1
|
Blanchet G, Bellinger MR, Kearns AM, Cortes-Rodriguez N, Masuda B, Campana MG, Rutz C, Fleischer RC, Sutton JT. Reduction of genetic diversity in 'Alalā (Hawaiian crow; Corvus hawaiiensis) between the late 1800s and the late 1900s. J Hered 2024; 115:32-44. [PMID: 37846510 DOI: 10.1093/jhered/esad063] [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: 06/18/2023] [Revised: 09/26/2023] [Accepted: 10/12/2023] [Indexed: 10/18/2023] Open
Abstract
Genetic and genomic data are increasingly used to aid conservation management of endangered species by providing insights into evolutionary histories, factors associated with extinction risks, and potential for future adaptation. For the 'Alalā, or Hawaiian crow (Corvus hawaiiensis), genetic concerns include negative correlations between inbreeding and hatching success. However, it is unclear if low genetic diversity and inbreeding depression are consequences of a historical population bottleneck, or if 'Alalā had historically low genetic diversity that predated human influence, perhaps as a result of earlier declines or founding events. In this study, we applied a hybridization-based sequence capture to generate a genome-wide single nucleotide polymorphism (SNP) dataset for comparing historical specimens collected in the 1890s, when 'Alalā were more numerous, to samples taken between 1973 and 1998, when 'Alalā population densities were near the lowest documented levels in the wild, prior to all individuals being collected for captive rearing. We found low genome-wide diversity in both sample groups, however, the modern sample group (1973 to 1998 cohort) exhibited relatively fewer polymorphic alleles, a lower proportion of polymorphic loci, and lower observed heterozygosity, consistent with a population decline and potential bottleneck effects. These results combined with a current low population size highlight the importance of continued efforts by conservation managers to mitigate inbreeding and maintain founder representation to preserve what genetic diversity remains.
Collapse
Affiliation(s)
- Geneviève Blanchet
- Department of Biology, University of Hawai'i at Hilo, 200 W Kāwili St, Hilo, Hawai'i 96720, United States
| | - M Renee Bellinger
- Department of Biology, University of Hawai'i at Hilo, 200 W Kāwili St, Hilo, Hawai'i 96720, United States
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, PO Box 44, Hawai'i National Park, Hawai'i 96718, United States
| | - Anna M Kearns
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington DC 20008, United States
| | - Nandadevi Cortes-Rodriguez
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington DC 20008, United States
| | - Bryce Masuda
- San Diego Zoo Wildlife Alliance, P.O. Box 39, Volcano, HI 96785, United States
| | - Michael G Campana
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington DC 20008, United States
| | - Christian Rutz
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews KY16 9TH, United Kingdom
| | - Robert C Fleischer
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington DC 20008, United States
| | - Jolene T Sutton
- Department of Biology, University of Hawai'i at Hilo, 200 W Kāwili St, Hilo, Hawai'i 96720, United States
| |
Collapse
|
2
|
Seidl CM, Ferreira FC, Parise KL, Paxton KL, Paxton EH, Atkinson CT, Fleischer RC, Foster JT, Marm Kilpatrick A. Linking avian malaria parasitemia estimates from quantitative PCR and microscopy reveals new infection patterns in Hawai'i. Int J Parasitol 2024; 54:123-130. [PMID: 37922977 DOI: 10.1016/j.ijpara.2023.10.001] [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] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/29/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Plasmodium parasites infect thousands of species and provide an exceptional system for studying host-pathogen dynamics, especially for multi-host pathogens. However, understanding these interactions requires an accurate assay of infection. Assessing Plasmodium infections using microscopy on blood smears often misses infections with low parasitemias (the fractions of cells infected), and biases in malaria prevalence estimates will differ among hosts that differ in mean parasitemias. We examined Plasmodium relictum infection and parasitemia using both microscopy of blood smears and quantitative polymerase chain reaction (qPCR) on 299 samples from multiple bird species in Hawai'i and fit models to predict parasitemias from qPCR cycle threshold (Ct) values. We used these models to quantify the extent to which microscopy underestimated infection prevalence and to more accurately estimate infection patterns for each species for a large historical study done by microscopy. We found that most qPCR-positive wild-caught birds in Hawaii had low parasitemias (Ct scores ≥35), which were rarely detected by microscopy. The fraction of infections missed by microscopy differed substantially among eight species due to differences in species' parasitemia levels. Infection prevalence was likely 4-5-fold higher than previous microscopy estimates for three introduced species, including Zosterops japonicus, Hawaii's most abundant forest bird, which had low average parasitemias. In contrast, prevalence was likely only 1.5-2.3-fold higher than previous estimates for Himatione sanguinea and Chlorodrepanis virens, two native species with high average parasitemias. Our results indicate that relative patterns of infection among species differ substantially from those observed in previous microscopy studies, and that differences depend on variation in parasitemias among species. Although microscopy of blood smears is useful for estimating the frequency of different Plasmodium stages and host attributes, more sensitive quantitative methods, including qPCR, are needed to accurately estimate and compare infection prevalence among host species.
Collapse
Affiliation(s)
- Christa M Seidl
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA; Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA.
| | - Francisco C Ferreira
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA; Center for Vector Biology, Rutgers University, New Brunswick, NJ, USA
| | - Katy L Parise
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Kristina L Paxton
- Hawai'i Volcanoes National Park, Resource Management, Hawai'i National Park, HI, USA
| | - Eben H Paxton
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, Hawai'i National Park, HI. USA
| | - Carter T Atkinson
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, Hawai'i National Park, HI. USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| |
Collapse
|
3
|
Mulder KP, Savage AE, Gratwicke B, Longcore JE, Bronikowski E, Evans M, Longo AV, Kurata NP, Walsh T, Pasmans F, McInerney N, Murray S, Martel A, Fleischer RC. Sequence capture identifies fastidious chytrid fungi directly from host tissue. Fungal Genet Biol 2024; 170:103858. [PMID: 38101696 DOI: 10.1016/j.fgb.2023.103858] [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] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
The chytrid fungus Batrachochytrium dendrobatidis (Bd) was discovered in 1998 as the cause of chytridiomycosis, an emerging infectious disease causing mass declines in amphibian populations worldwide. The rapid population declines of the 1970s-1990s were likely caused by the spread of a highly virulent lineage belonging to the Bd-GPL clade that was introduced to naïve susceptible populations. Multiple genetically distinct and regional lineages of Bd have since been isolated and sequenced, greatly expanding the known biological diversity within this fungal pathogen. To date, most Bd research has been restricted to the limited number of samples that could be isolated using culturing techniques, potentially causing a selection bias for strains that can grow on media and missing other unculturable or fastidious strains that are also present on amphibians. We thus attempted to characterize potentially non-culturable genetic lineages of Bd from distinct amphibian taxa using sequence capture technology on DNA extracted from host tissue and swabs. We focused our efforts on host taxa from two different regions that likely harbored distinct Bd clades: (1) wild-caught leopard frogs (Rana) from North America, and (2) a Japanese Giant Salamander (Andrias japonicus) at the Smithsonian Institution's National Zoological Park that exhibited signs of disease and tested positive for Bd using qPCR, but multiple attempts failed to isolate and culture the strain for physiological and genetic characterization. We successfully enriched for and sequenced thousands of fungal genes from both host clades, and Bd load was positively associated with number of recovered Bd sequences. Phylogenetic reconstruction placed all the Rana-derived strains in the Bd-GPL clade. In contrast, the A. japonicus strain fell within the Bd-Asia3 clade, expanding the range of this clade and generating additional genomic data to confirm its placement. The retrieved ITS locus matched public barcoding data from wild A. japonicus and Bd infections found on other amphibians in India and China, suggesting that this uncultured clade is widespread across Asia. Our study underscores the importance of recognizing and characterizing the hidden diversity of fastidious strains in order to reconstruct the spatiotemporal and evolutionary history of Bd. The success of the sequence capture approach highlights the utility of directly sequencing pathogen DNA from host tissue to characterize cryptic diversity that is missed by culture-reliant approaches.
Collapse
Affiliation(s)
- Kevin P Mulder
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium; Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA.
| | - Anna E Savage
- Department of Biology, University of Central Florida, Orlando, FL, USA
| | - Brian Gratwicke
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Joyce E Longcore
- School of Biology and Ecology, University of Maine, Orono, ME, USA
| | - Ed Bronikowski
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Matthew Evans
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Ana V Longo
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Naoko P Kurata
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA; Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, USA; Department of Ichthyology, American Museum of Natural History, New York, NY, USA
| | - Tim Walsh
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Frank Pasmans
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Nancy McInerney
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Suzan Murray
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - An Martel
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA
| |
Collapse
|
4
|
Navine AK, Paxton KL, Paxton EH, Hart PJ, Foster JT, McInerney N, Fleischer RC, Videvall E. Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria-resistant introduced birds. Mol Ecol 2023; 32:6659-6670. [PMID: 36281504 DOI: 10.1111/mec.16743] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 02/08/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/30/2022]
Abstract
Of the estimated 55 Hawaiian honeycreepers (subfamily Carduelinae) only 17 species remain, nine of which the International Union for Conservation of Nature considers endangered. Among the most pressing threats to honeycreeper survival is avian malaria, caused by the introduced blood parasite Plasmodium relictum, which is increasing in distribution in Hawai'i as a result of climate change. Preventing further honeycreeper decline will require innovative conservation strategies that confront malaria from multiple angles. Research on mammals has revealed strong connections between gut microbiome composition and malaria susceptibility, illuminating a potential novel approach to malaria control through the manipulation of gut microbiota. One honeycreeper species, Hawai'i 'amakihi (Chlorodrepanis virens), persists in areas of high malaria prevalence, indicating they have acquired some level of immunity. To investigate if avian host-specific microbes may be associated with malaria survival, we characterized cloacal microbiomes and malaria infection for 174 'amakihi and 172 malaria-resistant warbling white-eyes (Zosterops japonicus) from Hawai'i Island using 16S rRNA gene metabarcoding and quantitative polymerase chain reaction. Neither microbial alpha nor beta diversity covaried with infection, but 149 microbes showed positive associations with malaria survivors. Among these were Escherichia and Lactobacillus spp., which appear to mitigate malaria severity in mammalian hosts, revealing promising candidates for future probiotic research for augmenting malaria immunity in sensitive endangered species.
Collapse
Affiliation(s)
- Amanda K Navine
- Biology Department, University of Hawai'i at Hilo, Hilo, Hawaii, USA
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Kristina L Paxton
- Hawai'i Cooperative Studies Unit, University of Hawai'i at Hilo, Hawai'i National Park, Hawaii, USA
| | - Eben H Paxton
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, Hawai'i National Park, Hawaii, USA
| | - Patrick J Hart
- Biology Department, University of Hawai'i at Hilo, Hilo, Hawaii, USA
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Nancy McInerney
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Elin Videvall
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| |
Collapse
|
5
|
Paxton KL, Cassin-Sackett L, Atkinson CT, Videvall E, Campana MG, Fleischer RC. Gene expression reveals immune response strategies of naïve Hawaiian honeycreepers experimentally infected with introduced avian malaria. J Hered 2023; 114:326-340. [PMID: 36869776 DOI: 10.1093/jhered/esad017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 09/22/2022] [Accepted: 03/01/2023] [Indexed: 03/05/2023] Open
Abstract
The unprecedented rise in the number of new and emerging infectious diseases in the last quarter century poses direct threats to human and wildlife health. The introduction to the Hawaiian archipelago of Plasmodium relictum and the mosquito vector that transmits the parasite has led to dramatic losses in endemic Hawaiian forest bird species. Understanding how mechanisms of disease immunity to avian malaria may evolve is critical as climate change facilitates increased disease transmission to high elevation habitats where malaria transmission has historically been low and the majority of the remaining extant Hawaiian forest bird species now reside. Here, we compare the transcriptomic profiles of highly susceptible Hawai'i 'amakihi (Chlorodrepanis virens) experimentally infected with P. relictum to those of uninfected control birds from a naïve high elevation population. We examined changes in gene expression profiles at different stages of infection to provide an in-depth characterization of the molecular pathways contributing to survival or mortality in these birds. We show that the timing and magnitude of the innate and adaptive immune response differed substantially between individuals that survived and those that succumbed to infection, and likely contributed to the observed variation in survival. These results lay the foundation for developing gene-based conservation strategies for Hawaiian honeycreepers by identifying candidate genes and cellular pathways involved in the pathogen response that correlate with a bird's ability to recover from malaria infection.
Collapse
Affiliation(s)
- Kristina L Paxton
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
- Hawai'i Cooperative Studies Unit, University of Hawai'i Hilo, PO Box 44, Hawai'i National Park, HI 96718, USA
| | - Loren Cassin-Sackett
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
- Department of Biology, University of Louisiana, Lafayette, LA 70503, USA
| | - Carter T Atkinson
- U.S. Geological Survey Pacific Island Ecosystems Research Center, PO Box 44, Hawai'i National Park, HI 96718, USA
| | - Elin Videvall
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
| | - Michael G Campana
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
| |
Collapse
|
6
|
Kaganer AW, Ossiboff RJ, Keith NI, Schuler KL, Comizzoli P, Hare MP, Fleischer RC, Gratwicke B, Bunting EM. Immune priming prior to pathogen exposure sheds light on the relationship between host, microbiome and pathogen in disease. R Soc Open Sci 2023; 10:220810. [PMID: 36756057 PMCID: PMC9890126 DOI: 10.1098/rsos.220810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Dynamic interactions between host, pathogen and host-associated microbiome dictate infection outcomes. Pathogens including Batrachochytrium dendrobatidis (Bd) threaten global biodiversity, but conservation efforts are hindered by limited understanding of amphibian host, Bd and microbiome interactions. We conducted a vaccination and infection experiment using Eastern hellbender salamanders (Cryptobranchus alleganiensis alleganiensis) challenged with Bd to observe infection, skin microbial communities and gene expression of host skin, pathogen and microbiome throughout the experiment. Most animals survived high Bd loads regardless of their vaccination status and vaccination did not affect pathogen load, but host gene expression differed based on vaccination. Oral vaccination (exposure to killed Bd) stimulated immune gene upregulation while topically and sham-vaccinated animals did not significantly upregulate immune genes. In early infection, topically vaccinated animals upregulated immune genes but orally and sham-vaccinated animals downregulated immune genes. Bd increased pathogenicity-associated gene expression in late infection when Bd loads were highest. The microbiome was altered by Bd, but there was no correlation between anti-Bd microbe abundance or richness and pathogen burden. Our observations suggest that hellbenders initially generate a vigorous immune response to Bd, which is ineffective at controlling disease and is subsequently modulated. Interactions with antifungal skin microbiota did not influence disease progression.
Collapse
Affiliation(s)
- Alyssa W. Kaganer
- Department of Natural Resources and the Environment, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
| | - Robert J. Ossiboff
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Nicole I. Keith
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Biology Department, Hamilton College, Clinton, NY, 13323, USA
| | - Krysten L. Schuler
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Pierre Comizzoli
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Matthew P. Hare
- Department of Natural Resources and the Environment, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Robert C. Fleischer
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Brian Gratwicke
- Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA
| | - Elizabeth M. Bunting
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
7
|
Byerly PA, Chesser RT, Fleischer RC, McInerney N, Przelomska NAS, Leberg PL. Museum Genomics Provide Evidence for Persistent Genetic Differentiation in a Threatened Seabird Species in the Western Atlantic. Integr Comp Biol 2022; 62:1838-1848. [PMID: 35781565 DOI: 10.1093/icb/icac107] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 01/05/2023] Open
Abstract
Connectivity among wildlife populations facilitates exchange of genetic material between groups. Changes to historical connectivity patterns resulting from anthropogenic activities can therefore have negative consequences for genetic diversity, particularly for small or isolated populations. DNA obtained from museum specimens can enable direct comparison of temporal changes in connectivity among populations, which can aid in conservation planning and contribute to the understanding of population declines. However, museum DNA can be degraded and only available in low quantities, rendering it challenging for use in population genomic analyses. Applications of genomic methodologies such as targeted sequencing address this issue by enabling capture of shared variable sites, increasing quantity and quality of recovered genomic information. We used targeted sequencing of ultra-conserved Elements (UCEs) to evaluate potential changes in connectivity and genetic diversity of roseate terns (Sterna dougallii) with a breeding distribution in the northwestern Atlantic and the Caribbean. Both populations experienced range contractions and population declines due to anthropogenic activity in the 20th century, which has the potential to alter historical connectivity regimes. Instead, we found that the two populations were differentiated historically as well as contemporaneously, with little evidence of migration between them for either time period. We also found no evidence for temporal changes in genetic diversity, although these interpretations may have been limited due to sequencing artifacts caused by the degraded nature of the museum samples. Population structuring in migratory seabirds is typically reflective of low rates of divergence and high connectivity among geographically segregated subpopulations. Our contrasting results suggest the potential presence of ecological mechanisms driving population differentiation, and highlight the value of targeted sequencing on DNA derived from museum specimens to uncover long-term patterns of genetic differentiation in wildlife populations.
Collapse
Affiliation(s)
- Paige A Byerly
- University of Louisiana at Lafayette, 104 E University Ave, Lafayette, LA 70504, USA.,Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - R Terry Chesser
- Eastern Ecological Science Center, U.S. Geological Survey, 12100 Beech Forest Road, Laurel, MD 20708, USA.,National Museum of Natural History, 10th St. and Constitution Avenue, NW, Washington, DC 20560, USA
| | - Robert C Fleischer
- Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - Nancy McInerney
- Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - Natalia A S Przelomska
- National Museum of Natural History, 10th St. and Constitution Avenue, NW, Washington, DC 20560, USA.,Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA.,Royal Botanic Gardens, Kew, Richmond TW9 3AE, UK
| | - Paul L Leberg
- University of Louisiana at Lafayette, 104 E University Ave, Lafayette, LA 70504, USA
| |
Collapse
|
8
|
Ferreira FC, Videvall E, Seidl CM, Wagner NE, Kilpatrick AM, Fleischer RC, Fonseca DM. Transcriptional response of individual Hawaiian Culex quinquefasciatus mosquitoes to the avian malaria parasite Plasmodium relictum. Malar J 2022; 21:249. [PMID: 36038897 PMCID: PMC9422152 DOI: 10.1186/s12936-022-04271-x] [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] [Received: 06/17/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Plasmodium parasites that cause bird malaria occur in all continents except Antarctica and are primarily transmitted by mosquitoes in the genus Culex. Culex quinquefasciatus, the mosquito vector of avian malaria in Hawaiʻi, became established in the islands in the 1820s. While the deadly effects of malaria on endemic bird species have been documented for many decades, vector-parasite interactions in avian malaria systems are relatively understudied. Methods To evaluate the gene expression response of mosquitoes exposed to a Plasmodium infection intensity known to occur naturally in Hawaiʻi, offspring of wild-collected Hawaiian Cx. quinquefasciatus were fed on a domestic canary infected with a fresh isolate of Plasmodium relictum GRW4 from a wild-caught Hawaiian honeycreeper. Control mosquitoes were fed on an uninfected canary. Transcriptomes of five infected and three uninfected individual mosquitoes were sequenced at each of three stages of the parasite life cycle: 24 h post feeding (hpf) during ookinete invasion; 5 days post feeding (dpf) when oocysts are developing; 10 dpf when sporozoites are released and invade the salivary glands. Results Differential gene expression analyses showed that during ookinete invasion (24 hpf), genes related to oxidoreductase activity and galactose catabolism had lower expression levels in infected mosquitoes compared to controls. Oocyst development (5 dpf) was associated with reduced expression of a gene with a predicted innate immune function. At 10 dpf, infected mosquitoes had reduced expression levels of a serine protease inhibitor, and further studies should assess its role as a Plasmodium agonist in C. quinquefasciatus. Overall, the differential gene expression response of Hawaiian Culex exposed to a Plasmodium infection intensity known to occur naturally in Hawaiʻi was low, but more pronounced during ookinete invasion. Conclusions This is the first analysis of the transcriptional responses of vectors to malaria parasites in non-mammalian systems. Interestingly, few similarities were found between the response of Culex infected with a bird Plasmodium and those reported in Anopheles infected with human Plasmodium. The relatively small transcriptional changes observed in mosquito genes related to immune response and nutrient metabolism support conclusions of low fitness costs often documented in experimental challenges of Culex with avian Plasmodium. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04271-x.
Collapse
Affiliation(s)
- Francisco C Ferreira
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA. .,Center for Vector Biology, Entomology Department, Rutgers University, New Brunswick, NJ, 08901, USA.
| | - Elin Videvall
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA.,Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI, USA.,Institute at Brown for Environment and Society, Brown University, Providence, RI, USA.,Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Christa M Seidl
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Nicole E Wagner
- Center for Vector Biology, Entomology Department, Rutgers University, New Brunswick, NJ, 08901, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Dina M Fonseca
- Center for Vector Biology, Entomology Department, Rutgers University, New Brunswick, NJ, 08901, USA
| |
Collapse
|
9
|
Speer KA, Hawkins MTR, Flores MFC, McGowen MR, Fleischer RC, Maldonado JE, Campana MG, Muletz-Wolz CR. A comparative study of RNA yields from museum specimens, including an optimized protocol for extracting RNA from formalin-fixed specimens. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.953131] [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
Animal specimens in natural history collections are invaluable resources in examining the historical context of pathogen dynamics in wildlife and spillovers to humans. For example, natural history specimens may reveal new associations between bat species and coronaviruses. However, RNA viruses are difficult to study in historical specimens because protocols for extracting RNA from these specimens have not been optimized. Advances have been made in our ability to recover nucleic acids from formalin-fixed paraffin-embedded samples (FFPE) commonly used in human clinical studies, yet other types of formalin preserved samples have received less attention. Here, we optimize the recovery of RNA from formalin-fixed ethanol-preserved museum specimens in order to improve the usability of these specimens in surveys for zoonotic diseases. We provide RNA quality and quantity measures for replicate tissues subsamples of 22 bat specimens from five bat genera (Rhinolophus, Hipposideros, Megareops, Cynopterus, and Nyctalus) collected in China and Myanmar from 1886 to 2003. As tissues from a single bat specimen were preserved in a variety of ways, including formalin-fixed (8 bats), ethanol-preserved and frozen (13 bats), and flash frozen (2 bats), we were able to compare RNA quality and yield across different preservation methods. RNA extracted from historical museum specimens is highly fragmented, but usable for short-read sequencing and targeted amplification. Incubation of formalin-fixed samples with Proteinase-K following thorough homogenization improves RNA yield. This optimized protocol extends the types of data that can be derived from existing museum specimens and facilitates future examinations of host and pathogen RNA from specimens.
Collapse
|
10
|
Parker LD, Quinta JD, Rivera I, Cypher BL, Kelly EC, Campana MG, Fleischer RC, Boarman R, Boarman WI, Maldonado JE. Genetic analyses are more sensitive than morphological inspection at detecting the presence of threatened Mojave desert tortoise (
Gopherus agassizii
) remains in canid scat and raven pellets. Conservat Sci and Prac 2022. [DOI: 10.1111/csp2.12689] [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] Open
Affiliation(s)
- Lillian D. Parker
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
- School of Systems Biology George Mason University Virginia USA
| | - Jessica D. Quinta
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
| | - Isabel Rivera
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
| | - Brian L. Cypher
- Endangered Species Recovery Program California State University Stanislaus Turlock California USA
| | - Erica C. Kelly
- Endangered Species Recovery Program California State University Stanislaus Turlock California USA
| | - Michael G. Campana
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
- School of Systems Biology George Mason University Virginia USA
- Department of Environmental Science and Policy George Mason University Virginia USA
| | - Robert C. Fleischer
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
| | - Ryan Boarman
- Conservation Science Research and Consultation Spring Valley California USA
| | - William I. Boarman
- Conservation Science Research and Consultation Spring Valley California USA
| | - Jesús E. Maldonado
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
- School of Systems Biology George Mason University Virginia USA
- Department of Environmental Science and Policy George Mason University Virginia USA
| |
Collapse
|
11
|
Kearns AM, Campana MG, Slikas B, Berry L, Saitoh T, Cibois A, Fleischer RC. Conservation genomics and systematics of a near-extinct island radiation. Mol Ecol 2022; 31:1995-2012. [PMID: 35119154 DOI: 10.1111/mec.16382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/16/2022] [Accepted: 01/24/2022] [Indexed: 11/27/2022]
Abstract
Conservation benefits from incorporating genomics to explore the impacts of population declines, inbreeding, loss of genetic variation and hybridization. Here we use the near-extinct Mariana Islands reedwarbler radiation to showcase how ancient DNA approaches can allow insights into the population dynamics of extinct species and threatened populations for which historical museum specimens or material with low DNA yield (e.g., scats, feathers) are the only sources for DNA. Despite their having paraphyletic mtDNA, nuclear SNPs support the distinctiveness of critically endangered Acrocephalus hiwae and the other three species in the radiation that went extinct between the 1960s and 1990s. Two extinct species, A. yamashinae and A. luscinius, were deeply divergent from each other and from a third less differentiated lineage containing A. hiwae and extinct A. nijoi. Both mtDNA and SNPs suggest that the two isolated populations of A. hiwae from Saipan and Alamagan Islands are sufficiently distinct to warrant subspecies recognition and separate conservation management. We detected no significant differences in genetic diversity or inbreeding between Saipan and Alamagan, nor strong signatures of geographic structuring within either island. However, the implications of possible signatures of inbreeding in both Saipan and Alamagan, and long-term population declines in A. hiwae that predate modern anthropogenic threats require further study with denser population sampling. Our study highlights the value conservation genomics studies of island radiations have as windows onto the possible future for the world's biota as climate change and habitat destruction increasingly fragments their ranges and contributes to rapid declines in population abundances.
Collapse
Affiliation(s)
- Anna M Kearns
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Beth Slikas
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA.,Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Lainie Berry
- Department of Lands and Natural Resources, Commonwealth of the Northern Mariana Islands, Saipan, MP, 96950, USA.,Hawaii Department of Land and Natural Resources-Division of Forestry and Wildlife, Honolulu, HI, 96813, USA
| | - Takema Saitoh
- Yamashina Institute for Ornithology, 115 Konoyama, Abiko, Chiba, 270-1145, Japan
| | - Alice Cibois
- Natural History Museum of Geneva, CP, 6434, 1211, Geneva, Switzerland
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
| |
Collapse
|
12
|
Parker LD, Campana MG, Quinta JD, Cypher B, Rivera I, Fleischer RC, Ralls K, Wilbert TR, Boarman R, Boarman WI, Maldonado JE. An efficient method for simultaneous species, individual, and sex identification via in-solution single nucleotide polymorphism capture from low-quality scat samples. Mol Ecol Resour 2021; 22:1345-1361. [PMID: 34779133 DOI: 10.1111/1755-0998.13552] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/24/2021] [Accepted: 10/27/2021] [Indexed: 12/01/2022]
Abstract
Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful for the study of predators like canids that can be difficult to capture or directly observe. Here, we introduce the FAECES* method (Fast and Accurate Enrichment of Canid Excrement for Species* and other analyses) which expands the toolbox for canid researchers and conservationists by using in-solution hybridization sequence capture to produce single nucleotide polymorphism (SNP) genotypes for multiple canid species from scat-derived DNA using a single enrichment. We designed a set of hybridization probes to genotype both coyotes (Canis latrans) and kit foxes (Vulpes macrotis) at hundreds of polymorphic SNP loci and we tested the probes on both tissues and field-collected scat samples. We enriched and genotyped by sequencing 52 coyote and 70 kit fox scats collected in and around a conservation easement in the Nevada Mojave Desert. We demonstrate that the FAECES* method produces genotypes capable of differentiating coyotes and kit foxes, identifying individuals and their sex, and estimating genetic diversity and effective population sizes, even using highly degraded, low-quantity DNA extracted from scat. We found that the study area harbours a large and diverse population of kit foxes and a relatively smaller population of coyotes. By replicating our methods in the future, conservationists can assess the impacts of management decisions on canid populations. The method can also be adapted and applied more broadly to enrich and sequence multiple loci from any species of interest using scat or other noninvasive genetic samples.
Collapse
Affiliation(s)
- Lillian D Parker
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Jessica D Quinta
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Brian Cypher
- Endangered Species Recovery Program, California State University, Turlock, California, USA
| | - Isabel Rivera
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Katherine Ralls
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Tammy R Wilbert
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Ryan Boarman
- Conservation Science Research and Consultation, Spring Valley, California, USA
| | - William I Boarman
- Conservation Science Research and Consultation, Spring Valley, California, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| |
Collapse
|
13
|
Mulder KP, Alarcón-Ríos L, Nicieza AG, Fleischer RC, Bell RC, Velo-Antón G. Independent evolutionary transitions to pueriparity across multiple timescales in the viviparous genus Salamandra. Mol Phylogenet Evol 2021; 167:107347. [PMID: 34763070 DOI: 10.1016/j.ympev.2021.107347] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/21/2021] [Accepted: 11/03/2021] [Indexed: 02/07/2023]
Abstract
The ability to bear live offspring, viviparity, has evolved multiple times across the tree of life and is a remarkable adaptation with profound life-history and ecological implications. Within amphibians the ancestral reproductive mode is oviparity followed by a larval life stage, but viviparity has evolved independently in all three amphibian orders. Two types of viviparous reproduction can be distinguished in amphibians; larviparity and pueriparity. Larviparous amphibians deliver larvae into nearby ponds and streams, while pueriparous amphibians deliver fully developed juveniles and thus do not require waterbodies for reproduction. Among amphibians, the salamander genus Salamandra is remarkable as it exhibits both inter- and intraspecific variation in the occurrence of larviparity and pueriparity. While the evolutionary relationships among Salamandra lineages have been the focus of several recent studies, our understanding of how often and when transitions between modes occurred is still incomplete. Furthermore, in species with intraspecific variation, the reproductive mode of a given population can only be confirmed by direct observation of births and thus the prevalence of pueriparous populations is also incompletely documented. We used sequence capture to obtain 1,326 loci from 94 individuals from across the geographic range of the genus, focusing on potential reproductive mode transition zones. We also report additional direct observations of pueriparous births for 20 new locations and multiple lineages. We identify at least five independent transitions from the ancestral mode of larviparity to pueriparity among and within species, occurring at different evolutionary timescales ranging from the Pliocene to the Holocene. Four of these transitions occurred within species. Based on a distinct set of markers and analyses, we also confirm previous findings of introgression between species and the need for taxonomic revisions in the genus. We discuss the implications of our findings with respect to the evolution of this complex trait, and the potential of using five independent convergent transitions for further studies on the ecological context in which pueriparity evolves and the genetic architecture of this specialized reproductive mode.
Collapse
Affiliation(s)
- Kevin P Mulder
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC 20560, USA; Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA.
| | - Lucía Alarcón-Ríos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo UO, Oviedo, Spain
| | - Alfredo G Nicieza
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo UO, Oviedo, Spain; Biodiversity Research Institute (IMIB), University of Oviedo-Principality of Asturias-CSIC, 33600 Mieres, Spain
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC 20560, USA; Herpetology Department, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Guillermo Velo-Antón
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Universidade de Vigo, Grupo GEA, Departamento de Ecoloxía e Bioloxía Animal, Vigo, Spain.
| |
Collapse
|
14
|
Becker MH, Brophy JAN, Barrett K, Bronikowski E, Evans M, Glassey E, Kaganer AW, Klocke B, Lassiter E, Meyer AJ, Muletz-Wolz CR, Fleischer RC, Voigt CA, Gratwicke B. Genetically modifying skin microbe to produce violacein and augmenting microbiome did not defend Panamanian golden frogs from disease. ISME Commun 2021; 1:57. [PMID: 37938636 PMCID: PMC9723765 DOI: 10.1038/s43705-021-00044-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 04/21/2023]
Abstract
We designed two probiotic treatments to control chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd) on infected Panamanian golden frogs (Atelopus zeteki), a species that is thought to be extinct in the wild due to Bd. The first approach disrupted the existing skin microbe community with antibiotics then exposed the frogs to a core golden frog skin microbe (Diaphorobacter sp.) that we genetically modified to produce high titers of violacein, a known antifungal compound. One day following probiotic treatment, the engineered Diaphorobacter and the violacein-producing pathway could be detected on the frogs but the treatment failed to improve frog survival when exposed to Bd. The second approach exposed frogs to the genetically modified bacterium mixed into a consortium with six other known anti-Bd bacteria isolated from captive A. zeteki, with no preliminary antibiotic treatment. The consortium treatment increased the frequency and abundance of three probiotic isolates (Janthinobacterium, Chryseobacterium, and Stenotrophomonas) and these persisted on the skin 4 weeks after probiotic treatment. There was a temporary increase in the frequency and abundance of three other probiotics isolates (Masillia, Serratia, and Pseudomonas) and the engineered Diaphorobacter isolate, but they subsequently disappeared from the skin. This treatment also failed to reduce frog mortality upon exposure.
Collapse
Affiliation(s)
- Matthew H Becker
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA, USA
- Liberty University Department of Biology and Chemistry, Lynchburg, VA, USA
| | - Jennifer A N Brophy
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Ed Bronikowski
- Smithsonian's National Zoo and Conservation Biology Institute Reptile Discovery Center, Washington, DC, USA
| | - Matthew Evans
- Smithsonian's National Zoo and Conservation Biology Institute Reptile Discovery Center, Washington, DC, USA
| | - Emerson Glassey
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alyssa W Kaganer
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA, USA
| | - Blake Klocke
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA, USA
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Elliot Lassiter
- Smithsonian's National Zoo and Conservation Biology Institute Reptile Discovery Center, Washington, DC, USA
| | - Adam J Meyer
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carly R Muletz-Wolz
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Conservation Genetics, Washington, DC, 20001, USA
| | - Robert C Fleischer
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Conservation Genetics, Washington, DC, 20001, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian Gratwicke
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA, USA.
| |
Collapse
|
15
|
Campana MG, Corvelo A, Shelton J, Callicrate TE, Bunting KL, Riley-Gillis B, Wos F, DeGrazia J, Jarvis ED, Fleischer RC. Adaptive Radiation Genomics of Two Ecologically Divergent Hawai'ian Honeycreepers: The 'akiapōlā'au and the Hawai'i 'amakihi. J Hered 2021; 111:21-32. [PMID: 31723957 DOI: 10.1093/jhered/esz057] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 09/30/2019] [Indexed: 12/14/2022] Open
Abstract
The Hawai'ian honeycreepers (drepanids) are a classic example of adaptive radiation: they adapted to a variety of novel dietary niches, evolving a wide range of bill morphologies. Here we investigated genomic diversity, demographic history, and genes involved in bill morphology phenotypes in 2 honeycreepers: the 'akiapōlā'au (Hemignathus wilsoni) and the Hawai'i 'amakihi (Chlorodrepanis virens). The 'akiapōlā'au is an endangered island endemic, filling the "woodpecker" niche by using a unique bill morphology, while the Hawai'i 'amakihi is a dietary generalist common on the islands of Hawai'i and Maui. We de novo sequenced the 'akiapōlā'au genome and compared it to the previously sequenced 'amakihi genome. The 'akiapōlā'au is far less heterozygous and has a smaller effective population size than the 'amakihi, which matches expectations due to its smaller census population and restricted ecological niche. Our investigation revealed genomic islands of divergence, which may be involved in the honeycreeper radiation. Within these islands of divergence, we identified candidate genes (including DLK1, FOXB1, KIF6, MAML3, PHF20, RBP1, and TIMM17A) that may play a role in honeycreeper adaptations. The gene DLK1, previously shown to influence Darwin's finch bill size, may be related to honeycreeper bill morphology evolution, while the functions of the other candidates remain unknown.
Collapse
Affiliation(s)
- Michael G Campana
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC
| | | | | | - Taylor E Callicrate
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC.,Species Conservation Toolkit Initiative, Chicago Zoological Society, Brookfield, IL
| | | | | | - Frank Wos
- New York Genome Center, New York, NY
| | | | - Erich D Jarvis
- The Rockefeller University, New York, NY.,Howard Hughes Medical Institute, Chevy Chase, MD
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC
| |
Collapse
|
16
|
Videvall E, Paxton KL, Campana MG, Cassin‐Sackett L, Atkinson CT, Fleischer RC. Transcriptome assembly and differential gene expression of the invasive avian malaria parasite Plasmodium relictum in Hawai'i. Ecol Evol 2021; 11:4935-4944. [PMID: 33976860 PMCID: PMC8093664 DOI: 10.1002/ece3.7401] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/08/2021] [Accepted: 02/16/2021] [Indexed: 12/15/2022] Open
Abstract
The malaria parasite Plasmodium relictum (lineage GRW4) was introduced less than a century ago to the native avifauna of Hawai'i, where it has since caused major declines of endemic bird populations. One of the native bird species that is frequently infected with GRW4 is the Hawai'i 'amakihi (Chlorodrepanis virens). To achieve a better understanding of the transcriptional activities of this virulent parasite, we performed a controlled challenge experiment of 15 'amakihi that were infected with GRW4. Blood samples containing malaria parasites were collected at two time points (intermediate and peak infection stages) from host individuals that were either experimentally infected by mosquitoes or inoculated with infected blood. We then used RNA sequencing to assemble a high-quality blood transcriptome of P. relictum GRW4, allowing us to quantify parasite expression levels inside individual birds. We found few significant differences (one to two transcripts) in GRW4 expression levels between host infection stages and between inoculation methods. However, 36 transcripts showed differential expression levels among all host individuals, indicating a potential presence of host-specific gene regulation across hosts. To reduce the extinction risk of the remaining native bird species in Hawai'i, genetic resources of the local Plasmodium lineage are needed to enable further molecular characterization of this parasite. Our newly built Hawaiian GRW4 transcriptome assembly, together with analyses of the parasite's transcriptional activities inside the blood of Hawai'i 'amakihi, can provide us with important knowledge on how to combat this deadly avian disease in the future.
Collapse
Affiliation(s)
- Elin Videvall
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Kristina L. Paxton
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
- Present address:
Hawai‘i Cooperative Studies UnitUniversity of Hawai'i at HiloHawai‘i National ParkHIUSA
| | - Michael G. Campana
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Loren Cassin‐Sackett
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
- Department of BiologyUniversity of LouisianaLafayetteLAUSA
| | - Carter T. Atkinson
- U.S. Geological Survey Pacific Island Ecosystems Research CenterKilauea Field StationHawai‘i National ParkHIUSA
| | - Robert C. Fleischer
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| |
Collapse
|
17
|
Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, Andreu-Sánchez S, Margaryan A, Howard JT, Parent C, Pacheco G, Sinding MHS, Puetz L, Cavill E, Ribeiro ÂM, Eckhart L, Fjeldså J, Hosner PA, Brumfield RT, Christidis L, Bertelsen MF, Sicheritz-Ponten T, Tietze DT, Robertson BC, Song G, Borgia G, Claramunt S, Lovette IJ, Cowen SJ, Njoroge P, Dumbacher JP, Ryder OA, Fuchs J, Bunce M, Burt DW, Cracraft J, Meng G, Hackett SJ, Ryan PG, Jønsson KA, Jamieson IG, da Fonseca RR, Braun EL, Houde P, Mirarab S, Suh A, Hansson B, Ponnikas S, Sigeman H, Stervander M, Frandsen PB, van der Zwan H, van der Sluis R, Visser C, Balakrishnan CN, Clark AG, Fitzpatrick JW, Bowman R, Chen N, Cloutier A, Sackton TB, Edwards SV, Foote DJ, Shakya SB, Sheldon FH, Vignal A, Soares AER, Shapiro B, González-Solís J, Ferrer-Obiol J, Rozas J, Riutort M, Tigano A, Friesen V, Dalén L, Urrutia AO, Székely T, Liu Y, Campana MG, Corvelo A, Fleischer RC, Rutherford KM, Gemmell NJ, Dussex N, Mouritsen H, Thiele N, Delmore K, Liedvogel M, Franke A, Hoeppner MP, Krone O, Fudickar AM, Milá B, Ketterson ED, Fidler AE, Friis G, Parody-Merino ÁM, Battley PF, Cox MP, Lima NCB, Prosdocimi F, Parchman TL, Schlinger BA, Loiselle BA, Blake JG, Lim HC, Day LB, Fuxjager MJ, Baldwin MW, Braun MJ, Wirthlin M, Dikow RB, Ryder TB, Camenisch G, Keller LF, DaCosta JM, Hauber ME, Louder MIM, Witt CC, McGuire JA, Mudge J, Megna LC, Carling MD, Wang B, Taylor SA, Del-Rio G, Aleixo A, Vasconcelos ATR, Mello CV, Weir JT, Haussler D, Li Q, Yang H, Wang J, Lei F, Rahbek C, Gilbert MTP, Graves GR, Jarvis ED, Paten B, Zhang G. Author Correction: Dense sampling of bird diversity increases power of comparative genomics. Nature 2021; 592:E24. [PMID: 33833441 PMCID: PMC8081657 DOI: 10.1038/s41586-021-03473-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shaohong Feng
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,BGI-Shenzhen, Shenzhen, China
| | - Josefin Stiller
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yuan Deng
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joel Armstrong
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Qi Fang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Hart Reeve
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Duo Xie
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Guangji Chen
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Chunxue Guo
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Brant C Faircloth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Bent Petersen
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia.,Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zongji Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.,Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Wanjun Chen
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Sergio Andreu-Sánchez
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | | | | | - George Pacheco
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lara Puetz
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emily Cavill
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ângela M Ribeiro
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Jon Fjeldså
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Peter A Hosner
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robb T Brumfield
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Les Christidis
- Southern Cross University, Coffs Harbour, New South Wales, Australia
| | - Mads F Bertelsen
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Thomas Sicheritz-Ponten
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia.,Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Gerald Borgia
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Santiago Claramunt
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Irby J Lovette
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | - Saul J Cowen
- Biodiversity and Conservation Science, Department of Biodiversity Conservation and Attractions, Perth, Western Australia, Australia
| | - Peter Njoroge
- Ornithology Section, Zoology Department, National Museums of Kenya, Nairobi, Kenya
| | | | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA.,Evolution, Behavior, and Ecology, Division of Biology, University of California San Diego, La Jolla, CA, USA
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Western Australia, Perth, Australia
| | - David W Burt
- UQ Genomics, University of Queensland, Brisbane, Queensland, Australia
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
| | | | - Shannon J Hackett
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Peter G Ryan
- FitzPatrick Institute of African Ornithology, University of Cape Town, Cape Town, South Africa
| | - Knud Andreas Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ian G Jamieson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Rute R da Fonseca
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Alexander Suh
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - Suvi Ponnikas
- Department of Biology, Lund University, Lund, Sweden
| | - Hanna Sigeman
- Department of Biology, Lund University, Lund, Sweden
| | - Martin Stervander
- Department of Biology, Lund University, Lund, Sweden.,Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA.,Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA
| | | | - Rencia van der Sluis
- Focus Area for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Carina Visser
- Department of Animal Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | | - Reed Bowman
- Avian Ecology Program, Archbold Biological Station, Venus, FL, USA
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | | | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Dustin J Foote
- Department of Biology, East Carolina University, Greenville, NC, USA.,Sylvan Heights Bird Park, Scotland Neck, NC, USA
| | - Subir B Shakya
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Frederick H Sheldon
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Alain Vignal
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet-Tolosan, France
| | - André E R Soares
- Laboratório Nacional de Computação Científica, Petrópolis, Brazil.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.,Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Universitat de Barcelona, Barcelona, Spain
| | - Joan Ferrer-Obiol
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Julio Rozas
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Marta Riutort
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Anna Tigano
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Department of Biology, Queen's University, Kingston, Ontario, Canada
| | - Vicki Friesen
- Department of Biology, Queen's University, Kingston, Ontario, Canada
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Araxi O Urrutia
- Milner Centre for Evolution, University of Bath, Bath, UK.,Instituto de Ecologia, UNAM, Mexico City, Mexico
| | - Tamás Székely
- Milner Centre for Evolution, University of Bath, Bath, UK
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
| | | | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
| | - Kim M Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Nicolas Dussex
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden.,Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Henrik Mouritsen
- AG Neurosensory Sciences, Institut für Biologie und Umweltwissenschaften, University of Oldenburg, Oldenburg, Germany
| | - Nadine Thiele
- AG Neurosensory Sciences, Institut für Biologie und Umweltwissenschaften, University of Oldenburg, Oldenburg, Germany
| | - Kira Delmore
- Biology Department, Texas A&M University, College Station, TX, USA.,MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts- University of Kiel, Kiel, Germany
| | - Marc P Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrechts- University of Kiel, Kiel, Germany
| | - Oliver Krone
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Adam M Fudickar
- Environmental Resilience Institute, Indiana University, Bloomington, IN, USA
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | | | - Andrew Eric Fidler
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Guillermo Friis
- Center for Genomics and Systems Biology, Department of Biology, New York University - Abu Dhabi, Abu Dhabi, UAE
| | | | - Phil F Battley
- Wildlife and Ecology Group, Massey University, Palmerston North, New Zealand
| | - Murray P Cox
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Nicholas Costa Barroso Lima
- Laboratório Nacional de Computação Científica, Petrópolis, Brazil.,Departamento de Bioquímica e Biologia Molecular, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Rio de Janeiro, Brazil
| | | | - Barney A Schlinger
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Bette A Loiselle
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA.,Center for Latin American Studies, University of Florida, Gainesville, FL, USA
| | - John G Blake
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | - Haw Chuan Lim
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA.,Department of Biology, George Mason University, Fairfax, VA, USA
| | - Lainy B Day
- Department of Biology and Neuroscience Minor, University of Mississippi, University, MS, USA
| | - Matthew J Fuxjager
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | | | - Michael J Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, MD, USA
| | - Morgan Wirthlin
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA
| | - T Brandt Ryder
- Migratory Bird Center, Smithsonian National Zoological Park and Conservation Biology Institute, Washington, DC, USA
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | | | - Mark E Hauber
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matthew I M Louder
- Department of Biology, East Carolina University, Greenville, NC, USA.,Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,International Research Center for Neurointelligence, University of Tokyo, Tokyo, Japan
| | - Christopher C Witt
- Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology, Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Libby C Megna
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Matthew D Carling
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Biao Wang
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Glaucia Del-Rio
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Jason T Weir
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - David Haussler
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Qiye Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | | | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.,Institute of Ecology, Peking University, Beijing, China.,Department of Life Sciences, Imperial College London, Ascot, UK
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Gary R Graves
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Erich D Jarvis
- Duke University Medical Center, Durham, NC, USA.,The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA.
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| |
Collapse
|
18
|
Venkatraman M, Fleischer RC, Tsuchiya MTN. Comparative Analysis of Annotation Pipelines Using the First Japanese White-Eye (Zosterops japonicus) Genome. Genome Biol Evol 2021; 13:6184866. [PMID: 33760049 DOI: 10.1093/gbe/evab063] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2021] [Indexed: 11/14/2022] Open
Abstract
Introduced into Hawaii in the early 1900s, the Japanese white-eye or warbling white-eye (Zosterops japonicus) is now the most abundant land bird in the archipelago. Here, we present the first Z. japonicus genome, sequenced from an individual in its invasive range. This genome provides an important resource for future studies in invasion genomics. We annotated the genome using two workflows-standalone AUGUSTUS and BRAKER2. We found that AUGUSTUS was more conservative with gene predictions when compared with BRAKER2. The final number of annotated gene models was similar between the two workflows, but standalone AUGUSTUS had over 70% of gene predictions with Blast2GO annotations versus under 30% using BRAKER2. Additionally, we tested whether using RNA-seq data from 47 samples had a significant impact on annotation quality when compared with data from a single sample, as generating RNA-seq data for genome annotation can be expensive and requires well preserved tissue. We found that more data did not significantly change the number of annotated genes using AUGUSTUS but using BRAKER2 the number increased substantially. The results presented here will aid researchers in annotating draft genomes of nonmodel species as well as those studying invasion success.
Collapse
Affiliation(s)
- Madhvi Venkatraman
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Biological Sciences Graduate Program, University of Maryland, College Park, Maryland, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Mirian T N Tsuchiya
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia, USA
| |
Collapse
|
19
|
Muletz‐Wolz CR, Wilson Rankin E, McGrath‐Blaser S, Venkatraman M, Maldonado JE, Gruner DS, Fleischer RC. Identification of novel bacterial biomarkers to detect bird scavenging by invasive rats. Ecol Evol 2021; 11:1814-1828. [PMID: 33614005 PMCID: PMC7882976 DOI: 10.1002/ece3.7171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 01/04/2023] Open
Abstract
Rapid advances in genomic tools for use in ecological contexts and non-model systems allow unprecedented insight into interactions that occur beyond direct observation. We developed an approach that couples microbial forensics with molecular dietary analysis to identify species interactions and scavenging by invasive rats on native and introduced birds in Hawaii. First, we characterized bacterial signatures of bird carcass decay by conducting 16S rRNA high-throughput sequencing on chicken (Gallus gallus domesticus) tissues collected over an 11-day decomposition study in natural Hawaiian habitats. Second, we determined if field-collected invasive black rats (Rattus rattus; n = 51, stomach and fecal samples) had consumed birds using molecular diet analysis with two independent PCR assays (mitochondrial Cytochrome Oxidase I and Cytochrome b genes) and Sanger sequencing. Third, we characterized the gut microbiome of the same rats using 16S rRNA high-throughput sequencing and identified 15 bacterial taxa that were (a) detected only in rats that consumed birds (n = 20/51) and (b) were indicative of decaying tissue in the chicken decomposition experiment. We found that 18% of rats (n = 9/51) likely consumed birds as carrion by the presence of bacterial biomarkers of decayed tissue in their gut microbiome. One species of native bird (Myadestes obscurus) and three introduced bird species (Lophura leucomelanos, Meleagris gallopavo, Zosterops japonicus) were detected in the rats' diets, with individuals from these species (except L. nycthemera) likely consumed through scavenging. Bacterial biomarkers of bird carcass decay can persist through rat digestion and may serve as biomarkers of scavenging. Our approach can be used to reveal trophic interactions that are challenging to measure through direct observation.
Collapse
Affiliation(s)
- Carly R. Muletz‐Wolz
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Erin Wilson Rankin
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
- Department of EntomologyUniversity of MarylandCollege ParkMDUSA
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Sarah McGrath‐Blaser
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Madhvi Venkatraman
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
- Department of EntomologyUniversity of MarylandCollege ParkMDUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | | | - Robert C. Fleischer
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| |
Collapse
|
20
|
Dussex N, Kutschera VE, Wiberg RAW, Parker DJ, Hunt GR, Gray RD, Rutherford K, Abe H, Fleischer RC, Ritchie MG, Rutz C, Wolf JBW, Gemmell NJ. A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows. Mol Ecol 2020; 30:973-986. [PMID: 33305388 DOI: 10.1111/mec.15775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 12/30/2022]
Abstract
Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species). Here, we sequenced the genomes of two habitually tool-using and ten non-tool-using crow species to search for genomic signatures associated with a tool-using lifestyle. Using comparative genomic and population genetic approaches, we screened for signals of selection in protein-coding genes in the tool-using New Caledonian and Hawaiian crows. While we detected signals of recent selection in New Caledonian crows near genes associated with bill morphology, our data indicate that genetic changes in these two lineages are surprisingly subtle, with little evidence at present for convergence. We explore the biological explanations for these findings, such as the relative roles of gene regulation and protein-coding changes, as well as the possibility that statistical power to detect selection in recently diverged lineages may have been insufficient. Our study contributes to a growing body of literature aiming to decipher the genetic basis of recently evolved complex behaviour.
Collapse
Affiliation(s)
- Nicolas Dussex
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Department of Bioinformatics and Genetics, Centre for Palaeogenetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Verena E Kutschera
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - R Axel W Wiberg
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK.,Department of Environmental Sciences, Evolutionary Biology, University of Basel, Basel, Switzerland
| | - Darren J Parker
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Gavin R Hunt
- University of Auckland, Science Centre 302, Auckland, New Zealand
| | - Russell D Gray
- University of Auckland, Science Centre 302, Auckland, New Zealand.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Hideaki Abe
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - Christian Rutz
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - Jochen B W Wolf
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| |
Collapse
|
21
|
Savage AE, Gratwicke B, Hope K, Bronikowski E, Fleischer RC. Sustained immune activation is associated with susceptibility to the amphibian chytrid fungus. Mol Ecol 2020; 29:2889-2903. [PMID: 32700351 DOI: 10.1111/mec.15533] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 06/06/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022]
Abstract
The disease chytridiomycosis caused by the fungus Bd has devastated amphibian populations worldwide. Functional genomic contributions to host susceptibility remain enigmatic and vary between species and populations. We conducted experimental Bd infections in Rana yavapaiensis, a species with intraspecific variation in chytridiomycosis susceptibility, to assess the skin and spleen transcriptomic response to infection over time. We predicted that increased immune gene expression would be associated with a positive disease outcome, but we instead found that surviving frogs had significantly reduced immune gene expression compared to susceptible frogs and to uninfected controls. MHC class IIβ gene expression was also significantly higher in susceptible frogs compared to surviving frogs. Furthermore, susceptible frogs expressed a significantly larger number of distinct class IIβ alleles, demonstrating a negative correlation between class IIβ expression, functional diversity, and survival. Expression of the MHC class IIβ locus previously associated with Bd disease outcomes was a significant predictor of Bd infection intensity at early infection stages but not at late infection stages, suggesting initial MHC-linked immune processes are important for ultimate disease outcomes. We infer through disease association and phylogenetic analysis that certain MHC variants are linked to the immune expression that was negatively associated with survival, and we hypothesize that frogs that did not express these alleles could better survive infections. Our study finds that MHC expression at early and late infection stages predicts Bd infection intensity, and suggests that generating a sustained immune response against Bd may be counterproductive for surviving chytridiomycosis in this partially susceptible species.
Collapse
Affiliation(s)
- Anna E Savage
- Department of Biology, University of Central Florida, Orlando, FL, USA.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Brian Gratwicke
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Katharine Hope
- Center for Animal Care Sciences, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Edward Bronikowski
- Center for Animal Care Sciences, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| |
Collapse
|
22
|
Rao MV, Rice RA, Fleischer RC, Muletz-Wolz CR. Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador. PLoS One 2020; 15:e0231875. [PMID: 32330174 PMCID: PMC7182172 DOI: 10.1371/journal.pone.0231875] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 04/02/2020] [Indexed: 11/25/2022] Open
Abstract
Coffea arabica is a highly traded commodity worldwide, and its plantations are habitat to a wide range of organisms. Coffee farmers are shifting away from traditional shade coffee farms in favor of sun-intensive, higher yield farms, which can impact local biodiversity. Using plant-associated microorganisms in biofertilizers, particularly fungi collected from local forests, to increase crop yields has gained traction among coffee producers. However, the taxonomic and spatial distribution of many fungi in coffee soil, nearby forests and biofertilizers is unknown. We collected soil samples from a sun coffee system, shade coffee system, and nearby forest from Izalco, Sonsonate, El Salvador. At each coffee system, we collected soil from the surface (upper) and 10 cm below the surface (lower), and from the coffee plant drip line (drip line) and the walkway between two plants (walkway). Forest soils were collected from the surface only. We used ITS metabarcoding to characterize fungal communities in soil and in the biofertilizer (applied in both coffee systems), and assigned fungal taxa to functional guilds using FUNGuild. In the sun and shade coffee systems, we found that drip line soil had higher richness in pathotrophs, symbiotrophs, and saprotrophs than walkway soil, suggesting that fungi select for microhabitats closer to coffee plants. Upper and lower soil depths did not differ in fungal richness or composition, which may reflect the shallow root system of Coffea arabica. Soil from shade, sun, and forest had similar numbers of fungal taxa, but differed dramatically in community composition, indicating that local habitat differences drive fungal species sorting among systems. Yet, some fungal taxa were shared among systems, including seven fungal taxa present in the biofertilizer. Understanding the distribution of coffee soil mycobiomes can be used to inform sustainable, ecologically friendly farming practices and identify candidate plant-growth promoting fungi for future studies.
Collapse
Affiliation(s)
- Maya V. Rao
- Department of Biology, University of Maryland, College Park, MD, United States of America
- Center for Conservation Genomics, Smithsonian National Zoological Park & Conservation Biology Institute, Washington, DC, United States of America
| | - Robert A. Rice
- Migratory Bird Center, Smithsonian National Zoological Park & Conservation Biology Institute, Washington, DC, United States of America
| | - Robert C. Fleischer
- Center for Conservation Genomics, Smithsonian National Zoological Park & Conservation Biology Institute, Washington, DC, United States of America
| | - Carly R. Muletz-Wolz
- Center for Conservation Genomics, Smithsonian National Zoological Park & Conservation Biology Institute, Washington, DC, United States of America
- * E-mail:
| |
Collapse
|
23
|
McClure KM, Fleischer RC, Kilpatrick AM. The role of native and introduced birds in transmission of avian malaria in Hawaii. Ecology 2020; 101:e03038. [PMID: 32129884 DOI: 10.1002/ecy.3038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 01/09/2020] [Accepted: 01/30/2020] [Indexed: 01/07/2023]
Abstract
The introduction of nonnative species and reductions in native biodiversity have resulted in substantial changes in vector and host communities globally, but the consequences for pathogen transmission are poorly understood. In lowland Hawaii, bird communities are composed of primarily introduced species, with scattered populations of abundant native species. We examined the influence of avian host community composition, specifically the role of native and introduced species, as well as host diversity, on the prevalence of avian malaria (Plasmodium relictum) in the southern house mosquito (Culex quinquefasciatus). We also explored the reciprocal effect of malaria transmission on native host populations and demography. Avian malaria infection prevalence in mosquitoes increased with the density and relative abundance of native birds, as well as host community competence, but was uncorrelated with host diversity. Avian malaria transmission was estimated to reduce population growth rates of Hawai'i 'amakihi (Chlorodrepanis virens) by 7-14%, but mortality from malaria could not explain gaps in this species' distribution at our sites. Our results suggest that, in Hawaii, native host species increase pathogen transmission to mosquitoes, but introduced species can also support malaria transmission alone. The increase in pathogen transmission with native bird abundance leads to additional disease mortality in native birds, further increasing disease impacts in an ecological feedback cycle. In addition, vector abundance was higher at sites without native birds and this overwhelmed the effects of host community composition on transmission such that infected mosquito abundance was highest at sites without native birds. Higher disease risk at these sites due to higher vector abundance could inhibit recolonization and recovery of native species to these areas. More broadly, this work shows how differences in host competence for a pathogen among native and introduced taxa can influence transmission and highlights the need to examine this question in other systems to determine the generality of this result.
Collapse
Affiliation(s)
- Katherine M McClure
- Department Ecology and Evolutionary Biology, University of California, 130 McAllister Way, Santa Cruz, California, 95060, USA.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, USA
| | - A Marm Kilpatrick
- Department Ecology and Evolutionary Biology, University of California, 130 McAllister Way, Santa Cruz, California, 95060, USA
| |
Collapse
|
24
|
Lim HC, Shakya SB, Harvey MG, Moyle RG, Fleischer RC, Braun MJ, Sheldon FH. Opening the door to greater phylogeographic inference in Southeast Asia: Comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA. Ecol Evol 2020; 10:3222-3247. [PMID: 32273983 PMCID: PMC7141000 DOI: 10.1002/ece3.5964] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/02/2019] [Accepted: 12/06/2019] [Indexed: 12/30/2022] Open
Abstract
Indochina and Sundaland are biologically diverse, interconnected regions of Southeast Asia with complex geographic histories. Few studies have examined phylogeography of bird species that span the two regions because of inadequate population sampling. To determine how geographic barriers/events and disparate dispersal potential have influenced the population structure, gene flow, and demographics of species that occupy the entire area, we studied five largely codistributed rainforest bird species: Arachnothera longirostra, Irena puella, Brachypodius atriceps, Niltava grandis, and Stachyris nigriceps. We accomplished relatively thorough sampling and data collection by sequencing ultraconserved elements (UCEs) using DNA extracted from modern and older (historical) specimens. We obtained a genome-wide set of 753-4,501 variable loci and 3,919-18,472 single nucleotide polymorphisms. The formation of major within-species lineages occurred within a similar span of time (0.5-1.5 mya). Major patterns in population genetic structure are largely consistent with the dispersal potential and habitat requirements of the study species. A population break across the Isthmus of Kra was shared only by the two hill/submontane insectivores (N. grandis and S. nigriceps). Across Sundaland, there is little structure in B. atriceps, which is a eurytopic and partially frugivorous species that often utilizes forest edges. Two other eurytopic species, A. longirostra and I. puella, possess highly divergent populations in peripheral Sunda Islands (Java and/or Palawan) and India. These species probably possess intermediate dispersal abilities that allowed them to colonize new areas, and then remained largely isolated subsequently. We also observed an east-west break in Indochina that was shared by B. atriceps and S. nigriceps, species with very different habitat requirements and dispersal potential. By analyzing high-throughput DNA data, our study provides an unprecedented comparative perspective on the process of avian population divergence across Southeast Asia, a process that is determined by geography, species characteristics, and the stochastic nature of dispersal and vicariance events.
Collapse
Affiliation(s)
- Haw Chuan Lim
- Department of BiologyGeorge Mason UniversityFairfaxVirginia
- Department of Vertebrate ZoologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of Columbia
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
| | - Subir B. Shakya
- Museum of Natural Science and Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
| | - Michael G. Harvey
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTennessee
| | - Robert G. Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansas
| | - Robert C. Fleischer
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
| | - Michael J. Braun
- Department of Vertebrate ZoologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of Columbia
| | - Frederick H. Sheldon
- Museum of Natural Science and Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
| |
Collapse
|
25
|
Gillespie RG, Bennett GM, De Meester L, Feder JL, Fleischer RC, Harmon LJ, Hendry AP, Knope ML, Mallet J, Martin C, Parent CE, Patton AH, Pfennig KS, Rubinoff D, Schluter D, Seehausen O, Shaw KL, Stacy E, Stervander M, Stroud JT, Wagner C, Wogan GOU. Comparing Adaptive Radiations Across Space, Time, and Taxa. J Hered 2020; 111:1-20. [PMID: 31958131 PMCID: PMC7931853 DOI: 10.1093/jhered/esz064] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/28/2019] [Indexed: 01/02/2023] Open
Abstract
Adaptive radiation plays a fundamental role in our understanding of the evolutionary process. However, the concept has provoked strong and differing opinions concerning its definition and nature among researchers studying a wide diversity of systems. Here, we take a broad view of what constitutes an adaptive radiation, and seek to find commonalities among disparate examples, ranging from plants to invertebrate and vertebrate animals, and remote islands to lakes and continents, to better understand processes shared across adaptive radiations. We surveyed many groups to evaluate factors considered important in a large variety of species radiations. In each of these studies, ecological opportunity of some form is identified as a prerequisite for adaptive radiation. However, evolvability, which can be enhanced by hybridization between distantly related species, may play a role in seeding entire radiations. Within radiations, the processes that lead to speciation depend largely on (1) whether the primary drivers of ecological shifts are (a) external to the membership of the radiation itself (mostly divergent or disruptive ecological selection) or (b) due to competition within the radiation membership (interactions among members) subsequent to reproductive isolation in similar environments, and (2) the extent and timing of admixture. These differences translate into different patterns of species accumulation and subsequent patterns of diversity across an adaptive radiation. Adaptive radiations occur in an extraordinary diversity of different ways, and continue to provide rich data for a better understanding of the diversification of life.
Collapse
Affiliation(s)
- Rosemary G Gillespie
- University of California, Berkeley, Essig Museum of Entomology & Department of Environmental Science, Policy, and Management, Berkeley, CA
| | - Gordon M Bennett
- University of California Merced, Life and Environmental Sciences Unit, Merced, CA
| | - Luc De Meester
- University of Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Leuven, Belguim
| | - Jeffrey L Feder
- University of Notre Dame, Dept. of Biological Sciences, Notre Dame, IN
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
| | - Luke J Harmon
- University of Idaho, Dept. of Biological Sciences, Moscow, ID
| | | | | | | | - Christopher Martin
- University of California Berkeley, Integrative Biology and Museum of Vertebrate Zoology, Berkeley, CA
| | | | - Austin H Patton
- Washington State University, School of Biological Sciences, Pullman, WA
| | - Karin S Pfennig
- University of North Carolina at Chapel Hill, Department of Biology, Chapel Hill, NC
| | - Daniel Rubinoff
- University of Hawaiʻi at Manoa, Department of Plant and Environmental Protection Sciences, Honolulu, HI
| | | | - Ole Seehausen
- Institute of Ecology & Evolution, University of Bern, Bern, BE, Switzerland
- Center for Ecology, Evolution & Biogeochemistry, Eawag, Kastanienbaum, LU, Switzerland
| | - Kerry L Shaw
- Cornell University, Neurobiology and Behavior, Tower Road,, Ithaca, NY
| | - Elizabeth Stacy
- University of Nevada Las Vegas, School of Life Sciences, Las Vegas, NV
| | - Martin Stervander
- University of Oregon, Institute of Ecology and Evolution, Eugene, OR
| | - James T Stroud
- Washington University in Saint Louis, Biology, Saint Louis, MO
| | | | - Guinevere O U Wogan
- University of California Berkeley, Environmental Science Policy, and Management, Berkeley, CA
| |
Collapse
|
26
|
Lavretsky P, McInerney NR, Mohl JE, Brown JI, James HF, McCracken KG, Fleischer RC. Assessing changes in genomic divergence following a century of human-mediated secondary contact among wild and captive-bred ducks. Mol Ecol 2020; 29:578-595. [PMID: 31872482 DOI: 10.1111/mec.15343] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/09/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022]
Abstract
Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used worldwide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary timescales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (Anas platyrhynchos) throughout North America and two domestic mallard types (i.e., known game-farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (Anas rubripes) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game-farm mallards during the last ~100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game-farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.
Collapse
Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Nancy Rotzel McInerney
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
| | - Jonathon E Mohl
- Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, USA
| | - Joshua I Brown
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Helen F James
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Kevin G McCracken
- Department of Biology, University of Miami, Coral Gables, FL, USA.,Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL, USA.,Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Institute of Arctic Biology, University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
| |
Collapse
|
27
|
Kaiser SA, Martin TE, Oteyza JC, Danner JE, Armstad CE, Fleischer RC. Within-group relatedness and patterns of reproductive sharing and cooperation in the tropical chestnut-crested yuhina. Anim Behav 2019. [DOI: 10.1016/j.anbehav.2019.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
28
|
Card LR, McShea WJ, Fleischer RC, Maldonado JE, Stewardson K, Campana MG, Jansen PA, Calabrese JM. Tick Burdens in a Small-Mammal Community in Virginia. Northeast Nat (Steuben) 2019. [DOI: 10.1656/045.026.0317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Leah R. Card
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630
| | - William J. McShea
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630
| | - Robert C. Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute at the National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008
| | - Jesús. E. Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute at the National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008
| | - Kristin Stewardson
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute at the National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008
| | - Michael G. Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute at the National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008
| | - Patrick A. Jansen
- Center for Tropical Forest Science, Smithsonian Tropical Research Institute, Roosevelt Avenue, Balboa, Ancón, Republic of Panamá
| | - Justin M. Calabrese
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630
| |
Collapse
|
29
|
Muletz-Wolz CR, Kurata NP, Himschoot EA, Wenker ES, Quinn EA, Hinde K, Power ML, Fleischer RC. Diversity and temporal dynamics of primate milk microbiomes. Am J Primatol 2019; 81:e22994. [PMID: 31219214 DOI: 10.1002/ajp.22994] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/28/2019] [Accepted: 05/05/2019] [Indexed: 12/30/2022]
Abstract
Milk is inhabited by a community of bacteria and is one of the first postnatal sources of microbial exposure for mammalian young. Bacteria in breast milk may enhance immune development, improve intestinal health, and stimulate the gut-brain axis for infants. Variation in milk microbiome structure (e.g., operational taxonomic unit [OTU] diversity, community composition) may lead to different infant developmental outcomes. Milk microbiome structure may depend on evolutionary processes acting at the host species level and ecological processes occurring over lactation time, among others. We quantified milk microbiomes using 16S rRNA high-throughput sequencing for nine primate species and for six primate mothers sampled over lactation. Our data set included humans (Homo sapiens, Philippines and USA) and eight nonhuman primate species living in captivity (bonobo [Pan paniscus], chimpanzee [Pan troglodytes], western lowland gorilla [Gorilla gorilla gorilla], Bornean orangutan [Pongo pygmaeus], Sumatran orangutan [Pongo abelii], rhesus macaque [Macaca mulatta], owl monkey [Aotus nancymaae]) and in the wild (mantled howler monkey [Alouatta palliata]). For a subset of the data, we paired microbiome data with nutrient and hormone assay results to quantify the effect of milk chemistry on milk microbiomes. We detected a core primate milk microbiome of seven bacterial OTUs indicating a robust relationship between these bacteria and primate species. Milk microbiomes differed among primate species with rhesus macaques, humans and mantled howler monkeys having notably distinct milk microbiomes. Gross energy in milk from protein and fat explained some of the variations in microbiome composition among species. Microbiome composition changed in a predictable manner for three primate mothers over lactation time, suggesting that different bacterial communities may be selected for as the infant ages. Our results contribute to understanding ecological and evolutionary relationships between bacteria and primate hosts, which can have applied benefits for humans and endangered primates in our care.
Collapse
Affiliation(s)
- Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
| | - Naoko P Kurata
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
- The Graduate Center, The City University of New York, New York, New York
- Department of Ichthyology, American Museum of Natural History, New York, New York
| | - Elizabeth A Himschoot
- Nutrition Laboratory and Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
| | - Elizabeth S Wenker
- Nutrition Laboratory and Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
| | - Elizabeth A Quinn
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri
| | - Katie Hinde
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona
| | - Michael L Power
- Nutrition Laboratory and Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
| |
Collapse
|
30
|
Miller KL, Castañeda Rico S, Muletz-Wolz CR, Campana MG, McInerney N, Augustine L, Frere C, Peters AM, Fleischer RC. Parthenogenesis in a captive Asian water dragon (Physignathus cocincinus) identified with novel microsatellites. PLoS One 2019; 14:e0217489. [PMID: 31166974 PMCID: PMC6550409 DOI: 10.1371/journal.pone.0217489] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 05/12/2019] [Indexed: 11/19/2022] Open
Abstract
Reptiles show varying degrees of facultative parthenogenesis. Here we use genetic methods to determine that an isolated, captive female Asian water dragon produced at least nine offspring via parthenogenesis. We identified microsatellites for the species from shotgun genomic sequences, selected and optimized primer sets, and tested all of the offspring for a set of seven microsatellites that were heterozygous in the mother. We verified that the seven loci showed high levels of polymorphism in four wild Asian water dragons from Vietnam. In all cases, the offspring (unhatched, but developed eggs, or hatched young) had only a single allele at each locus, and contained only alleles present in the mother’s genotype (i.e., were homozygous or hemizygous). The probability that our findings resulted from the female mating with one or more males is extremely small, indicating that the offspring were derived from a single female gamete (either alone or via duplication and/or fusion) and implicating parthenogenesis. This is the first documented case of parthenogenesis in the Squamate family Agamidae.
Collapse
Affiliation(s)
- Kyle L. Miller
- Department of Animal Care Sciences, Smithsonian’s National Zoological Park Washington, District of Columbia, United States of America
- * E-mail:
| | - Susette Castañeda Rico
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, United States of America
- George Mason University, Fairfax, Virginia, United States of America
| | - Carly R. Muletz-Wolz
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, United States of America
| | - Michael G. Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, United States of America
| | - Nancy McInerney
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, United States of America
| | - Lauren Augustine
- Department of Animal Care Sciences, Smithsonian’s National Zoological Park Washington, District of Columbia, United States of America
- Saint Louis Zoo, One Government Drive, Saint Louis, Missouri, United States of America
| | - Celine Frere
- University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Alan M. Peters
- Department of Animal Care Sciences, Smithsonian’s National Zoological Park Washington, District of Columbia, United States of America
| | - Robert C. Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, United States of America
| |
Collapse
|
31
|
Muletz-Wolz CR, Fleischer RC, Lips KR. Fungal disease and temperature alter skin microbiome structure in an experimental salamander system. Mol Ecol 2019; 28:2917-2931. [PMID: 31066947 DOI: 10.1111/mec.15122] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/27/2019] [Accepted: 04/25/2019] [Indexed: 12/29/2022]
Abstract
Pathogens compete with host microbiomes for space and resources. Their shared environment impacts pathogen-microbiome-host interactions, which can lead to variation in disease outcome. The skin microbiome of red-backed salamanders (Plethodon cinereus) can reduce infection by the pathogen Batrachochytrium dendrobatidis (Bd) at moderate infection loads, with high species richness and high abundance of competitors as putative mechanisms. However, it is unclear if the skin microbiome can reduce epizootic Bd loads across temperatures. We conducted a laboratory experiment to quantify skin microbiome and host responses (P. cinereus: n = 87) to Bd at mimicked epizootic loads across temperatures (13, 17 and 21°C). We quantified skin microbiomes using 16S rRNA gene metabarcoding and identified operational taxonomic units (OTUs) taxonomically similar to culturable bacteria known to kill Bd (anti-Bd OTUs). Prior to pathogen exposure, temperature changed the microbiome (OTU richness decreased by 12% and the abundance of anti-Bd OTUs increased by 18% per degree increase in temperature), but these changes were not predictive of disease outcome. After exposure, Bd changed the microbiome (OTU richness decreased by 0.1% and the abundance of anti-Bd OTUs increased by 0.2% per 1% increase in Bd load) and caused high host mortality across temperatures (35/45: 78%). Temperature indirectly impacted microbiome change and mortality through its direct effect on pathogen load. We did not find support for the microbiome impacting Bd load or host survival. Our research reveals complex host, pathogen, microbiome and environmental interactions to demonstrate that during epizootic events the microbiome will be unlikely to reduce pathogen invasion, even for putatively Bd-resistant species.
Collapse
Affiliation(s)
- Carly R Muletz-Wolz
- Department of Biology, University of Maryland, College Park, Maryland.,Center for Conservation Genomics, Smithsonian National Zoological Park and Conservation Biology Institute, Washington, District of Columbia
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian National Zoological Park and Conservation Biology Institute, Washington, District of Columbia
| | - Karen R Lips
- Department of Biology, University of Maryland, College Park, Maryland
| |
Collapse
|
32
|
Yu JH, Durrant KL, Liu S, Carlin EP, Wang C, Rodriguez J, Bratthauer A, Walsh T, Valitutto MT, Fine L, Murray S, Fleischer RC. First Report of a Novel Hepatozoon sp. in Giant Pandas (Ailuropoda melanoleuca). Ecohealth 2019; 16:338-345. [PMID: 31147811 DOI: 10.1007/s10393-019-01416-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
The first report of giant pandas (Ailuropoda melanoleuca) infected with a novel Hepatozoon species is presented. An intraleukocytic parasite was detected via routine blood smear from a zoo-housed giant panda at the National Zoological Park. Ribosomal DNA sequences indicated a previously undescribed Hepatozoon species. Phylogenetic and distance analyses of the sequences placed it within its own branch, clustered with Old World species with carnivore (primarily ursid and mustelid) hosts. Retrospective and opportunistic testing of other individuals produced additional positive detections (17/23, 73.9%), demonstrating 100% prevalence (14/14) across five institutions. All animals were asymptomatic at time of sampling, and health implications for giant pandas remain unknown.
Collapse
Affiliation(s)
- Jennifer H Yu
- Global Health Program, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.
| | - Kate L Durrant
- School of Life Sciences, University of Nottingham, Nottingham, UK
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA
| | - Songrui Liu
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, People's Republic of China
| | - Ellen P Carlin
- Global Health Program, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA
- EcoHealth Alliance, New York, NY, USA
| | - Chengdong Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, People's Republic of China
| | - Juan Rodriguez
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA
| | - Ann Bratthauer
- Department of Pathology, Smithsonian National Zoological Park, Washington, DC, USA
| | - Tim Walsh
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Marc T Valitutto
- Global Health Program, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA
| | - Leah Fine
- Washington University in St. Louis, St. Louis, MO, USA
| | - Suzan Murray
- Global Health Program, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA
| |
Collapse
|
33
|
Mulder KP, Cortes‐Rodriguez N, Campbell Grant EH, Brand A, Fleischer RC. North-facing slopes and elevation shape asymmetric genetic structure in the range-restricted salamander Plethodon shenandoah. Ecol Evol 2019; 9:5094-5105. [PMID: 31110664 PMCID: PMC6509443 DOI: 10.1002/ece3.5064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 06/22/2018] [Revised: 02/17/2019] [Accepted: 02/27/2019] [Indexed: 12/28/2022] Open
Abstract
Species with narrow environmental tolerances are often distributed within fragmented patches of suitable habitat, and dispersal among these subpopulations can be difficult to directly observe. Genetic data can help quantify gene flow between localities, which is especially important for vulnerable species with a disjunct range. The Shenandoah salamander (Plethodon shenandoah) is a federally endangered species known only from three mountaintops in Virginia, USA. To reconstruct the evolutionary history and population connectivity of this species, we generated both mitochondrial and nuclear data using sequence capture from individuals collected across all three mountaintops. Applying population and landscape genetic methods, we found strong population structure that was independent of geographic distance. Both the nuclear markers and mitochondrial genomes indicated a deep split between the most southern population and the genetically similar central and northern populations. Although there was some mitochondrial haplotype-splitting between the central and northern populations, there was admixture in nuclear markers. This is indicative of either a recent split or current male-biased dispersal among mountain isolates. Models of landscape resistance found that dispersal across north-facing slopes at mid-elevation levels best explain the observed genetic structure among populations. These unexpected results highlight the importance of incorporating landscape features in understanding and predicting the movement and fragmentation of this range-restricted salamander species across space.
Collapse
Affiliation(s)
- Kevin P. Mulder
- Center for Conservation Genomics, National Zoological ParkSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
- Research Center in Biodiversity and Genetic ResourcesCIBIO/InBIOVairãoPortugal
- Departamento de BiologiaFaculdade de Ciências da Universidade do PortoPortoPortugal
- Department of Vertebrate Zoology, National Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of Columbia
| | - Nandadevi Cortes‐Rodriguez
- Center for Conservation Genomics, National Zoological ParkSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
- Department of BiologyIthaca CollegeIthacaNew York
| | - Evan H. Campbell Grant
- United States Geological Survey, Patuxent Wildlife Research CenterSO Conte Anadromous Fish Research LabTurners FallsMassachusetts
| | - Adrianne Brand
- United States Geological Survey, Patuxent Wildlife Research CenterSO Conte Anadromous Fish Research LabTurners FallsMassachusetts
| | - Robert C. Fleischer
- Center for Conservation Genomics, National Zoological ParkSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
| |
Collapse
|
34
|
|
35
|
|
36
|
Cassin-Sackett L, Callicrate TE, Fleischer RC. Parallel evolution of gene classes, but not genes: Evidence from Hawai'ian honeycreeper populations exposed to avian malaria. Mol Ecol 2018; 28:568-583. [PMID: 30298567 DOI: 10.1111/mec.14891] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 10/14/2018] [Accepted: 10/19/2018] [Indexed: 12/29/2022]
Abstract
Adaptation in nature is ubiquitous, yet characterizing its genomic basis is difficult because population demographics cause correlations with nonadaptive loci. Introduction events provide opportunities to observe adaptation over known spatial and temporal scales, facilitating the identification of genes involved in adaptation. The pathogen causing avian malaria, Plasmodium relictum, was introduced to Hawai'i in the 1930s and elicited extinctions and precipitous population declines in native honeycreepers. After a sharp initial population decline, the Hawai'i 'amakihi (Chlorodrepanis virens) has evolved tolerance to the parasite at low elevations where P. relictum exists, and can sustain infection without major fitness consequences. High-elevation, unexposed populations of 'amakihi display little to no tolerance. To explore the genomic basis of adaptation to P. relictum in low-elevation 'amakihi, we genotyped 125 'amakihi from the island of Hawai'i via hybridization capture to 40,000 oligonucleotide baits containing SNPs and used the reference 'amakihi genome to identify genes potentially under selection from malaria. We tested for outlier loci between low- and high-elevation population pairs and identified loci with signatures of selection within low-elevation populations. In some cases, genes commonly involved in the immune response (e.g., major histocompatibility complex) were associated with malaria presence in the population. We also detected several novel candidate loci that may be implicated in surviving malaria infection (e.g., beta-defensin, glycoproteins and interleukin-related genes). Our results suggest that rapid adaptation to pathogens may occur through changes in different immune genes, but in the same classes of genes, across populations.
Collapse
Affiliation(s)
- Loren Cassin-Sackett
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia.,Department of Integrative Biology, University of South Florida, Tampa, Florida
| | - Taylor E Callicrate
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia.,Species Conservation Toolkit Initiative, Department of Conservation Science, Chicago Zoological Society, Brookfield, Illinois
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia
| |
Collapse
|
37
|
Campana MG, Kurata NP, Foster JT, Helgen LE, Reeder DM, Fleischer RC, Helgen KM. White-Nose Syndrome Fungus in a 1918 Bat Specimen from France. Emerg Infect Dis 2018; 23:1611-1612. [PMID: 28820367 PMCID: PMC5572869 DOI: 10.3201/eid2309.170875] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
White-nose syndrome, first diagnosed in North America in 2006, causes mass deaths among bats in North America. We found the causative fungus, Pseudogymnoascusdestructans, in a 1918 sample collected in Europe, where bats have now adapted to the fungus. These results are consistent with a Eurasian origin of the pathogen.
Collapse
|
38
|
Kearns AM, Restani M, Szabo I, Schrøder-Nielsen A, Kim JA, Richardson HM, Marzluff JM, Fleischer RC, Johnsen A, Omland KE. Genomic evidence of speciation reversal in ravens. Nat Commun 2018; 9:906. [PMID: 29500409 PMCID: PMC5834606 DOI: 10.1038/s41467-018-03294-w] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/01/2018] [Indexed: 01/10/2023] Open
Abstract
Many species, including humans, have emerged via complex reticulate processes involving hybridisation. Under certain circumstances, hybridisation can cause distinct lineages to collapse into a single lineage with an admixed mosaic genome. Most known cases of such 'speciation reversal' or 'lineage fusion' involve recently diverged lineages and anthropogenic perturbation. Here, we show that in western North America, Common Ravens (Corvus corax) have admixed mosaic genomes formed by the fusion of non-sister lineages ('California' and 'Holarctic') that diverged ~1.5 million years ago. Phylogenomic analyses and concordant patterns of geographic structuring in mtDNA, genome-wide SNPs and nuclear introns demonstrate long-term admixture and random interbreeding between the non-sister lineages. In contrast, our genomic data support reproductive isolation between Common Ravens and Chihuahuan Ravens (C. cryptoleucus) despite extensive geographic overlap and a sister relationship between Chihuahuan Ravens and the California lineage. These data suggest that the Common Raven genome was formed by secondary lineage fusion and most likely represents a case of ancient speciation reversal that occurred without anthropogenic causes.
Collapse
Affiliation(s)
- Anna M Kearns
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway.
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, 20013-7012, DC, USA.
| | - Marco Restani
- Department of Biological Sciences, St. Cloud State University, 720 Fourth Avenue, St. Cloud, MN, 56301-4498, USA
| | - Ildiko Szabo
- Cowan Tetrapod Collection, Beaty Biodiversity Museum, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | | | - Jin Ah Kim
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Hayley M Richardson
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - John M Marzluff
- School of Environmental and Forest Sciences, University of Washington, Box 352100, Seattle, WA, 98195, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, 20013-7012, DC, USA
| | - Arild Johnsen
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway
| | - Kevin E Omland
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| |
Collapse
|
39
|
Titcomb G, Allan BF, Ainsworth T, Henson L, Hedlund T, Pringle RM, Palmer TM, Njoroge L, Campana MG, Fleischer RC, Mantas JN, Young HS. Interacting effects of wildlife loss and climate on ticks and tick-borne disease. Proc Biol Sci 2018; 284:rspb.2017.0475. [PMID: 28878055 DOI: 10.1098/rspb.2017.0475] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/24/2017] [Indexed: 01/18/2023] Open
Abstract
Both large-wildlife loss and climatic changes can independently influence the prevalence and distribution of zoonotic disease. Given growing evidence that wildlife loss often has stronger community-level effects in low-productivity areas, we hypothesized that these perturbations would have interactive effects on disease risk. We experimentally tested this hypothesis by measuring tick abundance and the prevalence of tick-borne pathogens (Coxiella burnetii and Rickettsia spp.) within long-term, size-selective, large-herbivore exclosures replicated across a precipitation gradient in East Africa. Total wildlife exclusion increased total tick abundance by 130% (mesic sites) to 225% (dry, low-productivity sites), demonstrating a significant interaction of defaunation and aridity on tick abundance. When differing degrees of exclusion were tested for a subset of months, total tick abundance increased from 170% (only mega-herbivores excluded) to 360% (all large wildlife excluded). Wildlife exclusion differentially affected the abundance of the three dominant tick species, and this effect varied strongly over time, likely due to differences among species in their host associations, seasonality, and other ecological characteristics. Pathogen prevalence did not differ across wildlife exclusion treatments, rainfall levels, or tick species, suggesting that exposure risk will respond to defaunation and climate change in proportion to total tick abundance. These findings demonstrate interacting effects of defaunation and aridity that increase disease risk, and they highlight the need to incorporate ecological context when predicting effects of wildlife loss on zoonotic disease dynamics.
Collapse
Affiliation(s)
- Georgia Titcomb
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA .,Mpala Research Centre, Box 555, Nanyuki, Kenya
| | - Brian F Allan
- Mpala Research Centre, Box 555, Nanyuki, Kenya.,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tyler Ainsworth
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Lauren Henson
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | - Tyler Hedlund
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Robert M Pringle
- Mpala Research Centre, Box 555, Nanyuki, Kenya.,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Todd M Palmer
- Mpala Research Centre, Box 555, Nanyuki, Kenya.,Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Laban Njoroge
- Invertebrate Zoology Section, National Museums of Kenya, Nairobi, Kenya
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | | | - Hillary S Young
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA.,Mpala Research Centre, Box 555, Nanyuki, Kenya
| |
Collapse
|
40
|
Pagenkopp Lohan KM, Hill-Spanik KM, Torchin ME, Fleischer RC, Carnegie RB, Reece KS, Ruiz GM. Phylogeography and connectivity of molluscan parasites: Perkinsus spp. in Panama and beyond. Int J Parasitol 2018; 48:135-144. [DOI: 10.1016/j.ijpara.2017.08.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/31/2017] [Accepted: 08/05/2017] [Indexed: 11/16/2022]
|
41
|
Kaiser SA, Martin TE, Oteyza JC, Armstad C, Fleischer RC. Direct fitness benefits and kinship of social foraging groups in an Old World tropical babbler. Behav Ecol 2018. [DOI: 10.1093/beheco/arx196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Sara A Kaiser
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Science Building, National Zoological Park, 3001 Connecticut Avenue NW., Washington, DC, USA
| | - Thomas E Martin
- U. S. Geological Survey, Montana Cooperative Wildlife Research Unit, University of Montana, Natural Sciences Room 205, Missoula, USA, Missoula, MT, USA
| | - Juan C Oteyza
- Montana Cooperative Wildlife Research Unit, University of Montana, MT, USA
| | - Connor Armstad
- Montana Cooperative Wildlife Research Unit, University of Montana, MT, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Science Building, National Zoological Park, 3001 Connecticut Avenue NW., Washington, DC, USA
| |
Collapse
|
42
|
Mulder KP, Cortazar-Chinarro M, Harris DJ, Crottini A, Campbell Grant EH, Fleischer RC, Savage AE. Evolutionary dynamics of an expressed MHC class IIβ locus in the Ranidae (Anura) uncovered by genome walking and high-throughput amplicon sequencing. Dev Comp Immunol 2017; 76:177-188. [PMID: 28587861 DOI: 10.1016/j.dci.2017.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 06/07/2023]
Abstract
The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and disease resistance. Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class IIβ chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a range of anuran taxa.
Collapse
Affiliation(s)
- Kevin P Mulder
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA; CIBIO/InBIO, Research Centre in Biodiversity and Genetic Resources, Rua Padre Armando Quintas 7, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Maria Cortazar-Chinarro
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - D James Harris
- CIBIO/InBIO, Research Centre in Biodiversity and Genetic Resources, Rua Padre Armando Quintas 7, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Angelica Crottini
- CIBIO/InBIO, Research Centre in Biodiversity and Genetic Resources, Rua Padre Armando Quintas 7, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Evan H Campbell Grant
- United States Geological Survey, Patuxent Wildlife Research Center, SO Conte Anadromous Fish Research Lab, 1 Migratory Way, Turner Falls, MA 01376, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA
| | - Anna E Savage
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA; Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA.
| |
Collapse
|
43
|
Loiseau C, Melo M, Lobato E, Beadell JS, Fleischer RC, Reis S, Doutrelant C, Covas R. Insularity effects on the assemblage of the blood parasite community of the birds from the Gulf of Guinea. J Biogeogr 2017; 44:2607-2617. [PMID: 29104347 PMCID: PMC5663302 DOI: 10.1111/jbi.13060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
AIM Lower species diversity, increased population densities and ecological niche enlargement are common characteristics of island faunas. However it remains to be determined if they extend to the parasite community. We tested if Haemosporidia parasite pressure varies between islands and the mainland with two different levels of analysis: i) at the host community level, and ii) with paired-species comparisons between islands and the mainland. LOCATION Gulf of Guinea, West Africa. METHODS We used molecular-based methods to identify avian Haemosporidian parasites (Plasmodium, Haemoproteus and Leucocytozoon) to describe their diversity, prevalence, host specificity and their phylogenetic relationships in five islands of the Gulf of Guinea and in nearby mainland areas. RESULTS We found reduced Haemosporidia diversity on islands for Haemoproteus and Leucocytozoon, but not for Plasmodium. In addition, lower parasite prevalence on islands was found using a paired-species approach. Although the mean host specificity of the parasite community on islands did not differ from the mainland, we found a very distinct parasite species assemblage on the islands, which was composed of both the most generalist and the most specialist lineages. MAIN CONCLUSIONS This study supports the hypothesis that parasite pressure is reduced on islands. Colonization is made by generalists with high host switching capacities, with some subsequently evolving into highly specialised parasites. This suggests that 'taxon cycle' dynamics may explain the assemblage of insular parasite communities.
Collapse
Affiliation(s)
- Claire Loiseau
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto. Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- Biology Department, Science Faculty, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- CEFE-CNRS, 1919 Route de Mende, 34293 Montpellier, France
| | - Martim Melo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto. Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- Percy Fitzpatrick Institute, DST/NRF Centre of Excellence, University of Cape Town, South Africa
| | - Elisa Lobato
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto. Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- CEFE-CNRS, 1919 Route de Mende, 34293 Montpellier, France
| | - Jon S Beadell
- Center for Conservation Genomics, National Zoological Park, Smithsonian Institution, 3001 Connecticut Ave., NW, Washington, DC 20008 USA
| | - Robert C Fleischer
- Center for Conservation Genomics, National Zoological Park, Smithsonian Institution, 3001 Connecticut Ave., NW, Washington, DC 20008 USA
| | - Sandra Reis
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto. Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | | | - Rita Covas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto. Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- Biology Department, Science Faculty, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Percy Fitzpatrick Institute, DST/NRF Centre of Excellence, University of Cape Town, South Africa
| |
Collapse
|
44
|
Klocke B, Becker M, Lewis J, Fleischer RC, Muletz-Wolz CR, Rockwood L, Aguirre AA, Gratwicke B. Batrachochytrium salamandrivorans not detected in U.S. survey of pet salamanders. Sci Rep 2017; 7:13132. [PMID: 29030586 PMCID: PMC5640657 DOI: 10.1038/s41598-017-13500-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/25/2017] [Indexed: 02/01/2023] Open
Abstract
We engaged pet salamander owners in the United States to screen their animals for two amphibian chytrid fungal pathogens Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal). We provided pet owners with a sampling kit and instructional video to swab the skin of their animals. We received 639 salamander samples from 65 species by mail, and tested them for Bd and Bsal using qPCR. We detected Bd on 1.3% of salamanders (95% CI 0.0053–0.0267) and did not detect Bsal (95% CI 0.0000–0.0071). If Bsal is present in the U.S. population of pet salamanders, it occurs at a very low prevalence. The United States Fish and Wildlife Service listed 201 species of salamanders as “injurious wildlife” under the Lacey Act (18 U.S.C. § 42) on January 28, 2016, a precautionary action to prevent the introduction of Bsal to the U.S. through the importation of salamanders. This action reduced the number of salamanders imported to the U.S. from 2015 to 2016 by 98.4%. Our results indicate that continued precautions should be taken to prevent the introduction and establishment of Bsal in the U.S., which is a hotspot of salamander biodiversity.
Collapse
Affiliation(s)
- Blake Klocke
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, 22030, United States of America. .,Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, United States of America. .,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, United States of America.
| | - Matthew Becker
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, United States of America.,Department of Biology and Chemistry, Liberty University, Lynchburg, Virginia, 24515, United States of America
| | - James Lewis
- Rainforest Trust, Warrenton, VA, 20187, United States of America
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, United States of America
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, United States of America
| | - Larry Rockwood
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, 22030, United States of America.,Department of Biology, George Mason University, Fairfax, Virginia, 22030, United States of America
| | - A Alonso Aguirre
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, 22030, United States of America
| | - Brian Gratwicke
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, United States of America
| |
Collapse
|
45
|
Muletz Wolz CR, Yarwood SA, Campbell Grant EH, Fleischer RC, Lips KR. Effects of host species and environment on the skin microbiome of Plethodontid salamanders. J Anim Ecol 2017; 87:341-353. [DOI: 10.1111/1365-2656.12726] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/08/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Carly R. Muletz Wolz
- Department of Biology; University of Maryland; College Park MD USA
- Center for Conservation Genomics; Smithsonian Conservation Biology Institute; National Zoological Park; Washington DC USA
| | - Stephanie A. Yarwood
- Department of Environmental Science & Technology; University of Maryland; College Park MD USA
| | - Evan H. Campbell Grant
- S.O. Conte Anadromous Fish Research Laboratory; United States Geological Survey Patuxent Wildlife Research Center; Turners Falls MA USA
| | - Robert C. Fleischer
- Center for Conservation Genomics; Smithsonian Conservation Biology Institute; National Zoological Park; Washington DC USA
| | - Karen R. Lips
- Department of Biology; University of Maryland; College Park MD USA
| |
Collapse
|
46
|
Fleischer RC, Rothstein SI. KNOWN SECONDARY CONTACT AND RAPID GENE FLOW AMONG SUBSPECIES AND DIALECTS IN THE BROWN-HEADED COWBIRD. Evolution 2017; 42:1146-1158. [PMID: 28581081 DOI: 10.1111/j.1558-5646.1988.tb04175.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/1987] [Accepted: 05/04/1988] [Indexed: 11/27/2022]
Abstract
We analyze geographic variation in morphology for Sierra Nevadan populations of Brown-headed Cowbirds (Molothrus ater) in relation to two levels of geographic structure of populations: 1) subspecies and 2) vocal dialects. Two morphologically distinct subspecies occupy opposite slopes of the Sierra Nevada: M. a artemisiae on the east slope is larger than M. a. obscurus on the west slope, and its juveniles have predominantly white versus yellow rictal (bill) flanges. Populations of obscurus moved into California from the lower Colorado River around 1900 and invaded the western Sierra during the 1930's. A relatively constant type of flight whistle occurs in obscurus populations up to 700 km apart, but east-slope artemisiae are divided into many distinct dialects. The means of seven morphological measurements and of principal component 1 (i.e., body size) for 2,287 individuals show similar clinal patterns for adult males, yearling males, and females over a 60-km north-south transect along the eastern Sierra Nevada: large sizes occur at the southernmost study site at Bishop, decrease clinally to the north to Mammoth Lakes, and then increase clinally to the north from Mammoth Lakes to the northernmost site at Lee Vining. This reversal in cline slope is reiterated for variation in the frequency of white-flanged juveniles. Our data do not support adaptive explanations for the clines. Rather, the most parsimonious explanation is that there has been flow of obscurus genes into artemisiae from the west slope across the crest of the Sierra Nevada into the Mammoth Lakes area. Concordantly, the Sierran crest at Mammoth Lakes is considerably lower than any other point within about 80 km to the north or 180 km to the south. Two other findings strongly support this interpretation. First, wing lengths of our longest-winged samples (at Bishop and Lee Vining) are significantly shorter than those of cowbirds collected in the same region between 1912 and 1922. Second, the wing lengths of Mammoth Lakes adult males and females during 1978-1981 are significantly larger than those of the 1982-1985 period. This putative hybridization must have been rapid, as there have been fewer than 50 years since secondary contact could have occurred. Calculation of the gene-flow parameter Ι of Endler (1977) indicates that the gene-flow rate reported here is higher than for nearly all of the species he surveyed. This gene flow occurs between two subspecies with different flight whistles and across several cowbird flight-whistle dialects within artemisiae. Therefore, vocal differences among these dialects do not appear to be a strong deterrent to gene flow.
Collapse
Affiliation(s)
- Robert C Fleischer
- Department of Biology, University of North Dakota, Grand Forks, ND, 58202-8238
| | - Stephen I Rothstein
- Department of Biological Sciences, University of California, Santa Barbara, CA, 93106
| |
Collapse
|
47
|
Pagenkopp Lohan KM, Fleischer RC, Carney KJ, Holzer KK, Ruiz GM. Inside Front Cover, Volume 23 Issue 6. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12599] [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: 12/01/2022] Open
|
48
|
Fleischer RC. A COMPARISON OF THEORETICAL AND ELECTROPHORETIC ASSESSMENTS OF GENETIC STRUCTURE IN POPULATIONS OF THE HOUSE SPARROW (PASSER DOMESTICUS). Evolution 2017; 37:1001-1009. [PMID: 28563548 DOI: 10.1111/j.1558-5646.1983.tb05628.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/1981] [Revised: 09/30/1982] [Indexed: 11/30/2022]
Affiliation(s)
- Robert C Fleischer
- Museum of Natural History, University of Kansas, Lawrence, Kansas, 66045
| |
Collapse
|
49
|
Good SV, Williams DF, Ralls K, Fleischer RC. POPULATION STRUCTURE OFDIPODOMYS INGENS(HETEROMYIDAE): THE ROLE OF SPATIAL HETEROGENEITY IN MAINTAINING GENETIC DIVERSITY. Evolution 2017; 51:1296-1310. [DOI: 10.1111/j.1558-5646.1997.tb03976.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/1996] [Accepted: 03/28/1997] [Indexed: 11/27/2022]
Affiliation(s)
- Sara V. Good
- Department of Biology and Molecular Evolutionary Genetics; Pennsylvania State University; University Park Pennsylvania 16802
| | - Daniel F. Williams
- San Joaquin Valley Endangered Species Recovery Planning Program; 1900 North Gateway Boulevard, Suite 101 Fresno California 93727
| | - Katherine Ralls
- Department of Zoological Research, National Zoological Park; Smithsonian Institution; Washington DC 20008
| | - Robert C. Fleischer
- Department of Zoological Research, National Zoological Park; Smithsonian Institution; Washington DC 20008
| |
Collapse
|
50
|
Danner JE, Fleischer RC, Danner RM, Moore IT. Genetic population structure in an equatorial sparrow: roles for culture and geography. J Evol Biol 2017; 30:1078-1093. [PMID: 28294451 DOI: 10.1111/jeb.13065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 11/29/2022]
Abstract
Female preference for local cultural traits has been proposed as a barrier to breeding among animal populations. As such, several studies have found correlations between male bird song dialects and population genetics over relatively large distances. To investigate whether female choice for local dialects could act as a barrier to breeding between nearby and contiguous populations, we tested whether variation in male song dialects explains genetic structure among eight populations of rufous-collared sparrows (Zonotrichia capensis) in Ecuador. Our study sites lay along a transect, and adjacent study sites were separated by approximately 25 km, an order of magnitude less than previously examined for this and most other species. This transect crossed an Andean ridge and through the Quijos River Valley, both of which may be barriers to gene flow. Using a variance partitioning approach, we show that song dialect is important in explaining population genetics, independent of the geographic variables: distance, the river valley and the Andean Ridge. This result is consistent with the hypothesis that song acts as a barrier to breeding among populations in close proximity. In addition, songs of contiguous populations differed by the same degree or more than between two populations previously shown to exhibit female preference for local dialect, suggesting that birds from these populations would also breed preferentially with locals. As expected, all geographic variables (distance, the river valley and the Andean Ridge) also predicted population genetic structure. Our results have important implications for the understanding whether, and at what spatial scale, culture can affect population divergence.
Collapse
Affiliation(s)
- J E Danner
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, Washington, DC, USA.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - R C Fleischer
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - R M Danner
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - I T Moore
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| |
Collapse
|