Divergent Pdf Indonesia

[Barbra Lidder]

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Genome sequences are known for two archaic hominins-Neanderthals and Denisovans-which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time.

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Known geographical distributions of the two species of Latimeria. The localities where specimens of L. menadoensis were captured are shown in bold, and the localities where this species has been observed in situ are in italics. The rectangle shows the limits of Fig. 5.

Uncorrected genetic distances for 16 genes of the mitogenome of Latimeria. Open symbols show distances between the two Indonesian specimens; filled symbols show distances between the new Indonesian specimen and a specimen of L. chalumnae.

In addition to the deletions noted above during alignment, the two Indonesian individuals showed 149 base differences, whereas the number of differences between two individuals of L. chalumnae varied between 0 and 10. Among the 13 proteins coded by the mitogenome, three had their genes sequenced in the new specimen: ND1, ND2, and COI. While no amino acid (AA) substitutions were observed among the 12 unique sequences of L. chalumnae, 35 AA replacements were observed between the Indonesian individuals and L. chalumnae (Table 1). Interestingly, it seems that all these replacements are the result of single events occurring on one of the three longest branches of the tree on Fig. 2. Among the 11 AA differences between the two Indonesian individuals, six can be inferred to result from substitutions that happened on the terminal branch leading to the new sequence, and five on the branch leading to GQ911586. The other 24 AA substitutions happened on the internal branch connecting the two main clades of Latimeria.

(A) Maximum likelihood phylogeny estimated with phangorn. The bold numbers give the node support bootstrap values (1000 replications). The branch lengths are in expected number of substitutions. (B) Dated phylogeny (chronogram) estimated by Bayesian inference. The rectangles show the credibility intervals from the highest posterior densities.

We acknowledge several limitations of our study with regard to relying on a mtDNA-only dataset from a single individual of the new population. For example, examining loci from both nuclear and mitochondrial genomes has revealed cases of cytonuclear discordance in other taxonomic groups19,20,21. In the current investigation, we may have detected a divergent mitochondrial lineage in L. menadoensis. However, nuclear loci may reveal contemporary gene flow between populations from Manado and Papua New Guinea. Sampling additional specimens and expanding future molecular investigations to include unlinked nuclear loci would extend our understanding of species limits and the evolutionary history of Latimeria. However, the most striking result from our analyses is the relatively deep but Neogene molecular divergence between the specimen from Papua and its counterpart representing the previously studied population from Manado. This divergence is apparent at the mitochondrial DNA level but also implied a substantial number of AA replacements in protein-coding mitochondrial genes, something that has not to-date been observed among L. chalumnae individuals. The ML bootstrap analysis of branches leading to the Indonesian coelacanth fish populations strongly suggests that molecular evolutionary rate was equal in these two lineages, thus supporting the hypothesis of a molecular clock for the mitochondrial genome within this clade. Furthermore, the number of amino acid substitutions were found to be almost the same on both branches (five and six, respectively).

The molecular divergence observed between the individuals from Waigeo and Manado is further evidence of a low rate of molecular evolution among the lineages of Latimeria. Remarkably, such a low rate of molecular evolution was observed in previous studies comparing the two species using mitochondrial13 or nuclear genomes30. The observed divergence for the COI-based barcode between the two Indonesian specimens (1.22%) was greater than among individuals of the same species for several groups of fishes which averaged 0.59%31, 0.89%32, or 0.29%33. This suggests that the new specimen is genetically distinct and may warrant formal recognition as a species, although in-depth taxonomic assessment would be required to test this hypothesis.

Based on the available information from our results, in combination with patterns of oceanic circulation from the region, we hypothesize that the Latimeria specimen captured in Waigeo in July 2018 belongs to L. menadoensis, although it is likely that this specimen belongs to a distinct and as-of-yet undescribed species or subspecies of Latimeria. We urgently call for future taxonomic studies integrating morphological and genetic data from multiple specimens from different L. menadoensis populations, in order to test this hypothesis. Nevertheless, our results suggest that L. menadoensis likely has a much wider geographical range than previously thought. Given the presence of this specimen nearby the New Guinea Coastal Current, we hypothesize that L. menadoensis populations can occur along the coast of New Guinea and probably further east of New Guinea. The waters of the northwest coast of New Guinea have been poorly sampled and it would not be surprising to find several populations of coelacanths in the region.

In light of our findings as well as the unique biology of coelacanths in general, we call for an international effort to take appropriate measures to protect these fascinating but vulnerable vertebrates. The conservation of relict species including the unique representatives of particular phylogenetic groups and their likely unique combinations of characters is key to conserve phylogenetic diversity represented by the Tree of Life. Yet, the existing global system of marine protected areas (MPAs) may fail to cover areas where these relict species are located34. If MPAs are to protect the unique and diverse marine lineages across the Tree of Life, we need to carefully reconsider the protection of East Indonesian coasts where this new lineage of coelacanth occurs.

We are extremely grateful to Mr. Dava Santoso who kindly provided a small piece of tissue of the coelacanth caught accidentally off Waigeo Island. We express thanks to the following persons who helped us during our investigation: Abdul Faris Umlati (Bupati Raja Ampat), Mayor Mar. Muh. Ali Wardana (DAN YONHARLAN XIV Sorong), Agus Darmawan, Andi Rusadi (Dirjend PRL KKP), Musa J. Telew (Karantina Ikan Sorong), Herwin Salurante (PSDKP Sorong), Yusuf Salim, Marthen L.R Bartholomeus and Yusdi N. Lamatenggo (PEMDA Raja Ampat), Saidin and Moch. Sayuti (Politeknik KP Sorong), Heri Triyono, and Kariza M. Puspita (Lab. Biologi dan Konservasi, STP Jakarta). We are grateful to two anonymous reviewers for their very positive and constructive comments. This is publication ISEM 2019-301 SUD.

K., L.P. and R.H. conceived and designed the study. K., H.Y.S., L.P., I.B.H., E.G., S.B.W., G.A. and F.W. performed the data acquisition. K., L.P., R.H., D.M. and E.P. analysed the data and wrote the manuscript. All authors reviewed, improved, and approved the manuscript.

The fast-growing Indo-Pacific region has drawn wide attention from both the European Union and the United States. The expanding engagement of the US and the EU with countries in Indo-Pacific serves as an essential pillar in the on-going global supply chain reconfiguration. This paper therefore conducts a preliminary comparative analysis of the EU and US imports from the Indo-Pacific region, in particular, South Korea, Japan, Taiwan, India and ASEAN. For the shipments with the aforementioned trade partners are tightly connected to Europe-Asia and Trans-Pacific containerized maritime transport.

Overall, from 2019 to 2023, the EU and the US import value from the countries studied in this article increased by 38% (Figure 1&2). India, South Korea, and Taiwan have all consolidated their positions in outbound trade to the EU and the US, while Japan's share eroded in both cases.

Despite sharing similarities, the EU and the US sourcing from ASEAN have gone in divergent directions (Figure 3). In contrast to the burgeoning ASEAN share in US imports, its share in EU imports has stagnated. In fact, in 2023, it was even lower than the pre-pandemic level. Furthermore, the growth of ASEAN trade with the EU from 2019 to 2023 also lagged behind the EU's total sourcing from outside the union during the same period.

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