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Publication Metadata only Author Correction: urbanization, climate and species traits shape mammal communities from local to continental scales(Nature Portfolio, 2024) Haight JD, Hall SJ, Fidino M, Adalsteinsson SA, Ahlers AA, Angstmann J, Anthonysamy WJB, Biro E, Collins MK, Dugelby B, Gallo T, Green AM, Hartley L, Jordan MJ, Kay CAM, Lehrer EW, Long RA, MacDougall B, Magle SB, Minier DE, Mowry C, Murray M, Nininger K, Pendergast ME, Remine KR, Ryan T, Salsbury C, Sander HA, Schell CJ, Shier CJ, Simon KC, St Clair CC, Stankowich T, Stevenson CJ, Wayne L, Will D, Williamson J, Wilson L, Zellmer AJ, Lewis JS.; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Department of Molecular Biology and Genetics; College of SciencesN/APublication Metadata only Avian responses to selective logging shaped by species traits and logging practices(The Royal Society, 2015) Burivalova, Zuzana; Lee, Tien Ming; Giam, Xingli; Wilcove, David S.; Koh, Lian Pin; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 327589Selective logging is one of the most common forms of forest use in the tropics. Although the effects of selective logging on biodiversity have been widely studied, there is little agreement on the relationship between life-history traits and tolerance to logging. In this study, we assessed how species traits and logging practices combine to determine species responses to selective logging, based on over 4000 observations of the responses of nearly 1000 bird species to selective logging across the tropics. Our analysis shows that species traits, such as feeding group and body mass, and logging practices, such as time since logging and logging intensity, interact to influence a species' response to logging. Frugivores and insectivores were most adversely affected by logging and declined further with increasing logging intensity. Nectarivores and granivores responded positively to selective logging for the first two decades, after which their abundances decrease below pre-logging levels. Larger species of omnivores and granivores responded more positively to selective logging than smaller species from either feeding group, whereas this effect of body size was reversed for carnivores, herbivores, frugivores and insectivores. Most importantly, species most negatively impacted by selective logging had not recovered approximately 40 years after logging cessation. We conclude that selective timber harvest has the potential to cause large and long-lasting changes in avian biodiversity. However, our results suggest that the impacts can be mitigated to a certain extent through specific forest management strategies such as Llengthening the rotation cycle and implementing reduced impact logging.Publication Open Access Existence of SARS-Cov-2 RNA on ambient particulate matter samples: a nationwide study in Turkey(Elsevier, 2021) Arı, Akif; Şahin, A. Ülkü; Gaga, O. Eftade; Kuzu, S. Levent; Arı Ertürk, Pelin; Odabaşı, Mustafa; Taşdemir, Yücel; Cindoruk, S. Sıddık; Esen, Fatma; Çalışkan, Burak; Sakin, Egemen; Tecer, H. Lokman; Fıçıcı, Merve; Altın, Ahmet; Onat, Burcu; Ayvaz, Coşkun; Uzun, Burcu; Saral, Arslan; Döğeroğlu, Tuncay; Malkoç, Semra; Üzmez, Ö. Özlem; Kunt, Fatma; Aydın, Senar; Kara, Melik; Yaman, Barış; Doğan, Güray; Olgun, Bihter; Dokumacı, N. Ebru; Güllü, Gülen; Uzunpınar, S. Elif; Kayalar, Özgecan; Konyalılar, Nur; Doğan, Özlem; Can, Füsun; Babuççu, Gizem; Bayram, Hasan; Researcher; PhD Student; Faculty Member; Faculty Member; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); School of Medicine; Graduate School of Health Sciences; N/A; N/A; 170418; 103165; N/A; 4890Coronavirus disease 2019 (COVID-19) is caused by the SARS-CoV-2 virus and has been affecting the world since the end of 2019. The disease led to significant mortality and morbidity in Turkey, since the first case was reported on March 11th, 2020. Studies suggest a positive association between air pollution and SARS-CoV-2 infection. The aim of the present study was to investigate the role of ambient particulate matters (PM), as potential carriers for SARS-CoV-2. Ambient PM samples in various size ranges were collected from 13 sites including urban and urban-background locations and hospital gardens in 10 cities across Turkey between 13th of May and 14th of June 2020 to investigate the possible presence of SARS-CoV-2 RNA on ambient PM. A total of 203 daily samples (TSP, n = 80; PM2.5, n = 33; PM2.5-10, n = 23; PM10?m, n = 19; and 6 size segregated PM, n = 48) were collected using various samplers. The N1 gene and RdRP gene expressions were analyzed for the presence of SARS-CoV-2, as suggested by the Centers for Disease Control and Prevention (CDC). According to real time (RT)-PCR and three-dimensional (3D) digital (d) PCR analysis, dual RdRP and N1 gene positivity were detected in 20 (9.8%) samples. Ambient PM-bound SARS-CoV-2 was analyzed quantitatively and the air concentrations of the virus ranged from 0.1 copies/m3 to 23 copies/m3. The highest percentages of virus detection on PM samples were from hospital gardens in Tekirdağ, Zonguldak, and Istanbul, especially in PM2.5 mode. Findings of this study have suggested that SARS-CoV-2 may be transported by ambient particles, especially at sites close to the infection hot-spots. However, whether this has an impact on the spread of the virus infection remains to be determined.Publication Metadata only Exploration behavior differs between Darwin's finch species and predicts territory defense and hatching success(Springer, 2024) Katsis, Andrew C.; Colombelli-Negrel, Diane; Common, Lauren K.; Garcia-Loor, Jefferson; Kleindorfer, Sonia; Department of Psychology; Akçay, Çağlar; Department of Psychology; College of Social Sciences and HumanitiesDarwin's finch species in the Galapagos Islands are famously distinguished by their morphology but less attention has been given to behavioral differences between species. In this study, we compared behavior between four Darwin's finch species on Floreana Island: small ground finch (Geospiza fuliginosa), medium ground finch (G. fortis), small tree finch (Camarhynchus parvulus), and medium tree finch (C. pauper). After capturing birds using mist-nets, we measured three behavioral traits: (1) boldness during human handling, (2) exploration in a novel environment, and (3) aggressiveness towards their mirror image. First, we found that ground finches were bolder and more exploratory than tree finches, consistent with their distinct ecological niches on Floreana Island and with the theoretical prediction that diet generalists should be less wary of novelty. Second, we tested the ecological validity of these behavioral variables at the individual level by relating them to territory defense behavior and breeding success. We found that males that were more exploratory in the novel environment also reacted more aggressively to a simulated territory intruder and showed lower offspring hatching success during the breeding season. Hence, our findings support previous work showing behavioral differences between Darwin's finch species and also suggest pathways by which behavioral differences among individuals might influence fitness. Significance statement Closely-related species that overlap in their geographical range may differ in their morphology and/or behavior, allowing them to occupy different ecological niches. In this study, we explored behavioral differences between four Darwin's finch species on Floreana Island in the Galapagos Archipelago. We found clear interspecies differences in behavior, with the ground finches struggling more often during handling (boldness) and visiting more sectors in a novel environment (exploration) compared to the tree finches. After birds were released, we continued to observe a subset of male finches in the wild. An individual's exploration behavior significantly predicted both its aggressive response to a territory intruder (simulated using song playback) and offspring hatching success during the breeding season. This suggests that individual differences in exploration behavior can potentially be used as a proxy for territorial behavior in the wild and may also predict fitness outcomes.Publication Metadata only Generation lengths of the world's birds and their implications for extinction risk(Wiley, 2020) Bird, Jeremy P.; Martin, Robert; Akcakaya, H. Resit; Gilroy, James; Burfield, Ian J.; Garnett, Stephen T.; Symes, Andy; Taylor, Joseph; Butchart, Stuart H. M.; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; N/A; 327589Birds have been comprehensively assessed on the International Union for Conservation of Nature (IUCN) Red List more times than any other taxonomic group. However, to date, generation lengths have not been systematically estimated to scale population trends when undertaking assessments, as required by the criteria of the IUCN Red List. We compiled information from major databases of published life-history and trait data for all birds and imputed missing life-history data as a function of species traits with generalized linear mixed models. Generation lengths were derived for all species, based on our modeled values of age at first breeding, maximum longevity, and annual adult survival. The resulting generation lengths varied from 1.42 to 27.87 years (median 2.99). Most species (61%) had generation lengths <3.33 years, meaning that the period of 3 generations-over which population declines are assessed under criterion A-was <10 years, which is the value used for IUCN Red List assessments of species with short generation times. For these species, our trait-informed estimates of generation length suggested that 10 years is a robust precautionary value for threat assessment. In other cases, however, for whole families, genera, or individual species, generation length had a substantial impact on their estimated extinction risk, resulting in higher extinction risk in long-lived species than in short-lived species. Although our approach effectively addressed data gaps, generation lengths for some species may have been underestimated due to a paucity of life-history data. Overall, our results will strengthen future extinction-risk assessments and augment key databases of avian life-history and trait data.Publication Open Access How COVID-19 financially hit urban refugees: evidence from mixed-method research with citizens and Syrian refugees in Turkey(Wiley, 2021) Kirişçioğlu, Eda; Department of International Relations; Elçi, Ezgi; Faculty Member; Department of International Relations; College of Administrative Sciences and Economics; Graduate School of Social Sciences and Humanities; 238439; N/APeering through a lens of disasters and inequalities, this article measures the financial impacts of Covid-19 on citizens and refugee communities in Turkey during a relatively early phase of the global pandemic. Our data comes from an online survey (N = 1749) conducted simultaneously with Turkish citizens and Syrian refugees living in Turkey, followed by in-depth online interviews with Syrian refugees. Our findings indicate that the initial Covid-19 measures had a higher financial impact on Syrians than on citizens when controlled for employment, wealth, and education, among other variables. In line with the literature, our research confirms that disasters' socio-economic effects disproportionally burden minority communities. We additionally discuss how Covid-19 measures have significantly accelerated effects on refugees compared to the local population, mainly due to the structural and policy context within which forcibly displaced Syrians have been received in Turkey.Publication Metadata only Mammal responses to global changes in human activity vary by trophic group and landscape(Nature Portfolio, 2024) Burton, A. Cole; Beirne, Christopher; Gayno, Kaitlyn M.; Sun, Catherine; Granados, Alys; Allen, Maximilian L.; Alston, Jesse M.; Alvarenga, Guilherme C.; Calderon, Francisco Samuel Alvarez; Amir, Zachary; Anhalt-Depies, Christine; Appel, Cara; Arroyo-Arce, Stephanny; Balme, Guy; Bar-Massada, Avi; Barcelos, Daniele; Barr, Evan; Barthelmess, Erika L.; Baruzzi, Carolina; Basak, Sayantani M.; Beenaerts, Natalie; Belmaker, Jonathan; Belova, Olgirda; Bezarevic, Branko; Bird, Tori; Bogan, Daniel A.; Bogdanovic, Neda; Boyce, Andy; Boyce, Mark; Brandt, LaRoy; Brodie, Jedediah F.; Brooke, Jarred; Bubnicki, Jakub W.; Cagnacci, Francesca; Carr, Benjamin Scott; Carvalho, Joao; Casaer, Jim; Cerne, Rok; Chen, Ron; Chow, Emily; Churski, Marcin; Cincotta, Connor; Cirovic, Dusko; Coates, T. D.; Compton, Justin; Coon, Courtney; Cove, Michael V.; Crupi, Anthony P.; Dal Farra, Simone; Darracq, Andrea K.; Davis, Miranda; Dawe, Kimberly; De Waele, Valerie; Descalzo, Esther; Diserens, Tom A.; Drimaj, Jakub; Dul'a, Martin; Ellis-Felege, Susan; Ellison, Caroline; Ertürk, Alper; Fantle-Lepczyk, Jean; Favreau, Jorie; Fennell, Mitch; Ferreras, Pablo; Ferretti, Francesco; Fiderer, Christian; Finnegan, Laura; Fisher, Jason T.; Fisher-Reid, M. Caitlin; Flaherty, Elizabeth A.; Flezar, Ursa; Flousek, Jiri; Foca, Jennifer M.; Ford, Adam; Franzetti, Barbara; Frey, Sandra; Fritts, Sarah; Frybova, Sarka; Furnas, Brett; Gerber, Brian; Geyle, Hayley M.; Gimenez, Diego G.; Giordano, Anthony J.; Gomercic, Tomislav; Gompper, Matthew E.; Grabin, Diogo Maia; Gray, Morgan; Green, Austin; Hagen, Robert; Hagen, Robert; Hammerich, Steven; Hanekom, Catharine; Hansen, Christopher; Hasstedt, Steven; Hebblewhite, Mark; Heurich, Marco; Hofmeester, Tim R.; Hubbard, Tru; Jachowski, David; Jansen, Patrick A.; Jaspers, Kodi Jo; Jensen, Alex; Jordan, Mark; Kaizer, Mariane C.; Kelly, Marcella J.; Kohl, Michel T.; Kramer-Schadt, Stephanie; Krofel, Miha; Krug, Andrea; Kuhn, Kellie M.; Kuijper, Dries P. J.; Kuprewicz, Erin K.; Kusak, Josip; Kutal, Miroslav; Lafferty, Diana J. R.; LaRose, Summer; Lashley, Marcus; Lathrop, Richard; Lee, Thomas E., Jr.; Lepczyk, Christopher; Lesmeister, Damon B.; Licoppe, Alain; Linnell, Marco; Loch, Jan; Long, Robert; Lonsinger, Robert C.; Louvrier, Julie; Luskin, Matthew Scott; MacKay, Paula; Maher, Sean; Manet, Benoit; Mann, Gareth K. H.; Marshall, Andrew J.; Mason, David; McDonald, Zara; McKay, Tracy; McShea, William J.; Mechler, Matt; Miaud, Claude; Millspaugh, Joshua J.; Monteza-Moreno, Claudio M.; Moreira-Arce, Dario; Mullen, Kayleigh; Nagy, Christopher; Naidoo, Robin; Namir, Itai; Nelson, Carrie; O'Neill, Brian; O'Mara, M. Teague; Oberosler, Valentina; Osorio, Christian; Ossi, Federico; Palencia, Pablo; Pearson, Kimberly; Pedrotti, Luca; Pekins, Charles E.; Pendergast, Mary; Pinho, Fernando F.; Plhal, Radim; Pocasangre-Orellana, Xochilt; Price, Melissa; Procko, Michael; Proctor, Mike D.; Ramalho, Emiliano Esterci; Ranc, Nathan; Reljic, Slaven; Remine, Katie; Rentz, Michael; Revord, Ronald; Reyna-Hurtado, Rafael; Risch, Derek; Ritchie, Euan G.; Romero, Andrea; Rota, Christopher; Rovero, Francesco; Rowe, Helen; Rutz, Christian; Salvatori, Marco; Sandow, Derek; Schalk, Christopher M.; Scherger, Jenna; Schipper, Jan; Scognamillo, Daniel G.; Semenzato, Paola; Sevin, Jennifer; Shamon, Hila; Shier, Catherine; Silva-Rodriguez, Eduardo A.; Sindicic, Magda; Smyth, Lucy K.; Soyumert, Anil; Sprague, Tiffany; St Clair, Colleen Cassady; Stenglein, Jennifer; Stephens, Philip A.; Stepniak, Kinga Magdalena; Stevens, Michael; Stevenson, Cassondra; Ternyik, Balint; Thomson, Ian; Torres, Rita T.; Tremblay, Joan; Urrutia, Tomas; Vacher, Jean-Pierre; Visscher, Darcy; Webb, Stephen L.; Weber, Julian; Weiss, Katherine C. B.; Whipple, Laura S.; Whittier, Christopher A.; Whittington, Jesse; Wierzbowska, Izabela; Wikelski, Martin; Williamson, Jacque; Wilmers, Christopher C.; Windle, Todd; Wittmer, Heiko U.; Zharikov, Yuri; Zorn, Adam; Kays, Roland.; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Department of Molecular Biology and Genetics; ; College of Sciences;Wildlife must adapt to human presence to survive in the Anthropocene, so it is critical to understand species responses to humans in different contexts. We used camera trapping as a lens to view mammal responses to changes in human activity during the COVID-19 pandemic. Across 163 species sampled in 102 projects around the world, changes in the amount and timing of animal activity varied widely. Under higher human activity, mammals were less active in undeveloped areas but unexpectedly more active in developed areas while exhibiting greater nocturnality. Carnivores were most sensitive, showing the strongest decreases in activity and greatest increases in nocturnality. Wildlife managers must consider how habituation and uneven sensitivity across species may cause fundamental differences in human-wildlife interactions along gradients of human influence. Analysing camera-trap data of 163 mammal species before and after the onset of COVID-19 lockdowns, the authors show that responses to human activity are dependent on the degree to which the landscape is modified by humans, with carnivores being especially sensitive.Publication Open Access Mismatch between bird species sensitivity and the protection of intact habitats across the Americas(Wiley, 2021) Cazalis, Victor; Barnes, Megan D.; Johnston, Alison; Watson, James E. M.; Rodrigues, Ana S. L.; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 327589Protected areas are highly heterogeneous in their effectiveness at buffering human pressure, which may hamper their ability to conserve species highly sensitive to human activities. Here, we use 60 million bird observations from eBird to estimate the sensitivity to human pressure of each bird species breeding in the Americas. Concerningly, we find that ecoregions hosting large proportions of high-sensitivity species, concentrated in tropical biomes, do not have more intact protected habitat. Moreover, 266 high-sensitivity species have little or no intact protected habitat within their distributions. Finally, we show that protected area intactness is decreasing faster where high-sensitivity species concentrate. Our results highlight a major mismatch between species conservation needs and the coverage of intact protected habitats, which likely hampers the long-term effectiveness of protected areas at retaining species. We highlight ecoregions where protection and management of intact habitats, complemented by restoration, is urgently needed.Publication Open Access Multi-modal communication: song sparrows increase signal redundancy in noise(The Royal Society, 2019) Beecher, Michael D.; Department of Psychology; Akçay, Çağlar; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; 272053Although the effects of anthropogenic noise on animal communication have been studied widely, most research on the effect of noise in communication has focused on signals in a single modality. Consequently, how multi-modal communication is affected by anthropogenic noise is relatively poorly understood. Here, we ask whether song sparrows (Melospiza melodia) show evidence of plasticity in response to noise in two aggressive signals in acoustic and visual modalities. We test two hypotheses: (i) that song sparrows will shift signalling effort to the visual modality (the multi-modal shift hypothesis) and (ii) that they will increase redundancy of their multi-modal signalling (the back-up signal hypothesis). We presented male song sparrows with song playback and a taxidermic mount with or without a low-frequency acoustic noise from a nearby speaker. We found that males did not switch their signalling effort to visual modality (i.e. wing waves) in response to the noise. However, the correlation between warbled soft songs and wing waves increased in the noise treatment, i.e. signals became more redundant. These results suggest that when faced with anthropogenic noise, song sparrows can increase the redundancy of their multi-modal signals, which may aid in the robustness of the communication system.Publication Open Access Re-emergence and diversification of a specialized antennal lobe morphology in ithomiine butterflies(Wiley, 2021) Morris, BJ.; Couto, A.; Montgomery, SH.; Aydın, Aslı; Undergraduate Student; School of MedicineHow an organism's sensory system functions is central to how it navigates its environment. The insect olfactory system is a prominent model for investigating how ecological factors impact sensory reception and processing. Notably, work in Lepidoptera led to the discovery of vastly expanded structures, termed macroglomerular complexes (MGCs), within the primary olfactory processing centre. MGCs typically process pheromonal cues, are usually larger in males, and provide classic examples of how variation in the size of neural structures reflects the importance of sensory cues. Though prevalent across moths, MGCs were lost during the origin of butterflies, consistent with evidence that courtship initiation in butterflies is primarily reliant on visual cues, rather than long distance chemical signals. However, an MGC was recently described in a species of ithomiine butterfly, suggesting that this once lost neural adaptation has re-emerged in this tribe. Here, we show that MGC-like morphologies are widely distributed across ithomiines, but vary in both their structure and prevalence of sexual dimorphism. Based on this interspecific variation we suggest that the ithomiine MGC is involved in processing both plant and pheromonal cues, which have similarities in their chemical constitution, and co-evolved with an increased importance of plant derived chemical compounds.