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Article ; Online: Immune genes are hotspots of shared positive selection across birds and mammals

Allison J Shultz / Timothy B Sackton

eLife, Vol

2019 Volume 8

Abstract: Consistent patterns of positive selection in functionally similar genes can suggest a common selective pressure across a group of species. We use alignments of orthologous protein-coding genes from 39 species of birds to estimate parameters related to ... ...

Abstract	Consistent patterns of positive selection in functionally similar genes can suggest a common selective pressure across a group of species. We use alignments of orthologous protein-coding genes from 39 species of birds to estimate parameters related to positive selection for 11,000 genes conserved across birds. We show that functional pathways related to the immune system, recombination, lipid metabolism, and phototransduction are enriched for positively selected genes. By comparing our results with mammalian data, we find a significant enrichment for positively selected genes shared between taxa, and that these shared selected genes are enriched for viral immune pathways. Using pathogen-challenge transcriptome data, we show that genes up-regulated in response to pathogens are also enriched for positively selected genes. Together, our results suggest that pathogens, particularly viruses, consistently target the same genes across divergent clades, and that these genes are hotspots of host-pathogen conflict over deep evolutionary time.
Keywords	birds ; host-pathogen co-evolution ; comparative genomics ; comparative transcriptomics ; viruses ; mammals ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Temporally Separated Data Sets Reveal Similar Traits of Birds Persisting in a United States Megacity

Daniel S. Cooper / Allison J. Shultz / Daniel T. Blumstein

Frontiers in Ecology and Evolution, Vol

2020 Volume 8

Abstract: We present an analysis of life history and behavioral traits associated with urbanization for 52 breeding bird species on 173 survey blocks in the Los Angeles area of southern California, United States, across two time periods, 1995–1999 and 2012–2016. ... ...

Abstract	We present an analysis of life history and behavioral traits associated with urbanization for 52 breeding bird species on 173 survey blocks in the Los Angeles area of southern California, United States, across two time periods, 1995–1999 and 2012–2016. We used observational data from two community science efforts and an estimate of urban land cover in each block to develop an index of urban association, and then modeled the relationship between species occurrence and eight traits likely associated with urban tolerance. We found two traits to be significantly associated with urbanization in both eras: Structure-nesting (i.e., the tendency to build nests on human-built structures) was positively associated, and cavity-nesting (i.e., the tendency to build nests in natural tree cavities) was negatively associated. Our analysis provides a template for mining historical community science data, and for “retrofitting” contemporary data to gain insights into ecological trends over time, and illustrates the persistence of ecological traits of species associated with urban areas even as the makeup of these species communities may change.
Keywords	community science ; citizen science ; California ; eBird ; breeding bird atlas ; life history traits ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
Subject code	590 ; 333
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Microstructures amplify carotenoid plumage signals in tanagers

Dakota E. McCoy / Allison J. Shultz / Charles Vidoudez / Emma van der Heide / Jacqueline E. Dall / Sunia A. Trauger / David Haig

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 20

Abstract: Abstract Brilliantly-colored birds are a model system for research into evolution and sexual selection. Red, orange, and yellow carotenoid-colored plumages have been considered honest signals of condition; however, sex differences in feather pigments and ...

Abstract	Abstract Brilliantly-colored birds are a model system for research into evolution and sexual selection. Red, orange, and yellow carotenoid-colored plumages have been considered honest signals of condition; however, sex differences in feather pigments and microstructures are not well understood. Here, we show that microstructures, rather than carotenoid pigments, seem to be a major driver of male–female color differences in the social, sexually-dimorphic tanager genus Ramphocelus. We comprehensively quantified feather (i) color (using spectrophotometry), (ii) pigments (using liquid chromatography–mass spectrometry (LC–MS)), and (iii) microstructures (using scanning electron microscopy (SEM) and finite-difference time-domain (FDTD) optical modeling). Males have significantly more saturated color patches than females. However, our exploratory analysis of pigments suggested that males and females have concordant carotenoid pigment profiles across all species (MCMCglmm model, female:male ratio = 0.95). Male, but not female, feathers have elaborate microstructures which amplify color appearance. Oblong, expanded feather barbs in males enhance color saturation (for the same amount of pigment) by increasing the transmission of optical power through the feather. Dihedral barbules (vertically-angled, strap-shaped barbules) in males reduce total reflectance to generate “super black” and “velvet red” plumage. Melanin in females explains some, but not all, of the male–female plumage differences. Our results suggest that a widely cited index of honesty, carotenoid pigments, cannot fully explain male appearance. We propose that males are selected to evolve amplifiers—in this case, microstructures that enhance appearance—that are not necessarily themselves linked to quality.
Keywords	Medicine ; R ; Science ; Q
Subject code	590
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Contrasting impacts of competition on ecological and social trait evolution in songbirds.

Jonathan P Drury / Joseph A Tobias / Kevin J Burns / Nicholas A Mason / Allison J Shultz / Hélène Morlon

PLoS Biology, Vol 16, Iss 1, p e

2018 Volume 2003563

Abstract: Competition between closely related species has long been viewed as a powerful selective force that drives trait diversification, thereby generating phenotypic diversity over macroevolutionary timescales. However, although the impact of interspecific ... ...

Abstract	Competition between closely related species has long been viewed as a powerful selective force that drives trait diversification, thereby generating phenotypic diversity over macroevolutionary timescales. However, although the impact of interspecific competition has been documented in a handful of iconic insular radiations, most previous studies have focused on traits involved in resource use, and few have examined the role of competition across large, continental radiations. Thus, the extent to which broad-scale patterns of phenotypic diversity are shaped by competition remain largely unclear, particularly for social traits. Here, we estimate the effect of competition between interacting lineages by applying new phylogenetic models that account for such interactions to an exceptionally complete dataset of resource-use traits and social signaling traits for the entire radiation of tanagers (Aves, Thraupidae), the largest family of songbirds. We find that interspecific competition strongly influences the evolution of traits involved in resource use, with a weaker effect on plumage signals, and very little effect on song. Our results provide compelling evidence that interspecific exploitative competition contributes to ecological trait diversification among coexisting species, even in a large continental radiation. In comparison, signal traits mediating mate choice and social competition seem to diversify under different evolutionary models, including rapid diversification in the allopatric stage of speciation.
Keywords	Biology (General) ; QH301-705.5
Subject code	580
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomics of host-pathogen interactions

Kathrin Näpflin / Emily A. O’Connor / Lutz Becks / Staffan Bensch / Vincenzo A. Ellis / Nina Hafer-Hahmann / Karin C. Harding / Sara K. Lindén / Morten T. Olsen / Jacob Roved / Timothy B. Sackton / Allison J. Shultz / Vignesh Venkatakrishnan / Elin Videvall / Helena Westerdahl / Jamie C. Winternitz / Scott V. Edwards

PeerJ, Vol 7, p e

challenges and opportunities across ecological and spatiotemporal scales

2019 Volume 8013

Abstract: Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater ... ...

Abstract	Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, ...
Keywords	Plasmodium ; MHC ; Immunotoxins ; Mucus ; Natural selection ; GWAS ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	333
Language	English
Publishing date	2019-11-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Research data: (with research data) Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient

TermignoniâGarcÃa, Flavia / Juan P. JaramilloâCorrea / Juan ChablÃ©âSantos / Mark Liu / Allison J. Shultz / Scott V. Edwards / Patricia EscalanteâPliego

Molecular ecology. 2017 Sept., v. 26, no. 17

2017

Abstract: Identifying the genetic basis of phenotypic variation and its relationship with the environment is key to understanding how local adaptations evolve. Such patterns are especially interesting among populations distributed across habitat gradients, where ... ...

Abstract	Identifying the genetic basis of phenotypic variation and its relationship with the environment is key to understanding how local adaptations evolve. Such patterns are especially interesting among populations distributed across habitat gradients, where genetic structure can be driven by isolation by distance (IBD) and/or isolation by environment (IBE). Here, we used variation in ~1,600 highâquality SNPs derived from pairedâend sequencing of doubleâdigest restriction siteâassociated DNA (ddRADâSeq) to test hypotheses related to IBD and IBE in the Yucatan jay (Cyanocorax yucatanicus), a tropical bird endemic to the YucatÃ¡n Peninsula. This peninsula is characterized by a precipitation and vegetation gradientâfrom dry to evergreen tropical forestsâthat is associated with morphological variation in this species. We found a moderate level of nucleotide diversity (ÏÂ =Â .008) and little evidence for genetic differentiation among vegetation types. Analyses of neutral and putatively adaptive SNPs (identified by complementary genomeâscan approaches) indicate that IBD is the most reliable explanation to account for frequency distribution of the former, while IBE has to be invoked to explain those of the later. These results suggest that selective factors acting along a vegetation gradient can promote local adaptation in the presence of gene flow in a vagile, nonmigratory and geographically restricted species. The putative candidate SNPs identified here are located within or linked to a variety of genes that represent ideal targets for future genomic surveys.
Keywords	DNA ; alloparental behavior ; frequency distribution ; gene flow ; genes ; genetic variation ; habitats ; phenotypic variation ; single nucleotide polymorphism ; surveys ; tropical birds ; vegetation types ; Mexico
Language	English
Dates of publication	2017-09
Size	p. 4483-4496.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Research data
Note	JOURNAL ARTICLE
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083 ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.14224
Database	NAL-Catalogue (AGRICOLA)

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Article: Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds

Burns, Kevin J / Allison J. Shultz / F. Keith Barker / Irby J. Lovette / John Klicka / Nicholas A. Mason / Pascal O. Title / Scott M. Lanyon

Molecular phylogenetics and evolution. 2014 June, v. 75

2014

Abstract: Thraupidae is the second largest family of birds and represents about 4% of all avian species and 12% of the Neotropical avifauna. Species in this family display a wide range of plumage colors and patterns, foraging behaviors, vocalizations, ecotypes, ... ...

Abstract	Thraupidae is the second largest family of birds and represents about 4% of all avian species and 12% of the Neotropical avifauna. Species in this family display a wide range of plumage colors and patterns, foraging behaviors, vocalizations, ecotypes, and habitat preferences. The lack of a complete phylogeny for tanagers has hindered the study of this evolutionary diversity. Here, we present a comprehensive, species-level phylogeny for tanagers using six molecular markers. Our analyses identified 13 major clades of tanagers that we designate as subfamilies. In addition, two species are recognized as distinct branches on the tanager tree. Our topologies disagree in many places with previous estimates of relationships within tanagers, and many long-recognized genera are not monophyletic in our analyses. Our trees identify several cases of convergent evolution in plumage ornaments and bill morphology, and two cases of social mimicry. The phylogeny produced by this study provides a robust framework for studying macroevolutionary patterns and character evolution. We use our new phylogeny to study diversification processes, and find that tanagers show a background model of exponentially declining diversification rates. Thus, the evolution of tanagers began with an initial burst of diversification followed by a rate slowdown. In addition to this background model, two later, clade-specific rate shifts are supported, one increase for Darwinâs finches and another increase for some species of Sporophila. The rate of diversification within these two groups is exceptional, even when compared to the overall rapid rate of diversification found within tanagers. This study provides the first robust assessment of diversification rates for the Darwinâs finches in the context of the larger group within which they evolved.
Keywords	color ; convergent evolution ; ecotypes ; foraging ; genetic markers ; habitat preferences ; models ; monophyly ; plumage ; songbirds ; Thraupidae ; tropics ; vocalization
Language	English
Dates of publication	2014-06
Size	p. 41-77.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2014.02.006
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Specimen collection is essential for modern science.

Michael W Nachman / Elizabeth J Beckman / Rauri Ck Bowie / Carla Cicero / Chris J Conroy / Robert Dudley / Tyrone B Hayes / Michelle S Koo / Eileen A Lacey / Christopher H Martin / Jimmy A McGuire / James L Patton / Carol L Spencer / Rebecca D Tarvin / Marvalee H Wake / Ian J Wang / Anang Achmadi / Sergio Ticul Álvarez-Castañeda / Michael J Andersen /

Jairo Arroyave / Christopher C Austin / F Keith Barker / Lisa N Barrow / George F Barrowclough / John Bates / Aaron M Bauer / Kayce C Bell / Rayna C Bell / Allison W Bronson / Rafe M Brown / Frank T Burbrink / Kevin J Burns / Carlos Daniel Cadena / David C Cannatella / Todd A Castoe / Prosanta Chakrabarty / Jocelyn P Colella / Joseph A Cook / Joel L Cracraft / Drew R Davis / Alison R Davis Rabosky / Guillermo D'Elía / John P Dumbacher / Jonathan L Dunnum / Scott V Edwards / Jacob A Esselstyn / Julián Faivovich / Jon Fjeldså / Oscar A Flores-Villela / Kassandra Ford / Jérôme Fuchs / Matthew K Fujita / Jeffrey M Good / Eli Greenbaum / Harry W Greene / Shannon Hackett / Amir Hamidy / James Hanken / Tri Haryoko / Melissa Tr Hawkins / Lawrence R Heaney / David M Hillis / Bradford D Hollingsworth / Angela D Hornsby / Peter A Hosner / Mohammad Irham / Sharon Jansa / Rosa Alicia Jiménez / Leo Joseph / Jeremy J Kirchman / Travis J LaDuc / Adam D Leaché / Enrique P Lessa / Hernán López-Fernández / Nicholas A Mason / John E McCormack / Caleb D McMahan / Robert G Moyle / Ricardo A Ojeda / Link E Olson / Chan Kin Onn / Lynne R Parenti / Gabriela Parra-Olea / Bruce D Patterson / Gregory B Pauly / Silvia E Pavan / A Townsend Peterson / Steven Poe / Daniel L Rabosky / Christopher J Raxworthy / Sushma Reddy / Alejandro Rico-Guevara / Awal Riyanto / Luiz A Rocha / Santiago R Ron / Sean M Rovito / Kevin C Rowe / Jodi Rowley / Sara Ruane / David Salazar-Valenzuela / Allison J Shultz / Brian Sidlauskas / Derek S Sikes / Nancy B Simmons / Melanie L J Stiassny / Jeffrey W Streicher / Bryan L Stuart / Adam P Summers / Jose Tavera / Pablo Teta / Cody W Thompson / Robert M Timm / Omar Torres-Carvajal / Gary Voelker / Robert S Voss / Kevin Winker / Christopher Witt / Elizabeth A Wommack / Robert M Zink

PLoS Biology, Vol 21, Iss 11, p e

2023 Volume 3002318

Abstract: Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ... ...

Abstract	Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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