Highly restricted gene flow and deep evolutionary lineages in the giant clam Tridacna maxima

Abstract

The tropical Indo-West Pacific is the biogeographic region with the highest diversity of marine shallow water species, with its centre in the Indo-Malay Archipelago. However, due to its high endemism, the Red Sea is also considered as an important centre of evolution. Currently, not much is known about exchange among the Red Sea, Indian Ocean and West Pacific, as well as connectivity within the Indo-Malay Archipelago, even though such information is important to illuminate ecological and evolutionary processes that shape marine biodiversity in these regions. In addition, the inference of connectivity among populations is important for conservation. This study aims to test the hypothesis that the Indo-Malay Archipelago and the Red Sea are important centres of evolution by studying the genetic population structure of the giant clam Tridacna maxima. This study is based on a 484-bp fragment of the cytochrome c oxidase I gene from 211 individuals collected at 14 localities in the Indo-West Pacific to infer lineage diversification and gene flow as a measure for connectivity. The analysis showed a significant genetic differentiation among sample sites in the Indo-West Pacific (U st = 0.74, P \ 0.001) and across the Indo-Malay Archipelago (U st = 0.72, P \ 0.001), indicating restricted gene flow. Hierarchical AMOVA revealed the highest fixation index (U ct = 0.8, P \ 0.001) when sample sites were assigned to the following regions: (1) Red Sea, (2) Indian Ocean and Java Sea, (3) Indonesian throughflow and seas in the East of Sulawesi, and (4) Western Pacific. Geological history as well as oceanography are important factors that shape the genetic structure of T. maxima in the Indo-Malay Archipelago and Red Sea. The observed deep evolutionary lineages might include cryptic species and this result supports the notion that the Indo-Malay Archipelago and the Red Sea are important centres of evolution.

Phylogeography of the neon damselfish Pomacentrus coelestis indicates a cryptic species and different species origins in the West Pacific Ocean

“…Most of the past research supports the Center of Origin hypothesis (Barber et al 2006, Williams 2007, Timm & Kochzius 2008, Nuryanto & Kochzius 2009). In contrast, relatively few cases substantiate the Center of Overlap (Teske et al 2005, Gaither et al 2011) and Center of Accumulation hypotheses (Wilson et al 2001, Drew & Barber 2009).…”

“…However, Cende rawasih Bay was the only population har boring extremely low haplotype (0.1538 ± 0.1261) and nucleotide (0.0005 ± 0.0008) diversity, indicating that the population may have suffered a recent bottleneck or founder event (Grant & Bowen 1998). Previous phylogeographic studies of various marine taxa have also found unique genetic diversity in the Cenderawasih Bay region (Barber et al 2006, Crandall et al 2008, Nuryanto & Kochzius 2009. Allen & Erdmann (2006) hypothesized that the bay was essentially isolated for substantial periods over the past 5 million years.…”

Karakterisasi Molekuler Ikan Gurami Soang (Osphronemus gouramy Lac.) yang Mati pada Rentang Waktu Berbeda Menggunakan PCR-RFLP Gen Major Histocompatibility Complex Kelas II B

“…Menurut Weeden et al (1992), hasil isolasi DNA tersebut masih bisa digunakan sebagai template yang cukup baik untuk reaksi PCR. Kondisi tersebut juga pernah dilaporkan pada beberapa penelitian terdahulu yang memperoleh produk PCR dengan kuantitas dan kualitas yang baik meskipun menggunakan templat DNA berupa DNA smear (Nuryanto & Kochzius, 2009;Nuryanto et al, 2012;Azizah et al, 2015).…”

Seascape genetics of Indo-Pacific reef organisms: methodologies and case studies for an emerging discipline

“…crocea throughout Wallacea using mitochondrial (mtDNA) markers [24][25][26], allozymes [27,28], and microsatellites [29]. Both T. crocea and T. maxima have been shown to contain distinct mtDNA clades associated with Sumatra (Sunda), Wallacea, and northwest New Guinea (Sahul, particularly in Cenderawasih Bay) [24][25][26].…”

“…Both T. crocea and T. maxima have been shown to contain distinct mtDNA clades associated with Sumatra (Sunda), Wallacea, and northwest New Guinea (Sahul, particularly in Cenderawasih Bay) [24][25][26]. These lineages are sympatric in some populations, for instance T. maxima from northern Java has both Sumatran and Wallacean mitotypes, and similarly T. crocea populations from Halmahera eastward through Cenderawasih Bay contain both Wallacean and northwest New…”