Article
Biochemistry & Molecular Biology
Jurjan P. van der Zee, Marjolijn J. A. Christianen, Martine Berube, Mabel Nava, Sietske van der Wal, Jessica Berkel, Tadzio Bervoets, Melanie Meijer zu Schlochtern, Leontine E. Becking, Per J. Palsboll
Summary: The study tracked changes in shallow marine habitat availability due to Pleistocene sea level fluctuations and assessed correlations with past changes in genetic diversity in Caribbean hawksbill turtles. Results showed a strong correlation between changes in habitat availability and genetic diversity of hawksbill turtles, with a rapid increase in both factors after the Last Glacial Maximum. These findings suggest a positive correlation between Pleistocene environmental changes, habitat availability, and species' demography.
Article
Biotechnology & Applied Microbiology
Shreya M. Banerjee, Jamie Adkins Stoll, Camryn D. Allen, Jennifer M. Lynch, Heather S. Harris, Lauren Kenyon, Richard E. Connon, Eleanor J. Sterling, Eugenia Naro-Maciel, Kathryn McFadden, Margaret M. Lamont, James Benge, Nadia B. Fernandez, Jeffrey A. Seminoff, Scott R. Benson, Rebecca L. Lewison, Tomoharu Eguchi, Tammy M. Summers, Jessy R. Hapdei, Marc R. Rice, Summer Martin, T. Todd Jones, Peter H. Dutton, George H. Balazs, Lisa M. Komoroske
Summary: Transcriptomic data has demonstrated the utility of physiological diversity and responses to environmental stressors in marine turtles. The study generated high quality blood transcriptome assemblies for multiple turtle species, showing distinct gene expression signatures between species and foraging aggregations, providing valuable insights into functional genomics underlying diversity and evolutionary ecology in marine turtles.
Article
Biochemistry & Molecular Biology
Giulia Secci-Petretto, Gernot K. Englmaier, Steven J. Weiss, Alexander Antonov, Henri Persat, Gael P. J. Denys, Tamara Schenekar, Vladimir I. Romanov, Eric B. Taylor, Elsa Froufe
Summary: Hybridization and introgression are common among freshwater fishes, leading to discordant paths of evolution for mitochondrial and nuclear genomes. Using ddRADseq, a genome-wide SNP dataset was obtained for Thymallus species, revealing phylogenetic relationships and gene flow among species. The analysis showed discordances between mitochondrial and nuclear genomes, as well as signs of mitochondrial capture and limited nuclear introgression in contact zones.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Genetics & Heredity
Jennifer M. Korstian, Nicole S. Paulat, Roy N. Platt, Richard D. Stevens, David A. Ray
Summary: Using presence/absence data from over 10,000 Ves SINE insertions, the researchers reconstructed a phylogeny for 11 Myotis species. They found that phylogenetic conflict was rampant in this genus, with almost one-third of individual gene trees being discordant with the overall species tree. The study suggests that incomplete lineage sorting (ILS) is a major contributor to the discordance. The researchers also observed signs of introgression between Old and New World taxa, as well as within the New World Myotis species. The findings highlight the role of hybridization in the evolutionary history of Myotis.
Article
Biochemistry & Molecular Biology
Kyle R. Piller, Elyse Parker, Alan R. Lemmon, Emily Moriarty Lemmon
Summary: This study investigated the phylogenetic relationships among families within the Cyprinodontiformes using the anchored hybrid enrichment method. The results revealed new sets of relationships and confirmed the monophyly of two well-established clades. The assessment of gene tree discordance provided support for alternative topological hypotheses. This study provides a robust framework for further investigation in biogeography, taxonomy, ecology, and physiology of these fishes.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Evolutionary Biology
Vlatka Cubric-Curik, Dinko Novosel, Vladimir Brajkovic, Omar Rota Stabelli, Stefan Krebs, Johann Solkner, Dragica Salamon, Strahil Ristov, Beate Berger, Stamatina Trivizaki, Iosif Bizelis, Maja Ferencakovic, Sophie Rothammer, Elisabeth Kunz, Mojca Simcic, Peter Dovc, Gojko Bunevski, Hysen Bytyqi, Bozidarka Markovic, Muhamed Brka, Kristaq Kume, Srctan Stojanovid, Vasil Nikolov, Natalia Zinovieva, Anna Amanda Schonherz, Bernt Guldbrandtsen, Mato Cacic, Sinisa Radovic, Preston Miracle, Cristiano Vernesi, Ino Curik, Ivica Medugorac
Summary: This study conducted a comprehensive analysis of the mitochondrial genome of cattle, revealing different haplotypes and classifications, as well as providing evidence for interactions between wild aurochs and domesticated cattle during the domestication and dispersal of cattle in Europe.
EVOLUTIONARY APPLICATIONS
(2022)
Review
Veterinary Sciences
Valentina Virginia Ebani
Summary: Sea turtles are endangered by infectious and parasitic pathogens present in the marine environment, which can cause diseases in both sea turtles and other animals. While sea turtles are not a major source of infection for humans compared to other animals, they can still contribute to the spread of zoonotic bacteria, including antibiotic-resistant ones. Therefore, contact with sea turtles, their products, and their habitat poses a One Health threat.
VETERINARY SCIENCES
(2023)
Article
Evolutionary Biology
Elize Y. X. Ng, Siqi Li, Dezhi Zhang, Kritika M. Garg, Gang Song, Jonathan Martinez, Le Manh Hung, Vuong Tan Tu, Jerome Fuchs, Lu Dong, Urban Olsson, Yuan Huang, Per Alstrom, Frank E. Rheindt, Fumin Lei
Summary: Morphology has long been a reliable tool for taxonomic classification, but recent genetic and genomic advancements have shown that it can lead to erroneous classifications. In our study on Asian Cyornis flycatchers, we used thousands of genomic markers to confirm that two previously recognized species are actually a single species, and we also discovered interbreeding between two different species, highlighting their ability to hybridize even after long periods of divergence. This research demonstrates the importance of incorporating genomic data into taxonomic studies for a more comprehensive understanding of species relationships.
Article
Microbiology
Jun Chen, Haoxin Lv, Zhixia Zhang, Hua Zhang, Bei Zhang, Xing Wang, Yuan Liu, Miao Zhang, Huili Pang, Guangyong Qin, Lei Wang, Zhongfang Tan
Summary: In this study, 45 Leuconostoc mesenteroides strains isolated from different plants and dairy products in Qinghai-Tibet Plateau were analyzed using MLST with eight housekeeping genes. A total of 25 sequence types were identified, which were grouped into one clonal complexes, 3 doublets and 17 singletons. The results indicated a weak relationship between the strains from the Qinghai-Tibet Plateau and the isolated region, but a close relationship between the genotypes of the strains and the type of isolated sample.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kylie Chen, Jiri C. Moravec, Alex Gavryushkin, David Welch, Alexei J. Drummond
Summary: Single-cell sequencing provides a new approach to explore the evolutionary history of cells, preserving the information about the origin of sequences. However, single-cell data are more prone to errors due to limited genomic material available per cell. This study presents error and mutation models within the Bayesian framework BEAST2, allowing for accurate evolutionary inference of single-cell data and integration with biologically informative models.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Lucinda P. Lawson, Jose Alfredo Samaniego Castruita, James S. Haile, Cristiano Vernesi, Francesco Rovero, Eline D. Lorenzen
Summary: Through analysis of mitochondrial genomes, high levels of gene introgression were found among giant sengi species, primarily occurring in the eastern Udzungwa Mountains forests in Tanzania. However, nuclear gene data showed a different pattern, indicating the need for further genome-wide analysis and increased spatial sampling to clarify aspects of diversification and introgression in this group.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Genetics & Heredity
Henry D. Kunerth, Joaquim T. Tapisso, Raul Valente, Maria da Luz Mathias, Paulo C. Alves, Jeremy B. Searle, Rodrigo Vega, Joana Pauperio
Summary: The phenomenon of mitochondrial introgression raises questions about biogeography, reproductive isolation, and natural selection in the Sorex araneus complex. Previous research has shown hybridization between Sorex granarius and the Carlit chromosomal race of S. araneus, leading to introgression of the S. araneus mitochondrial genome into S. granarius. The current study further examines this phenomenon and suggests recent hybridization and introgression between S. coronatus and S. granarius, as well as between S. araneus and S. coronatus.
Article
Agriculture, Dairy & Animal Science
Edward McGinley, Avery Cogley, Leslie Palmer, Patricia McCaul, Lilli Longo, Jasmine Silvennoinen, Angela Martin, Josalyn Gomez, Sydney Bachmaier, Michaela Mackey, Chris Kao, Scott Eastman, Catherine Eastman
Summary: This study conducted an 18-month observation on juvenile green sea turtles feeding on algae in the local marinas in Florida. The researchers successfully identified 195 individual turtles and found that the numbers were highest in summer and lowest in winter. These findings provide valuable information for conservation efforts.
Article
Evolutionary Biology
Jimmy A. Mcguire, Xiaoting Huang, Sean B. Reilly, Djoko T. Iskandar, Cynthia Y. Wang-Claypool, Sarah Werning, Rebecca A. Chong, Shobi Z. S. Lawalata, Alexander L. Stubbs, Jeffrey H. Frederick, Rafe M. Brown, Ben J. Evans, Umilaela Arifin, Awal Riyanto, Amir Hamidy, Evy Arida, Michelle S. Koo, Jatna Supriatna, Noviar Andayani, Robert Hall
Summary: The biota of Sulawesi is known for its unique species and diversification. In this study, the diversification history of Sulawesi flying lizards, an endemic group to Sulawesi, was explored using a geological framework. The analysis revealed that there are more Draco species in Sulawesi than previously thought, with cryptic and arrested speciation events and ancient hybridization affecting the phylogenetic analyses. The colonization of Sulawesi by the common ancestor of the Draco lineatus Group occurred around 11 million years ago, followed by radiations and dynamic species interactions.
SYSTEMATIC BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Eduardo Ascarrunz, Julien Claude, Walter G. Joyce
Summary: Quantitative analyses examining the placement of Messel geoemydids in a reference tree generated from molecular data show that their position remains uncertain, with different methods yielding varied results. Parsimony suggests placement as sister to two different species, but with weak support, highlighting the challenge of determining the relationships within this group.
Article
Biodiversity Conservation
Ana Carolina Oliveira de Meirelles, Danielle dos Santos Lima, Maria Danise de Oliveira Alves, Joao Carlos Gomes Borges, Miriam Marmontel, Vitor Luz Carvalho, Fabricio Rodrigues dos Santos
Summary: Sirenians play a unique ecological role in coastal ecosystems and require special conservation attention. The West Indian manatee is classified as Vulnerable globally and as Endangered in Brazil. Using available data, the species' extinction risk in Brazil was assessed, with scenarios projecting significant population declines and even extinction. The results highlight the need for reassessment of the species' national extinction risk and evaluation of the effectiveness of the National Action Plan.
JOURNAL FOR NATURE CONSERVATION
(2022)
Article
Ecology
Caroline Batistim Oswald, Priscila Lemes, Maria Tereza C. Thome, Tiago Leite Pezzuti, Fabricio Rodrigues Santos, Paulo Christiano de Anchietta Garcia, Felipe Sa Fortes Leite, Rafael Felix Magalhaes
Summary: This study investigated the distribution and diversification of the ledge treefrog in Brazilian mountains, finding four evolutionary significant lineages and suggesting a Pleistocene jump-dispersal scenario as the best explanation for diversification. These findings challenge previous views on the endemism in the Espinhaco Range, indicating recent dispersal, habitat expansion, and colonization as important factors in explaining the current distribution and genetic diversity.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Biodiversity Conservation
Jose Eustaquio Santos Junior, Paul H. Williams, Cayo A. Rocha Dias, Fernando A. Silveira, Pierre Faux, Raphael T. F. Coimbra, Davidson P. Campos, Fabricio Rodrigues Santos
Summary: This study sequenced the DNA of nine Brazilian bumblebee species to construct a detailed phylogenetic tree, and used fossil dating to analyze the timeline of bumblebee diversification. The results showed that the ancestral Bombus lineage originated between 47.08 and 34.27 million years ago in the Holarctic region, and was mainly distributed in the eastern Old World. The Neotropical bumblebees likely originated from North American lineages and colonized South America after 29 million years ago.
Article
Biodiversity Conservation
Raphael T. F. Coimbra, Rafael F. Magalhaes, Priscila Lemes, Flavia R. Miranda, Fabricio R. Santos
Summary: In this study, the phylogeography, distribution, ecology, and historical demography of the Brazilian populations of giant anteaters were investigated. The research found two distinct mtDNA clusters and highlighted the importance of the Brazilian Cerrado as a priority biome for the conservation of the species.
Article
Zoology
Flavia R. Miranda, Guilherme S. T. Garbino, Fabio A. Machado, Fernando A. Perini, Fabricio R. Santos, Daniel M. Casali
Summary: A taxonomic revision of maned sloths revealed the presence of two species: the northern maned sloth and the southern maned sloth. These species diverged in the Early Pliocene and are distributed allopatrically. The conservation status of both species needs to be reassessed.
JOURNAL OF MAMMALOGY
(2023)
Article
Ecology
Sarah Maria Vargas, Ana Carolina Barcelos, Rita Gomes Rocha, Paula Guimaraes, Lais Amorim, Arturo Martinelli, Fabricio Rodrigues Santos, Jose Erickson, Ana Claudia Jorge Marcondes, Sandra Ludwig
Summary: This study conducted genetic assessment of the South West Atlantic subpopulation of leatherback turtles and found genetic differences and two different genetic clusters. The low number of reproductive females in the subpopulation may be due to breeding occurrence in other nesting areas, as well as mating behaviors and inbreeding avoidance. The low remigration rates estimated for the subpopulation may be related to high mortality rates at sea.
REGIONAL STUDIES IN MARINE SCIENCE
(2022)
Article
Biodiversity Conservation
Roberto Biello, Andrea Brunelli, Giulia Sozio, Katja Havenstein, Alessio Mortelliti, Valerio Ketmaier, Sibelle Torres Vilaca, Giorgio Bertorelle
Summary: The negative impact of habitat fragmentation due to human activities on different species co-existing in the same area can vary, affecting the development of environmental protection plans. This study examined the effects of natural and anthropic landscape features on gene flow patterns in two sympatric species with different specializations. The results revealed that the dispersal abilities of a generalist and specialist species were reflected in their genetic structure despite extensive habitat changes caused by human activities. The negative effects of fragmentation due to urbanization were partially mitigated by cultivated terrains subdivided by hedgerows for both species.
CONSERVATION GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Sibelle T. Vilaca, Francesco Maroso, Paulo Lara, Benoit de Thoisy, Damien Chevallier, Larissa Souza Arantes, Fabricio R. Santos, Giorgio Bertorelle, Camila J. Mazzoni
Summary: Hybridization and introgression patterns in the Brazilian sea turtle population were investigated using RAD-Seq markers, mitogenomes, and satellite telemetry. The study found that all adult hybrids were first generation (F1) and most displayed loggerhead migratory behavior. Paternal leakage and different proportions of mitochondria from maternal and paternal species were also detected.
Article
Genetics & Heredity
Jose R. Sandoval, Susana Revollo, Cinthia Cuellar, Daniela R. Lacerda, Marilza S. Jota, Ricardo Fujita, Fabricio R. Santos
Summary: During the colonial period in South America, the genetic makeup of autochthonous populations was impacted and reconfigured due to relocation by European missionary reductions and other factors. This study used DNA comparison studies to explore the genetic relationships among Takanan and Panoan-speaking peoples in the Amazonian areas of Peru, Bolivia, and Brazil. The results revealed a shared ancestry between these groups, consistent with linguistic evidence and indicating an early Arawak expansion in the western Amazonia.
ANNALS OF HUMAN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Sibelle T. Vilaca, Michael E. Donaldson, Andrea Benazzo, Tyler J. Wheeldon, Maria Teresa Vizzari, Giorgio Bertorelle, Brent R. Patterson, Christopher J. Kyle
Summary: Eastern wolves (Canis lycaon) in southeastern Canada have been a topic of controversy. Mitochondrial DNA analysis suggests that they evolved in North America, while nuclear genome studies indicate they are a hybrid entity. By sequencing whole genomes, it was discovered that eastern wolves are a distinct taxonomic entity that evolved separately from grey wolves for about 67,000 years with a hybridization event with coyotes about 37,000 years ago. Great Lakes wolves originated from admixture between grey wolves and eastern wolves after the last glaciation, while eastern coyotes originated from admixture between western coyotes and eastern wolves in the last century. Eastern wolf nuclear genomes show signs of historical and contemporary gene flow with grey wolves and coyotes.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Caroline Batistim Oswald, Rafael Felix de Magalhaes, Paulo C. A. Garcia, Fabricio R. Santos, Selvino Neckel-Oliveira
Summary: This study investigates the distribution of the threatened frog Ischnocnema manezinho and confirms its restricted range to Santa Catarina Island in Brazil. It also highlights the threat posed by urban expansion and emphasizes the need for protection and monitoring.
Article
Ecology
Madison Wikston, Brie-Anne A. Breton, Sibelle Torres Vilaca, Amanda M. M. Bennett, Christopher J. J. Kyle, David V. V. Beresford, David Lesbarreres, Chris C. C. Wilson, David M. M. Green, Marie-Josee Fortin, Dennis L. L. Murray
Summary: Documenting biodiversity and species occurrence is challenging due to the complex life history and behavior of anurans. Traditional amphibian monitoring techniques may be complemented by the use of environmental DNA (eDNA) surveys, which have shown promising results. In this study, we compared the efficacy of eDNA detection using quantitative PCR (qPCR) with three conventional survey methods for anuran detection. Our results showed that all methods had imperfect detection, but eDNA surveys detected the highest species richness and required fewer sampling events. The composition of amphibian communities varied among survey methods and sampling events, highlighting the need for multiple monitoring methods tailored to individual species or communities.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Archaeology
Anna L. Gosling, Edana Lord, James Boocock, Sophia Cameron-Christie, K. Ann Horsburgh, Olga Kardailsky, Stefan Prost, Stephen Wilcox, David Addison, Adam Thompson, John Kalolo, Andrew C. Clarke, Elizabeth A. Matisoo-Smith
Summary: This study compares the genomic data of the current population and ancient individuals from Tokelau, finding less genetic diversity compared to other Polynesian populations. Rare mitochondrial lineages suggest prehistoric settlement by people from the northwest. Ancient DNA data supports the previous population abandonment and resettlement on Atafu, the northernmost atoll of Tokelau, from a population of Samoan or Samoan-origin. The study also reveals links between Tokelau and other atoll populations in the western Pacific.
JOURNAL OF ISLAND & COASTAL ARCHAEOLOGY
(2023)