Strong genetic population structure in the boring giant clam, <i>Tridacna crocea,</i> across the Indo‐Malay Archipelago: implications related to evolutionary processes and connectivity

Kochzius, Marc; Nuryanto, Agus

doi:10.1111/j.1365-294x.2008.03803.x

Cited by 120 publications

(199 citation statements)

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“…This result in accordance with Kochzius & Nuryanto (2008) that nucleotide diversity value less than 0.01 refers to low-level diversity. All genetic parameters indicate that the studied giant gourami strains had low genetic diversity in their cytochrome b gene.…”

Section: Resultssupporting

confidence: 75%

Molecular Characteristics of Batanghari, Tambago, Orange, and Mandiangin Giant Gourami Strains

Nuryanto

Pulungsari

2017

J Bio Bio Edu

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Morphological variations among geographic and can be identified as different species. However, a lot of studies proved that morphological variations are also common in conspecific individuals. Therefore, precise identification using additional characters is vital, such as using a molecular marker. Here, we characterized Batanghari, Tambago, Orange, and Mandiangin gourami strains using the cytochrome b gene to evaluate their taxonomic status. Partial sequences of cytochrome b gene were sequenced for 40 individuals. Taxonomic status was checked for giant gourami sequences available in GenBank. Kimura 2-Parameter genetic distances were calculated in MEGA6 software. Haplotype and nucleotide diversity within population and Φ st -value among populations were estimated in Arlequin software. Phylogenetic relationship was reconstructed using the neighbor-joining method in MEGA6 software based on Kimura 2-parameter model with 1000 pseudobootstraps. Taxonomic identification results in 99% sequences homology to Osphronemus goramy sequences (accession number KU984978.1 and AY763768.1), means that all strains belong to single species. Low genetic distances, medium haplotype and low-level nucleotide diversity were observed among strains. Pairwise Φ st -comparison indicates no genetic differences among Sumatera strain, whereas strong genetic structures observed between Sumatera and Mandiangin strains. The phylogenetic tree showed that Mandiangin formed separate subclades from other strains with bootstraps value of 100%. This finding has important implication for breeding sciences and efforts.

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Section: Resultssupporting

confidence: 75%

Molecular Characteristics of Batanghari, Tambago, Orange, and Mandiangin Giant Gourami Strains

Nuryanto

Pulungsari

2017

J Bio Bio Edu

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“…Tridacna crocea and T. squamosa are sister species, with T. maxima basal to them (Schneider & Foighil 1999). Additional phylogenetic structure is apparent within host species, with distinct COI clades present in T. crocea (DeBoer et al 2008, Kochzius & Nuryanto 2008 and T. maxima, but not in T. squamosa (Fig. 3).…”

Section: Host -Symbiont Specificitymentioning

confidence: 88%

Patterns of Symbiodinium distribution in three giant clam species across the biodiverse Bird’s Head region of Indonesia

DeBoer¹,

Baker²,

Erdmann³

et al. 2012

Mar. Ecol. Prog. Ser.

111

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The formation and persistence of modern coral reefs depends largely on organisms that host dinoflagellate algal symbionts of the genus Symbiodinium. There are important ecological and physiological differences among Symbiodinium types, and many host species are able to associate with multiple types, which may facilitate adaptation to local environmental change. Using denaturing gradient gel electrophoresis (DGGE) and sequencing of internal transcribed spacer-2 (ITS2) ribosomal DNA, we identified 11 Symbiodinium types belonging to clades A, C, and D in 250 host animals from 3 Tridacna species in eastern Indonesia. Individuals with multiple symbiont types were common: 42% of all clams had symbionts from multiple clades and 15% of all clams had multiple types from a single clade. T. crocea associated more often with clade C symbionts and less frequently with clade D symbionts. T. squamosa associated more frequently with clade D and less often with clade C symbionts. T. maxima did not preferentially associate with a particular Symbiodinium clade, but sample sizes were low. We used both satellite sea surface temperature and in situ recordings to characterize the thermal environment in the study area. Clams with clade C and D symbionts were located in areas with higher mean temperatures, while clams with clade A symbionts were in cooler areas. This is consistent with previous research indicating that clade C and D types may be more heat-tolerant than clade A. These results support the hypothesis that giant clams can associate with different symbiont types based on local environmental conditions. KEY WORDS: Symbiodinium · Tridacna spp. · Thermal tolerance · Climate change · Coral reef · IndonesiaResale or republication not permitted without written consent of the publisher

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“…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…”

Section: Discussionmentioning

confidence: 99%

“…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].…”

Section: Discussionmentioning

confidence: 99%

“…4.0.3). In addition, the NCBI repository of nucleotide sequences was searched for all published Tridacna COI and 16S sequences (August 2012) representing both intraspecific [24][25][26]41] and interspecific [9,15,16] surveys. These sequences were manually aligned [42] against our new sequences and against outgroups (Hippopus hippopus, Hippopus porcellanus, Cerastoderma glaucum, Fragum sueziense, and Corculum cardissa) and trimmed to a common length.…”

Section: Dna Sequencesmentioning

confidence: 99%

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

Liggins¹

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Which factors shape population connectivity and the consistency of their influence across species and seascapes is largely unresolved. This thesis takes a comparative genetic approach to investigate the influences of seascape topology (past sea level changes, contemporary oceanography, and geography) and species biology on the genetic connectivity among coral reefs around Australia, the Indo-Australasian Archipelago (IAA), and the wider Indo-Pacific. I focus on a suite of common, codistributed coral reef fishes and invertebrates that differ in life history characteristics. In the introductory chapter of my thesis I discuss population connectivity in marine systems, the contribution of seascape genetics to marine population connectivity research, and the state of our knowledge in the Indian and Pacific Oceans (Chapter One). Chapters Two and Three review the field of seascape genetics and the methodologies used in seascape genetic studies, respectively. My empirical research (Chapters Four-Six) takes a broad, yet integrated approach to describe and understand the processes underlying seascape genetic patterns around Australia, the IAA, and the Indo-Pacific. First, I investigate historical spatial genetic (mitochondrial DNA, mtDNA) patterns and processes using a comparative, multi-species framework (Chapter Four). I extend typical methods of comparative phylogeography to include: a matrix comparison method that allows the quantitative characterization of spatial genetic patterns; and a multiple regression modeling approach to identify the processes underlying the spatial genetic patterns for each species. I find that despite being subjected to common geographic and seascape influences, spatial genetic patterns differ across four common coral reef fishes (Acanthurus triostegus, Dascyllus trimaculatus, Halichoeres hortulanus, Pomacentrus coelestis). Although species with similar dispersal potential (based on egg type and pelagic larval duration) have the most similar spatial genetic patterns, the seascape features and processes (e.g. previous landbridges and oceanographic distances) underlying the genetic patterns are not always shared among species. Second, I characterize the latitude-wide genetic patterns of one species (P. coelestis) and extend methods typically used in such investigations by borrowing concepts and measures more commonly used for analyses of community composition (Chapter Five). Genealogical analyses reveal that levels of population genetic diversity in the core of the species range are elevated by the co-occurrence of two cryptic clades. Furthermore, the application of partitioned -diversity measures and nestedness analyses reveal that differing demographic processes underlie the genetic patterns observed at the northern and southern latitudinal peripheries of the species range. Last, I focus on edge-of-range genetic patterns for two tropical echinoderm species (Acanthaster planci and Tripneustes gratilla) at a little-studied high latitude peripheral population, Kermadec Islands, New Zea...

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Strong genetic population structure in the boring giant clam, Tridacna crocea, across the Indo‐Malay Archipelago: implications related to evolutionary processes and connectivity

Cited by 120 publications

References 95 publications

Molecular Characteristics of Batanghari, Tambago, Orange, and Mandiangin Giant Gourami Strains

Molecular Characteristics of Batanghari, Tambago, Orange, and Mandiangin Giant Gourami Strains

Patterns of Symbiodinium distribution in three giant clam species across the biodiverse Bird’s Head region of Indonesia

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

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