Article
Plant Sciences
Tam Minh Nguyen, Duy Dinh Vu, Hien Phan Dang, Xuan Thi Tuyet Bui, Hong Phan Lan Nguyen, Duc Minh Nguyen
Summary: Moderate levels of genetic diversity and differentiation were found in Anisoptera costata. Population divergence during the Younger Dryas was detected. The anthropogenic disturbance significantly impacted the genetic diversity of the species in low tropical forests.
Article
Biotechnology & Applied Microbiology
Junfeng Liu, Xianchao Ji, Hua Chen
Summary: This study introduced a new method called Beta-PSMC, which refines population history in each time interval by incorporating a beta distribution into the Pairwise Sequentially Markovian Coalescent model. Compared to traditional methods, Beta-PSMC achieved more detailed results and demonstrated higher accuracy and resolution in simulation experiments. It was also successfully applied to infer the population history of Adelie penguin, showing contrasting population size fluctuations with temperature changes 15-27 thousand years ago.
Article
Biochemistry & Molecular Biology
Simon Bober, Matthias Glaubrecht, Bernhard Hausdorf, Marco T. Neiber
Summary: The two endemic species Hemicycla mascaensis and H. diegoi in Tenerife show differences in shell morphology and genital anatomy, with molecular analysis indicating they are reciprocally monophyletic. Species delimitation methods tend to recognize them as distinct species, while anatomical comparisons suggest differentiation within H. mascaensis. Thus, despite recognition as distinct species, there is still potential for further taxonomic study, including the possibility of recognizing them as subspecies.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Rohan S. Mehta, Mike Steel, Noah A. Rosenberg
Summary: Monophyly is a feature used to evaluate phylogenetic and species range, and the probability of joint monophyly (JM) has been widely used in these evaluations. This study derives the probability of JM for arbitrary numbers of separate groups in arbitrary species trees based on coalescent theory, and investigates the impact of tree height, sample size, and number of species on the JM probability.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tianqi Zhu, Ziheng Yang
Summary: This study investigated the identifiability, consistency, and efficiency of different species tree methods in the case of three species and three sequences under the molecular clock using mathematical analysis and computer simulation. The results suggest that full-likelihood methods are considerably more efficient than summary methods and can provide estimates of important parameters.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Fabien Leprieur, Loic Pellissier, David Mouillot, Theo Gaboriau
Summary: The study found that past environmental changes had a relatively small impact on the diversification of tropical reef fish. While habitat fragmentation was found to drive diversification in some clades, overall, no significant associations were identified between diversification dynamics and paleo-habitat fragmentation, contrary to theoretical predictions.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Matthew J. Christmas, Julia C. Jones, Anna Olsson, Ola Wallerman, Ignas Bunikis, Marcin Kierczak, Valentina Peona, Kaitlyn M. Whitley, Tuuli Larva, Alexander Suh, Nicole E. Miller-Struttmann, Jennifer C. Geib, Matthew T. Webster
Summary: Evidence suggests that gene flow commonly occurs between recently diverged species, despite barriers to gene flow. Genetic barriers to gene flow often accumulate in regions of low recombination and near centromeres.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Jeet Sukumaran, Mark T. Holder, L. Lacey Knowles
Summary: The traditional multispecies coalescent (MSC) model fails to distinguish genetic structures between species and within species, leading to the emergence of artifactual species under high-resolution data. The new species delimitation approach explicitly models speciation as an extended process, allowing for more accurate discrimination between genetic structures corresponding to species lineages and population lineages within species, providing insights into the relationship between population and species-level processes.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
George P. Tiley, Tobias van Elst, Helena Teixeira, Dominik Schussler, Jordi Salmona, Marina B. Blanco, Jose M. Ralison, Blanchard Randrianambinina, Rodin M. Rasoloarison, Amanda R. Stahlke, Paul A. Hohenlohe, Lounes Chikhi, Edward E. Louis, Ute Radespiel, Anne D. Yoder
Summary: Madagascar's Central Highlands consist of grasslands and scattered patches of forest. Recent evidence suggests that grasslands were a natural component of the pre-human Central Highlands vegetation, challenging the previous belief that they were anthropogenic. Through population genomic investigation of Goodman's mouse lemur, we found that open habitats have ancient origins in the Central Highlands, and forest fragmentation occurred naturally during a period of decreased precipitation. Our findings also suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene. Furthermore, we found evidence for human-mediated population declines, highlighting the vulnerability of species threatened by deforestation.
Article
Biochemistry & Molecular Biology
Zeqi Yao, Kehui Liu, Shanjun Deng, Xionglei He
Summary: The study introduces a new coalescent method, i-coalescent analysis, which computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles. It accurately reconstructs population size dynamics of highly structured populations, although larger sample sizes are often required for structured populations.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Article
Plant Sciences
Juan J. Ancona, Juan P. Pinzon-Esquivel, Eduardo Ruiz-Sanchez, Clarisse Palma-Silva, Juan J. Ortiz-Diaz, Juan Tun-Garrido, German Carnevali, Nestor E. Raigoza
Summary: Cryptic species refer to independent evolutionary lineages without phenotypic variation as a criterion for delimitation. This study aims to evaluate T. ionantha complex populations and delimit the species using multilocus data, phylogenetic analysis, and coalescent model. Phylogenetic analysis reveals that T. ionantha is polyphyletic with eight lineages. Strong population structure and high genetic differentiation are observed among populations. Multispecies coalescent analysis supports the recognition of these eight lineages as different species.
Article
Agriculture, Dairy & Animal Science
Flor Hernandez, Joshua I. Brown, Marissa Kaminski, Michael G. Harvey, Philip Lavretsky
Summary: The study explores hybridization among introduced feral Rock Pigeon and Eurasian Collared-Dove and native White-winged and Mourning doves in southwestern North America, finding limited evidence of extensive hybridization but detecting six putative contemporary late-stage hybrids involving the Mourning Dove. The research highlights the importance of using multiple marker types to infer complex evolutionary histories and considers important factors when analyzing populations that were recently established or of domestic origins.
Article
Evolutionary Biology
Benjamin J. Cooper, Michael J. Moore, Norman A. Douglas, Warren L. Wagner, Matthew G. Johnson, Rick P. Overson, Sylvia P. Kinosian, Angela J. McDonnell, Rachel A. Levin, Robert A. Raguso, Hilda Flores Olvera, Helga Ochoterena, Jeremie B. Fant, Krissa A. Skogen, Norman J. Wickett
Summary: This study used target enrichment, gene tree/species tree methods, and morphological analysis to reconstruct the phylogenetic history and evaluate taxon circumscriptions of Oenothera sect. Calylophus. The study found improved support for species relationships by combining exons and flanking noncoding regions. It also discovered evidence for multiple evolutionary origins of bee pollination, edaphic specialization on gypsum, and permanent translocation heterozygosity in the group. The study applied newly emerging techniques and dense infraspecific sampling to effectively reconstruct the complex history of the rapid radiation.
SYSTEMATIC BIOLOGY
(2023)
Article
Evolutionary Biology
Matthew Wascher, Laura Kubatko
Summary: The study reveals that SVDQuartets is statistically consistent for all data types, while ML is consistent only for CIS data under the JC69 model. Proof of consistency for the more general multilocus case remains challenging.
SYSTEMATIC BIOLOGY
(2021)
Review
Multidisciplinary Sciences
Xiyun Jiao, Tomas Flouri, Ziheng Yang
Summary: The Multispecies Coalescent (MSC) model extends the single-population coalescent model to multiple species, allowing for estimation of species divergence times, population sizes, species trees, and inference of cross-species gene flow and species delimitation. This framework faces statistical and computational challenges, but research advancements are leading the way towards breakthroughs in the field in the next few years.
NATIONAL SCIENCE REVIEW
(2021)
Article
Ecology
Joseph D. Manthey, Robert G. Moyle, Dency F. Gawin, Mustafa Abdul Rahman, Mohamad Fizl Sidq Ramji, Frederick H. Sheldon
JOURNAL OF BIOGEOGRAPHY
(2017)
Article
Evolutionary Biology
Joseph D. Manthey, Robert G. Moyle, Stephane Boissinot
GENOME BIOLOGY AND EVOLUTION
(2018)
Article
Evolutionary Biology
Yann Bourgeois, Robert P. Ruggiero, Joseph D. Manthey, Stephane Boissinot
GENOME BIOLOGY AND EVOLUTION
(2019)
Article
Genetics & Heredity
Luke C. Campillo, Kevin J. Burns, Robert G. Moyle, Joseph D. Manthey
MITOCHONDRIAL DNA PART B-RESOURCES
(2019)
Article
Audiology & Speech-Language Pathology
John Peacock, Garth M. Spellman, Nathaniel T. Greene, Daniel J. Tollin
Article
Audiology & Speech-Language Pathology
John Peacock, Garth M. Spellman, Daniel J. Tollin, Nathaniel T. Greene
Article
Evolutionary Biology
Luke C. Campillo, Joseph D. Manthey, Robert C. Thomson, Peter A. Hosner, Robert G. Moyle
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2020)
Correction
Ecology
A. M. Carpenter, B. A. Graham, G. M. Spellman, T. M. Burg
Article
Biochemistry & Molecular Biology
Joseph D. Manthey, Yann Bourgeois, Yonas Meheretu, Stephane Boissinot
Summary: This study utilized whole-genome sequencing data to characterize genomic variation in populations of six Ethiopian Highlands forest bird species separated by a lowland biogeographic barrier, the Great Rift Valley (GRV). It was found that the GRV acts as a substantial biogeographic barrier even in highly dispersive species like birds, with species' dispersal ability negatively correlated with levels of population differentiation.
Article
Ecology
Joseph D. Manthey, Jennifer C. Giron, Jack P. Hruska
Summary: This study found a coevolutionary relationship between carpenter ants and their Blochmannia endosymbionts, with Blochmannia genes evolving at a faster pace than their hosts and positively associated with host rates of molecular evolution. Host demography was associated with increased selection strengths in Blochmannia, but not with other evolutionary processes.
ECOLOGY AND EVOLUTION
(2022)
Article
Biodiversity Conservation
Matthew G. DeSaix, T. Luke George, Amy E. Seglund, Garth M. Spellman, Erika S. Zavaleta, Kristen C. Ruegg
Summary: This study integrates ecological and evolutionary factors to reveal the vulnerability of Brown-capped Rosy-Finch populations to climate change. The results showed that precipitation as snow plays a crucial role in habitat suitability and genetic variation. Future climate change is predicted to lead to a contraction of suitable habitat at high elevations and a shift in population allele frequencies to adapt to novel climate conditions.
DIVERSITY AND DISTRIBUTIONS
(2022)
Article
Entomology
B. A. Meadows, M. Emad, J. P. Hruska, J. Silva, G. J. Behrends, J. C. Giron, J. D. Manthey
Summary: Scientists used genome-wide single-nucleotide polymorphism data to study social structure and relatedness estimation in three Nearctic ant species. The results showed that allele-frequency-free inference can accurately determine kinship and be used in population genetics studies of haplodiploid organisms. The findings also aligned with previous research in the field.
Article
Ecology
Amie E. E. Settlecowski, Ben D. D. Marks, Joseph D. D. Manthey
Summary: This study aims to identify the most efficient method and DNA source for collecting whole genome sequencing (WGS) data from avian museum specimens. The results show that the single-stranded DNA (ssDNA) multi-tube method can achieve higher endogenous DNA content, average read length, and sequencing efficiency compared to other tested methods. In addition, a predigestion step can further reduce exogenous DNA. These findings have the potential to significantly increase WGS coverage of historical DNA from bird specimens.
ECOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Jack P. Hruska, Joseph D. Manthey
Summary: This study presents a highly contiguous de novo genome assembly of the northern flicker, containing 18,745 genes and approximately 28.0% repetitive elements. The assembly, estimated to have a mutation rate of 4.007 x 10(-9) substitutions/site/year, serves as a valuable resource for future research on the genomics of the species and the comparative evolution of woodpeckers.
G3-GENES GENOMES GENETICS
(2021)
Article
Ornithology
Joseph D. Manthey, Stephane Boissinot, Robert G. Moyle