David K. Jacobs

David K. Jacobs
University of California, Los Angeles | UCLA · Department of Ecology and Evolutionary Biology

PHD, 1990 VPI & SU

About

225
Publications
37,330
Reads
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5,495
Citations
Citations since 2017
36 Research Items
1672 Citations
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2017201820192020202120222023050100150200250300
2017201820192020202120222023050100150200250300
2017201820192020202120222023050100150200250300
Additional affiliations
January 1994 - December 2007
January 1994 - December 2007
January 1990 - present

Publications

Publications (225)
Article
Full-text available
Habitat loss, flood control infrastructure, and drought have left most of southern California and northern Baja California’s native freshwater fish near extinction, including the endangered unarmored threespine stickleback (Gasterosteus aculeatus williamsoni). This subspecies, an unusual morph lacking the typical lateral bony plates of the G. acule...
Article
Full-text available
DNA methylation, an important component of eukaryotic epigenetics, varies in pattern and function across Metazoa. Notably, bilaterian vertebrates and invertebrates differ dramatically in gene body methylation (GbM). Using the frequency of cytosine-phospho-guanines (CpGs), which are lost through mutation when methylated, we report the first broad su...
Article
Full-text available
Scleractinian corals typically form a robust calcium carbonate skeleton beneath their living tissue. This skeleton, through its trace element composition and isotope ratios, may record environmental conditions of water surrounding the coral animal. While bulk unrecrystallized aragonite coral skeletons can be used to reconstruct past ocean condition...
Article
The extinction of California’s flightless duck, Chendytes lawi, stands out in the faunal history of North America because it involved a marine animal that disappeared in the late Holocene, not in the terminal Pleistocene when humans arrived from Asia, nor with the more recent entry of Europeans and associated resource exploitation. Here we evaluate...
Article
Full-text available
Here we report the first recovery, sequencing, and identification of fossil biomineral proteins from a Pleistocene fossil invertebrate, the stony coral Orbicella annularis. This fossil retains total hydrolysable amino acids of a roughly similar composition to extracts from modern O. annularis skeletons, with the amino acid data rich in Asx (Asp + A...
Article
Full-text available
We are among the scientists who have documented the environmental and ecological changes to the Upper Gulf of California following the reduction in the Colorado River’s flow. We object to any suggestion that our research supports Manjarrez-Bringas et al.’s conclusion that the decline in the Colorado River’s flow is the reason for the decline in the...
Article
Full-text available
We present the genome of the moon jellyfish Aurelia, a genome from a cnidarian with a medusa life stage. Our analyses suggest that gene gain and loss in Aurelia is comparable to what has been found in its morphologically simpler relatives—the anthozoan corals and sea anemones. RNA sequencing analysis does not support the hypothesis that taxonomical...
Preprint
Full-text available
In his enthusiasm to highlight the impacts of fisheries in the Gulf of California, Richard Brusca (Brusca 2018) attacks our paper which is about a largely separate issue, makes false claims, does a disservice to his own cause, and undermines science. Brusca sets out to defame our work because, as he states, he fears that third parties will misuse w...
Preprint
Full-text available
In his enthusiasm to highlight the impacts of fisheries in the Gulf of California, Richard Brusca (Brusca 2018) attacks our paper which is about a largely separate issue, makes false claims, does a disservice to his own cause, and undermines science. Brusca sets out to defame our work because, as he states, he fears that third parties will misuse w...
Article
Plate tectonics and sediment processes control regional continental shelf topography. We examine the genetic consequences of how glacial-associated sea-level change interacted with variable near-shore topography since the last glaciation. We reconstructed the size and distribution of areas suitable for tidal estuary formation from the Last Glacial...
Article
Full-text available
We investigate hybridization and introgression between ecologically distinct sister species of silverside fish in the Gulf of California through combined analysis of morphological, sequence, and genotypic data. Water diversions in the past century turned the Colorado River Delta from a normal estuary to a hypersaline inverse estuary, raising concer...
Data
Radiographs of vertebral differences Radiographs of a C. hubbsi specimen (A) and a C. regis specimen (B); arrow in (B) shows the expanded process in the hemal spines of C. regis.
Data
Boxplots of the DAPC coordinates for specimens in the hybrid zone
Data
Microsatellite allele frequencies Frequencies of each microsatellite alleles at each sampling locale. Microsatellite alleles are arranged by size. Number in parentheses under each locale denotes number of individuals analyzed.
Data
C. regis Cyt b sequence data
Data
C. hubbsi Cyt b sequence data
Data
STRUCTURE assignment of individuals to groups (K = 3 and K = 4) Structure plots for the correlated allele frequency model for K = 3 (top) and K = 4 (bottom).
Data
External morphological measurements of a historic collection of Colpichthys Measurements of the external morphology of C. regis specimens collected in 1968 at the San Felipe site. SL, standard length; Snout-D1, length from snout to first dorsal fin origin; DLS, dorsolateral scale count. Measurements for specimen 16 (in bold) identify it as C. hubbs...
Data
Description of raw data formats
Article
Full-text available
Chendytes lawi, an extinct flightless diving anseriform from coastal California, was traditionally classified as a sea duck, tribe Mergini, based on similarities in osteological characters. We recover and analyze mitochondrial genomes of C. lawi and five additional Mergini species, including the extinct Labrador Duck, Camptorhyncus labradorius. Des...
Preprint
Full-text available
We investigate hybridization and introgression between ecologically distinct sister species of silverside fish in the Gulf of California through combined analysis of morphological, sequence, and genotypic data. Water diversions in the past century turned the Colorado River Delta from a normal estuary to a hypersaline inverse estuary, raising concer...
Preprint
Full-text available
We investigate hybridization and introgression between ecologically distinct sister species of silverside fish in the Gulf of California through combined analysis of morphological, sequence, and genotypic data. Water diversions in the past century turned the Colorado River Delta from a normal estuary to a hypersaline inverse estuary, raising concer...
Article
Full-text available
Using a novel combination of palaeohabitat modelling and genetic mixture analyses, we identify and assess a sea-level-driven recolonization process following the Last Glacial Maximum (LGM). Our palaeohabitat modelling reveals dramatic changes in estuarine habitat distribution along the coast of California (USA) and Baja California (Mexico). At the...
Article
Full-text available
The moon jellyfish Aurelia exhibits a dramatic reorganization of tissue during its metamorphosis from planula larva to polyp. There are currently two competing hypotheses regarding the fate of embryonic germ layers during this metamorphosis. In one scenario, the original endoderm undergoes apoptosis and is replaced by a secondary endoderm derived f...
Article
Full-text available
A geographically isolated set of southern localities of the formerly monotypic goby genus Eucyclogobius is known to be reciprocally monophyletic and substantially divergent in mito-chondrial sequence and nuclear microsatellite-based phylogenies relative to populations to the north along the California coast. To clarify taxonomic and conservation st...
Data
Locality information used in mapping. These data are mapped in Fig 6, and S1–S3 Figs. (DOCX)
Data
Synonymy and Valid Literature References. (DOCX)
Data
Distribution of E. newberryi from Santa Cruz County to North Santa Barbara County. See S1 Text for mapped data. (TIF)
Data
Size adjusted data for discriminant analyses. (XLSX)
Data
Distribution of E. newberryi in del Norte and Humboldt Counties. See S1 Text for mapped data. (TIF)
Data
Distribution of E. newberryi from Mendocino County to San Mateo County. See S1 Text for mapped data. (TIF)
Data
Measures and counts used in analyses. (XLSX)
Data
Fin ray and vertebral counts from both species of Eucyclogobius. (XLSX)
Data
Free neuromast and shoulder papillae counts from both species of Eucyclogobius. See Fig 2 for location of lines of neuromasts. (XLSX)
Conference Paper
The endangered closed-estuary specialist goby genus Eucyclogobius, the tidewater gobies, is the most locally-differentiated vertebrate taxon on the Pacific coast. It is subdivided into regional clades, which are further subdivided into long-isolated entities. Clades and subclades exhibit regionally distinct metapopulation processes. In addition, th...
Article
Full-text available
Intermittent estuaries are temporarily open to exchange with the open ocean, and the influence of their entrance opening regime on hydrological and ecological function has received considerable attention. Here we consider the influence of tectonic, climatic and geomorphic controls on the distribution of estuarine habitats by contrasting two setting...
Article
Full-text available
Despite numerous attempts, classification of the Precambrian fossil Dickinsonia has eluded scientific consensus. This is largely because Dickinsonia and its relatives are structurally simple, lacking morphological synapomorphies to clarify their relationship to modern taxa. However, there is increasing precedence for using ontogeny to constrain eni...
Article
Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction-colonization are potentially fraught with detection bias and have rarely been validated. Here we provide a comparison of molecular and field-based approaches for assessment of the ext...
Article
Full-text available
Tentacles armed with stinging cells (cnidocytes) are a defining trait of the cnidarians, a phy-lum that includes sea anemones, corals, jellyfish, and hydras. While cnidarian tentacles are generally characterized as structures evolved for feeding and defense, significant variation exists between the tentacles of different species, and within the sam...
Article
Full-text available
In Bilateria, Pax6, Six, Eya and Dach families of transcription factors underlie the development and evolution of morphologically and phyletically distinct eyes, including the compound eyes in Drosophila and the camera-type eyes in vertebrates, indicating that bilaterian eyes evolved under the strong influence of ancestral developmental gene regula...
Data
Full-text available
The chambered cephalopod shell has long been a subject of scientific investigation. However, a rudimentary understanding of the function of the shell in supporting external pressure was not achieved until the early 1960s. This functional issue is a relatively simple one: Did the chambered shell contain pressurized gas opposing the external water pr...
Conference Paper
Full-text available
Pleistocene glacial cycles are a foremost influence on the genetic diversity and species distribution patterns observed today. Though much work has centered on biotic response to such climatic forcing, little of it has regarded estuarine or other aquatic coastal taxa whose habitat formation is a function of sea level, hydrography, and coastal geomo...
Article
Full-text available
The POU genes represent a diverse class of animal-specific transcription factors that play important roles in neurogenesis, pluripotency, and cell-type specification. Although previous attempts have been made to reconstruct the evolution of the POU class, these studies have been limited by a small number of representative taxa, and a lack of sequen...
Conference Paper
Full-text available
Much work has centered on understanding the impact of Pleistocene glacial cycles on patterns of genetic diversity and ranges of modern species. Here we address such questions comparatively across three fishes in the estuaries of southern and Baja California where slope and bathymetry exert primary control over habitat formation through time. We pre...
Data
##Assembly-Data-START## Assembly Method :: Trinity v. trinityrnaseq_r2013_08_14. Sequencing Technology :: Illumina ##Assembly-Data-END##
Data
##Assembly-Data-START## Assembly Method :: Trinity v. trinityrnaseq_r2013_08_14. Sequencing Technology :: Illumina ##Assembly-Data-END##
Data
##Assembly-Data-START## Assembly Method :: Trinity v. trinityrnaseq_r2013_08_14. Sequencing Technology :: Illumina ##Assembly-Data-END##
Data
##Assembly-Data-START## Assembly Method :: Trinity v. trinityrnaseq_r2013_08_14. Sequencing Technology :: Illumina ##Assembly-Data-END##