55 Works

A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily

Hong-Xin Wang, Diego F. Morales-Briones, Michael Moore, Jun Wen & Hua-Feng Wang
The use of diverse datasets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we employed target enrichment data and species tree and species network approaches to infer the backbone phylogeny of the family Caprifoliaceae, while distinguishing among sources of incongruence. We used 713 nuclear loci and...

Video recordings of polynoid (Annelida) swimming and crawling

Marc Christian Allentoft-Larsen, Brett C. Gonzalez, Joost Daniels, Kakani Katija, Karen Osborn & Katrine Worsaae
Annelids are predominantly found along the seafloor, but over time have colonised a vast diversity of habitats, such as the water column, where different modes of locomotion are necessary. Yet, little is known about their potential muscular adaptation to the continuously swimming required in the water column. The musculature and motility were examined for five scale worm species of Polynoidae (Aphroditiformia, Annelida) found in shallow waters, deep sea and caves that exhibit crawling, occasional swimming...

Pelagomacellicephala iliffei MicroCT-Scans for 3D reconstruction

Marc Christian Allentoft-Larsen, Brett C. Gonzalez, Joost Daniels, Kakani Katija, Karen Osborn & Katrine Worsaae
Annelids are predominantly found along the seafloor, but over time have colonised a vast diversity of habitats, such as the water column, where different modes of locomotion are necessary. Yet, little is known about their potential muscular adaptation to the continuously swimming required in the water column. The musculature and motility were examined for five scale worm species of Polynoidae (Aphroditiformia, Annelida) found in shallow waters, deep sea and caves that exhibit crawling, occasional swimming...

Leaf water relations in epiphytic ferns

Courtney Campany, Jarmila Pittermann, Alex Baer, Helen Holmlund, Eric Schuettpelz, Klaus Mehltreter &
Opportunistic diversification has allowed ferns to radiate into epiphytic niches in angiosperm dominated landscapes. However, our understanding of how ecophysiological function allowed establishment in the canopy and the potential transitionary role of the hemi-epiphytic life form remain unclear. Here, we surveyed 39 fern species in Costa Rican tropical forests to explore epiphytic trait divergence in a phylogenetic context. We examined leaf responses to water deficits in terrestrial, hemi-epiphytic, and epiphytic ferns and related these findings...

Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families

Nicholas Crouch, Stewart Edie, Katie Collins, Rüdiger Bieler & David Jablonski
Analyses of evolutionary dynamics can be profoundly affected by age calibrations of phylogenetic nodes under different models of lineage branching. Most time-calibrated molecular phylogenies of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. Lineages can also split via budding, in which a parent lineage persists following the origin of a daughter lineage, and nodes are calibrated using the age...

Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)

Xiu-Rong Ke, Diego F. Morales-Briones, Hong-Xin Wang, Qing-Hui Sun, Jacob B. Landis, Jun Wen & Hua-Feng Wang
Understanding biological diversity and the mechanisms of the Sino-Japanese disjunctions are major challenges in eastern Asia biogeography. The Sino-Japanese flora has been broadly studied as an ideal model for plant phylogeography. Diabelia (Caprifoliaceae) is an East Asian genus, with a disjunctive distribution across the Sino-Japanese region. However, relationships within Diabelia remain elusive. In this study, we reconstructed the phylogeny of Diabelia and inferred historical biogeography and evolutionary patterns based on nuclear and plastid sequences from...

Data for: Freeze tolerance influenced forest cover and hydrology during the Pennsylvanian

William Matthaeus, Sophia I. Macarewich, Jon D. Richey, Jonathan P. Wilson, Jennifer C. McElwin, Isabel P. Montañez, William A. DiMichele, Michael T. Hren, Christopher J. Poulsen & Joseph D. White
Global forest cover affects the Earth system by altering surface mass and energy exchange. Physiology determines plant environmental limits and influences geographical vegetation distribution. Ancient plant physiology, therefore, likely affected vegetation-climate feedbacks. We combine climate modeling and ecosystem-process modeling to simulate arboreal vegetation in the late Paleozoic ice age. Using GENESIS V3 GCM simulations, varying pCO2, pO2, and ice extent for the Pennsylvanian, and fossil-derived leaf C:N, maximum stomatal conductance, and specific conductivity for several...

Bay of Panama Water Quality Monitoring Project, Site 1 of 7

Steve Paton
Bay of Panama water quality monitoring program. Site #1 (of 7).
Location: 8° 38.743'N, 79° 2.887'W
Weekly depth profile (approximately 5m intervals) using YSI EXO 2 sonde.
Parameters measured temperature, salinity, conductivity, pH, turbidity, chlorophyll, Dissolved Oxygen

Bay of Panama Water Quality Monitoring Project_Temperature, all stations

Steve Paton
Bay of Panama water quality monitoring program.
Initiated July 2017

Temperature data for all stations

Depth profiles at 7 locations. Approximately 5m depth intervals

Sampling Sites
1 8° 38.743'N 79° 2.887'W
2 8° 42.498'N 78° 57.855'W
3 8° 41.894'N 79° 9.648'W
4 8° 44.138'N 79° 15.955'W
5 8° 45.670'N 79° 21.906'W
6 8° 47.078'N 79° 27.968'W
7 8° 51.308'N 79° 28.162'W

Weekly depth profile (approximately 5m intervals) using YSI EXO 2 sonde.

Bay of Panama Water Quality Monitoring Project_Dissolved Oxygen, all stations

Steve Paton
Bay of Panama water quality monitoring program.
Initiated July 2017

Dissolved Oxygen for all stations
Depth profiles at 7 locations. Approximately 5m depth intervals

Sampling Sites
1 8° 38.743'N 79° 2.887'W
2 8° 42.498'N 78° 57.855'W
3 8° 41.894'N 79° 9.648'W
4 8° 44.138'N 79° 15.955'W
5 8° 45.670'N 79° 21.906'W
6 8° 47.078'N 79° 27.968'W
7 8° 51.308'N 79° 28.162'W

Weekly depth profile (approximately 5m intervals) using YSI EXO 2 sonde.

Bay of Panama Water Quality Monitoring Project_pH, all stations

Steve Paton
Bay of Panama water quality monitoring program.
Initiated July 2017

pH data for all stations
Depth profiles at 7 locations. Approximately 5m depth intervals

Sampling Sites
1 8° 38.743'N 79° 2.887'W
2 8° 42.498'N 78° 57.855'W
3 8° 41.894'N 79° 9.648'W
4 8° 44.138'N 79° 15.955'W
5 8° 45.670'N 79° 21.906'W
6 8° 47.078'N 79° 27.968'W
7 8° 51.308'N 79° 28.162'W

Weekly depth profile (approximately 5m intervals) using YSI EXO 2 sonde.

Bay of Panama Water Quality Monitoring Project_Dissolved Organic matter, all stations

Steve Paton
Bay of Panama water quality monitoring program.
Initiated July 2017

Dissolved Oxygen measurements for all stations
Depth profiles at 7 locations. Approximately 5m depth intervals

Sampling Sites
1 8° 38.743'N 79° 2.887'W
2 8° 42.498'N 78° 57.855'W
3 8° 41.894'N 79° 9.648'W
4 8° 44.138'N 79° 15.955'W
5 8° 45.670'N 79° 21.906'W
6 8° 47.078'N 79° 27.968'W
7 8° 51.308'N 79° 28.162'W

Weekly depth profile (approximately 5m intervals) using YSI EXO 2 sonde.

Gesiella jameensis MicroCT-scans for 3D reconstruction

Marc Christian Allentoft-Larsen, Brett C. Gonzalez, Joost Daniels, Kakani Katija, Karen Osborn & Katrine Worsaae
Annelids are predominantly found along the seafloor, but over time have colonised a vast diversity of habitats, such as the water column, where different modes of locomotion are necessary. Yet, little is known about their potential muscular adaptation to the continuously swimming required in the water column. The musculature and motility were examined for five scale worm species of Polynoidae (Aphroditiformia, Annelida) found in shallow waters, deep sea and caves that exhibit crawling, occasional swimming...

Drieschia sp. MicroCT-Scans for 3D reconstruction

Marc Christian Allentoft-Larsen, Brett C. Gonzalez, Joost Daniels, Kakani Katija, Karen Osborn & Katrine Worsaae
Annelids are predominantly found along the seafloor, but over time have colonised a vast diversity of habitats, such as the water column, where different modes of locomotion are necessary. Yet, little is known about their potential muscular adaptation to the continuously swimming required in the water column. The musculature and motility were examined for five scale worm species of Polynoidae (Aphroditiformia, Annelida) found in shallow waters, deep sea and caves that exhibit crawling, occasional swimming...

Bay of Panama Water Quality Monitoring Project_Salinity, all stations

Steve Paton
Bay of Panama water quality monitoring program.
Initiated July 2017

Salinity and conductivity for all stations

Depth profiles at 7 locations. Approximately 5m depth intervals

Sampling Sites
1 8° 38.743'N 79° 2.887'W
2 8° 42.498'N 78° 57.855'W
3 8° 41.894'N 79° 9.648'W
4 8° 44.138'N 79° 15.955'W
5 8° 45.670'N 79° 21.906'W
6 8° 47.078'N 79° 27.968'W
7 8° 51.308'N 79° 28.162'W

Weekly depth profile (approximately 5m intervals) using YSI EXO 2 sonde.

Data from: Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data

Xuankun Li, Ryan St Laurent, Chandra Earl, Camiel Doorenweerd, Erik Van Nieukerken, Don Davis, Atsushi Kawakita, Shigeki Kobayashi, Andreas Zwick, Carlos Lopez-Vaamonde, Issei Ohshima & Akito Kawahara
Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially at the subfamily level, remain largely uncertain. Genomic data (83 taxa and 589 loci) were integrated with Sanger data (130 taxa and...

Environmental DNA in a global biodiversity hotspot: Lessons from coral reef fish diversity across the Indonesian archipelago

Onny Marwayana, Zachary Gold, Christopher Meyer & Paul Barber
Indonesia is the heart of the Coral Triangle, the world’s most diverse marine ecosystem. Preserving the biological and economic value of this marine biodiversity requires efficient and economical ecosystem monitoring, yet our understanding of marine biodiversity in this region remains limited. Towards this end, this study uses environmental DNA (eDNA) to survey fish communities across a well-documented biodiversity gradient in Indonesia. A total of 6,608,693 sequence reads of MiFish 12S rRNA from 39 sites spanning...

Phylogenomic reconstruction reveals new insights into the evolution and biogeography of Atta leaf-cutting ants (Hymenoptera: Formicidae)

Corina Barrera, Jeffrey Sosa-Calvo, Ted Schultz, Christian Rabeling & Maurício Bacci
Atta Fabricius is an ecologically dominant leaf-cutting ant genus, the major herbivore of the Neotropics, and an agricultural pest of great economic importance. Phylogenetic relationships within Atta have until now remained uncertain, and the delimitation and identification of a subset of Atta species are problematic. To address these phylogenetic uncertainties, we reconstruct the most comprehensive phylogenetic estimate to date of Atta by employing ultraconserved elements (UCEs). We recovered 2340 UCE loci from 224 Atta specimens,...

Supplementary information for Paleoceanographic changes in the late Pliocene promoted rapid diversification in pelagic seabirds

Joan Ferrer Obiol, Helen F. James, R. Terry Chesser, Vincent Bretagnolle, Jacob González-Solís, Julio Rozas, Andreanna J. Welch & Marta Riutort
Aim: Paleoceanographic changes can act as drivers of diversification and speciation, even in highly mobile marine organisms. Shearwaters are a group of globally distributed and highly mobile pelagic seabirds. Despite a recent well resolved phylogeny, shearwaters have controversial species limits, and show periods of both slow and rapid diversification. Here, we explore the role of paleoceanographic changes on the diversification and speciation in these highly mobile pelagic seabirds. We investigate shearwater biogeography and the evolution...

Noachian Bedrock at Endeavour Crater: Data Tables, Statistical Modeling and Locator Images

David Mittlefehldt, Ralf Gellert, Scott VanBommel, Raymond Arvidson, James W. Ashley, Benton Clark, Larry S. Crumpler, William H. Farrand, Matthew Golombek, John Grant, Richard Morris & Christian Schröder

Moorea Biocode

Neil Davies
The core goal of the Moorea Biocode Project (MBP) is to genetically barcode every non-microbial species on Moorea. We will thus create a professionally produced, verifiable (vouchered) All Taxa Biotic Inventory (ATBI) of Moorea (Output 1), together with the informatics services needed for ATBI and biocode-enabled research in Model Ecosystems (Outcome 2). We will also design a long-term plan (business model) to ensure the financial self-sustainability of biocode services, and carry out proof of concept...

Macellicephala longipalpa MicroCT-scans for 3d reconstruction

Marc Christian Allentoft-Larsen, Brett C. Gonzalez, Joost Daniels, Kakani Katija, Karen Osborn & Katrine Worsaae
Annelids are predominantly found along the seafloor, but over time have colonised a vast diversity of habitats, such as the water column, where different modes of locomotion are necessary. Yet, little is known about their potential muscular adaptation to the continuously swimming required in the water column. The musculature and motility were examined for five scale worm species of Polynoidae (Aphroditiformia, Annelida) found in shallow waters, deep sea and caves that exhibit crawling, occasional swimming...

Branchipolynoe sp. MicroCT-Scans for 3D reconstruction

Marc Christian Allentoft-Larsen, Brett C. Gonzalez, Joost Daniels, Kakani Katija, Karen Osborn & Katrine Worsaae
Annelids are predominantly found along the seafloor, but over time have colonised a vast diversity of habitats, such as the water column, where different modes of locomotion are necessary. Yet, little is known about their potential muscular adaptation to the continuously swimming required in the water column. The musculature and motility were examined for five scale worm species of Polynoidae (Aphroditiformia, Annelida) found in shallow waters, deep sea and caves that exhibit crawling, occasional swimming,...

Bipartite network datasets for Permian host-plant--insect herbivory

Anshuman Swain, S. Augusta Maccracken, William Fagan & Conrad Labandeira
Plant–insect associations have been a significant component of terrestrial ecology for over 400 million years. Exploring these interactions in the fossil record, through novel perspectives, provides a window into understanding evolutionary and ecological forces that shaped these interactions. For the past several decades, researchers have documented, described and categorized fossil evidence of these interactions. Drawing on powerful tools from network science, we propose here a bipartite network representation of fossilized plants and their herbivore-induced leaf...

Evolutionary tradeoffs between male secondary sexual traits revealed by a phylogeny of the hyperdiverse tribe Eumaeini (Lepidoptera: Lycaenidae)

Wendy A. Valencia-Montoya, Tiago B. Quental, João Filipe R. Tonini, Gerard Talavera, James D. Crall, Gerardo Lamas, Robert C. Busby, Ana Paula S. Carvalho, Ana B. Morais, Nicolás Oliveira Mega, Helena Piccoli Romanowski, Marjorie A. Liénard, Shayla Salzman, Melissa R. L. Whitaker, Akito Y. Kawahara, David J. Lohman, Robert K. Robbins & Naomi E. Pierce
Male butterflies in the hyperdiverse tribe Eumaeini possess an unusually complex and diverse repertoire of secondary sexual characteristics involved in pheromone production and dissemination. Maintaining multiple sexually selected traits is likely to be metabolically costly, potentially resulting in trade-offs in the evolution of male signals. However, a phylogenetic framework to test hypotheses regarding the evolution and maintenance of male sexual traits in Eumaeini has been lacking. Here, we infer a comprehensive, time-calibrated phylogeny from 379...

Registration Year

  • 2021
    55

Resource Types

  • Dataset
    54
  • Output Management Plan
    1

Affiliations

  • Smithsonian Institution
    55
  • Monterey Bay Aquarium Research Institute
    7
  • University of Copenhagen
    7
  • University of Chicago
    3
  • University of Florida
    3
  • Centre d'Etudes Biologiques de Chizé
    2
  • Durham University
    2
  • Washington University in St. Louis
    2
  • University of Barcelona
    2
  • Hainan University
    2