Expanding Southwest Pacific mitochondrial haplogroups P and Q

Modern humans have occupied New Guinea and the nearby Bismarck and Solomon archipelagos of Island Melanesia for at least 40,000 years. Previous mitochondrial DNA (mtDNA) studies indicated that two common lineages in this region, haplogroups P and Q, were particularly diverse, with the coalescence for P considered significantly older than that for Q. In this study, we expand the definition of haplogroup Q so that it includes three major branches, each separated by multiple mutational distinctions (Q1, equivalent to the earlier definition of Q, plus Q2 and Q3). We report three whole-mtDNA genomes that establish Q2 as a major Q branch. In addition, we describe 314 control region sequences that belong to the expanded haplogroups P and Q from our Southwest Pacific collection. The coalescence dates for the largest P and Q branches (P1 and Q1) are similar to each other (approximately 50,000 years old) and considerably older than prior estimates. Newly identified Q2, which was found in Island Melanesian samples just to the east, is somewhat younger by more than 10,000 years. Our coalescence estimates should be more reliable than prior ones because they were based on significantly larger samples as well as complete mtDNA-coding region sequencing. Our estimates are roughly in accord with the current suggested dates for the first settlement of New Guinea-Sahul. The phylogeography of P and Q indicates almost total (female) isolation of ancient New Guinea-Island Melanesia from Australia that may have existed from the time of the first settlement. While Q subsequently diversified extensively in New Guinea-Island Melanesia, it has not been found in Australia. The only shared mtDNA haplogroup between Australia and New Guinea identified to date remains one minor branch of P.     

Hermaphroditism in two populations of Chiton articulatus (Mollusca: Polyplacophora) from the eastern tropical coast of México

Through histological analyses, this study reveals an unusually high incidence of hermaphroditism in Chiton articulatus. Specimens were sampled every 30?days between September 2010 and September 2011 at two locations (Las Brisas and Jaramillo beaches, Acapulco) on the tropical eastern Pacific coast of Mexico. At both sites, hermaphroditism was found throughout the year, although in varying proportions. Higher percentages of hermaphroditism were found during the pre-spawning summer months (Las Brisas Beach 63%, Jaramillo Beach 68%). Two different kinds of hermaphroditic gonads were found, showing a preponderance of either male or female tissues but, commonly, female tissues occupied the greatest part of the gonad cross sections. Similar to other species of polyplacophorans, there was a predominance of males, although M:F sex ratios ranged from 0.7 to 4.5: 1 at Las Brisas Beach and 0.3–8: 1 at Jaramillo Beach.     

Unexpected NRY chromosome variation in Northern Island Melanesia

To investigate the paternal population history of populations in Northern Island Melanesia, 685 paternally unrelated males from 36 populations in this region and New Guinea were analyzed at 14 regionally informative binary markers and 7 short tandem repeat (STR) loci from the nonrecombining portion of the Y chromosome. Three newly defined binary markers (K6-P79, K7-P117, and M2-P87) aided in identifying considerable heterozygosity that would have otherwise gone undetected. Judging from their geographic distributions and network analyses of their associated STR profiles, 4 lineages appear to have developed in this region and to be of considerable age: K6-P79, K7-P117, M2-P87, and M2a-P22. The origins of K5-M230 and M-M4 are also confirmed as being located further west, probably in New Guinea. In the 25 adequately sampled populations, the number of different haplogroups ranged from 2 in the single most isolated group (the Aita of Bougainville), to 9, and measures of molecular diversity were generally not particularly low. The resulting pattern contradicts earlier findings that suggested far lower male-mediated diversity and gene exchange rates in the region. However, these earlier studies had not included the newly defined haplogroups. We could only identify a very weak signal of recent male Southeast Asian genetic influence (<10%), which was almost entirely restricted to Austronesian (Oceanic)-speaking groups. This contradicts earlier assumptions on the ancestral composition of these groups and requires a revision of hypotheses concerning the settlement of the islands of the central Pacific, which commenced from this region.     

Diatom-inferred productivity changes in the eastern equatorial Pacific: The quaternary record of ODP leg 111, site 677

Recent marine planktonic diatom assemblages from 47 sediment surface samples retrieved from the eastern equatorial Pacific yielded four significant Q-mode factors that are related to surface water properties. They include a northern subtropical (Factor 1), a southern subtropical (Factor 2), a Peru Current (Factor 3) and an eastern Equatorial Pacific (Factor 4) factor.A transfer function (based on 42 surface sediment samples) with a productivity range of 109 to 210 gC m^–2 y^–1 was defined using the geographic distribution of the northern and southern subtropical assemblages (Factor 1 and 2) and their relation to mapped surface water primary productivity. This transfer function has a standard error of estimate of 11.9 gC m^–2 y^–1 and it is used to estimate late Pleistocene paleo-productivity changes at ODP Leg 111 Site 677 off Ecuador.The Site 677 samples (usually spaced 10 cm apart and with a linear sedimentation rate of 4.3 cm y^–3) were the same samples that were used for stable oxygen/carbon isotopic analysis from planktonic Foraminifera. The well constrained oxygen isotope stratigraphy permitted assignment of accurate ages to downcore samples.The interval between oxygen isotope stages 3 and 9 had variable productivity that is generally higher than present values of 175 gC m^–2 y^–1 A major decline in paleo-productivity below the present value occurred in stage 9, the early part of stage 8 and in the early and late stage 5.     

OBSERVATIONS OF AN UNIDENTIFIED BEAKED WHALE (MESOPLODON SP.) IN THE EASTERN TROPICAL PACIFIC

Multiple sightings of a distinctive but unidentified species of beaked whale have been made in the eastern tropical Pacific. The unidentified whale has two color morphs: a conspicuously marked black and white form (judged to be larger), and a uniformly gray-brown form. Maximum length estimates have been 5–5.5 m. Other features include a relatively flat head, with a small, distinct melon; a moderately long beak; and a low, wide-based, triangular dorsal fin. On most animals the trailing edge of the dorsal fin is only slightly falcate and often appears straight. On the black and white morph, a broad white or cream-colored swathe originates immediately posterior to the dorsal surface of the head and runs posterio-ventrally on either side of the animal. The prevalence of scarring on the black and white animals suggests sexual dimorphism and that these larger, more conspicuously marked animals are adult males, while the smaller, browner, unscarred animals are females and young. Possibilities for identification include: 1) a well-marked race of a known Mesoplodon sp., 2) Mesoplodon (Indopacetus) pacificus or 3) an undescribed species.     

The signal crayfish is not a single species: cryptic diversity and invasions in the Pacific Northwest range of Pacifastacus leniusculus

1. We used historical sources, morphology‐based taxonomy and mtDNA sequence data to address questions about the signal crayfish Pacifastacus leniusculus. These included evaluating unrecognised cryptic diversity and investigating the extent to which P. leniusculus may have been introduced within its presumed native range in the Pacific Northwest region of North America. Our study builds and expands on Pacific Northwest phylogeographic knowledge, particularly related to patterns of glacial refugia for freshwater species. 2. Extensive collections (824 specimens) from British Columbia (Canada), Idaho, Nevada, Oregon and Washington (United States) were used to characterise P. leniusculus at the mitochondrial 16S rRNA gene. Genetic groups within the species were elucidated by phylogenetics and amova ; evolutionary relationships within the most common and diverse group were investigated using a statistical parsimony haplotype network, a nested amova , and tests of isolation by distance. Morphological measurements were used to relate findings of molecular analyses to three historically recognised P. leniusculus subspecies and characterise cryptic diversity by morphology. 3. We found substantial cryptic diversity, with three groups highly distinct from P. leniusculus in discrete geographic regions: the Chehalis River glacial refugium, Central Oregon and the Okanagan Plateau. Disjunct distributions of P. leniusculus relative to these cryptic groups and known patterns of Pleistocene glaciation and landscape evolution cast doubt on whether P. leniusculus is native to some areas such as coastal drainages of northern Washington and southern British Columbia. Morphological traits previously used to characterise P. leniusculus subspecies still persist but may be incapable of distinguishing P. leniusculus from newly discovered cryptic groups. 4. Cryptic diversity found within P. leniusculus highlights the pressing need for a thorough investigation of the genus Pacifastacus using data based on more extensive gene and taxon sampling. It also warrants conservation attention, as introductions of P. leniusculus within the Pacific Northwest may carry risks of hybridisation and introgression for cryptic groups. Owing to high genetic diversity and limited dispersal capacity relative to more vagile organisms like freshwater fish, crayfish of the genus Pacifastacus offer powerful potential insights into the geological history and phylogeography of the Pacific Northwest region. Finally, by shedding light on the long‐neglected native range of P. leniusculus, our results should also better inform our understanding of potential source populations for, and the ecology of, this important invasive species in regions including Europe, Japan and elsewhere in North America.     

Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America

Glacial cycles have played a dominant role in shaping the genetic structure and distribution of biota in northwestern North America. The two major ice age refugia of Beringia and the Pacific Northwest were connected by major mountain chains and bordered by the Pacific Ocean. As a result, numerous refugial options were available for the regions taxa during glacial advances. We reviewed the importance of glaciations and refugia in shaping northwestern North America’s phylogeographic history. We also tested whether ecological variables were associated with refugial history. The recurrent phylogeographic patterns that emerged were the following: (i) additional complexity, i.e. refugia within refugia, in both Beringia and the Pacific Northwest; and (ii) strong evidence for cryptic refugia in the Alexander Archipelago and Haida Gwaii, the Canadian Arctic and within the ice‐sheets. Species with contemporary ranges that covered multiple refugia, or those with high dispersal ability, were significantly more likely to have resided in multiple refugia. Most of the shared phylogeographic patterns can be attributed to multiple refugial locales during the last glacial maximum or major physiographic barriers like rivers and glaciers. However, some of the observed patterns are much older and appear connected to the orogeny of the Cascade‐Sierra chain or allopatric differentiation during historic glacial advances. The emergent patterns from this review suggest we should refine the classic Beringian‐southern refugial paradigm for northwestern North American biota and highlight the ecological and evolutionary consequences of colonization from multiple refugia.