A list of the top 50 Whale Rock Capital Management holdings showing which stocks are owned by Alex Sacerdote's hedge fund.

The National Marine Fisheries Service (NMFS) has conducted shore-based counts of the Eastern North Pacific stock of gray whales (Eschrichtius robustus) 26 years from 1967 to 2008 at Granite Canyon (or nearby at Yankee Point), 13 km south of Carmel, in central California. Convenient access to the Granite Canyon research station (owned by NOAA but operated by the State of California Department of Fish and Game) and the narrowness of the whales' migratory corridor in this area permitted an efficient counting process at this site. All counts were conducted during the 2-month southbound migration (mid-December to late February) rather than the protracted 3-month northbound migration. The routine nature of these counts and the consistency in research protocol lend themselves to inter-annual trend analyses. Research protocol has been based on single observers independently searching for whales and recording data on environmental conditions and the time, location, count, and direction of travel for each sighting. The counting system and observer performance has been tested through paired, independent observational effort; aerial surveys; thermal imagery; radio-tagging of whales; systematic observations through high-powered (25x) binoculars; and teams of observers tracking specific whale pods through the viewing area.

The difficulties associated with detecting population boundaries have long constrained the conservation and management of highly mobile marine species, especially for wide-ranging cetaceans such as killer whales (Orcinus orca). In this study, we use molecular genetic data to test a priori hypotheses about population subdivisions generated from a decade of killer whale surveys across the northern North Pacific. A total of 462 skin biopsies were collected from free-swimming killer whales from 1990 to 2010 between the northern Gulf of Alaska in the east and the Sea of Okhotsk in the west, representing both the piscivorous resident and the mammal-eating Biggs (or transient) killer whales. Geographic patterns of genetic differentiation were supported by significant regions of genetic discontinuity providing evidence of population structuring within both lineages, and corroborating direct observations of restricted movements of individual whales. In the Aleutian Islands (Alaska), population strata were largely delimited by major oceanographic boundaries for resident killer whales. In contrast, subdivisions among Biggs killer whales indicated multiple genetic clusters in the Eastern Aleutians and Bering Sea. The presence of sympatric genetic clusters within Biggs whales suggests the presence of isolating mechanisms other than geographic distance within this highly mobile top predator.

Density dependence only affects increase rates in baleen whale populations at high abundance levels

Overview of files hosted on Dryad

Each file contains a time series of catch records by species/population and location, with two columns: 1. year, and 2. catch number.

Models

"StanSimulation0.stan" (Stan code for the logistic model with fixed z =2.39)

"StanSimulation.stan" (Stan code for the logistic model with estimating z value)

Overview of files hosted on Zenodo

Abundance time-series

"Abund.Bowhead.csv" (Abundance data for bowhead whales)

"Abund.GR.csv" (Abundance data for gray whales)

"Abund.Hbk.csv" (Abundance data for USWC humpback whales)

"Abund.HbkAusNoad2019.csv" (Abundance data for EAUS humpback whales)

"Abund.HbkAusSpueBb.csv" (Relative abundance data for EAUS humpback whales)

"Abund.HbkAusSpueppc.csv" (Relative abundance data for EAUS humpback whales)

"Abund.HbkAusSpuesol.csv" (Relative abundance data for EAUS humpback whales)

Descrip...

This dataset is comprised of data from ice-based visual census studies to estimate the abundance of the Bering-Chukchi-Beaufort Seas (BCBS) stock of bowhead whales (Balaena mysticetus). These counts take place off Point Barrow, Alaska, in the spring, as the whales migrate from the Bering to the Beaufort Sea. They were conducted annually from 1978 to 1988 and again in 1993 and 2001. Adverse environmental conditions led to counts inadequate to support abundance estimates in 1979 and 1984. The data provide an estimate of the number of whales that passed within the 4km visual range of the observation perch from which the whales are counted. This dataset is part of the Pacific Marine Arctic Regional Synthesis (PacMARS) Project.

Gray whale SNP genotypesThe data include SNP genotypes from gray whales for genic regions.SNP_genotypes_gray_whales.txt

Southern Resident Killer Whales (SRKW) are listed as a Distinct Population Segment under the Endangered Species Act. Data concerning their prey species and stock specific consumption estimates for SRKW in their summer range is important to understand trophic effects influencing their distribution and abundance. Estimates of these parameters allow prediction of population level responses to prey...

Once hunted to the brink of extinction, humpback whales (Megaptera novaeangliae) in the North Atlantic have recently been increasing in numbers. However, uncertain information on past abundance makes it difficult to assess the extent of the recovery in this species. While estimates of pre-exploitation abundance based upon catch data suggest the population might be approaching pre-whaling numbers, estimates based on mtDNA genetic diversity suggest they are still only a fraction of their past abundance levels. The difference between the two estimates could be accounted for by inaccuracies in the catch record, by uncertainties surrounding the genetic estimate, or by differences in the timescale to which the two estimates apply. Here we report an estimate of long-term population size based on nuclear gene diversity. We increase the reliability of our genetic estimate by increasing the number of loci, incorporating uncertainty in each parameter and increasing sampling across the geographic range. We report an estimate of long-term population size in the North Atlantic humpback of ~112,000 individuals (95% CI: 45,000 – 235,000). This value is 2-3 fold higher than estimates based upon catch data. This persistent difference between estimates parallels difficulties encountered by population models in explaining the historical crash of North Atlantic humpback whales. The remaining discrepancy between genetic and catch-record values, and the failure of population models, highlights a need for continued evaluation of whale population growth and shifts over time, and continued caution about changing the conservation status of this population.

Southern right whale population modelThis is the R script used to conduct the population assessments. Two example calls are also given.SRW_SIR_pop_model_REV.rSouthern right whale catch series for New Zealand and Southeast PacificCatch series data, as described in Carroll et al. 2014 (PLoS One 9:e93789), for input into population assessment model.Catch_inputs.csv

Humpback whales undertake one of the longest known migrations of any mammal. While their migration route generally extends between latitudes, the breeding stocks are longitudinally separated and display high site fidelity to their feeding grounds. While there is an indication of certain breeding stocks overlapping with each other, the current information on the migration routes of humpback whales within the Southern Hemisphere limits our understanding on the extent of this exchange. Here, we present the longest documented great-circle distance between sightings on wintering grounds of two different Ocean basins of an adult male humpback whale between two breeding stocks in the eastern Pacific (stock G) and Southwest Indian Ocean (stock C). These two stocks were separated by a minimum of 120° longitude, and 13,046 km of a great-circle distance. These extreme distances movements demonstrate behavioural plasticity, which may play an important role in adaptation strategies to global environ..., The data have been collected on the dedicated vessel-based surveys in Colombia and Tanzania. Location, behaviour, group type, group size, spatial distribution, and photo-identification images were collected in all locations. Fluke images were uploaded to Happywhale.com a web-based cetacean photo-ID platform., , # Interbreeding area movement of an adult humpback whale between the East Pacific Ocean and Southwest Indian Ocean

https://doi.org/10.5061/dryad.bzkh189k2

Description of the data and file structure

The GIS coordinates for the encountered individual Humpback Whale (Megaptera novaeangliae) on a small boat surveys in Colombia and Zanzibar have been obtained along with the following data - species, country, date, coordinates, group size and group type.Â

Files and variables

File: Sighting_Coordinates_Colombia_Zanzibar_Data.xls

**Description:Â **Â The dataset contains records of the humpback whale encountered on a dedicated vessel based surveys in the northern Colombian Pacific in 2013 and 2017, and in Southwest Indian Ocean in 2022, and consist of the 3 records of the same humpback whale individual, with indication of the country and date where and when it was encountered, as well as coordinates of each sighting, group size an...

This project consists of a large-scale genetic study of the Western Australian Humpback (Antarctic Area Group IV). The primary aim of this study is to determine whether humpback whales in Western Australia (Antarctic Area Group IV) comprise distinct genetic subgroups and therefore unique conservation units. The purpose of Muriel's research is to find out as much as possible about the humpback whale in WA in order to manage and protect this very valuable stock by determining which subgroups may be susceptible to impact by human activities.

Data was collected in the Antarctic Peninsula and greater Scotia Sea using standard distance sampling methodology. The dataset includes both raw data in Microsoft Access format, as well as processed R objects.

A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as “Endangered” on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to “Critically Endangered” on the IUCN Red List.

Transient killers whales inhabit the West Coast of the United States. Their range and movement patterns are difficult to ascertain, but are vital to understanding killer whale population dynamics and abundance trends. Satellite tagging of West Coast transient killer whales to determine range and movement patterns will provide data to assist in understanding transient killer whale populations. L...

The eastern population of the North Pacific right whale (Eubalaena japonica) is the most endangered stock of whales in the world, with recent abundance estimates indicating a population size of approximately 30 animals. Photo-identification of the naturally occurring callosity patterns on the chin, rostrum, lips and post blowhole, and the lip and fluke trailing edge crenulations together represent a nonintrusive technique for obtaining information on their life history parameters, distribution and movements, stock structure, health assessment, and population size. As part of a study funded by the Minerals Management Service and North Pacific Research Board, a North Pacific right whale photo-identification catalog has been established using sighting data recorded since the late 1970s by various dedicated surveys and opportunistic sighting platforms. Date, time, position, photographer, picture quality and notes are documented for each of the approximately 1,780 photographs in the catalog. Within the catalog, there are 18 individual animals with both a high-quality left and right side oblique photograph or a high-quality aerial photograph of the head and dorsal surface; this should be considered the conservative minimum number of individuals catalogued. There are nine other animals with a high quality left or right oblique photograph, but not both. There are eight additional animals with the full suite of required photographs, but the images are of poor quality and cannot be reliably matched. Seven individuals were seen between years (over a period of 11 years), and one of those whales was seen in five separate years within that same period. Data from this catalog have been used to calculate the first abundance estimates for the population. Additionally, the first known match between high and low latitudes (the Bering Sea and Hawaii) was discovered in the catalog. Tracking the within- and between-year sighting histories of photo-identified individuals over decades broadens our knowledge of how these animals use their habitat, and can significantly assist the conservation and management of the species.

The calf counts over time, as a csv file.

Genetic diversity is declining globally, a trend that may particularly impact exploited populations that must adapt to rapid environmental change and other threats. Estimated genomic changes in effective population size mirrored known whaling history and shifts in technology. In the Southern Ocean, a comparison of genomes from historical and contemporary populations indicated that the contemporary genomes have less diversity and an elevated realised mutation load for moderately deleterious mutations, likely due to the effects of whaling. Our results demonstrate that the relatively recent, brief, and drastic depletion of humpback whale populations by whaling likely had subtle but discernible, negative, and lasting effects on the whales’ genomes. Thus, even as some humpback whale populations are now recovering to pre-exploitation numbers, they likely do so with a diminished adaptive capacity in the face of future conditions and threats.

The blue whale is an endangered and globally distributed species of baleen whale with multiple described subspecies assignments, including the morphologically and molecularly distinct pygmy blue whale, among others. North Atlantic and North Pacific populations, however, are currently regarded as a single subspecies despite being separated by continental land masses and differences in their acoustic communication. To determine the degree of isolation among the Northern Hemisphere populations, fourteen North Pacific and six Western Australian blue whale nuclear and mitochondrial genomes were sequenced and analyzed combinedly with eleven publicly available North Atlantic blue whale genomes. This allowed to contrast the genetic differentiation and genetic exchange among Northern Hemisphere populations to the Western Australian pygmy blue whale subspecies. Population genomic analyses revealed distinctly differentiated clusters and limited exchange among all three populations, indicating a hi..., We sequenced the genomes from 20 blue whale specimens gathered from the North Pacific blue whale and West-Australian pygmy blue whale populations and analyze the data together with 12 publicly available genomes of other blue whales, including those of the North-Atlantic blue whales (Jossey et al., 2024). This sampling is further complemented by three genomes of the closely related sei whale (Balaenoptera borealis), of which one is sequenced in this study. All Illumina paired-end libraries were prepared by Novogene, Cambridge, United Kingdom using the NEBNEXT DNA LIBRARY PREP kit with a read length of 150 base pairs (bp) and an insert size of 350 bp. Illumina sequencing was performed on a NovaSeq 6000 platform targeting ~20x coverage per individual. A comprehensive pipeline used to process the data and perform many of the here presented downstream analyses can be found on GitHub: mag-wolf/RESEQ-to-Popanalyses/. Short read data were trimmed for quality and adapter sequences using FASTP V0..., Usage Notes: All variance sets are contained in zipped vcf files and might be viewed and altered with BCFTOOLS (Danecek et al., 2021). While the genome wide set only contains SNPs, the haploid mitochondrial and sex-chromosomal data contain also conserved sites!, # Supporting Data for: Ocean-wide conservation genomics of blue whales suggest new Northern Hemisphere subspecies

[Access this dataset on Dryad: https://doi.org/10.5061/dryad.47d7wm3jz]

We sequenced the genomes from 20 blue whale specimens gathered from the North Pacific blue whale and West-Australian pygmy blue whale populations and analyze the data together with 12 publicly available genomes of other blue whales, including those of the North-Atlantic blue whales (Jossey et al., 2024). The data was used for SNP calling of genomic, mitogenomic, mt_Marker region, and y-chromosomal data. The SNPs were subsequently used for population genetic analyses regarding gene flow, genetic divergence, phylogenetic reconstruction and genetic viability.

Description of the data and file structure

In this data repository, we provide filtered, high-quality SNPs called from our genomic resequencing and subsequent mapping to the blue whale reference genome...

State-space modelled data and README files associated with Riekkola et al. (2018). Application of a multi-disciplinary approach to reveal population structure and Southern Ocean feeding grounds of humpback whales. Ecological Indicators, 89, 455-465.AbstractObtaining direct measurements to characterise ecosystem function can be hindered by remote or inaccessible regions. Next-generation satellite tags that inform increasingly sophisticated movement models, and the miniaturisation of animal-borne loggers, have enabled the use of animals as tools to collect habitat data in remote environments, such as the Southern Ocean. Research on the distribution, habitat use and recovery of Oceania’s humpback whales (Megaptera novaeangliae) has been constrained by the inaccessibility to their Antarctic feeding grounds and the limitations of technology. In this multi-disciplinary study, we combine innovative analytical tools to comprehensively assess the distribution and population structure of this marine predator throughout their entire migratory range. We used genotypeand photo-identification matches and conducted a genetic mixed-stock analysis to identify the breeding ground origins of humpback whales migrating past the Kermadec Islands, New Zealand. Satellite tracking data and a state-space model were then used to identify the migratory paths and behaviour of 18 whales, and to reveal their Antarctic feeding ground destinations. Additionally, we conducted progesterone assays and epigenetic aging to determine the pregnancy rate and age-profile of the population. Humpback whales passing the Kermadec Islands did not assign to a single breeding ground origin, but instead came from a range of breeding grounds spanning ∼3500 km of ocean. Sampled whales ranged from calves to adults of up to 67 years of age, and a pregnancy rate of 57% was estimated from 30 adult females. The whales migrated to the Southern Ocean (straight-line distances of up to 7000 km) and spanned ∼4500 km across their Antarctic feeding grounds. All fully tracked females with a dependent calf (n = 4) migrated to the Ross Sea region, while 70% of adults without calves (n = 7) travelled further east to the Amundsen and Bellingshausen Seas region. By combining multiple research and analytical tools we obtained a comprehensive understanding of this wide-ranging, remote population of whales. Our results indicate a population recovering from exploitation, and their feeding ground distribution serves as an indicator of the resources available in these environments. The unexpected Kermadec Islands migratory bottle-neck of whales from several breeding grounds, variable distribution patterns by life history stage and high pregnancy rates will be important in informing conservation and management planning, and for understanding how this, as well as other whale populations, might respond to emerging threats such as climate change.

AbstractGenetic diversity is declining globally, a trend that may particularly impact exploited populations that must adapt to rapid environmental change and other threats. Estimated genomic changes in effective population size mirrored known whaling history and shifts in technology. In the Southern Ocean, a comparison of genomes from historical and contemporary populations indicated that the contemporary genomes have less diversity and an elevated realised mutation load for moderately deleterious mutations, likely due to the effects of whaling. Our results demonstrate that the relatively recent, brief, and drastic depletion of humpback whale populations by whaling likely had subtle but discernible, negative, and lasting effects on the whales’ genomes. Thus, even as some humpback whale populations are now recovering to pre-exploitation numbers, they likely do so with a diminished adaptive capacity in the face of future conditions and threats.