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1. Phylogenetic classification of the world's tropical forests

Author

Slik, J. W. F., Franklin, J., Arroyo-Rodríguez, V., Field, R., Aguilar, S., Aguirre, N., Ahumada, J., Aiba, S.-I., Alves, L. F., Anitha, K., Avella, A., Mora, F., Aymard, G. A. C., Báez, S., Balvanera, P., Bastian, M. L., Bastin, J.-F., Bellingham, P. J., Van Den Berg, E., Da Conceição Bispo, P., Boeckx, P., Boehning-Gaese, K., Bongers, F., Boyle, B., Brambach, F., Brearley, F. Q., Brown, S., Chai, S.-L., Chazdon, R. L., Chen, S., Chhang, P., Chuyong, G., Ewango, C., Coronado, I. M., Cristóbal-Azkarate, J., Culmsee, H., Damas, K., Dattaraja, H. S., Davidar, P., DeWalt, S. J., DIn, H., Drake, D. R., Duque, A., Durigan, G., Eichhorn, K., Eler, E. S., Enoki, T., Ensslin, A., Fandohan, A. B., Farwig, N., Feeley, K. J., Fischer, M., Forshed, O., Garcia, Q. S., Garkoti, S. C., Gillespie, T. W., Gillet, J.-F., Gonmadje, C., Granzow-De La Cerda, I., Griffith, D. M., Grogan, J., Hakeem, K. R., Harris, D. J., Harrison, R. D., Hector, A., Hemp, A., Homeier, J., Hussain, M. S., Ibarra-Manríquez, G., Hanum, I. F., Imai, N., Jansen, P. A., Joly, C. A., Joseph, S., Kartawinata, K., Kearsley, E., Kelly, D. L., Kessler, M., Killeen, T. J., Kooyman, R. M., Laumonier, Y., Laurance, S. G., Laurance, W. F., Lawes, M. J., Letcher, S. G., Lindsell, J., Lovett, J., Lozada, J., Lu, X., Lykke, A. M., Bin Mahmud, K., Mahayani, N. P. D., Mansor, A., Marshall, A. R., Martin, E. H., Matos, D. C. L., Meave, J. A., Melo, F. P. L., Mendoza, Z. H. A., Metali, F., Medjibe, V. P., Metzger, J. P., Metzker, T., Mohandass, D., Munguía-Rosas, M. A., Muñoz, R., Nurtjahy, E., De Oliveira, E. L., Onrizal, Parolin, P., Parren, M., Parthasarathy, N., Paudel, E., Perez, R., Pérez-García, E. A., Pommer, U., Poorter, L., Qi, L., Piedade, M. T. F., Pinto, J. R. R., Poulsen, A. D., Poulsen, J. R., Powers, J. S., Prasad, R. C., Puyravaud, J.-P., Rangel, O., Reitsma, J., Rocha, D. S. B., Rolim, S., Rovero, F., Rozak, A., Ruokolainen, K., Rutishauser, E., Rutten, G., Mohd Said, M. N., Saiter, F. Z., Saner, P., Santos, B., Dos Santos, J. R., Sarker, S. K., Schmitt, C. B., Schoengart, J., Schulze, M., Sheil, D., Sist, P., Souza, A. F., Spironello, W. R., Sposito, T., Steinmetz, R., Stevart, T., Suganuma, M. S., Sukri, R., Sultana, A., Sukumar, R., Sunderland, T., Supriyadi, Suresh, H. S., Suzuki, E., Tabarelli, M., Tang, J., Tanner, E. V. J., Targhetta, N., Theilade, I., Thomas, D., Timberlake, J., De Morisson Valeriano, M., Van Valkenburg, J., Van Do, T., Van Sam, H., Vandermeer, J. H., Verbeeck, H., Vetaas, O. R., Adekunle, V., Vieira, S. A., Webb, C. O., Webb, E. L., Whitfeld, T., Wich, S., Williams, J., Wiser, S., Wittmann, F., Yang, X., Yao, C. Y. A., Yap, S. L., Zahawi, R. A., Zakaria, R., and Zang, R.

Subjects
15. Life on land

2. Mapping of SINEs in the genome of Proechimys (Mammalia: Rodentia).

Author

Cardoso Soares S, Schmidt Eler E, Eduardo Faresin E Silva C, Francisco Souza E Sousa J, Nazareth Ferreira da Silva M, Pereira Araújo N, Svartman M, and Feldberg E

Subjects
Animals, Genome genetics, Chromosome Mapping, Karyotyping methods, Evolution, Molecular, Chromosomes, Mammalian genetics, Rodentia genetics, Rodentia classification, Short Interspersed Nucleotide Elements genetics, Karyotype
Abstract

This study aimed to analyze the distribution of short interspersed elements (SINEs) in the chromosomes of five species of rodents of the genus Proechimys and in a variant karyotype of P. guyannensis. Molecular cytogenetic techniques were used to characterize the sequences of the B1, B4, MAR and THER SINEs, which were used as probes for hybridization in metaphase chromosomes. A wide distribution of SINEs was observed in the chromosomes of the Proechimys species examined, thus indicating differentiation of these retroelements. The signal of the B4 SINE was more evident than that of the B1 SINE, especially in P. echinothrix, P. longicaudatus, and P. cuvieri. Although the signal of the MAR SINE was more explosive than that of the THER SINE, in the species P. echinothrix, P. guyannensis (2n = 46) and P. longicaudatus, its distribution in the karyotypes was similar. The signals of these retroelements occurred at specific heterochromatic sites and were centromeric/pericentromeric and at the terminal regions in most chromosomes. This appears to be a typical distribution pattern of the SINEs and may indicate involvement with rearrangements during karyotypic diversification in Proechimys. The variation of the SINEs in the genome of Proechimys species demonstrates that these elements are distributed in a specific way in this genus and the preference for some sites, considered hotspots for chromosomal breakage, allows us to propose that these elements are related to the karyotypic evolution of Proechimys., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Published
2024
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3. An estimate of the number of tropical tree species.

Author

Slik JW, Arroyo-Rodríguez V, Aiba S, Alvarez-Loayza P, Alves LF, Ashton P, Balvanera P, Bastian ML, Bellingham PJ, van den Berg E, Bernacci L, da Conceição Bispo P, Blanc L, Böhning-Gaese K, Boeckx P, Bongers F, Boyle B, Bradford M, Brearley FQ, Breuer-Ndoundou Hockemba M, Bunyavejchewin S, Calderado Leal Matos D, Castillo-Santiago M, Catharino EL, Chai SL, Chen Y, Colwell RK, Chazdon RL, Clark C, Clark DB, Clark DA, Culmsee H, Damas K, Dattaraja HS, Dauby G, Davidar P, DeWalt SJ, Doucet JL, Duque A, Durigan G, Eichhorn KA, Eisenlohr PV, Eler E, Ewango C, Farwig N, Feeley KJ, Ferreira L, Field R, de Oliveira Filho AT, Fletcher C, Forshed O, Franco G, Fredriksson G, Gillespie T, Gillet JF, Amarnath G, Griffith DM, Grogan J, Gunatilleke N, Harris D, Harrison R, Hector A, Homeier J, Imai N, Itoh A, Jansen PA, Joly CA, de Jong BH, Kartawinata K, Kearsley E, Kelly DL, Kenfack D, Kessler M, Kitayama K, Kooyman R, Larney E, Laumonier Y, Laurance S, Laurance WF, Lawes MJ, Amaral IL, Letcher SG, Lindsell J, Lu X, Mansor A, Marjokorpi A, Martin EH, Meilby H, Melo FP, Metcalfe DJ, Medjibe VP, Metzger JP, Millet J, Mohandass D, Montero JC, de Morisson Valeriano M, Mugerwa B, Nagamasu H, Nilus R, Ochoa-Gaona S, Onrizal, Page N, Parolin P, Parren M, Parthasarathy N, Paudel E, Permana A, Piedade MT, Pitman NC, Poorter L, Poulsen AD, Poulsen J, Powers J, Prasad RC, Puyravaud JP, Razafimahaimodison JC, Reitsma J, Dos Santos JR, Roberto Spironello W, Romero-Saltos H, Rovero F, Rozak AH, Ruokolainen K, Rutishauser E, Saiter F, Saner P, Santos BA, Santos F, Sarker SK, Satdichanh M, Schmitt CB, Schöngart J, Schulze M, Suganuma MS, Sheil D, da Silva Pinheiro E, Sist P, Stevart T, Sukumar R, Sun IF, Sunderland T, Suresh HS, Suzuki E, Tabarelli M, Tang J, Targhetta N, Theilade I, Thomas DW, Tchouto P, Hurtado J, Valencia R, van Valkenburg JL, Van Do T, Vasquez R, Verbeeck H, Adekunle V, Vieira SA, Webb CO, Whitfeld T, Wich SA, Williams J, Wittmann F, Wöll H, Yang X, Adou Yao CY, Yap SL, Yoneda T, Zahawi RA, Zakaria R, Zang R, de Assis RL, Garcia Luize B, and Venticinque EM

Subjects
Conservation of Natural Resources, Databases, Factual, Ecosystem, Phylogeography, Rainforest, Species Specificity, Statistics, Nonparametric, Biodiversity, Forests, Trees classification, Tropical Climate
Abstract

The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼ 40,000 and ∼ 53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼ 19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼ 4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.

Published
2015
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4. Fast demographic traits promote high diversification rates of Amazonian trees.

Author

Baker TR, Pennington RT, Magallon S, Gloor E, Laurance WF, Alexiades M, Alvarez E, Araujo A, Arets EJ, Aymard G, de Oliveira AA, Amaral I, Arroyo L, Bonal D, Brienen RJ, Chave J, Dexter KG, Di Fiore A, Eler E, Feldpausch TR, Ferreira L, Lopez-Gonzalez G, van der Heijden G, Higuchi N, Honorio E, Huamantupa I, Killeen TJ, Laurance S, Leaño C, Lewis SL, Malhi Y, Marimon BS, Marimon Junior BH, Monteagudo Mendoza A, Neill D, Peñuela-Mora MC, Pitman N, Prieto A, Quesada CA, Ramírez F, Ramírez Angulo H, Rudas A, Ruschel AR, Salomão RP, de Andrade AS, Silva JN, Silveira M, Simon MF, Spironello W, ter Steege H, Terborgh J, Toledo M, Torres-Lezama A, Vasquez R, Vieira IC, Vilanova E, Vos VA, and Phillips OL

Subjects
South America, Tropical Climate, Biodiversity, Models, Biological, Trees physiology
Abstract

The Amazon rain forest sustains the world's highest tree diversity, but it remains unclear why some clades of trees are hyperdiverse, whereas others are not. Using dated phylogenies, estimates of current species richness and trait and demographic data from a large network of forest plots, we show that fast demographic traits--short turnover times--are associated with high diversification rates across 51 clades of canopy trees. This relationship is robust to assuming that diversification rates are either constant or decline over time, and occurs in a wide range of Neotropical tree lineages. This finding reveals the crucial role of intrinsic, ecological variation among clades for understanding the origin of the remarkable diversity of Amazonian trees and forests., (© 2014 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.)

Published
2014
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5. Comparative cytogenetics of spiny rats of the genus Proechimys (Rodentia, Echimyidae) from the Amazon region.

Author

Eler ES, da Silva MN, Silva CE, and Feldberg E

Subjects
Animals, Brazil, Chromosome Banding, Karyotyping, Rodentia genetics
Abstract

We made a comparative analysis of the cytogenetics of spiny rat species of the genus Proechimys collected from several sites of the Madeira River basin (Amazonas State, Brazil) and Jari River valley (Pará State, Brazil). Individuals were assigned to three groups based on diploid and fundamental numbers: 2n = 28, FN = 46 (P. cuvieri and P. gr. longicaudatus); 2n = 38, FN = 52 (Proechimys gr. guyannensis), and 2n = 40, FN = 54 (P. gardneri). The nucleolar organizer region (NOR) was interstitial on the long arm of one submetacentric pair, as seen in all species of Proechimys analyzed thus far. However, its position in the karyotype was variable. A duplication of the NOR in one of the homologues was detected in P. gr. longicaudatus from the Aripuanã basin along the mid Madeira. The C-band pattern varied between species and, together with the NOR, allowed the identification of two evolutionary units in P. gr. longicaudatus in the region of the mid Madeira River (cytotypes A and B). The morphology and banding of the sex chromosomes were species specific. A range extension is suggested for the geographic distribution of P. gardneri and P. gr. longicaudatus. Moreover, we suggest that species of Proechimys with 2n = 38 chromosomes are restricted to east of the Negro River and north of the Amazon River. We also revised the published chromosome data available for Proechimys.

Published
2012
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