103 Works

Data from: High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

James Starrett, Shahan Derkarabetian, Marshal Hedin, , John E. McCormack, Brant C. Faircloth & Robert W. Bryson
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic...

Data from: European ornamental garden flora as an invasion debt under climate change

Emily Haeuser, Wayne Dawson, Wilfried Thuiller, Stefan Dullinger, Svenja Block, Oliver Bossdorf, Marta Carboni, Luisa Conti, Iwona Dullinger, Franz Essl, Günther Klonner, Dietmar Moser, Tamara Muenkemueller, Madalin Parepa, Matthew V. Talluto, Holger Kreft, Jan Pergl, Petr Pyšek, Patrick Weigelt, Marten Winter, Martin Hermy, Sebastiaan Van Der Veken, Cristina Roquet & Mark Van Kleunen
1.Most naturalized and invasive alien plant species were originally introduced to regions for horticultural purposes. However, many regions now face an invasion debt from ornamental alien species, which have not yet naturalized. In this regard, climate change represents a threat as it may lower the barriers to naturalization for some ornamental alien species. Identifying those species is extremely important for anticipating impending invasions. 2.To identify predictors of naturalization, we modelled the effects of climate, nursery...

Data from: Phylogenomic reclassification of the world’s most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution

Marshal Hedin, Shahan Derkarabetian, Martín J. Ramírez, Cor Vink & Jason E. Bond
Here we show that the most venomous spiders in the world are phylogenetically misplaced. Australian atracine spiders (family Hexathelidae), including the notorious Sydney funnel-web spider Atrax robustus, produce venom peptides that can kill people. Intriguingly, eastern Australian mouse spiders (family Actinopodidae) are also medically dangerous, possessing venom peptides strikingly similar to Atrax hexatoxins. Based on the standing morphology-based classification, mouse spiders are hypothesized distant relatives of atracines, having diverged over 200 million years ago. Using...

Data from: Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux

Erin A. Lynch, Morgan G. I. Langille, Aaron Darling, Elizabeth G. Wilbanks, Caitlin Haltiner, Katie S. Y. Shao, Michael O. Starr, Clotilde Teiling, Timothy T. Harkins, Robert A. Edwards, Jonathan A. Eisen, Marc T. Facciotti & Lennart Randau
We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications. Seven genomes were sequenced to ~20×coverage and assembled to an average of 50 contigs...

Data from: Sky island diversification meets the multispecies coalescent – divergence in the spruce-fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia

Marshal Hedin, Dave Carlson & Fred Coyle
Microhexura montivaga is a miniature tarantula-like spider endemic to the highest peaks of the southern Appalachian mountains and is known only from six allopatric, highly disjunct montane populations. Because of severe declines in spruce-fir forest in the late 20th century, M. montivaga was formally listed as a US federally endangered species in 1995. Using DNA sequence data from one mitochondrial and seven nuclear genes, patterns of multigenic genetic divergence were assessed for six montane populations....

Data from: Black abalone (Haliotis cracherodii) population structure shifts through deep time: Management implications for southern California's northern Channel Islands

Hannah Haas, Todd J. Braje, Matthew S. Edwards, Jon M. Erlandson & Steven G. Whitaker
For over 10,000 years, black abalone (Haliotis cracherodii) were an important resource in southern California, first for coastal Native Americans, then beginning in the nineteenth century, as one of the state's first commercial shellfisheries. By 1993, after years of heavy fishing, rising sea surface temperatures (SST), and the spread of withering syndrome (WS), black abalone populations declined dramatically, resulting in the closure of the Alta California fishery. After nearly 25 years of management and recovery...

Dataset for: Conservation genomics of federally endangered Texella harvester species (Arachnida, Opiliones, Phalangodidae) from cave and karst habitats of central Texas

Marshal Hedin, Shahan Derkarabetian, James Reddell & Pierre Paquin
Genomic-scale data for non-model taxa are providing new insights into landscape genomic structuring and species limits, leading to more informed conservation decisions, particularly in taxa with extremely restricted microhabitat preferences and small geographic distributions. This study applied sequence capture of ultraconserved elements (UCEs) to gather genomic-scale data for two federally endangered Texella harvester species distributed in Edwards Formation cave and karst habitats of central Texas, near Austin. We gathered UCE data for 51 T. reyesi...

The biogeography of community assembly: latitude and predation drive variation in community trait distribution in a guild of epifaunal crustaceans

Collin Gross, Collin Gross, J Duffy, Kevin Hovel, Melissa Kardish, Pamela Reynolds, Christoffer Boström, Katharyn Boyer, Mathiew Cusson, Johan Eklöf, Aschwin Engelen, Klemens Eriksson, Joel Fodrie, John Griffin, Clara Hereu, Masakazu Hori, A Randall Hughes, Mikhail Ivanov, Pablo Jorgensen, Claudia Kruschel, Kun-Seop Lee, Jonathan Lefcheck, Karen McGlathery, Per-Olav Moksnes, Masahiro Nakaoka … & Jay Stachowicz
While considerable evidence exists of biogeographic patterns in the intensity of species interactions, the influence of these patterns on variation in community structure is less clear. Using a model selection approach on measures of trait dispersion in crustaceans associated with eelgrass (Zostera marina) spanning 30º of latitude in two oceans, we found that dispersion strongly increased with increasing predation and decreasing latitude. Ocean and epiphyte load appeared as secondary predictors; Pacific communities were more overdispersed...

Data from: Phylogenomics of paleoendemic lampshade spiders (Araneae, Hypochilidae, Hypochilus), with description of a new species from montane California

Erik Ciaccio, Andrew Debray & Marshal Hedin
The spider genus Hypochilus is a relictual lineage of Nearctic species distributed disjunctly across the United States in three montane regions (California, southern Rocky Mountains, southern Appalachia). Phylogenetic resolution of species relationships in Hypochilus has been challenging, with different data types recovering sometimes conflicting topologies. Furthermore, conserved morphology coupled with extreme genetic divergence and paraphyletic topologies at the species level has led to uncertain species limits in some complexes. Using a combination of ultraconserved elements...

Coupled changes in pH, temperature and dissolved oxygen impact the physiology and ecology of herbivorous kelp forest grazers

Emily Donham, Lauren Strope, Scott Hamilton & Kristy Kroeker
Understanding species’ responses to upwelling may be especially important in light of ongoing environmental change. Upwelling frequency and intensity are expected to increase in the future, while ocean acidification and deoxygenation are expected to decrease the pH and dissolved oxygen of upwelled waters. However, the acute effects of a single upwelling event and the integrated effects of multiple upwelling events on marine organisms are poorly understood. Here, we use in situ measurements of pH, temperature,...

Sitticine jumping spiders: phylogeny, classification and chromosomes (Araneae: Salticidae: Sitticini)

Wayne Maddison, David Maddison, Shahan Derkarabetian & Marshal Hedin
We review the systematics of sitticine jumping spiders, with a focus on the Palearctic and Nearctic regions, in order to revise their generic classification, clarify the species of one region (Canada), and study their chromosomes. A genome-wide molecular phylogeny of 23 sitticine species, using more than 700 loci from the arachnid Ultra-Conserved Element (UCE) probeset, confirms the Neotropical origins of sitticines, whose basal divergence separates the new subtribe Aillutticina (a group of 5 Neotropical genera)...

Data from: Phosphorus alleviation of nitrogen-suppressed methane sink in global grasslands

Lihua Zhang, Fenghui Yuan, Junhong Bai, Hongtao Duan, Xueying Gu, Longyu Hou, Yao Huang, Mingan Yang, Jinsheng He, Zhenghua Zhang, Lijun Yu, Changchun Song, David Lipson, Donatella Zona, Walter Oechel, Ivan Janssens & Xiaofeng Xu
Grassland ecosystems account for more than 10% of the global CH4 sink in soils. A 4-year field experiment found that addition of P alone did not affect CH4 uptake and experimental addition of N alone significantly suppressed CH4 uptake, while concurrent N and P additions suppressed CH4 uptake to a lesser degree. A meta-analysis including 382 data points in global grasslands corroborated these findings. Global extrapolation with an empirical modeling approach estimated that contemporary N...

Evolutionary divergences mirror Pleistocene paleodrainages in a rapidly-evolving complex of oasis-dwelling jumping spiders (Salticidae, Habronattus tarsalis)

Marshal Hedin, Steven Foldi & Brendan Rajah-Boyer
We aimed to understand the diversification history of jumping spiders in the Habronattus tarsalis species complex, with particular emphasis on how history in this system might illuminate biogeographic patterns and processes in deserts of the western United States. Desert populations of H. tarsalis are now confined to highly discontinuous oasis-like habitats, but these habitats would have been periodically more connected during multiple pluvial periods of the Pleistocene. We estimated divergence times using relaxed molecular clock...

Bill size, bill shape, and body size constrain bird song evolution on a macroevolutionary scale

Amelia-Juliette Demery, Kevin Burns & Nicholas Mason
Studying macroevolutionary patterns of phenotypic variation and their driving forces in large radiations can shed light on how biodiversity is generated across broad spatiotemporal scales. In this study, we integrated song and morphological variation across more than 300 species representing the largest family of songbirds, the tanagers (Thraupidae), to uncover how morphological variables of the vocal tract combine to shape vocal evolution on a macroevolutionary scale. We found that body size correlated with multiple frequency...

Data from: Accounting for variation in temperature and oxygen availability when quantifying marine ecosystem metabolism

Matthew Bracken, Luke Miller, Sarah Mastroni, Stephany Lira & Cascade Sorte
Given human modification of Earth’s ecosystems, it is essential to understand how these changes are influencing ecosystem functioning, including net and gross community production and community respiration. These responses are often estimated by measuring oxygen production in the light (net community production) and consumption in the dark (community respiration). These values can then be combined to estimate gross community production. However, the method used to create “dark” conditions – either experimental darkening during the day...

Soil dissolved organic carbon in terrestrial ecosystems: global budget, spatial distribution and controls

Xiaofeng Xu, Ziyu Guo, Yihui Wang & Zhongmei Wan
Aims: Soil dissolved organic carbon (DOC) is a primary form of labile carbon in terrestrial ecosystems and therefore plays a vital role in soil carbon cycling. This study aims to quantify the budgets of soil DOC at biome- and global levels and to examine the variations in soil DOC and their environmental controls. Location: Global Time period: 1981 - 2019 Method: We compiled a global dataset and analyzed the concentration and distribution of DOC across...

Automated total and heterotrophic soil respiration in semi-arid shrubland and annual invasive patches

Marguerite Mauritz & David A Lipson
Soil respiration (Rs) is the largest terrestrial source of carbon (C) flux to the atmosphere but our understanding of Rs controls with shifts in plant-community composition remains limited. We used high frequency soil respiration measurements and root exclusion to evaluate how Rs component fluxes, autotrophic respiration (Ra) and heterotrophic respiration (Rh), vary between a perennial semi-arid shrub community and annual invasive community.

Data from: Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux

Erin A. Lynch, Morgan G. I. Langille, Aaron Darling, Elizabeth G. Wilbanks, Caitlin Haltiner, Katie S. Y. Shao, Michael O. Starr, Clotilde Teiling, Timothy T. Harkins, Robert A. Edwards, Jonathan A. Eisen & Marc T. Facciotti
We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications. Seven genomes were sequenced to ~20×coverage and assembled to an average of 50 contigs...

Data from: Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes

David E. Carlson & Marshal Hedin
Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus...

Data from: Integrative taxonomy and species delimitation in harvestmen: a revision of the western North American genus Sclerobunus (Opiliones: Laniatores: Travunioidea)

Shahan Derkarabetian & Marshal Hedin
Alpha taxonomy, and specifically the delimitation of species, is becoming increasingly objective and integrative. The use of coalescent-based methods applied to genetic data is providing new tools for the discovery and delimitation of species. Here, we use an integrative approach via a combination of discovery-based multivariate morphological analyses to detect potential new species. These potential species are then used as a priori species in hypothesis-driven validation analyses with genetic data. This research focuses on the...

Data from: Potential limitations of behavioral plasticity and the role of egg relocation in climate change mitigation for a thermally-sensitive endangered species

Michael J. Liles, Tarla Rai Peterson, Jeffrey A. Seminoff, Alexander R. Gaos, Eduardo Altamirano, Ana V. Henríquez, Velkiss Gadea, Sofía Chavarría, José Urteaga, Bryan P. Wallace & Markus J. Peterson
Anthropogenic climate change is widely considered a major threat to global biodiversity, such that the ability of a species to adapt will determine its likelihood of survival. Egg-burying reptiles that exhibit temperature-dependent sex determination, such as critically endangered hawksbill turtles (Eretmochelys imbricata), are particularly vulnerable to changes in thermal regimes because nest temperatures affect offspring sex, fitness, and survival. It is unclear whether hawksbills possess sufficient behavioral plasticity of nesting traits (i.e., redistribution of nesting...

Data from: Post-fire recovery in coastal sage scrub: seed rain and community trajectory

Erin Conlisk, Rebecca Swab, Alejandra Martínez-Berdeja & Matthew P. Daugherty
Disturbance is a primary mechanism structuring ecological communities. However, human activity has the potential to alter the frequency and intensity of natural disturbance regimes, with subsequent effects on ecosystem processes. In Southern California, human development has led to increased fire frequency close to urban areas that can form a positive feedback with invasive plant spread. Understanding how abiotic and biotic factors structure post-fire plant communities is a critical component of post-fire management and restoration. In...

Data from: Dynamic measurements of black oystercatcher (Haematopus bachmani) predation on mussels (Mytilus californianus)

Luke P. Miller & William W. Dowd
Intertidal zone mussels can face threats from a variety of predatory species during high and low tides, and they must balance the threat of predation against other needs such as feeding and aerobic respiration. Black oystercatchers (Haematopus bachmani) on the Pacific coast of North America can depend on the mussel Mytilus californianus for a substantial portion of their diet. Observations suggest that oystercatchers tend to focus on mussels beginning to gape their valves during rising...

Data from: Determinants of predation success: how to survive an attack from a rattlesnake

Malachi D. Whitford, Grace A. Freymiller, Timothy E. Higham & Rulon W. Clark
1. The selection pressures that arise from capturing prey and avoiding predators are some of the strongest biotic forces shaping animal form and function. Examining how performance (i.e., athletic ability) affects the outcomes of encounters between free-ranging predators and prey is essential for understanding the factors that determine predation success rates and broad scale predator–prey dynamics, but quantifying these encounters in natural situations is logistically challenging. 2. The goal of our study was to examine...

Data from: A global dataset for economic losses of extreme hydrological events during 1960-2014

Bo Tao, Liping Gao, Yunxuan Miao, Lihua Zhang, Xia Song, Wei Ren, Liyuan He & Xiaofeng Xu
A comprehensive dataset of extreme hydrological events (EHEs) – floods and droughts, consisting of 2,171 occurrences worldwide, during 1960‐2014 was compiled, and then their economic losses were normalized using a price index in U.S. dollar. The dataset showed a significant increasing trend of EHEs before 2000, while a slight post‐2000 decline. Correspondingly, the EHEs‐caused economic losses increased obviously before 2000 followed by a slight decrease; the post‐2000 decline could be partially attributed to the decreases...

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