1
|
Zhang T, Jing H, Wang J, Zhao L, Liu Y, Rossiter SJ, Lu H, Li G. Evolution of olfactory receptor superfamily in bats based on high throughput molecular modelling. Mol Ecol Resour 2024:e13958. [PMID: 38567648 DOI: 10.1111/1755-0998.13958] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
The origin of flight and laryngeal echolocation in bats is likely to have been accompanied by evolutionary changes in other aspects of their sensory biology. Of all sensory modalities in bats, olfaction is perhaps the least well understood. Olfactory receptors (ORs) function in recognizing odour molecules, with crucial roles in evaluating food, as well as in processing social information. Here we compare OR repertoire sizes across taxa and apply a new pipeline that integrates comparative genome data with protein structure modelling and then we employ molecular docking techniques with small molecules to analyse OR functionality based on binding energies. Our results suggest a sharp contraction in odorant recognition of the functional OR repertoire during the origin of bats, consistent with a reduced dependence on olfaction. We also compared bat lineages with contrasting different ecological characteristics and found evidence of differences in OR gene expansion and contraction, and in the composition of ORs with different tuning breadths. The strongest binding energies of ORs in non-echolocating fruit-eating bats were seen to correspond to ester odorants, although we did not detect a quantitative advantage of functional OR repertoires in these bats compared with echolocating insectivorous species. Overall, our findings based on molecular modelling and computational docking suggest that bats have undergone olfactory evolution linked to dietary adaptation. Our results from extant and ancestral bats help to lay the groundwork for targeted experimental functional tests in the future.
Collapse
Affiliation(s)
- Tianmin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Haohao Jing
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Le Zhao
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London, UK
| | - Huimeng Lu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| |
Collapse
|
2
|
Zhou W, Furey NM, Soisook P, Thong VD, Lim BK, Rossiter SJ, Mao X. Corrigendum to "Diversification and introgression in four chromosomal taxa of the Pearson's horseshoe bat (Rhinolophus pearsoni) group" [Mol. Phylogenet. Evol. 183 (2023) 107784]. Mol Phylogenet Evol 2023; 189:107943. [PMID: 37845160 DOI: 10.1016/j.ympev.2023.107943] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Affiliation(s)
- Weiwei Zhou
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China
| | - Neil M Furey
- Fauna & Flora International (Cambodia), PO Box 1380, No. 19, Street 360, Boeng Keng Kong 1, Phnom Penh 12000, Cambodia
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Vu D Thong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Viet Nam; Graduate University of Science and Technology, VAST, Viet Nam
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China.
| |
Collapse
|
3
|
Anthwal N, Hall RP, de la Rosa Hernandez FA, Koger M, Yohe LR, Hedrick BP, Davies KTJ, Mutumi GL, Roseman CC, Dumont ER, Dávalos LM, Rossiter SJ, Sadier A, Sears KE. Cochlea development shapes bat sensory system evolution. Anat Rec (Hoboken) 2023. [PMID: 37994725 DOI: 10.1002/ar.25353] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023]
Abstract
Sensory organs must develop alongside the skull within which they are largely encased, and this relationship can manifest as the skull constraining the organs, organs constraining the skull, or organs constraining one another in relative size. How this interplay between sensory organs and the developing skull plays out during the evolution of sensory diversity; however, remains unknown. Here, we examine the developmental sequence of the cochlea, the organ responsible for hearing and echolocation, in species with distinct diet and echolocation types within the ecologically diverse bat super-family Noctilionoidea. We found the size and shape of the cochlea largely correlates with skull size, with exceptions of Pteronotus parnellii, whose high duty cycle echolocation (nearly constant emission of sound pulses during their echolocation process allowing for detailed information gathering, also called constant frequency echolocation) corresponds to a larger cochlear and basal turn, and Monophyllus redmani, a small-bodied nectarivorous bat, for which interactions with other sensory organs restrict cochlea size. Our findings support the existence of developmental constraints, suggesting that both developmental and anatomical factors may act synergistically during the development of sensory systems in noctilionoid bats.
Collapse
Affiliation(s)
- Neal Anthwal
- King's College London, Centre for Craniofacial and Regenerative Biology, London, UK
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Ronald P Hall
- Department of Life and Environment Sciences, University of California Merced, Merced, California, USA
| | | | - Michael Koger
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Laurel R Yohe
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, Charlotte, North Carolina, USA
| | - Brandon P Hedrick
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Kalina T J Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Gregory L Mutumi
- Department of Life and Environment Sciences, University of California Merced, Merced, California, USA
| | - Charles C Roseman
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, USA
| | - Elizabeth R Dumont
- Department of Life and Environment Sciences, University of California Merced, Merced, California, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution and Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, USA
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California Los Angeles, Los Angeles, California, USA
| |
Collapse
|
4
|
Li Y, Jiao H, Sin SYW, Wang R, Rossiter SJ, Zhao H. Common ancestors of bats were omnivorous suggested by resurrection of ancestral sweet receptors. Sci Bull (Beijing) 2023; 68:1748-1751. [PMID: 37500405 DOI: 10.1016/j.scib.2023.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/29/2023] [Accepted: 06/21/2023] [Indexed: 07/29/2023]
Affiliation(s)
- Yingcan Li
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau of the Ministry of Education, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hengwu Jiao
- School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Ruiqi Wang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau of the Ministry of Education, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Huabin Zhao
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau of the Ministry of Education, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| |
Collapse
|
5
|
Mutumi GL, Hall RP, Hedrick BP, Yohe LR, Sadier A, Davies KTJ, Rossiter SJ, Sears KE, Dávalos LM, Dumont ER. Disentangling Mechanical and Sensory Modules in the Radiation of Noctilionoid Bats. Am Nat 2023; 202:216-230. [PMID: 37531274 DOI: 10.1086/725368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
AbstractWith diverse mechanical and sensory functions, the vertebrate cranium is a complex anatomical structure whose shifts between modularity and integration, especially in mechanical function, have been implicated in adaptive diversification. Yet how mechanical and sensory systems and their functions coevolve, as well as how their interrelationship contributes to phenotypic disparity, remain largely unexplored. To examine the modularity, integration, and evolutionary rates of sensory and mechanical structures within the head, we analyzed hard and soft tissue scans from ecologically diverse bats in the superfamily Noctilionoidea, a clade that ranges from insectivores and carnivores to frugivores and nectarivores. We identified eight regions that evolved in a coordinated fashion, thus recognizable as evolutionary modules: five associated with bite force and three linked to olfactory, visual, and auditory systems. Interrelationships among these modules differ between Neotropical leaf-nosed bats (family Phyllostomidae) and other noctilionoids. Consistent with the hypothesis that dietary transitions begin with changes in the capacity to detect novel food items followed by adaptations to process them, peak rates of sensory module evolution predate those of some mechanical modules. We propose that the coevolution of structures influencing bite force, olfaction, vision, and hearing constituted a structural opportunity that allowed the phyllostomid ancestor to take advantage of existing ecological opportunities and contributed to the clade's remarkable radiation.
Collapse
|
6
|
Zhou W, Furey NM, Soisook P, Thong VD, Lim BK, Rossiter SJ, Mao X. Diversification and introgression in four chromosomal taxa of the Pearson's horseshoe bat (Rhinolophus pearsoni) group. Mol Phylogenet Evol 2023; 183:107784. [PMID: 37040825 DOI: 10.1016/j.ympev.2023.107784] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/11/2023] [Accepted: 04/07/2023] [Indexed: 04/13/2023]
Abstract
Chromosomal variation among closely related taxa is common in both plants and animals, and can reduce rates of introgression as well as promote reproductive isolation and speciation. In mammals, studies relating introgression to chromosomal variation have tended to focus on a few model systems and typically characterized levels of introgression using small numbers of loci. Here we took a genome-wide approach to examine how introgression rates vary among four closely related horseshoe bats (Rhinolophus pearsoni group) that possess different diploid chromosome numbers (2n = 42, 44, 46, and 60) resulting from Robertsonian (Rb) changes (fissions/fusions). Using a sequence capture we obtained orthologous loci for thousands of nuclear loci, as well as mitogenomes, and performed phylogenetic and population genetic analyses. We found that the taxon with 2n = 60 was the first to diverge in this group, and that the relationships among the three other taxa (2n = 42, 44 and 46) showed discordance across our different analyses. Our results revealed signatures of multiple ancient introgression events between the four taxa, with evidence of mitonuclar discordance in phylogenetic trees and reticulation events in their evolutionary history. Despite this, we found no evidence of recent and/or ongoing introgression between taxa. Overall, our results indicate that the effects of Rb changes on the reduction of introgression are complicated and that these may contribute to reproductive isolation and speciation in concert with other factors (e.g. phenotypic and genic divergence).
Collapse
Affiliation(s)
- Weiwei Zhou
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China
| | - Neil M Furey
- Fauna & Flora International (Cambodia), PO Box 1380, No. 19, Street 360, Boeng Keng Kong 1, Phnom Penh 12000, Cambodia
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Vu D Thong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Viet Nam; Graduate University of Science and Technology, VAST, Viet Nam
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China.
| |
Collapse
|
7
|
Tian S, Zeng J, Jiao H, Zhang D, Zhang L, Lei CQ, Rossiter SJ, Zhao H. Comparative analyses of bat genomes identify distinct evolution of immunity in Old World fruit bats. Sci Adv 2023; 9:eadd0141. [PMID: 37146151 PMCID: PMC10162675 DOI: 10.1126/sciadv.add0141] [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] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Bats have been identified as natural reservoir hosts of several zoonotic viruses, prompting suggestions that they have unique immunological adaptations. Among bats, Old World fruit bats (Pteropodidae) have been linked to multiple spillovers. To test for lineage-specific molecular adaptations in these bats, we developed a new assembly pipeline to generate a reference-quality genome of the fruit bat Cynopterus sphinx and used this in comparative analyses of 12 bat species, including six pteropodids. Our results reveal that immunity-related genes have higher evolutionary rates in pteropodids than in other bats. Several lineage-specific genetic changes were shared across pteropodids, including the loss of NLRP1, duplications of PGLYRP1 and C5AR2, and amino acid replacements in MyD88. We introduced MyD88 transgenes containing Pteropodidae-specific residues into bat and human cell lines and found evidence of dampened inflammatory responses. By uncovering distinct immune adaptations, our results could help explain why pteropodids are frequently identified as viral hosts.
Collapse
Affiliation(s)
- Shilin Tian
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Jiaming Zeng
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Hengwu Jiao
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Dejing Zhang
- Novogene Bioinformatics Institute, Beijing 100015, China
| | - Libiao Zhang
- Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Cao-Qi Lei
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Huabin Zhao
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| |
Collapse
|
8
|
Guo J, Chi H, Zhang L, Song S, Rossiter SJ, Liu Y. Convergent evolutionary shifts in rhodopsin retinal release explain shared opsin repertoires in monotremes and crocodilians. Proc Biol Sci 2023; 290:20230530. [PMID: 37040807 PMCID: PMC10089720 DOI: 10.1098/rspb.2023.0530] [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] [Indexed: 04/13/2023] Open
Abstract
The visual ecology of early mammals remains poorly resolved. Studies of ancestral photopigments suggest an ancient transition from nocturnal to more crepuscular conditions. By contrast, the phenotypic shifts following the split of monotremes and therians-which lost their SWS1 and SWS2 opsins, respectively-are less clear. To address this, we obtained new phenotypic data on the photopigments of extant and ancestral monotremes. We then generated functional data for another vertebrate group that shares the same photopigment repertoire as monotremes: the crocodilians. By characterizing resurrected ancient pigments, we show that the ancestral monotreme underwent a dramatic acceleration in its rhodopsin retinal release rate. Moreover, this change was likely mediated by three residue replacements, two of which also arose on the ancestral branch of crocodilians, which exhibit similarly accelerated retinal release. Despite this parallelism in retinal release, we detected minimal to moderate changes in the spectral tuning of cone visual pigments in these groups. Our results imply that ancestral forms of monotremes and crocodilians independently underwent niche expansion to encompass quickly changing light conditions. This scenario-which accords with reported crepuscular activity in extant monotremes-may help account for their loss of the ultraviolet-sensitive SWS1 pigment but retention of the blue-sensitive SWS2.
Collapse
Affiliation(s)
- Jinqu Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Hai Chi
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Linghan Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Shengjing Song
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London E1 4NS, UK
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| |
Collapse
|
9
|
Kemp VA, Grey J, Hemprich‐Bennett D, Rossiter SJ, Lewis OT, Wilkinson CL, Clare EL, Kratina P. Changes in trophic ecology of mobile predators in response to rainforest degradation. J Appl Ecol 2023. [DOI: 10.1111/1365-2664.14396] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Victoria A. Kemp
- School of Biological and Behavioural Sciences Queen Mary University of London London United Kingdom
| | - Jonathan Grey
- School of Biological and Behavioural Sciences Queen Mary University of London London United Kingdom
- Lancaster Environment Centre Lancaster University Bailrigg Lancaster United Kingdom
| | - David Hemprich‐Bennett
- School of Biological and Behavioural Sciences Queen Mary University of London London United Kingdom
- Department of Biology University of Oxford South Parks Road Oxford United Kingdom
| | - Stephen J. Rossiter
- School of Biological and Behavioural Sciences Queen Mary University of London London United Kingdom
| | - Owen T. Lewis
- Department of Biology University of Oxford South Parks Road Oxford United Kingdom
| | - Clare L. Wilkinson
- Department of Biological Sciences National University of Singapore 16 Science Drive 4 Singapore Singapore
| | - Elizabeth L. Clare
- School of Biological and Behavioural Sciences Queen Mary University of London London United Kingdom
- Department of Biology York University 4700 Keele Streer Toronto Canada
| | - Pavel Kratina
- School of Biological and Behavioural Sciences Queen Mary University of London London United Kingdom
| |
Collapse
|
10
|
Struebig MJ, Aninta SG, Beger M, Bani A, Barus H, Brace S, Davies ZG, Brauwer M, Diele K, Djakiman C, Djamaluddin R, Drinkwater R, Dumbrell A, Evans D, Fusi M, Herrera-Alsina L, Iskandar DT, Jompa J, Juliandi B, Lancaster LT, Limmon G, Lo MGY, Lupiyaningdyah P, McCannon M, Meijaard E, Mitchell SL, Mumbunan S, O'Connell D, Osborne OG, Papadopulos AST, Rahajoe JS, Rossiter SJ, Rustiami H, Salzmann U, Sudiana IM, Sukara E, Tasirin JS, Tjoa A, Travis JMJ, Trethowan L, Trianto A, Utteridge T, Voigt M, Winarni N, Zakaria Z, Edwards DP, Frantz L, Supriatna J. Safeguarding Imperiled Biodiversity and Evolutionary Processes in the Wallacea Center of Endemism. Bioscience 2022; 72:1118-1130. [PMID: 36325105 PMCID: PMC9618277 DOI: 10.1093/biosci/biac085] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Wallacea-the meeting point between the Asian and Australian fauna-is one of the world's largest centers of endemism. Twenty-three million years of complex geological history have given rise to a living laboratory for the study of evolution and biodiversity, highly vulnerable to anthropogenic pressures. In the present article, we review the historic and contemporary processes shaping Wallacea's biodiversity and explore ways to conserve its unique ecosystems. Although remoteness has spared many Wallacean islands from the severe overexploitation that characterizes many tropical regions, industrial-scale expansion of agriculture, mining, aquaculture and fisheries is damaging terrestrial and aquatic ecosystems, denuding endemics from communities, and threatening a long-term legacy of impoverished human populations. An impending biodiversity catastrophe demands collaborative actions to improve community-based management, minimize environmental impacts, monitor threatened species, and reduce wildlife trade. Securing a positive future for Wallacea's imperiled ecosystems requires a fundamental shift away from managing marine and terrestrial realms independently.
Collapse
|
11
|
Yohe LR, Fabbri M, Lee D, Davies KTJ, Yohe TP, Sánchez MKR, Rengifo EM, Hall RP, Mutumi G, Hedrick BP, Sadier A, Simmons NB, Sears KE, Dumont E, Rossiter SJ, Bhullar BAS, Dávalos LM. Ecological constraints on highly evolvable olfactory receptor genes and morphology in neotropical bats. Evolution 2022; 76:2347-2360. [PMID: 35904467 DOI: 10.1111/evo.14591] [Citation(s) in RCA: 1] [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: 12/13/2021] [Revised: 05/06/2022] [Accepted: 05/13/2022] [Indexed: 01/22/2023]
Abstract
Although evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with constant exposure to a changing odorant landscape; detecting adaptation amidst extensive chemosensory diversity is an open challenge. In phyllostomid bats, an ecologically diverse clade that evolved plant visiting from a presumed insectivorous ancestor, the evolution of novel food detection mechanisms is suggested to be a key innovation, as plant-visiting species rely strongly on olfaction, supplementarily using echolocation. If this is true, exceptional variation in underlying olfactory genes and phenotypes may have preceded dietary diversification. We compared olfactory receptor (OR) genes sequenced from olfactory epithelium transcriptomes and olfactory epithelium surface area of bats with differing diets. Surprisingly, although OR evolution rates were quite variable and generally high, they are largely independent of diet. Olfactory epithelial surface area, however, is relatively larger in plant-visiting bats and there is an inverse relationship between OR evolution rates and surface area. Relatively larger surface areas suggest greater reliance on olfactory detection and stronger constraint on maintaining an already diverse OR repertoire. Instead of the typical case in which specialization and elaboration are coupled with rapid diversification of associated genes, here the relevant genes are already evolving so quickly that increased reliance on smell has led to stabilizing selection, presumably to maintain the ability to consistently discriminate among specific odorants-a potential ecological constraint on sensory evolution.
Collapse
Affiliation(s)
- Laurel R Yohe
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794, USA.,Deaprtment of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, 28223, USA.,North Carolina Research Campus, Kannapolis, North Carolina, 28081, USA
| | - Matteo Fabbri
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, 60605, USA
| | - Daniela Lee
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Harvard School of Medicine, Cambridge, Massachusetts, 02115, USA
| | - Kalina T J Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | | | - Miluska K R Sánchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, 20004, Peru
| | - Edgardo M Rengifo
- Programa de Pós-Graduação Interunidades em Ecologia Aplicada, Escola Superior de Agricultura 'Luiz de Queiroz', Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, 13416-970, Brazil.,Centro de Investigación Biodiversidad Sostenible (BioS), Lima, 15073, Peru
| | - Ronald P Hall
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Gregory Mutumi
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Brandon P Hedrick
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, 90095, USA
| | - Nancy B Simmons
- Department of Mammalogy, American Museum of Natural History, New York, New York, 10024, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, 90095, USA
| | - Elizabeth Dumont
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Bhart-Anjan S Bhullar
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Yale Peabody Museum of Natural History, Yale University, New Haven, Connecticut, 06511, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794, USA.,Center for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, 11794, USA
| |
Collapse
|
12
|
Tanshi I, Obitte BC, Monadjem A, Rossiter SJ, Fisher‐Phelps M, Kingston T. Multiple dimensions of biodiversity in paleotropical hotspots reveal comparable bat diversity. Biotropica 2022. [DOI: 10.1111/btp.13143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Iroro Tanshi
- Department of Biological Sciences Texas Tech University Lubbock Texas USA
- Department of Biology University of Washington Seattle Washington USA
- Department of Animal and Environmental Biology University of Benin Benin City Nigeria
- Small Mammal Conservation Organization Benin City Nigeria
| | - Benneth C. Obitte
- Department of Biological Sciences Texas Tech University Lubbock Texas USA
- Small Mammal Conservation Organization Benin City Nigeria
| | - Ara Monadjem
- Department of Biological Sciences University of Eswatini Kwaluseni Eswatini
- Department of Zoology & Entomology, Mammal Research Institute University of Pretoria Hatfield South Africa
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - Marina Fisher‐Phelps
- Department of Biological Sciences Texas Tech University Lubbock Texas USA
- National Audubon Society Dallas Texas USA
| | - Tigga Kingston
- Department of Biological Sciences Texas Tech University Lubbock Texas USA
| |
Collapse
|
13
|
Gilbert JD, Rossiter SJ, Bennett NC, Faulkes CG. The elusive role of prolactin in the sociality of the naked mole-rat. Horm Behav 2022; 143:105196. [PMID: 35597054 DOI: 10.1016/j.yhbeh.2022.105196] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/13/2022] [Accepted: 05/05/2022] [Indexed: 12/01/2022]
Abstract
Despite decades of research into the evolutionary drivers of sociality, we know relatively little about the underlying proximate mechanisms. Here we investigate the potential role of prolactin in the highly social naked mole-rat. Naked mole-rats live in large social groups but, only a small number of individuals reproduce. The remaining non-breeders are reproductively suppressed and contribute to burrow maintenance, foraging, and allo-parental care. Prolactin has well-documented links with reproductive timing and parental behaviour, and the discovery that non-breeding naked mole-rats have unusually high prolactin levels has led to the suggestion that prolactin may help maintain naked mole-rat sociality. To test this idea, we investigated whether urinary prolactin was correlated with cooperative behaviour and aggression. We then administered the prolactin-suppressing drug Cabergoline to eight female non-breeders for eight weeks and assessed the physiology and behaviour of the animals relative to controls. Contrary to the mammalian norm, and supporting previous findings for plasma, we found non-breeders had elevated urinary prolactin concentrations that were similar to breeding females. Further, prolactin levels were higher in heavier, socially dominant non-breeders. Urinary prolactin concentrations did not explain variation in working behaviour or patterns of aggression. Furthermore, females receiving Cabergoline did not show any behavioural or hormonal (progesterone) differences, and urinary prolactin did not appear to be suppressed in individuals receiving Cabergoline. While the results add to the relatively limited literature experimentally manipulating prolactin to investigate its role in reproduction and behaviour, they fail to explain why prolactin levels are high in non-breeding naked mole-rats, or how female non-breeding phenotypes are maintained.
Collapse
Affiliation(s)
- James D Gilbert
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom of Great Britain and Northern Ireland.
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom of Great Britain and Northern Ireland
| | - Nigel C Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Christopher G Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom of Great Britain and Northern Ireland.
| |
Collapse
|
14
|
Marsh CJ, Sica YV, Burgin CJ, Dorman WA, Anderson RC, del Toro Mijares I, Vigneron JG, Barve V, Dombrowik VL, Duong M, Guralnick R, Hart JA, Maypole JK, McCall K, Ranipeta A, Schuerkmann A, Torselli MA, Lacher T, Mittermeier RA, Rylands AB, Sechrest W, Wilson DE, Abba AM, Aguirre LF, Arroyo‐Cabrales J, Astúa D, Baker AM, Braulik G, Braun JK, Brito J, Busher PE, Burneo SF, Camacho MA, Cavallini P, de Almeida Chiquito E, Cook JA, Cserkész T, Csorba G, Cuéllar Soto E, da Cunha Tavares V, Davenport TRB, Deméré T, Denys C, Dickman CR, Eldridge MDB, Fernandez‐Duque E, Francis CM, Frankham G, Franklin WL, Freitas T, Friend JA, Gadsby EL, Garbino GST, Gaubert P, Giannini N, Giarla T, Gilchrist JS, Gongora J, Goodman SM, Gursky‐Doyen S, Hackländer K, Hafner MS, Hawkins M, Helgen KM, Heritage S, Hinckley A, Hintsche S, Holden M, Holekamp KE, Honeycutt RL, Huffman BA, Humle T, Hutterer R, Ibáñez Ulargui C, Jackson SM, Janecka J, Janecka M, Jenkins P, Juškaitis R, Juste J, Kays R, Kilpatrick CW, Kingston T, Koprowski JL, Kryštufek B, Lavery T, Lee TE, Leite YLR, Novaes RLM, Lim BK, Lissovsky A, López‐Antoñanzas R, López‐Baucells A, MacLeod CD, Maisels FG, Mares MA, Marsh H, Mattioli S, Meijaard E, Monadjem A, Morton FB, Musser G, Nadler T, Norris RW, Ojeda A, Ordóñez‐Garza N, Pardiñas UFJ, Patterson BD, Pavan A, Pennay M, Pereira C, Prado J, Queiroz HL, Richardson M, Riley EP, Rossiter SJ, Rubenstein DI, Ruelas D, Salazar‐Bravo J, Schai‐Braun S, Schank CJ, Schwitzer C, Sheeran LK, Shekelle M, Shenbrot G, Soisook P, Solari S, Southgate R, Superina M, Taber AB, Talebi M, Taylor P, Vu Dinh T, Ting N, Tirira DG, Tsang S, Turvey ST, Valdez R, Van Cakenberghe V, Veron G, Wallis J, Wells R, Whittaker D, Williamson EA, Wittemyer G, Woinarski J, Zinner D, Upham NS, Jetz W. Expert range maps of global mammal distributions harmonised to three taxonomic authorities. J Biogeogr 2022; 49:979-992. [PMID: 35506011 PMCID: PMC9060555 DOI: 10.1111/jbi.14330] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 01/05/2022] [Accepted: 01/13/2022] [Indexed: 06/01/2023]
Abstract
AIM Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroecology. We provide global range maps for the native ranges of all extant mammal species harmonised to the taxonomy of the Mammal Diversity Database (MDD) mobilised from two sources, the Handbook of the Mammals of the World (HMW) and the Illustrated Checklist of the Mammals of the World (CMW). LOCATION Global. TAXON All extant mammal species. METHODS Range maps were digitally interpreted, georeferenced, error-checked and subsequently taxonomically aligned between the HMW (6253 species), the CMW (6431 species) and the MDD taxonomies (6362 species). RESULTS Range maps can be evaluated and visualised in an online map browser at Map of Life (mol.org) and accessed for individual or batch download for non-commercial use. MAIN CONCLUSION Expert maps of species' global distributions are limited in their spatial detail and temporal specificity, but form a useful basis for broad-scale characterizations and model-based integration with other data. We provide georeferenced range maps for the native ranges of all extant mammal species as shapefiles, with species-level metadata and source information packaged together in geodatabase format. Across the three taxonomic sources our maps entail, there are 1784 taxonomic name differences compared to the maps currently available on the IUCN Red List website. The expert maps provided here are harmonised to the MDD taxonomic authority and linked to a community of online tools that will enable transparent future updates and version control.
Collapse
Affiliation(s)
- Charles J. Marsh
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Yanina V. Sica
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Connor J. Burgin
- Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Wendy A. Dorman
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Robert C. Anderson
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Isabel del Toro Mijares
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Jessica G. Vigneron
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Vijay Barve
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | - Victoria L. Dombrowik
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Michelle Duong
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Robert Guralnick
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | - Julie A. Hart
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
- New York Natural Heritage ProgramState University of New York College of Environmental Science and ForestryAlbanyNew YorkUSA
| | - J. Krish Maypole
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Kira McCall
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Ajay Ranipeta
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Anna Schuerkmann
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Michael A. Torselli
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Thomas Lacher
- Department of Ecology and Conservation BiologyTexas A&M UniversityCollege StationTexasUSA
- Re:wildAustinTexasUSA
| | | | | | | | - Don E. Wilson
- National Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Agustín M. Abba
- Centro de Estudios Parasitológicos y de Vectores (CEPAVE‐UNLP‐CONICET)La Plata, Buenos AiresArgentina
| | - Luis F. Aguirre
- Centro de Biodiversidad y GenéticaUniversidad Mayor de San SimónCochabambaBolivia
| | | | - Diego Astúa
- Departamento de ZoologiaUniversidade Federal de PernambucoRecifePernambucoBrazil
| | - Andrew M. Baker
- School of Biology and Environmental Science, Faculty of ScienceQueensland University of TechnologyBrisbaneQueenslandAustralia
- Biodiversity and Geosciences ProgramQueensland MuseumBrisbaneQueenslandAustralia
| | - Gill Braulik
- School of BiologyUniversity of St. AndrewsSt. Andrews, FifeUK
| | | | - Jorge Brito
- Instituto Nacional de Biodiversidad (INABIO)QuitoEcuador
| | - Peter E. Busher
- College of General StudiesBoston UniversityBostonMassachusettsUSA
| | - Santiago F. Burneo
- Sección Mastozoología, Museo de Zoología, Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
| | - M. Alejandra Camacho
- Sección Mastozoología, Museo de Zoología, Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
| | | | | | - Joseph A. Cook
- Museum of Southwestern Biology and Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Tamás Cserkész
- Department of ZoologyHungarian Natural History MuseumBudapestHungary
| | - Gábor Csorba
- Department of ZoologyHungarian Natural History MuseumBudapestHungary
| | | | - Valeria da Cunha Tavares
- Vale Technological InstituteBelémParáBrazil
- Laboratório de Mamíferos, Departamento de Sistemática e Ecologia, CCEN/DSEUniversidade Federal da ParaíbaJoão PessoaPBBrazil
| | - Tim R. B. Davenport
- Species Conservation & Science (Africa)Wildlife Conservation Society (WCS)ArushaTanzania
| | | | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB)Muséum national d'Histoire naturelle (CNRS)ParisFrance
| | - Christopher R. Dickman
- Desert Ecology Research Group, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - Mark D. B. Eldridge
- Australian Museum Research InstituteAustralian MuseumSydneyNew South WalesAustralia
| | - Eduardo Fernandez‐Duque
- Department of Anthropology and School of the EnvironmentYale UniversityNew HavenConnecticutUSA
| | - Charles M. Francis
- Canadian Wildlife ServiceEnvironment and Climate Change CanadaOttawaOntarioCanada
| | - Greta Frankham
- Australian Museum Research InstituteAustralian MuseumSydneyNew South WalesAustralia
| | - William L. Franklin
- Deparment of Natural Resource Ecology and EnvironmentIowa State UniversityAmesIowaUSA
| | - Thales Freitas
- Departamento de GenéticaUniversidade Federal do Rio Grande do SulPorto AlegreRio Grande do SulBrazil
| | - J. Anthony Friend
- Department of BiodiversityConservation and AttractionsAlbanyWestern AustraliaAustralia
| | | | | | - Philippe Gaubert
- Laboratoire Évolution & Diversité BiologiqueUniversité Toulouse III Paul SabatierToulouseFrance
| | - Norberto Giannini
- Unidad Ejecutora LilloCONICET ‐ Fundación Miguel LilloSan Miguel de Tucumán, TucumánArgentina
| | - Thomas Giarla
- Department of BiologySiena CollegeLoudonvilleNew YorkUSA
| | | | - Jaime Gongora
- Sydney School of Veterinary Science, Faculty of ScienceThe University of SydneySydneyNew South WalesAustralia
| | - Steven M. Goodman
- Negaunee Integrative Research Center, Field Museum of Natural HistoryChicagoIllinoisUSA
| | | | - Klaus Hackländer
- Institute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life SciencesWienAustria
| | - Mark S. Hafner
- Museum of Natural ScienceLouisiana State UniversityBaton RougeLouisianaUSA
| | - Melissa Hawkins
- National Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Kristofer M. Helgen
- Australian Museum Research InstituteAustralian MuseumSydneyNew South WalesAustralia
| | - Steven Heritage
- Duke Lemur Center, Museum of Natural HistoryDuke UniversityDurhamNorth CarolinaUSA
| | | | | | - Mary Holden
- Department of MammalogyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Kay E. Holekamp
- Department of Integrative BiologyMichigan State UniversityEast LansingMichiganUSA
| | | | | | - Tatyana Humle
- Durrell Institute of Conservation and EcologySchool of Anthropology and Conservation, University of KentCanterburyUK
| | | | | | | | - Jan Janecka
- Department of Biological SciencesDuquesne UniversityPittsburghPennsylvaniaUSA
| | - Mary Janecka
- Department of Biological SciencesUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Paula Jenkins
- Mammal Group, Vertebrates DivisionDepartment of Life Sciences, The Natural History MuseumLondonUK
| | | | | | - Roland Kays
- North Carolina Museum of Natural SciencesRaleighNorth CarolinaUSA
| | | | - Tigga Kingston
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
| | | | | | - Tyrone Lavery
- Fenner School of Environment and SocietyThe Australian National UniversityActonAustralian Capital TerritoryAustralia
| | - Thomas E. Lee
- Department of BiologyAbilene Christian UniversityAbileneTexasUSA
| | - Yuri L. R. Leite
- Departamento de Ciências BiológicasUniversidade Federal do Espírito SantoVitóriaEspiríto SantoBrazil
| | | | - Burton K. Lim
- Department of Natural HistoryRoyal Ontario MuseumTorontoOntarioCanada
| | | | - Raquel López‐Antoñanzas
- Institut des Sciences de l'Évolution de Montpellier (ISE‐M, UMR 5554, UM/CNRS/IRD/EPHE)MontpellierFrance
| | | | | | - Fiona G. Maisels
- Wildlife Conservation SocietyGlobal Conservation ProgramNew YorkNew YorkUSA
- Faculty of Natural SciencesUniversity of StirlingStirlingUK
| | | | - Helene Marsh
- Division of Tropical Environments and SocietiesCentre for Tropical Water and Aquatic Ecosystem Research, James Cook UniversityTownsvilleQueenslandAustralia
| | - Stefano Mattioli
- Research Unit of Behavioural Ecology, Ethology and Wildlife Management, Department of Life SciencesUniversity of SienaSienaItaly
| | - Erik Meijaard
- Borneo FuturesBandar Seri BegawanBABrunei Darussalam
| | - Ara Monadjem
- Department of Biological SciencesUniversity of EswatiniKwaluseniEswatini
- Department of Zoology & Entomology, Mammal Research InstituteUniversity of PretoriaPretoriaSouth Africa
| | | | - Grace Musser
- Jackson School of GeosciencesUniversity of Texas at AustinAustinTexasUSA
| | - Tilo Nadler
- Cuc Phuong CommuneNho Quan DistrictNinh BInh, ProvinceVietnam
| | - Ryan W. Norris
- Evolution, Ecology and Organismal BiologyThe Ohio State UniversityLimaOhioUSA
| | - Agustina Ojeda
- Instituto Argentino de Zonas Áridas (IADIZA)‐CCT Mendoza‐CONICETMendozaArgentina
| | | | | | - Bruce D. Patterson
- Negaunee Integrative Research Center, Field Museum of Natural HistoryChicagoIllinoisUSA
| | - Ana Pavan
- Universidade de São PauloSão PauloBrazil
| | - Michael Pennay
- NSW National Parks and Wildlife ServiceQueanbeyanNew South WalesAustralia
| | | | | | - Helder L. Queiroz
- Instituto de Desenvolvimento Sustentável Mamirauá – IDSMTeféAmazonasBrazil
| | | | - Erin P. Riley
- Department of AnthropologySan Diego State UniversitySan DiegoCaliforniaUSA
| | - Stephen J. Rossiter
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Daniel I. Rubenstein
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
| | - Dennisse Ruelas
- Museo de Historia NaturalUniversidad Nacional Mayor de San Marcos, LimaLimaPeru
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS‐IRD‐UM)Université de MontpellierMontpellier Cedex 5France
| | | | - Stéphanie Schai‐Braun
- Institute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life SciencesViennaAustria
| | - Cody J. Schank
- Re:wildAustinTexasUSA
- Department of Geography and the EnvironmentThe University of Texas at AustinAustinTexasUSA
| | | | - Lori K. Sheeran
- Department of Anthropology and Museum StudiesCentral Washington UniversityEllensburgWAUSA
| | - Myron Shekelle
- Department of AnthropologyWestern Washington UniversityBellinghamWAUSA
| | - Georgy Shenbrot
- Mitrani Department of Desert EcologyJacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History MuseumPrince of Songkhla UniversityHatyai, SongkhlaThailand
| | - Sergio Solari
- Instituto de BiologíaUniversidad de AntioquiaMedellínColombia
| | | | - Mariella Superina
- IMBECU, CCT CONICET Mendoza – UNCuyoParque Gral. San MartínMendozaArgentina
| | - Andrew B. Taber
- Forestry DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Maurício Talebi
- Laboratório de Ecologia e Conservação da NaturezaDeptartamento de Ciências AmbientaisUniversidade Federal de São Paulo (UNIFESP) ‐ Campus Diadema, DiademaSão PauloBrazil
| | | | - Thong Vu Dinh
- Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHanoiVietnam
| | - Nelson Ting
- Department of AnthropologyUniversity of OregonEugeneOregonUSA
| | | | - Susan Tsang
- Department of MammalogyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | | | - Raul Valdez
- Department of Fish, Wildlife, and Conservation EcologyNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Victor Van Cakenberghe
- Laboratory for Functional Morphology, Biology DepartmentUniversity of Antwerp, Campus Drie EikenAntwerpen (Wilrijk)Belgium
| | - Geraldine Veron
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRSSorbonne Université, EPHE, Université des AntillesParisFrance
| | | | - Rod Wells
- Biological Sciences, College of Science and EngineeringFlinders UniversityAdelaideSouth AustraliaAustralia
| | - Danielle Whittaker
- BEACON Center for the Study of Evolution in ActionMichigan State UniversityEast LansingMichiganUSA
| | | | - George Wittemyer
- Department of Fish, Wildlife and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - John Woinarski
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityCasuarinaNorthern TerritoryAustralia
| | - Dietmar Zinner
- German Primate Center (DPZ)Leibniz Institute for Primate ResearchGöttingenGermany
| | - Nathan S. Upham
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Walter Jetz
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| |
Collapse
|
15
|
Williamson J, Teh E, Jucker T, Brindle M, Bush E, Chung AYC, Parrett J, Lewis OT, Rossiter SJ, Slade EM. Local‐scale temperature gradients driven by human disturbance shape the physiological and morphological traits of dung beetle communities in a Bornean oil‐palm‐forest mosaic. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14062] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Joseph Williamson
- School of Biological and Behavioural Sciences Queen Mary University of London, Mile End Road London UK
| | - Enoch Teh
- Asian School of the Environment Nanyang Technological University, 50 Nanyang Avenue Singapore City Singapore
| | - Tommaso Jucker
- School of Biological Sciences University of Bristol, 24 Tyndall Ave Bristol UK
| | - Matilda Brindle
- Department of Anthropology University College London 14 Taviton Street London
| | - Emma Bush
- Royal Botanic Garden Edinburgh, Arboretum Pl Edinburgh UK
| | - Arthur Y. C. Chung
- Forest Research Centre, Sabah Forestry Department, P.O. Box 1407, 90715 Sandakan Sabah Malaysia
| | - Jonathan Parrett
- Evolutionary Biology Group, Faculty of Biology Adam Mickiewicz University ul. Uniwersytetu Poznańskiego 6 Poznań Poland
| | - Owen T. Lewis
- Department of Zoology University of Oxford Oxford UK
| | - Stephen J. Rossiter
- School of Biological and Behavioural Sciences Queen Mary University of London, Mile End Road London UK
| | - Eleanor M. Slade
- Asian School of the Environment Nanyang Technological University, 50 Nanyang Avenue Singapore City Singapore
- Department of Zoology University of Oxford Oxford UK
| |
Collapse
|
16
|
Xia Y, Cui Y, Wang A, Liu F, Chi H, Potter JHT, Williamson J, Chen X, Rossiter SJ, Liu Y. Convergent Phenotypic Evolution of Rhodopsin for Dim-Light Sensing across Deep-Diving Vertebrates. Mol Biol Evol 2021; 38:5726-5734. [PMID: 34463769 PMCID: PMC8662592 DOI: 10.1093/molbev/msab262] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rhodopsin comprises an opsin attached to a retinal chromophore and is the only visual pigment conferring dim-light vision in vertebrates. On activation by photons, the retinal group becomes detached from the opsin, which is then inactive until it is recharged. Of all vertebrate species, those that dive face unique visual challenges, experiencing rapid decreases in light level and hunting in near darkness. Here, we combine sequence analyses with functional assays to show that the rhodopsin pigments of four divergent lineages of deep-diving vertebrates have undergone convergent increases in their retinal release rate. We compare gene sequences and detect parallel amino acids between penguins and diving mammals and perform mutagenesis to show that a single critical residue fully explains the observed increases in retinal release rate in both the emperor penguin and beaked whale. At the same time, we find that other shared sites have no significant effect on retinal release, implying that convergence does not always signify adaptive significance. We propose that accelerated retinal release confers rapid rhodopsin recharging, enabling the visual systems of diving species to adjust quickly to changing light levels as they descend through the water column. This contrasts with nocturnal species, where adaptation to darkness has been attributed to slower retinal release rates.
Collapse
Affiliation(s)
- Yu Xia
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yimeng Cui
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | | | - Fangnan Liu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Hai Chi
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Joshua H T Potter
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Joseph Williamson
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | | | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Zoonosis of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| |
Collapse
|
17
|
Hemprich-Bennett DR, Kemp VA, Blackman J, Lewis OT, Struebig MJ, Bernard H, Kratina P, Rossiter SJ, Clare EL. Selective Logging Shows No Impact on the Dietary Breadth of a Generalist Bat Species: The Fawn Leaf-Nosed Bat (Hipposideros cervinus). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.750269] [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: 11/13/2022] Open
Abstract
Logging activities degrade forest habitats across large areas of the tropics, but the impacts on trophic interactions that underpin forest ecosystems are poorly understood. DNA metabarcoding provides an invaluable tool to investigate such interactions, allowing analysis at a far greater scale and resolution than has previously been possible. We analysed the diet of the insectivorous fawn leaf-nosed bat Hipposideros cervinus across a forest disturbance gradient in Borneo, using a dataset of ecological interactions from an unprecedented number of bat-derived faecal samples. Bats predominantly consumed insects from the orders Lepidoptera, Diptera, Blattodea, and Coleoptera, and the taxonomic composition of their diet remained relatively consistent across sites regardless of logging disturbance. There was little difference in the richness of prey consumed per-bat in each logging treatment, indicating potential resilience of this species to habitat degradation. In fact, bats consumed a high richness of prey items, and intensive sampling is needed to reliably compare feeding ecology over multiple sites. Multiple bioinformatic parameters were used, to assess how they altered our perception of sampling completeness. While parameter choice altered estimates of completeness, a very high sampling effort was always required to detect the entire prey community.
Collapse
|
18
|
Nesi N, Tsagkogeorga G, Tsang SM, Nicolas V, Lalis A, Scanlon AT, Riesle-Sbarbaro SA, Wiantoro S, Hitch AT, Juste J, Pinzari CA, Bonaccorso FJ, Todd CM, Lim BK, Simmons NB, McGowen MR, Rossiter SJ. Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae). Syst Biol 2021; 70:1077-1089. [PMID: 33693838 PMCID: PMC8513763 DOI: 10.1093/sysbio/syab013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 11/12/2019] [Revised: 04/27/2021] [Accepted: 03/03/2021] [Indexed: 11/14/2022] Open
Abstract
The family Pteropodidae (Old World fruit bats) comprises $>$200 species distributed across the Old World tropics and subtropics. Most pteropodids feed on fruit, suggesting an early origin of frugivory, although several lineages have shifted to nectar-based diets. Pteropodids are of exceptional conservation concern with $>$50% of species considered threatened, yet the systematics of this group has long been debated, with uncertainty surrounding early splits attributed to an ancient rapid diversification. Resolving the relationships among the main pteropodid lineages is essential if we are to fully understand their evolutionary distinctiveness, and the extent to which these bats have transitioned to nectar-feeding. Here we generated orthologous sequences for $>$1400 nuclear protein-coding genes (2.8 million base pairs) across 114 species from 43 genera of Old World fruit bats (57% and 96% of extant species- and genus-level diversity, respectively), and combined phylogenomic inference with filtering by information content to resolve systematic relationships among the major lineages. Concatenation and coalescent-based methods recovered three distinct backbone topologies that were not able to be reconciled by filtering via phylogenetic information content. Concordance analysis and gene genealogy interrogation show that one topology is consistently the best supported, and that observed phylogenetic conflicts arise from both gene tree error and deep incomplete lineage sorting. In addition to resolving long-standing inconsistencies in the reported relationships among major lineages, we show that Old World fruit bats have likely undergone at least seven independent dietary transitions from frugivory to nectarivory. Finally, we use this phylogeny to identify and describe one new genus. [Chiroptera; coalescence; concordance; incomplete lineage sorting; nectar feeder; species tree; target enrichment.].
Collapse
Affiliation(s)
- Nicolas Nesi
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Susan M Tsang
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
- Zoology Section, National Museum of Natural History, Manila, Philippines
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Aude Lalis
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Annette T Scanlon
- School of Natural and Built Environments, University of South Australia, Mawson Lakes, SA, Australia
| | - Silke A Riesle-Sbarbaro
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Institute of Zoology, Zoological Society of London, London, UK
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Sigit Wiantoro
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Alan T Hitch
- Department of Wildlife, Fish, and Conservation Biology, University of California Davis, CA, USA
| | - Javier Juste
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| | | | | | - Christopher M Todd
- The Hawkesbury institute for the Environment, Western Sydney University, Australia
| | - Burton K Lim
- Royal Ontario Museum, Toronto, ON M5S 2C6, Canada
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
| | - Michael R McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| |
Collapse
|
19
|
Potter JHT, Davies KTJ, Yohe LR, Sanchez MKR, Rengifo EM, Struebig M, Warren K, Tsagkogeorga G, Lim BK, Reis MD, Dávalos LM, Rossiter SJ. Erratum to: Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution. Mol Biol Evol 2021; 38:4657. [PMID: 34405236 PMCID: PMC8476151 DOI: 10.1093/molbev/msab204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
20
|
Zhang X, Chi H, Li G, Irwin DM, Zhang S, Rossiter SJ, Liu Y. Parallel Independent Losses of G-Type Lysozyme Genes in Hairless Aquatic Mammals. Genome Biol Evol 2021; 13:6358722. [PMID: 34450623 PMCID: PMC8449827 DOI: 10.1093/gbe/evab201] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 12/03/2022] Open
Abstract
Lysozyme enzymes provide classic examples of molecular adaptation and parallel evolution, however, nearly all insights to date come from chicken-type (c-type) lysozymes. Goose-type (g-type) lysozymes occur in diverse vertebrates, with multiple independent duplications reported. Most mammals possess two g-type lysozyme genes (Lyg1 and Lyg2), the result of an early duplication, although some lineages are known to have subsequently lost one copy. Here we examine g-type lysozyme evolution across >250 mammals and reveal widespread losses of either Lyg1 or Lyg2 in several divergent taxa across the mammal tree of life. At the same time, we report strong evidence of extensive losses of both gene copies in cetaceans and sirenians, with an additional putative case of parallel loss in the tarsier. To validate these findings, we inspected published short-read data and confirmed the presence of loss of function mutations. Despite these losses, comparisons of selection pressures between intact g- and c-type lysozyme genes showed stronger purifying selection in the former, indicative of conserved function. Although the reasons for the evolutionary loss of g-type lysozymes in fully aquatic mammals are not known, we suggest that this is likely to at least partially relate to their hairlessness. Indeed, although Lyg1 does not show tissue-specific expression, recent studies have linked Lyg2 expression to anagen hair follicle development and hair loss. Such a role for g-type lysozyme would explain why the Lyg2 gene became obsolete when these taxa lost their body hair.
Collapse
Affiliation(s)
- Xiaoqing Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Hai Chi
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Zoonosis of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| |
Collapse
|
21
|
Drinkwater R, Williamson J, Clare EL, Chung AYC, Rossiter SJ, Slade E. Dung beetles as samplers of mammals in Malaysian Borneo-a test of high throughput metabarcoding of iDNA. PeerJ 2021; 9:e11897. [PMID: 34447624 PMCID: PMC8366524 DOI: 10.7717/peerj.11897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 02/17/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022] Open
Abstract
Invertebrate-derived DNA (iDNA) sampling in biodiversity surveys is becoming increasingly widespread, with most terrestrial studies relying on DNA derived from the gut contents of blood-feeding invertebrates, such as leeches and mosquitoes. Dung beetles (superfamily Scarabaeoidea) primarily feed on the faecal matter of terrestrial vertebrates and offer several potential benefits over blood-feeding invertebrates as samplers of vertebrate DNA. Importantly, these beetles can be easily captured in large numbers using simple, inexpensive baited traps, are globally distributed, and occur in a wide range of habitats. To build on the few existing studies demonstrating the potential of dung beetles as sources of mammalian DNA, we subjected the large-bodied, Bornean dung beetle (Catharsius renaudpauliani) to a controlled feeding experiment. We analysed DNA from gut contents at different times after feeding using qPCR techniques. Here, we first describe the window of DNA persistence within a dung beetle digestive tract. We found that the ability to successfully amplify cattle DNA decayed over relatively short time periods, with DNA copy number decreasing by two orders of magnitude in just 6 h. In addition, we sampled communities of dung beetles from a lowland tropical rainforest in Sabah, Malaysia, in order to test whether it is possible to identify vertebrate sequences from dung beetle iDNA. We sequenced both the gut contents from large dung beetle species, as well as whole communities of smaller beetles. We successfully identified six mammalian species from our samples, including the bearded pig (Sus barbatus) and the sambar deer (Rusa unicolor)—both vulnerable species on the IUCN red list. Our results represent the first use of dung beetle iDNA to sample Southeast Asian vertebrate fauna, and highlight the potential for dung beetle iDNA to be used in future biodiversity monitoring surveys.
Collapse
Affiliation(s)
- Rosie Drinkwater
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Joseph Williamson
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Arthur Y C Chung
- Sabah Forestry Department, Forest Research Centre, Sandakan, Malaysia
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Eleanor Slade
- Asian School of the Environment, Nanyang Technological University, Singapore City, Singapore.,Department of Zoology, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
22
|
Hemprich-Bennett DR, Kemp VA, Blackman J, Struebig MJ, Lewis OT, Rossiter SJ, Clare EL. Altered structure of bat-prey interaction networks in logged tropical forests revealed by metabarcoding. Mol Ecol 2021; 30:5844-5857. [PMID: 34437745 DOI: 10.1111/mec.16153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 07/29/2020] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 11/27/2022]
Abstract
Habitat degradation is pervasive across the tropics and is particularly acute in Southeast Asia, with major implications for biodiversity. Much research has addressed the impact of degradation on species diversity; however, little is known about how ecological interactions are altered, including those that constitute important ecosystem functions such as consumption of herbivores. To examine how rainforest degradation alters trophic interaction networks, we applied DNA metabarcoding to construct interaction networks linking forest-dwelling insectivorous bat species and their prey, comparing old-growth forest and forest degraded by logging in Sabah, Borneo. Individual bats in logged rainforest consumed a lower richness of prey than those in old-growth forest. As a result, interaction networks in logged forests had a less nested structure. These network structures were associated with reduced network redundancy and thus increased vulnerability to perturbations in logged forests. Our results show how ecological interactions change between old-growth and logged forests, with potentially negative implications for ecosystem function and network stability.
Collapse
Affiliation(s)
- David R Hemprich-Bennett
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Victoria A Kemp
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Joshua Blackman
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Matthew J Struebig
- Durrell Institute of Conservation and Ecology, University of Kent, Canterbury, Kent, UK
| | - Owen T Lewis
- Department of Zoology, University of Oxford, Oxford, UK
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.,Department of Biology, York University, Toronto, Ontario, Canada
| |
Collapse
|
23
|
Potter JHT, Davies KTJ, Yohe LR, Sanchez MKR, Rengifo EM, Struebig M, Warren K, Tsagkogeorga G, Lim BK, dos Reis M, Dávalos LM, Rossiter SJ. Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution. Mol Biol Evol 2021; 38:3864-3883. [PMID: 34426843 PMCID: PMC8382914 DOI: 10.1093/molbev/msab028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dietary adaptation is a major feature of phenotypic and ecological diversification, yet the genetic basis of dietary shifts is poorly understood. Among mammals, Neotropical leaf-nosed bats (family Phyllostomidae) show unmatched diversity in diet; from a putative insectivorous ancestor, phyllostomids have radiated to specialize on diverse food sources including blood, nectar, and fruit. To assess whether dietary diversification in this group was accompanied by molecular adaptations for changing metabolic demands, we sequenced 89 transcriptomes across 58 species and combined these with published data to compare ∼13,000 protein coding genes across 66 species. We tested for positive selection on focal lineages, including those inferred to have undergone dietary shifts. Unexpectedly, we found a broad signature of positive selection in the ancestral phyllostomid branch, spanning genes implicated in the metabolism of all major macronutrients, yet few positively selected genes at the inferred switch to plantivory. Branches corresponding to blood- and nectar-based diets showed selection in loci underpinning nitrogenous waste excretion and glycolysis, respectively. Intriguingly, patterns of selection in metabolism genes were mirrored by those in loci implicated in craniofacial remodeling, a trait previously linked to phyllostomid dietary specialization. Finally, we show that the null model of the widely-used branch-site test is likely to be misspecified, with the implication that the test is too conservative and probably under-reports true cases of positive selection. Our findings point to a complex picture of adaptive radiation, in which the evolution of new dietary specializations has been facilitated by early adaptations combined with the generation of new genetic variation.
Collapse
Affiliation(s)
- Joshua H T Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Department of Earth and Planetary Science, Yale University, 210 Whitney Ave, New Haven, CT, USA
| | - Miluska K R Sanchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, Peru
| | - Edgardo M Rengifo
- Escola Superior de Agricultura ‘Luiz de Queiroz,’ Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
- Centro de Investigación Biodiversidad Sostenible (BioS), Lima, Peru
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kim Warren
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Mario dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| |
Collapse
|
24
|
Zou D, Tian S, Zhang T, Zhuoma N, Wu G, Wang M, Dong L, Rossiter SJ, Zhao H. Vulture Genomes Reveal Molecular Adaptations Underlying Obligate Scavenging and Low Levels of Genetic Diversity. Mol Biol Evol 2021; 38:3649-3663. [PMID: 33944941 PMCID: PMC8382910 DOI: 10.1093/molbev/msab130] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Obligate scavenging on the dead and decaying animal matter is a rare dietary specialization that in extant vertebrates is restricted to vultures. These birds perform essential ecological services, yet many vulture species have undergone recent steep population declines and are now endangered. To test for molecular adaptations underlying obligate scavenging in vultures, and to assess whether genomic features might have contributed to their population declines, we generated high-quality genomes of the Himalayan and bearded vultures, representing both independent origins of scavenging within the Accipitridae, alongside a sister taxon, the upland buzzard. By comparing our data to published sequences from other birds, we show that the evolution of obligate scavenging in vultures has been accompanied by widespread positive selection acting on genes underlying gastric acid production, and immunity. Moreover, we find evidence of parallel molecular evolution, with amino acid replacements shared among divergent lineages of these scavengers. Our genome-wide screens also reveal that both the Himalayan and bearded vultures exhibit low levels of genetic diversity, equating to around a half of the mean genetic diversity of other bird genomes examined. However, demographic reconstructions indicate that population declines began at around the Last Glacial Maximum, predating the well-documented dramatic declines of the past three decades. Taken together, our genomic analyses imply that vultures harbor unique adaptations for processing carrion, but that modern populations are genetically depauperate and thus especially vulnerable to further genetic erosion through anthropogenic activities.
Collapse
Affiliation(s)
- Dahu Zou
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shilin Tian
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Nima Zhuoma
- Research Center for Ecology, College of Science, Tibet University, Lhasa, China
| | - Guosheng Wu
- Xining Wildlife Park of Qinghai Province, Xining, China
| | - Muyang Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Huabin Zhao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- Research Center for Ecology, College of Science, Tibet University, Lhasa, China
| |
Collapse
|
25
|
Moreno Santillán DD, Lama TM, Gutierrez Guerrero YT, Brown AM, Donat P, Zhao H, Rossiter SJ, Yohe LR, Potter JH, Teeling EC, Vernes SC, Davies KTJ, Myers E, Hughes GM, Huang Z, Hoffmann F, Corthals AP, Ray DA, Dávalos LM. Large-scale genome sampling reveals unique immunity and metabolic adaptations in bats. Mol Ecol 2021; 30:6449-6467. [PMID: 34146369 DOI: 10.1111/mec.16027] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/27/2021] [Accepted: 06/03/2021] [Indexed: 11/28/2022]
Abstract
Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species, one generated in this study, encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defence receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defence response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance antiviral immune response while dampening inflammatory signalling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.
Collapse
Affiliation(s)
| | - Tanya M Lama
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Yocelyn T Gutierrez Guerrero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Mexico City, Mexico
| | - Alexis M Brown
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Paul Donat
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Huabin Zhao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Laurel R Yohe
- Department of Earth & Planetary Science, Yale University, New Haven, Connecticut, USA
| | - Joshua H Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,School of Biology, The University of St Andrews, Fife, UK
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Eugene Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Graham M Hughes
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Federico Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Angelique P Corthals
- Department of Sciences, John Jay College of Criminal Justice, New York, New York, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Consortium for Inter- Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, USA
| |
Collapse
|
26
|
Hall RP, Mutumi GL, Hedrick BP, Yohe LR, Sadier A, Davies KTJ, Rossiter SJ, Sears K, Dávalos LM, Dumont ER. Find the food first: An omnivorous sensory morphotype predates biomechanical specialization for plant based diets in phyllostomid bats. Evolution 2021; 75:2791-2801. [PMID: 34021589 DOI: 10.1111/evo.14270] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 03/27/2020] [Revised: 03/03/2021] [Accepted: 04/05/2021] [Indexed: 11/30/2022]
Abstract
The role of mechanical morphologies in the exploitation of novel niche space is well characterized; however, the role of sensory structures in unlocking new niches is less clear. Here, we investigate the relationship between the evolution of sensory structures and diet during the radiation of noctilionoid bats. With a broad range of foraging ecologies and a well-supported phylogeny, noctilionoids constitute an ideal group for studying this relationship. We used diffusible iodine-based contrast enhanced computed tomography scans of 44 noctilionoid species to analyze relationships between the relative volumes of three sensory structures (olfactory bulbs, orbits, and cochleae) and diet. We found a positive relationship between frugivory and both olfactory and orbit size. However, we also found a negative relationship between nectarivory and cochlea size. Ancestral state estimates suggest that larger orbits and olfactory bulbs were present in the common ancestor of family Phyllostomidae, but not in other noctilionoid. This constellation of traits indicates a shift toward omnivory at the base of Phyllostomidae, predating their radiation into an exceptionally broad range of dietary niches. This is consistent with a scenario in which changes in sensory systems associated with foraging and feeding set the stage for subsequent morphological modification and diversification.
Collapse
Affiliation(s)
- Ronald P Hall
- Life and Environmental Sciences, University of California-Merced, Merced, California
| | - Gregory L Mutumi
- Life and Environmental Sciences, University of California-Merced, Merced, California
| | - Brandon P Hedrick
- Department of Cell Biology and Anatomy, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Laurel R Yohe
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut
| | - Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Karen Sears
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York.,Consortium for Inter-Disciplinary Environmental Research, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York
| | - Elizabeth R Dumont
- Life and Environmental Sciences, University of California-Merced, Merced, California
| |
Collapse
|
27
|
Chen S, Juan C, Rossiter SJ, Kinjo T, Fukui D, Kawai K, Tsang SM, Veluz MJ, Sakurai H, Lin H, Jang‐Liaw N, Osawa K, Ko W, Izawa M. Population genetic structure of the insular Ryukyu flying fox
Pteropus dasymallus. Biotropica 2021. [DOI: 10.1111/btp.12897] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shiang‐Fan Chen
- Center for General Education National Taipei University New Taipei City Taiwan
| | - Chung‐Hao Juan
- Center for General Education National Taipei University New Taipei City Taiwan
| | | | | | - Dai Fukui
- The University of Tokyo Hokkaido Forest The University of Tokyo Hokkaido Japan
| | - Kuniko Kawai
- Department of Biology Tokai University Hokkaido Japan
| | - Susan M. Tsang
- Department of Mammalogy American Museum of Natural History New York NY USA
- Mammalogy Section National Museum of Natural History Manila Philippines
| | | | | | - Hua‐Ching Lin
- Forestry Bureau Council of Agriculture Taipei Taiwan
| | | | | | - Wen‐Ya Ko
- Department of Life Sciences and Institute of Genome Sciences National Yang‐Ming University Taipei Taiwan
| | - Masako Izawa
- Biology Program Faculty of Science University of the Ryukyus Okinawa Japan
| |
Collapse
|
28
|
McGowen MR, Tsagkogeorga G, Álvarez-Carretero S, Dos Reis M, Struebig M, Deaville R, Jepson PD, Jarman S, Polanowski A, Morin PA, Rossiter SJ. Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture. Syst Biol 2020; 69:479-501. [PMID: 31633766 PMCID: PMC7164366 DOI: 10.1093/sysbio/syz068] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 10/02/2019] [Accepted: 10/06/2019] [Indexed: 12/20/2022] Open
Abstract
The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$\sim $\end{document}3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$>$\end{document}38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.]
Collapse
Affiliation(s)
- Michael R McGowen
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.,Department of Vertebrate Zoology, Smithsonian Museum of Natural History, 10th & Constitution Ave. NW, Washington DC 20560, USA
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Sandra Álvarez-Carretero
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Robert Deaville
- Institute of Zoology, Zoological Society of London, Outer Circle, London NW1 4RY, UK
| | - Paul D Jepson
- Institute of Zoology, Zoological Society of London, Outer Circle, London NW1 4RY, UK
| | - Simon Jarman
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth WA 6009, Australia
| | - Andrea Polanowski
- Australian Antarctic Division, 203 Channel Highway, Kingston TAS 7050, Australia
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla CA 92037 USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| |
Collapse
|
29
|
Drinkwater R, Jucker T, Potter JHT, Swinfield T, Coomes DA, Slade EM, Gilbert MTP, Lewis OT, Bernard H, Struebig MJ, Clare EL, Rossiter SJ. Leech blood-meal invertebrate-derived DNA reveals differences in Bornean mammal diversity across habitats. Mol Ecol 2020; 30:3299-3312. [PMID: 33171014 PMCID: PMC8359290 DOI: 10.1111/mec.15724] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 12/29/2022]
Abstract
The application of metabarcoding to environmental and invertebrate‐derived DNA (eDNA and iDNA) is a new and increasingly applied method for monitoring biodiversity across a diverse range of habitats. This approach is particularly promising for sampling in the biodiverse humid tropics, where rapid land‐use change for agriculture means there is a growing need to understand the conservation value of the remaining mosaic and degraded landscapes. Here we use iDNA from blood‐feeding leeches (Haemadipsa picta) to assess differences in mammalian diversity across a gradient of forest degradation in Sabah, Malaysian Borneo. We screened 557 individual leeches for mammal DNA by targeting fragments of the 16S rRNA gene and detected 14 mammalian genera. We recorded lower mammal diversity in the most heavily degraded forest compared to higher quality twice logged forest. Although the accumulation curves of diversity estimates were comparable across these habitat types, diversity was higher in twice logged forest, with more taxa of conservation concern. In addition, our analysis revealed differences between the community recorded in the heavily logged forest and that of the twice logged forest. By revealing differences in mammal diversity across a human‐modified tropical landscape, our study demonstrates the value of iDNA as a noninvasive biomonitoring approach in conservation assessments.
Collapse
Affiliation(s)
- Rosie Drinkwater
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Tommaso Jucker
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Joshua H T Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Tom Swinfield
- Department of Plant Sciences, Forest and Ecology Conservation Group, University of Cambridge, Cambridge, UK
| | - David A Coomes
- Department of Plant Sciences, Forest and Ecology Conservation Group, University of Cambridge, Cambridge, UK
| | - Eleanor M Slade
- Department of Zoology, University of Oxford, Oxford, UK.,Asian School of the Environment, Nanyang Technological University, Singapore City, Singapore
| | - M Thomas P Gilbert
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Owen T Lewis
- Department of Zoology, University of Oxford, Oxford, UK
| | - Henry Bernard
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Sabah, Malaysia
| | - Matthew J Struebig
- Durrell Institute of Conservation and Ecology (DICE), School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| |
Collapse
|
30
|
Hemprich-Bennett DR, Oliveira HFM, Le Comber SC, Rossiter SJ, Clare EL. Assessing the impact of taxon resolution on network structure. Ecology 2020; 102:e03256. [PMID: 33226629 DOI: 10.1002/ecy.3256] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/01/2020] [Accepted: 09/18/2020] [Indexed: 01/04/2023]
Abstract
Constructing ecological networks has become an indispensable approach in understanding how different taxa interact. However, the methods used to generate data in network research vary widely among studies, potentially limiting our ability to compare results meaningfully. In particular, methods of classifying nodes vary in their precision, likely altering the architecture of the network studied. For example, rather than being classified as Linnaean species, taxa are regularly assigned to morphospecies in observational studies, or to molecular operational taxonomic units (MOTUs) in molecular studies, with the latter defined based on an arbitrary threshold of sequence similarity. Although the use of MOTUs in ecological networks holds great potential, especially for allowing rapid construction of large data sets of interactions, it is unclear how the choice of clustering threshold can influence the conclusions obtained. To test the impact of taxonomic precision on network architecture, we obtained and analyzed 16 data sets of ecological interactions, inferred from metabarcoding and observations. Our comparisons of networks constructed under a range of sequence thresholds for assigning taxa demonstrate that even small changes in node resolution can cause wide variation in almost all key metric values. Moreover, relative values of commonly used metrics such as robustness were seen to fluctuate continuously with node resolution, thereby potentially causing error in conclusions drawn when comparing multiple networks. In observational networks, we found that changing node resolution could, in some cases, lead to substantial changes to measurements of network topology. Overall, our findings highlight the importance of classifying nodes to the greatest precision possible, and demonstrate the need for caution when comparing networks that differ with respect to node resolution, even where taxonomic groups and interaction types are similar. In such cases, we recommend that comparisons of networks should focus on relative differences rather than absolute values between the networks studied.
Collapse
Affiliation(s)
- David R Hemprich-Bennett
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.,Department of Zoology, Zoology Research and Administration Building, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Hernani F M Oliveira
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Steven C Le Comber
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| |
Collapse
|
31
|
Williamson J, Slade EM, Luke SH, Swinfield T, Chung AYC, Coomes DA, Heroin H, Jucker T, Lewis OT, Vairappan CS, Rossiter SJ, Struebig MJ. Riparian buffers act as microclimatic refugia in oil palm landscapes. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13784] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph Williamson
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - Eleanor M. Slade
- Asian School of the EnvironmentNanyang Technological University Singapore City Singapore
| | - Sarah H. Luke
- Durrell Institute of Conservation and Ecology (DICE) School of Anthropology and Conservation University of Kent Canterbury UK
- Department of Zoology University of Cambridge Cambridge UK
| | - Tom Swinfield
- Department of Plant Sciences University of Cambridge Conservation Research Institute Cambridge UK
| | | | - David A. Coomes
- Department of Plant Sciences University of Cambridge Conservation Research Institute Cambridge UK
| | - Herry Heroin
- Institute for Tropical Biology and Conservation Universiti Malaysia Sabah Kota Kinabalu Sabah Malaysia
| | - Tommaso Jucker
- School of Biological Sciences University of Bristol Bristol UK
| | - Owen T. Lewis
- Department of Zoology University of Oxford Oxford UK
| | - Charles S. Vairappan
- Institute for Tropical Biology and Conservation Universiti Malaysia Sabah Kota Kinabalu Sabah Malaysia
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - Matthew J. Struebig
- Durrell Institute of Conservation and Ecology (DICE) School of Anthropology and Conservation University of Kent Canterbury UK
| |
Collapse
|
32
|
Gilbert JD, Rossiter SJ, Faulkes CG. The relationship between individual phenotype and the division of labour in naked mole-rats: it's complicated. PeerJ 2020; 8:e9891. [PMID: 33062418 PMCID: PMC7531346 DOI: 10.7717/peerj.9891] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 05/21/2020] [Accepted: 08/17/2020] [Indexed: 11/20/2022] Open
Abstract
Background The naked mole-rat (Heterocephalus glaber) is among the most social mammals on the planet, living in eusocial groups of up to 300 individuals that contain a single reproductive female and up to three reproductive males. A critical aspect of their complex social system is the division of labour that allows non-breeders to form an effective workforce. Age- or weight-based polyethisms are widely cited as explanations for how labour is divided, but evidence in support of these hypotheses has been equivocal. Methods To assess the extent to which individual working behaviour is determined by sex, age, weight and social rank, we studied the behaviours of 103 animals from eight captive colonies. We performed focal sampling and ran mixed-effects models to assess which factors explained variation in working behaviour during six ten-minute observation periods per individual. Results Contrary to widely-held beliefs, we found that working behaviour did not decrease linearly with weight, although polynomial regressions indicated younger and medium-sized individuals worked most frequently, while high-ranking individuals worked for the shortest periods of time. Working behaviour and its relationship with individual characteristics also varied between colonies. Conclusions While age- or size-based polyethisms may have some influence on working behaviour, we argue that other characteristics of the individual and colony are also important. In particular, the interactions of individual, social and environmental factors must be considered in order to understand the emergence and effectiveness of the division of labour that is so critical to many social organisms.
Collapse
Affiliation(s)
- James D Gilbert
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Chris G Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| |
Collapse
|
33
|
Sun H, Chen W, Wang J, Zhang L, Rossiter SJ, Mao X. Echolocation call frequency variation in horseshoe bats: molecular basis revealed by comparative transcriptomics. Proc Biol Sci 2020; 287:20200875. [PMID: 32900318 DOI: 10.1098/rspb.2020.0875] [Citation(s) in RCA: 5] [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] [Indexed: 01/11/2023] Open
Abstract
Recently diverged taxa with contrasting phenotypes offer opportunities for unravelling the genetic basis of phenotypic variation in nature. Horseshoe bats are a speciose group that exhibit a derived form of high-duty cycle echolocation in which the inner ear is finely tuned to echoes of the narrowband call frequency. Here, by focusing on three recently diverged subspecies of the intermediate horseshoe bat (Rhinolophus affinis) that display divergent echolocation call frequencies, we aim to identify candidate loci putatively involved in hearing frequency variation. We used de novo transcriptome sequencing of two mainland taxa (himalayanus and macrurus) and one island taxon (hainanus) to compare expression profiles of thousands of genes. By comparing taxa with divergent call frequencies (around 15 kHz difference), we identified 252 differentially expressed genes, of which six have been shown to be involved in hearing or deafness in human/mouse. To obtain further validation of these results, we applied quantitative reverse transcription-PCR to the candidate gene FBXL15 and found a broad association between the level of expression and call frequency across taxa. The genes identified here represent strong candidate loci associated with hearing frequency variation in bats.
Collapse
Affiliation(s)
- Haijian Sun
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, People's Republic of China
| | - Wenli Chen
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, People's Republic of China
| | - Jiaying Wang
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, People's Republic of China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou 510260, People's Republic of China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, People's Republic of China.,Institute of Eco-Chongming (IEC), East China Normal University, Shanghai 200062, People's Republic of China
| |
Collapse
|
34
|
Kelly LJ, Plumb WJ, Carey DW, Mason ME, Cooper ED, Crowther W, Whittemore AT, Rossiter SJ, Koch JL, Buggs RJA. Convergent molecular evolution among ash species resistant to the emerald ash borer. Nat Ecol Evol 2020; 4:1116-1128. [PMID: 32451426 PMCID: PMC7610378 DOI: 10.1038/s41559-020-1209-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 11/25/2019] [Accepted: 04/16/2020] [Indexed: 11/08/2022]
Abstract
Recent studies show that molecular convergence plays an unexpectedly common role in the evolution of convergent phenotypes. We exploited this phenomenon to find candidate loci underlying resistance to the emerald ash borer (EAB, Agrilus planipennis), the United States' most costly invasive forest insect to date, within the pan-genome of ash trees (the genus Fraxinus). We show that EAB-resistant taxa occur within three independent phylogenetic lineages. In genomes from these resistant lineages, we detect 53 genes with evidence of convergent amino acid evolution. Gene-tree reconstruction indicates that, for 48 of these candidates, the convergent amino acids are more likely to have arisen via independent evolution than by another process such as hybridization or incomplete lineage sorting. Seven of the candidate genes have putative roles connected to the phenylpropanoid biosynthesis pathway and 17 relate to herbivore recognition, defence signalling or programmed cell death. Evidence for loss-of-function mutations among these candidates is more frequent in susceptible species than in resistant ones. Our results on evolutionary relationships, variability in resistance, and candidate genes for defence response within the ash genus could inform breeding for EAB resistance, facilitating ecological restoration in areas invaded by this beetle.
Collapse
Affiliation(s)
- Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
- Royal Botanic Gardens, Kew, Richmond, UK.
| | - William J Plumb
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Royal Botanic Gardens, Kew, Richmond, UK
- Forestry Development Department, Teagasc, Dublin, Republic of Ireland
| | - David W Carey
- United States Department of Agriculture, Forest Service, Northern Research Station, Delaware, OH, USA
| | - Mary E Mason
- United States Department of Agriculture, Forest Service, Northern Research Station, Delaware, OH, USA
| | - Endymion D Cooper
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - William Crowther
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Alan T Whittemore
- United States Department of Agriculture, Agricultural Research Service, US National Arboretum, Washington, DC, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Jennifer L Koch
- United States Department of Agriculture, Forest Service, Northern Research Station, Delaware, OH, USA
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
- Royal Botanic Gardens, Kew, Richmond, UK.
| |
Collapse
|
35
|
Mao X, Rossiter SJ. Genome-wide data reveal discordant mitonuclear introgression in the intermediate horseshoe bat (Rhinolophus affinis). Mol Phylogenet Evol 2020; 150:106886. [PMID: 32534185 DOI: 10.1016/j.ympev.2020.106886] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 10/10/2019] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 10/24/2022]
Abstract
Closely related taxa often exhibit mitonuclear discordance attributed to introgression of mitochondrial DNA (mtDNA), yet few studies have considered the underlying causes of mtDNA introgression. Here we test for demographic versus adaptive processes as explanations for mtDNA introgression in three subspecies of the intermediate horseshoe bat (Rhinolophus affinis). We generated sequences of 1692 nuclear genes and 13 mitochondrial protein-coding genes for 48 individuals. Phylogenetic reconstructions based on 320 exon sequences and 2217 single nucleotide polymorphisms (SNPs) both revealed conflicts between the species tree and mtDNA tree. These results, together with geographic patterns of mitonuclear discordance, and shared identical or near-identical mtDNA sequences, suggest extensive introgression of mtDNA between the two parapatric mainland subspecies. Under demographic hypotheses, we would also expect to uncover traces of ncDNA introgression, however, population structure and gene flow analyses revealed little nuclear admixture. Furthermore, we found inconsistent estimates of the timing of population expansion and that of the most recent common ancestor for the clade containing introgressed haplotypes. Without a clear demographic explanation, we also examined whether introgression likely arises from adaptation. We found that five mtDNA genes contained fixed amino acid differences between introgressed and non-introgressed individuals, including putative positive selection found in one codon, although this did not show introgression. While our evidence for rejecting demographic hypotheses is arguably stronger than that for rejecting adaptation, we find no definitive support for either explanation. Future efforts will focus on larger-scale resequencing to decipher the underlying causes of discordant mitonuclear introgression in this system.
Collapse
Affiliation(s)
- Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China; Institute of Eco-Chongming (IEC), East China Normal University, Shanghai 200062, China.
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK.
| |
Collapse
|
36
|
Davies KTJ, Yohe LR, Almonte J, Sánchez MKR, Rengifo EM, Dumont ER, Sears KE, Dávalos LM, Rossiter SJ. Foraging shifts and visual preadaptation in ecologically diverse bats. Mol Ecol 2020; 29:1839-1859. [PMID: 32293071 DOI: 10.1111/mec.15445] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 10/17/2019] [Revised: 02/28/2020] [Accepted: 03/31/2020] [Indexed: 12/11/2022]
Abstract
Changes in behaviour may initiate shifts to new adaptive zones, with physical adaptations for novel environments evolving later. While new mutations are commonly considered engines of adaptive change, sensory evolution enabling access to new resources might also arise from standing genetic diversity, and even gene loss. We examine the relative contribution of molecular adaptations, measured by positive and relaxed selection, acting on eye-expressed genes associated with shifts to new adaptive zones in ecologically diverse bats from the superfamily Noctilionoidea. Collectively, noctilionoids display remarkable ecological breadth, from highly divergent echolocation to flight strategies linked to specialized insectivory, the parallel evolution of diverse plant-based diets (e.g., nectar, pollen and fruit) from ancestral insectivory, and-unusually for echolocating bats-often have large, well-developed eyes. We report contrasting levels of positive selection in genes associated with the development, maintenance and scope of visual function, tracing back to the origins of noctilionoids and Phyllostomidae (the bat family with most dietary diversity), instead of during shifts to novel diets. Generalized plant visiting was not associated with exceptional molecular adaptation, and exploration of these novel niches took place in an ancestral phyllostomid genetic background. In contrast, evidence for positive selection in vision genes was found at subsequent shifts to either nectarivory or frugivory. Thus, neotropical noctilionoids that use visual cues for identifying food and roosts, as well as for orientation, were effectively preadapted, with subsequent molecular adaptations in nectar-feeding lineages and the subfamily Stenodermatinae of fig-eating bats fine-tuning pre-existing visual adaptations for specialized purposes.
Collapse
Affiliation(s)
- Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Laurel R Yohe
- Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, USA.,Department of Geology & Geophysics, Yale University, New Haven, CT, USA
| | - Jesus Almonte
- Independent Scientist, Santo Domingo, Dominican Republic
| | - Miluska K R Sánchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, Peru
| | - Edgardo M Rengifo
- Programa de Pós-Graduação Interunidades em Ecologia Aplicada, Escola Superior de Agricultura 'Luiz de Queiroz', Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil.,Centro de Investigación Biodiversidad Sostenible (BioS), Lima, Peru
| | - Elizabeth R Dumont
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, USA.,Consortium for Inter-Disciplinary Environmental Research, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| |
Collapse
|
37
|
Magalhães de Oliveira HF, Camargo NF, Hemprich-Bennett DR, Rodríguez-Herrera B, Rossiter SJ, Clare EL. Wing morphology predicts individual niche specialization in Pteronotus mesoamericanus (Mammalia: Chiroptera). PLoS One 2020; 15:e0232601. [PMID: 32392221 PMCID: PMC7213686 DOI: 10.1371/journal.pone.0232601] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 10/21/2019] [Accepted: 04/17/2020] [Indexed: 12/30/2022] Open
Abstract
Morphological variation between individuals can increase niche segregation and decrease intraspecific competition when heterogeneous individuals explore their environment in different ways. Among bat species, wing shape correlates with flight maneuverability and habitat use, with species that possess broader wings typically foraging in more cluttered habitats. However, few studies have investigated the role of morphological variation in bats for niche partitioning at the individual level. To determine the relationship between wing shape and diet, we studied a population of the insectivorous bat species Pteronotus mesoamericanus in the dry forest of Costa Rica. Individual diet was resolved using DNA metabarcoding, and bat wing shape was assessed using geometric morphometric analysis. Inter-individual variation in wing shape showed a significant relationship with both dietary dissimilarity based on Bray-Curtis estimates, and nestedness derived from an ecological network. Individual bats with broader and more rounded wings were found to feed on a greater diversity of arthropods (less nested) in comparison to individuals with triangular and pointed wings (more nested). We conclude that individual variation in bat wing morphology can impact foraging efficiency leading to the observed overall patterns of diet specialization and differentiation within the population.
Collapse
Affiliation(s)
- Hernani Fernandes Magalhães de Oliveira
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, United States of America
- School of Biological and Chemical Sciences, Queen Mary University of London, London, England, United Kingdom
| | | | - David R. Hemprich-Bennett
- School of Biological and Chemical Sciences, Queen Mary University of London, London, England, United Kingdom
- Department of Zoology, University of Oxford, Oxford, England, United Kingdom
| | | | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, England, United Kingdom
| | - Elizabeth L. Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, England, United Kingdom
| |
Collapse
|
38
|
Drinkwater R, Williamson J, Swinfield T, Deere NJ, Struebig MJ, Clare EL, Coomes D, Rossiter SJ. Occurrence of blood‐feeding terrestrial leeches (Haemadipsidae) in a degraded forest ecosystem and their potential as ecological indicators. Biotropica 2020. [DOI: 10.1111/btp.12686] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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)
- Rosie Drinkwater
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - Joseph Williamson
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - Tom Swinfield
- Department of Plant Sciences University of Cambridge Cambridge UK
| | - Nicolas J. Deere
- School of Anthropology and Conservation University of Kent Canterbury UK
| | | | - Elizabeth L. Clare
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - David Coomes
- Department of Plant Sciences University of Cambridge Cambridge UK
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| |
Collapse
|
39
|
Amorim F, Razgour O, Mata VA, Lopes S, Godinho R, Ibáñez C, Juste J, Rossiter SJ, Beja P, Rebelo H. Evolutionary history of the European free‐tailed bat, a tropical affinity species spanning across the Mediterranean Basin. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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)
- Francisco Amorim
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
- Departamento de Biologia, Faculdade de Ciências Universidade do Porto Porto Portugal
| | - Orly Razgour
- Biological Sciences University of Southampton Southampton UK
| | - Vanessa A. Mata
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
- Departamento de Biologia, Faculdade de Ciências Universidade do Porto Porto Portugal
| | - Susana Lopes
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
| | - Raquel Godinho
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
- Departamento de Biologia, Faculdade de Ciências Universidade do Porto Porto Portugal
- Department of Zoology University of Johannesburg South Africa
| | | | - Javier Juste
- Estación Biológica de Doñana (CSIC) Seville Spain
| | - Stephen J. Rossiter
- School of Biological & Chemical Sciences Queen Mary University of London London UK
| | - Pedro Beja
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, Institute of Agronomy University of Lisbon Lisbon Portugal
| | - Hugo Rebelo
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, Institute of Agronomy University of Lisbon Lisbon Portugal
| |
Collapse
|
40
|
Yohe LR, Devanna P, Davies KT, Potter JH, Rossiter SJ, Teeling EC, Vernes SC, Dávalos LM. Tissue Collection of Bats for -Omics Analyses and Primary Cell Culture. J Vis Exp 2019. [DOI: 10.3791/59505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
|
41
|
Yohe LR, Davies KTJ, Simmons NB, Sears KE, Dumont ER, Rossiter SJ, Dávalos LM. Evaluating the performance of targeted sequence capture, RNA-Seq, and degenerate-primer PCR cloning for sequencing the largest mammalian multigene family. Mol Ecol Resour 2019; 20:140-153. [PMID: 31523924 DOI: 10.1111/1755-0998.13093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 04/20/2019] [Revised: 08/27/2019] [Accepted: 09/06/2019] [Indexed: 12/18/2022]
Abstract
Multigene families evolve from single-copy ancestral genes via duplication, and typically encode proteins critical to key biological processes. Molecular analyses of these gene families require high-confidence sequences, but the high sequence similarity of the members can create challenges for sequencing and downstream analyses. Focusing on the common vampire bat, Desmodus rotundus, we evaluated how different sequencing approaches performed in recovering the largest mammalian protein-coding multigene family: olfactory receptors (OR). Using the genome as a reference, we determined the proportion of intact protein-coding receptors recovered by: (a) amplicons from degenerate primers sequenced via Sanger technology, (b) RNA-Seq of the main olfactory epithelium, and (c) those genes captured with probes designed from transcriptomes of closely-related species. Our initial re-annotation of the high-quality vampire bat genome resulted in >400 intact OR genes, more than doubling the original estimate. Sanger-sequenced amplicons performed the poorest among the three approaches, detecting <33% of receptors in the genome. In contrast, the transcriptome reliably recovered >50% of the annotated genomic ORs, and targeted sequence capture recovered nearly 75% of annotated genes. Each sequencing approach assembled high-quality sequences, even if it did not recover all receptors in the genome. While some variation may be due to limitations of the study design (e.g., different individuals), variation among approaches was mostly caused by low coverage of some receptors rather than high rates of assembly error. Given this variability, we caution against using the counts of intact receptors per species to model the birth-death process of multigene families. Instead, our results support the use of orthologous sequences to explore and model the evolutionary processes shaping these genes.
Collapse
Affiliation(s)
- Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.,Department of Geology and Geophysics, Yale University, Stony Brook, NY, USA
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - Elizabeth R Dumont
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| |
Collapse
|
42
|
Mao X, Tsagkogeorga G, Thong VD, Rossiter SJ. Resolving evolutionary relationships among six closely related taxa of the horseshoe bats (Rhinolophus) with targeted resequencing data. Mol Phylogenet Evol 2019; 139:106551. [DOI: 10.1016/j.ympev.2019.106551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/11/2019] [Accepted: 07/01/2019] [Indexed: 01/04/2023]
|
43
|
Yohe LR, Davies KTJ, Rossiter SJ, Dávalos LM. Expressed Vomeronasal Type-1 Receptors (V1rs) in Bats Uncover Conserved Sequences Underlying Social Chemical Signaling. Genome Biol Evol 2019; 11:2741-2749. [PMID: 31424505 PMCID: PMC6777432 DOI: 10.1093/gbe/evz179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2019] [Indexed: 01/08/2023] Open
Abstract
In mammals, social and reproductive behaviors are mediated by chemical cues encoded by hyperdiverse families of receptors expressed in the vomeronasal organ. Between species, the number of intact receptors can vary by orders of magnitude. However, the evolutionary processes behind variation in receptor number, and its link to fitness-related behaviors are not well understood. From vomeronasal transcriptomes, we discovered the first evidence of intact vomeronasal type-1 receptor (V1r) genes in bats, and we tested whether putatively functional bat receptors were orthologous to those of related taxa, or whether bats have evolved novel receptors. Instead of lineage-specific duplications, we found that bat V1rs show high levels of orthology to those of their relatives, and receptors are under comparative levels of purifying selection as non-bats. Despite widespread vomeronasal organ loss in bats, V1r copies have been retained for >65 million years. The highly conserved nature of bat V1rs challenges our current understanding of mammalian V1r function and suggests roles other than conspecific recognition or mating initiation in social behavior.
Collapse
Affiliation(s)
- Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, NY
- Department of Geology & Geophysics, Yale University, New Haven, CT
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, NY
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY
| |
Collapse
|
44
|
Hedrick BP, Mutumi GL, Munteanu VD, Sadier A, Davies KTJ, Rossiter SJ, Sears KE, Dávalos LM, Dumont E. Morphological Diversification under High Integration in a Hyper Diverse Mammal Clade. J MAMM EVOL 2019. [DOI: 10.1007/s10914-019-09472-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
45
|
Abstract
Long-term suppression of recombination ultimately leads to gene loss, as demonstrated by the depauperate Y and W chromosomes of long-established pairs of XY and ZW chromosomes. The young social supergene of the Solenopsis invicta red fire ant provides a powerful system to examine the effects of suppressed recombination over a shorter timescale. The two variants of this supergene are carried by a pair of heteromorphic chromosomes, referred to as the social B and social b (SB and Sb) chromosomes. The Sb variant of this supergene changes colony social organization and has an inheritance pattern similar to a Y or W chromosome because it is unable to recombine. We used high-resolution optical mapping, k-mer distribution analysis, and quantification of repetitive elements on haploid ants carrying alternate variants of this young supergene region. We find that instead of shrinking, the Sb variant of the supergene has increased in length by more than 30%. Surprisingly, only a portion of this length increase is due to consistent increases in the frequency of particular classes of repetitive elements. Instead, haplotypes of this supergene variant differ dramatically in the amounts of other repetitive elements, indicating that the accumulation of repetitive elements is a heterogeneous and dynamic process. This is the first comprehensive demonstration of degenerative expansion in an animal and shows that it occurs through nonlinear processes during the early evolution of a region of suppressed recombination.
Collapse
Affiliation(s)
- Eckart Stolle
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.,Institut für Biologie, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, Halle, Germany
| | - Rodrigo Pracana
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Philip Howard
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Carolina I Paris
- Departamento Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Susan J Brown
- Division of Biology, Kansas State University, Manhattan, Kansas
| | | | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Yannick Wurm
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| |
Collapse
|
46
|
Stolle E, Pracana R, Howard P, Paris CI, Brown SJ, Castillo-Carrillo C, Rossiter SJ, Wurm Y. Erratum to: Degenerative Expansion of a Young Supergene. Mol Biol Evol 2019; 36:1111. [DOI: 10.1093/molbev/msz056] [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: 11/13/2022] Open
|
47
|
Liu Y, Chi H, Li L, Rossiter SJ, Zhang S. Molecular Data Support an Early Shift to an Intermediate-Light Niche in the Evolution of Mammals. Mol Biol Evol 2019; 35:1130-1134. [PMID: 29462332 DOI: 10.1093/molbev/msy019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The visual ability and associated photic niche of early mammals is debated. The theory that ancestral mammals were nocturnal is supported by diverse adaptations. However, others argue that photopigment repertoires of early mammals are more consistent with a crepuscular niche, and support for this also comes from inferred spectral tuning of middle/long wavelength-sensitive (M/LWS) opsin sequences. Functional studies have suggested that the M/LWS pigment in the ancestor of Mammalia was either red- or green-sensitive; however, these were based on outdated phylogenies with key lineages omitted. By performing the most detailed study to date of middle/long-wave mammalian color vision, we provide the first experimental evidence that the M/LWS pigment of amniotes underwent a 9-nm spectral shift towards shorter wavelengths in the Mammalia ancestor, exceeding predictions from known critical sites. Our results suggest early mammals were yellow-sensitive, possibly representing an adaptive trade-off for both crepuscular (twilight) and nocturnal (moonlight) niches.
Collapse
Affiliation(s)
- Yang Liu
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Hai Chi
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Longfei Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Shuyi Zhang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| |
Collapse
|
48
|
Drinkwater R, Schnell IB, Bohmann K, Bernard H, Veron G, Clare E, Gilbert MTP, Rossiter SJ. Using metabarcoding to compare the suitability of two blood-feeding leech species for sampling mammalian diversity in North Borneo. Mol Ecol Resour 2019; 19:105-117. [PMID: 30225935 PMCID: PMC7379310 DOI: 10.1111/1755-0998.12943] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 01/09/2023]
Abstract
The application of high-throughput sequencing (HTS) for metabarcoding of mixed samples offers new opportunities in conservation biology. Recently, the successful detection of prey DNA from the guts of leeches has raised the possibility that these, and other blood-feeding invertebrates, might serve as useful samplers of mammals. Yet little is known about whether sympatric leech species differ in their feeding preferences, and whether this has a bearing on their relative suitability for monitoring local mammalian diversity. To address these questions, we collected spatially matched samples of two congeneric leech species Haemadipsa picta and Haemadipsa sumatrana from lowland rainforest in Borneo. For each species, we pooled ~500 leeches into batches of 10 individuals, performed PCR to target a section of the mammalian 16S rRNA locus and undertook sequencing of amplicon libraries using an Illumina MiSeq. In total, we identified sequences from 14 mammalian genera, spanning nine families and five orders. We found greater numbers of detections, and higher diversity of OTUs, in H. picta compared with H. sumatrana, with rodents only present in the former leech species. However, comparison of samples from across the landscape revealed no significant difference in mammal community composition between the leech species. We therefore suggest that H. picta is the more suitable iDNA sampler in this degraded Bornean forest. We conclude that the choice of invertebrate sampler can influence the detectability of different mammal groups and that this should be accounted for when designing iDNA studies.
Collapse
Affiliation(s)
- Rosie Drinkwater
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | | | - Kristine Bohmann
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- School of Biological SciencesUniversity of East Anglia, Norwich Research ParkNorwich, NorfolkUK
| | - Henry Bernard
- Institute for Tropical Biology and ConservationUniversiti Malaysia Sabah, Jalan UMSKota KinabaluSabahMalaysia
| | - Géraldine Veron
- Institut Systématique Evolution Biodiversité (ISYEB)Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHEParis CedexFrance
| | - Elizabeth Clare
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - M. Thomas P. Gilbert
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- NTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Stephen J. Rossiter
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| |
Collapse
|
49
|
Simões BF, Foley NM, Hughes GM, Zhao H, Zhang S, Rossiter SJ, Teeling EC. As Blind as a Bat? Opsin Phylogenetics Illuminates the Evolution of Color Vision in Bats. Mol Biol Evol 2019; 36:54-68. [PMID: 30476197 PMCID: PMC6340466 DOI: 10.1093/molbev/msy192] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Through their unique use of sophisticated laryngeal echolocation bats are considered sensory specialists amongst mammals and represent an excellent model in which to explore sensory perception. Although several studies have shown that the evolution of vision is linked to ecological niche adaptation in other mammalian lineages, this has not yet been fully explored in bats. Recent molecular analysis of the opsin genes, which encode the photosensitive pigments underpinning color vision, have implicated high-duty cycle (HDC) echolocation and the adoption of cave roosting habits in the degeneration of color vision in bats. However, insufficient sampling of relevant taxa has hindered definitive testing of these hypotheses. To address this, novel sequence data was generated for the SWS1 and MWS/LWS opsin genes and combined with existing data to comprehensively sample species representing diverse echolocation types and niches (SWS1 n = 115; MWS/LWS n = 45). A combination of phylogenetic analysis, ancestral state reconstruction, and selective pressure analyses were used to reconstruct the evolution of these visual pigments in bats and revealed that although both genes are evolving under purifying selection in bats, MWS/LWS is highly conserved but SWS1 is highly variable. Spectral tuning analyses revealed that MWS/LWS opsin is tuned to a long wavelength, 555-560 nm in the bat ancestor and the majority of extant taxa. The presence of UV vision in bats is supported by our spectral tuning analysis, but phylogenetic analyses demonstrated that the SWS1 opsin gene has undergone pseudogenization in several lineages. We do not find support for a link between the evolution of HDC echolocation and the pseudogenization of the SWS1 gene in bats, instead we show the SWS1 opsin is functional in the HDC echolocator, Pteronotus parnellii. Pseudogenization of the SWS1 is correlated with cave roosting habits in the majority of pteropodid species. Together these results demonstrate that the loss of UV vision in bats is more widespread than was previously considered and further elucidate the role of ecological niche specialization in the evolution of vision in bats.
Collapse
Affiliation(s)
- Bruno F Simões
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
- School of Earth Science, University of Bristol, Bristol, United Kingdom
- School of Biological Science, The University of Adelaide, South Australia, Australia
| | - Nicole M Foley
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Graham M Hughes
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Huabin Zhao
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Emma C Teeling
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| |
Collapse
|
50
|
Sadier A, Davies KT, Yohe LR, Yun K, Donat P, Hedrick BP, Dumont ER, Dávalos LM, Rossiter SJ, Sears KE. Multifactorial processes underlie parallel opsin loss in neotropical bats. eLife 2018; 7:37412. [PMID: 30560780 PMCID: PMC6333445 DOI: 10.7554/elife.37412] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 04/10/2018] [Accepted: 12/04/2018] [Indexed: 12/27/2022] Open
Abstract
The loss of previously adaptive traits is typically linked to relaxation in selection, yet the molecular steps leading to such repeated losses are rarely known. Molecular studies of loss have tended to focus on gene sequences alone, but overlooking other aspects of protein expression might underestimate phenotypic diversity. Insights based almost solely on opsin gene evolution, for instance, have made mammalian color vision a textbook example of phenotypic loss. We address this gap by investigating retention and loss of opsin genes, transcripts, and proteins across ecologically diverse noctilionoid bats. We find multiple, independent losses of short-wave-sensitive opsins. Mismatches between putatively functional DNA sequences, mRNA transcripts, and proteins implicate transcriptional and post-transcriptional processes in the ongoing loss of S-opsins in some noctilionoid bats. Our results provide a snapshot of evolution in progress during phenotypic trait loss, and suggest vertebrate visual phenotypes cannot always be predicted from genotypes alone. Bats are famous for using their hearing to explore their environments, yet fewer people are aware that these flying mammals have both good night and daylight vision. Some bats can even see in color thanks to two light-sensitive proteins at the back of their eyes: S-opsin which detects blue and ultraviolet light and L-opsin which detects green and red light. Many species of bat, however, are missing one of these proteins and cannot distinguish any colors; in other words, they are completely color-blind. Some bat species found in Central and South America have independently lost their ability to see blue-ultraviolet light and have thus also lost their color vision. These bats have diverse diets – ranging from insects to fruits and even blood – and being able to distinguish color may offer an advantage in many of their activities, including hunting or foraging. The vision genes in these bats, therefore, give scientists an opportunity to explore how a seemingly important trait can be lost at the molecular level. Sadier, Davies et al. now report that S-opsin has been lost more than a dozen times during the evolutionary history of these Central and South American bats. The analysis used samples from 55 species, including animals caught from the wild and specimens from museums. As with other proteins, the instructions encoded in the gene sequence for S opsin need to be copied into a molecule of RNA before they can be translated into protein. As expected, S-opsin was lost several times because of changes in the gene sequence that disrupted the formation of the protein. However, at several points in these bats’ evolutionary history, additional changes have taken place that affected the production of the RNA or the protein, without an obvious change to the gene itself. This finding suggests that other studies that rely purely on DNA to understand evolution may underestimate how often traits may be lost. By capturing ‘evolution in action’, these results also provide a more complete picture of the molecular targets of evolution in a diverse set of bats.
Collapse
Affiliation(s)
- Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, United States
| | - Kalina Tj Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, New York, United States.,Geology & Geophysics, Yale University, New Haven, United States
| | - Kun Yun
- Department of Animal Biology, University of Illinois, Urbana, United States
| | - Paul Donat
- Department of Ecology and Evolution, Stony Brook University, New York, United States
| | - Brandon P Hedrick
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - Elizabeth R Dumont
- School of Natural Sciences, University of California, Merced, United States
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, New York, United States.,Consortium for Inter-Disciplinary Environmental Research, School of Marine and Atmospheric Sciences, Stony Brook University, New York, United States
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, United States
| |
Collapse
|