In the past decade much attention has focused on the role that genetics can play in the formation of management strategies in conservation. Here, we describe genetic diversity in the world's largest lizard, the Komodo dragon (Varanus komodoensis), examining the evolutionary relationships and population genetic history of the four islands in south-east Indonesia, which form the vast majority of its range. We identify distinct genetic groups for conservation. The population on the island of Komodo shows by far the largest values of genetic divergence and is proposed that it should be a separate conservation management unit. Other populations, surviving either on small islands with substantially reduced genetic variability, or in isolated patches, are identified as particularly vulnerable to stochastic threats and habitat loss. Our results provide an example of how data defining intraspecific levels of genetic divergence can provide information to help management plans, ensure the maintenance of genetic variability across populations and identify evolutionary potential within endangered species.

/pdf/genetic-divergence-and-units-for-conservation-in-the-komodo-213h0bpn9m.pdf

Genetic divergence and units for conservation in the Komodo dragon Varanus komodoensis

Mesoplodon perrini, a new species of beaked whale is described on the basis of five animals stranded on the coast of California (between 32°55′N, 117°15′W and 36°37′N, 121°55′W) from May 1975 to September 1997. Four of these animals were initially identified as Hector's beaked whales M. hectori based on cranial morphology (Mead 1981). A fifth specimen was initially identified as a neonate Cuvier's beaked whale Ziphius cavirostris based on external features. These specimens were first recognized as representatives of an undescribed species through phylogenetic analysis of mitochondrial (mt) DNA control region and cytochrome b sequence data. Although similar morphologically, the genetic data do not support a close evolutionary relationship between M. perrini and M. hectori. Instead, these data suggest a possible sister species relationship with the lesser beaked whale M. peruvianus. Sightings of two small beaked whales off California in the 1970s which were tentatively identified as M. hectori are also likely to be M. perrini. We suggest that M. hectori is confined to the Southern Hemisphere, while M. perrini is known to date only from the North Pacific.

/pdf/a-new-species-of-beaked-whale-mesoplodon-perrini-sp-n-1486nf1mxl.pdf

A new species of beaked whale mesoplodon perrini sp. n. (cetacea: ziphiidae) discovered through phylogenetic analyses of mitochondrial dna sequences

Pinnipeds are charismatic but difficult to study, and taxonomy is poorly under- stood. An accurate taxonomic framework is essential for studies of biogeography, ecology and conservation. 2. Morphologic and genetic criteria used to recognize pinniped species and subspe- cies are evaluated individually for all taxa in the three families: Otariidae (sea lions and fur seals), Odobenidae (walruses) and Phocidae (seals). We advocate a pragmatic approach that, in general, follows the Evolutionary Species Concept and 'diagnos- ability' criterion for subspecies delimitations. 3. Of the 33 species, all have at least two lines of evidence to distinguish them, and of the 29 subspecies, 24 have at least one line of evidence, but five have inadequate support. We present a composite phylogeny for pinnipeds. 4. We propose that the genus Arctocephalus be limited to Arctocephalus pusillus, and we resurrect the name Arctophoca for at least six species and subspecies. 5. We recommend large sample sizes and broad, random sampling in further research on pinniped taxonomy. Taxa should be described based on robust statistical analysis, not by arbitrary division of characters, and molecular research should include analysis of mtDNA and nuDNA. 6. Finally, we offer suggestions for further taxonomic research (on hybridization in otariids, and to allow consideration of life history data in sampling) in an effort to improve our understanding of pinniped diversity. Even for taxa which are already protected, better understanding of their taxonomy can only enhance their conser- vation status and facilitate efforts to protect their habitats.

Pinniped taxonomy: review of currently recognized species and subspecies, and evidence used for their description

Abstract Previous hypotheses for the origin and diversification of pinnipeds have followed a narrative approach based mostly on dispersalist (i.e., center of origin) explanations. Using an analytical approach, we present a testable hypothesis to explain the evolutionary biogeography of pinnipedimorphs (fur seals, sea lions, walruses, seals, and their fossil relatives) based on both dispersal and vicariant events in the context of a species-level phylogenetic framework. This integrated hypothesis considers many lines of evidence, including physical and ecologic factors controlling modern pinniped distributions, past geologic events related to opening and closing of seaways, paleoceanographic models, the improving pinniped fossil record, and pinniped phylogenetic analyses based on both morphologic and molecular data sets. Oceanic biogeographic regions and faunal provinces are defined and oceanic circulation patterns discussed with reference to the distribution of extant and fossil species. Paleobiogeographic hypotheses for each of the major pinniped lineages are presented using area cladograms and paleogeographic maps showing oceanographic and tectonic changes during successive intervals of the Cenozoic. Our biogeographic hypothesis supports an eastern North Pacific origin for pinnipedimorphs during the late Oligocene coincident with initiation of glaciation in Antarctica. During the early Miocene, pinnipedimorphs remained restricted to the eastern North Pacific, where they began to diversify. Otariids (fur seals and sea lions) are first known from the late Miocene in the North Pacific, where they remained restricted until the late Pliocene. A transequatorial dispersal into the western South Pacific at this time preceded the rapid diversification of this group that occurred during the Pleistocene in the Southern Ocean. Odobenids (walruses) evolved in the North Pacific during the late early Miocene and underwent dramatic diversification in the late Miocene with later members of the odobenine lineage dispersing into the North Atlantic, most likely via an Arctic route. Extinct archaic phocoids, the desmatophocids, known only from the early to late Miocene, were confined to the eastern and western North Pacific. Phocids, although postulated here to have a North Pacific origin, are first known as fossils from the middle Miocene in the eastern and western North Atlantic region, as well as the Paratethys. Both monachine and phocine seals are distinct lineages beginning in the middle Miocene in the eastern and western provinces of the North Atlantic. During the late Miocene, phocids underwent a dramatic diversification. The early biogeographic history of phocine seals is centered in the Arctic and North Atlantic. Subsequent dispersal of phocines into the Paratethys and Pacific occurred during the Pleistocene. In contrast, monachine seals have a southern hemisphere center of diversity, especially the lobodontines of the Southern Ocean. Southern dispersal of this clade most likely occurred through the Neogene Central American Seaway prior to its closure in the mid-Pliocene. The pagophilic nature of extant phocine and lobodontine seals is largely a function of Pleistocene glacioeustatic events.

Chapter 3: Pinnipedimorph Evolutionary Biogeography

Commercial sealing in the 18th and 19th centuries had a major impact on the Antarctic and subantarctic fur seal populations (Arctocephalus gazella and A. tropicalis) in the Southern Ocean. The intensive and unrestricted nature of the industry ensured substantial reductions in population sizes and resulted in both species becoming locally extinct at some sites. However, both species are continuing to recover, through the recolonization of islands across their former range and increasing population size. This study investigated the extent and pattern of genetic variation in each species to examine the hypothesis that higher levels of historic sealing in A. gazella have resulted in a greater loss of genetic variability and population structure compared with A. tropicalis. A 316-bp section of the mitochondrial control region was sequenced and revealed nucleotide diversities of 3.2% and 4.8% for A. gazella and A. tropicalis, respectively. There was no geographical distribution of lineages observed within either species, although the respective PhiST values of 0.074 and 0.19 were significantly greater than zero. These data indicate low levels of population structure in A. gazella and relatively high levels in A. tropicalis. Additional samples screened with restriction endonucleases were incorporated, and the distribution of restriction fragment length polymorphism (RFLP) and sequence haplotypes were examined to identify the main source populations of newly recolonized islands. For A. tropicalis, the data suggest that Macquarie Island and Iles Crozet were probably recolonized by females from Marion Island, and to a lesser extent Ile Amsterdam. Although there was less population structure within A. gazella, there were two geographical regions identified: a western region containing the populations of South Georgia and Bouvetoya, which were the probable sources for populations at Marion, the South Shetland and Heard Islands; and an eastern region containing the panmictic populations of Iles Kerguelen and Macquarie Island. The latter region may be a result of a pronounced founder effect, or represent a remnant population that survived sealing at Iles Kerguelen.

/pdf/postsealing-genetic-variation-and-population-structure-of-41iimyoaha.pdf

Postsealing genetic variation and population structure of two species of fur seal (Arctocephalus gazella and A-tropicalis)

We have examined phylogenetic and geographic patterns of variation in the mitochondrial cytochrome b gene of Southern Hemisphere fur seals (Arctocephalus spp.). Our survey of 106 individuals from four putative species reveals three distinct patterns of variation reflecting ancient, recent historic, and contemporary gene flow. For the combined samples of Subantarctic (Arctocephalus tropicalis) and Antarctic (Arctocephalus gazella) fur seals, we find low levels of sequence diversity and reciprocal paraphyly of hapiotypes (where representative haplotypes of a species are found to occur infrequently in another species and vice versa). For the Australian and Cape fur seal subspecies (Arctocephalus pusillus doriferus and A. p. pusillus, respectively), we find low levels of sequence diversity but significant differences in the regional distribution of haplotypes that are consistent with, but not conclusive of, the current subspecies definition based on nonmolecular data. For the New Zealand fur seal (Arctocephalus forsteri), we find high levels of average sequence diversity because of the survival of two divergent lineages of mitochondrial hapiotypes with differences approaching that found in interspecific comparisons of other mammals. The two divergent clades are distributed sympatrically in some regions, but the overall geographic structure of the variation is significant across the range of this species. These new molecular data are inconsistent with current taxonomic definitions of species within the Southern Hemisphere fur seals and argue for reevaluation of these "species" definitions. For management purposes, the definition of evolutionarily significant units (Ryder 1986) and genetic management units (Moritz 1994) in relation to these species may also be evaluated in light of this molecular genetic information.

/pdf/genetic-variation-of-southern-hemisphere-fur-seals-47bqg35xzu.pdf

Genetic Variation of Southern Hemisphere Fur Seals (Arctocephalus spp.): Investigation of Population Structure and Species Identity

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Genetic Variation of Southern Hemisphere Fur Seals (Arctocephalus spp.): Investigation of Population Structure and Species Identity