Article
Biochemistry & Molecular Biology
Lu Jin, Jia-Jia Liu, Tian-Wen Xiao, Qiao-Ming Li, Li-Xiang Lin, Xiao-Na Shao, Chen-Xin Ma, Bu-Hang Li, Xiang-Cheng Mi, Hai-Bao Ren, Xiu-Juan Qiao, Ju-Yu Lian, Gang Hao, Xue-Jun Ge
Summary: Plastome-trees exhibit higher resolution and support for species relationships compared to barcode-trees and synthetic-trees. For local phylogenetic structure, all three trees showed consistent results with Faith's PD and MPD, but only the synthetic-tree showed significant clustering patterns using MNTD in some plots. In terms of functional traits, both barcode-tree and plastome-tree detected phylogenetic signal in maximum height, while only the plastome-tree detected signal in leaf width.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Ecology
Marta A. Jarzyna, Ignacio Quintero, Walter Jetz
Summary: This study documents variations in avian functional and phylogenetic diversity along major elevational gradients worldwide, revealing strong latitudinal differences. Assemblages in warm tropical lowlands and cold temperate highlands exhibit high functional overdispersion and distinctiveness, while tropical highlands and temperate lowlands show strong functional clustering and redundancy.
Article
Forestry
Sergio Henrique Borges, Tarcisio do R. S. Tavares, Nicholas M. A. Crouch, Fabricio Baccaro
Summary: The study found that total species richness and evenness were similar between secondary and old growth forests, but there were more bird species and disturbance-vulnerable species in the controls of old growth forests. Additionally, bird abundance with distinct functional traits differed between secondary forest age categories, and phylogenetic diversity was higher compared to old growth forests, suggesting a positive conservation value of secondary forests for bird diversity.
FOREST ECOLOGY AND MANAGEMENT
(2021)
Article
Biochemistry & Molecular Biology
Tara A. Pelletier, Danielle J. Parsons, Sydney K. Decker, Stephanie Crouch, Eric Franz, Jeffery Ohrstrom, Bryan C. Carstens
Summary: Patterns of genetic diversity contain valuable information about the history of a species. The phylogatR database and tools allow for efficient repurposing and analysis of existing genetic data, enabling large-scale meta-analyses and introducing genetic analysis to a broader audience.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Luz Boyero, Javier Perez, Naiara Lopez-Rojo, Alan M. Tonin, Francisco Correa-Araneda, Richard G. Pearson, Jaime Bosch, Ricardo J. Albarino, Sankarappan Anbalagan, Leon A. Barmuta, Leah Beesley, Francis J. Burdon, Adriano Caliman, Marcos Callisto, Ian C. Campbell, Bradley J. Cardinale, J. Jesus Casas, Ana M. Chara-Serna, Szymon Ciapala, Eric Chauvet, Checo Colon-Gaud, Aydee Cornejo, Aaron M. Davis, Monika Degebrodt, Emerson S. Dias, Maria E. Diaz, Michael M. Douglas, Arturo Elosegi, Andrea C. Encalada, Elvira de Eyto, Ricardo Figueroa, Alexander S. Flecker, Tadeusz Fleituch, Andre Frainer, Juliana S. Franca, Erica A. Garcia, Gabriela Garcia, Pavel Garcia, Mark O. Gessner, Paul S. Giller, Jesus E. Gomez, Sergio Gomez, Jose F. Goncalves, Manuel A. S. Graca, Robert O. Hall, Neusa Hamada, Luiz U. Hepp, Cang Hui, Daichi Imazawa, Tomoya Iwata, S. A. Junior Edson, Samuel Kariuki, Andrea Landeira-Dabarca, Maria Leal, Kaisa Lehosmaa, Charles M'Erimba, Richard Marchant, Renato T. Martins, Frank O. Masese, Megan Camden, Brendan G. McKie, Adriana O. Medeiros, Jen A. Middleton, Timo Muotka, Junjiro N. Negishi, Jesus Pozo, Alonso Ramirez, Renan S. Rezende, John S. Richardson, Jose Rincon, Juan Rubio-Rios, Claudia Serrano, Angela R. Shaffer, Fran Sheldon, Christopher M. Swan, Nathalie S. D. Tenkiano, Scott D. Tiegs, Janine R. Tolod, Michael Vernasky, Anne Watson, Mourine J. Yegon, Catherine M. Yule
Summary: The study found significant differences in the impact of litter functional diversity on decomposition processes across different latitudes, indicating distinct evolutionary adaptations of litter-consuming detritivores at low and high latitudes.
Article
Biodiversity Conservation
Myung-Bok Lee
Summary: The study found that taxonomic and functional diversity in southern pine forests increased with agricultural cover within the landscape, while insectivores and tree nesters, negatively correlated with urban and agricultural covers, showed a negative response to this variable.
BIODIVERSITY AND CONSERVATION
(2022)
Article
Horticulture
Daouda Coulibaly, Xiao Huang, Shi Ting, Shahid Iqbal, Zhaojun Ni, Kenneth Omondi Ouma, Faisal Hayat, Wei Tan, Guofeng Hu, Chengdong Ma, Benjamin Karikari, Mahmoud Magdy, Zhihong Gao
Summary: This study compared the agronomical and chloroplast genome characteristics of ten Japanese apricot accessions from three Chinese provinces, revealing significant differences in phenotype and genome composition among accessions from different provinces, leading to clustering based on geographic origin.
Article
Environmental Sciences
Dorota Jozwicki, Puneet Sharma, Ingrid Mann, Ulf-Peter Hoppe
Summary: This paper presents an approach to segment Polar Mesospheric Summer Echoes (PMSE) from datasets obtained from EISCAT VHF radar data. The method involves manual labeling of data into different categories and using random forests algorithm to segment the PMSE. The results show that random forests can effectively segment the PMSE and the weighted-down labels technique improves the performance.
Article
Ecology
Axel Arango, Fabricio Villalobos, David A. Prieto-Torres, Roger Guevara
Summary: The study investigates the reverse latitudinal species richness gradient of the Neotropical seasonally dry tropical forests (SDTF), finding an increase in phylogenetic diversity away from the Equator, likely driven by species richness. The phylogenetic structure of SDTF assemblages showed spatial patterning, with significant phylogenetic clustering in certain regions like Mesoamerica and Caatinga. The findings suggest that the phylogenetic history influenced the diversity patterns differently across the Neotropics, with no relationship to climatic stability since the Last Glacial Maximum.
JOURNAL OF BIOGEOGRAPHY
(2021)
Article
Biotechnology & Applied Microbiology
Muhammad Asghar Hassan, Zhixiang Tan, Rongrong Shen, Jichun Xing
Summary: The phylogenetic position and classification of Athysanini, a tribe including a large group of polyphyletic genera, are poorly defined. In this study, we compared the complete mitochondrial genomes of three species of the bamboo-feeding leafhopper genus Abrus. The results showed that these species have highly conserved mitogenomes with similar gene order and biased nucleotide composition. Phylogenetic analyses consistently recovered the monophyletic Athysanini based on limited available mitogenome sequence data.
Article
Biodiversity Conservation
Kyle R. Grant, T. Jonathan Davies, Sachin Medigeshi Harish, Javid Ahmad Dar, Subashree Kothandaraman, Tapas Ray, Dinesh Malasiya, Selvadurai Dayanandan, Mohammed Latif Khan
Summary: This study used an eco-phylogenetic approach to investigate the diversity and assembly patterns of tropical dry forests in Central India. The aim was to inform conservation and restoration practices by identifying potential habitats of conservation significance and vulnerable elements of regional biodiversity.
DIVERSITY AND DISTRIBUTIONS
(2023)
Article
Statistics & Probability
Arkajyoti Saha, Sumanta Basu, Abhirup Datta
Summary: Spatial linear mixed-models are widely used for geospatial data analysis but often ignore spatial correlation in the presence of nonlinear covariate effects. Random forests, a popular method for estimating nonlinear functions, also suffer from the same issue. We propose a novel extension called RF-GLS that incorporates the spatial correlation modeled using Gaussian process in random forests, and show its superior performance in estimation and prediction compared to traditional random forests.
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
(2023)
Article
Biodiversity Conservation
Dehui Meng, Yiming Zuo, Huayun Wang, Gang Feng
Summary: Forest bird communities in China captured by camera traps show significant taxonomic, phylogenetic, and functional diversity. Most of the bird species observed are ground-dwelling, representing approximately 21% of all Chinese bird species. The phylogenetic diversity and functional diversity of understory birds comprise 28% and 51% of all Chinese bird species, respectively.
GLOBAL ECOLOGY AND CONSERVATION
(2021)
Article
Genetics & Heredity
Yong Wang, Jing Yu, Yu-Kai Chen, Zhu-Cheng Wang
Summary: This study sequenced, assembled, and annotated the chloroplast genome of Dendropanax oligodontus for the first time, providing crucial insights into its genetic and phylogenetic evolution. Analysis of the genome can help study genetic diversity, conservation, and phylogenetic relationships within the Araliaceae family.
Article
Plant Sciences
Erin T. H. Crockett, Mark Vellend, Elena M. Bennett
Summary: At global scales, species richness is declining. However, at local scales, understanding exactly how, where and why biodiversity is changing becomes challenging since researchers have assessed biodiversity trends using different indicators, data sources and methods. In this study, the authors present a multifaceted analysis of biodiversity change in Quebec, Canada's temperate and boreal forests, exploring various levels, dimensions, metrics and spatial scales of analysis. They found no evidence of declines in alpha or beta diversity, but observed temporal turnover in composition. Their results emphasize the need for nuanced discussions around 'biodiversity change' rather than blanket descriptions of 'biodiversity loss'.
JOURNAL OF ECOLOGY
(2022)
Article
Ecology
Emanuel M. Fonseca, Marcelo Gehara, Fernanda P. Werneck, Flavia M. Lanna, Guarino R. Colli, Jack W. Sites, Miguel T. Rodrigues, Adrian A. Garda
JOURNAL OF BIOGEOGRAPHY
(2018)
Article
Biochemistry & Molecular Biology
Flavia Lanna, Fernanda Werneck, Marcelo Gehara, Emanuel Fonseca, Guarino Colli, Jack Sites, Miguel Rodrigues, Adrian Garda
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2018)
Article
Biodiversity Conservation
Emanuel M. Fonseca, Fernanda P. Werneck, Marcelo Gehara, Eliana F. Oliveira, Felipe de M. Magalhaes, Flavia M. Lanna, Guilherme S. Lima, Ricardo Marques, Daniel O. Mesquita, Gabriel C. Costa, Guarino R. Colli, Adrian A. Garda
BIODIVERSITY AND CONSERVATION
(2019)
Article
Evolutionary Biology
Flavia M. Lanna, Marcelo Gehara, Fernanda P. Werneck, Emanuel M. Fonseca, Guarino R. Colli, Jack W. Sites, Miguel T. Rodrigues, Adrian A. Garda
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2020)
Article
Ecology
Jessica Fenker, Fabricius M. C. B. Domingos, Leonardo G. Tedeschi, Dan F. Rosauer, Fernanda P. Werneck, Guarino R. Colli, Roger M. D. Ledo, Emanuel M. Fonseca, Adrian A. Garda, Derek Tucker, Jack W. Sites, Maria F. Breitman, Flavia Soares, Lilian G. Giugliano, Craig Moritz
JOURNAL OF BIOGEOGRAPHY
(2020)
Article
Ecology
Felipe Camurugi, Marcelo Gehara, Emanuel M. Fonseca, Kelly R. Zamudio, Celio F. B. Haddad, Guarino R. Colli, Maria Tereza C. Thome, Cynthia P. A. Prado, Marcelo F. Napoli, Adrian A. Garda
Summary: This study reveals two genetic lineages of a widespread South American treefrog that diverged in the mid-Pleistocene with continued gene flow. The scenario of isolation with migration until the Last Glacial Maximum was supported, followed by recent population expansion in northeastern Brazil and stability in southwest South America. Isolation by environment was the best predictor of genetic distance between populations, indicating the importance of environmental niches in shaping genetic differentiation.
JOURNAL OF BIOGEOGRAPHY
(2021)
Article
Ecology
Emanuel M. Fonseca, Drew J. Duckett, Bryan C. Carstens
Summary: The research team developed a software package to assess the fit of the GMYC model with empirical data, recommending its use when applying the GMYC method to identify unknown species boundaries. The package has modest computational requirements, is user-friendly, and can complete analyses on a typical laptop within minutes to an hour.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Emanuel M. Fonseca, Guarino R. Colli, Fernanda P. Werneck, Bryan C. Carstens
Summary: The discipline of phylogeography has rapidly advanced in utilizing a wide range of analytical tools for analyzing large genomic data sets. This study demonstrates the effectiveness of convolutional neural networks (CNNs) in accurately assessing demographic models in South American lizards, with a model accuracy exceeding 98% for all lineages. This highlights the potential of CNNs as a valuable addition to the phylogeographer's toolkit.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Ecology
Emanuel M. Fonseca, Adrian A. Garda, Eliana F. Oliveira, Felipe Camurugi, Felipe de M. Magalhaes, Flavia M. Lanna, Juan Pablo Zurano, Ricardo Marques, Miguel Vences, Marcelo Gehara
Summary: Rivers, landscape, and climate can alter patterns of gene flow and shape intraspecific genetic variation. The study on highly aquatic frog Pseudis tocantins in central Brazil found that genetic differentiation among localities is mostly explained by river connectivity, while elevation, slope, and climate have little impact. Migration patterns took place directionally from upstream to downstream sites.
Review
Ecology
Bryan C. Carstens, Megan L. Smith, Drew J. Duckett, Emanuel M. Fonseca, M. Tereza C. Thome
Summary: Phylogeographic studies rely on complex demographic models and large data sets, but researchers face challenges in choosing appropriate models, interpreting results, and evaluating model fit. Currently, most attention is given to interpreting results, while model selection and evaluation are often overlooked.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Emanuel M. Fonseca, Drew J. Duckett, Filipe G. Almeida, Megan L. Smith, Maria Tereza C. Thome, Bryan C. Carstens
Summary: P2C2M.Skyline is a tool designed to evaluate model adequacy for BSPs, helping researchers detect model violations to avoid spurious results. It successfully identified model violations in simulated datasets and showed low false positive rates under simulated BSP models. The tool also performed well in empirical systems.
Article
Evolutionary Biology
Emanuel M. Fonseca, Tara A. Pelletier, Sydney K. Decker, Danielle J. Parsons, Bryan C. Carstens
Summary: This study demonstrated that tropical species have higher levels of intraspecific genetic diversity compared to non-tropical species. Additionally, the data suggests that non-tropical species show deviations from neutral expectations, indicating historical population fluctuations possibly associated with Pleistocene glacial cycles. These findings suggest that Quaternary climate perturbations may play a more significant role in driving the latitudinal gradient in species richness than previously thought.
Article
Evolutionary Biology
Coleen E. P. Thompson, Tara A. Pelletier, Bryan C. Carstens
Summary: The study compared genetic diversity inside and outside of protected areas in 44 vertebrate species and found that 48% of species showed significant differences in nucleotide diversity between the two areas. However, it remains unclear what factors influence the relative amount of genetic diversity in protected areas across different species.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)