scholarly journals Geographic origin and timing of colonization of the Pacific Coast of North America by the rocky shore gastropod Littorina sitkana

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7987
Author(s):  
Peter B. Marko ◽  
Nadezhda I. Zaslavskaya
Keyword(s):  
Fossil Record ◽  
Rocky Shore ◽  
Sequence Data ◽  
Demographic History ◽  
Geographic Origin ◽  
Kamchatka Peninsula ◽  
Population Divergence ◽  
Northwestern Pacific ◽  
Mtdna Sequence ◽  
Littorina Sitkana

The demographic history of a species can have a lasting impact on its contemporary population genetic structure. Northeastern Pacific (NEP) populations of the rocky shore gastropod Littorina sitkana have very little mitochondrial DNA (mtDNA) sequence diversity and show no significant population structure despite lacking dispersive planktonic larvae. A contrasting pattern of high mtDNA diversity in the northwestern Pacific (NWP) suggests that L. sitkana may have recently colonized the NEP from the NWP via stepping-stone colonization through the Aleutian-Commander Archipelago (ACA) following the end of the last glacial 20,000 years ago. Here, we use multi-locus sequence data to test that hypothesis using a combination of descriptive statistics and population divergence modeling aimed at resolving the timing and the geographic origin of NEP populations. Our results show that NEP populations share a common ancestor with a population of L. sitkana on the Kamchatka Peninsula ∼46,900 years ago and that NEP populations diverged from each other ∼21,400 years ago. A more recent population divergence between Kamchatka and NEP populations, than between Kamchatka and other populations in the NWP, suggests that the ACA was the most probable dispersal route. Taking into account the confidence intervals for the estimates, we conservatively estimate that L. sitkana arrived in the NEP between 107,400 and 4,100 years ago, a range of dates that is compatible with post-glacial colonization of the NEP. Unlike other congeners that are relatively abundant in the Pleistocene fossil record of the NEP, only one report of L. sitkana exists from the NEP fossil record. Although broadly consistent with the molecular data, the biogeographic significance of these fossils is difficult to evaluate, as the shells cannot be distinguished from the closely-related congener L. subrotundata.

scholarly journals Genetic structure of the grey side-gilled sea slug (Pleurobranchaea maculata) in coastal waters of New Zealand

2017 ◽  
Author(s):  
Yeşerin Yıldırım ◽  
Marti J. Anderson ◽  
Selina Patel ◽  
Craig D. Millar ◽  
Paul B. Rainey
Keyword(s):  
New Zealand ◽  
Genetic Structure ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Haplotype Network ◽  
Founding Population ◽  
Mtdna Sequence ◽  
Expansion Time ◽  
History Of

AbstractPleurobranchaea maculatais a rarely studied species of the Heterobranchia found throughout the south and western Pacific – and recently recorded in Argentina – whose population genetic structure is unknown. Interest in the species was sparked in New Zealand following a series of dog deaths caused by ingestions of slugs containing high levels of the neurotoxin tetrodotoxin. Here we describe the genetic structure and demographic history ofP. maculatapopulations from five principle locations in New Zealand based on extensive analyses of 12 microsatellite loci and theCOIandCytBregions of mitochondrial DNA (mtDNA). Microsatellite data showed significant differentiation between northern and southern populations with population structure being associated with previously described regional variations in tetrodotoxin concentrations. However, mtDNA sequence data did not support such structure, revealing a star-shaped haplotype network with estimates of expansion time suggesting a population expansion in the Pleistocene era. Inclusion of publicly available mtDNA sequence from Argentinian sea slugs did not alter the star-shaped network. We interpret our data as indicative of a single founding population that fragmented following geographical changes that brought about the present day north-south divide in New Zealand waters. Lack of evidence of cryptic species supports data indicating that differences in toxicity of individuals among regions are a consequence of differences in diet.

New species of Patellogastropoda (Mollusca) from the Cretaceous of Hokkaido, Japan and Sakhalin, Russia

1996 ◽  
Vol 70 (5) ◽  
pp. 762-771 ◽  
Author(s):  
Tomoki Kase ◽  
Yasunari Shigeta
Keyword(s):  
South Africa ◽  
New Species ◽  
Shell Structure ◽  
Fossil Record ◽  
Rocky Shore ◽  
The Other ◽  
Northwestern Pacific ◽  
Worldwide Distribution ◽  
Eastern Russia ◽  
Northern Japan

Rare patellogastropod limpets are described from the Cenomanian to Campanian (Cretaceous) age sediments in Hokkaido, northern Japan and Sakhalin, eastern Russia. Shell structure analysis has revealed the presence of five shell structure groups within six species, permitting the allocation of three of the species identified to modern clades. However, the other three species recorded belong to shell-structure groups not known at the present day. The species described in this paper are Patella soyaensis new species, Patella sp., Patelloida obirensis new species, ?Patelloida miyauchii new species, an indeterminate species of the Lottiinae, and an indeterminate species and belonging to an unknown family. Two species are recognized as belonging to the Patellidae and three species to the Lottiidae, demonstrating that two of the three major families found to inhabit present-day rocky shore environments already existed in the Cretaceous. The discovery of two Patella species belonging to a modern clade found in South Africa indicates that the fossil record of the clade dates back more than 80 Ma and the distribution of the clade has changed markedly since that time. The occurrence of Patelloida from the northwestern Pacific further elucidates the worldwide distribution for this genus during the Cretaceous.

scholarly journals Demographic History of Indigenous Populations in Mesoamerica Based on mtDNA Sequence Data

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0131791 ◽  
Author(s):  
Antonio González-Martín ◽  
Amaya Gorostiza ◽  
Lucía Regalado-Liu ◽  
Sergio Arroyo-Peña ◽  
Sergio Tirado ◽  
...  
Keyword(s):  
Sequence Data ◽  
Demographic History ◽  
Indigenous Populations ◽  
Mtdna Sequence ◽  
History Of

Genus Arctomelon (Gastropoda, Volutidae) in the Tertiary of the northwestern Pacific: Evolution and adaptations

1996 ◽  
Vol 70 (2) ◽  
pp. 236-246 ◽  
Author(s):  
Anton E. Oleinik
Keyword(s):  
Fossil Record ◽  
Cold Water ◽  
Middle Eocene ◽  
Major Change ◽  
Kamchatka Peninsula ◽  
Shell Morphology ◽  
Northwestern Pacific ◽  
Water Conditions ◽  
Northeastern Pacific ◽  
Change Of Life

The fossil record of the volutid gastropod Arctomelon is represented by three species from the Koryak Upland and the Kamchatka Peninsula (Russian northeast), ranging in age from late middle Eocene to early Miocene. Although Recent Arctomelon stearnsii (Dall, 1872) from the northeastern Pacific is a cold-water species, paleontological data point to the origin of the genus in shallow, warm-water conditions that existed in high latitudes of the northwestern Pacific during Paleogene time. The fossil record also indicates survival of the genus during the climatic coolings through the Cenozoic. It is apparent that Arctomelon successfully adapted to the new cooler and deeper-water conditions. Despite this major change of life habit, shell morphology has remained fairly unchanged since the Eocene. Two new species of the genus Arctomelon, A. harasewychi sp. nov. and A. rateginense sp. nov., are described.

scholarly journals PSI-40 Two mitochondrial lineages revealed in North American yak

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 477-477
Author(s):  
Leah K Treffer ◽  
Edward S Rice ◽  
Anna M Fuller ◽  
Samuel Cutler ◽  
Jessica L Petersen
Keyword(s):  
Sequence Data ◽  
Haplotype Network ◽  
Ovis Aries ◽  
Similar Species ◽  
Nucleotide Polymorphisms ◽  
Mt Dna ◽  
Protein Coding ◽  
Sister Clade ◽  
Mtdna Sequence ◽  
The Impact

Abstract Domestic yak (Bos grunniens) are bovids native to the Asian Qinghai-Tibetan Plateau. Studies of Asian yak have revealed that introgression with domestic cattle has contributed to the evolution of the species. When imported to North America (NA), some hybridization with B. taurus did occur. The objective of this study was to use mitochondrial (mt) DNA sequence data to better understand the mtDNA origin of NA yak and their relationship to Asian yak and related species. The complete mtDNA sequence of 14 individuals (12 NA yak, 1 Tibetan yak, 1 Tibetan B. indicus) was generated and compared with sequences of similar species from GeneBank (B. indicus, B. grunniens (Chinese), B. taurus, B. gaurus, B. primigenius, B. frontalis, Bison bison, and Ovis aries). Individuals were aligned to the B. grunniens reference genome (ARS_UNL_BGru_maternal_1.0), which was also included in the analyses. The mtDNA genes were annotated using the ARS-UCD1.2 cattle sequence as a reference. Ten unique NA yak haplotypes were identified, which a haplotype network separated into two clusters. Variation among the NA haplotypes included 93 nonsynonymous single nucleotide polymorphisms. A maximum likelihood tree including all taxa was made using IQtree after the data were partitioned into twenty-two subgroups using PartitionFinder2. Notably, six NA yak haplotypes formed a clade with B. indicus; the other four haplotypes grouped with B. grunniens and fell as a sister clade to bison, gaur and gayal. These data demonstrate two mitochondrial origins of NA yak with genetic variation in protein coding genes. Although these data suggest yak introgression with B. indicus, it appears to date prior to importation into NA. In addition to contributing to our understanding of the species history, these results suggest the two major mtDNA haplotypes in NA yak may functionally differ. Characterization of the impact of these differences on cellular function is currently underway.

scholarly journals An Integrated Framework for the Inference of Viral Population History From Reconstructed Genealogies

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1429-1437
Author(s):  
Oliver G Pybus ◽  
Andrew Rambaut ◽  
Paul H Harvey
Keyword(s):  
Maximum Likelihood ◽  
Sequence Data ◽  
Demographic History ◽  
Population History ◽  
Maximum Likelihood Estimates ◽  
Viral Population ◽  
True Parameter ◽  
Subtype B ◽  
Exponential Growth Model ◽  
Parameter Values

Abstract We describe a unified set of methods for the inference of demographic history using genealogies reconstructed from gene sequence data. We introduce the skyline plot, a graphical, nonparametric estimate of demographic history. We discuss both maximum-likelihood parameter estimation and demographic hypothesis testing. Simulations are carried out to investigate the statistical properties of maximum-likelihood estimates of demographic parameters. The simulations reveal that (i) the performance of exponential growth model estimates is determined by a simple function of the true parameter values and (ii) under some conditions, estimates from reconstructed trees perform as well as estimates from perfect trees. We apply our methods to HIV-1 sequence data and find strong evidence that subtypes A and B have different demographic histories. We also provide the first (albeit tentative) genetic evidence for a recent decrease in the growth rate of subtype B.

scholarly journals Molecular clocks and the early evolution of metazoan nervous systems

2015 ◽  
Vol 370 (1684) ◽  
pp. 20150046 ◽  
Author(s):  
Gregory A. Wray
Keyword(s):  
Sensory Processing ◽  
Fossil Record ◽  
Sequence Data ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Sense Organs ◽  
Animal Evolution ◽  
Nervous Systems ◽  
Nervous System Evolution ◽  
Fossil Records

The timing of early animal evolution remains poorly resolved, yet remains critical for understanding nervous system evolution. Methods for estimating divergence times from sequence data have improved considerably, providing a more refined understanding of key divergences. The best molecular estimates point to the origin of metazoans and bilaterians tens to hundreds of millions of years earlier than their first appearances in the fossil record. Both the molecular and fossil records are compatible, however, with the possibility of tiny, unskeletonized, low energy budget animals during the Proterozoic that had planktonic, benthic, or meiofaunal lifestyles. Such animals would likely have had relatively simple nervous systems equipped primarily to detect food, avoid inhospitable environments and locate mates. The appearance of the first macropredators during the Cambrian would have changed the selective landscape dramatically, likely driving the evolution of complex sense organs, sophisticated sensory processing systems, and diverse effector systems involved in capturing prey and avoiding predation.

scholarly journals Reef development and Sea level changes drive Acanthaster Population Expansion in the Indo-Pacific region

2020 ◽  
Author(s):  
P.C. Pretorius ◽  
T.B. Hoareau
Keyword(s):  
Population Size ◽  
Sea Level ◽  
Environmental Changes ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Population Level ◽  
Sea Level Changes ◽  
Reef Development ◽  
Curve Fitting Method

AbstractMolecular clock calibration is central in population genetics as it provides an accurate inference of demographic history, whereby helping with the identification of driving factors of population changes in an ecosystem. This is particularly important for coral reef species that are seriously threatened globally and in need of conservation. Biogeographic events and fossils are the main source of calibration, but these are known to overestimate timing and parameters at population level, which leads to a disconnection between environmental changes and inferred reconstructions. Here, we propose the Last Glacial Maximum (LGM) calibration that is based on the assumptions that reef species went through a bottleneck during the LGM, which was followed by an early yet marginal increase in population size. We validated the LGM calibration using simulations and genetic inferences based on Extended Bayesian Skyline Plots. Applying it to mitochondrial sequence data of crown-of-thorns starfish Acanthaster spp., we obtained mutation rates that were higher than phylogenetically based calibrations and varied among populations. The timing of the greatest increase in population size differed slightly among populations, but all started between 10 and 20 kya. Using a curve-fitting method, we showed that Acanthaster populations were more influenced by sea-level changes in the Indian Ocean and by reef development in the Pacific Ocean. Our results illustrate that the LGM calibration is robust and can probably provide accurate demographic inferences in many reef species. Application of this calibration has the potential to help identify population drivers that are central for the conservation and management of these threatened ecosystems.

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