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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. https://doi.org/10.3390/d12010030
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.
Interspecific Eavesdropping on Ant Chemical CommunicationAdams, Rachelle M. M.Wells, Rachel L.Yanoviak, Stephen P.Frost, Christopher J.Fox, Eduardo G. P.2020DOI: info:10.3389/fevo.2020.00024Frontiers in Ecology and Evolutionv. 82424LAUSANNE; AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLANDFRONTIERS MEDIA SA24–242296-701X
Adams, Rachelle M. M., Wells, Rachel L., Yanoviak, Stephen P., Frost, Christopher J., and Fox, Eduardo G. P. 2020. "Interspecific Eavesdropping on Ant Chemical Communication." Frontiers in Ecology and Evolution 8:24–24. https://doi.org/10.3389/fevo.2020.00024
ID: 155290
Type: article
Authors: Adams, Rachelle M. M.; Wells, Rachel L.; Yanoviak, Stephen P.; Frost, Christopher J.; Fox, Eduardo G. P.
Keywords: NMNH; NH-Entomology; STRI
Abstract: Chemical communication is a fundamental, highly complex component of social insect societies. Ants in particular employ a remarkable diversity of chemical signals to maintain social cohesion among nestmates, gain essential resources through coordinated foraging, and warn of danger. Although the chemicals used can be functionally specific, they are vulnerable to exploitation by eavesdropping natural enemies (e.g., parasitoids, predators, parasites) and other associates (e.g., myrmecophiles). Ant nests are nutrient hotspots due to their collection of resources warranting keen defense systems; yet the heavily defended hideouts are frequently invaded. Many organisms exploit ant species, but how they locate hosts-including what host-derived cues are used-is still poorly understood. Here, we review current knowledge about how ant chemical communication systems can be exploited by unintended receivers. We take a case study approach and illustrate the diversity of ant associates and host traits that may predispose ants to exploitation. We identify knowledge gaps by reviewing host systems and listing: (1) the types of associates (e.g., fly, wasp, beetle) where eavesdropping is likely occurring, organized by the host communication system that is being exploited; (2) the ant parasites that exploit trail pheromones; and (3) the experimentally determined chemicals (i.e., alarm/defensive pheromones), used by eavesdroppers. At least 25 families of arthropods (10 orders) potentially eavesdrop on ant communication systems and nearly 20 host ant species are vulnerable to trail parasite ant species. We also propose future research that will improve our understanding of community assembly by examining host traits (e.g., latitude, nest characteristics, trail system) that influence their susceptibility to eavesdropping associates.
Fossil sea catfish (Siluriformes; Ariidae) otoliths and in-skull otoliths from the Neogene of the Western Central AtlanticAguilera, OrangelLopes, Ricardo T.Rodriguez, Felixdos Santos, Thaís M.Rodrigues-Almeida, CarolineAlmeida, PauloMachado, Alessandra S.Moretti, Tailan2020DOI: info:10.1016/j.jsames.2020.102619Journal of South American Earth Sciencesv. 1011026191026190895-9811
Aguilera, Orangel, Lopes, Ricardo T., Rodriguez, Felix, dos Santos, Thaís M., Rodrigues-Almeida, Caroline, Almeida, Paulo, Machado, Alessandra S., and Moretti, Tailan. 2020. "Fossil sea catfish (Siluriformes; Ariidae) otoliths and in-skull otoliths from the Neogene of the Western Central Atlantic." Journal of South American Earth Sciences 101:102619. https://doi.org/10.1016/j.jsames.2020.102619
ID: 155492
Type: article
Authors: Aguilera, Orangel; Lopes, Ricardo T.; Rodriguez, Felix; dos Santos, Thaís M.; Rodrigues-Almeida, Caroline; Almeida, Paulo; Machado, Alessandra S.; Moretti, Tailan
Keywords: STRI
Abstract: The examined Ariidae marine catfish from the Neogene of tropical America consisted of isolated skulls, otoliths and bone fragments, some of which were described independently as otolith-based species or skull-based species. We used three-dimensional digital rendering (microCT) of skull and otolith reconstructions to recognize anatomical patterns including skull-otolith morphology, spatial allocations of otoliths in the endocranium for taxonomic identifications. We recognized isolated Proto-Caribbean otoliths of Cathorops sp. from the late early Miocene to early Pliocene formations and isolated otoliths of †Aspistor verumquadriscutis, †Bagre urumacoensis and Notarius sp. from the late Miocene. We explored the endocrania of four fossil Ariidae skulls from the late Oligocene to late early Miocene Proto-Caribbean to determine their internal otolith-cranial morphology, and we identified and described the skulls of †Bagre protocaribbeanus and †Cantarius nolfi and erected the new species of †Bagre castilloensi n. sp. and †Bagre ornatus n. sp. based on the internal otolith-skull association. The first fossil record of Bagre marinus from the early Pliocene Cubagua Formation to the late Pliocene San Gregorio Formation completed the ariid geochronological sequence. We discuss the differential stages of fossil preservation of bioapatite skulls and aragonite otoliths according to the diagenetic processes as well as the paleoenvironmental conditions in the sedimentary basins. Detailed microCT, 3D reconstructions, X-rays, dry prepared skeletons and digital photos of otolith and skull are shown to elucidate the in-skull otoliths species descriptions.
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. https://doi.org/10.1016/j.marmicro.2019.101813
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
First host plant record for Pacarina (Hemiptera, Cicadidae)Aiello, AnnetteStucky, Brian J.2020DOI: info:10.3897/neotropical.15.e49013Neotropical Biology and Conservationv. 15No. 17788Sofia, BulgariaPensoft Publishers77–882236-3777
Aiello, Annette and Stucky, Brian J. 2020. "First host plant record for Pacarina (Hemiptera, Cicadidae)." Neotropical Biology and Conservation 15 (1):77–88. https://doi.org/10.3897/neotropical.15.e49013
ID: 155018
Type: article
Authors: Aiello, Annette; Stucky, Brian J.
Keywords: STRI
Abstract: Twenty-nine Pacarina (Hemiptera: Cicadidae) adults, 12 males and 17 females, emerged from the soil of a potted Dracaena trifasciata (Asparagaceae) in Arraiján, Republic of Panama, providing the first rearing records and the first definitive host plant records for any species of Pacarina. These reared Pacarina appear to be morphologically distinct from all known species of Pacarina and likely represent an undescribed species. In light of this finding, we also discuss the taxonomy, biogeography, and ecology of Pacarina.
Exceptionally preserved 'skin' in an Early Cretaceous fish from ColombiaAlfonso-Rojas, AndrCadena, Edwin-Alberto2020DOI: info:10.7717/peerj.9479PeerJv. 81231–232167-8359
Alfonso-Rojas, Andr and Cadena, Edwin-Alberto. 2020. "Exceptionally preserved 'skin' in an Early Cretaceous fish from Colombia." PeerJ 8:1–23. https://doi.org/10.7717/peerj.9479
ID: 156751
Type: article
Authors: Alfonso-Rojas, Andr; Cadena, Edwin-Alberto
Keywords: STRI
Abstract: Studies of soft tissue, cells and original biomolecular constituents preserved in fossil vertebrates have increased greatly in recent years. Here we report preservation of 'skin' with chemical and molecular characterization from a three-dimensionally preserved caudal portion of an aspidorhynchid Cretaceous fish from the equatorial Barremian of Colombia, increasing the number of localities for which exceptional preservation is known. We applied several analytical techniques including SEM-EDS, FTIR and ToF-SIMS to characterize the micromorphology and molecular and elemental composition of this fossil. Here, we show that the fossilized 'skin' exhibits similarities with those from extant fish, including the wrinkles after suffering compression stress and flexibility, as well as architectural and tissue aspects of the two main layers (epidermis and dermis). This similarity extends also to the molecular level, with the demonstrated preservation of potential residues of original proteins not consistent with a bacterial source. Our results show a potential preservation mechanism where scales may have acted as an external barrier and together with an internal phosphate layer resulting from the degradation of the dermis itself creating an encapsulated environment for the integument.
Population Genomics and Phylogeography of a Clonal Bryophyte With Spatially Separated Sexes and Extreme Sex RatiosAlonso-García, MartaCarlos, Villarreal A., JuanMcFarland, KennethGoffinet, Bernard2020DOI: info:10.3389/fpls.2020.00495Frontiers in Plant Sciencev. 111664-462X
Alonso-García, Marta, Carlos, Villarreal A., Juan, McFarland, Kenneth, and Goffinet, Bernard. 2020. "Population Genomics and Phylogeography of a Clonal Bryophyte With Spatially Separated Sexes and Extreme Sex Ratios." Frontiers in Plant Science 11:https://doi.org/10.3389/fpls.2020.00495
ID: 156581
Type: article
Authors: Alonso-García, Marta; Carlos, Villarreal A., Juan; McFarland, Kenneth; Goffinet, Bernard
Keywords: STRI
Abstract: The southern Appalachian (SA) is one of the most biodiversity-rich areas in North America and has been considered a refugium for many disjunct plant species, from the last glacial period to the present. Our study focuses on the SA clonal hornwort, Nothoceros aenigmaticus J. C. Villarreal & K. D. McFarland. This hornwort was described from North Carolina and is widespread in the SA, growing on rocks near or submerged in streams in six and one watersheds of the Tennessee (TR) and Alabama (AR) Rivers, respectively. Males and female populations occur in different watersheds, except in the Little Tennessee (TN) River where an isolated male population exists ca. 48 km upstream from the female populations. The sex ratio of 1:0 seems extreme in each population. In this study, we use nuclear and organellar microsatellites from 250 individuals from six watersheds (seven populations) in the SA region and two populations from Mexico (23 individuals). We, then, selected 86 individuals from seven populations and used genotyping by sequencing to sample over 600 bi-allelic markers. Our results suggest that the SA N. aenigmaticus and Mexican plants are a nested within a clade of sexual tropical populations. In the US populations, we confirm an extreme sex ratio and only contiguous US watersheds share genotypes. The phylogenetic analysis of SNP data resolves four clusters: Mexican populations, male plants (Little Pigeon and Pigeon river watersheds) and two clusters of female plants; one from the Little Tennessee and Hiwassee Rivers (TR) and the other from the Ocoee (TR) and Coosa (AR) Rivers. All clusters are highly differentiated (Fst values over 0.9). In addition, our individual assignment analyses and PCAs reflect the phylogenetic results grouping the SA samples in three clades and recovering males and female plants with high genetic differentiation (Fst values between 0.5 and 0.9 using microsatellites and bi-allelic markers). Our results point to Pleistocene events shaping the biogeographical pattern seen in US populations. The extreme sex ratio reflects isolation and highlights the high vulnerability of the populations in the SA.
Long-Term Impacts of Invasive Insects and Pathogens on Composition, Biomass, and Diversity of Forests in Virginia's Blue Ridge MountainsAnderson-Teixeira, Kristina J.Herrmann, ValentineCass, Wendy B.Williams, Alan B.Paull, Stephen J.Gonzalez-Akre, Erika B.Helcoski, RyanTepley, Alan J.Bourg, Norman A.Cosma, Christopher T.Ferson, Abigail E.Kittle, CarolineMeakem, VictoriaMcGregor, Ian R.Prestipino, Maya N.Scott, Michael K.Terrell, Alyssa R.Alonso, AlfonsoDallmeier, FranciscoMcShea, William J.2020DOI: info:10.1007/s10021-020-00503-wEcosystemsNew YorkSpringer1432-9840
Anderson-Teixeira, Kristina J., Herrmann, Valentine, Cass, Wendy B., Williams, Alan B., Paull, Stephen J., Gonzalez-Akre, Erika B., Helcoski, Ryan, Tepley, Alan J., Bourg, Norman A., Cosma, Christopher T., Ferson, Abigail E., Kittle, Caroline, Meakem, Victoria, McGregor, Ian R., Prestipino, Maya N., Scott, Michael K., Terrell, Alyssa R., Alonso, Alfonso, Dallmeier, Francisco, and McShea, William J. 2020. "Long-Term Impacts of Invasive Insects and Pathogens on Composition, Biomass, and Diversity of Forests in Virginia's Blue Ridge Mountains." Ecosystems https://doi.org/10.1007/s10021-020-00503-w
ID: 155476
Type: article
Authors: Anderson-Teixeira, Kristina J.; Herrmann, Valentine; Cass, Wendy B.; Williams, Alan B.; Paull, Stephen J.; Gonzalez-Akre, Erika B.; Helcoski, Ryan; Tepley, Alan J.; Bourg, Norman A.; Cosma, Christopher T.; Ferson, Abigail E.; Kittle, Caroline; Meakem, Victoria; McGregor, Ian R.; Prestipino, Maya N.; Scott, Michael K.; Terrell, Alyssa R.; Alonso, Alfonso; Dallmeier, Francisco; McShea, William J.
Keywords: NZP; STRI
Abstract: Exotic forest insects and pathogens (EFIP) have become regular features of temperate forest ecosystems, yet we lack a long-term perspective on their net impacts on tree mortality, carbon sequestration, and tree species diversity. Here, we analyze 3 decades (1987-2019) of forest monitoring data from the Blue Ridge Mountains ecoregion in eastern North America, including 67 plots totaling 29.4 ha, along with a historical survey from 1939. Over the past century, EFIP substantially affected at least eight tree genera. Tree host taxa had anomalously high mortality rates (>= 6% year(-1) from 2008 to 2019 vs 1.4% year(-1) for less-impacted taxa). Following the arrival of EFIP, affected taxa declined in abundance (- 25 to - 100%) and live aboveground biomass (AGB; - 13 to - 100%) within our monitoring plots. We estimate that EFIP were responsible for 21-29% of ecosystem AGB loss through mortality (- 87 g m(-2) year(-1)) from 1991 to 2013 across 66 sites. Over a century, net AGB loss among affected species totaled roughly 6.6-10 kg m(-2). The affected host taxa accounted for 23-29% of genera losses at the plot scale, with mixed net effects on alpha-diversity. Several taxa were lost from our monitoring plots but not completely extirpated from the region. Despite these losses, both total AGB and alpha-diversity were largely recovered through increases in sympatric genera. These results indicate that EFIP have been an important force shaping forest composition, carbon cycling, and diversity. At the same time, less-affected taxa in these relatively diverse temperate forests have conferred substantial resilience with regard to biomass and alpha-diversity.
Review of Scolia (Hymenoptera: Scoliidae) from Central America, Including Seasonal Flight Activity in Scolia GuttataAnino, Yostin J.Cambra, Roberto A.Windsor, Donald M.Zuniga, RonaldQuintero, Diomedes2020DOI: info:10.15446/abc.v25n2.77590Acta Biológica Colombianav. 25No. 2202209202–2090120-548X
Anino, Yostin J., Cambra, Roberto A., Windsor, Donald M., Zuniga, Ronald, and Quintero, Diomedes. 2020. "Review of Scolia (Hymenoptera: Scoliidae) from Central America, Including Seasonal Flight Activity in Scolia Guttata." Acta Biológica Colombiana 25 (2):202–209. https://doi.org/10.15446/abc.v25n2.77590
ID: 156578
Type: article
Authors: Anino, Yostin J.; Cambra, Roberto A.; Windsor, Donald M.; Zuniga, Ronald; Quintero, Diomedes
Keywords: STRI
Abstract: A taxonomic revision of the genus Scolia Fabricius, 1775 (Hymenoptera: Scoliidae) from Central America is presented. Two species of Scolia are present in Central America: S. (Discolia) guttata Burmeister, 1853 and S. (Hesperoscolia) rufiventris Fabricius, 1804, the latter representing the first record for Costa Rica, Panama and Colombia. The male of S. rufiventris is described and illustrated for the first time. Seasonal flight activity for S. guttata from two years of continuous Malaise trapping in Barro Colorado Island, Panama, is described
Occurrence in seeds and potential seed transmission of Xanthomonas vasicola pv. vasculorum in maize in the United StatesArias, SilvinaBlock, CharlesMayfield, Derrick A.Santillana, Gem E.Stulberg, Michael E.Broders, KirkJackson-Ziems, TamraMunkvold, Gary P.2020DOI: info:10.1094/PHYTO-08-19-0306-RPhytopathologyv. 110No. 6113911461139–11460031-949X
Arias, Silvina, Block, Charles, Mayfield, Derrick A., Santillana, Gem E., Stulberg, Michael E., Broders, Kirk, Jackson-Ziems, Tamra, and Munkvold, Gary P. 2020. "Occurrence in seeds and potential seed transmission of Xanthomonas vasicola pv. vasculorum in maize in the United States." Phytopathology 110 (6):1139–1146. https://doi.org/10.1094/PHYTO-08-19-0306-R
ID: 155710
Type: article
Authors: Arias, Silvina; Block, Charles; Mayfield, Derrick A.; Santillana, Gem E.; Stulberg, Michael E.; Broders, Kirk; Jackson-Ziems, Tamra; Munkvold, Gary P.
Keywords: STRI
Abstract: This paper reports original evidence regarding the potential role of seed transmission of Xanthomonas vasicola pv. vasculorum (Xvv) in the epidemiology of bacterial leaf streak (BLS) in maize. We evaluated the occurrence of the pathogen on seeds from diseased fields and its subsequent transmission to seedlings. In 2016 and 2017, Xvv was detected by TaqMan PCR from 22 of 41 maize seed lots harvested from naturally-infected fields in Colorado (CO), Nebraska (NE) and Iowa (IA). However, many of the PCR-positive samples did not yield culturable Xvv colonies. The highest levels of seed contamination were detected in dent maize and popcorn from NE and CO. Seed transmission was evaluated in greenhouse grow-outs from eight seed lots, totaling more than 14,000 plants. Putative seed transmission events from naturally contaminated seed lots, estimated from PCR results, occurred at a frequency between 0.1 and 0.5% in 10-seedling pooled samples and at a frequency of 2.7% from individual plant assays. However, no seedling symptoms were observed during these assays and live Xvv colonies were not recovered from PCR-positive seedlings. In contrast, seed transmission was readily demonstrated from artificially contaminated seed lots, including typical symptoms and recovery of live bacteria. Seed transmission consistently occurred from seeds soaked in bacterial suspensions with concentrations of ≥106 CFU per mL, suggesting that a threshold population of the bacterium is necessary for the development of BLS-symptoms and recovery of live bacteria. The low bacterial populations on naturally contaminated seeds apparently were not sufficient to result in diseased seedlings.
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. https://doi.org/10.1002/ecy.2937
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. https://doi.org/10.1128/mBio.02475-19
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.
Early Eocene spore and pollen assemblages from the Laguna del Hunco fossil-lake beds, Patagonia, ArgentinaBarreda, Viviana D.Zamaloa, María del CarmenGandolfo, María A.Jaramillo, CarlosWilf, Peter2020DOI: info:10.1086/708386International journal of plant sciencesv. 181No. 61221–221058-5893
Barreda, Viviana D., Zamaloa, María del Carmen, Gandolfo, María A., Jaramillo, Carlos, and Wilf, Peter. 2020. "Early Eocene spore and pollen assemblages from the Laguna del Hunco fossil-lake beds, Patagonia, Argentina." International journal of plant sciences 181 (6):1–22. https://doi.org/10.1086/708386
ID: 156400
Type: article
Authors: Barreda, Viviana D.; Zamaloa, María del Carmen; Gandolfo, María A.; Jaramillo, Carlos; Wilf, Peter
Keywords: STRI
Costs and compensation in zooplankton pigmentation under countervailing threats of ultraviolet radiation and predationBashevkin, Samuel M.Christy, John H.Morgan, Steven G.2020DOI: info:10.1007/s00442-020-04648-2Oecologia1131–130029-8549
Bashevkin, Samuel M., Christy, John H., and Morgan, Steven G. 2020. "Costs and compensation in zooplankton pigmentation under countervailing threats of ultraviolet radiation and predation." Oecologia 1–13. https://doi.org/10.1007/s00442-020-04648-2
ID: 155497
Type: article
Authors: Bashevkin, Samuel M.; Christy, John H.; Morgan, Steven G.
Keywords: STRI
Enemy-free space and the distribution of ants, springtails and termites in the soil of one tropical rainforestBasset, YvesPalacios-Vargas, JosDonoso, David A.Castaño-Meneses, GabrielaDecaëns, ThibaudLamarre, Greg P.De León, Luis F.Rivera, MarlenyGarcía-Gómez, ArturoPerez, FilonilaBobadilla, RicardoLopez, YacksecariRamirez, José AlejandroCruz, Maira MontejoGalván, Angela ArangoMejía-Recamier, Blanca E.Barrios, Héctor2020DOI: info:10.1016/j.ejsobi.2020.103193European Journal of Soil Biologyv. 991031931031931164-5563
Basset, Yves, Palacios-Vargas, Jos, Donoso, David A., Castaño-Meneses, Gabriela, Decaëns, Thibaud, Lamarre, Greg P., De León, Luis F., Rivera, Marleny, García-Gómez, Arturo, Perez, Filonila, Bobadilla, Ricardo, Lopez, Yacksecari, Ramirez, José Alejandro, Cruz, Maira Montejo, Galván, Angela Arango, Mejía-Recamier, Blanca E., and Barrios, Héctor. 2020. "Enemy-free space and the distribution of ants, springtails and termites in the soil of one tropical rainforest." European Journal of Soil Biology 99:103193. https://doi.org/10.1016/j.ejsobi.2020.103193
ID: 155908
Type: article
Authors: Basset, Yves; Palacios-Vargas, Jos; Donoso, David A.; Castaño-Meneses, Gabriela; Decaëns, Thibaud; Lamarre, Greg P.; De León, Luis F.; Rivera, Marleny; García-Gómez, Arturo; Perez, Filonila; Bobadilla, Ricardo; Lopez, Yacksecari; Ramirez, José Alejandro; Cruz, Maira Montejo; Galván, Angela Arango; Mejía-Recamier, Blanca E.; Barrios, Héctor
Keywords: STRI
On the efficacy of an Ascophyllum-based, soluble extract in association with standard plant growth regulators on the micropropagation of the agarophyte, Gracilaria blodgettii, from seaweed farms located at the northern entrance of the Panama CanalBatista de Vega, GloriaUlloque N, Carlos E.Hurtado, Anicia Q.Cornish, LynnCritchley, Alan T.2020DOI: info:10.1007/s10811-020-02168-3Journal of Applied PhycologySpringer0921-8971
Batista de Vega, Gloria, Ulloque N, Carlos E., Hurtado, Anicia Q., Cornish, Lynn, and Critchley, Alan T. 2020. "On the efficacy of an Ascophyllum-based, soluble extract in association with standard plant growth regulators on the micropropagation of the agarophyte, Gracilaria blodgettii, from seaweed farms located at the northern entrance of the Panama Canal." Journal of Applied Phycology https://doi.org/10.1007/s10811-020-02168-3
ID: 156401
Type: article
Authors: Batista de Vega, Gloria; Ulloque N, Carlos E.; Hurtado, Anicia Q.; Cornish, Lynn; Critchley, Alan T.
Keywords: STRI
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 https://doi.org/10.1002/edn3.66
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.
Scaphokogia totajpe, sp. nov., a new bulky-faced pygmy sperm whale (Kogiidae) from the late Miocene of PeruBenites-Palomino, AldoVelez-Juarbe, JorgeSalas-Gismondi, RodolfoUrbina, Mario2020DOI: info:10.1080/02724634.2019.1728538Journal of Vertebrate PaleontologyAricle e1728538Philadelphia, PennsylvaniaTaylor & Francis IncorporatedAricle e17285380272-4634
Benites-Palomino, Aldo, Velez-Juarbe, Jorge, Salas-Gismondi, Rodolfo, and Urbina, Mario. 2020. "Scaphokogia totajpe, sp. nov., a new bulky-faced pygmy sperm whale (Kogiidae) from the late Miocene of Peru." Journal of Vertebrate Paleontology Aricle e1728538. https://doi.org/10.1080/02724634.2019.1728538
ID: 155361
Type: article
Authors: Benites-Palomino, Aldo; Velez-Juarbe, Jorge; Salas-Gismondi, Rodolfo; Urbina, Mario
Keywords: NMNH; NH-Paleobiology; STRI
Abstract: The modern pygmy and dwarf sperm whales (Physeteroidea, Kogiidae) are remnants of a highly diverse group, which flourished in the Miocene oceans. Unlike their modern suction-feeding, deep-diving relatives, the past diversity of this family includes animals with disparate ecological habits. Here, we describe Scaphokogia totajpe, sp. nov., a new species of kogiid based on a well-preserved skull from the upper Miocene strata of the Pisco Formation, Peru. A phylogenetic analysis places S. totajpe as sister taxon of S. cochlearis and divides Kogiidae into two clades: the first including both species of Scaphokogia and the second including Kogia, Koristocetus, Praekogia, and Nanokogia. Similar to S. cochlearis, S. totajpe has a tubular rostrum with a hypertrophied mesorostral canal, a large supracranial basin, and a leftward deviated facial sagittal crest, but it differs by possessing a proportionately shorter rostrum, a reduced projection of the lacrimojugal between the frontal and the maxilla, and a flat occipital shield. The cranial morphology of Scaphokogia indicates that the extent of the nasal complex was greater than in modern kogiids. Furthermore, the overall rostrum shape and the reconstructed muscle insertion sites indicate that Scaphokogia retained some plesiomorphic features related to a more generalist ecology. Inclusion of S. totajpe into the context of the Pisco Formation indicates that during the late Miocene, the Peruvian coastal system was a hot spot for the diversification of physeteroids, with at least four species coexisting. Finally, Scaphokogia totajpe highlights a late Miocene diversity peak for sperm whales in the global oceans, before the Pliocene odontocete turnover.
Molecular detection of rickettsial agents of hard ticks (Acari: Ixodidae) collected from wild birds of PanamaBermúdez, SergioDomínguez, LillianOchoa, IsisOliveira, Jonathan GonçalvesDe Lemos, Elba,Regina SampaioCastillo, BernardoSmith, DioreneHerrera, JorgeOgrzewalska, Maria2020DOI: info:10.11158/saa.25.4.3Systematic and Applied Acarologyv. 25No. 4622632London, EnglandSystematic and Applied Acarology Society622–6321362-1971
Bermúdez, Sergio, Domínguez, Lillian, Ochoa, Isis, Oliveira, Jonathan Gonçalves, De Lemos, Elba,Regina Sampaio, Castillo, Bernardo, Smith, Diorene, Herrera, Jorge, and Ogrzewalska, Maria. 2020. "Molecular detection of rickettsial agents of hard ticks (Acari: Ixodidae) collected from wild birds of Panama." Systematic and Applied Acarology 25 (4):622–632. https://doi.org/10.11158/saa.25.4.3
ID: 154934
Type: article
Authors: Bermúdez, Sergio; Domínguez, Lillian; Ochoa, Isis; Oliveira, Jonathan Gonçalves; De Lemos, Elba,Regina Sampaio; Castillo, Bernardo; Smith, Diorene; Herrera, Jorge; Ogrzewalska, Maria
Keywords: STRI
Abstract: Ticks (Acari: Ixodidae) collected from wild birds in Panama were tested for the presence of tick-borne pathogens as Rickettsia, Anaplasma, Ehrlichia, Bartonella, Borrelia, Hepatozoon sp., and Babesia. Overall 124 ticks were found in 57 birds belonging to 28 species: Amblyomma longirostre (32 larvae, 1 nymph), Amblyomma nodosum (30 nymphs), Amblyomma geayi (15 larvae, 1 nymph), Amblyomma varium (5 larvae, 2 nymphs), Amblyomma naponense (2 larvae), Amblyomma ovale (2 larvae), and Amblyomma calcaratum (1 larva). DNA of Rickettsia amblyommatis was detected in 65% of A. longirostre, 69% of A. geayi and 14% of A. varium. Moreover, results from two larvae of A. longirostre showed DNA of unidentified Rickettsia sp. No DNA of Borrelia, Bartonella, Anaplasmataceae neither Babesia nor Hepatozoon was detected. These results expand knowledge about the host for immature Amblyomma ticks in Panama and show the first data of Rickettsia in ticks collected from birds in this country.
Framework species approach proves robust in restoring forest on fire prone invasive grass: A case study from PanamaBoeschoten, Laura E.Breugel, Michiel vanBailon, MarioBalbuena, JohanaNuñez, MiguelCerezo, ArturoHall, Jefferson S.2020DOI: info:10.1080/10549811.2020.1746915Journal of Sustainable Forestry1191–191054-9811
Boeschoten, Laura E., Breugel, Michiel van, Bailon, Mario, Balbuena, Johana, Nuñez, Miguel, Cerezo, Arturo, and Hall, Jefferson S. 2020. "Framework species approach proves robust in restoring forest on fire prone invasive grass: A case study from Panama." Journal of Sustainable Forestry 1–19. https://doi.org/10.1080/10549811.2020.1746915
ID: 155212
Type: article
Authors: Boeschoten, Laura E.; Breugel, Michiel van; Bailon, Mario; Balbuena, Johana; Nuñez, Miguel; Cerezo, Arturo; Hall, Jefferson S.
Keywords: STRI
Abstract: Grasses and fire pose a major challenge for forest restoration. Here we evaluate a case study of reforestation in an area invaded by the tall invasive grass Saccharum spontaneum in the Panama Canal Watershed. The project objectives were to (1) replace Saccharum with a forest, (2) restore a stratified mixed species forest and (3) sequester carbon. We aimed to compare the practice of forest restoration with a treatment grounded in theory. Therefore, the first species selection method followed business-as-usual: contractors planted any combination of 130 prescribed species. The second method followed the framework species approach, a mixture of 22 species was planted to ensure early shade, create a stratified forest over time, attract seed dispersers, and for their potential to fix N2. Both treatments showed successful restoration trajectories 8.5 years after planting, they did not differ in structural characteristics (stem density, basal area, aboveground biomass, height, and amount of Saccharum). However, based on the species present, the framework approach shows more potential to become a stratified forest. As the framework approach also withstood fires much better than the business-as-usual approach, we conclude that it improves restoration success in this human-dominated landscape.