scholarly journals Evolution of initiation rites during the Austronesian dispersal

2021 ◽  
Vol 104 (3) ◽  
pp. 003685042110313
Author(s):  
R Alexander Bentley ◽  
William R Moritz ◽  
Damian J Ruck ◽  
Michael J O’Brien
Keyword(s):  
Adaptive Systems ◽  
Bayes Factor ◽  
Phylogenetic Analyses ◽  
Complex Societies ◽  
Data Set ◽  
Initiation Rites ◽  
Austronesian Language ◽  
The Pacific ◽  
Phylogenetic Model ◽  
Foundational Work

As adaptive systems, kinship and its accompanying rules have co-evolved with elements of complex societies, including wealth inheritance, subsistence, and power relations. Here we consider an aspect of kinship evolution in the Austronesian dispersal that began from about 5500 BP in Taiwan, reaching Melanesia about 3200 BP, and dispersing into Micronesia by 1500 BP. Previous, foundational work has used phylogenetic comparative methods and ethnolinguistic information to infer matrilocal residence in proto-Austronesian societies. Here we apply Bayesian phylogenetic analyses to a data set on Austronesian societies that combines existing data on marital residence systems with a new set of ethnographic data, introduced here, on initiation rites. Transition likelihoods between cultural-trait combinations were modeled on an ensemble of 1000 possible Austronesian language trees, using Reversible Jump Markov Chain Monte Carlo (RJ-MCMC) simulations. Compared against a baseline phylogenetic model of independent evolution, a phylogenetic model of correlated evolution between female and male initiation rites is substantially more likely (log Bayes factor: 17.9). This indicates, over the generations of Austronesian dispersal, initiation rites were culturally stable when both female and male rites were in the same state (both present or both absent), yet relatively unstable for female-only rites. The results indicate correlated phylogeographic evolution of cultural initiation rites in the prehistoric dispersal of Austronesian societies across the Pacific. Once acquired, male initiation rites were more resilient than female-only rites among Austronesian societies.

scholarly journals The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 995-1010 ◽  
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Living Fossil ◽  
Latimeria Chalumnae ◽  
Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

Minimal clustering and species delimitation based on multi-locus alignments vs SNPs: the case of the Seriphium plumosum L. complex (Gnaphalieae: Asteraceae)

2021 ◽  
Author(s):  
Zaynab Shaik ◽  
Nicola Georgina Bergh ◽  
Bengt Oxelman ◽  
Anthony George Verboom
Keyword(s):  
Species Delimitation ◽  
Bayes Factor ◽  
Cape Floristic Region ◽  
Parametric Models ◽  
Western Cape ◽  
Nucleotide Polymorphisms ◽  
Sequence Alignments ◽  
Separate Species ◽  
Multiple Sequence ◽  
Data Set

We applied species delimitation methods based on the Multi-Species Coalescent (MSC) model to 500+ loci derived from genotyping-by-sequencing on the South African Seriphium plumosum (Asteraceae) species complex. The loci were represented either as multiple sequence alignments or single nucleotide polymorphisms (SNPs), and analysed by the STACEY and Bayes Factor Delimitation (BFD)/SNAPP methods, respectively. Both methods supported species taxonomies where virtually all of the 32 sampled individuals, each representing its own geographical population, were identified as separate species. Computational efforts required to achieve adequate mixing of MCMC chains were considerable, and the species/minimal cluster trees identified similar strongly supported clades in replicate runs. The resolution was, however, higher in the STACEY trees than in the SNAPP trees, which is consistent with the higher information content of full sequences. The computational efficiency, measured as effective sample sizes of likelihood and posterior estimates per time unit, was consistently higher for STACEY. A random subset of 56 alignments had similar resolution to the 524-locus SNP data set. The STRUCTURE-like sparse Non-negative Matrix Factorisation (sNMF) method was applied to six individuals from each of 48 geographical populations and 28023 SNPs. Significantly fewer (13) clusters were identified as optimal by this analysis compared to the MSC methods. The sNMF clusters correspond closely to clades consistently supported by MSC methods, and showed evidence of admixture, especially in the western Cape Floristic Region. We discuss the significance of these findings, and conclude that it is important to a priori consider the kind of species one wants to identify when using genome-scale data, the assumptions behind the parametric models applied, and the potential consequences of model violations may have.

Integrated geophysical modelling of terranes and other structural features along the western Canadian margin

1992 ◽  
Vol 29 (7) ◽  
pp. 1492-1508 ◽  
Author(s):  
S. A. Dehler ◽  
R. M. Clowes
Keyword(s):  
Seismic Refraction ◽  
Vancouver Island ◽  
Structural Features ◽  
Pacific Rim ◽  
Data Set ◽  
Reflection Seismic ◽  
Barkley Sound ◽  
The Pacific ◽  
Wrangellia Terrane ◽  
Lower Crustal

An integrated geophysical data set has been used to develop structural models across the continental margin west of Vancouver Island, Canada. A modern accretionary complex underlies the continental slope and shelf and rests against and below the allochthonous Crescent and Pacific Rim terranes. These terranes in turn abut against the pre-Tertiary Wrangellia terrane that constitutes most of the island. Gravity and magnetic anomaly data, constrained by seismic reflection, seismic refraction, and other data, were interpreted to determine the offshore positions of these terranes and related features. Iterative 2.5-dimensional forward models of anomaly profiles were stepped laterally along the margin to extend areal coverage over a 70 km wide swath oriented normal to the tectonic features. An average model was then developed to represent this part of the margin. The Pacific Rim terrane appears to be continuous and close to the coastline along the length of Vancouver Island, consistent with emplacement by strike-slip motion along the margin. The Westcoast fault, the boundary between the Pacific Rim and Wrangellia terranes, is interpreted to be 15 km farther seaward than in previous interpretations in the region of Barkley Sound. The Crescent terrane forms a thin landward-dipping slab along the southern half of the Vancouver Island margin, and cannot be confirmed along the northern part. Model results suggest the slab has buckled into an anticline beneath southern Vancouver Island and Juan de Fuca Strait, uplifting high-density lower crustal or upper mantle material close to the surface to produce the observed intense positive gravity anomaly. This geometry is consistent with emplacement of the Crescent terrane by oblique subduction.

scholarly journals The political biogeography of migratory marine predators

2019 ◽  
Author(s):  
Autumn-Lynn Harrison
Keyword(s):  
Pacific Ocean ◽  
The Political ◽  
Migratory Species ◽  
Data Set ◽  
Leatherback Turtles ◽  
Annual Cycles ◽  
Marine Predators ◽  
The Pacific ◽  
The Pacific Ocean ◽  
International Strategies

We synthesized a large tracking data set from the Tagging of Pacific Predators to show how the movements and migratory phenology of 1,648 individuals representing 14 species—from leatherback turtles to white sharks—relate to the geopolitical boundaries of the Pacific Ocean throughout species’ annual cycles. Cumulatively, these species visited 86% of Pacific Ocean countries and some spent three-quarters of their annual cycles in the high seas. With our results, we offer answers to questions posed when designing international strategies for managing migratory species.

scholarly journals Micromorphological, anatomical and molecular study of Hedera species (Araliaceae) in Iran

2020 ◽  
Vol 63 (2) ◽  
pp. 91-101
Author(s):  
Elham Amini ◽  
Fatemeh Nasrollahi ◽  
Ali Sattarian ◽  
Mahboobeh Haji Moradkhani ◽  
Sohrab Boozarpour ◽  
...  
Keyword(s):  
North Africa ◽  
Phylogenetic Analyses ◽  
Molecular Study ◽  
Molecular Characteristics ◽  
Nrdna Its ◽  
Anticlinal Wall ◽  
Data Set ◽  
Phylogenetic Methods ◽  
Extant Species ◽  
Qualitative Characters

Hedera, with 12 extant species, is a genus of evergreen climbers native to Europe, north Africa, and south Asia. In this study, the micromorphological, anatomical structure and molecular evidences of 11 populations from two species of Hedera (H. helix and H. pastuchovii) have been considered to evaluate the relationships in Hedera. In total, seven quantitative and qualitative characters of pollen were selected and measured. Based on this study, the anticlinal wall and surface sculpturing of seed support for separation of two species of Hedera. Micromorphology of epidermis illustrated two types of epidermal cells: puzzle-shaped and polygonal cells. Using nuclear (nrDNA ITS) marker, we reconstructed phylogenetic relationships within two species of Hedera. This data set was analyzed by phylogenetic methods including Bayesian inference, maximum likelihood, and maximum parsimony. In phylogenetic analyses, all members of two species formed a well-supported clade (PP = 1; ML/BS = 100/100) and divided into two major clades (A and B). Neighbor Net diagram demonstrated separation of the studied populations. The results showed that these taxa differ in taxonomically important micromorphological, anatomical and molecular characteristics and these data provide reliable evidence for separation of these two species.

scholarly journals Phylogenetic placement of enigmatic Astianthus (Bignoniaceae) based on molecular data, wood and bark anatomy

2021 ◽  
Vol 99 (2) ◽  
pp. 398-412
Author(s):  
Marcelo R. Pace ◽  
Brenda Hernández-Hernández ◽  
Esteban M. Martínez Salas ◽  
Lúcia G. Lohmann ◽  
N. Ivalu Cacho
Keyword(s):  
Pacific Coast ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Placement ◽  
The Pacific ◽  
Molecular Phylogenetic ◽  
Phloem Fibers ◽  
Plastid Markers ◽  
Bark Anatomy

Background: Astianthus is a monospecific arborescent genus of Bignoniaceae that occur in the Pacific Coast of central Mexico and northern Central America, where it grows in dense populations along riversides. Its phylogenetic placement has remained controversial since Astianthus has unusual morphological characters such as a four-loculed ovary, and simple, pulvinate, verticillate leaves. Methods: Here we used three plastid markers ndhF, rbcL, and trnL-F, wood, and bark anatomical data to investigate the phylogenetic placement of Astianthus and assign it to one of Bignoniaceae’s main clades. Results: Our molecular phylogenetic analyses indicated that Astianthus belongs in tribe Tecomeae s.s., where other charismatic Neotropical Bignoniaceae genera such as Campsis and Tecoma are currently placed. Wood and bark anatomy support this placement, as Astianthus reunites a unique combination of features only known from members of Tecomeae s.s., such as storied axial parenchyma, the co-occurrence of homo- and heterocellular rays, septate fibers, and scattered phloem fibers in the bark. Conclusions: The placement of Astianthus within Tecomeae s.s. provides further support to previous proposals for the Neotropical origin of this Pantropical tribe.

scholarly journals Novel Cell-Virus-Virophage Tripartite Infection Systems Discovered in the Freshwater Lake Dishui Lake in Shanghai, China

2020 ◽  
Vol 94 (11) ◽  
Author(s):  
Shengzhong Xu ◽  
Liang Zhou ◽  
Xiaosha Liang ◽  
Yifan Zhou ◽  
Hao Chen ◽  
...  
Keyword(s):  
Green Algae ◽  
Green Alga ◽  
Phylogenetic Analyses ◽  
Freshwater Lake ◽  
Metagenomic Data ◽  
Data Sets ◽  
Data Set ◽  
Dna Viruses ◽  
Oligonucleotide Frequency ◽  
Dsdna Viruses

ABSTRACT Virophages are small parasitic double-stranded DNA (dsDNA) viruses of giant dsDNA viruses infecting unicellular eukaryotes. Except for a few isolated virophages characterized by parasitization mechanisms, features of virophages discovered in metagenomic data sets remain largely unknown. Here, the complete genomes of seven virophages (26.6 to 31.5 kbp) and four large DNA viruses (190.4 to 392.5 kbp) that coexist in the freshwater lake Dishui Lake, Shanghai, China, have been identified based on environmental metagenomic investigation. Both genomic and phylogenetic analyses indicate that Dishui Lake virophages (DSLVs) are closely related to each other and to other lake virophages, and Dishui Lake large DNA viruses are affiliated with the micro-green alga-infecting Prasinovirus of the Phycodnaviridae (named Dishui Lake phycodnaviruses [DSLPVs]) and protist (protozoan and alga)-infecting Mimiviridae (named Dishui Lake large alga virus [DSLLAV]). The DSLVs possess more genes with closer homology to that of large alga viruses than to that of giant protozoan viruses. Furthermore, the DSLVs are strongly associated with large green alga viruses, including DSLPV4 and DSLLAV1, based on codon usage as well as oligonucleotide frequency and correlation analyses. Surprisingly, a nonhomologous CRISPR-Cas like system is found in DSLLAV1, which appears to protect DSLLAV1 from the parasitization of DSLV5 and DSLV8. These results suggest that novel cell-virus-virophage (CVv) tripartite infection systems of green algae, large green alga virus (Phycodnaviridae- and Mimiviridae-related), and virophage exist in Dishui Lake, which will contribute to further deep investigations of the evolutionary interaction of virophages and large alga viruses as well as of the essential roles that the CVv plays in the ecology of algae. IMPORTANCE Virophages are small parasitizing viruses of large/giant viruses. To our knowledge, the few isolated virophages all parasitize giant protozoan viruses (Mimiviridae) for propagation and form a tripartite infection system with hosts, here named the cell-virus-virophage (CVv) system. However, the CVv system remains largely unknown in environmental metagenomic data sets. In this study, we systematically investigated the metagenomic data set from the freshwater lake Dishui Lake, Shanghai, China. Consequently, four novel large alga viruses and seven virophages were discovered to coexist in Dishui Lake. Surprisingly, a novel CVv tripartite infection system comprising green algae, large green alga viruses (Phycodnaviridae- and Mimiviridae-related), and virophages was identified based on genetic link, genomic signature, and CRISPR system analyses. Meanwhile, a nonhomologous CRISPR-like system was found in Dishui Lake large alga viruses, which appears to protect the virus host from the infection of Dishui Lake virophages (DSLVs). These findings are critical to give insight into the potential significance of CVv in global evolution and ecology.

scholarly journals Large-Volume WOCE Radiocarbon Sampling in the Pacific Ocean

Radiocarbon ◽  
1996 ◽  
Vol 38 (3) ◽  
pp. 519-561 ◽  
Author(s):  
Minze Stuiver ◽  
H. G. Östlund ◽  
Robert M. Key ◽  
Paula J. Reimer
Keyword(s):  
Pacific Ocean ◽  
Large Volume ◽  
University Of Washington ◽  
Data Set ◽  
Comprehensive Data ◽  
The Pacific ◽  
The Pacific Ocean ◽  
University Of Miami ◽  
The University

At the University of Miami Tritium Laboratory and the University of Washington Quaternary Isotope Laboratory, more than 1000 large-volume Pacific Ocean radiocarbon samples were measured for the WOCE program. Here we present a comprehensive data set, and a brief discussion of our findings.

scholarly journals Novel Viruses Found in Antricola Ticks Collected in Bat Caves in the Western Amazonia of Brazil

Viruses ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 48 ◽  
Author(s):  
Anne-Lie Blomström ◽  
Hermes R. Luz ◽  
Pontus Öhlund ◽  
Matthew Lukenge ◽  
Paulo Eduardo Brandão ◽  
...  
Keyword(s):  
Rna Viruses ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Blood Feeding ◽  
Dominant Group ◽  
Data Set ◽  
Adult Feeding ◽  
Viral Sequences ◽  
Negative Sense ◽  
Bat Guano

In this study, we describe the viral composition of adult Antricola delacruzi ticks collected in a hot bat cave in the state of Rondônia, Western Amazonia, Brazil. A. delacruzi ticks, are special, compared to many other ticks, in that they feed on both bats (larval blood feeding) and bat guano (nymphal and adult feeding) instead of feeding exclusively on vertebrate hosts (blood feeding). Considering this unique life-cycle it is potentially possible that these ticks can pick up/be infected by viruses not only present in the blood of viremic bats but also by virus shed through the bat guano. The viral metagenomic investigation of adult ticks showed that single-stranded negative-sense RNA viruses were the dominant group of viruses identified in the investigated ticks. Out of these, members of the Nairoviridae family were in clear majority constituting 88% of all viral reads in the data set. Genetic and phylogenetic analyses indicate the presence of several different orthonairoviruses in the investigated ticks with only distant relationship to previously described ones. In addition, identification of viral sequences belonging to Orthomyxoviridae, Iflaviridae, Dicistroviridae, Polycipiviridae, Reoviridae and different unclassified RNA viruses showed the presence of viruses with low sequence similarity to previously described viruses.

scholarly journals Oceanic Radiocarbon Between Antarctica and South Africa Along Woce Section 16 at 30°E

Radiocarbon ◽  
1999 ◽  
Vol 41 (1) ◽  
pp. 51-73 ◽  
Author(s):  
Viviane Leboucher ◽  
James Orr ◽  
Philippe Jean-Baptiste ◽  
Maurice Arnold ◽  
Patrick Monfray ◽  
...  
Keyword(s):  
South Africa ◽  
Surface Waters ◽  
Polar Front ◽  
Return Flow ◽  
Intermediate Water ◽  
Data Set ◽  
Deep Waters ◽  
The Pacific ◽  
Ocean Carbon ◽  
The Antarctic

Accelerator mass spectrometry (AMS) radiocarbon measurements were made on 120 samples collected between Antarctica and South Africa along 30°E during the WOCE-France CIVA1 campaign in February 1993. Our principal objective was to complement the Southern Ocean's sparse existing data set in order to improve the 14C benchmark used for validating ocean carbon-cycle models, which disagree considerably in this region. Measured 14C is consistent with the θ-S characteristics of CIVA1. Antarctic Intermediate Water (AAIW) forming north of the Polar Front (PF) is rich in 14C, whereas surface waters south of the PF are depleted in 14C. A distinct old 14C signal was found for the contribution of the Pacific Deep Water (PDW) to the return flow of Circumpolar Deep Waters (CDW). Comparison to previous measurements shows a 14C decrease in surface waters, consistent with northward displacement of surface waters, replacement by old deep waters upwelled at the Antarctic Divergence, and atmospheric decline in 14C. Conversely, an increase was found in deeper layers, in the AAIW. Large uncertainties, associated with previous methods for separating natural and bomb 14C when in the Southern Ocean south of 45°S, motivated us to develop a new approach that relies on a simple mixing model and on chlorofluorocarbon (CFC) measurements also taken during CIVA1. This approach leads to inventories for CIVA1 that are equal to or higher than those calculated with previous methods. Differences between old and new methods are especially high south of approximately 55°S, where bomb 14C inventories are relatively modest.

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