Michelle Koo
University of California, Berkeley, Museum of Vertebrate Zoology, Department Member
- Evolutionary Biology, Biogeography, Evolutionary Ecology, Herpetology, Ornithology, Mammalogy, and 21 moreSpatial Modeling, Biodiversity Informatics, Data Visualization, Phylogeography, Amphibians, Burma, Animal Species Loss and Decline, California, Hemidactylus, Sage Sparrow, Species diversification, Crotaphytus, Grinnellian niche, Biology, Ecology, Geography, Geographic Information Systems (GIS), Cartography, Conservation, Reptiles, and Species Distributionedit
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The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island’s long period of isolation and dynamic tectonic history have been implicated as drivers... more
The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island’s long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses o...
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Many countries have responded to the current global biodiversity crisis by committing to protect 30% of the Earth by 2030, a goal known as “30 x 30”. However, an excessive emphasis on megafauna to the exclusion of other species weakens... more
Many countries have responded to the current global biodiversity crisis by committing to protect 30% of the Earth by 2030, a goal known as “30 x 30”. However, an excessive emphasis on megafauna to the exclusion of other species weakens our current protected area (PA) network. This limited perspective overvalues large, connected PAs, while disregarding the potential impacts of small PAs in preserving biodiversity. Using public databases of 31,828 terrestrial vertebrate species we demonstrate that range sizes for the most vulnerable class of vertebrates, the amphibians, are smaller than those of reptiles, birds, and mammals and suggest that small PAs are overlooked as conservation tools for this group. We found that, though each of many endangered amphibians could have their entire distribution protected by a single microreserve (< 10 km2), the current PA network fails at adequately protecting most threatened amphibian species. Furthermore, we show that many current microreserves h...
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IntroductionEmerging infectious diseases are increasingly recognized as a global threat to wildlife. Pandemics in amphibians, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), have resulted in biodiversity loss at a... more
IntroductionEmerging infectious diseases are increasingly recognized as a global threat to wildlife. Pandemics in amphibians, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), have resulted in biodiversity loss at a global scale. Genomic data suggest a complex evolutionary history of Bd lineages that vary in pathogenicity. Africa harbors a significant proportion of global amphibian biodiversity, and multiple Bd lineages are known to occur there; yet, despite the decline of many host species, there are currently no described Bd-epizootics. Here, we describe the historical and recent biogeographical spread of Bd and assess its risk to amphibians across the continent of Africa.MethodsWe provide a 165-year view of host-pathogen interactions by (i) employing a Bd assay to test 4,623 specimens (collected 1908–2013); (ii) compiling 12,297 published Bd records (collected 1852–2017); (iii) comparing the frequency of Bd-infected amphibians through time by both country and reg...
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Bell’s and Sagebrush sparrows (Artemisiospiza belli and A. nevadensis) are phenotypically and genetically distinct, but data have yielded contradictory findings for A. belli subspecies. Disjunct populations of A. b. canescens from the San... more
Bell’s and Sagebrush sparrows (Artemisiospiza belli and A. nevadensis) are phenotypically and genetically distinct, but data have yielded contradictory findings for A. belli subspecies. Disjunct populations of A. b. canescens from the San Joaquin Valley and Mojave Desert are phenotypically indistinguishable but diagnosable from Coast Range A. b. belli. However, San Joaquin Valley A. b. canescens shares allozymes and mtDNA with A. b. belli whereas Mojave Desert A. b. canescens is genetically distinct. Furthermore, Great Basin A. nevadensis is closer in mtDNA to non-desert A. belli subspecies than to Mojave Desert A. b. canescens, with whom it contacts across an aridland transition. We assessed concordance of song with genetics and phenotype for these taxa, and also analyzed songs and mtDNA for A. b. clementeae which is endemic to arid San Clemente Island off the coast of southern California. Songs of open, arid habitat populations (A. nevadensis, A. b. canescens, A. b. clementeae) are consistently more similar to each other than they are to songs of coastal A. b. belli. We examined bioclimatic and land cover conditions to understand the basis for these patterns across ecoregions, and discuss the effect of the acoustic environment on song
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The role of the environmental niche in fostering ecological divergence during adaptive radiation remains enigmatic. In this study, we examine the interplay between environmental niche divergence and conservatism in the context of adaptive... more
The role of the environmental niche in fostering ecological divergence during adaptive radiation remains enigmatic. In this study, we examine the interplay between environmental niche divergence and conservatism in the context of adaptive radiation on oceanic islands, by characterizing the niche breadth of four Hawaiian arthropod radiations: Tetragnatha spiders (Tetragnathidae Latreille, 1804), Laupala crickets (Gryllidae Otte, 1994), a clade of Drosophila flies (Drosophilidae Fallén, 1823) and Nesosydne planthoppers (Delphacidae Kirkaldy, 1907). We assembled occurrence datasets for the four lineages, modelled their distributions and quantified niche overlap. All four groups occupy the islands in distinct ways, highlighting the contrasting axes of diversification for different lineages. Laupala and Nesosydne have opposite environmental niche extents (broad and narrow, respectively), whereas Tetragnatha and Drosophila share relatively intermediate tolerances. Temperature constrains t...
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Amphibians are a clade of over 8,400 species that provide unique research opportunities and challenges. With amphibians undergoing severe global declines, we posit that assessing our current understanding of amphibians is imperative.... more
Amphibians are a clade of over 8,400 species that provide unique research opportunities and challenges. With amphibians undergoing severe global declines, we posit that assessing our current understanding of amphibians is imperative. Focusing on the past five years (2016–2020), we examine trends in amphibian research, data, and systematics. New species of amphibians continue to be described at a pace of ~150 per year. Phylogenomic studies are increasing, fueling a growing consensus in the amphibian tree of life. Over 3,000 species of amphibians are now represented by expert-curated accounts or data in AmphibiaWeb, AmphibiaChina, BioWeb, or the Amphibian Disease Portal. Nevertheless, many species lack basic natural history data (e.g., diet records, morphological measurements, call recordings) and major gaps exist for entire amphibian clades. Genomic resources appear on the cusp of a rapid expansion, but large, repetitive amphibian genomes still pose significant challenges. Conservati...
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We studied the feeding ecology of California Kingsnakes (Lampropeltis californiae) based on stomach contents of 2,662 museum specimens, 90 published records, and 92 unpublished observations. These snakes typically are diurnal,... more
We studied the feeding ecology of California Kingsnakes (Lampropeltis californiae) based on stomach contents of 2,662 museum specimens, 90 published records, and 92 unpublished observations. These snakes typically are diurnal, wide-foraging generalists and ingest prey headfirst. Twenty-nine percent of 447 diet items were mammals, 29% were snakes, 25% were lizards, 11% were birds, 4% were squamate eggs, 1% were unidentified squamates, and 1% were amphibians. We detected no differences in diet based on kingsnake sex or color pattern, nor evidence of individual specialization. Rodents, lizards, and birds were eaten more frequently by larger individuals; snakes were eaten with similar frequency independent of predator size. Predation on mammals, birds, and lizards, but not snakes, was seasonally restricted. Kingsnakes from arid bioregions consumed more snakes, fewer rodents, and fewer lizards than did those from non-arid bioregions. Overall frequencies were similar for rodents and snakes, yet snakes accounted for 45% of prey biomass; among snakes, rattlesnakes comprised 24% by frequency and 37% of snake prey biomass and energy. Prey-predator mass ratios averaged 0.24 ± 0.19 (range 0.01-0.73; n = 43); a positive relationship exists between prey mass and snake mass, but larger snakes also consumed small prey items. Rattlesnakes, amounting to only 7% of overall diet and 16% of total biomass and energy value, are available throughout the active season and provide higher payoff per item than other diet types. Our findings thus provide a resolution to the paradox that this generalist predator is specialized (i.e., venom immunity) to feed on rattlesnakes, a rare prey type.
The emerging fungal pathogen, Batrachochytrium dendrobatidis (Bd), which can cause a fatal disease called chytridiomycosis, is implicated in the collapse of hundreds of host amphibian species. We describe chytridiomycosis dynamics in two... more
The emerging fungal pathogen, Batrachochytrium dendrobatidis (Bd), which can cause a fatal disease called chytridiomycosis, is implicated in the collapse of hundreds of host amphibian species. We describe chytridiomycosis dynamics in two co-occurring terrestrial salamander species, the Santa Lucia Mountains slender salamander, Batrachoseps luciae, and the arboreal salamander, Aneides lugubris. We (1) conduct a retrospective Bd-infection survey of specimens collected over the last century, (2) estimate present-day Bd infections in wild populations, (3) use generalized linear models (GLM) to identify biotic and abiotic correlates of infection risk, (4) investigate susceptibility of hosts exposed to Bd in laboratory trials, and (5) examine the ability of host skin bacteria to inhibit Bd in culture. Our historical survey of 2,866 specimens revealed that for most of the early 20th century (~1920–1969), Bd was not detected in either species. By the 1990s the proportion of infected specime...
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These datasets are associated with the study entitled, "Continent-wide recent emergence of a global pathogen in African amphibians." In this study we describe the historical and recent biogeographical spread of a fungal pathogen... more
These datasets are associated with the study entitled, "Continent-wide recent emergence of a global pathogen in African amphibians." In this study we describe the historical and recent biogeographical spread of a fungal pathogen of amphibians, <em>Batrachochytrium dendrobatidis</em> (<em>Bd</em>) and assess its risk to amphibians across the continent of Africa. The larger combined file, "AfricaBd_CombinedFile_LitReview_BdMaps_GhoseData.xlsx", contains <em>Bd</em> occurrence records processed by the authors of the study (N=4,623) and previously published records (N=12,297). Of the previously published records, 12,234 records came from studies reporting both <em>Bd</em>-negative and <em>Bd</em>-positive records (i.e. prevalence) that we used along with our data (N=4,623) to assess emergence of <em>Bd</em> in African amphibians. The file "AfricaBd_Ghosedata_Hirschfelddata_ZimkusCameroondata...
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AmphibiaWeb Team Kellie Whittaker AmphibiaWeb Coordinator University of California at Berkeley David B. Wake Director and Founder University of California at Berkeley Vance Vredenburg Associate Director, and Founder San Francisco State... more
AmphibiaWeb Team Kellie Whittaker AmphibiaWeb Coordinator University of California at Berkeley David B. Wake Director and Founder University of California at Berkeley Vance Vredenburg Associate Director, and Founder San Francisco State University Joyce Gross Database Programmer, and Founder University of California at Berkeley David C. Blackburn Senior Associate California Academy of Sciences (as of September 2011) David C. Cannatella Senior Associate University of Texas, Austin Michelle S. Koo Senior Associate University of California at Berkeley Carol L. Spencer Senior Associate University of California at Berkeley Arie van der Meijden Senior Associate CIBIO Institute, Portugal
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Resurveys of historical collecting localities have revealed range shifts, primarily leading edge expansions, which have been attributed to global warming. However, there have been few spatially replicated community-scale resurveys testing... more
Resurveys of historical collecting localities have revealed range shifts, primarily leading edge expansions, which have been attributed to global warming. However, there have been few spatially replicated community-scale resurveys testing whether species' responses are spatially consistent. Here we repeated early twentieth century surveys of small mammals along elevational gradients in northern, central and southern regions of montane California. Of the 34 species we analysed, 25 shifted their ranges upslope or downslope in at least one region. However, two-thirds of ranges in the three regions remained stable at one or both elevational limits and none of the 22 species found in all three regions shifted both their upper and lower limits in the same direction in all regions. When shifts occurred, high-elevation species typically contracted their lower limits upslope, whereas low-elevation species had heterogeneous responses. For high-elevation species, site-specific change in te...
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A newly described pathogen poses a major threat to salamanders via trade
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The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an... more
The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expres...
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Editorials Announcement of the International Symposium on Natural History and Conservation of Amphibians and Reptiles at the 6th World Congress of Herpetology. Robert... more
Editorials Announcement of the International Symposium on Natural History and Conservation of Amphibians and Reptiles at the 6th World Congress of Herpetology. Robert Brodman…………………….……………….............................................................................................. ....................... ... Articles Distribution and Relative Abundance of Tennessee Cave Salamanders (Gyrinophilus palleucus and Gyrinophilus gulolineatus) with an Emphasis on Tennessee Populations. Brian T. Miller and Matthew L. Neimiller…………………………………………… ...
The Tahoe National Forest comprises an area of approximately 800,000 acres, which has been relatively unstudied with respect to the amphibian and reptile fauna.-Other than Hayes and Cliff (1982) who report on the amphibians and reptiles... more
The Tahoe National Forest comprises an area of approximately 800,000 acres, which has been relatively unstudied with respect to the amphibian and reptile fauna.-Other than Hayes and Cliff (1982) who report on the amphibians and reptiles of Butte County, north of the Tahoe National Forest, there are no other published accounts on the region's general herpetology. Thus, biologists of the Tahoe National 'Forest have had to rely on published sources, which address the herpetofauna at a larger geographic scale and consequently ...
Abstract.—Monitoring the distribution, population size, and trends of declining species is necessary to evaluate their vulnerability to extinction. It is the responsibility of scientists to alert management professionals of the need for... more
Abstract.—Monitoring the distribution, population size, and trends of declining species is necessary to evaluate their vulnerability to extinction. It is the responsibility of scientists to alert management professionals of the need for preemptive action if a species approaches imminent, regional extirpation. This is the case with Rana cascadae (Cascades Frog) populations near Lassen Peak. From 1993 to 2007, we conducted 1,873 amphibian surveys at 856 sites within Lassen Volcanic National Park and Lassen National Forest, California, ...
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The push and pull of climate change causes heterogeneous shift in avian elevational ranges
George R. Zug1, Jens V. Vindum2, and Michelle S. Koo3 1 Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560 USA.; Email: zugg@si.edu; 2 Department of Herpetology, California... more
George R. Zug1, Jens V. Vindum2, and Michelle S. Koo3 1 Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560 USA.; Email: zugg@si.edu; 2 Department of Herpetology, California Academy of Sciences, San Francisco, CA, 94103 USA; Email: jvindum@calacademy.org; 3 Museum of Vertebrate Zoology, University of California, Berkeley, CA. 94720 USA
Research Interests: Burma and Hemidactylus
Understanding variation of traits within and among species through time and across space is central to many questions in biology. Many resources have been developed to assemble trait data at the species level, but the underlying data and... more
Understanding variation of traits within and among species through time and across space is central to many questions in biology. Many resources have been developed to assemble trait data at the species level, but the underlying data and metadata about those trait measurements are often not reported, limiting broadest utility. Here we introduce FuTRES (Functional Trait Resource for Environmental Studies), a datastore and community resource for individual-level trait reporting that utilizes a strong semantic framework and best practices approach to overcome previous limitations. FuTRES already stores millions of trait measurements that span across multiple time scales, including zooarchaeological and paleobiological specimens, with a current focus on mammals. Two case studies showcase the promise of FuTRES. The first compares dynamically derived extant mammal species' body size estimates with summary values from other compilations, highlighting potential issues with simply reporting a single mean estimate. The second shows that FuTRES data improves estimates of body mass – including uncertainty – for zooarchaeological specimens. FuTRES facilitates trait data integration and discoverability, accelerating new research agendas, especially scaling from intra- to interspecific trait variability.