@article{Hoover2018,
abstract = {Studies of MHC-based mate choice in wild populations often test hypotheses on species exhibiting female choice and male-male competition, which reflects the general prevalence of females as the choosy sex in natural systems. Here, we examined mutual mate-choice patterns in a small burrow-nesting seabird, the Leach's storm-petrel (Oceanodroma leucorhoa), using the major histocompatibility complex (MHC). The life history and ecology of this species are extreme: both partners work together to fledge a single chick during the breeding season, a task that requires regularly travelling hundreds of kilometres to and from foraging grounds over a 6- to 8-week provisioning period. Using a 5-year data set unprecedented for this species (n = 1078 adults and 925 chicks), we found a positive relationship between variation in the likelihood of female reproductive success and heterozygosity at Ocle-DAB2, a MHC class IIB locus. Contrary to previous reports rejecting disassortative mating as a mechanism for maintaining genetic polymorphism in this species, here we show that males make significant disassortative mate-choice decisions. Variability in female reproductive success suggests that the most common homozygous females (Ocle-DAB2*01/Ocle-DAB2*01) may be physiologically disadvantaged and, therefore, less preferred as lifelong partners for choosy males. The results from this study support the role of mate choice in maintaining high levels of MHC variability in a wild seabird species and highlight the need to incorporate a broader ecological framework and sufficient sample sizes into studies of MHC-based mating patterns in wild populations in general.},
author = {Hoover, Brian and Alcaide, Miguel and Jennings, Sarah and Sin, Simon Yung Wa and Edwards, Scott V. and Nevitt, Gabrielle A.},
doi = {10.1111/mec.14801},
issn = {09621083},
journal = {Molecular Ecology},
keywords = {heterozygosity,major histocompatibility complex,mate choice,seabirds,sexual selection},
month = {aug},
number = {16},
pages = {3371--3385},
pmid = {30010226},
title = {{Ecology can inform genetics: Disassortative mating contributes to MHC polymorphism in Leach's storm-petrels ( {\textless}i{\textgreater}Oceanodroma leucorhoa{\textless}/i{\textgreater} )}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/30010226 http://doi.wiley.com/10.1111/mec.14801},
volume = {27},
year = {2018}
}
@article{Tang2018,
abstract = {Multi-locus data have proven invaluable in phylogenetic reconstruction and species delimitation. However, the mixed genetic signal from different loci can make inference of evolutionary history challenging and may produce incongruences depending on analytical and marker choice. Aside from incomplete lineage sorting (ILS) following diversification events that have had little time for deep differentiation, the most common causes of incongruent phylogenies are genetic introgression confounding a bifurcating evolutionary trajectory. In this study, we used multi-locus analytical approaches on sequence data of nine loci from 80 individuals of over 20 Neotropical Elaenia flycatcher species to examine the systematics, molecular phylogeny and species limits of this complex genus. Our results provide a robust phylogeny and estimates of species limits within Elaenia, but point to important cases of incongruences among phylogenies based on different analytical approaches. Simulations and estimates of divergence times provide reasonable explanations for the incongruent placement of some Elaenia taxa, pointing to multiple cases of both ILS and introgression within the genus. Molecular dating of major evolutionary events revealed intensive diversification during the Pleistocene, suggesting a central role of climate oscillations in the evolution of Elaenia flycatchers.},
author = {Tang, Qian and Edwards, Scott V and Rheindt, Frank E},
doi = {10.1016/j.ympev.2018.05.008},
issn = {1095-9513},
journal = {Molecular phylogenetics and evolution},
keywords = {Elaenia flycatchers,Incomplete lineage sorting,Introgression,Phylogenetic incongruence,Pleistocene climate oscillations},
month = {oct},
pages = {522--533},
pmid = {29758274},
title = {{Rapid diversification and hybridization have shaped the dynamic history of the genus Elaenia.}},
url = {https://linkinghub.elsevier.com/retrieve/pii/S105579031730667X http://www.ncbi.nlm.nih.gov/pubmed/29758274},
volume = {127},
year = {2018}
}
@article{Antonelli2018,
abstract = {{\textless}p{\textgreater}The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of “trans-disciplinary biogeography,” which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.{\textless}/p{\textgreater}},
author = {Antonelli, Alexandre and Ariza, Mar{\'{i}}a and Albert, James and Andermann, Tobias and Azevedo, Josu{\'{e}} and Bacon, Christine and Faurby, S{\o}ren and Guedes, Thais and Hoorn, Carina and Lohmann, L{\'{u}}cia G. and Matos-Marav{\'{i}}, P{\'{a}}vel and Ritter, Camila D. and Sanmart{\'{i}}n, Isabel and Silvestro, Daniele and Tejedor, Marcelo and ter Steege, Hans and Tuomisto, Hanna and Werneck, Fernanda P. and Zizka, Alexander and Edwards, Scott V.},
doi = {10.7717/peerj.5644},
issn = {2167-8359},
journal = {PeerJ},
month = {oct},
pages = {e5644},
title = {{Conceptual and empirical advances in Neotropical biodiversity research}},
url = {https://peerj.com/articles/5644},
volume = {6},
year = {2018}
}
@article{Schmitt2019,
abstract = {Natural history museums and the specimen collections they curate are vital scientific infrastructure, a fact as true today as it was when biologists began collecting and preserving specimens over 200 years ago. The importance of museum specimens in studies of taxonomy, systematics, ecology and evolutionary biology is evidenced by a rich and abundant literature, yet creative and novel uses of specimens are constantly broadening the impact of natural history collections on biodiversity science and global sustainability. Excellent examples of the critical importance of specimens come from their use in documenting the consequences of environmental change, which is particularly relevant considering the alarming rate at which we now modify our planet in the Anthropocene. In this review, we highlight the important role of bird, mammal and amphibian specimens in documenting the Anthropocene and provide examples that underscore the need for continued collection of museum specimens.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.},
author = {Schmitt, C. Jonathan and Cook, Joseph A. and Zamudio, Kelly R. and Edwards, Scott V.},
doi = {10.1098/rstb.2017.0387},
issn = {0962-8436},
journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
keywords = {Anthropocene,climate change,contamination,emergent disease,museum specimens},
month = {jan},
number = {1763},
pages = {20170387},
pmid = {30455205},
title = {{Museum specimens of terrestrial vertebrates are sensitive indicators of environmental change in the Anthropocene}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/30455205 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC6282080 http://www.royalsocietypublishing.org/doi/10.1098/rstb.2017.0387},
volume = {374},
year = {2019}
}
@article{Lewin2018,
abstract = {Increasing our understanding of Earth's biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet's organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project's goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.},
author = {Lewin, Harris A. and Robinson, Gene E. and Kress, W. John and Baker, William J. and Coddington, Jonathan and Crandall, Keith A. and Durbin, Richard and Edwards, Scott V. and Forest, F{\'{e}}lix and Gilbert, M. Thomas P. and Goldstein, Melissa M. and Grigoriev, Igor V. and Hackett, Kevin J. and Haussler, David and Jarvis, Erich D. and Johnson, Warren E. and Patrinos, Aristides and Richards, Stephen and Castilla-Rubio, Juan Carlos and van Sluys, Marie-Anne and Soltis, Pamela S. and Xu, Xun and Yang, Huanming and Zhang, Guojie},
doi = {10.1073/pnas.1720115115},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
keywords = {access and benefit sharing,biodiversity,data science,genome sequencing,genomics},
month = {apr},
number = {17},
pages = {4325--4333},
pmid = {29686065},
title = {{Earth BioGenome Project: Sequencing life for the future of life}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/29686065 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5924910 http://www.pnas.org/lookup/doi/10.1073/pnas.1720115115},
volume = {115},
year = {2018}
}
@article{Bravo,
abstract = {Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are},
author = {Bravo, Gustavo A and Antonelli, Alexandre and Bacon, Christine D and Bartoszek, Krzysztof and Blom, Mozes P K and Huynh, Stella and Jones, Graham and Knowles, L Lacey and Lamichhaney, Sangeet and Marcussen, Thomas and Morlon, H{\'{e}}l{\`{e}}ne and Nakhleh, Luay K and Oxelman, Bengt and Pfeil, Bernard and Schliep, Alexander and Wahlberg, Niklas and Werneck, Fernanda P and Wiedenhoeft, John and Willows-Munro, Sandi and Edwards, Scott V},
doi = {10.7717/peerj.6399},
file = {::},
title = {{Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics Distributed under Creative Commons CC-BY 4.0}},
url = {https://peerj.com/articles/6399.pdf}
}
@article{Hu2019,
author = {Hu, Zhirui and Sackton, Timothy B and Edwards, Scott V and Liu, Jun S},
doi = {10.1093/molbev/msz049},
editor = {Pond, Sergei Kosakovsky},
issn = {0737-4038},
journal = {Molecular Biology and Evolution},
month = {mar},
title = {{Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees}},
url = {https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msz049/5372678},
year = {2019}
}
@article{Sackton2019,
abstract = {A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which are corroborated as enhancers by open chromatin states during development, identified 2355 independent accelerations along lineages of flightless paleognaths, with functional consequences for driving gene expression in the developing forelimb. Our results suggest that the genomic landscape associated with morphological convergence in ratites has a substantial shared regulatory component.},
author = {Sackton, Timothy B and Grayson, Phil and Cloutier, Alison and Hu, Zhirui and Liu, Jun S and Wheeler, Nicole E and Gardner, Paul P and Clarke, Julia A and Baker, Allan J and Clamp, Michele and Edwards, Scott V},
doi = {10.1126/science.aat7244},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
month = {apr},
number = {6435},
pages = {74--78},
pmid = {30948549},
publisher = {American Association for the Advancement of Science},
title = {{Convergent regulatory evolution and loss of flight in paleognathous birds.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/30948549},
volume = {364},
year = {2019}
}