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Article: Disentangling drivers of thermal physiology: Community‐wide cold shock recovery of butterflies under natural conditions

Khazan, Emily S. / Haggard, Jaime / Ríos‐Málaver, Indiana Cristobal / Shirk, Philip / Scheffers, Brett R.

Biotropica. 2022 Jan., v. 54, no. 1

2022

Abstract: Physiological strategies of terrestrial ectotherms are a delicate interplay between species’ traits and their physical environment. Several theories and overarching hypotheses seek to explain strategies related to thermal physiology with respect to ... ...

Abstract	Physiological strategies of terrestrial ectotherms are a delicate interplay between species’ traits and their physical environment. Several theories and overarching hypotheses seek to explain strategies related to thermal physiology with respect to organisms and their environments. However, most of these have been investigated under controlled laboratory conditions with lab‐reared or otherwise acclimated individuals, removing the effect of environmental acclimation. This study examines an in‐situ physiological trait, cold shock recovery, across butterfly communities of the Colombian Andes from different environments, elevations, and ambient conditions. We explored four non‐mutually exclusive hypotheses—1) intrinsic (species) traits dictate response hypothesis; 2) extrinsic (environmental) traits dictate response hypothesis; 3) climate variability hypothesis; 4) thermal melanism hypothesis—to explain cold shock recovery of wild‐caught butterflies from high (1800 m.a.s.l) and low (600 m.a.s.l.) elevations in two habitat types (open and closed canopy). Cold shock recovery was measured as the time following a cold shock to full recovery, that is, flight. Ambient conditions and the thermal melanism hypothesis, which posits an interaction between pigmentation and solar intensity, best explained cold‐shock recovery. Higher temperatures and light exposure reduced recovery time. Dark butterflies under high solar intensity recovered from cold shock faster than light butterflies or those under low solar intensity regardless of species identity, morphology, or habitat characteristics. These results highlight the importance of ambient conditions and the interaction between pigmentation of tropical ectotherms and their physical thermal environments, patterns that may render populations vulnerable to the thermal impacts of climate change and development. Abstract in Spanish is available with online material.
Keywords	acclimation ; butterflies ; canopy ; climate ; climate change ; cold stress ; ectothermy ; flight ; habitats ; laboratory rearing ; melanosis ; pigmentation ; Andes region
Language	English
Dates of publication	2022-01
Size	p. 205-214.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2052061-X
ISSN	1744-7429 ; 0006-3606
ISSN (online)	1744-7429
ISSN	0006-3606
DOI	10.1111/btp.13046
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Early Estimates of Updated 2023-2024 (Monovalent XBB.1.5) COVID-19 Vaccine Effectiveness Against Symptomatic SARS-CoV-2 Infection Attributable to Co-Circulating Omicron Variants Among Immunocompetent Adults - Increasing Community Access to Testing Program, United States, September 2023-January 2024.

Link-Gelles, Ruth / Ciesla, Allison Avrich / Mak, Josephine / Miller, Joseph D / Silk, Benjamin J / Lambrou, Anastasia S / Paden, Clinton R / Shirk, Philip / Britton, Amadea / Smith, Zachary R / Fleming-Dutra, Katherine E

MMWR. Morbidity and mortality weekly report

2024 Volume 73, Issue 4, Page(s) 77–83

Abstract: On September 12, 2023, CDC's Advisory Committee on Immunization Practices recommended updated 2023-2024 (updated) COVID-19 vaccination with a monovalent XBB.1.5-derived vaccine for all persons aged ≥6 months to prevent COVID-19, including severe disease. ...

Abstract	On September 12, 2023, CDC's Advisory Committee on Immunization Practices recommended updated 2023-2024 (updated) COVID-19 vaccination with a monovalent XBB.1.5-derived vaccine for all persons aged ≥6 months to prevent COVID-19, including severe disease. During fall 2023, XBB lineages co-circulated with JN.1, an Omicron BA.2.86 lineage that emerged in September 2023. These variants have amino acid substitutions that might increase escape from neutralizing antibodies. XBB lineages predominated through December 2023, when JN.1 became predominant in the United States. Reduction or failure of spike gene (S-gene) amplification (i.e., S-gene target failure [SGTF]) in real-time reverse transcription-polymerase chain reaction testing is a time-dependent, proxy indicator of JN.1 infection. Data from the Increasing Community Access to Testing SARS-CoV-2 pharmacy testing program were analyzed to estimate updated COVID-19 vaccine effectiveness (VE) (i.e., receipt versus no receipt of updated vaccination) against symptomatic SARS-CoV-2 infection, including by SGTF result. Among 9,222 total eligible tests, overall VE among adults aged ≥18 years was 54% (95% CI = 46%-60%) at a median of 52 days after vaccination. Among 2,199 tests performed at a laboratory with SGTF testing, VE 60-119 days after vaccination was 49% (95% CI = 19%-68%) among tests exhibiting SGTF and 60% (95% CI = 35%-75%) among tests without SGTF. Updated COVID-19 vaccines provide protection against symptomatic infection, including against currently circulating lineages. CDC will continue monitoring VE, including for expected waning and against severe disease. All persons aged ≥6 months should receive an updated COVID-19 vaccine dose.
MeSH term(s)	United States/epidemiology ; Adult ; Humans ; Adolescent ; COVID-19 Vaccines ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/prevention & control ; Vaccine Efficacy ; SARS-CoV-2
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2024-02-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	412775-4
ISSN	1545-861X ; 0149-2195
ISSN (online)	1545-861X
ISSN	0149-2195
DOI	10.15585/mmwr.mm7304a2
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Article ; Online: Spike Gene Target Amplification in a Diagnostic Assay as a Marker for Public Health Monitoring of Emerging SARS-CoV-2 Variants - United States, November 2021-January 2023.

Scobie, Heather M / Ali, Akilah R / Shirk, Philip / Smith, Zachary R / Paul, Prabasaj / Paden, Clinton R / Hassell, Norman / Zheng, Xiao-Yu / Lambrou, Anastasia S / Kondor, Rebecca / MacCannell, Duncan / Thornburg, Natalie J / Miller, Joseph / Wentworth, Dave / Silk, Benjamin J

MMWR. Morbidity and mortality weekly report

2023 Volume 72, Issue 5, Page(s) 125–127

Abstract: Monitoring emerging SARS-CoV-2 lineages and their epidemiologic characteristics helps to inform public health decisions regarding vaccine policy, the use of therapeutics, and health care capacity. When the SARS-CoV-2 Alpha variant emerged in late 2020, a ...

Abstract	Monitoring emerging SARS-CoV-2 lineages and their epidemiologic characteristics helps to inform public health decisions regarding vaccine policy, the use of therapeutics, and health care capacity. When the SARS-CoV-2 Alpha variant emerged in late 2020, a spike gene (S-gene) deletion (Δ69-70) in the N-terminal region, which might compensate for immune escape mutations that impair infectivity (1), resulted in reduced or failed S-gene target amplification in certain multitarget reverse transcription-polymerase chain reaction (RT-PCR) assays, a pattern referred to as S-gene target failure (SGTF) (2). The predominant U.S. SARS-CoV-2 lineages have generally alternated between SGTF and S-gene target presence (SGTP), which alongside genomic sequencing, has facilitated early monitoring of emerging variants. During a period when Omicron BA.5-related sublineages (which exhibit SGTF) predominated, an XBB.1.5 sublineage with SGTP has rapidly expanded in the northeastern United States and other regions.
MeSH term(s)	United States/epidemiology ; Humans ; Public Health ; SARS-CoV-2/genetics ; COVID-19/epidemiology ; Mutation ; COVID-19 Testing
Language	English
Publishing date	2023-02-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	412775-4
ISSN	1545-861X ; 0149-2195
ISSN (online)	1545-861X
ISSN	0149-2195
DOI	10.15585/mmwr.mm7205e2
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Article ; Online: Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron Lineages - United States, January 2022-May 2023.

Ma, Kevin C / Shirk, Philip / Lambrou, Anastasia S / Hassell, Norman / Zheng, Xiao-Yu / Payne, Amanda B / Ali, Akilah R / Batra, Dhwani / Caravas, Jason / Chau, Reina / Cook, Peter W / Howard, Dakota / Kovacs, Nicholas A / Lacek, Kristine A / Lee, Justin S / MacCannell, Duncan R / Malapati, Lakshmi / Mathew, Sandra / Mittal, Neha /

Nagilla, Roopa R / Parikh, Rishika / Paul, Prabasaj / Rambo-Martin, Benjamin L / Shepard, Samuel S / Sheth, Mili / Wentworth, David E / Winn, Amber / Hall, Aron J / Silk, Benjamin J / Thornburg, Natalie / Kondor, Rebecca / Scobie, Heather M / Paden, Clinton R

MMWR. Morbidity and mortality weekly report

2023 Volume 72, Issue 24, Page(s) 651–656

Abstract: CDC has used national genomic surveillance since December 2020 to monitor SARS-CoV-2 variants that have emerged throughout the COVID-19 pandemic, including the Omicron variant. This report summarizes U.S. trends in variant proportions from national ... ...

Abstract	CDC has used national genomic surveillance since December 2020 to monitor SARS-CoV-2 variants that have emerged throughout the COVID-19 pandemic, including the Omicron variant. This report summarizes U.S. trends in variant proportions from national genomic surveillance during January 2022-May 2023. During this period, the Omicron variant remained predominant, with various descendant lineages reaching national predominance (>50% prevalence). During the first half of 2022, BA.1.1 reached predominance by the week ending January 8, 2022, followed by BA.2 (March 26), BA.2.12.1 (May 14), and BA.5 (July 2); the predominance of each variant coincided with surges in COVID-19 cases. The latter half of 2022 was characterized by the circulation of sublineages of BA.2, BA.4, and BA.5 (e.g., BQ.1 and BQ.1.1), some of which independently acquired similar spike protein substitutions associated with immune evasion. By the end of January 2023, XBB.1.5 became predominant. As of May 13, 2023, the most common circulating lineages were XBB.1.5 (61.5%), XBB.1.9.1 (10.0%), and XBB.1.16 (9.4%); XBB.1.16 and XBB.1.16.1 (2.4%), containing the K478R substitution, and XBB.2.3 (3.2%), containing the P521S substitution, had the fastest doubling times at that point. Analytic methods for estimating variant proportions have been updated as the availability of sequencing specimens has declined. The continued evolution of Omicron lineages highlights the importance of genomic surveillance to monitor emerging variants and help guide vaccine development and use of therapeutics.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Pandemics ; COVID-19/epidemiology ; Genomics
Language	English
Publishing date	2023-06-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	412775-4
ISSN	1545-861X ; 0149-2195
ISSN (online)	1545-861X
ISSN	0149-2195
DOI	10.15585/mmwr.mm7224a2
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Article: Impact of habitat alteration on endemic Afromontane chameleons: evidence for historical population declines using hierarchical spatial modelling

Shirk, Philip L / Linden, Daniel W / Patrick, David A / Howell, Kim M / Harper, Elizabeth B / Vonesh, James R / Fitzpatrick, Matthew

Diversity & distributions. 2014 Oct., v. 20, no. 10

2014

Abstract: AIM: We map estimated historical population declines resulting from species‐specific models of sensitivity to habitat fragmentation for three forest‐dependent chameleons. LOCATION: East Usambara Mountains, Eastern Arc Mountains, Tanzania. METHODS: We ... ...

Abstract	AIM: We map estimated historical population declines resulting from species‐specific models of sensitivity to habitat fragmentation for three forest‐dependent chameleons. LOCATION: East Usambara Mountains, Eastern Arc Mountains, Tanzania. METHODS: We surveyed three chameleon species (Rhampholeon spinosus, Rhampholeon temporalis and Trioceros deremensis) along 32.2� km of transects and used a hierarchical, distance‐sampling model to estimate densities. The model included habitat characteristics at the landscape (patch) and local (transect) scales while accounting for detectability. By analysing the model in a Bayesian framework, we were able to propagate error through the entire analysis and obtain exact solutions despite small sample sizes. We then used our estimated relationships between habitat and density to project chameleon population sizes across current and historical land cover maps of the study area (230� km²), giving an estimate of the impact of anthropogenic habitat alteration on these species. RESULTS: Species’ densities increased in larger patches and further from patch edges and varied seasonally. Local vegetation characteristics had significant relationships with expected chameleon densities, though effect sizes were small. Estimates of total current population sizes varied by two orders of magnitude among species, but each was 49–79% higher than detection‐naïve estimates. All three declined from estimated historical levels by approximately 60% in the study area, approximately one‐third more than would be expected from forest loss alone. Remaining populations of the study species are predominantly located in protected nature reserves, so the future of these species will likely be determined by the degree of protection offered by the nature reserves. MAIN CONCLUSIONS: Habitat loss and fragmentation have greatly reduced forest‐dependent chameleon population sizes in the East Usambara Mountains. Populations of these species in other areas are experiencing higher rates of habitat loss. Efforts aimed at ensuring the efficacy of protected forests may be a key to conserving remaining populations.
Keywords	Chamaeleonidae ; anthropogenic activities ; conservation areas ; forests ; habitat destruction ; habitat fragmentation ; habitats ; land cover ; landscapes ; models ; mountains ; population dynamics ; population size ; Tanzania
Language	English
Dates of publication	2014-10
Size	p. 1186-1199.
Publishing place	Blackwell Science
Document type	Article
ZDB-ID	2020139-4
ISSN	1366-9516 ; 1472-4642
ISSN (online)	1366-9516
ISSN	1472-4642
DOI	10.1111/ddi.12239
Database	NAL-Catalogue (AGRICOLA)

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Article: Globally Threatened Biodiversity of the Eastern Arc Mountains and Coastal Forests of Kenya and Tanzania

Gereau, Roy E / Cumberlidge Neil / Hemp Claudia / Hochkirch Axel / Jones Trevor / Kariuki Mercy / Lange Charles N / Loader Simon P / Malonza Patrick K / Menegon Michele / Ndang'ang'a P. Kariuki / Rovero Francesco / Shirk Philip

Journal of East African natural history. 2016 Mar., v. 105, no. 1

2016

Abstract: We present an account of the 909 globally threatened taxa (793 species, 74 subspecies, 42 varieties) of animals and plants in the Eastern Arc Mountains and Coastal Forests of Kenya and Tanzania and the sites in which they occur based upon a review of the ...

Abstract	We present an account of the 909 globally threatened taxa (793 species, 74 subspecies, 42 varieties) of animals and plants in the Eastern Arc Mountains and Coastal Forests of Kenya and Tanzania and the sites in which they occur based upon a review of the 2015 IUCN Red List of Threatened Species. Results for animals are summarised by Class (Amphibia, Aves, Gastropoda, Insecta, Malacostraca, Mammalia, Reptilia) and presented for plants as a whole (Classes Bryopsida, Cycadopsida, Jungermanniopsida, Liliopsida, Lycopodiopsida, Magnoliopsida, Pinopsida, Polypodiopsida). We analyse the status of previously known and newly identified sites in which globally threatened biodiversity occurs and summarise the current state of research on the globally threatened and ecologically critical biodiversity of the EACF. We then provide recommendations for future research, environmental regulations, and management regimes based upon comprehensive and reliable data to ensure the continued survival of the EACF's biodiversity within the context of sustainable resource utilisation.
Keywords	Amphibia ; animals ; Aves ; biodiversity ; Bryopsida ; coastal forests ; Cycadopsida ; environmental law ; Gastropoda ; Insecta ; Jungermanniopsida ; Liliopsida ; Lycopodiopsida ; Magnoliopsida ; Malacostraca ; Mammalia ; mountains ; Pinopsida ; plants (botany) ; Polypodiopsida ; Reptilia ; threatened species ; Kenya ; Tanzania
Language	English
Dates of publication	2016-03
Size	p. 115-201.
Publishing place	Nature Kenya
Document type	Article
DOI	10.2982/028.105.0104
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants - United States, June 2021-January 2022.

Lambrou, Anastasia S / Shirk, Philip / Steele, Molly K / Paul, Prabasaj / Paden, Clinton R / Cadwell, Betsy / Reese, Heather E / Aoki, Yutaka / Hassell, Norman / Zheng, Xiao-Yu / Talarico, Sarah / Chen, Jessica C / Oberste, M Steven / Batra, Dhwani / McMullan, Laura K / Halpin, Alison Laufer / Galloway, Summer E / MacCannell, Duncan R / Kondor, Rebecca /

Barnes, John / MacNeil, Adam / Silk, Benjamin J / Dugan, Vivien G / Scobie, Heather M / Wentworth, David E / Caravas, Jason / Kovacs, Nicholas A / Gerhart, Jonathan G / Jia Ng, Han / Beck, Andrew / Chau, Reina / Cintron, Roxana / Cook, Peter W / Gulvik, Christopher A / Howard, Dakota / Jang, Yunho / Knipe, Kristen / Lacek, Kristine A / Moser, Kara A / Paskey, Adrian C / Rambo-Martin, Benjamin L / Nagilla, Roopa R / Retchless, Adam C / Schmerer, Matthew W / Seby, Sandra / Shepard, Samuel S / Stanton, Richard A / Stark, Thomas J / Uehara, Anna / Unoarumhi, Yvette / Bentz, Meghan L / Burgin, Alex / Burroughs, Mark / Davis, Morgan L / Keller, Matthew W / Keong, Lisa M / Le, Shoshona S / Lee, Justin S / Madden Jr, Joseph C / Nobles, Sarah / Owuor, D. Collins / Padilla, Jasmine / Sheth, Mili / Wilson, Malania M

MMWR. Morbidity and mortality weekly report

2022 Volume 71, Issue 6, Page(s) 206–211

Abstract: Genomic surveillance is a critical tool for tracking emerging variants of SARS-CoV-2 (the virus that causes COVID-19), which can exhibit characteristics that potentially affect public health and clinical interventions, including increased ... ...

Abstract	Genomic surveillance is a critical tool for tracking emerging variants of SARS-CoV-2 (the virus that causes COVID-19), which can exhibit characteristics that potentially affect public health and clinical interventions, including increased transmissibility, illness severity, and capacity for immune escape. During June 2021-January 2022, CDC expanded genomic surveillance data sources to incorporate sequence data from public repositories to produce weighted estimates of variant proportions at the jurisdiction level and refined analytic methods to enhance the timeliness and accuracy of national and regional variant proportion estimates. These changes also allowed for more comprehensive variant proportion estimation at the jurisdictional level (i.e., U.S. state, district, territory, and freely associated state). The data in this report are a summary of findings of recent proportions of circulating variants that are updated weekly on CDC's COVID Data Tracker website to enable timely public health action.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/virology ; Centers for Disease Control and Prevention, U.S. ; Genomics ; Humans ; Prevalence ; Public Health Surveillance/methods ; SARS-CoV-2/genetics ; United States/epidemiology
Language	English
Publishing date	2022-02-11
Publishing country	United States
Document type	Technical Report
ZDB-ID	412775-4
ISSN	1545-861X ; 0149-2195
ISSN (online)	1545-861X
ISSN	0149-2195
DOI	10.15585/mmwr.mm7106a4
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Article: Disentangling drivers of thermal physiology: Community‐wide cold shock recovery of butterflies under natural conditions

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Article ; Online: Spike Gene Target Amplification in a Diagnostic Assay as a Marker for Public Health Monitoring of Emerging SARS-CoV-2 Variants - United States, November 2021-January 2023.

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Article ; Online: Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron Lineages - United States, January 2022-May 2023.

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Article: Impact of habitat alteration on endemic Afromontane chameleons: evidence for historical population declines using hierarchical spatial modelling

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Article: Globally Threatened Biodiversity of the Eastern Arc Mountains and Coastal Forests of Kenya and Tanzania

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Article ; Online: Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants - United States, June 2021-January 2022.

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