Molecular phylogeny of extant horseshoe crabs (Xiphosura, Limulidae) indicates Paleogene diversification of Asian species

Obst, Matthias; Faurby, Søren; Bussarawit, Somchai; Funch, Peter

doi:10.1016/j.ympev.2011.08.025

Cited by 61 publications

(68 citation statements)

References 34 publications

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“…Relationships among the paralog groups were identical to those recovered in a previous study [31]. Within the chelicerate orders, relationships of the three xiphosuran genera could only be assessed by one paralog (Hc1/A is the only hemocyanin sequenced for Tachypleus tridentatus), but are consistent with a recent multilocus phylogeny of Xiphosura using a separate set of molecular loci [36]. Among the better-sampled spiders, the expected basal relationship of (Mesothelae, (Mygalomorphae + Araneomorphae)) was obtained in only two out of six subtrees wherein all three lineages were represented.…”

Section: Resultssupporting

confidence: 83%

Cross-bracing uncalibrated nodes in molecular dating improves congruence of fossil and molecular age estimates

Sharma

Wheeler

2014

Front Zool

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Introduction: The practice of molecular dating is an essential tool for hypothesis testing in evolutionary biology. Vagaries of fossilization and taphonomic bias commonly engender high uncertainty in molecular dating in taxonomic groups wherein few fossils can be unambiguously assigned to phylogenetic nodes. A recent and novel implementation in molecular dating, "cross-bracing", exploits gene duplications by formally linking calibrated node dates throughout the paralogous subtrees through hierarchical Bayesian models. An unexplored refinement of this method is cross-bracing nodes with unknown dates, in addition to calibrated nodes, such that all nodes representing the same cladogenetic events have linked priors. We applied such a refinement to molecular dating in chelicerates, one of the earliest groups of arthropods present in the fossil record, but whose molecular dating has been greatly inconsistent in the literature. We inferred divergence times using hemocyanin paralogs isolated from de novo assembled transcriptomic libraries, and multiple fossil calibrations. Results: We show that extending cross-bracing to uncalibrated nodes greatly reduced variance in estimates of divergence times throughout the phylogeny, particularly for estimated diversification ages of spiders and scorpions, whereas cross-bracing calibrated nodes alone did not affect age estimation for uncalibrated, derived clades. Comparing ages inferred with extended cross-bracing to the fossil record, we observe smaller gaps between diversification and the first appearance of crown group fossils than have previously been inferred, particularly for spiders. Our dating indicates that scorpions have a Silurian origin, but diversification of extant lineages occurred near the Triassic-Jurassic boundary, falsifying previous inference of Permian diversification age based on extant distribution alone. Conclusion: The significant reduction of variance in divergence time estimates upon extending cross-bracing to uncalibrated nodes makes this approach greatly suited for evolutionary inference in groups with poor fossil records, with particular reference to terrestrial arthropods.

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Section: Resultssupporting

confidence: 83%

Cross-bracing uncalibrated nodes in molecular dating improves congruence of fossil and molecular age estimates

Sharma

Wheeler

2014

Front Zool

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“…Present xiphosuran diversity is limited to just four species, L. polyphemus found in the Atlantic, and C. rotundicauda, Tachypleus gigas and Tachypleus tridentatus found in Southeast Asia. These species separated from one another relatively recently,~135 million years before the present day ( Figure 2b, Obst et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs

et al. 2015

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Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs-Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates 4135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.

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“…Hewan ini telah mengalami diversifikasi sejak zaman paleogene (65-23 Mya) (Obst et al, 2012) dan di Indonesia merupakan salah satu sumber daya genetik yang dilindungi sesuai dengan SK Menteri Kehutanan No. 12/Kpts-II/1987 dan Peraturan Pemerintah RI No.…”

Section: Pendahuluanunclassified

“…Hal ini menunjukkan bahwa ketiga spesies tersebut memiliki karakter nukleutida yang berbeda dibandingkan dengan outgroups (Negara lain). Menurut penelitian yang telah dilakukan oleh Obst et al (2012) dengan menggunakan fragmen gen 16S, 228S, dan CO1 diperoleh hasil bahwa konstruksi pohon filogeni C. rotundicuada terpisah dengan genus Tachypleus, hal ini juga berkaitan dengan perbedaan ekologi. C. rotundicuada merupakan spesies yang memiliki keragaman genetik paling tinggi dibandingkan dengan genus Tachypleus dan Limulus, hal ini disebabkan oleh perbedaan faktor ekologi C. Rotundicuada yang berhabitat di estuari dan mangrove.…”

Section: Pembahasanunclassified

MORPHOLOGICAL CHARACTER AND MOLECULAR IDENTIFICATION WITH COI GENE MARKER OF HORSESHOE CRABS (Tachypleus gigas) AT COASTAL WATERS OF NORTHERN JAVA ISLAND

Meilana

Wardiatno

Butet

et al. 2016

J. Ilmu dan Teknologi Kelautan Tropis

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The existence of horseshoe crabs Tachypleus gigas is currently on the threatened condition and its population status is also unclear. The objectives of this research were to asses the horseshoe crabs morphological characters and to identify based on molecular marker of Cytochrome ABSTRAKKeberadaan spesies mimi T. gigas saat ini sudah pada kondisi terancam dan status populasinya juga belum diketahui dengan jelas. Tujuan penelitian ini adalah untuk meneliti karakteristik morfologi mimi berdasarkan 27 karakter morfologi dan mengidentifikasi mimi berdasarkan marka gen Cytochrome Oxydase Subunit I (COI). Sampel diambil dari lima lokasi (Segara Menyan Subang, Ujung Kulon Banten, Tambak Lorok Semarang, Betah Walang Demak, dan Kenjeran Surabaya) pada bulan Oktober 2014 sampai Juni 2015. Sebanyak 27 karakter morfologi dari 62 individu digunakan untuk mengetahui konektivitas dan karakteristik antar populasi. Pengujian data dilakukan dengan menggunakan analisis non-parametrik. Sedangkan, 5 individu dari masing masing lokasi digunakan untuk analisis molekuler yang meliputi beberapa tahapan diantaranya yaitu ekstraksi DNA genomik, elektroforesis DNA, amplifikasi dan visualisasi fragmen DNA, serta sekuensing DNA. Hasil penelitian menunjukkan bahwa T. gigas Surabaya membentuk kelompok tersendiri karena memiliki ukuran tubuh (X1-X2 dan X4-X16) lebih besar dan 5 anggota tubuh (X22, X23, X26-X28) yang relatif lebih besar dibandingkan Semarang, Demak, Subang, dan Banten. Tidak terdapat konektivitas antar populasi berdasarkan karakter mor-fologi. Dihasilkan nukleotida dengan panjang 650 pb bersifat conserve. Analisis menggunakan soft-ware MEGA 5.0 menunjukkan sebanyak 73 situs spesifik yang merupakan penciri yang membedakan T. gigas in groups dengan T. gigas dari Central Arabian Sea, T. tridentatus dari Sweden dan Car-cinoscorpius rotundicauda dari USA sebagai outgroups.

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Molecular phylogeny of extant horseshoe crabs (Xiphosura, Limulidae) indicates Paleogene diversification of Asian species

Cited by 61 publications

References 34 publications

Cross-bracing uncalibrated nodes in molecular dating improves congruence of fossil and molecular age estimates

Cross-bracing uncalibrated nodes in molecular dating improves congruence of fossil and molecular age estimates

Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs

MORPHOLOGICAL CHARACTER AND MOLECULAR IDENTIFICATION WITH COI GENE MARKER OF HORSESHOE CRABS (Tachypleus gigas) AT COASTAL WATERS OF NORTHERN JAVA ISLAND

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