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Dalapicolla J, Weir JT, Vilaça ST, Quaresma TF, Schneider MPC, Vasconcelos ATR, Aleixo A. Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary. Ecol Evol 2024; 14:e11250. [PMID: 38660467 PMCID: PMC11040105 DOI: 10.1002/ece3.11250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
The "Amazon tipping point" is a global change scenario resulting in replacement of upland terra-firme forests by large-scale "savannization" of mostly southern and eastern Amazon. Reduced rainfall accompanying the Last Glacial Maximum (LGM) has been proposed to have acted as such a tipping point in the past, with the prediction that terra-firme inhabiting species should have experienced reductions in population size as drier habitats expanded. Here, we use whole-genomes of an Amazonian endemic organism (Scale-backed antbirds - Willisornis spp.) sampled from nine populations across the region to test this historical demography scenario. Populations from southeastern Amazonia and close to the Amazon-Cerrado ecotone exhibited a wide range of demographic patterns, while most of those from northern and western Amazonia experienced uniform expansions between 400 kya and 80-60 kya, with gradual declines toward 20 kya. Southeastern populations of Willisornis were the last to diversify and showed smaller heterozygosity and higher runs of homozygosity values than western and northern populations. These patterns support historical population declines throughout the Amazon that affected more strongly lineages in the southern and eastern areas, where historical "tipping point" conditions existed due to the widespread replacement of humid forest by drier and open vegetation during the LGM.
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Affiliation(s)
- Jeronymo Dalapicolla
- Instituto Tecnológico ValeBelémParáBrazil
- Departamento de Sistemática e EcologiaUniversidade Federal da Paraíba, João PessoaParaíbaBrazil
| | - Jason T. Weir
- Department of Biological SciencesUniversity of Toronto ScarboroughTorontoOntarioCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of Natural History, Royal Ontario MuseumTorontoOntarioCanada
| | | | | | - Maria P. C. Schneider
- Laboratório de Genômica e BiotecnologiaInstituto de Ciências Biológicas, UFPABelémBrazil
| | - Ana Tereza R. Vasconcelos
- Laboratório de BioinformáticaLaboratório Nacional de Computação Científica, PetrópolisRio de JaneiroBrazil
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2
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Mikkelsen EK, Weir JT. Phylogenomics Reveals that Mitochondrial Capture and Nuclear Introgression Characterizes Skua Species Proposed to be of Hybrid Origin. Syst Biol 2022; 72:78-91. [DOI: 10.1093/sysbio/syac078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Abstract
The skuas and jaegers (Stercorariidae) are an enigmatic family of seven seabird species that breed at Arctic and Antarctic latitudes. The phylogenetic relationships amongst the species have been controversial, with one of the biggest enigmas involving the Pomarine Jaeger (Stercorarius pomarinus), which has been proposed to represent a hybrid species originating from the merging of distant lineages within the complex. We inferred a phylogeny for the family using multispecies coalescent methods with whole-genome sequencing for all seven species of Stercorariidae, and document an evolutionary history rich in introgression. We uncover evidence for mitochondrial capture and nuclear introgression between S. pomarinus and S. skua, providing a potential avenue for adaptive introgression. One candidate for adaptive introgression is the MC1R plumage gene which appears to have introgressed from one of the large skuas into S. pomarinus, where it now forms the basis of the dark-morph colour polymorphism of that species. We further highlight a complex biogeographical history of interchange between the Arctic and Antarctic, with unexpected close ancestry between S. skua of the northern hemisphere and S. antarcticus of the southern hemisphere. These results highlight the dynamic history of introgression during a pelagic seabird radiation.
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Affiliation(s)
- Else K Mikkelsen
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto , ON, Canada
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto , ON, Canada
- Department of Biology, University of Toronto at Scarborough, Toronto , ON, Canada
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3
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Abstract
After decades of debate, biologists today largely agree that most speciation events require an allopatric phase (that is, geographic separation), but the role of adaptive ecological divergence during this critical period is still unknown. Here, we show that relatively few allopatric pairs of birds, mammals, or amphibians exhibit trait differences consistent with models of divergent adaptation in each of many ecologically relevant traits. By fitting new evolutionary models to numerous sets of sister-pair trait differences, we find that speciating and recently speciated allopatric taxa seem to overwhelmingly evolve under similar rather than divergent macro-selective pressures. This contradicts the classical view of divergent adaptation as a prominent driver of the early stages of speciation and helps synthesize two historical controversies regarding the ecology and geography of species formation.
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Affiliation(s)
- Sean A S Anderson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Biological Sciences, University of Toronto at Scarborough, Toronto, ON, Canada.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Biological Sciences, University of Toronto at Scarborough, Toronto, ON, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
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4
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Anderson SAS, López-Fernández H, Weir JT. Ecology and the origin of non-ephemeral species. Am Nat 2022; 201:619-638. [PMID: 37130236 DOI: 10.1086/723763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractResearch over the past three decades has shown that ecology-based extrinsic reproductive barriers can rapidly arise to generate incipient species-but such barriers can also rapidly dissolve when environments change, resulting in incipient species collapse. Understanding the evolution of unconditional, "intrinsic" reproductive barriers is therefore important for understanding the longer-term buildup of biodiversity. In this article, we consider ecology's role in the evolution of intrinsic reproductive isolation. We suggest that this topic has fallen into a gap between disciplines: while evolutionary ecologists have traditionally focused on the rapid evolution of extrinsic isolation between co-occurring ecotypes, speciation geneticists studying intrinsic isolation in other taxa have devoted little attention to the ecological context in which it evolves. We argue that for evolutionary ecology to close this gap, the field will have to expand its focus beyond rapid adaptation and its traditional model systems. Synthesizing data from several subfields, we present circumstantial evidence for and against different forms of ecological adaptation as promoters of intrinsic isolation and discuss alternative forces that may be significant. We conclude by outlining complementary approaches that can better address the role of ecology in the evolution of nonephemeral reproductive barriers and, by extension, less ephemeral species.
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5
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Bemmels JB, Haddrath O, Colbourne RM, Robertson HA, Weir JT. Legacy of supervolcanic eruptions on population genetic structure of brown kiwi. Curr Biol 2022; 32:3389-3397.e8. [PMID: 35728597 DOI: 10.1016/j.cub.2022.05.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/09/2022] [Accepted: 05/31/2022] [Indexed: 10/18/2022]
Abstract
Supervolcanoes are volcanoes capable of mega-colossal eruptions that emit more than 1,000 km3 of ash and other particles.1 The earth's most recent mega-colossal eruption was the Oruanui eruption of the Taupo supervolcano 25,580 years before present (YBP) on the central North Island of New Zealand.2 This eruption blanketed major swaths of the North Island in thick layers of ash and igneous rock,2,3 devastating habitats and likely causing widespread population extinctions.4-7 An additional devastating super-colossal eruption (>100 km3) of the Taupo supervolcano occurred approximately 1,690 YBP.8 The impacts of such massive but ephemeral natural disasters on contemporary population genetic structure remain underexplored. Here, we combined data for 4,951 SNPs with spatially explicit demographic and coalescent models within an approximate Bayesian computation framework to test the drivers of genetic structure in brown kiwi (Apteryx mantelli). Our results strongly support the importance of eruptions of the Taupo supervolcano in restructuring pre-existing geographic patterns of population differentiation and genetic diversity. Range shifts due to climatic oscillations-a frequent explanation for genetic structure9-are insufficient to fully explain the empirical data. Meanwhile, recent range contraction and fragmentation due to historically documented anthropogenic habitat alteration adds no explanatory power to our models. Our results support a major role for cycles of destruction and post-volcanic recolonization in restructuring the population genomic landscape of brown kiwi and highlight how ancient and ephemeral mega-disasters may leave a lasting legacy on patterns of intraspecific genetic variation.
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Affiliation(s)
- Jordan B Bemmels
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
| | - Oliver Haddrath
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada
| | - Rogan M Colbourne
- Department of Conservation, PO Box 10420, Wellington 6140, New Zealand
| | - Hugh A Robertson
- Department of Conservation, PO Box 10420, Wellington 6140, New Zealand
| | - Jason T Weir
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada.
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6
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Barrera-Guzmán AO, Aleixo A, Faccio M, de Melo Dantas S, Weir JT. Gene flow, genomic homogenization and the timeline to speciation in Amazonian manakins. Mol Ecol 2022; 31:4050-4066. [PMID: 35665558 DOI: 10.1111/mec.16562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/28/2022] [Accepted: 05/12/2022] [Indexed: 11/26/2022]
Abstract
Phylogeographic studies of the most species rich region of the planet - the Amazon basin - repeatedly uncover genetically distinctive, allopatric lineages within currently named species, but understanding whether such lineages are reproductively isolated species is challenging. Here we harness the power of genome-wide datasets together with detailed phylogeographic sampling to both characterize the number of unique lineages and infer levels of reproductive isolation for three parapatric manakin species that make up the genus Pipra. The mitochondrial and nuclear genomes both support six distinctive lineages. The youngest lineages are now highly admixed with each other across major portions of their geographic ranges with one lineage now extinct in a genomically unadmixed state. In contrast, the oldest sets of lineages - dated to 1.4 million years - exhibit narrow hybrid zones. By fitting demographic models to parapatric lineage pairs we found that levels of gene flow and genomic homogenization decline with increasing evolutionary age. Only lineages descending from the 1.4 Ma basal node in the genus experience negligible gene flow, possess genomes resistant to homogenization and are separated by narrow hybrid zones. We conclude that a million years or more were required for Pipra manakins to become reproductively isolated. We suggest the six lineages be reclassified as two or three reproductively isolated species. Our unique approach to quantifying reproductive isolation in parapatric lineages could be applied broadly to other phylogeographic studies and would help determine species classification of the plethora of newly identified lineages in the Amazon basin and other regions.
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Affiliation(s)
- Alfredo O Barrera-Guzmán
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada.,Departamento de Biología Marina, Campus de Ciencias biológicas y Agropecuarias, Universidad Autónoma de Yucatán
| | - Alexandre Aleixo
- Pós-graduação em Biodiversidade e Evolução, Museu Paraense Emílio Goeldi, Belém, Brazil.,Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Maya Faccio
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Sidnei de Melo Dantas
- Pós-graduação em Biodiversidade e Evolução, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada.,Department of ornithology, Royal Ontario Museum, Toronto, Ontario, Canada
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7
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Lujan NK, Colm JE, Weir JT, Montgomery FA, Noonan BP, Lovejoy NR, Mandrak NE. Genomic population structure of Grass Pickerel (Esox americanus vermiculatus) in Canada: management guidance for an at-risk fish at its northern range limit. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01450-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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8
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Bemmels JB, Mikkelsen EK, Haddrath O, Colbourne RM, Robertson HA, Weir JT. Demographic decline and lineage-specific adaptations characterize New Zealand kiwi. Proc Biol Sci 2021; 288:20212362. [PMID: 34905706 PMCID: PMC8670953 DOI: 10.1098/rspb.2021.2362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/19/2021] [Indexed: 12/24/2022] Open
Abstract
Small and fragmented populations may become rapidly differentiated due to genetic drift, making it difficult to distinguish whether neutral genetic structure is a signature of recent demographic events, or of long-term evolutionary processes that could have allowed populations to adaptively diverge. We sequenced 52 whole genomes to examine Holocene demographic history and patterns of adaptation in kiwi (Apteryx), and recovered 11 strongly differentiated genetic clusters corresponding to previously recognized lineages. Demographic models suggest that all 11 lineages experienced dramatic population crashes relative to early- or mid-Holocene levels. Small population size is associated with low genetic diversity and elevated genetic differentiation (FST), suggesting that population declines have strengthened genetic structure and led to the loss of genetic diversity. However, population size is not correlated with inbreeding rates. Eight lineages show signatures of lineage-specific selective sweeps (284 sweeps total) that are unlikely to have been caused by demographic stochasticity. Overall, these results suggest that despite strong genetic drift associated with recent bottlenecks, most kiwi lineages possess unique adaptations and should be recognized as separate adaptive units in conservation contexts. Our work highlights how whole-genome datasets can address longstanding uncertainty about the evolutionary and conservation significance of small and fragmented populations of threatened species.
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Affiliation(s)
- Jordan B. Bemmels
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada ON M1C 1A4
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada ON M5S 3B2
| | - Else K. Mikkelsen
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada ON M1C 1A4
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada ON M5S 3B2
| | - Oliver Haddrath
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada ON M5S 3B2
- Department of Natural History, Royal Ontario Museum, Toronto, Canada ON M5S 2C6
| | | | | | - Jason T. Weir
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada ON M1C 1A4
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada ON M5S 3B2
- Department of Natural History, Royal Ontario Museum, Toronto, Canada ON M5S 2C6
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9
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E Luzuriaga-Aveiga V, Ugarte M, Weir JT. Distinguishing genomic homogenization from parapatric speciation in an elevationally replacing pair of Ramphocelus tanagers. Mol Ecol 2021; 30:5517-5529. [PMID: 34403554 DOI: 10.1111/mec.16128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022]
Abstract
Geographically connected species pairs with weakly differentiated genomes could either represent cases of genomic homogenization in progress or of incipient parapatric speciation. Discriminating between these processes is difficult because intermediate stages of either may produce weakly differentiated genomes that diverge at few locations. We used coalescent modelling applied to a genome-wide sample of SNPs to discriminate between speciation with gene flow and genomic homogenization in two phenotypically distinct but genomically weakly diverged species of elevationally replacing Ramphocelus tanagers, forming a hybrid zone in the Andean foothills. We found overwhelming support for a model of genomic homogenization following secondary contact. Simulating under this model suggested that our species pair was differentiated (FST = 0.30) at secondary contact but that most of the genome has rapidly homogenized during 254 Ky of high gene flow towards the present (FST = 0.02). Despite extensive genome-wide homogenization, plumage remains distinctive with a narrower than expected geographic cline width, indicating divergent selection on colour. We found two SNPs significantly associated with plumage colour, which retain moderately high FST . We conclude that the majority of the genome has fused, but that divergent selection on select loci probably maintains the geographically structured colour differences between these incipient species.
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Affiliation(s)
- Vanessa E Luzuriaga-Aveiga
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Mauricio Ugarte
- Área de Ornitología, Universidad Nacional de San Agustín de Arequipa, Museo de Historia Natural Arequipa, Peru
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada.,Department of Ornithology, Royal Ontario Museum, Toronto, Ontario, Canada
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10
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Bemmels JB, Bramwell AC, Anderson SAS, Luzuriaga-Aveiga VE, Mikkelsen EK, Weir JT. Geographic contact drives increased reproductive isolation in two cryptic Empidonax flycatchers. Mol Ecol 2021; 30:4833-4844. [PMID: 34347907 DOI: 10.1111/mec.16105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/05/2021] [Accepted: 07/28/2021] [Indexed: 01/02/2023]
Abstract
Geographic contact between sister lineages often occurs near the final stages of speciation, but its role in speciation's completion remains debated. Reproductive isolation may be essentially complete prior to secondary contact. Alternatively, costly interactions between partially reproductively isolated species - such as maladaptive hybridization or competition for resources - may select for divergence, increasing reproductive isolation and driving speciation toward completion. Here, we use coalescent demographic modelling and whole-genome data sets to show that a period of contact and elevated hybridization between sympatric eastern North American populations of two cryptic bird species preceded a major increase in reproductive isolation between these populations within the last 10,000 years. In contrast, substantial introgression continues to the present in a western contact zone where geographic overlap is much narrower and probably of more recent origin. In the sympatric eastern region where reproductive isolation has increased, it is not accompanied by character displacement in key morphometric traits, plumage coloration, or ecological traits. While the precise trait and underlying mechanism driving increased reproductive isolation remains unknown, we discuss several possibilities and outline avenues for future research. Overall, our results highlight how demographic models can reveal the geographic context in which reproductive isolation was completed, and demonstrate how contact can accelerate the final stages of speciation.
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Affiliation(s)
- Jordan B Bemmels
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Ashley C Bramwell
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Sean A S Anderson
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Vanessa E Luzuriaga-Aveiga
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Else K Mikkelsen
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Jason T Weir
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
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11
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Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, Andreu-Sánchez S, Margaryan A, Howard JT, Parent C, Pacheco G, Sinding MHS, Puetz L, Cavill E, Ribeiro ÂM, Eckhart L, Fjeldså J, Hosner PA, Brumfield RT, Christidis L, Bertelsen MF, Sicheritz-Ponten T, Tietze DT, Robertson BC, Song G, Borgia G, Claramunt S, Lovette IJ, Cowen SJ, Njoroge P, Dumbacher JP, Ryder OA, Fuchs J, Bunce M, Burt DW, Cracraft J, Meng G, Hackett SJ, Ryan PG, Jønsson KA, Jamieson IG, da Fonseca RR, Braun EL, Houde P, Mirarab S, Suh A, Hansson B, Ponnikas S, Sigeman H, Stervander M, Frandsen PB, van der Zwan H, van der Sluis R, Visser C, Balakrishnan CN, Clark AG, Fitzpatrick JW, Bowman R, Chen N, Cloutier A, Sackton TB, Edwards SV, Foote DJ, Shakya SB, Sheldon FH, Vignal A, Soares AER, Shapiro B, González-Solís J, Ferrer-Obiol J, Rozas J, Riutort M, Tigano A, Friesen V, Dalén L, Urrutia AO, Székely T, Liu Y, Campana MG, Corvelo A, Fleischer RC, Rutherford KM, Gemmell NJ, Dussex N, Mouritsen H, Thiele N, Delmore K, Liedvogel M, Franke A, Hoeppner MP, Krone O, Fudickar AM, Milá B, Ketterson ED, Fidler AE, Friis G, Parody-Merino ÁM, Battley PF, Cox MP, Lima NCB, Prosdocimi F, Parchman TL, Schlinger BA, Loiselle BA, Blake JG, Lim HC, Day LB, Fuxjager MJ, Baldwin MW, Braun MJ, Wirthlin M, Dikow RB, Ryder TB, Camenisch G, Keller LF, DaCosta JM, Hauber ME, Louder MIM, Witt CC, McGuire JA, Mudge J, Megna LC, Carling MD, Wang B, Taylor SA, Del-Rio G, Aleixo A, Vasconcelos ATR, Mello CV, Weir JT, Haussler D, Li Q, Yang H, Wang J, Lei F, Rahbek C, Gilbert MTP, Graves GR, Jarvis ED, Paten B, Zhang G. Author Correction: Dense sampling of bird diversity increases power of comparative genomics. Nature 2021; 592:E24. [PMID: 33833441 PMCID: PMC8081657 DOI: 10.1038/s41586-021-03473-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shaohong Feng
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,BGI-Shenzhen, Shenzhen, China
| | - Josefin Stiller
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yuan Deng
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joel Armstrong
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Qi Fang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Hart Reeve
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Duo Xie
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Guangji Chen
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Chunxue Guo
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Brant C Faircloth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Bent Petersen
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia.,Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zongji Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.,Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Wanjun Chen
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Sergio Andreu-Sánchez
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | | | | | - George Pacheco
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lara Puetz
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emily Cavill
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ângela M Ribeiro
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Jon Fjeldså
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Peter A Hosner
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robb T Brumfield
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Les Christidis
- Southern Cross University, Coffs Harbour, New South Wales, Australia
| | - Mads F Bertelsen
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Thomas Sicheritz-Ponten
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia.,Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Gerald Borgia
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Santiago Claramunt
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Irby J Lovette
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | - Saul J Cowen
- Biodiversity and Conservation Science, Department of Biodiversity Conservation and Attractions, Perth, Western Australia, Australia
| | - Peter Njoroge
- Ornithology Section, Zoology Department, National Museums of Kenya, Nairobi, Kenya
| | | | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA.,Evolution, Behavior, and Ecology, Division of Biology, University of California San Diego, La Jolla, CA, USA
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Western Australia, Perth, Australia
| | - David W Burt
- UQ Genomics, University of Queensland, Brisbane, Queensland, Australia
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
| | | | - Shannon J Hackett
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Peter G Ryan
- FitzPatrick Institute of African Ornithology, University of Cape Town, Cape Town, South Africa
| | - Knud Andreas Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ian G Jamieson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Rute R da Fonseca
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Alexander Suh
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - Suvi Ponnikas
- Department of Biology, Lund University, Lund, Sweden
| | - Hanna Sigeman
- Department of Biology, Lund University, Lund, Sweden
| | - Martin Stervander
- Department of Biology, Lund University, Lund, Sweden.,Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA.,Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA
| | | | - Rencia van der Sluis
- Focus Area for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Carina Visser
- Department of Animal Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | | - Reed Bowman
- Avian Ecology Program, Archbold Biological Station, Venus, FL, USA
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | | | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Dustin J Foote
- Department of Biology, East Carolina University, Greenville, NC, USA.,Sylvan Heights Bird Park, Scotland Neck, NC, USA
| | - Subir B Shakya
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Frederick H Sheldon
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Alain Vignal
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet-Tolosan, France
| | - André E R Soares
- Laboratório Nacional de Computação Científica, Petrópolis, Brazil.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.,Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Universitat de Barcelona, Barcelona, Spain
| | - Joan Ferrer-Obiol
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Julio Rozas
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Marta Riutort
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Anna Tigano
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Department of Biology, Queen's University, Kingston, Ontario, Canada
| | - Vicki Friesen
- Department of Biology, Queen's University, Kingston, Ontario, Canada
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Araxi O Urrutia
- Milner Centre for Evolution, University of Bath, Bath, UK.,Instituto de Ecologia, UNAM, Mexico City, Mexico
| | - Tamás Székely
- Milner Centre for Evolution, University of Bath, Bath, UK
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
| | | | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
| | - Kim M Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Nicolas Dussex
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden.,Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Henrik Mouritsen
- AG Neurosensory Sciences, Institut für Biologie und Umweltwissenschaften, University of Oldenburg, Oldenburg, Germany
| | - Nadine Thiele
- AG Neurosensory Sciences, Institut für Biologie und Umweltwissenschaften, University of Oldenburg, Oldenburg, Germany
| | - Kira Delmore
- Biology Department, Texas A&M University, College Station, TX, USA.,MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts- University of Kiel, Kiel, Germany
| | - Marc P Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrechts- University of Kiel, Kiel, Germany
| | - Oliver Krone
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Adam M Fudickar
- Environmental Resilience Institute, Indiana University, Bloomington, IN, USA
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | | | - Andrew Eric Fidler
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Guillermo Friis
- Center for Genomics and Systems Biology, Department of Biology, New York University - Abu Dhabi, Abu Dhabi, UAE
| | | | - Phil F Battley
- Wildlife and Ecology Group, Massey University, Palmerston North, New Zealand
| | - Murray P Cox
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Nicholas Costa Barroso Lima
- Laboratório Nacional de Computação Científica, Petrópolis, Brazil.,Departamento de Bioquímica e Biologia Molecular, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Rio de Janeiro, Brazil
| | | | - Barney A Schlinger
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Bette A Loiselle
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA.,Center for Latin American Studies, University of Florida, Gainesville, FL, USA
| | - John G Blake
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | - Haw Chuan Lim
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA.,Department of Biology, George Mason University, Fairfax, VA, USA
| | - Lainy B Day
- Department of Biology and Neuroscience Minor, University of Mississippi, University, MS, USA
| | - Matthew J Fuxjager
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | | | - Michael J Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, MD, USA
| | - Morgan Wirthlin
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA
| | - T Brandt Ryder
- Migratory Bird Center, Smithsonian National Zoological Park and Conservation Biology Institute, Washington, DC, USA
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | | | - Mark E Hauber
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matthew I M Louder
- Department of Biology, East Carolina University, Greenville, NC, USA.,Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,International Research Center for Neurointelligence, University of Tokyo, Tokyo, Japan
| | - Christopher C Witt
- Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology, Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Libby C Megna
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Matthew D Carling
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Biao Wang
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Glaucia Del-Rio
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Jason T Weir
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - David Haussler
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Qiye Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | | | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.,Institute of Ecology, Peking University, Beijing, China.,Department of Life Sciences, Imperial College London, Ascot, UK
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Gary R Graves
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Erich D Jarvis
- Duke University Medical Center, Durham, NC, USA.,The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA.
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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12
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Elmore JA, Hager SB, Cosentino BJ, O'Connell TJ, Riding CS, Anderson ML, Bakermans MH, Boves TJ, Brandes D, Butler EM, Butler MW, Cagle NL, Calderón-Parra R, Capparella AP, Chen A, Cipollini K, Conkey AAT, Contreras TA, Cooper RI, Corbin CE, Curry RL, Dosch JJ, Dyson KL, Fraser EE, Furbush RA, Hagemeyer NDG, Hopfensperger KN, Klem D, Lago EA, Lahey AS, Machtans CS, Madosky JM, Maness TJ, McKay KJ, Menke SB, Ocampo-Peñuela N, Ortega-Álvarez R, Pitt AL, Puga-Caballero A, Quinn JE, Roth AM, Schmitz RT, Schnurr JL, Simmons ME, Smith AD, Varian-Ramos CW, Walters EL, Walters LA, Weir JT, Winnett-Murray K, Zuria I, Vigliotti J, Loss SR. Correlates of bird collisions with buildings across three North American countries. Conserv Biol 2021; 35:654-665. [PMID: 32537779 DOI: 10.1111/cobi.13569] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Collisions with buildings cause up to 1 billion bird fatalities annually in the United States and Canada. However, efforts to reduce collisions would benefit from studies conducted at large spatial scales across multiple study sites with standardized methods and consideration of species- and life-history-related variation and correlates of collisions. We addressed these research needs through coordinated collection of data on bird collisions with buildings at sites in the United States (35), Canada (3), and Mexico (2). We collected all carcasses and identified species. After removing records for unidentified carcasses, species lacking distribution-wide population estimates, and species with distributions overlapping fewer than 10 sites, we retained 269 carcasses of 64 species for analysis. We estimated collision vulnerability for 40 bird species with ≥2 fatalities based on their North American population abundance, distribution overlap in study sites, and sampling effort. Of 10 species we identified as most vulnerable to collisions, some have been identified previously (e.g., Black-throated Blue Warbler [Setophaga caerulescens]), whereas others emerged for the first time (e.g., White-breasted Nuthatch [Sitta carolinensis]), possibly because we used a more standardized sampling approach than past studies. Building size and glass area were positively associated with number of collisions for 5 of 8 species with enough observations to analyze independently. Vegetation around buildings influenced collisions for only 1 of those 8 species (Swainson's Thrush [Catharus ustulatus]). Life history predicted collisions; numbers of collisions were greatest for migratory, insectivorous, and woodland-inhabiting species. Our results provide new insight into the species most vulnerable to building collisions, making them potentially in greatest need of conservation attention to reduce collisions and into species- and life-history-related variation and correlates of building collisions, information that can help refine collision management.
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Affiliation(s)
- Jared A Elmore
- Department of Natural Resource Ecology and Management, Oklahoma State University, 008C Ag Hall, Stillwater, OK, 74078, U.S.A
| | - Stephen B Hager
- Department of Biology, Augustana College, Rock Island, IL, 61201, U.S.A
| | - Bradley J Cosentino
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, 14456, U.S.A
| | - Timothy J O'Connell
- Department of Natural Resource Ecology and Management, Oklahoma State University, 008C Ag Hall, Stillwater, OK, 74078, U.S.A
| | - Corey S Riding
- Department of Natural Resource Ecology and Management, Oklahoma State University, 008C Ag Hall, Stillwater, OK, 74078, U.S.A
- Current address: Department of Biology, Salt Lake Community College, 4600 South Redwood Road, Salt Lake City, Utah, 84123, U.S.A
| | - Michelle L Anderson
- Department of Biology, The University of Montana Western, 710 S. Atlantic St., Dillon, MT, 59725, U.S.A
| | - Marja H Bakermans
- Worcester Polytechnic Institute, Goddard Hall 128, 100 Institute Road, Worcester, MA, 01609, U.S.A
| | - Than J Boves
- Department of Biological Sciences, Arkansas State University, State University, PO Box 599, Jonesboro, AR, 72467, U.S.A
| | - David Brandes
- Acopian Engineering Center 320, Lafayette College, Easton, 18042, PA, U.S.A
| | - Eric M Butler
- Shaw University, 118 E. South Street, Raleigh, NC, 27601, U.S.A
| | - Michael W Butler
- Department of Biology, Lafayette College, 213 Kunkel Hall, Easton, 18042, PA, U.S.A
| | - Nicolette L Cagle
- Duke University, BOX 90328, 9 Circuit Drive, Durham, NC, 27708, U.S.A
| | - Rafael Calderón-Parra
- Iniciativa para la Conservación de las Aves de América del Norte-México (NABCI-México), Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO), Liga Periférico-Insurgentes Sur, No. 4903, Col. Parques del Pedregal, Delegación Tlalpan, Distrito Federal, 14010, Mexico
- Current address: Av. La Garita And. 17 #22 Casa 3 Col. Narciso Mendoza Villa Coapa, C.P., Ciudad de México, 14390, Mexico
| | - Angelo P Capparella
- School of Biological Sciences, Illinois State University, Normal, IL, 61790, U.S.A
| | - Anqi Chen
- University of Washington, Gould Hall Box 355740, Seattle, WA, 98195, U.S.A
- Current address: 3010 Remington Ct, San Jose, CA, 95148, U.S.A
| | - Kendra Cipollini
- Wilmington College, 1870 Quaker Way, Wilmington, OH, 45177, U.S.A
| | - April A T Conkey
- Department of Animal, Rangeland, & Wildlife Sciences, Texas A&M University-Kingsville, Kingsville, TX, 78363, U.S.A
| | - Thomas A Contreras
- Biology Department, Washington and Jefferson College, 60 S. Lincoln St., Washington, PA, 15301, U.S.A
| | - Rebecca I Cooper
- Department of Biological Sciences, Arkansas State University, State University, PO Box 599, Jonesboro, AR, 72467, U.S.A
| | - Clay E Corbin
- Department of Biological Sciences, Bloomsburg University, 400 E 2nd Street, Bloomsburg, PA, 17815, U.S.A
| | - Robert L Curry
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, PA, 19085, U.S.A
| | - Jerald J Dosch
- Biology Department, Macalester College, 1600 Grand Avenue, St. Paul, MN, 55105, U.S.A
| | - Karen L Dyson
- University of Washington, Gould Hall Box 355740, Seattle, WA, 98195, U.S.A
| | - Erin E Fraser
- Environmental Science (Biology), Memorial University of Newfoundland, Grenfell Campus, 20 University Drive, Corner Brook, NL, A2H 5G4, Canada
| | - Ross A Furbush
- Principia College, 1 Front Gate Road, Elsah, IL, 62028, U.S.A
- Current address: 1115 N Pitt St., Alexandria, VA, 22314, U.S.A
| | - Natasha D G Hagemeyer
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, 23529, U.S.A
| | - Kristine N Hopfensperger
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41099, U.S.A
| | - Daniel Klem
- Acopian Center for Ornithology, Muhlenberg College, 2400 Chew St., Allentown, 18104, PA, U.S.A
| | - Elizabeth A Lago
- Department of Biological Sciences, Florida International University, 11200 SW 8th St., Miami, FL, 33199, U.S.A
| | - Ally S Lahey
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, 23529, U.S.A
- Current address: 305 Kabler Road, Virginia Beach, VA, 23456, U.S.A
| | - Craig S Machtans
- Environment and Climate Change Canada, Canadian Wildlife Service, 91780 Alaska Highway, Whitehorse, YT, Y1A 5 × 7, Canada
| | - Jessa M Madosky
- Warren Wilson College, 701 Warren Wilson College Rd, Swannanoa, NC, 28778, U.S.A
- Current address: University of Tampa, 401 W Kennedy Blvd., Tampa, FL, 33606, U.S.A
| | - Terri J Maness
- School of Biological Sciences, Louisiana Tech University, Ruston, LA, 71272, U.S.A
| | - Kelly J McKay
- BioEco Research and Monitoring Center, P.O. Box 452, Hampton, IL, 61256, U.S.A
| | - Sean B Menke
- Lake Forest College, 555 N. Sheridan Rd., Lake Forest, IL, 60045, U.S.A
| | - Natalia Ocampo-Peñuela
- Nicholas School of the Environment, Duke University, 9 Circuit Drive, Durham, NC, 27708, U.S.A
- Current address: Department of Environmental Systems Science, ETH Zurich, Universitatstrasse 16, Zurich, 8092, Switzerland
| | - Rubén Ortega-Álvarez
- Iniciativa para la Conservación de las Aves de América del Norte-México (NABCI-México), Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO), Liga Periférico-Insurgentes Sur, No. 4903, Col. Parques del Pedregal, Delegación Tlalpan, Distrito Federal, 14010, Mexico
- Current address: Grupo de Ecología Evolutiva y Demografía Animal, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Distrito Federal, 04510, Mexico
| | - Amber L Pitt
- Department of Biological Sciences, Bloomsburg University, 400 E 2nd Street, Bloomsburg, PA, 17815, U.S.A
- Current address: Environmental Science Program & Biology Department, Trinity College, 300 Summit Street, Hartford, CT, 06106, U.S.A
| | - Aura Puga-Caballero
- Museo de Zoología Alfonso L. Herrera, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 3000, Circuito Exterior S/N, Delegación Coyoacán, C.P. 04510, Ciudad Universitaria, Distrito Federal, Mexico
| | - John E Quinn
- Furman University, 3300 Poinsett Highway, Greenville, SC, 29613, U.S.A
| | - Amber M Roth
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, U.S.A
- Current address: University of Maine, 5755 Nutting Hall, Orono, ME, 04469, U.S.A
| | - Ryan T Schmitz
- University of Wisconsin-Platteville, 1 University Plaza, Platteville, WI, 53818, U.S.A
| | | | - Matthew E Simmons
- University of Minnesota Crookston, 2900 University Ave Crookston, Crookston, MN, 56716, U.S.A
| | - Alexis D Smith
- University of Illinois at Chicago, 845 W Taylor St, Chicago, IL, 60607, U.S.A
| | - Claire W Varian-Ramos
- Biology Department, Colorado State University - Pueblo, 2200 Bonforte Blvd., Pueblo, CO, 81001, U.S.A
| | - Eric L Walters
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, 23529, U.S.A
| | - Lindsey A Walters
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41099, U.S.A
| | - Jason T Weir
- University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario, MIC 1A4, Canada
| | - Kathy Winnett-Murray
- Department of Biology, Hope College, 35 E. 12th Street, Holland, MI, 49423, U.S.A
| | - Iriana Zuria
- Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Hidalgo, Km 4.5 carr. Pachuca-Tulancingo s/n, col. Carboneras, Mineral de la Reforma, Hidalgo, C.P. 42184, Mexico
| | - Jesse Vigliotti
- Environment and Climate Change Canada, Canadian Wildlife Service, 91780 Alaska Highway, Whitehorse, YT, Y1A 5 × 7, Canada
- Current address: PO Box 40118, Station Main, Whitehorse, Y1A 6M7, Yukon, Canada
| | - Scott R Loss
- Department of Natural Resource Ecology and Management, Oklahoma State University, 008C Ag Hall, Stillwater, OK, 74078, U.S.A
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13
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Cronemberger ÁA, Aleixo A, Mikkelsen EK, Weir JT. Postzygotic isolation drives genomic speciation between highly crypticHypocnemisantbirds from Amazonia. Evolution 2020; 74:2512-2525. [DOI: 10.1111/evo.14103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 08/28/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Áurea A. Cronemberger
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Canada
- Department of Biological Sciences University of Toronto Scarborough Toronto Canada
- Pós‐graduação em Biodiversidade e Evolução Museu Paraense Emílio Goeldi Belém Brazil
| | - Alexandre Aleixo
- Pós‐graduação em Biodiversidade e Evolução Museu Paraense Emílio Goeldi Belém Brazil
- Finnish Museum of Natural History University of Helsinki Helsinki Finland
| | - Else K. Mikkelsen
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Canada
- Department of Biological Sciences University of Toronto Scarborough Toronto Canada
| | - Jason T. Weir
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Canada
- Department of Biological Sciences University of Toronto Scarborough Toronto Canada
- Department of Natural History Royal Ontario Museum Toronto Canada
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14
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Abstract
AbstractEcological differentiation between lineages is widely considered to be an important driver of speciation, but support for this hypothesis is mainly derived from the detailed study of a select set of model species pairs. Mounting evidence from nonmodel taxa, meanwhile, suggests that speciation often occurs with minimal differentiation in ecology or ecomorphology, calling into question the true contribution of divergent adaptation to species richness in nature. To better understand divergent ecological adaptation and its role in speciation generally, researchers require a comparative approach that can distinguish its signature from alternative processes, such as drift and parallel selection, in data sets containing many species pairs. Here we introduce new statistical models of divergent adaptation in the continuous traits of paired lineages. In these models, ecomorphological characters diverge as two lineages adapt toward alternative phenotypic optima following their departure from a common ancestor. The absolute distance between optima measures the extent of divergent selection and provides a basis for interpretation. We encode the models in the new R package diverge and extend them to allow the distance between optima to vary across continuous and categorical variables. We test model performance using simulation and demonstrate model application using published data sets of trait divergence in birds and mammals. Our framework provides the first explicit test for signatures of divergent selection in trait divergence data sets, and it will enable empiricists from a wide range of fields to better understand the dynamics of divergent adaptation and its prevalence in nature beyond just our best-studied model systems.
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15
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Mikkelsen EK, Weir JT. The genome of the Xingu scale-backed antbird (Willisornis vidua nigrigula) reveals lineage-specific adaptations. Genomics 2020; 112:4552-4560. [PMID: 32771623 DOI: 10.1016/j.ygeno.2020.07.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/08/2020] [Accepted: 07/30/2020] [Indexed: 12/23/2022]
Abstract
Antbirds (Thamnophilidae) are a large neotropical family of passerine bird renowned for the ant-following foraging strategies of several members of this clade. The high diversity of antbirds provides ample opportunity for speciation studies, however these studies can be hindered by the lack of an annotated antbird reference genome. In this study, we produced a high-quality annotated reference genome for the Xingu Scale-backed Antbird (Willisornis vidua nigrigula) using 10X Genomics Chromium linked-reads technology. The assembly is 1.09 Gb, with a scaffold N50 of 12.1 Mb and 17,475 annotated protein coding genes. We compare the proteome of W. v. nigrigula to several other passerines, and produce annotations for two additional antbird genomes in order to identify genes under lineage-specific positive selection and gene families with evidence for significant expansions in antbirds. Several of these genes have functions potentially related to the lineage-specific traits of antbirds, including adaptations for thermoregulation in a humid tropical environment.
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Affiliation(s)
- Else K Mikkelsen
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto M5S 3B2, ON, Canada.
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto M5S 3B2, ON, Canada; Department of Biological Sciences, University of Toronto Scarborough, Toronto M1C 1A4, ON, Canada; Department of Ornithology, Royal Ontario Museum, Toronto, Canada
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16
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Lujan NK, Weir JT, Noonan BP, Lovejoy NR, Mandrak NE. Is Niagara Falls a barrier to gene flow in riverine fishes? A test using genome-wide SNP data from seven native species. Mol Ecol 2020; 29:1235-1249. [PMID: 32202354 DOI: 10.1111/mec.15406] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/17/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022]
Abstract
Since the early Holocene, fish population genetics in the Laurentian Great Lakes have been shaped by the dual influences of habitat structure and post-glacial dispersal. Riverscape genetics theory predicts that longitudinal habitat corridors and unidirectional downstream water-flow drive the downstream accumulation of genetic diversity, whereas post-glacial dispersal theory predicts that fish genetic diversity should decrease with increasing distance from glacial refugia. This study examines populations of seven native fish species codistributed above and below the 58 m high Niagara Falls - a hypothesized barrier to gene flow in aquatic species. A better understanding of Niagara Falls' role as a barrier to gene flow and dispersal is needed to identify drivers of Great Lakes genetic diversity and guide strategies to limit exotic species invasions. We used genome-wide SNPs and coalescent models to test whether populations are: (a) genetically distinct, consistent with the Niagara Falls barrier hypothesis; (b) more genetically diverse upstream, consistent with post-glacial expansion theory, or downstream, consistent with the riverscape habitat theory; and (c) have migrated either upstream or downstream past Niagara Falls. We found that genetic diversity is consistently greater below Niagara Falls and the falls are an effective barrier to migration, but two species have probably dispersed upstream past the falls after glacial retreat yet before opening of the Welland Canal. Models restricting migration to after opening of the Welland Canal were generally rejected. These results help explain how river habitat features affect aquatic species' genetic diversity and highlight the need to better understand post-glacial dispersal pathways.
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Affiliation(s)
- Nathan K Lujan
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Biological Sciences, University of Mississippi, Oxford, MS, USA
| | - Jason T Weir
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Brice P Noonan
- Department of Biological Sciences, University of Mississippi, Oxford, MS, USA
| | - Nathan R Lovejoy
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Nicholas E Mandrak
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
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17
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Pulido‐Santacruz P, Aleixo A, Weir JT. Genomic data reveal a protracted window of introgression during the diversification of a neotropical woodcreeper radiation*. Evolution 2020; 74:842-858. [DOI: 10.1111/evo.13902] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 10/31/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Paola Pulido‐Santacruz
- Department of Ecology and Evolutionary BiologyUniversity of Toronto Toronto Canada
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Bogotá Colombia
- Current address: Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Calle 28A No. 15 – 09 Bogotá Colombia
| | | | - Jason T. Weir
- Department of Ecology and Evolutionary BiologyUniversity of Toronto Toronto Canada
- Department of Biological SciencesUniversity of Toronto Scarborough Toronto Canada
- Department of OrnithologyRoyal Ontario Museum Toronto Canada
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18
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Weir JT, Price TD. Song playbacks demonstrate slower evolution of song discrimination in birds from Amazonia than from temperate North America. PLoS Biol 2019; 17:e3000478. [PMID: 31639139 PMCID: PMC6804960 DOI: 10.1371/journal.pbio.3000478] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/17/2019] [Indexed: 11/19/2022] Open
Abstract
Genetic data indicate differences in speciation rate across latitudes, but underlying causes have been difficult to assess because a critical phase of the speciation process is initiated in allopatry, in which, by definition, individuals from different taxa do not interact. We conducted song playback experiments between 109 related pairs of mostly allopatric bird species or subspecies in Amazonia and North America to compare the rate of evolution of male discrimination of songs. Relative to local controls, the number of flyovers and approach to the speaker were higher in Amazonia. We estimate that responses to songs of relatives are being lost about 6 times more slowly in Amazonia than in North America. The slow loss of response holds even after accounting for differences in song frequency and song length. Amazonian species with year-round territories are losing aggressive responses especially slowly. We suggest the presence of many species and extensive interspecific territoriality favors recognition of songs sung by sympatric heterospecifics, which results in a broader window of recognition and hence an ongoing response to novel similar songs. These aggressive responses should slow the establishment of sympatry between recently diverged forms. If male responses to novel allopatric taxa reflect female responses, then premating reproductive isolation is also evolving more slowly in Amazonia. The findings are consistent with previously demonstrated slower recent rates of expansion of sister taxa into sympatry, slower rates of evolution of traits important for premating isolation, and slower rates of speciation in general in Amazonia than in temperate North America.
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Affiliation(s)
- Jason T. Weir
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology and Evolutionary Biology and Department of Biological Sciences, University of Toronto, Toronto, Canada
- Department of Natural History, Royal Ontario Museum, Toronto, Canada
- * E-mail:
| | - Trevor D. Price
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
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19
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Luzuriaga-Aveiga VE, Weir JT. Elevational differentiation accelerates trait evolution but not speciation rates in Amazonian birds. Ecol Lett 2019; 22:624-633. [PMID: 30714311 DOI: 10.1111/ele.13229] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/15/2018] [Accepted: 01/04/2019] [Indexed: 01/21/2023]
Abstract
The importance of ecologically mediated divergent selection in accelerating trait evolution has been poorly studied in the most species-rich biome of the planet, the continental Neotropics. We performed macroevolutionary analyses of trait divergence and diversification rates across closely related pairs of Andean and Amazonian passerine birds, to assess whether the difference in elevational range separating species pairs - a proxy for the degree of ecological divergence - influences the speed of trait evolution and diversification rates. We found that elevational differentiation is associated with faster divergence of song frequency, a trait important for pre-mating isolation, and several morphological traits, which may contribute to extrinsic post-mating isolation. However, elevational differentiation did not increase recent speciation rates, possibly due to early bursts of diversification during the uplift of the eastern Andes followed by a slow-down in speciation rate. Our results suggest that ecological differentiation may speed up trait evolution, but not diversification of Neotropical birds.
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Affiliation(s)
- Vanessa E Luzuriaga-Aveiga
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M1C 1A4, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M1C 1A4, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada.,Department of Ornithology, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, M5S 2C6, Canada
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20
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Abstract
We possess limited understanding of how speciation unfolds in the most species-rich region of the planet-the Amazon basin. Hybrid zones provide valuable information on the evolution of reproductive isolation, but few studies of Amazonian vertebrate hybrid zones have rigorously examined the genome-wide underpinnings of reproductive isolation. We used genome-wide genetic datasets to show that two deeply diverged, but morphologically cryptic sister species of forest understorey birds show little evidence for prezygotic reproductive isolation, but substantial postzygotic isolation. Patterns of heterozygosity and hybrid index revealed that hybrid classes with heavily recombined genomes are rare and closely match simulations with high levels of selection against hybrids. Genomic and geographical clines exhibit a remarkable similarity across loci in cline centres, and have exceptionally narrow cline widths, suggesting that postzygotic isolation is driven by genetic incompatibilities at many loci, rather than a few loci of strong effect. We propose Amazonian understorey forest birds speciate slowly via gradual accumulation of postzygotic genetic incompatibilities, with prezygotic barriers playing a less important role. Our results suggest old, cryptic Amazonian taxa classified as subspecies could have substantial postzygotic isolation deserving species recognition and that species richness is likely to be substantially underestimated in Amazonia.
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Affiliation(s)
| | - Alexandre Aleixo
- Department of Zoology, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada .,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada
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21
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Ramón‐Laca A, White DJ, Weir JT, Robertson HA. Extraction of DNA from captive-sourced feces and molted feathers provides a novel method for conservation management of New Zealand kiwi ( Apteryx spp.). Ecol Evol 2018; 8:3119-3130. [PMID: 29607011 PMCID: PMC5869209 DOI: 10.1002/ece3.3795] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 11/01/2017] [Accepted: 12/06/2017] [Indexed: 11/17/2022] Open
Abstract
Although some taxa are increasing in number due to active management and predator control, the overall number of kiwi (Apteryx spp.) is declining. Kiwi are cryptic and rare, meaning current monitoring tools, such as call counts, radio telemetry, and surveys using detection dogs are labor-intensive, yield small datasets, and require substantial resources or provide inaccurate estimates of population sizes. A noninvasive genetic approach could help the conservation effort. We optimized a panel of 23 genetic markers (22 autosomal microsatellite loci and an allosomal marker) to discriminate between all species of kiwi and major lineages within species, while simultaneously determining sex. Markers successfully amplified from both fecal and shed feather DNA samples collected in captivity. We found that DNA extraction was more efficient from shed feathers, but DNA quality was greater with feces, although this was sampling dependent. Our microsatellite panel was able to distinguish between contemporary kiwi populations and lineages and provided PI values in the range of 4.3 × 10-5 to 2.0 × 10-19, which in some cases were sufficient for individualization and mark-recapture studies. As such, we have tested a wide-reaching, noninvasive molecular approach that will improve conservation management by providing better parameter estimates associated with population ecology and demographics such as abundance, growth rates, and genetic diversity.
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Affiliation(s)
| | - Daniel J. White
- Landcare ResearchAucklandNew Zealand
- School of Biological SciencesUniversity of Western AustraliaPerthWAAustralia
| | - Jason T. Weir
- Department of Biological SciencesUniversity of TorontoTorontoONCanada
- Department of Ecology and EvolutionUniversity of TorontoTorontoONCanada
| | - Hugh A. Robertson
- Department of ConservationNew Zealand GovernmentWellingtonNew Zealand
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22
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Cooney CR, Tobias JA, Weir JT, Botero CA, Seddon N. Sexual selection, speciation and constraints on geographical range overlap in birds. Ecol Lett 2017; 20:863-871. [DOI: 10.1111/ele.12780] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/06/2017] [Accepted: 04/03/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher R. Cooney
- Department of Zoology; Edward Grey Institute; University of Oxford; South Parks Road Oxford OX1 3PS UK
- Department of Animal and Plant Sciences; University of Sheffield; Western Bank Sheffield S10 2TN UK
| | - Joseph A. Tobias
- Department of Zoology; Edward Grey Institute; University of Oxford; South Parks Road Oxford OX1 3PS UK
- Department of Life Sciences; Imperial College London; Silwood Park Buckhurst Road Ascot Berkshire SL5 7PY UK
| | - Jason T. Weir
- Department Ecology and Evolution and Department of Biological Sciences; University of Toronto Scarborough; Toronto ON M1C 1A4 Canada
| | - Carlos A. Botero
- Department of Biology; Washington University in Saint Louis; St. Louis MO 63130-4899 USA
| | - Nathalie Seddon
- Department of Zoology; Edward Grey Institute; University of Oxford; South Parks Road Oxford OX1 3PS UK
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23
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Germain RM, Weir JT, Gilbert B. Species coexistence: macroevolutionary relationships and the contingency of historical interactions. Proc Biol Sci 2016; 283:20160047. [PMID: 27009226 DOI: 10.1098/rspb.2016.0047] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 02/23/2016] [Indexed: 11/12/2022] Open
Abstract
Evolutionary biologists since Darwin have hypothesized that closely related species compete more intensely and are therefore less likely to coexist. However, recent theory posits that species diverge in two ways: either through the evolution of 'stabilizing differences' that promote coexistence by causing individuals to compete more strongly with conspecifics than individuals of other species, or through the evolution of 'fitness differences' that cause species to differ in competitive ability and lead to exclusion of the weaker competitor. We tested macroevolutionary patterns of divergence by competing pairs of annual plant species that differ in their phylogenetic relationships, and in whether they have historically occurred in the same region or different regions (sympatric versus allopatric occurrence). For sympatrically occurring species pairs, stabilizing differences rapidly increased with phylogenetic distance. However, fitness differences also increased with phylogenetic distance, resulting in coexistence outcomes that were unpredictable based on phylogenetic relationships. For allopatric species, stabilizing differences showed no trend with phylogenetic distance, whereas fitness differences increased, causing coexistence to become less likely among distant relatives. Our results illustrate the role of species' historical interactions in shaping how phylogenetic relationships structure competitive dynamics, and offer an explanation for the evolution of invasion potential of non-native species.
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Affiliation(s)
- Rachel M Germain
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5 Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada M1C 1A4
| | - Benjamin Gilbert
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
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24
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Pulido-Santacruz P, Weir JT. Extinction as a driver of avian latitudinal diversity gradients. Evolution 2016; 70:860-72. [DOI: 10.1111/evo.12899] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 12/22/2022]
Affiliation(s)
| | - Jason T. Weir
- Current Address: Department of Ecology and Evolutionary Biology; University of Toronto; 1265 Military Trail Scarborough Ontario M1C 1A4 Canada
- Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario Canada
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25
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Abstract
Are rates of evolution and speciation fastest where diversity is greatest - the tropics? A commonly accepted theory links the latitudinal diversity gradient to a speciation pump model whereby the tropics produce species at a faster rate than extra-tropical regions. In this issue of Molecular Ecology, Botero et al. () test the speciation pump model using subspecies richness patterns for more than 9000 species of birds and mammals as a proxy for incipient speciation opportunity. Rather than using latitudinal centroids, the authors investigate the role of various environmental correlates of latitude as drivers of subspecies richness. Their key finding points to environmental harshness as a positive predictor of subspecies richness. The authors link high subspecies richness in environmental harsh areas to increased opportunities for geographic range fragmentation and/or faster rates of trait evolution as drivers of incipient speciation. Because environmental harshness generally increases with latitude, these results suggest that opportunity for incipient speciation is lowest where species richness is highest. The authors interpret this finding as incompatible with the view of the tropics as a cradle of diversity. Their results are consistent with a growing body of evidence that reproductive isolation and speciation occur fastest at high latitudes.
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Affiliation(s)
- Jason T Weir
- Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada, M1C 1A4
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26
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Affiliation(s)
- Jason T. Weir
- Department of Biological Sciences University of Toronto Scarborough Toronto ON M1C 1A4 Canada
- Department of Ecology and Evolutionary Biology University of Toronto Scarborough Toronto ON M1C 1A4 Canada
| | - Adam Lawson
- Department of Biological Sciences University of Toronto Scarborough Toronto ON M1C 1A4 Canada
- Department of Ecology and Evolutionary Biology University of Toronto Scarborough Toronto ON M1C 1A4 Canada
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27
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Weir JT, Faccio MS, Pulido-Santacruz P, Barrera-Guzmán AO, Aleixo A. Hybridization in headwater regions, and the role of rivers as drivers of speciation in Amazonian birds. Evolution 2015; 69:1823-34. [DOI: 10.1111/evo.12696] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 04/29/2015] [Accepted: 04/29/2015] [Indexed: 01/19/2023]
Affiliation(s)
- Jason T. Weir
- Department of Biological Sciences; University of Toronto Scarborough; Toronto Canada
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Canada
| | - Maya S. Faccio
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Canada
| | | | | | - Alexandre Aleixo
- Department of Zoology; Museu Paraense Emílio Goeldi; Belém Brazil
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28
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Rowe M, Albrecht T, Cramer ERA, Johnsen A, Laskemoen T, Weir JT, Lifjeld JT. Postcopulatory sexual selection is associated with accelerated evolution of sperm morphology. Evolution 2015; 69:1044-52. [PMID: 25655075 DOI: 10.1111/evo.12620] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/16/2015] [Indexed: 01/31/2023]
Abstract
Rapid diversification of sexual traits is frequently attributed to sexual selection, though explicit tests of this hypothesis remain limited. Spermatozoa exhibit remarkable variability in size and shape, and studies report a correlation between sperm morphology (sperm length and shape) and sperm competition risk or female reproductive tract morphology. However, whether postcopulatory processes (e.g., sperm competition and cryptic female choice) influence the speed of evolutionary diversification in sperm form is unknown. Using passerine birds, we quantified evolutionary rates of sperm length divergence among lineages (i.e., species pairs) and determined whether these rates varied with the level of sperm competition (estimated as relative testes mass). We found that relative testes mass was significantly and positively associated with more rapid phenotypic divergence in sperm midpiece and flagellum lengths, as well as total sperm length. In contrast, there was no association between relative testes mass and rates of evolutionary divergence in sperm head size, and models suggested that head length is evolutionarily constrained. Our results are the first to show an association between the strength of sperm competition and the speed of sperm evolution, and suggest that postcopulatory sexual selection promotes rapid evolutionary diversification of sperm morphology.
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Affiliation(s)
- Melissah Rowe
- Natural History Museum, University of Oslo, PO Box 1172, Blindern, 0318, Oslo, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway.
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29
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Lawson AM, Weir JT. Latitudinal gradients in climatic-niche evolution accelerate trait evolution at high latitudes. Ecol Lett 2014; 17:1427-36. [PMID: 25168260 DOI: 10.1111/ele.12346] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/12/2014] [Accepted: 07/28/2014] [Indexed: 11/26/2022]
Abstract
Despite the importance of divergent selection to the speed of evolution, it remains poorly understood if divergent selection is more prevalent in the tropics (where species richness is highest), or at high latitudes (where paleoclimate change has been most intense). We tested whether the rate of climatic-niche evolution - one proxy for divergent selection - varies with latitude for 111 pairs of bird species. Using Brownian motion and Ornsetin-Ulhenbeck models, we show that evolutionary rates along two important axes of the climatic-niche - temperature and seasonality - have been faster at higher latitudes. We then tested whether divergence of the climatic-niche was associated with evolution in traits important in ecological differentiation (body mass) and reproductive isolation (song), and found that climatic divergence is associated with faster rates in both measures. These results highlight the importance of climate-mediated divergent selection pressures in driving evolutionary divergence and reproductive isolation at high latitudes.
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Affiliation(s)
- Adam M Lawson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M1C 1A4, Canada
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30
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Lepais O, Weir JT. SimRAD: an R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches. Mol Ecol Resour 2014; 14:1314-21. [DOI: 10.1111/1755-0998.12273] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 04/30/2014] [Accepted: 04/30/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Olivier Lepais
- INRA; UMR 1224; Ecologie Comportementale et Biologie des Populations de Poissons; INRA; Saint Pée sur Nivelle France
- Univ Pau & Pays Adour; UMR 1224; Ecologie Comportementale et Biologie des Populations de Poissons; UFR Sciences et Techniques de la Côte Basque; Univ Pau and Pays Adour; Anglet France
| | - Jason T. Weir
- Department of Biological Sciences, and Department of Ecology and Evolutionary Biology; University of Toronto Scarborough; Toronto ON M1C 1A4 Canada
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31
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Seddon N, Botero CA, Tobias JA, Dunn PO, Macgregor HEA, Rubenstein DR, Uy JAC, Weir JT, Whittingham LA, Safran RJ. Sexual selection accelerates signal evolution during speciation in birds. Proc Biol Sci 2013; 280:20131065. [PMID: 23864596 PMCID: PMC3730587 DOI: 10.1098/rspb.2013.1065] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Sexual selection is proposed to be an important driver of diversification in animal systems, yet previous tests of this hypothesis have produced mixed results and the mechanisms involved remain unclear. Here, we use a novel phylogenetic approach to assess the influence of sexual selection on patterns of evolutionary change during 84 recent speciation events across 23 passerine bird families. We show that elevated levels of sexual selection are associated with more rapid phenotypic divergence between related lineages, and that this effect is restricted to male plumage traits proposed to function in mate choice and species recognition. Conversely, we found no evidence that sexual selection promoted divergence in female plumage traits, or in male traits related to foraging and locomotion. These results provide strong evidence that female choice and male-male competition are dominant mechanisms driving divergence during speciation in birds, potentially linking sexual selection to the accelerated evolution of pre-mating reproductive isolation.
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Affiliation(s)
- Nathalie Seddon
- Edward Grey Institute, University of Oxford, , South Parks Road, Oxford OX1 3PS, UK.
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Bloom DD, Weir JT, Piller KR, Lovejoy NR. DO FRESHWATER FISHES DIVERSIFY FASTER THAN MARINE FISHES? A TEST USING STATE-DEPENDENT DIVERSIFICATION ANALYSES AND MOLECULAR PHYLOGENETICS OF NEW WORLD SILVERSIDES (ATHERINOPSIDAE). Evolution 2013; 67:2040-57. [DOI: 10.1111/evo.12074] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 02/04/2013] [Indexed: 12/17/2022]
Affiliation(s)
- Devin D. Bloom
- Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario M1C 1A4 Canada
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Jason T. Weir
- Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario M1C 1A4 Canada
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Kyle R. Piller
- Department of Biological Sciences; Southeastern Louisiana University; Hammond Louisiana 70402
| | - Nathan R. Lovejoy
- Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario M1C 1A4 Canada
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
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Desantis LM, Delehanty B, Weir JT, Boonstra R. Mediating free glucocorticoid levels in the blood of vertebrates: are corticosteroid-binding proteins always necessary? Funct Ecol 2013. [DOI: 10.1111/1365-2435.12038] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lanna M. Desantis
- Centre for the Neurobiology of Stress; Department of Biological Sciences; University of Toronto Scarborough; Toronto; Ontario; M1C 1A4; Canada
| | - Brendan Delehanty
- Centre for the Neurobiology of Stress; Department of Biological Sciences; University of Toronto Scarborough; Toronto; Ontario; M1C 1A4; Canada
| | - Jason T. Weir
- Department of Biological Sciences; University of Toronto Scarborough; Toronto; Ontario; M1C 1A4; Canada
| | - Rudy Boonstra
- Centre for the Neurobiology of Stress; Department of Biological Sciences; University of Toronto Scarborough; Toronto; Ontario; M1C 1A4; Canada
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Kennedy JD, Weir JT, Hooper DM, Tietze DT, Martens J, Price TD. ECOLOGICAL LIMITS ON DIVERSIFICATION OF THE HIMALAYAN CORE CORVOIDEA. Evolution 2012; 66:2599-613. [DOI: 10.1111/j.1558-5646.2012.01618.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Just as features of the physical and biotic environment constrain evolution of ecological and morphological traits, they may also affect evolution of communication systems. Here we analyze constraints on rates of vocal evolution, using a large dataset of New World avian sister taxa. We show that species breeding in tropical forests sing at generally lower frequencies and across narrower bandwidths than species breeding in open habitats, or at high latitudes. We attribute these restrictions on birdsong frequency to the presence of high-frequency insect noise and greater degradation of high-frequency sounds in tropical forests. We fit Ornstein-Uhlenbeck models to show that recent evolution of song frequency has been more greatly constrained in tropical forests than elsewhere, that is, songs have shown less tendency to diverge over time in tropical forests, consistent with inferred acoustic restrictions. In addition, we find that song frequency has evolved more rapidly overall at high latitudes in both forest and open habitats. Besides a larger available sound window, other factors contributing to more rapid divergence at high latitudes may include an overall increased intensity of sexual selection, occupation of more divergent habitats, and the presence of fewer competing species.
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Affiliation(s)
- Jason T Weir
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
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Affiliation(s)
- Jaime A Chaves
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, 619 Charles E. Young Dr. South, La Kretz Hall, Suite 300, Los Angeles, CA 90095-1496, USA.
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Weir JT, Price TD. Limits to Speciation Inferred from Times to Secondary Sympatry and Ages of Hybridizing Species along a Latitudinal Gradient. Am Nat 2011; 177:462-9. [DOI: 10.1086/658910] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Weir JT, Schluter D. Are rates of molecular evolution in mammals substantially accelerated in warmer environments? Proc Biol Sci 2011; 278:1291-3; discussion 1294-7. [PMID: 21288954 DOI: 10.1098/rspb.2010.0388] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jason T Weir
- Department of Ecology and Evolution, University of Chicago, Chicago 60637, USA.
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Abstract
We ask whether rates of evolution in traits important for reproductive isolation vary across a latitudinal gradient, by quantifying evolutionary rates of two traits important for pre-mating isolation-avian syllable diversity and song length. We analyse over 2500 songs from 116 pairs of closely related New World passerine bird taxa to show that evolutionary rates for the two main groups of passerines-oscines and suboscines-doubled with latitude in both groups for song length. For syllable diversity, oscines (who transmit song culturally) evolved more than 20 times faster at high latitudes than in low latitudes, whereas suboscines (whose songs are innate in most species and who possess very simple song with few syllable types) show no clear latitudinal gradient in rate. Evolutionary rates in oscines and suboscines were similar at tropical latitudes for syllable complexity as well as for song length. These results suggest that evolutionary rates in traits important to reproductive isolation and speciation are influenced by latitude and have been fastest, not in the tropics where species diversity is highest, but towards the poles.
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Affiliation(s)
- Jason T Weir
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada.
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Harmon LJ, Losos JB, Jonathan Davies T, Gillespie RG, Gittleman JL, Bryan Jennings W, Kozak KH, McPeek MA, Moreno-Roark F, Near TJ, Purvis A, Ricklefs RE, Schluter D, Schulte Ii JA, Seehausen O, Sidlauskas BL, Torres-Carvajal O, Weir JT, Mooers AØ. EARLY BURSTS OF BODY SIZE AND SHAPE EVOLUTION ARE RARE IN COMPARATIVE DATA. Evolution 2010; 64:2385-96. [PMID: 20455932 DOI: 10.1111/j.1558-5646.2010.01025.x] [Citation(s) in RCA: 345] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luke J Harmon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, USA.
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Abstract
The sudden exchange of mammals over the land bridge between the previously isolated continents of North and South America is among the most celebrated events in the faunal history of the New World. This exchange resulted in the rapid merging of continental mammalian faunas that had evolved in almost complete isolation from each other for tens of millions of years. Yet, the wider importance of land bridge-mediated interchange to faunal mixing in other groups is poorly known because of the incompleteness of the fossil record. In particular, the ability of birds to fly may have rendered a land bridge unnecessary for faunal merging. Using molecular dating of the unique bird faunas of the two continents, we show that rates of interchange increased dramatically after land bridge completion in tropical forest-specializing groups, which rarely colonize oceanic islands and have poor dispersal abilities across water barriers, but not in groups comprised of habitat generalists. These results support the role of the land bridge in the merging of the tropical forest faunas of North and South America. In contrast to mammals, the direction of traffic across the land bridge in birds was primarily south to north. The event transformed the tropical avifauna of the New World.
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Affiliation(s)
- Jason T Weir
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.
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Miller MJ, Bermingham E, Klicka J, Escalante P, do Amaral FSR, Weir JT, Winker K. Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher. Proc Biol Sci 2008; 275:1133-42. [PMID: 18285279 PMCID: PMC2602697 DOI: 10.1098/rspb.2008.0015] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Revised: 02/01/2008] [Accepted: 02/04/2008] [Indexed: 11/12/2022] Open
Abstract
Most Neotropical lowland forest taxa occur exclusively on one side of the Andes despite the availability of appropriate habitat on both sides. Almost all molecular phylogenies and phylogenetic analyses of species assemblages (i.e. area cladograms) have supported the hypothesis that Andean uplift during the Late Pliocene created a vicariant barrier affecting lowland lineages in the region. However, a few widespread plant and animal species occurring in lowland forests on both sides of the Andes challenge the generality of this hypothesis. To understand the role of the Andes in the history of such organisms, we reconstructed the phylogeographic history of a widespread Neotropical flycatcher (Mionectes oleagineus) in the context of the other four species in the genus. A molecular phylogeny based on nuclear and mitochondrial sequences unambiguously showed an early basal split between montane and lowland Mionectes. The phylogeographic reconstruction of lowland taxa revealed a complex history, with multiple cases in which geographically proximate populations do not represent sister lineages. Specifically, three populations of M. oleagineus west of the Andes do not comprise a monophyletic clade; instead, each represents an independent lineage with origins east of the Andes. Divergence time estimates suggest that at least two cross-Andean dispersal events post-date Andean uplift.
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Weir JT, Bermingham E, Miller MJ, Klicka J, González MA. Phylogeography of a morphologically diverse Neotropical montane species, the Common Bush-Tanager (Chlorospingusophthalmicus). Mol Phylogenet Evol 2008; 47:650-64. [DOI: 10.1016/j.ympev.2008.02.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 02/03/2008] [Accepted: 02/07/2008] [Indexed: 10/22/2022]
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Affiliation(s)
- J T Weir
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
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Affiliation(s)
- Luke J Harmon
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
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Abstract
Although the tropics harbor greater numbers of species than do temperate zones, it is not known whether the rates of speciation and extinction also follow a latitudinal gradient. By sampling birds and mammals, we found that the distribution of the evolutionary ages of sister species-pairs of species in which each is the other's closest relative-adheres to a latitudinal gradient. The time to divergence for sister species is shorter at high latitudes and longer in the tropics. Birth-death models fitting these data estimate that the highest recent speciation and extinction rates occur at high latitudes and decline toward the tropics. These results conflict with the prevailing view that links high tropical diversity to elevated tropical speciation rates. Instead, our findings suggest that faster turnover at high latitudes contributes to the latitudinal diversity gradient.
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Affiliation(s)
- Jason T Weir
- Biodiversity Research Center and Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Weir JT. Divergent timing and patterns of species accumulation in lowland and highland neotropical birds. Evolution 2006; 60:842-55. [PMID: 16739464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Late Pliocene and Pleistocene climatic instability has been invoked to explain the buildup of Neotropical biodiversity, although other theories date Neotropical diversification to earlier periods. If these climatic fluctuations drove Neotropical diversification, then a large proportion of species should date to this period and faunas should exhibit accelerated rates of speciation. However, the unique role of recent climatic fluctuations in promoting diversification could be rejected if late Pliocene and Pleistocene rates declined. To test these temporal predictions, dateable molecular phylogenies for 27 avian taxa were used to contrast the timing and rates of diversification in lowland and highland Neotropical faunas. Trends in diversification rates were analyzed in two ways. First, rates within taxa were analyzed for increasing or decreasing speciation rates through time. There was a significant trend within lowland taxa towards decreasing speciation rates, but no significant trend was observed within most highland taxa. Second, fauna wide diversification rates through time were estimated during one-million-year intervals by combining rates across taxa. In the lowlands, rates were highest during the late Miocene and then decreased towards the present. The decline in rates observed both within taxa and for the fauna as a whole probably resulted from density dependent cladogenesis. In the highlands, faunawide rates did not vary greatly before the Pleistocene but did increase significantly during the last one million years of the Pleistocene following the onset of severe glacial cycles in the Andes. These contrasting patterns of species accumulation suggest that lowland and highland regions were affected differently by recent climatic fluctuations. Evidently, habitat alterations associated with global climate change were not enough to promote an increase in the rate of diversification in lowland faunas. In contrast, direct fragmentation of habitats by glaciers and severe altitudinal migration of montane vegetation zones during climatic cycles may have resulted in the late Pleistocene increase in highland diversification rates. This increase resulted in a fauna with one third of its species dating to the last one million years.
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Affiliation(s)
- Jason T Weir
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
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