A Test of Computer-assisted Matching Using the North Pacific Humpback Whale, Megaptera novaeangliae, Tail Flukes Photograph Collection

Testing was conducted of a computer-assisted system for matching humpback whale tail flukes photographs. Trials with a 12,000-photographs database found no differences in match success between matching by computer and matching by comparing smaller catalogs ranging in size from 200 to 400 photographs. Tests with a 24,000-photographs database showed that, on average, the first match was found after examining about 130 photographs whether the photograph quality was excellent, good, or poor. Match success did not appear to be strongly related to whether the tail flukes had especially distinctive markings or pigment patterns (recognition quality). An advantage of computer-assisted matching is the ability to compare new photographs to the entire North Pacific collection, where no bias is introduced based on expectation of resightings within or between specific areas, or based on expectation of behavioral role (e.g. matching “known” females to “known” females)

Killer whales and marine mammal trends in the North Pacific : a re-examination of evidence for sequential megafauna collapse and the prey-switching hypothesis

This paper is not subject to U.S. copyright. The definitive version was published in Marine Mammal Science 23 (2007): 766–802, doi:10.1111/j.1748-7692.2006.00093.x.Springer et al. (2003) contend that sequential declines occurred in North Pacific populations of harbor and fur seals, Steller sea lions, and sea otters. They hypothesize that these were due to increased predation by killer whales, when industrial whaling's removal of large whales as a supposed primary food source precipitated a prey switch. Using a regional approach, we reexamined whale catch data, killer whale predation observations, and the current biomass and trends of potential prey, and found little support for the prey-switching hypothesis. Large whale biomass in the Bering Sea did not decline as much as suggested by Springer et al., and much of the reduction occurred 50–100 yr ago, well before the declines of pinnipeds and sea otters began; thus, the need to switch prey starting in the 1970s is doubtful. With the sole exception that the sea otter decline followed the decline of pinnipeds, the reported declines were not in fact sequential. Given this, it is unlikely that a sequential megafaunal collapse from whales to sea otters occurred. The spatial and temporal patterns of pinniped and sea otter population trends are more complex than Springer et al. suggest, and are often inconsistent with their hypothesis. Populations remained stable or increased in many areas, despite extensive historical whaling and high killer whale abundance. Furthermore, observed killer whale predation has largely involved pinnipeds and small cetaceans; there is little evidence that large whales were ever a major prey item in high latitudes. Small cetaceans (ignored by Springer et al.) were likely abundant throughout the period. Overall, we suggest that the Springer et al. hypothesis represents a misleading and simplistic view of events and trophic relationships within this complex marine ecosystem

Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly

The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 380 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively 'trivial' aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic

Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly

© The Authors, 2019. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 4.0 International License. The definitive version was published in Molecular Phylogenetics and Evolution (2019), doi:10.1016/j.ympev.2019.02.003.The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1,676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 358 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively “trivial” aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic.We are grateful to Hanne Jørgensen, Anna Sellas, Mary Beth Rew and Christina Færch-Jensen for technical assistance. We thank Drs. P. E. Rosel and K. D. Mullin (U.S. National Marine Fisheries Service Southeast Fisheries Science Center) and members of the U.S. Northeast and Southeast Region Marine Mammal Stranding Network and its response teams, including the International Fund for Animal Welfare, the Marine Mammal Stranding Center, Mystic Aquarium, the Riverhead Foundation for Marine Research and Preservation (K. Durham) and the Marine Mammal Stranding Program of the University of North Carolina Wilmington for access to fin whale samples from the western North Atlantic. We thank Gisli Vikingsson for providing samples. We are indebted to Dr. Eduardo Secchi for facilitating data sharing. Data collection in the Southern Ocean was conducted under research projects Baleias (CNPq grants 557064/2009-0 and 408096/2013-6), INTERBIOTA (CNPq 407889/2013-2) and INCT-APA (CNPq 574018/2008-5), of the Brazilian Antarctic Program and a contribution by the research consortium ‘Ecology and Conservation of Marine Megafauna – EcoMega-CNPq’. MAS was supported through a FCT Investigator contract funded by POPH, QREN European Social Fund, and Portuguese Ministry for Science and Education. Data collection in the Azores was funded by TRACE-PTDC/MAR/74071/2006 and MAPCET-M2.1.2/F/012/2011 [FEDER, COMPETE, QREN European Social Fund, and Proconvergencia Açores/EU Program]. Fin whale illustration herein is used with the permission of Frédérique Lucas. We acknowledge the Center for Information Technology of the University of Groningen for IT support and access to the Peregrine high performance-computing cluster

Movements and Population Structure of Humpback Whales in the North Pacific

Despite the extensive use of photographic identification methods to investigate humpback whales in the North Pacific, few quantitative analyses have been conducted. We report on a comprehensive analysis of interchange in the North Pacific among three wintering regions (Mexico, Hawaii, and Japan) each with two to three subareas, and feeding areas that extended from southern California to the Aleutian Islands. Of the 6,413 identification photographs of humpback whales obtained by 16 independent research groups between 1990 and 1993 and examined for this study, 3,650 photographs were determined to be of suitable quality. A total of 1,241 matches was found by two independent matching teams, identifying 2,712 unique whales in the sample (seen one to five times). Site fidelity was greatest at feeding areas where there was a high rate of resightings in the same area in different years and a low rate of interchange among different areas. Migrations between winter regions and feeding areas did not follow a simple pattern, although highest match rates were found for whales that moved between Hawaii and southeastern Alaska, and between mainland and Baja Mexico and California. Interchange among subareas of the three primary wintering regions was extensive for Hawaii, variable (depending on subareas) for Mexico, and low for Japan and reflected the relative distances among subareas. Interchange among these primary wintering regions was rare. This study provides the first quantitative assessment of the migratory structure of humpback whales in the entire North Pacific basin

Estimating the mortality rate of humpback whale calves in the central North Pacific ocean.

Sighting histories of individually identified female humpback whales (Megaptera novaeangliae) in their winter and summer ranges were used to investigate mortality of North Pacific humpback whale calves. We compiled records collected between 1979 and 1995 by eight independent research groups, which yielded 29 cases where 25 different mothers sighted in Hawai'i were identified later the same year in Alaska. In 7 of 29 cases, a calf sighted with its mother in Hawai'i was missing from its mother's Alaska sighting(s). After investigating many factors, we determined that the largest potential bias would occur in late-autumn observations, when calf absences might indicate weaning or temporary mother–calf separation rather than calf mortality. Our minimal and most robust estimate excluded all mortalities and survivals based on sightings of the mother after October 31; 3 of 20 cases or 0.150 (95% confidence intervals (CI) = 0.032, 0.378). The maximal calf mortality rate, derived from all the available data, was 7 of 29 cases or 0.241 (95% CI = 0.103, 0.434). An intermediate estimate that excluded all cases based on single Alaska sightings and omitted late-season sightings (2 of 11 cases or 0.182; 95% CI = 0.023, 0.518) is perhaps closest to the actual first-year mortality rate for humpback whale calves, although it is compromised by its small sample size. Our results demonstrate both the value and the limitations of using longitudinal data to determine the life-history parameters that are essential for documenting the recovery of endangered populations

Baleen whales are not important as prey for killer whales Orcinus orca in high-latitude regions

Author Posting. © Inter-Research, 2007. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Marine Ecology Progress Series 348 (2007): 297-307, doi:10.3354/meps07015.Certain populations of killer whales Orcinus orca feed primarily or exclusively on marine mammals. However, whether or not baleen whales represent an important prey source for killer whales is debatable. A hypothesis by Springer et al. (2003) suggested that overexploitation of large whales by industrial whaling forced killer whales to prey-switch from baleen whales to pinnipeds and sea otters, resulting in population declines for these smaller marine mammals in the North Pacific and southern Bering Sea. This prey-switching hypothesis is in part contingent upon the idea that killer whales commonly attack mysticetes while they are in these high-latitude areas. In this study, we used photographic and sighting data from long-term studies of baleen whales in 24 regions worldwide to determine the proportion of whales that bear scars (rake marks) from killer whale attacks, and to examine the timing of scar acquisition. The results of this study show that there is considerable geographic variation in the proportion of whales with rake marks, ranging from 0% to >40% in different regions. In every region, the great majority of the scars seen were present on the whales’ bodies when the animals were first sighted. Less than 7% (9 of 132) of scarred humpback whales with multi-year sighting histories acquired new scars after the first sighting. This suggests that most killer whale attacks on baleen whales target young animals, probably calves on their first migration from low-latitude breeding and calving areas to high-latitude feeding grounds. Overall, our results imply that adult baleen whales are not an important prey source for killer whales in high latitudes, and therefore that one of the primary assumptions underlying the Springer et al. (2003) prey-switching hypothesis (and its purported link to industrial whaling) is invalid.This study was supported in part by funding from the Marine Mammal Commission

Data from: Fin whale (Balaenoptera physalus) mitogenomics: a cautionary tale of defining sub-species from mitochondrial sequence monophyly

The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1,676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 358 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively “trivial” aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic

Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly

The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 380 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively “trivial” aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic