Naupaka Zimmerman | University of San Francisco (original) (raw)

Papers by Naupaka Zimmerman

Research paper thumbnail of Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota)

Molecular Phylogenetics and Evolution, 2016

The Xylariaceae (Sordariomycetes) comprise one of the largest and most diverse families of Ascomy... more The Xylariaceae (Sordariomycetes) comprise one of the largest and most diverse families of Ascomycota, with at least 85 accepted genera and ca. 1343 accepted species. In addition to their frequent occurrence as saprotrophs, members of the family often are found as endophytes in living tissues of phylogenetically diverse plants and lichens. Many of these endophytes remain sterile in culture, precluding identification based on morphological characters. Previous studies indicate that endophytes are highly diverse and represent many xylariaceous genera; however, phylogenetic analyses at the family level generally have not included endophytes, such that their contributions to understanding phylogenetic relationships of Xylariaceae are not well known. Here we use a multi-locus, cumulative supermatrix approach to integrate 92 putative species of fungi isolated from plants and lichens into a phylogenetic framework for Xylariaceae. Our collection spans 1933 isolates from living and senescent tissues in five biomes across the continental United States, and here is analyzed in the context of previously published sequence data from described species and additional taxon sampling of type specimens from culture collections. We found that the majority of strains obtained in our surveys can be classified in the hypoxyloid and xylaroid subfamilies, although many also were found outside of these lineages (as currently circumscribed). Many endophytes were placed in lineages previously not known for endophytism. Most endophytes appear to represent novel species, but inferences are limited by potential gaps in public databases. By linking our data, publicly available sequence data, and records of ascomata, we identify many geographically widespread, host-generalist clades capable of symbiotic associations with diverse photosynthetic partners. Concomitant with such cosmopolitan host use and distributions, many xylariaceous endophytes appear to inhabit both living and non-living plant tissues, with potentially important roles as saprotrophs. Overall, our study reveals major gaps in the availability of multi-locus datasets and metadata for this iconic family, and provides new hypotheses regarding the ecology and evolution of endophytism and other trophic modes across the family Xylariaceae.

Research paper thumbnail of Altitudinal shifts of the native and introduced flora of California in the context of 20th-century warming

Global Ecology and Biogeography, 2016

Research paper thumbnail of The Tao of Open Science for Ecology

Research paper thumbnail of Ecology Postdocs in Academia: Primary Concerns and Possible Solutions

Bulletin of the Ecological Society of America, 2015

Research paper thumbnail of Leaf endophytes and Populus genotype affect severity of damage from the necrotrophic leaf pathogen, Drepanopeziza populi

Ecosphere, 2013

2013. Leaf endophytes and Populus genotype affect severity of damage from the necrotrophic leaf p... more 2013. Leaf endophytes and Populus genotype affect severity of damage from the necrotrophic leaf pathogen, Drepanopeziza populi. Ecosphere 4(10):125. http://dx.

Research paper thumbnail of The next generation of action ecology: novel approaches towards global ecological research

Advances in the acquisition and dissemination of knowledge over the last decade have dramatically... more Advances in the acquisition and dissemination of knowledge over the last decade have dramatically reshaped the way that ecological research is conducted. The advent of large, technology-based resources such as iNaturalist, Genbank, or the Global Biodiversity Information Facility (GBIF) allow ecologists to work at spatio-temporal scales previously unimaginable. This has generated a new approach in ecological research: one that relies on large datasets and rapid synthesis for theory testing and development, and findings that provide specific recommendations to policymakers and managers. This new approach has been termed action ecology, and here we aim to expand on earlier definitions to delineate its characteristics so as to distinguish it from related subfields in applied ecology and ecological management. Our new, more nuanced definition describes action ecology as ecological research that is (1) explicitly motivated by the need for immediate insights into current, pressing problems, (2) collaborative and transdisciplinary, incorporating sociological in addition to ecological considerations throughout all steps of the research, (3) technology-mediated, innovative, and aggregative (i.e., reliant on ‘big data'), and (4) designed and disseminated with the intention to inform policy and management. We provide tangible examples of existing work in the domain of action ecology, and offer suggestions for its implementation and future growth, with explicit recommendations for individuals, research institutions, and ecological societies.

Research paper thumbnail of Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond

We present a case for using Global Community Innovation Platforms (GCIPs), an approach to improve... more We present a case for using Global Community Innovation Platforms (GCIPs), an approach to improve innovation and knowledge exchange in international scientific communities through a common and open online infrastructure. We highlight the value of GCIPs by focusing on recent efforts targeting the ecological sciences, where GCIPs are of high relevance given the urgent need for interdisciplinary, geographical, and cross-sector collaboration to cope with growing challenges to the environment as well as the scientific community itself. Amidst the emergence of new international institutions, organizations, and meetings, GCIPs provide a stable international infrastructure for rapid and long-term coordination that can be accessed by any individual. This accessibility can be especially important for researchers early in their careers. Recent examples of early-career GCIPs complement an array of existing options for early-career scientists to improve skill sets, increase academic and social impact, and broaden career opportunities. We v www.esajournals.org 1 April 2015 v Volume 6(4) v Article 68 provide a number of examples of existing early-career initiatives that incorporate elements from the GCIPs approach, and highlight an in-depth case study from the ecological sciences: the International Network of Next-Generation Ecologists (INNGE), initiated in 2010 with support from the International Association for Ecology and 20 member institutions from six continents.

Research paper thumbnail of The next generation of action ecology: novel approaches towards global ecological research

Advances in the acquisition and dissemination of knowledge over the last decade have dramatically... more Advances in the acquisition and dissemination of knowledge over the last decade have dramatically reshaped the way that ecological research is conducted. The advent of large, technology-based resources such as iNaturalist, Genbank, or the Global Biodiversity Information Facility (GBIF) allow ecologists to work at spatio-temporal scales previously unimaginable. This has generated a new approach in ecological research: one that relies on large datasets and rapid synthesis for theory testing and development, and findings that provide specific recommendations to policymakers and managers. This new approach has been termed action ecology, and here we aim to expand on earlier definitions to delineate its characteristics so as to distinguish it from related subfields in applied ecology and ecological management. Our new, more nuanced definition describes action ecology as ecological research that is (1) explicitly motivated by the need for immediate insights into current, pressing problems, (2) collaborative and transdisciplinary, incorporating sociological in addition to ecological considerations throughout all steps of the research, (3) technology-mediated, innovative, and aggregative (i.e., reliant on ‘big data'), and (4) designed and disseminated with the intention to inform policy and management. We provide tangible examples of existing work in the domain of action ecology, and offer suggestions for its implementation and future growth, with explicit recommendations for individuals, research institutions, and ecological societies.

Read More: http://www.esajournals.org/doi/abs/10.1890/ES14-00485.1#.VdVi-pTu4lU.twitter

Research paper thumbnail of The unseen world: environmental microbial sequencing and identification methods for ecologists

Frontiers in Ecology and the Environment, May 2014

Research paper thumbnail of Lack of quantitative training among early-career ecologists: a survey of the problem and potential solutions

PeerJ, 2014

Proficiency in mathematics and statistics is essential to modern ecological science, yet few stud... more Proficiency in mathematics and statistics is essential to modern ecological science, yet few studies have assessed the level of quantitative training received by ecologists. To do so, we conducted an online survey. The 937 respondents were mostly early-career scientists who studied biology as undergraduates. We found a clear self-perceived lack of quantitative training: 75% were not satisfied with their understanding of mathematical models; 75% felt that the level of mathematics was "too low" in their ecology classes; 90% wanted more mathematics classes for ecologists; and 95% more statistics classes. Respondents thought that 30% of classes in ecology-related degrees should be focused on quantitative disciplines, which is likely higher than for most existing programs. The main suggestion to improve quantitative training was to relate theoretical and statistical modeling to applied ecological problems. Improving quantitative training will require dedicated, quantitative classes for ecology-related degrees that contain good mathematical and statistical practice. How to cite this article Barraquand et al. (2014), Lack of quantitative training among early-career ecologists: a survey of the problem and potential solutions. PeerJ 2:e285; . Volterra V. 1931. Leçons sur la théorie mathématique de la lutte pour la vie. Paris: Gauthier-Villars. Williams B, Nichols J, Conroy M. 2002. Analysis and management of animal populations: modeling, estimation, and decision making. San Diego, CA: Academic Press.

Research paper thumbnail of Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape

Abstract We surveyed endophytic fungal communities in leaves of a single tree species (Metrosider... more Abstract We surveyed endophytic fungal communities in leaves of a single tree species (Metrosideros polymorpha) across wide environmental gradients (500���5,500 mm of rain/y; 10���22 C mean annual temperature) spanning short geographic distances on Mauna Loa Volcano, Hawai'i. Using barcoded amplicon pyrosequencing at 13 sites (10 trees/site; 10 leaves/tree), we found very high levels of diversity within sites (a mean of 551��134 taxonomic units per site).

Research paper thumbnail of The Nature of Identity and the Identity of Nature: Hawaiian Perspectives on Persons and Place

Academia.edu helps academics follow the latest research.

Research paper thumbnail of The next generation of peer reviewing

… in Ecology and …, Jan 1, 2011

Research paper thumbnail of Patterns of Primary Succession of Native and Introduced Plants In Lowland Wet Forests In Eastern Hawai'I

…, Jan 1, 2008

The majority of Hawaii's lowland wet forests no longer exist, with many of the last remaining pat... more The majority of Hawaii's lowland wet forests no longer exist, with many of the last remaining patches found on the eastern, windward sides of the largest islands. To better understand successional patterns and invasion in these native systems, we quantified basal area (BA) and densities of woody species and understory cover at nine sites in the Puna district on the Island of Hawai'i, representing age gradients of native stand development on both 'a'ā and pāhoehoe lava flows. On both flow types, BA of native species increased (from 5 to 50 m 2 /ha) and stem densities decreased (from 3700 to 2600 stems/ha) with increasing stand/flow age. Both native and introduced species compositions diverged between substrate types on older flows. We found that lowland wet native forests remain at least partially intact in several locations, but their functional and compositional integrity is increasingly compromised by invasion of nonnative species, such as Psidium cattleianum and Melastoma candidum, which become more common at sites greater than 300-yr old. This time period may represent a threshold, after which abiotic environmental conditions no longer constrain recruitment of introduced species. On older flows, nonnative stem densities swamped those of native species by an order of magnitude, with nonnative stems (height > 1.3 m) achieving densities as high as 18,000 stems/ha. In addition, all stands lacked recruitment of native woody species in the understory, suggesting that without management, the native componentsof these forests may soon no longer be self-sustaining.

Conference Presentations by Naupaka Zimmerman

Research paper thumbnail of Widespread plant movement in response to 20th century warming disproportionately affects endemic species

The differential responses of plant species to global warming are of great interest and grave con... more The differential responses of plant species to global warming are of great interest and grave concern for scientists and conservationists. We used> 650,000 herbaria records to estimate geographic and climatic shifts over> 100 years in 4300 plant taxa from a wide range of bioclimatic zones, functional types, and phylogeographic origins.

Research paper thumbnail of Pyrosequencing of tropical fungal endophytes provides evidence for adaptation to high elevation

Fungal endophytes, the fungi that inhabit the asymptomatic leaves of all plants surveyed to date,... more Fungal endophytes, the fungi that inhabit the asymptomatic leaves of all plants surveyed to date, represent a large and unknown component of global fungal diversity. Previous studies have shown them to exhibit a diverse range of functional roles in ecosystems, including protecting their plant host from herbivory or pathogen damage, reducing host nutrient and/or water stress, and as latent decomposers.

Research paper thumbnail of Fungals in the Jungles: Endophytic fungal diversity at the landscape scale

eco.confex.com

Academia.edu helps academics follow the latest research.

Data by Naupaka Zimmerman

Research paper thumbnail of Data from: Patterns of primary succession of native and introduced plants in lowland wet forests in eastern Hawai 'i

Abstract The majority of Hawaii's lowland wet forests no longer exist, with many of the ... more Abstract The majority of Hawaii's lowland wet forests no longer exist, with many of the last remaining patches found on the eastern, windward sides of the largest islands. To better understand successional patterns and invasion in these native systems, we quantified ...

Research paper thumbnail of Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota)

Molecular Phylogenetics and Evolution, 2016

The Xylariaceae (Sordariomycetes) comprise one of the largest and most diverse families of Ascomy... more The Xylariaceae (Sordariomycetes) comprise one of the largest and most diverse families of Ascomycota, with at least 85 accepted genera and ca. 1343 accepted species. In addition to their frequent occurrence as saprotrophs, members of the family often are found as endophytes in living tissues of phylogenetically diverse plants and lichens. Many of these endophytes remain sterile in culture, precluding identification based on morphological characters. Previous studies indicate that endophytes are highly diverse and represent many xylariaceous genera; however, phylogenetic analyses at the family level generally have not included endophytes, such that their contributions to understanding phylogenetic relationships of Xylariaceae are not well known. Here we use a multi-locus, cumulative supermatrix approach to integrate 92 putative species of fungi isolated from plants and lichens into a phylogenetic framework for Xylariaceae. Our collection spans 1933 isolates from living and senescent tissues in five biomes across the continental United States, and here is analyzed in the context of previously published sequence data from described species and additional taxon sampling of type specimens from culture collections. We found that the majority of strains obtained in our surveys can be classified in the hypoxyloid and xylaroid subfamilies, although many also were found outside of these lineages (as currently circumscribed). Many endophytes were placed in lineages previously not known for endophytism. Most endophytes appear to represent novel species, but inferences are limited by potential gaps in public databases. By linking our data, publicly available sequence data, and records of ascomata, we identify many geographically widespread, host-generalist clades capable of symbiotic associations with diverse photosynthetic partners. Concomitant with such cosmopolitan host use and distributions, many xylariaceous endophytes appear to inhabit both living and non-living plant tissues, with potentially important roles as saprotrophs. Overall, our study reveals major gaps in the availability of multi-locus datasets and metadata for this iconic family, and provides new hypotheses regarding the ecology and evolution of endophytism and other trophic modes across the family Xylariaceae.

Research paper thumbnail of Altitudinal shifts of the native and introduced flora of California in the context of 20th-century warming

Global Ecology and Biogeography, 2016

Research paper thumbnail of The Tao of Open Science for Ecology

Research paper thumbnail of Ecology Postdocs in Academia: Primary Concerns and Possible Solutions

Bulletin of the Ecological Society of America, 2015

Research paper thumbnail of Leaf endophytes and Populus genotype affect severity of damage from the necrotrophic leaf pathogen, Drepanopeziza populi

Ecosphere, 2013

2013. Leaf endophytes and Populus genotype affect severity of damage from the necrotrophic leaf p... more 2013. Leaf endophytes and Populus genotype affect severity of damage from the necrotrophic leaf pathogen, Drepanopeziza populi. Ecosphere 4(10):125. http://dx.

Research paper thumbnail of The next generation of action ecology: novel approaches towards global ecological research

Advances in the acquisition and dissemination of knowledge over the last decade have dramatically... more Advances in the acquisition and dissemination of knowledge over the last decade have dramatically reshaped the way that ecological research is conducted. The advent of large, technology-based resources such as iNaturalist, Genbank, or the Global Biodiversity Information Facility (GBIF) allow ecologists to work at spatio-temporal scales previously unimaginable. This has generated a new approach in ecological research: one that relies on large datasets and rapid synthesis for theory testing and development, and findings that provide specific recommendations to policymakers and managers. This new approach has been termed action ecology, and here we aim to expand on earlier definitions to delineate its characteristics so as to distinguish it from related subfields in applied ecology and ecological management. Our new, more nuanced definition describes action ecology as ecological research that is (1) explicitly motivated by the need for immediate insights into current, pressing problems, (2) collaborative and transdisciplinary, incorporating sociological in addition to ecological considerations throughout all steps of the research, (3) technology-mediated, innovative, and aggregative (i.e., reliant on ‘big data'), and (4) designed and disseminated with the intention to inform policy and management. We provide tangible examples of existing work in the domain of action ecology, and offer suggestions for its implementation and future growth, with explicit recommendations for individuals, research institutions, and ecological societies.

Research paper thumbnail of Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond

We present a case for using Global Community Innovation Platforms (GCIPs), an approach to improve... more We present a case for using Global Community Innovation Platforms (GCIPs), an approach to improve innovation and knowledge exchange in international scientific communities through a common and open online infrastructure. We highlight the value of GCIPs by focusing on recent efforts targeting the ecological sciences, where GCIPs are of high relevance given the urgent need for interdisciplinary, geographical, and cross-sector collaboration to cope with growing challenges to the environment as well as the scientific community itself. Amidst the emergence of new international institutions, organizations, and meetings, GCIPs provide a stable international infrastructure for rapid and long-term coordination that can be accessed by any individual. This accessibility can be especially important for researchers early in their careers. Recent examples of early-career GCIPs complement an array of existing options for early-career scientists to improve skill sets, increase academic and social impact, and broaden career opportunities. We v www.esajournals.org 1 April 2015 v Volume 6(4) v Article 68 provide a number of examples of existing early-career initiatives that incorporate elements from the GCIPs approach, and highlight an in-depth case study from the ecological sciences: the International Network of Next-Generation Ecologists (INNGE), initiated in 2010 with support from the International Association for Ecology and 20 member institutions from six continents.

Research paper thumbnail of The next generation of action ecology: novel approaches towards global ecological research

Advances in the acquisition and dissemination of knowledge over the last decade have dramatically... more Advances in the acquisition and dissemination of knowledge over the last decade have dramatically reshaped the way that ecological research is conducted. The advent of large, technology-based resources such as iNaturalist, Genbank, or the Global Biodiversity Information Facility (GBIF) allow ecologists to work at spatio-temporal scales previously unimaginable. This has generated a new approach in ecological research: one that relies on large datasets and rapid synthesis for theory testing and development, and findings that provide specific recommendations to policymakers and managers. This new approach has been termed action ecology, and here we aim to expand on earlier definitions to delineate its characteristics so as to distinguish it from related subfields in applied ecology and ecological management. Our new, more nuanced definition describes action ecology as ecological research that is (1) explicitly motivated by the need for immediate insights into current, pressing problems, (2) collaborative and transdisciplinary, incorporating sociological in addition to ecological considerations throughout all steps of the research, (3) technology-mediated, innovative, and aggregative (i.e., reliant on ‘big data'), and (4) designed and disseminated with the intention to inform policy and management. We provide tangible examples of existing work in the domain of action ecology, and offer suggestions for its implementation and future growth, with explicit recommendations for individuals, research institutions, and ecological societies.

Read More: http://www.esajournals.org/doi/abs/10.1890/ES14-00485.1#.VdVi-pTu4lU.twitter

Research paper thumbnail of The unseen world: environmental microbial sequencing and identification methods for ecologists

Frontiers in Ecology and the Environment, May 2014

Research paper thumbnail of Lack of quantitative training among early-career ecologists: a survey of the problem and potential solutions

PeerJ, 2014

Proficiency in mathematics and statistics is essential to modern ecological science, yet few stud... more Proficiency in mathematics and statistics is essential to modern ecological science, yet few studies have assessed the level of quantitative training received by ecologists. To do so, we conducted an online survey. The 937 respondents were mostly early-career scientists who studied biology as undergraduates. We found a clear self-perceived lack of quantitative training: 75% were not satisfied with their understanding of mathematical models; 75% felt that the level of mathematics was "too low" in their ecology classes; 90% wanted more mathematics classes for ecologists; and 95% more statistics classes. Respondents thought that 30% of classes in ecology-related degrees should be focused on quantitative disciplines, which is likely higher than for most existing programs. The main suggestion to improve quantitative training was to relate theoretical and statistical modeling to applied ecological problems. Improving quantitative training will require dedicated, quantitative classes for ecology-related degrees that contain good mathematical and statistical practice. How to cite this article Barraquand et al. (2014), Lack of quantitative training among early-career ecologists: a survey of the problem and potential solutions. PeerJ 2:e285; . Volterra V. 1931. Leçons sur la théorie mathématique de la lutte pour la vie. Paris: Gauthier-Villars. Williams B, Nichols J, Conroy M. 2002. Analysis and management of animal populations: modeling, estimation, and decision making. San Diego, CA: Academic Press.

Research paper thumbnail of Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape

Abstract We surveyed endophytic fungal communities in leaves of a single tree species (Metrosider... more Abstract We surveyed endophytic fungal communities in leaves of a single tree species (Metrosideros polymorpha) across wide environmental gradients (500���5,500 mm of rain/y; 10���22 C mean annual temperature) spanning short geographic distances on Mauna Loa Volcano, Hawai'i. Using barcoded amplicon pyrosequencing at 13 sites (10 trees/site; 10 leaves/tree), we found very high levels of diversity within sites (a mean of 551��134 taxonomic units per site).

Research paper thumbnail of The Nature of Identity and the Identity of Nature: Hawaiian Perspectives on Persons and Place

Academia.edu helps academics follow the latest research.

Research paper thumbnail of The next generation of peer reviewing

… in Ecology and …, Jan 1, 2011

Research paper thumbnail of Patterns of Primary Succession of Native and Introduced Plants In Lowland Wet Forests In Eastern Hawai'I

…, Jan 1, 2008

The majority of Hawaii's lowland wet forests no longer exist, with many of the last remaining pat... more The majority of Hawaii's lowland wet forests no longer exist, with many of the last remaining patches found on the eastern, windward sides of the largest islands. To better understand successional patterns and invasion in these native systems, we quantified basal area (BA) and densities of woody species and understory cover at nine sites in the Puna district on the Island of Hawai'i, representing age gradients of native stand development on both 'a'ā and pāhoehoe lava flows. On both flow types, BA of native species increased (from 5 to 50 m 2 /ha) and stem densities decreased (from 3700 to 2600 stems/ha) with increasing stand/flow age. Both native and introduced species compositions diverged between substrate types on older flows. We found that lowland wet native forests remain at least partially intact in several locations, but their functional and compositional integrity is increasingly compromised by invasion of nonnative species, such as Psidium cattleianum and Melastoma candidum, which become more common at sites greater than 300-yr old. This time period may represent a threshold, after which abiotic environmental conditions no longer constrain recruitment of introduced species. On older flows, nonnative stem densities swamped those of native species by an order of magnitude, with nonnative stems (height > 1.3 m) achieving densities as high as 18,000 stems/ha. In addition, all stands lacked recruitment of native woody species in the understory, suggesting that without management, the native componentsof these forests may soon no longer be self-sustaining.

Research paper thumbnail of Widespread plant movement in response to 20th century warming disproportionately affects endemic species

The differential responses of plant species to global warming are of great interest and grave con... more The differential responses of plant species to global warming are of great interest and grave concern for scientists and conservationists. We used> 650,000 herbaria records to estimate geographic and climatic shifts over> 100 years in 4300 plant taxa from a wide range of bioclimatic zones, functional types, and phylogeographic origins.

Research paper thumbnail of Pyrosequencing of tropical fungal endophytes provides evidence for adaptation to high elevation

Fungal endophytes, the fungi that inhabit the asymptomatic leaves of all plants surveyed to date,... more Fungal endophytes, the fungi that inhabit the asymptomatic leaves of all plants surveyed to date, represent a large and unknown component of global fungal diversity. Previous studies have shown them to exhibit a diverse range of functional roles in ecosystems, including protecting their plant host from herbivory or pathogen damage, reducing host nutrient and/or water stress, and as latent decomposers.

Research paper thumbnail of Fungals in the Jungles: Endophytic fungal diversity at the landscape scale

eco.confex.com

Academia.edu helps academics follow the latest research.

Research paper thumbnail of Data from: Patterns of primary succession of native and introduced plants in lowland wet forests in eastern Hawai 'i

Abstract The majority of Hawaii's lowland wet forests no longer exist, with many of the ... more Abstract The majority of Hawaii's lowland wet forests no longer exist, with many of the last remaining patches found on the eastern, windward sides of the largest islands. To better understand successional patterns and invasion in these native systems, we quantified ...