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Veale A, Reudink MW, Burg TM. Neutral markers reveal complex population structure across the range of a widespread songbird. Ecol Evol 2024; 14:e11638. [PMID: 38979005 PMCID: PMC11228359 DOI: 10.1002/ece3.11638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/17/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024] Open
Abstract
Understanding how both contemporary and historical physical barriers influence gene flow is key to reconstructing evolutionary histories and can allow us to predict species' resilience to changing environmental conditions. During the last glacial maximum (LGM), many high latitude North American bird species were forced into glacial refugia, including mountain bluebirds (Silia currucoides). Within their current breeding range, mountain bluebirds still experience a wide variety of environmental conditions and barriers that may disrupt gene flow and isolate populations. Using single nucleotide polymorphisms (SNPs) obtained through restriction site-associated DNA sequencing, we detected at least four genetically distinct mountain bluebird populations. Based on this structure, we determined that isolation-by-distance, the northern Rocky Mountains, and discontinuous habitat are responsible for the low connectivity and the overall history of each population going back to the last glacial maximum. Finally, we identified five candidate genes under balancing selection and three loci under diversifying selection. This study provides the first look at connectivity and gene flow across the range of these high-altitude and high latitude songbirds.
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Affiliation(s)
- Aaron Veale
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
| | - Matthew W. Reudink
- Department of Biological SciencesThompson Rivers UniversityKamloopsBritish ColumbiaCanada
| | - Theresa M. Burg
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
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Edwards SV, Cloutier A, Cockburn G, Driver R, Grayson P, Katoh K, Baldwin MW, Sackton TB, Baker AJ. A nuclear genome assembly of an extinct flightless bird, the little bush moa. SCIENCE ADVANCES 2024; 10:eadj6823. [PMID: 38781323 DOI: 10.1126/sciadv.adj6823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Glenn Cockburn
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Robert Driver
- Department of Biology, East Carolina University, E 5th Street, Greenville, NC 27605, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Kazutaka Katoh
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Timothy B Sackton
- Informatics Group, Harvard University, 38 Oxford Street, Cambridge, MA 02138, USA
| | - Allan J Baker
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, ON M5S 3B2, Canada
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON M5S 2C6, Canada
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Gozashti L, Hoekstra HE. Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome Biol 2024; 25:4. [PMID: 38166955 PMCID: PMC10763064 DOI: 10.1186/s13059-023-03118-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
Transposable elements (TEs) are important drivers of genome evolution. Nonetheless, TE annotation remains a complex and challenging task. As more genomes from phylogenetically diverse species are published, a comprehensive pipeline for accurate annotation of diverse TEs is increasingly important. Recently, (Ou et al. Genome Biol. 20:275, 2019) developed a new comprehensive pipeline, Extensive De novo Transposable element Annotator (EDTA), and benchmarked its performance on the genomes of three species: maize, wheat, and fruit fly. Because TE landscapes can vary tremendously across species, we tested EDTA's performance on four additional genomes with different TE landscapes: mouse, zebrafish, zebra finch, and chicken. Our analysis reveals that EDTA faces challenges with repeat classification in these genomes and underperforms overall relative to its benchmark dataset. Notably, EDTA consistently misclassifies nonLTR retrotransposons as DNA transposons, resulting in erroneous TE annotations for species with considerable repertoires of nonLTR retrotransposons. Overall, we set expectations for EDTA's performance on genomes spanning additional diversity, urge caution when using EDTA on genomes with divergent TE repertoires from the species on which it was initially benchmarked, and hope to motivate the development of methods that are robust to both the diversity of TEs and TE landscapes observed across species.
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Affiliation(s)
- Landen Gozashti
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Hopi E Hoekstra
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA.
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Edwards SV, Tonini JFR, Mcinerney N, Welch C, Beerli P. Multilocus phylogeography, population genetics and niche evolution of Australian brown and black-tailed treecreepers (Aves: Climacteris). Biol J Linn Soc Lond 2023. [DOI: 10.1093/biolinnean/blac144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Abstract
The Carpentarian barrier across north-eastern Australia is a major biogeographic barrier and a generator of biodiversity within the Australian Monsoonal Tropics. Here we present a continent-wide analysis of mitochondrial (control region) and autosomal (14 anonymous loci) sequence and indel variation and niche modelling of brown and black-tailed treecreepers (Climacteris picumnus and Climacteris melanurus), a clade with a classic distribution on either side of the Carpentarian barrier. mtDNA control region sequences exhibited reciprocal monophyly and strong differentiation (Fst = 0.91), and revealed a signature of a recent selective sweep in C. picumnus. A variety of tests support an isolation-with-migration model of divergence, albeit with low levels of gene flow across the Carpentarian barrier and a divergence time between species of ~1.7–2.8 Mya. Palaeoecological niche models show that both range size as measured by available habitat and estimated historical population sizes of both species declined in the past ~600 kyr and that the area of interspecific range overlap was never historically large, perhaps decreasing opportunities for extensive gene flow. The relatively long divergence time and low opportunity for gene flow may have facilitated speciation more so than in other co-distributed bird taxa across the Australian Monsoonal Tropics.
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Affiliation(s)
- Scott V Edwards
- Museum of Comparative Zoology, Harvard University , Cambridge, MA 02138 , USA
- Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
| | - João F R Tonini
- Museum of Comparative Zoology, Harvard University , Cambridge, MA 02138 , USA
- Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
- Department of Biology, University of Richmond , Richmond, VA 23217 , USA
| | - Nancy Mcinerney
- Smithsonian's National Zoo and Conservation Biology Institute , NW, Washington, DC 20008 , USA
| | - Corey Welch
- Department of Biology and Burke Museum, University of Washington , Seattle, WA 98195 , USA
- STEM Scholars Program, Student Innovation Center, Iowa State University , Ames, IA 50011 , USA
| | - Peter Beerli
- Department of Scientific Computing, Florida State University, Florida State University , Tallahassee, FL 32306 , USA
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Starkloff NC, Galen SC. Coinfection rates of avian blood parasites increase with latitude in parapatric host species. Parasitology 2023; 150:1-8. [PMID: 36597832 PMCID: PMC10090641 DOI: 10.1017/s0031182022001792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023]
Abstract
Animals are frequently coinfected with multiple parasites concurrently, and advances in our sampling of these complex intra-host parasite communities have revealed important ecological impacts on their hosts. However, the spatial distributions and environmental determinants of parasite coinfection remain infrequently studied. Here, we investigated the drivers of haemosporidian blood parasite coinfection in the Bicknell's thrush (Catharus bicknelli) and grey-cheeked thrush (Catharus minimus), parapatric sister species that occur across a broad latitudinal range in northern North America. Using 298 samples from across the distributions of these species, we found high overall infection (86%) and coinfection (41%) rates within host populations. Coinfection rates within populations were highly variable across sampling sites, ranging from 7 to 75%. Latitude was a more important predictor of coinfection frequency than host species identity, with coinfections becoming more abundant at higher latitudes. The 2 host species exhibited similar parasite faunas, and an analysis of the co-occurrence patterns among haemosporidians showed that host species identity was largely not a factor in structuring which parasites were found within coinfections. To our knowledge, this is the first study to illustrate a reverse latitudinal gradient in coinfection frequency in a eukaryotic parasite system. Further work is necessary to determine whether vector ecology or some other factor is the primary proximate driver of this pattern.
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Affiliation(s)
- Naima C. Starkloff
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
- New York State Museum, Albany, NY 12230, USA
| | - Spencer C. Galen
- Biology Department, Loyola Science Center, University of Scranton, Scranton, PA 18510, USA
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Abstract
The detection and quantification of transposable elements (TE) are notoriously challenging despite their relevance in evolutionary genomics and molecular ecology. The main hurdle is caused by the dependence of numerous tools on genome assemblies, whose level of completion directly affects the comparability of the results across species or populations. dnaPipeTE, whose use is demonstrated here, tackles this issue by directly performing TE detection, classification, and quantification from unassembled short reads. This chapter details all the required steps to perform a comparative analysis of the TE content between two related species, starting from the installation of a recently containerized version of the program to the post-processing of the outputs.
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Affiliation(s)
- Clément Goubert
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada.
- McGill Genome Centre, Montreal, QC, Canada.
- Human Genetics, McGill University, Montreal, QC, Canada.
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McGrath C. Highlight: Comparative Population Genomics—Answering Old Questions with New Data. Genome Biol Evol 2022. [PMCID: PMC8743037 DOI: 10.1093/gbe/evab278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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