Howard C. Rosenbaum

Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific

The population structure of variation in a nuclear actin intron and the control region of mitochondrial DNA is described for humpback whales from eight regions in the North Pacific Ocean: central California, Baja Peninsula, nearshore Mexico (Bahia Banderas), offshore Mexico (Socorro Island), southeastern Alaska, central Alaska (Prince Williams Sound), Hawaii and Japan (Ogasawara Islands). Primary mtDNA haplotypes and intron alleles were identified using selected restriction fragment length polymorphisms of target sequences amplified by the polymerase chain reaction (PCR–RFLP). There was little evidence of heterogeneity in the frequencies of mtDNA haplotypes or actin intron alleles due to the year or sex composition of the sample. However, frequencies of four mtDNA haplotypes showed marked regional differences in their distributions (ΦST = 0.277; P < 0.001; n = 205 individuals) while the two alleles showed significant, but less marked, regional differences (ΦST = 0.033; P < 0.013; n = 400 chromosomes). An hierarchical analysis of variance in frequencies of haplotypes and alleles supported the grouping of six regions into a central and eastern stock with further partitioning of variance among regions within stocks for haplotypes but not for alleles. Based on available genetic and demographic evidence, the southeastern Alaska and central California feeding grounds were selected for additional analyses of nuclear differentiation using allelic variation at four microsatellite loci. All four loci showed significant differences in allele frequencies (overall FST = 0.043; P < 0.001; average n = 139 chromosomes per locus), indicating at least partial reproductive isolation between the two regions as well as the segregation of mtDNA lineages. Although the two feeding grounds were not panmictic for nuclear or mitochondrial loci, estimates of long‐term migration rates suggested that male‐mediated gene flow was several‐fold greater than female gene flow. These results include and extend the range and sample size of previously published work, providing additional evidence for the significance of genetic management units within oceanic populations of humpback whales.

World-wide genetic differentiation of Eubalaena: Questioning the number of right whale species

Few studies have examined systematic relationships of right whales (Eubalaena spp.) since the original species descriptions, even though they are one of the most endangered large whales. Little morphological evidence exists to support the current species designations for Eubalaena glacialis in the northern hemisphere and E. australis in the southern hemisphere. Differences in migratory behaviour or antitropical distribution between right whales in each hemisphere are considered a barrier to gene flow and maintain the current species distinctions and geographical populations. However, these distinctions between populations have remained controversial and no study has included an analysis of all right whales from the three major ocean basins. To address issues of genetic differentiation and relationships among right whales, we have compiled a database of mitochondrial DNA control region sequences from right whales representing populations in all three ocean basins that consist of: western North Atlantic E. glacialis, multiple geographically distributed populations of E. australis and the first molecular analysis of historical and recent samples of E. glacialis from the western and eastern North Pacific Ocean. Diagnostic characters, as well as phylogenetic and phylogeographic analyses, support the possibility that three distinct maternal lineages exist in right whales, with North Pacific E. glacialis being more closely related to E. australis than to North Atlantic E. glacialis. Our genetic results provide unequivocal character support for the two usually recognized species and a third distinct genetic lineage in the North Pacific under the Phylogenetic Species Concept, as well as levels of genetic diversity among right whales world‐wide.

What Does It Mean to Successfully Conserve a (Vertebrate) Species

The conservation of species is one of the foundations of conservation biology. Successful species conservation has often been defined as simply the avoidance of extinction. We argue that this focus, although important, amounts to practicing conservation at the “emergency room door,” and will never be a sufficient approach to conserving species. Instead, we elaborate a positive definition of species conservation on the basis of six attributes and propose a categorization of different states of species conservation using the extent of human management and the degree to which each of the attributes is conserved. These states can be used to develop a taxonomy of species “recovery” that acknowledges there are multiple stable points defined by ecological and social factors. “With this approach, we hope to contribute to a new, optimistic conservation biology that is not based on underambitious goals and that seeks to create the conditions under which Earths biological systems can thrive.

Habitat preference reflects social organization of humpback whales ( Megaptera novaeangliae ) on a wintering ground

Habitat preference is driven by a complex interaction among behavioural patterns, biological requirements, and environmental conditions. These variables are difficult to determine for any species but are further complicated for migratory marine mammals, such as humpback whales Megaptera novaeangliae . Patterns of habitat use in relation to social organization potentially exist for this species on their wintering grounds. Using an integrated GIS approach, we examined the degree to which spatial patterns of habitat stratification are correlated within different humpback whale group types from 6 years of sighting data (1996–2001) collected on the Antongil Bay, Madagascar, wintering ground. Stratification of humpback whale sightings by behavioural classification showed significant variation in depth and distance from shore. Distribution by depth could not be described as a function of group size but could be described as a function of social organization, with mother–calf pairs showing a strong preference for shallower water compared to all other group types. Group size and social organization seem to be factors in distribution by distance from shore. Significant diurnal patterns in distribution by depth and distance from shore also exist, where mother–calf groups maintain a relatively stable distribution and pairs and competitive groups are the most variable. Patterns of habitat preference on this wintering ground appear to be guided by social organization, where distribution by depth and distance from shore highlight areas critical to conservation.

Population structure of humpback whales from their breeding grounds in the South Atlantic and Indian oceans

Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region.

Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?

The conservation of humpback dolphins, distributed in coastal waters of the Indo‐West Pacific and eastern Atlantic Oceans, has been hindered by a lack of understanding about the number of species in the genus (Sousa) and their population structure. To address this issue, we present a combined analysis of genetic and morphologic data collected from beach‐cast, remote‐biopsied and museum specimens from throughout the known Sousa range. We extracted genetic sequence data from 235 samples from extant populations and explored the mitochondrial control region and four nuclear introns through phylogenetic, population‐level and population aggregation frameworks. In addition, 180 cranial specimens from the same geographical regions allowed comparisons of 24 morphological characters through multivariate analyses. The genetic and morphological data showed significant and concordant patterns of geographical segregation, which are typical for the kind of demographic isolation displayed by species units, across the Sousa genus distribution range. Based on our combined genetic and morphological analyses, there is convincing evidence for at least four species within the genus (S. teuszii in the Atlantic off West Africa, S. plumbea in the central and western Indian Ocean, S. chinensis in the eastern Indian and West Pacific Oceans, and a new as‐yet‐unnamed species off northern Australia).

Estimates of relatedness in groups of humpback whales (Megaptera novaeangliae) on two wintering grounds of the Southern Hemisphere

Group formation in humpback whales has been described in relation to different components of the migratory cycle, yet it is debated whether such groups represent real social bonding or ephemeral aggregations. Cooperative behaviours are exhibited during feeding activities, and it has been suggested that males may cooperate during competition for mates. Since most cooperative behaviours are expected to originate among kin, genetic relatedness represents a critical variable in the understanding of any social phenomenon, especially when cooperation cannot be confirmed unequivocally. Using an approach combining multi‐locus microsatellite genotyping and several genetic relatedness estimators, we analyzed whale associations for two different wintering grounds in the Southern Hemisphere. The analyses included 648 whales sampled from 292 groups off the coast of Gabon and Northeast Madagascar, and screened for eleven microsatellite loci. Through simulations, we assessed the performance of three pairwise relatedness estimators. The individuals were molecularly sexed and their associations were investigated in the context of sex and group type. No significant association among relatives was found with the exception of mother–offspring pairs, supporting previous indications of extended maternal care. The analysis from the Gabon population also suggests that related males may avoid each other during competitive activities. Our results demonstrate that if cooperative behaviours occur on wintering grounds they are not favoured by kin selection.

DNA Isolation Procedures

Literally hundreds of protocols for DNA preparation from various sources of tissue have been published over the last few decades. To display all of these preparations would take volumes of manual space so instead we present in this chapter several of the preparations that have been used successfully in our laboratories. We also present a few “classical” procedures that are “tried and true” and nearly always work. In addition the www is an excellent source for protocols. Some forums exist for the dissemination of protocols for DNA and RNA isolation (DNA isolation protocols forums: http://www.nwfsc.noaa.gov/protocols.html, http://bric.postech.ac.kr/resources/rprotocol/; RNA isolation protocols forum: http://www.nwfsc.noaa.gov/protocols/methods/RNAMethodsMenu.html).

Migration redefined? Seasonality, movements and group composition of humpback whales Megaptera novaeangliae off the west coast of South Africa

The migration of Southern Hemisphere humpback whales Megaptera novaeangliae between their feeding and breeding areas has thus far been considered a highly predictable and seasonal event. However, previous observations on the humpbacks that pass through the nearshore waters of the west coast of South Africa have revealed deviations from the behaviour and seasonality expected during a typical migration. This ‘anomaly’ is hypothesised to be associated with prey availability in the region. Shore-based observations between July 2001 and February 2003 from North Head, Saldanha Bay, in the Western Cape province, yielded relative abundances that again did not support a classical migration pattern, with the highest sighting rates from mid-spring through summer. Movement parameters (actual swimming speed, direction and linearity) of humpback groups tracked by theodolite showed mid-spring to be a turning point in their behaviour, after which we observed a significant reduction in actual swimming speed, an increase in ‘non-directional’ movement, and a distribution farther from shore than in other seasons. Additional data on group composition and sex collected between 1993 and 2008 showed a significantly female-biased sex ratio during mid-spring, the first such recorded for any region. Direct observation of feeding on crustacean prey during spring and summer further supports the notion that humpbacks may have more flexible foraging habits than previously appreciated, and that the southern Benguela upwelling region may function as an important feeding area for these whales.

Molecular ecology meets remote sensing: environmental drivers to population structure of humpback dolphins in the Western Indian Ocean

Genetic analyses of population structure can be placed in explicit environmental contexts if appropriate environmental data are available. Here, we use high-coverage and high-resolution oceanographic and genetic sequence data to assess population structure patterns and their potential environmental influences for humpback dolphins in the Western Indian Ocean. We analyzed mitochondrial DNA data from 94 dolphins from the coasts of South Africa, Mozambique, Tanzania and Oman, employing frequency-based and maximum-likelihood algorithms to assess population structure and migration patterns. The genetic data were combined with 13 years of remote sensing oceanographic data of variables known to influence cetacean dispersal and population structure. Our analyses show strong and highly significant genetic structure between all putative populations, except for those in South Africa and Mozambique. Interestingly, the oceanographic data display marked environmental heterogeneity between all sampling areas and a degree of overlap between South Africa and Mozambique. Our combined analyses therefore suggest the occurrence of genetically isolated populations of humpback dolphins in areas that are environmentally distinct. This study highlights the utility of molecular tools in combination with high-resolution and high-coverage environmental data to address questions not only pertaining to genetic population structure, but also to relevant ecological processes in marine species.