Hasil Pencarian  ::  Simpan CSV :: Kembali

"Several series of trawl surveys were carried out in the waters of Perhentian Islands using commercial trawlers.16S mithochondrial rRNA gene sequences were used to infer the phylogenetic relationship among nine morphospecies of leiognathids...."

"Isolasi merupakan faktor utama dalam biogeografi pulau, disini kami mencoba memahami fenomena filogeografi kelompok londok pohon Asia Tenggara yaitu genus Bronchocela di Kepulauan Indonesia dengan dukungan data morfologi (ukuran tengkorak), molekuler (DNA mitokondria dan inti) dan data evolusi. Genus Bronchocela kosmopolit, morfologi sangat bervariasi tersebar dan terisolasi di hutan yang terfragmentasi di kepulauan Indonesia. Variasi yang kompleks pada genus ini menyebabkan kesulitan dalam penentuan batas spesies dengan jelas. Sebanyak 520 individu spesimen koleksi museum telah diperiksa untuk diuji mengenai dampak isolasi pulau secara geografis terhadap struktur morfologi populasi. Uji statistic dilakukan dengan menggunkan analisis univariat dan multivariat. Sejauh ini baru diketahui hanya hanya empat spesies yang teridentifikasi di wilayah Indonesia, setelah dilakukannya penelitian ini setidaknya teridentifikasi menjadi enam spesies. Rekonstruksi pohon filogenetik dilakukan berdasarkan marka DNA mitokondria yaitu 16s rRNA (~500 bp) dan ND2 (~1300 bp) serta gen inti yaitu oocyte maturation factor mos (CMOS). Hasil penelitian menunjukkan bahwa B. cristatella yang tersebar luas, dalam penelitian ini terbukti sebagai spesies kompleks yang setidaknya terdiri atas tiga spesies berbeda. Rekonstruksi pohon filogenetik DNA mitokondria dan inti menggunakan Maximum Likelihood (ML) dan Bayesian Inference (BI) menunjukkan adanya enam garis keturunan evolusi Bronchocela di Indonesia. Tingkat variasi selama ini mungkin diremehkan karena tingginya tingkat kesamaan morfologi yang disebabkan oleh sifat arboreal. Haplotipe network berdasarkan gen mitokondria ND2 dengan jelas menunjukkan adanya delapan garis keturunan. Indeks isolasi diestimasi melalui uji interaksi dua arah (ANOVA) antara luas daratan dan ukuran tubuh dari setiap populasi. Hasil penelitian ini menunjukkan pulau-pulau yang lebih besar mendukung kehidupan londok yang berukuran besar dibandingkan dengan pulau-pulau yang lebih kecil (fenomena dwarfisme pulau) dan sejalan dengan teori isolasi pulau. Hasil analisis waktu BEAST berbasis penggabungan menghasilkan pohon filogenetik dengan dua klade utama dan mengungkapkan nenek moyang terbaru atau most recent common ancestor (MRCA) untuk Bronchocela berasal sekitar 42 juta tahun yang lalu di daratan Asia. Pohon filogenetik menununjukkan bahwa klade basal Bronchocela terdiri dari B. burmana dan taksa nenek moyangnya yang sebagian besar terbatas di Semenanjung Malaysia. Pohon kredibilitas clade maksimum atau Maximum Credibility Clade (MCC) skala waktu geologi menunjukkan bahwa genus Bronchocela berevolusi pada zaman Miosen awal (~18,7 juta tahun yang lalu) dan memulai spesiasi cepat pada Miosen akhir. Pohon filogenetik menununjukkan bahwa klade basal Bronchocela terdiri dari B. burmana dan taksa nenek moyangnya yang sebagian besar terbatas di Semenanjung Malaysia. Dalam penelitian ini, distribusi klade berdasarkan keberadaan spesies londok dalam pohon filogenetik. Model State-dependent Speciation and Extinction (SSE) digunakan untuk merekonstruksi Ancestral Range Estimation (ARE). Hasil simulasi silsilah Bronchocela dengan ARE sesuai hipotesis kami bahwa daratan Sunda merupakan asal muasal genus ini dan menjalan kepulauan Sunda Besar, kepulauan Sulu, Sulawesi, dan Maluku utara pada zaman Miosen. Penelitian ini memberikan wawasan baru mengenai isolasi pulau di wilayah yang belum pernah diteliti sebelumnya dan hal ini menyiratkan bahwa pola distribusi Bronchocela sebagian besar dibentuk oleh peristiwa dispersal pada pra-Pliosen yang diikuti oleh peristiwa vicarian yang mendalam. Penelitian ini juga menunjukkan bahwa perubahan iklim Pliosen dapat berdampak besar pada diversifikasi spesies dan demografi spesies-spesies hutan ini.

---

Isolation is the main factor in insular biogeography, here we try to understand the insular biogeographical phenomenon of the southeast Asian arboreal lizard genus Bronchocela across the Indonesian Archipelago with the support of morphological (including skull morphology), molecular (mitochondrial and nuclear DNA) and evolutionary data. The morphologically highly variable, cosmopolitan arboreal forest lizards of the genus, Bronchocela are dispersed and isolated in fragmented island forests across the Indonesian Archipelago. These species exhibit complex morphological variations, which weaken clear species delimitation. To determine the effects of geographical island isolation on the morphological structure of the populations, 520 individuals of museum specimens (including name-bearing types) were examined across Peninsular Malaysia and the Indonesian Archipelago. Both univariate and multivariate analyses were conducted on morphometric characters. So far only four species have been identified within Indonesian territory and after evaluating morphological and morphometric evidence at least six distinct species have been recognised. We screened two mitochondrial markers comprising 16s rRNA (~500 bp) and ND2 (~1300 bp), with intervening nuclear loci (CMOS) to obtain a robust phylogenetic hypothesis. Based on both morphology and genetics, we delimit potential biogeographic boundaries of the species composition. The previously widely distributed Bronchocela cristatella is here considered as a species complex with at least three distinct species. The phylogeny of mitochondrial and nuclear DNA using Maximum likelihood (ML) and Bayesian Inference (BI) revealed at least six evolutionary lineages within the Indonesian Bronchocela. This level of variation has probably been underestimated because of the high levels of morphological similarity brought about by the arboreal lifestyle. The haplotype networks based on the ND2 mitochondrial gene differentiated the eight lineages. An isolation index was estimated and defined for each island landmass based on its area and tested for two‐way interactions (ANOVA) between landmass and the mean body sizes of each population. Our results show the significant influence of the larger islands supporting larger-bodied lizards compared to the smaller islands, agreeing with the island theory. The coalescent-based BEAST time-analysis yielded a phylogenetic tree with two major clades. It revealed that the most recent common ancestor (MRCA) for the Bronchocela genus originated approximately 42 MYA in mainland Asia. The basal clade of Bronchocela consists of B. burmana and its ancestral taxa which are mostly confined to the Malay Peninsula. The geological time-scaled maximum clade credibility (MCC) tree indicated that the genus Bronchocela evolved in the early Miocene epoch (~18.7 MYA) and started rapid speciation in the late Miocene. We divided the distribution of the clade into regions based on the species in the phylogenetic tree by its presence in those regions, and we used the State-dependent Speciation and Extinction (SSE) models to reconstruct Ancestral Range Estimation (ARE). As we hypothesised, ancestral Range Estimation (ARE) analyses supported that mainland Sundaland served as the origin for Bronchocela, which colonized the Great Sundaic Islands, the Sulu Archipelago, Sulawesi, and Northern Moluccas during the Miocene epoch. Our results provide new insights into insular isolation in a previously unstudied region, and it implies that the distribution pattern of Bronchocela has been largely shaped by pre-Pliocene dispersal followed by deep vicariance events. We further demonstrate that Pliocene climatic changes can have profound effects on species diversification and demography in these forest species."

"The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters. "

"Asian tropical forests are among the most diverse on the planet, a richness that belies the fact that they are dominated by a single tropical tree family, the Dipterocarpaceae. Many other families contribute to Asias natural diversity, but few compare to the dipterocarps in the number and variety of species that occupy the forest canopy. Understanding the ecology and dynamics of Asian forests is, to a very great extent, a study of the Dipterocarpaceae. This book synthesizes current knowledge on the dipterocarps. The family is explored through ecological, evolutionary, and biogeographic perspectives. The variety of dipterocarp forest formations in both the ever-wet and seasonal tropics is described, with due consideration given to the poorly known African and South American dipterocarp species. The considerable progress on the phylogeny and biogeography of the family is synthesized. A chapter on dipterocarp reproductive ecology, and particularly masting behaviour, reflects the considerable research interest attributed to this subject and its importance in shaping the ecology of Asian lowland rain forests in particular. Ecophysiological responses to light, water, and nutrients, which underlie mechanisms that maintain dipterocarp species richness, are addressed in separate chapters. At broader scales, dipterocarp responses to variation in soil, topography, climate, and natural disturbance regimes are explored from population and community perspectives in two additional chapters. The book concludes with a consideration of the economic values of dipterocarps and the recent and ongoing threats to dipterocarp forests. Looking to the future, a scientific foundation is required to capitalize on opportunities for conservation and restoration, and it is this to which this book aims to contribute."

"Penelitian ini bertujuan untuk mengetahui keragaman genetik dan kekerabatan ikan cupang menggunakan sekuens Cytochrome Oxidase I. Keragaman genetik diketahui menggunakan sekuens Cytochrome Oxidase I. Amplifikasi Cytochrome Oxidase I dilakukan menggunakan primer HCO dan LCO dengan hasil sekuens yang diperoleh berukuran 680 pb. Hasil alignment sekuens menunjukkan keragaman genetik yang kurang signifikan pada B. imbellis, sedangkan pada B. pallifina, B. patoti, dan B. unimaculata menunjukkan keragaman yang cukup signifikan. Tiga spesies ikan cupang dari Kalimantan memiliki kekerabatan yang dekat. Namun demikian, kekerabatan ikan cupang dari Kalimantan dengan ikan cupang dari Sumatera cukup jauh.

---

This study aims to determine the genetic diversity and kinship of fighting fish using Cytochrome Oxidase I. Cytochrome Oxidase I is used to know the genetic diversity of fighting fish. Primer HCO and LCO were used to amplify 680 bp of Cytochrome Oxidase I. The results of sequence alignment showed less significant genetic diversity for B. imbellis, whereas B. pallifina, B. patoti, and B. unimaculata show significant diversity. Three species of fighting fish from Kalimantan are closely related. However, the kinship of fighting fish from Kalimantan with fighting fish from Sumatra are far enough."