A5030022002- Amphibian and Reptile Biology
- Species Distribution and Climate Change
- Genetic diversity and population structure
- Plant and animal studies
- Genomics and Phylogenetic Studies
- Animal Behavior and Reproduction
- Evolution and Paleontology Studies
- Ecology and Vegetation Dynamics Studies
- Primate Behavior and Ecology
- Environmental DNA in Biodiversity Studies
- Bat Biology and Ecology Studies
- Wildlife Ecology and Conservation
- Physiological and biochemical adaptations
- Animal and Plant Science Education
- Turtle Biology and Conservation
- Molecular Biology Techniques and Applications
- Antimicrobial Peptides and Activities
- Knee injuries and reconstruction techniques
- Total Knee Arthroplasty Outcomes
- Identification and Quantification in Food
- Plant Diversity and Evolution
- Spider Taxonomy and Behavior Studies
- Morphological variations and asymmetry
- Viral Infections and Vectors
- Paleontology and Evolutionary Biology
Museum of Vertebrate Zoology
2016-2025
University of California, Berkeley
2016-2025
University of California System
2008-2025
Berkeley College
2025
Indonesian Institute of Sciences
2022
Google (United States)
2019
Bandung Institute of Technology
2014
Integra (United States)
2004-2013
Stevens Institute of Technology
2009-2010
Marquette University
2010
The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs increase sequencing efficiency, with concomitant development improved annotation technology and, therefore, propose to create collection tissue DNA specimens 10 000 specifically designated the very near future. For this purpose, we, Genome 10K Community...
Until recently, it was believed that complex phylogenies might be extremely difficult to reconstruct due the phenomenal rate of increase in number possible as taxa increases. However, Hillis (1996) showed through simulation that, for at least one phylogeny angiosperms with 228 taxa, reconstruction far more accurate than expected, even relatively modest amounts DNA sequence data. This led a flurry papers on subject taxon sampling and phylogenetic reconstruction, focus quickly shifting from...
How biotic interactions, current and historical environment, biogeographic barriers determine community structure is a fundamental question in ecology evolution, especially diverse tropical regions. To evaluate patterns of local regional diversity, we quantified the phylogenetic composition 189 hummingbird communities Ecuador. We assessed how species changed along environmental gradients across barriers. show that humid, low-elevation are phylogenetically overdispersed (coexistence distant...
Abstract Batesian mimicry, in which harmless species (mimics) deter predators by deceitfully imitating the warning signals of noxious (models), generates striking cases phenotypic convergence that are classic examples evolution natural selection. However, mimicry venomous coral snakes has remained controversial because unresolved conflict between predictions theory and empirical patterns distribution abundance snakes. Here we integrate distributional, phylogenetic data across all New World...
Rosenberg and Kumar (2001) addressed the importance of taxon sampling in phylogenetic analysis concluded that error is “largely independent sample size” (2001:10756) their “results do not provide evidence favor adding taxa to problematic phylogenies” (2001:10756). In response these conclusions, Zwickl Hillis (2002) Pollock et al. conducted additional simulations reanalyzed data presented by (2001). showed conclusions could be supported either analyses original or new corrected a number...
We investigate the roles of mitochondrial introgression and incomplete lineage sorting during phylogenetic history crotaphytid lizards. Our Bayesian estimate for Crotaphytidae is based on analysis DNA sequence data 408 individuals representing 12 extant species Crotaphytus Gambelia. The phylogeny disagrees in several respects with a previously published morphological tree, as well conventional designations, we conclude that some this disagreement stems from hybridization-mediated...
Hummingbirds are an important model system in avian biology, but to date the group has been subject of remarkably few phylogenetic investigations. Here we present partitioned Bayesian and maximum likelihood analyses for 151 approximately 330 species hummingbirds 12 outgroup taxa based on two protein-coding mitochondrial genes (ND2 ND4), flanking tRNAs, nuclear introns (AK1 BFib). We analyzed these data under several partitioning strategies ranging between unpartitioned a nine partitions. In...
Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, these contingent properties of species provide the operational criteria necessary for delimitation. We inferred historical lineage formation in coast horned lizard (Phrynosoma coronatum) complex by evaluating diversity criteria, including mtDNA (98 specimens; 2,781 bp) nuclear loci (RAG-1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic...
The interface of the Asian and Australian faunal zones is defined by a network deep ocean trenches that separate intervening islands Philippines Wallacea (Sulawesi, Lesser Sundas, Moluccas). Studies this region Wallace marked genesis field biogeography, yet few workers have used molecular methods to investigate biogeography taxa whose distribution spans interface. Some taxa, such as fanged frogs ranid genus Limnonectes, distributions on either side zoogeographical lines Huxley, offering an...
Recent phylogenetic analyses of cetacean relationships based on DNA sequence data have challenged the traditional view that baleen whales (Mysticeti) and toothed (Odontoceti) are each monophyletic, arguing instead sister group odontocete family Physeteridae (sperm whales). We reexamined this issue in light a morphological set composed 207 characters molecular sets published 12S, 16S, cytochrome b mitochondrial sequences. reach four primary conclusions: (1) Our strongly supports monophyly;...
Animals that sustain high levels of aerobic activity under hypoxic conditions (e.g., birds fly at altitude) face the physiological challenge jointly optimizing blood-O2 affinity for O2 loading in pulmonary circulation and unloading systemic circulation. At altitude, this is especially acute small endotherms like hummingbirds have exceedingly mass-specific metabolic rates. Here we report an experimental analysis hemoglobin (Hb) function South American revealed a positive correlation between...
A biomechanically parsimonious hypothesis for the evolution of flapping flight in terrestrial vertebrates suggests progression within an arboreal context from jumping to directed aerial descent, gliding with control via appendicular motions, and ultimately powered flight. The more than 30 phylogenetically independent lineages vertebrate gliders lend strong indirect support ecological feasibility such a trajectory. Insect likely followed similar sequence, but is unresolved paleontologically....
We describe a new species of fanged frog (Limnonectes larvaepartus) that is unique among anurans in having both internal fertilization and birth tadpoles. The endemic to Sulawesi Island, Indonesia. This the fourth valid Limnonectes described from despite radiation includes at least 15 possibly many more. Fewer than dozen 6455 frogs world are known have fertilization, these, all but either deposit fertilized eggs or give froglets.
For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological (i.e. amphibians reptiles), attempts to extract sequence DNA from formalin-fixed, ethanol-preserved specimens-particularly use phylogenetic analyses-has been laborious largely ineffective due highly fragmented nature DNA. As a result, tens thousands have not available sequence-based studies....
Abstract Aim To investigate the association between hummingbird–plant network structure and species richness, phylogenetic signal on species' interaction pattern, insularity historical current climate. Location Fifty‐four communities along a c . 10,000 km latitudinal gradient across A mericas (39° N –32° S ), ranging from sea level to 3700 m a.s.l., located mainland islands covering wide range of climate regimes. Methods We measured specialization modularity in mutualistic plant–hummingbird...
The recent description of Cyrtodactylus tahuna from Sangihe Island and descriptions other new species remote islands in the Indo-Australian Archipelago indicate important role oceanic dispersal isolation evolution diversification genus Cyrtodactylus. We provide another example involving Tanahjampea Island, a island 155 km south Southwestern Peninsula Sulawesi, Indonesia. Here, we describe on basis 11 specimens collected that island. This is an intermediate sized with snout–vent length up to...
Lepidodactylus pantai is a new species of gecko from the Kei Islands, Maluku, Indonesia that closely associated with intertidal habitats. This does not fit cleanly into any three groups described for genus because it possesses unique combination both divided terminal scansors on all toes and nearly completely cylindrical tail without fringes or evidence dorsoventral compression. A phylogenetic analysis including this demonstrates sister taxon population Palau, clade to containing Group III...
We describe the sixth species of bent-toed gecko from Lesser Sunda Islands, Indonesia. This was first collected on banks Oi Marai River low northern slopes Gunung (Mount) Tambora Sumbawa Island. The new is differentiated Greater Islands (including Sulawesi) and congeners by having following unique combination characters: (1) two scales between second pair postmentals in contact with pair; (2) dorsal surface antebrachium tuberculate; (3) no tubercles brachium; (4) surfaces thigh crus (5) 18...
Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics phylogenetics of nonmodel organisms. To multiplex large numbers indexed samples while predominantly orthologous, targeted regions the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes enrich pools genomic subset interest. The sequence using PCR-generated (SCPP) protocol requires no...
Abstract Parasite host switches may trigger disease emergence, but prehistoric ranges are often unknowable. Lymphatic filariasis and loiasis major human diseases caused by the insect-borne filarial nematodes Brugia , Wuchereria Loa . Here we show that genomes of these seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83–99% nucleotide identity between genomes, their phylogenetic distribution,...
Field biology is an area of research that involves working directly with living organisms in situ through a practice known as "fieldwork." Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting local communities at field sites, and collaborative led by one few the core team members. However, existing power imbalances stemming from geopolitical history, discrimination, professional position, among other factors, perpetuate...