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Simple Summary: Cetacean strandings are regularly recorded along the coast of Chile. However, crucial information such as species and sex of the individuals involved in these events can often be difficult to assess. In this context, the use of molecular tools as a complementary method can improve a stranding database, particularly by correcting misidentifications and providing new data for unidentified samples. This new information is especially important in the case of species that are poorly known or of high conservation interest. In this study, we evaluate how molecular tools can support and complement the field work records of strandings in Chile by identifying, corroborating, or correcting the identification of the species and sex of the recorded individuals. We obtained samples through a collaboration with the government agency that is in charge of assisting with cetacean strandings and collected the relevant information. Multidisciplinary approaches like this, and inter-institutional collaborations, can improve the study of cetacean strandings and the decisions in management and conservation policies around them. Cetacean strandings are a valuable source of information for several studies from species richness to conservation and management. During the examination of strandings, taxonomic and sex identification might be hindered for several reasons. Molecular techniques are valuable tools to obtain that missing information. This study evaluates how gene fragment amplification protocols can support the records of strandings done in the field in Chile by identifying, corroborating, or correcting the identification of the species and sex of the recorded individuals. Through a collaboration between a scientific laboratory and government institution in Chile, 63 samples were analyzed. Thirty-nine samples were successfully identified to the species level. In total, 17 species of six families were detected, including six species of conservation interest. Of the 39 samples, 29 corresponded to corroborations of field identifications. Seven corresponded to unidentified samples and three to corrected misidentifications, adding up to 28% of the identified samples. Sex was successfully identified for 58 of the 63 individuals. Twenty were corroborations, 34 were previously unidentified, and four were corrections. Applying this method improves the stranding database of Chile and provides new data for future management and conservation tasks. [ABSTRACT FROM AUTHOR]

Understanding genetic differentiation and speciation processes in marine species with high dispersal capabilities is challenging. The Chilean dolphin, Cephalorhynchus eutropia, is the only endemic cetacean of Chile and is found in two different coastal habitats: a northern habitat with exposed coastlines, bays and estuaries from Valparaíso (33°02′S) to Chiloé (42°00′S), and a southern habitat with highly fragmented inshore coastline, channels and fjords between Chiloé and Navarino Island (55°14′S). With the aim of evaluating the potential existence of conservation units for this species, we analyzed the genetic diversity and population structure of the Chilean dolphin along its entire range. We genotyped 21 dinucleotide microsatellites for 53 skin samples collected between 1998 and 2012 (swab: n = 8, biopsy: n = 38, entanglement n = 7). Bayesian clustering and spatial model analyses identified two genetically distinct populations corresponding to the northern and southern habitats. Genetic diversity levels were similar in the two populations (He: 0.42 v/s 0.45 for southern and northern populations, respectively), while effective size population was higher in the southern area (Ne: 101 v/s 39). Genetic differentiation between these two populations was high and significant (FST = 0.15 and RST = 0.19), indicating little or no current gene flow. Because of the absence of evident geographical barriers between the northern and southern populations, we propose that genetic differentiation may reflect ecological adaptation to the different habitat conditions and resource uses. Therefore, the two genetic populations of this endemic and Near Threatened species should be considered as different conservation units with independent management strategies. [ABSTRACT FROM AUTHOR]

The widely distributed long-finned pilot whale ( Globicephala melas) has been reported off the Chilean coast, from Iquique (20°12′S) south to Navarino Island (55°15′S; 67°30′W), but little is known about its biology or ecology in the region. Here, we report on the prey of this species, identified by stomach content analyses from animals stranded on Holget Islets, Beagle Channel, southern Chile in August 2006. The stomachs of seven individuals (six females and one male) contained cephalopod remains. The prey composition found in these southern Chilean pilot whales was similar to that described in other parts of the world and the Southern Ocean. This is the first report on the feeding habits of this species from Chile. [ABSTRACT FROM AUTHOR]

The occurrence of dwarf minke whales ( Balaenoptera acutorostrata subsp.) around the Antarctic Peninsula was examined based on 406 sightings of minke whales recorded during the Chilean Antarctic Scientific Expeditions and other opportunistic cetacean surveys. Identification of the species was made only for the whales sighted in the proximity of the vessels when the specific diagnostic characters could be confirmed. Of the 406 sightings, 296 were assigned to Antarctic (519 individuals), nine (11 individuals) to dwarf and 101 to unidentified minke whales (149 individuals). Dwarf minke whales were identified by the reported external diagnostic characters for this species. Seven animals occurred around the South Shetland Island and four in the Gerlache Strait. In addition, another two animals were identified as dwarf minke whales in the Bellinghausen Sea in winter 1993, being these the most southern records for this species. These results confirm the occurrence of dwarf minke whales around the Antarctic Peninsula during the summer seasons, as well as in the Bellinghausen Sea in winter. The geographical range of these sightings was comprised between 61°03′ and 69°25′S and between 55°29′ and 86°53′W. These results also suggest that some dwarf minke whales remain in the Antarctic during the austral winter. [ABSTRACT FROM AUTHOR]

The common bottlenose dolphin (Tursiops truncatus) is a cosmopolitan species that does not range to latitudes greater than 45° in either hemisphere, with a few exceptions. In South American waters, this species is generally distributed in the Atlantic Ocean south to Chubut province (ca. 46° S), while in the eastern South Pacific this species has been recorded in northern and central Chile, with a few records south to 40° S. Here we summarize recent records of common bottlenose dolphins obtained during systematic marine mammal surveys in the Chilean Patagonian and Fuegian channels and fjords (the Los Lagos, Aysén, and Magallanes regions of Chile). These data suggest an extension of the documented range of the species southwards, indicating that bottlenose dolphins may have colonized new areas in the eastern South Pacific or as the result of an increase in survey efforts by scientists in the region. [ABSTRACT FROM AUTHOR]

The article presents a study on the lack of divergence in the mitochondrial cytochrome b gene between the Macruronus novaezelandiae and Macruronus magellanicus grenadiers in the Southern Hemisphere. It investigates on the extent of genetic difference between the two putative species by using partial sequences of the mitochondrial deoxyribonucleic acid (DNA) cytochrome b in a phylogenetic analysis and in an analysis of molecular variance (AMOVA).

The 20th century commercial whaling industry severely reduced populations of great whales throughout the Southern Hemisphere. The effect of this exploitation on genetic diversity and population structure remains largely undescribed. Here, we compare pre- and post-whaling diversity of mitochondrial DNA (mtDNA) control region sequences for 3 great whales in the South Atlantic, such as the blue, humpback, and fin whale. Pre-whaling diversity is described from mtDNA extracted from bones collected near abandoned whaling stations, primarily from the South Atlantic island of South Georgia. These bones are known to represent the first stage of 20th century whaling and thus pre-whaling diversity of these populations. Post-whaling diversity is described from previously published studies reporting large-scale sampling of living whales in the Southern Hemisphere. Despite relatively high levels of surviving genetic diversity in the post-whaling populations, we found evidence of a probable loss of mtDNA lineages in all 3 species. This is evidenced by the detection of a large number of haplotypes found in the pre-whaling samples that are not present in the post-whaling samples. A rarefaction analysis further supports a loss of haplotypes in the South Atlantic humpback and Antarctic blue whale populations. The bones from former whaling stations in the South Atlantic represent a remarkable molecular archive for further investigation of the decline and ongoing recovery in the great whales of the Southern Hemisphere. [ABSTRACT FROM AUTHOR]

The matrilineal long-finned pilot whale presents an antitropical distribution and is divided into two subspecies, one in the temperate seas of the Southern Hemisphere and the other restricted to the North Atlantic and Mediterranean. Until now, population genetic and phylogeographic studies have included localities of most of its Northern Hemisphere distribution, while only the southwestern Pacific has been sampled in the Southern Hemisphere. We add new genetic data from the southeastern Pacific to the published sequences. Low mitochondrial and nuclear diversity was encountered in this new area, as previously reported for other localities. Four haplotypes were found with only one new for the species. Fifteen haplotypes were detected in the global dataset, underlining the species' low diversity. As previously reported, the subspecies shared two haplotypes and presented a strong phylogeographic structure. The extant distribution of this species has been related to dispersal events during the Last Glacial Maximum. Using the genetic data and Approximate Bayesian Calculations, this study supports this historical biogeographic scenario. From a taxonomic perspective, even if genetic analyses do not support the subspecies category, this study endorses the incipient divergence process between hemispheres, thus maintaining their status and addressing them as Demographically Independent Populations is recommended. [ABSTRACT FROM AUTHOR]

Humpback whales (Megaptera novaeangliae) seasonally migrate between their corresponding breeding and feeding grounds; however, some individual whales deviate from this pattern migrating to different breeding or feeding grounds. Here, we report the first recorded movement of a humpback whale between the Antarctic Peninsula and the east coast of Australia. The individual whale, a known female, was identified by natural markings in the Antarctic Peninsula feeding area, and then photographed 15 years later in Byron Bay, on the eastern coast of Australia. This constitutes the longest migration for any humpback whale documented to date in the South Pacific Ocean and in the Southern Hemisphere (143° of longitude). Although the route is uncertain and the cues may be environmental, social or demographic, or some combinations thereof, this exceptional movement between two distant Breeding Stocks in the South Pacific Ocean demonstrates that longitudinal long-distance migrations among humpback whale populations do take place, at least occasionally, and perhaps may not be as atypical as it has been thought. [ABSTRACT FROM AUTHOR]

The article discusses a study which reports new mitochondrial DNA (mtDNA) control region analysis of the genetic diversity of humpback whales or Megaptera novaeangliae wintering off Ecuador. The study extracted mtDNA and sequenced from 230 skin samples which are collected between 2002 and 2008 to establish the genetic diversity of its population. The study found 41 haplotypes from 182 usable samples, in which haplotype diversity was estimated to be 0.922 ‡ while the nucleotide diversity is 0.019 ‡ 0.009. Results show that the exact test or population differentiation indicated differences in haplotype frequencies.

We test the ability of Very High Resolution satellite (VHR) imagery to detect stranded whales using both manual and automated methods. We use the 2015 mass mortality event in the Gulf of Penas locality, central Patagonia, Chile, as an initial case study. This event was the largest known mass mortality of baleen whales, with at least 343 whales, mainly sei whales (Balaenoptera borealis), documented as stranding. However, even with such a large number of whales, due to the remote location of the gulf the strandings went unrecorded for several weeks. Aerial and boat surveys of the area were conducted two to four months after the mortality event. In this study we use 50cm resolution WorldView2 imagery to identify and count strandings from two archival images acquired just after the stranding event and two months before the aerial and ground surveys, and to test manual and automated methods of detecting stranded whales. Our findings show that whales are easily detected manually in the images but due to the heterogeneous colouration of decomposing whales, spectral indices are unsuitable for automatic detection. Our satellite counts suggest that, at the time the satellite images were taken, more whales were stranded than recorded in the aerial survey, possibly due to the non-comprehensive coverage of the aerial survey or movement of the carcases between survey acquisition. With even higher resolution imagery now available, satellite imagery may be a cost effective alternative to aerial surveys for future assessment of the extent of mass whale stranding events, especially in remote and inaccessible areas. [ABSTRACT FROM AUTHOR]

The South American sea lion (Otaria flavescens) is widely distributed along the southern Atlantic and Pacific coasts of South America with a history of significant commercial exploitation. We aimed to evaluate the population genetic structure and the evolutionary history of South American sea lion along its distribution by analyses of mitochondrial DNA (mtDNA) and 10 nuclear microsatellites loci. We analyzed 147 sequences of mtDNA control region and genotyped 111 individuals of South American sea lion for 10 microsatellite loci, representing six populations (Peru, Northern Chile, Southern Chile, Uruguay (Brazil), Argentina and Falkland (Malvinas) Islands) and covering the entire distribution of the species. The mtDNA phylogeny shows that haplotypes from the two oceans comprise two very divergent clades as observed in previous studies, suggesting a long period (>1 million years) of low inter-oceanic female gene flow. Bayesian analysis of bi-parental genetic diversity supports significant (but less pronounced than mitochondrial) genetic structure between Pacific and Atlantic populations, although also suggested some inter-oceanic gene flow mediated by males. Higher male migration rates were found in the intra-oceanic population comparisons, supporting very high female philopatry in the species. Demographic analyses showed that populations from both oceans went through a large population expansion ~10,000 years ago, suggesting a very similar influence of historical environmental factors, such as the last glacial cycle, on both regions. Our results support the proposition that the Pacific and Atlantic populations of the South American sea lion should be considered distinct evolutionarily significant units, with at least two managements units in each ocean. [ABSTRACT FROM AUTHOR]

Since the decimation of the southern right whale Eubalaena australis population in New Zealand by whaling, research on its recovery has focused on the wintering ground at the Auckland Islands, neglecting potentially important wintering habitat at Campbell Island. For the first time in 20 years we conducted an expedition to sub-Antarctic Campbell Island to document and describe E. australis occupying this wintering habitat. We used a variety of methods including photo-identification, genetic and stable isotope analyses of tissue samples, and visual surveys of abundance and distribution, to provide details on the demography, population connectivity and ecology of E. australis wintering at Campbell Island. Our primary findings include (1) a lack of calves observed at Campbell Island, (2) an age-class bias toward sub-adults encountered at Campbell Island, (3) nine photo-identification matches between individuals observed at Campbell Island and previously documented elsewhere in New Zealand, (4) no genetic differentiation between E. australis at Campbell Island and the broader New Zealand population, (5) increased abundance estimates of E. australis at Campbell Island over the last 20 years, and (6) indications that E. australis forage within the sub-Antarctic region based on stable isotope analyses. Our results confirm that the Auckland Islands are currently the only significant calving area for E. australis in New Zealand, and therefore previous abundance estimates based on demographic data from the Auckland Islands are applicable to the entire New Zealand population of E. australis. However, future periodic surveys to Campbell Island are recommended to monitor population recovery and expansion. [ABSTRACT FROM AUTHOR]

Recent photo-identification and genetic studies have identified at least five discrete breeding populations in Australia and Oceania: western Australia (D), eastern Australia (E (i)), New Caledonia (E (ii)), Tonga (E (iii)), French Polynesia and the Cook Islands (F). Also evident are low levels of intermingling among breeding populations consistent with the degree of genetic differentiation. Photo-identification has confirmed linkages between Area V feeding areas and eastern Australia breeding grounds and one genotype match has been reported between Area V feeding areas and Oceania breeding grounds. Recent abundance estimates show strong increases in the eastern Australian population, and some recovery in the New Caledonia and Tonga populations, but with little evidence of recovery at other known Oceania breeding grounds or New Zealand. Studies to date have provided no conclusive evidence of the migratory destination of humpback whales passing through New Zealand waters en route between Antarctic feeding areas and tropical breeding grounds. Photo-identification comparisons were undertaken between humpback whale fluke catalogues from eastern Australia (EA, 1315), Oceania east (OE, 513), Oceania west (OW, 166) and New Zealand (NZ, 13). Five matches were found between OE/OW, four matches between OW/EA and three matches between NZ/EA. The data are used to investigate and discuss the migratory destination and breeding ground migratory interchange of humpback whales travelling through New Zealand waters. The data confirm that humpback whales with site fidelity to eastern Australia migrate past New Zealand including through the Cook Strait and Foveaux Strait. [ABSTRACT FROM AUTHOR]

In understanding the impact of commercial whaling, it is important to estimate the mixing of low latitude breeding populations on Antarctic feeding grounds, particularly the endangered humpback whale populations of Oceania. This paper estimates the degree of genetic differentiation among the putative populations of Oceania (New Caledonia, Tonga, the Cook Islands and French Polynesia) and Australia (western Australia and eastern Australia) using ten microsatellite loci and mtDNA, assesses the power of the data for a mixed-stock analysis, determines ways to improve statistical power for future studies and estimates the population composition of Antarctic samples collected in 2010 south of New Zealand and eastern Australia. A large proportion of individuals could not be assigned to a population of origin (> 52%) using a posterior probability threshold of > 0.90. The mixed-stock analysis simulations however, produced accurate results with humpback whales reapportioned to their population of origin above the 90% threshold for western Australia, New Caledonia and Oceania grouped using a combined mtDNA and microsatellite dataset. Removing the Cook Islands, considered a transient region for humpback whales, from the simulation analysis increased the ability to reapportion Tonga from 86% to 89% and French Polynesia from 89% to 92%. Breeding ground sample size was found to be a factor influencing the accuracy of population reapportionment whereas increasing the mixture or feeding ground sample size improved the precision of results. The mixed-stock analysis of our Antarctic samples revealed substantial contributions from both eastern Australia (53.2%, 6.8% SE) and New Caledonia (43.7%, 5.5% SE) [with Oceania contributing 46.8% (5.9% SE)] but not western Australia. Despite the need for more samples to improve estimates of population allocation, our study strengthens the emerging genetic and non-genetic evidence that Antarctic waters south of New Zealand and eastern Australia are used by humpback whales from both eastern Australia and the more vulnerable breeding population of New Caledonia, representing Oceania. [ABSTRACT FROM AUTHOR]

Background: A number of studies have described the extension of ice cover in western Patagonia during the Last Glacial Maximum, providing evidence of a complete cover of terrestrial habitat from 41°S to 56°S and two main refugia, one in south-eastern Tierra del Fuego and the other north of the Chiloé Island. However, recent evidence of high genetic diversity in Patagonian river species suggests the existence of aquatic refugia in this region. Here, we further test this hypothesis based on phylogeographic inferences from a semi-aquatic species that is a top predator of river and marine fauna, the huillín or Southern river otter (Lontra provocax). Results: We examined mtDNA sequences of the control region, ND5 and Cytochrome-b (2151 bp in total) in 75 samples of L. provocax from 21 locations in river and marine habitats. Phylogenetic analysis illustrates two main divergent clades for L. provocax in continental freshwater habitat. A highly diverse clade was represented by haplotypes from the marine habitat of the Southern Fjords and Channels (SFC) region (43°38' to 53°08'S), whereas only one of these haplotypes was paraphyletic and associated with northern river haplotypes. Conclusions: Our data support the hypothesis of the persistence of L. provocax in western Patagonia, south of the ice sheet limit, during last glacial maximum (41°S latitude). This limit also corresponds to a strong environmental change, which might have spurred L. provocax differentiation between the two environments. [ABSTRACT FROM AUTHOR]

A study is presented which provides information on the Chilean dolphin Cephalorhynchus eutropia's occurrence and distribution along the central-southern coast of Chile from January 2000 to March 2001. The dolphins were sighted in 83% of the surveys and the relative abundance was significantly higher in the northern than the southern area. Feeding, socializing and traveling were the three behavior categories being recorded in both areas, but were more frequently observed in the northern area. The study shows a year-round occurrence of these dolphins in the study area which is possibly a critical habitat for the species.

We have employed electron microscopic, biochemical, and molecular techniques to clarify the species of origin of the "Chilean Blob," the remains of a large sea creature that beached on the Chilean coast in July 2003. Electron microscopy revealed that the remains are largely composed of an acellular, fibrous network reminiscent of the collagen fiber network in whale blubber. Amino acid analyses of an acid hydrolysate indicated that the fibers are composed of 31% glycine residues and also contain hydroxyproline and hydroxylysine, all diagnostic of collagen. Using primers designed to the mitochondrial gene nad2, an 800-bp product of the polymerase chain reaction (PCR) was amplified from DNA that had been purified from the carcass. The DNA sequence of the PCR product was 100% identical to nad2 of sperm whale (Physeter catadon). These results unequivocally demonstrate that the Chilean Blob is the almost completely decomposed remains of the blubber layer of a sperm whale. This identification is the same as those we have obtained before from other relics such as the so-called giant octopus of St. Augustine (Florida), the Tasmanian West Coast Monster, two Bermuda Blobs, and the Nantucket Blob. It is clear now that all of these blobs of popular and cryptozoological interest are, in fact, the decomposed remains of large cetaceans. [ABSTRACT FROM AUTHOR]

Humpback whales (Megaptera novaeangliae) annually undertake the longest migrations between seasonal feeding and breeding grounds of any mammal. Despite this dispersal potential, discontinuous seasonal distributions and migratory patterns suggest that humpbacks form discrete regional populations within each ocean. To better understand the worldwide population history of humpbacks, and the interplay of this species with the oceanic environment through geological time, we assembled mitochondrial DNA control region sequences representing approximately 2700 individuals (465 bp, 219 haplotypes) and eight nuclear intronic sequences representing approximately 70 individuals (3700 bp, 140 alleles) from the North Pacific, North Atlantic and Southern Hemisphere. Bayesian divergence time reconstructions date the origin of humpback mtDNA lineages to the Pleistocene (880 ka, 95% posterior intervals 550-1320 ka) and estimate radiation of current Northern Hemisphere lineages between 50 and 200 ka, indicating colonization of the northern oceans prior to the Last Glacial Maximum. Coalescent analyses reveal restricted gene flow between ocean basins, with long-term migration rates (individual migrants per generation) of less than 3.3 for mtDNA and less than 2 for nuclear genomic DNA. Genetic evidence suggests that humpbacks in the North Pacific, North Atlantic and Southern Hemisphere are on independent evolutionary trajectories, supporting taxonomic revision of M. novaeangliae to three subspecies. [ABSTRACT FROM AUTHOR]