confirms the shift in processes controlling Si availability between the carbonate and silicate weathering domains. Overall, our results show a nonlinear response of plant-available Si to long-term pedogenesis, with likely important implications for the Si-related functioning of terrestrial ecosystems.
Evaluating amphibian biobanking and reproduction for captive breeding programs according to the Amphibian Conservation Action Plan objectivesDella Togna, GinaHowell, Lachlan G.Clulow, John C.Langhorne, Cecilia J.Marcec-Greaves, RuthCalatayud, Natalie E.2020DOI: info:10.1016/j.theriogenology.2020.02.024Theriogenology0093-691X
Della Togna, Gina, Howell, Lachlan G., Clulow, John C., Langhorne, Cecilia J., Marcec-Greaves, Ruth, and Calatayud, Natalie E. 2020. "Evaluating amphibian biobanking and reproduction for captive breeding programs according to the Amphibian Conservation Action Plan objectives." Theriogenology
ID: 154736
Type: article
Authors: Della Togna, Gina; Howell, Lachlan G.; Clulow, John C.; Langhorne, Cecilia J.; Marcec-Greaves, Ruth; Calatayud, Natalie E.
Keywords: STRI
Abstract: The Amphibian Conservation Action Plan (ACAP), published in 2007, is a formal document of international significance that proposed eleven relevant actions for global amphibian conservation. Action seven of the ACAP document addresses the use of amphibian captive programs as a conservation tool. Appendix material under this action explores the potential use of Genome Resource Banking (biobanking) as an urgently needed tool for these captive programs. ACAP proposed twelve objectives for Genome Resource Banking which exhibit little emphasis on reproduction as a vital underlying science for amphibian Captive Breeding Programs (CBP's). Here we have reassessed the original twelve ACAP objectives for amphibian reproduction and biobanking for CBP's as a contribution to future ACAP review processes. We have reviewed recent advances since the original objectives, as well as highlighted weaknesses and strengths for each of these objectives. We make various scientific, policy and economic recommendations based on the current reality and recent advances in relevant science in order to inform future ACAP towards new global objectives. The number of amphibian CBP'S has escalated in recent years and reproductive success is not always easily accomplished. Increases in applied and fundamental research on the natural history and reproductive biology of these species, followed by the appropriate development and application of artificial reproductive technologies (ART's) and the incorporation of genome resource banks (GRB's), may turn CBP's into a more powerful tool for amphibian conservation.
Interpreting insect declines: seven challenges and a way forwardDidham, Raphael K.Basset, YvesCollins, C. M.Leather, Simon R.Littlewood, Nick A.Menz, Myles H. M.Müller, JörgPacker, LaurenceSaunders, Manu E.Schönrogge, KarstenStewart, Alan J. A.Yanoviak, Stephen P.Hassall, Christopher2020DOI: info:10.1111/icad.12408Insect Conservation and Diversityv. 13No. 2103114103–1141752-4598
Didham, Raphael K., Basset, Yves, Collins, C. M., Leather, Simon R., Littlewood, Nick A., Menz, Myles H. M., Müller, Jörg, Packer, Laurence, Saunders, Manu E., Schönrogge, Karsten, Stewart, Alan J. A., Yanoviak, Stephen P., and Hassall, Christopher. 2020. "Interpreting insect declines: seven challenges and a way forward." Insect Conservation and Diversity 13 (2):103–114.
ID: 154847
Type: article
Authors: Didham, Raphael K.; Basset, Yves; Collins, C. M.; Leather, Simon R.; Littlewood, Nick A.; Menz, Myles H. M.; Müller, Jörg; Packer, Laurence; Saunders, Manu E.; Schönrogge, Karsten; Stewart, Alan J. A.; Yanoviak, Stephen P.; Hassall, Christopher
Keywords: STRI
Abstract: Many insect species are under threat from the anthropogenic drivers of global change. There have been numerous well-documented examples of insect population declines and extinctions in the scientific literature, but recent weaker studies making extreme claims of a global crisis have drawn widespread media coverage and brought unprecedented public attention. This spotlight might be a double-edged sword if the veracity of alarmist insect decline statements do not stand up to close scrutiny. We identify seven key challenges in drawing robust inference about insect population declines: establishment of the historical baseline, representativeness of site selection, robustness of time series trend estimation, mitigation of detection bias effects, and ability to account for potential artefacts of density dependence, phenological shifts and scale-dependence in extrapolation from sample abundance to population-level inference. Insect population fluctuations are complex. Greater care is needed when evaluating evidence for population trends and in identifying drivers of those trends. We present guidelines for best-practise approaches that avoid methodological errors, mitigate potential biases and produce more robust analyses of time series trends. Despite many existing challenges and pitfalls, we present a forward-looking prospectus for the future of insect population monitoring, highlighting opportunities for more creative exploitation of existing baseline data, technological advances in sampling and novel computational approaches. Entomologists cannot tackle these challenges alone, and it is only through collaboration with citizen scientists, other research scientists in many disciplines, and data analysts that the next generation of researchers will bridge the gap between little bugs and big data.
Dermal denticle assemblages in coral reef sediments correlate with conventional shark surveysDillon, Erin M.Lafferty, Kevin D.McCauley, Douglas J.Bradley, DarcyNorris, Richard D.Caselle, Jennifer E.DiRenzo, Graziella V.Gardner, Jonathan P. A.O'Dea, AaronHsiang Liow, Lee2020DOI: info:10.1111/2041-210X.13346Methods in Ecology and EvolutionArticle13346Article–133462041-210X
Dillon, Erin M., Lafferty, Kevin D., McCauley, Douglas J., Bradley, Darcy, Norris, Richard D., Caselle, Jennifer E., DiRenzo, Graziella V., Gardner, Jonathan P. A., and O'Dea, Aaron. 2020. "Dermal denticle assemblages in coral reef sediments correlate with conventional shark surveys." Methods in Ecology and Evolution Article–13346.
ID: 154029
Type: article
Authors: Dillon, Erin M.; Lafferty, Kevin D.; McCauley, Douglas J.; Bradley, Darcy; Norris, Richard D.; Caselle, Jennifer E.; DiRenzo, Graziella V.; Gardner, Jonathan P. A.; O'Dea, Aaron
Keywords: STRI
Abstract: 1. It is challenging to assess long-term trends in mobile, long-lived and relatively rare species such as sharks. Despite ongoing declines in many coastal shark populations, conventional surveys might be too fleeting and too recent to describe population trends over decades to millennia. Placing recent shark declines into historical context should improve management efforts as well as our understanding of past ecosystem dynamics. 2. A new palaeoecological approach for surveying shark abundance on coral reefs is to quantify dermal denticle assemblages preserved in sediments. This approach assumes that denticle accumulation rates correlate with shark abundances. Here, we test this assumption by comparing the denticle record in surface sediments to three conventional shark survey methods at Palmyra Atoll, Line Islands, central Pacific Ocean, where shark density is high and spatially heterogeneous. 3. We generally found a significant positive correlation between denticle accumulation rates and shark abundances derived from underwater visual census, baited remote underwater video and hook and line surveys. 4. Denticle accumulation rates reflected shark abundances, suggesting that denticle assemblages can preserve a signal of time-averaged shark abundance in lowenergy coral reef environments. We offer suggestions for applying this tool to measure shark abundance over long time-scales in other contexts
Microbial colonization of microplastics in the Caribbean SeaDudek, Kassandra L.Cruz, Bianca N.Polidoro, BethNeuer, Susanne2020DOI: info:10.1002/lol2.10141Limnology and Oceanography Lettersv. 5No. 15175–172378-2242
Dudek, Kassandra L., Cruz, Bianca N., Polidoro, Beth, and Neuer, Susanne. 2020. "Microbial colonization of microplastics in the Caribbean Sea." Limnology and Oceanography Letters 5 (1):5–17.
ID: 154062
Type: article
Authors: Dudek, Kassandra L.; Cruz, Bianca N.; Polidoro, Beth; Neuer, Susanne
Keywords: STRI
Abstract: Microplastics in the ocean function as an artificial microbial reef, with diverse communities of eukaryotic and bacterial microbiota colonizing its surface. It is not well understood if these communities are specific for the type of microplastic on which they develop. Here, we carried out a 6-week long incubation experiment of six common plastic polymers in Bocas del Toro, Panama. The community composition of prokaryotes based on 16S rRNA gene sequencing data, when judged under a null model analysis, shows that neither plastic polymer type nor time exposed to the environment plays a significant role in shaping biofilm communities. However, the null model analyses of eukaryotic communities based on 18S rRNA gene sequences reveal that they can be significantly influenced by plastic polymer type and time incubated. This was confirmed by scanning electron microscopy, which allowed us to distinguish plastic-specific diatom communities by the end of the incubation period.
Habitat Use and Abundance of Island-Endemic White-Tailed Deer in PanamaDuquette, Jared F.Flores, Eric E.Ureña, LuisOrtega, JosuéCisneros, IlianaMoreno, RicardoLoman, Zachary2020DOI: info:10.3106/ms2019-0036Mammal Studyv. 45No. 11131–131343-4152
Duquette, Jared F., Flores, Eric E., Ureña, Luis, Ortega, Josué, Cisneros, Iliana, Moreno, Ricardo, and Loman, Zachary. 2020. "Habitat Use and Abundance of Island-Endemic White-Tailed Deer in Panama." Mammal Study 45 (1):1–13.
ID: 154321
Type: article
Authors: Duquette, Jared F.; Flores, Eric E.; Ureña, Luis; Ortega, Josué; Cisneros, Iliana; Moreno, Ricardo; Loman, Zachary
Keywords: STRI
Abstract: Although white-tailed deer (Odocoileus virginianus) have been studied extensively, ecological information lacks for O. virginianus rothschildi, a subspecies endemic to Coiba Island, Panama. A combination of camera traps (n = 29) deployed during March–July 2015 and Royle–Nichols occupancy model were used to estimate the sex-related detection, habitat use, and abundance of unmarked deer. No covariates influenced detection of individual sexes, but detection of sexes combined was greater on wildlife trails than maintained human foot trails and negatively related to daily maximum temperature. Predicted abundance of sexes combined and females were greatest along an ecotone of secondary forest and feral fields, whereas male abundance was greatest at an ecotone of secondary and primary forest. Results corroborated the common mixed edge habitat use of O. virginianus, with likely partitioning of resources between sexes due to differing habitat needs. Although primary forest dominants Coiba Island, lesser use of this habitat suggests that it may provide poorer resources for deer, at least during the period of this study. Additionally, habitat use suggested potential avoidance of areas with greater feral livestock and tourist use. Further research is needed to understand the ecology of this endemic subspecies, including potential anthropogenic threats.