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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Nuryadi, Handung; Mandagi, Ixchel; Masengi, Kawilarang; Kusumi, Junko; +2 Authors

    Heteroplasmy, the presence of multiple mitochondrial DNA (mtDNA) haplotypes within cells of an individual, is caused by mutation or paternal leakage. However, heteroplasmy is usually resolved to homoplasmy within a few generations because of germ-line bottlenecks; therefore, instances of heteroplasmy are limited in nature. Here, we report heteroplasmy in the ricefish species Oryzias matanensis, endemic to Lake Matano, an ancient lake in Sulawesi Island, in which one individual was known to have many heterozygous sites in the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. In this study, we cloned the ND2 gene for some additional individuals with heterozygous sites and demonstrated that they are truly heteroplasmic. Phylogenetic analysis revealed that the extra haplotype within the heteroplasmic O. matanensis individuals clustered with haplotypes of O. marmoratus, a congeneric species inhabiting adjacent lakes. This indicated that the heteroplasmy originated from paternal leakage due to interspecific hybridisation. The extra haplotype was unique and contained two nonsynonymous substitutions. These findings demonstrate that this hybridisation-driven heteroplasmy was maintained across generations for a long time to the extent that the extra mitochondria evolved within the new host. ## Data set from Nuryadi et al. 2023 Biology Letters. The data set accompanies four Dryad data files. Uploaded: November 2023 Revised: Contact: Kazunori Yamahira (yamahira@lab.u-ryukyu.ac.jp) *** File\_01\_Fasta\_ND2\_all.fas The fasta file containing mitochondrial ND2 sequences (1053 bp) of Oryzias species endemic to the Malili Lake system, which was used for the ML phylogeny in figure 2. *** File\_02\_Fasta\_ND2\_unique.fas The fasta file containing mitochondrial ND2 sequences (1053 bp) of the 52 unique haplotypes among Oryzias species endemic to the Malili Lake system, which was used for the ML phylogeny in figure S1. *** File\_03\_Fasta\_ND2\_unique\_only\_HapB\_Mar.fas The fasta file containing mitochondrial ND2 sequences (1053 bp) of the 10 unique haplotypes from Oryzias marmoratus and the O. matanensis extra haplotype, which was used in EasyCodeML. *** File\_04\_Newick\_ND2\_unique\_only\_HapB\_Mar.txt The newick file containing a topology among the 10 unique haplotypes from Oryzias marmoratus and the O. matanensis extra haplotype, which was used in EasyCodeML.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DRYAD; ZENODOarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DRYAD; ZENODO
    Dataset . 2023
    License: CC 0
    Data sources: ZENODO; Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DRYAD; ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DRYAD; ZENODO
      Dataset . 2023
      License: CC 0
      Data sources: ZENODO; Datacite
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Yang, Bin; Cui, Leilei; Perez-Enciso, Miguel; Traspov, Aleksei; +18 Authors

    [Results]: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. [Conclusions]: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation. [Background]: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. Usage Notes: Description_data_GSE_Global_pigs Table describing the samples. Note that the submitted data includes a few animals that were removed from the paper due to additional constraints applied in the review process. GSE_global_pigs.map PLINK MAP file, describing the SNPs used. GSE_global_pigs.ped Genotype data used in PLINK PED file format. Peer reviewed

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    DRYAD; NARCIS; ZENODO
    Dataset . 2018
    License: CC 0
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DANS-EASY
    Dataset . 2017
    Data sources: B2FIND
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      DRYAD; NARCIS; ZENODO
      Dataset . 2018
      License: CC 0
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DANS-EASY
      Dataset . 2017
      Data sources: B2FIND
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  • Authors: Prasetyo, Teguh Budi;
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    Authors: Baru Sakka, Sakka;

    - Tinjauan Agroklimatologi Kelapa Sawit Berbasis Sistem Informasi dan Geografis (SIG) di PT. Perkebunan Nusantara XIV Sulawesi Selatan

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Hasanuddin Universit...arrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Hasanuddin Universit...arrow_drop_down
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    Authors: Reilly, Sean; Karin, Benjamin; Stubbs, Alexander L.; Arida, Evy; +6 Authors

    The archipelagos of Wallacea extend between the Sunda and Sahul Shelves, serving as a semi-permeable two-way filter influencing faunal exchange between Asia and Australo-Papua. Forest skinks (Genus Sphenomorphus) are widespread throughout southern Wallacea and exhibit complex clinal, ontogenetic, sexual, and seasonal morphological variation rendering species delimitation difficult. We screened a mitochondrial marker for 245 Sphenomorphus specimens from this area to inform the selection of 104 samples from which we used targeted sequence-capture to generate a dataset of 1154 nuclear genes (~1.8 Mb) plus complete mitochondrial genomes. Phylogenomic analyses recovered many deeply divergent lineages, three of which are now sympatric, that began to diversify in the late Miocene shortly after the oldest islands are thought to have become emergent. We infer a complex and non-stepping-stone pattern of island colonization, with the group having originated in the Sunda Arc islands before using Sumba as a springboard for colonization of the Banda Arcs. Estimates of population structure and gene flow across the region suggest total isolation except between two Pleistocene Aggregate Island Complexes that become episodically land-bridged during glacial maxima. These historical processes have resulted in at least 11 Sphenomorphus species in the region, nine of which require formal description. This fine-scale geographic partitioning of undescribed species highlights the importance of utilizing comprehensive genomic studies for defining biodiversity hotspots to be considered for conservation protection. See supplementary methods for a detailed description of the datasets, which include mitochondrial ND4 sequence data (GenBank accession numbers MW291696–291940), and a targeted sequence capture dataset that includes 1,154 nuclear loci and complete mitochondrial genomes for 104 samples. The targeted capture dataset was sequenced on the Illumina platform with paired end 100 bp reads that have been deposited in the NCBI sequence read archive under accession number PRJNA682772.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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    ZENODO
    Dataset . 2022
    License: CC 0
    Data sources: ZENODO
    DRYAD
    Dataset . 2022
    License: CC 0
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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      ZENODO
      Dataset . 2022
      License: CC 0
      Data sources: ZENODO
      DRYAD
      Dataset . 2022
      License: CC 0
      Data sources: Datacite
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Hapsari, K. Anggi; Jennerjahn, Tim; Nugroho, Septriono Hari; Yulianto, Eko; +1 Authors

    Southeast Asian peatlands, along with their various important ecosystem services, are mainly distributed in the coastal areas of Sumatra and Borneo. These ecosystems are threatened by coastal development, global warming and sea level rise (SLR). Despite receiving growing attention for their biodiversity and as massive carbon stores, there is still a lack of knowledge on how they initiated and evolved over time, and how they responded to past environmental change, i.e., precipitation, sea level and early anthropogenic activities. To improve our understanding thereof, we conducted multi-proxy palaeoecological studies in the Kampar Peninsula and Katingan peatlands in the coastal area of Riau and Central Kalimantan, Indonesia. The results indicate that the initiation timing and environment of both peatlands are very distinct, suggesting that peat could form under various vegetation as soon as there is sufficient moisture to limit organic matter decomposition. The past dynamics of both peatlands were mainly attributable to natural drivers, while anthropogenic activities were hardly relevant. Changes in precipitation and sea level led to shifts in peat swamp forest vegetation, peat accumulation rates, and fire regimes at both sites. We infer that the simultaneous occurrence of El Niño-Southern Oscillation (ENSO) events and SLR resulted in synergistic effects which led to the occurrenceere fires in a pristine coastal peatland ecosystem, however, it did not interrupt peat accretion. In the future, SLR, combined with the projected increase in frequency and intensity of ENSO, can potentially amplify the negative effects of anthropogenic peatland fires. This prospectively stimulates massive carbon release, thus could, in turn, contribute to worsening the global climate crisis especially once an as yet unknown threshold is crossed and peat accretion is halted, i.e., peatlands lose their carbon sink function. Given the current rapid SLR, coastal peatland managements should start develop fire risk reduction or mitigation strategies. The investigation including pollen and spore, loss-on-ignition, total organic carbon, stable carbon isotope and micro- and macrocharcoal was carried out on a peat core collected from coastal area in eastern Sumatra. Pollen, spore and charcoal extraction and identification, as well as Loss-On-Igntition analysis were conducted at the Dept. Palynology and Climate Dynamics, University of Goettingen. Organic carbon content and isotopes were determined in Euro EA3000 elemental analyzer and Thermo Finnigan Delta Plus mass spectrometer, respectively, at the Leibniz Centre for Tropical Marine Research (ZMT), Bremen. Fossil pollen and spore are in counts.

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    DRYAD; ZENODO
    Dataset . 2022
    License: CC 0
    Data sources: ZENODO; Datacite
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      DRYAD; ZENODO
      Dataset . 2022
      License: CC 0
      Data sources: ZENODO; Datacite
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  • Authors: Prasetyo, Teguh Budi;
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    Authors: Stelbrink, Björn; Stöger, Isabella; Hadiaty, Renny K.; Schliewen, Ulrich K.; +1 Authors

    Background: The Malili Lakes system in central Sulawesi (Indonesia) is a hotspot of freshwater biodiversity in the Wallacea, characterized by endemic species flocks like the sailfin silversides (Teleostei: Atherinomorpha: Telmatherinidae) radiation. Phylogenetic reconstructions of these freshwater fishes have previously revealed two Lake Matano Telmatherina lineages (sharpfins and roundfins) forming an ancient monophyletic group, which is however masked by introgressive hybridization of sharpfins with riverine populations. The present study uses mitochondrial data, newly included taxa, and different external calibration points, to estimate the age of speciation and hybridization processes, and to test for phylogeographic relationships between Kalyptatherina from ancient islands off New Guinea, Marosatherina from SW Sulawesi, and the Malili Lakes flock. Results: Contrary to previous expectations, Kalyptatherina is the closest relative to the Malili Lakes Telmatherinidae, and Marosatherina is the sister to this clade. Palaeogeographic reconstructions of Sulawesi suggest that the closer relationship of the Malili Lakes radiation to Kalypatherina might be explained by a 'terrane-rafting' scenario, while proto-Marosatherina might have colonized Sulawesi by marine dispersal. The most plausible analysis conducted here implies an age of c. 1.9 My for the onset of divergence between the two major clades endemic to Lake Matano. Diversification within both lineages is apparently considerably more recent (c. 1.0 My); stream haplotypes present in the sharpfins are of even more recent origin (c. 0.4 My). Conclusions: Sulawesi's Telmatherinidae have most likely originated in the Sahul Shelf area, have possibly reached the island by both, marine dispersal and island/terrane-rafting, and have colonized the Malili Lakes system from rivers. Estimates for the split between the epibenthic sharpfins and the predominantly pelagic to benthopelagic roundfins in Lake Matano widely coincide with geological age estimates of this rift lake. Diversification within both clades clearly predates hybridization events with stream populations. For Lake Matano, these results support a scenario of initial benthic-pelagic divergence after colonization of the lake by riverine populations, followed by rapid radiation within both clades within the last 1 My. Secondary hybridization of stream populations with the sharpfins occurred more recently, and has thus most likely not contributed to the initial divergence of this benthic species flock. BEAST tree filesBEAST MCC tree files of analyses [A]-[D].BEAST_tree_files.zip

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    DANS-EASY
    Dataset . 2014
    Data sources: B2FIND
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    DRYAD; NARCIS; ZENODO
    Dataset . 2014
    License: CC 0
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      DANS-EASY
      Dataset . 2014
      Data sources: B2FIND
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      DRYAD; NARCIS; ZENODO
      Dataset . 2014
      License: CC 0
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  • Authors: Tirtoni, Feri;

    ini adalah sebuah Video Dokumentasi Riset Instutusi di SD Kejaten 1 sidoarjo, 2019, Feri Tirtoni

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  • Authors: Ulfa Farrah Lisa, Ulfa;

    SK Dekan Dosen Pengajar MK Elektif Kewirausahaan Prodi S1 Kebidanan 2018/2019

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Nuryadi, Handung; Mandagi, Ixchel; Masengi, Kawilarang; Kusumi, Junko; +2 Authors

    Heteroplasmy, the presence of multiple mitochondrial DNA (mtDNA) haplotypes within cells of an individual, is caused by mutation or paternal leakage. However, heteroplasmy is usually resolved to homoplasmy within a few generations because of germ-line bottlenecks; therefore, instances of heteroplasmy are limited in nature. Here, we report heteroplasmy in the ricefish species Oryzias matanensis, endemic to Lake Matano, an ancient lake in Sulawesi Island, in which one individual was known to have many heterozygous sites in the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. In this study, we cloned the ND2 gene for some additional individuals with heterozygous sites and demonstrated that they are truly heteroplasmic. Phylogenetic analysis revealed that the extra haplotype within the heteroplasmic O. matanensis individuals clustered with haplotypes of O. marmoratus, a congeneric species inhabiting adjacent lakes. This indicated that the heteroplasmy originated from paternal leakage due to interspecific hybridisation. The extra haplotype was unique and contained two nonsynonymous substitutions. These findings demonstrate that this hybridisation-driven heteroplasmy was maintained across generations for a long time to the extent that the extra mitochondria evolved within the new host. ## Data set from Nuryadi et al. 2023 Biology Letters. The data set accompanies four Dryad data files. Uploaded: November 2023 Revised: Contact: Kazunori Yamahira (yamahira@lab.u-ryukyu.ac.jp) *** File\_01\_Fasta\_ND2\_all.fas The fasta file containing mitochondrial ND2 sequences (1053 bp) of Oryzias species endemic to the Malili Lake system, which was used for the ML phylogeny in figure 2. *** File\_02\_Fasta\_ND2\_unique.fas The fasta file containing mitochondrial ND2 sequences (1053 bp) of the 52 unique haplotypes among Oryzias species endemic to the Malili Lake system, which was used for the ML phylogeny in figure S1. *** File\_03\_Fasta\_ND2\_unique\_only\_HapB\_Mar.fas The fasta file containing mitochondrial ND2 sequences (1053 bp) of the 10 unique haplotypes from Oryzias marmoratus and the O. matanensis extra haplotype, which was used in EasyCodeML. *** File\_04\_Newick\_ND2\_unique\_only\_HapB\_Mar.txt The newick file containing a topology among the 10 unique haplotypes from Oryzias marmoratus and the O. matanensis extra haplotype, which was used in EasyCodeML.

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    DRYAD; ZENODO
    Dataset . 2023
    License: CC 0
    Data sources: ZENODO; Datacite
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      DRYAD; ZENODO
      Dataset . 2023
      License: CC 0
      Data sources: ZENODO; Datacite
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    Authors: Yang, Bin; Cui, Leilei; Perez-Enciso, Miguel; Traspov, Aleksei; +18 Authors

    [Results]: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. [Conclusions]: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation. [Background]: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. Usage Notes: Description_data_GSE_Global_pigs Table describing the samples. Note that the submitted data includes a few animals that were removed from the paper due to additional constraints applied in the review process. GSE_global_pigs.map PLINK MAP file, describing the SNPs used. GSE_global_pigs.ped Genotype data used in PLINK PED file format. Peer reviewed

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    DRYAD; NARCIS; ZENODO
    Dataset . 2018
    License: CC 0
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    DANS-EASY
    Dataset . 2017
    Data sources: B2FIND
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      DRYAD; NARCIS; ZENODO
      Dataset . 2018
      License: CC 0
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      DANS-EASY
      Dataset . 2017
      Data sources: B2FIND
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  • Authors: Prasetyo, Teguh Budi;
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    Authors: Baru Sakka, Sakka;

    - Tinjauan Agroklimatologi Kelapa Sawit Berbasis Sistem Informasi dan Geografis (SIG) di PT. Perkebunan Nusantara XIV Sulawesi Selatan

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    Authors: Reilly, Sean; Karin, Benjamin; Stubbs, Alexander L.; Arida, Evy; +6 Authors

    The archipelagos of Wallacea extend between the Sunda and Sahul Shelves, serving as a semi-permeable two-way filter influencing faunal exchange between Asia and Australo-Papua. Forest skinks (Genus Sphenomorphus) are widespread throughout southern Wallacea and exhibit complex clinal, ontogenetic, sexual, and seasonal morphological variation rendering species delimitation difficult. We screened a mitochondrial marker for 245 Sphenomorphus specimens from this area to inform the selection of 104 samples from which we used targeted sequence-capture to generate a dataset of 1154 nuclear genes (~1.8 Mb) plus complete mitochondrial genomes. Phylogenomic analyses recovered many deeply divergent lineages, three of which are now sympatric, that began to diversify in the late Miocene shortly after the oldest islands are thought to have become emergent. We infer a complex and non-stepping-stone pattern of island colonization, with the group having originated in the Sunda Arc islands before using Sumba as a springboard for colonization of the Banda Arcs. Estimates of population structure and gene flow across the region suggest total isolation except between two Pleistocene Aggregate Island Complexes that become episodically land-bridged during glacial maxima. These historical processes have resulted in at least 11 Sphenomorphus species in the region, nine of which require formal description. This fine-scale geographic partitioning of undescribed species highlights the importance of utilizing comprehensive genomic studies for defining biodiversity hotspots to be considered for conservation protection. See supplementary methods for a detailed description of the datasets, which include mitochondrial ND4 sequence data (GenBank accession numbers MW291696–291940), and a targeted sequence capture dataset that includes 1,154 nuclear loci and complete mitochondrial genomes for 104 samples. The targeted capture dataset was sequenced on the Illumina platform with paired end 100 bp reads that have been deposited in the NCBI sequence read archive under accession number PRJNA682772.

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    ZENODO
    Dataset . 2022
    License: CC 0
    Data sources: ZENODO
    DRYAD
    Dataset . 2022
    License: CC 0
    Data sources: Datacite
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      ZENODO
      Dataset . 2022
      License: CC 0
      Data sources: ZENODO
      DRYAD
      Dataset . 2022
      License: CC 0
      Data sources: Datacite
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    Authors: Hapsari, K. Anggi; Jennerjahn, Tim; Nugroho, Septriono Hari; Yulianto, Eko; +1 Authors

    Southeast Asian peatlands, along with their various important ecosystem services, are mainly distributed in the coastal areas of Sumatra and Borneo. These ecosystems are threatened by coastal development, global warming and sea level rise (SLR). Despite receiving growing attention for their biodiversity and as massive carbon stores, there is still a lack of knowledge on how they initiated and evolved over time, and how they responded to past environmental change, i.e., precipitation, sea level and early anthropogenic activities. To improve our understanding thereof, we conducted multi-proxy palaeoecological studies in the Kampar Peninsula and Katingan peatlands in the coastal area of Riau and Central Kalimantan, Indonesia. The results indicate that the initiation timing and environment of both peatlands are very distinct, suggesting that peat could form under various vegetation as soon as there is sufficient moisture to limit organic matter decomposition. The past dynamics of both peatlands were mainly attributable to natural drivers, while anthropogenic activities were hardly relevant. Changes in precipitation and sea level led to shifts in peat swamp forest vegetation, peat accumulation rates, and fire regimes at both sites. We infer that the simultaneous occurrence of El Niño-Southern Oscillation (ENSO) events and SLR resulted in synergistic effects which led to the occurrenceere fires in a pristine coastal peatland ecosystem, however, it did not interrupt peat accretion. In the future, SLR, combined with the projected increase in frequency and intensity of ENSO, can potentially amplify the negative effects of anthropogenic peatland fires. This prospectively stimulates massive carbon release, thus could, in turn, contribute to worsening the global climate crisis especially once an as yet unknown threshold is crossed and peat accretion is halted, i.e., peatlands lose their carbon sink function. Given the current rapid SLR, coastal peatland managements should start develop fire risk reduction or mitigation strategies. The investigation including pollen and spore, loss-on-ignition, total organic carbon, stable carbon isotope and micro- and macrocharcoal was carried out on a peat core collected from coastal area in eastern Sumatra. Pollen, spore and charcoal extraction and identification, as well as Loss-On-Igntition analysis were conducted at the Dept. Palynology and Climate Dynamics, University of Goettingen. Organic carbon content and isotopes were determined in Euro EA3000 elemental analyzer and Thermo Finnigan Delta Plus mass spectrometer, respectively, at the Leibniz Centre for Tropical Marine Research (ZMT), Bremen. Fossil pollen and spore are in counts.

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    DRYAD; ZENODO
    Dataset . 2022
    License: CC 0
    Data sources: ZENODO; Datacite
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      DRYAD; ZENODO
      Dataset . 2022
      License: CC 0
      Data sources: ZENODO; Datacite
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  • Authors: Prasetyo, Teguh Budi;
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    Authors: Stelbrink, Björn; Stöger, Isabella; Hadiaty, Renny K.; Schliewen, Ulrich K.; +1 Authors

    Background: The Malili Lakes system in central Sulawesi (Indonesia) is a hotspot of freshwater biodiversity in the Wallacea, characterized by endemic species flocks like the sailfin silversides (Teleostei: Atherinomorpha: Telmatherinidae) radiation. Phylogenetic reconstructions of these freshwater fishes have previously revealed two Lake Matano Telmatherina lineages (sharpfins and roundfins) forming an ancient monophyletic group, which is however masked by introgressive hybridization of sharpfins with riverine populations. The present study uses mitochondrial data, newly included taxa, and different external calibration points, to estimate the age of speciation and hybridization processes, and to test for phylogeographic relationships between Kalyptatherina from ancient islands off New Guinea, Marosatherina from SW Sulawesi, and the Malili Lakes flock. Results: Contrary to previous expectations, Kalyptatherina is the closest relative to the Malili Lakes Telmatherinidae, and Marosatherina is the sister to this clade. Palaeogeographic reconstructions of Sulawesi suggest that the closer relationship of the Malili Lakes radiation to Kalypatherina might be explained by a 'terrane-rafting' scenario, while proto-Marosatherina might have colonized Sulawesi by marine dispersal. The most plausible analysis conducted here implies an age of c. 1.9 My for the onset of divergence between the two major clades endemic to Lake Matano. Diversification within both lineages is apparently considerably more recent (c. 1.0 My); stream haplotypes present in the sharpfins are of even more recent origin (c. 0.4 My). Conclusions: Sulawesi's Telmatherinidae have most likely originated in the Sahul Shelf area, have possibly reached the island by both, marine dispersal and island/terrane-rafting, and have colonized the Malili Lakes system from rivers. Estimates for the split between the epibenthic sharpfins and the predominantly pelagic to benthopelagic roundfins in Lake Matano widely coincide with geological age estimates of this rift lake. Diversification within both clades clearly predates hybridization events with stream populations. For Lake Matano, these results support a scenario of initial benthic-pelagic divergence after colonization of the lake by riverine populations, followed by rapid radiation within both clades within the last 1 My. Secondary hybridization of stream populations with the sharpfins occurred more recently, and has thus most likely not contributed to the initial divergence of this benthic species flock. BEAST tree filesBEAST MCC tree files of analyses [A]-[D].BEAST_tree_files.zip

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    DANS-EASY
    Dataset . 2014
    Data sources: B2FIND
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    DRYAD; NARCIS; ZENODO
    Dataset . 2014
    License: CC 0
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DANS-EASYarrow_drop_down
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      DANS-EASY
      Dataset . 2014
      Data sources: B2FIND
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DRYAD; NARCIS; ZENODO
      Dataset . 2014
      License: CC 0
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  • Authors: Tirtoni, Feri;

    ini adalah sebuah Video Dokumentasi Riset Instutusi di SD Kejaten 1 sidoarjo, 2019, Feri Tirtoni