Beyond the Coral Triangle: high genetic diversity and near panmixia in Singapore's populations of the broadcast spawning sea star
            Protoreaster nodosus

The Coral Triangle is widely considered the most important centre of marine biodiversity in Asia while areas on its periphery such as the South China Sea, have received much less interest. Here, we demonstrate that a small population of the knobbly sea star Protoreaster nodosus in Singapore has similarly high levels of genetic diversity as comparable Indonesian populations from the Coral Triangle. The high genetic diversity of this population is remarkable because it is maintained despite decades of continued anthropogenic disturbance. We postulate that it is probably due to broadcast spawning which is likely to maintain high levels of population connectivity. To test this, we analysed 6140 genome-wide single nucleotide polymorphism (SNP) loci for Singapore's populations and demonstrate a pattern of near panmixia. We here document a second case of high genetic diversity and low genetic structure for a broadcast spawner in Singapore, which suggests that such species have high resilience against anthropogenic disturbances. The study demonstrates the feasibility and power of using genome-wide SNPs for connectivity studies of marine invertebrates without a sequenced genome.

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Differences in genetic diversity and divergence between brooding and broadcast spawning corals across two spatial scales in the Coral Triangle region

Marine Biology ◽

10.1007/s00227-020-03813-8 ◽

2021 ◽

Vol 168 (2) ◽

Author(s):

Rosa Maria van der Ven ◽

Hanneloor Heynderickx ◽

Marc Kochzius

Keyword(s):

Genetic Diversity ◽

Spatial Scales ◽

Allelic Diversity ◽

Marine Biodiversity ◽

Coral Triangle ◽

Broadcast Spawning ◽

Acropora Millepora ◽

Dispersal Barriers ◽

Seriatopora Hystrix ◽

Spermonde Archipelago

AbstractThe Coral Triangle region contains the world’s highest marine biodiversity, however, these reefs are also the most threatened by global and local threats. A main limitation that prevents the implementation of adequate conservation measures is that connectivity and genetic structure of populations is poorly known. The aim of this study was to investigate the genetic diversity, population structure and connectivity patterns of tropical corals in Indonesia on two different spatial scales, as well as by comparing two different reproduction strategies. Genotyping was based on microsatellite markers for 316 individual Seriatopora hystrix colonies and 142 Acropora millepora colonies sampled in Pulau Seribu and Spermonde Archipelago in 2012 and 2013. Differences in allelic diversity and a strong signature of divergence associated with historical land barriers at the Sunda Shelf were found for the brooding coral Seriatopora hystrix. However, differences in diversity and divergence were not pronounced in the broadcast spawning coral Acropora millepora. Within Spermonde Archipelago, two groups were identified: (1) sites of the sheltered inner-shelf and mid-shelf, which were found to be highly interconnected and (2) mid-shelf and outer-shelf sites characterised by higher differentiation. These patterns of contemporary dispersal barriers and genetic diversity can be explained by the differences in life history of the corals, as well as by oceanographic conditions facilitating larval dispersal. The contemporary dispersal barriers found within the Spermonde Archipelago emphasise the need for incorporating connectivity data in future conservation efforts.

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Genetic population structure of the blue sea star Linckia laevigata in the Visayas (Philippines)

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315415000971 ◽

2015 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Diana Sr Alcazar ◽

Marc Kochzius

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Flow ◽

Comparative Analysis ◽

Marine Invertebrates ◽

Genetic Population Structure ◽

Sea Star ◽

Genetic Population ◽

Gene Coi ◽

Linckia Laevigata

Coral reef associated marine invertebrates, such as the blue sea starLinckia laevigata, have a life history with two phases: sedentary adults and planktonic larvae. On the one hand it is hypothesised that the long pelagic larval duration facilitates large distance dispersal. On the other hand, complex oceanographic and geographic characteristics of the Visayan seascape could cause isolation of populations. The study aims to investigate the genetic diversity, genetic population structure and gene flow inL. laevigatato reveal connectivity among populations in the Visayas. The analysis is based on partial sequences (626 bp in length) of the mitochondrial cytochrome oxidase I gene (COI) from 124 individuals collected from five localities in the Visayas. A comparative analysis of these populations with populations from the Indo-Malay Archipelago (IMA) published previously is also presented. Genetic diversity was high (h = 0.98, π = 1.6%) and comparable with preceding studies. Analyses of molecular variance (AMOVA) revealed a lack of spatial population differentiation among sample sites in the Visayas (ΦST-value = 0.009;P > 0.05). The lack of genetic population structure indicates high gene flow among populations ofL. laevigatain the Visayas. Comparative analysis with data from the previous study indicates high connectivity of the Visayas with the central part of the IMA.

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Linkage disequilibrium and within-breed genetic diversity in Iranian Zandi sheep

Archives Animal Breeding ◽

10.5194/aab-62-143-2019 ◽

2019 ◽

Vol 62 (1) ◽

pp. 143-151 ◽

Cited By ~ 6

Author(s):

Seyed Mohammad Ghoreishifar ◽

Hossein Moradi-Shahrbabak ◽

Nahid Parna ◽

Pourya Davoudi ◽

Majid Khansefid

Keyword(s):

Genetic Diversity ◽

Linkage Disequilibrium ◽

Association Studies ◽

Genome Wide Association Studies ◽

Effective Population ◽

High Genetic Diversity ◽

Single Nucleotide ◽

Genome Wide ◽

Snp Panel ◽

Zandi Sheep

Abstract. This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (Ne), and runs of homozygosity (ROHs) in one of the major Iranian sheep breeds (Zandi) using 96 samples genotyped with Illumina Ovine SNP50 BeadChip. The amount of LD (r2) for single-nucleotide polymorphism (SNP) pairs in short distances (10–20 kb) was 0.21±0.25 but rapidly decreased to 0.10±0.16 by increasing the distance between SNP pairs (40–60 kb). The Ne of Zandi sheep in past (approximately 3500 generations ago) and recent (five generations ago) populations was estimated to be 6475 and 122, respectively. The ROH-based inbreeding was 0.023. We found 558 ROH regions, of which 37 % were relatively long (> 10 Mb). Compared with the rate of LD reduction in other species (e.g., cattle and pigs), in Zandi, it was reduced more rapidly by increasing the distance between SNP pairs. According to the LD pattern and high genetic diversity of Zandi sheep, we need to use an SNP panel with a higher density than Illumina Ovine SNP50 BeadChip for genomic selection and genome-wide association studies in this breed.

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Broad-scale puma connectivity could restore genomic diversity to fine-scale coastal populations

10.1101/2021.10.08.463677 ◽

2021 ◽

Author(s):

Kyle D Gustafson ◽

Roderick B Gagne ◽

Michael R Buchalski ◽

T Winston Vickers ◽

Seth PD Riley ◽

...

Keyword(s):

Genetic Diversity ◽

Linkage Disequilibrium ◽

Puma Concolor ◽

Genomic Diversity ◽

Strong Linkage Disequilibrium ◽

Fine Scale ◽

High Genetic Diversity ◽

Population Genomic ◽

Genome Wide ◽

Genetic Clusters

Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California's central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double-digest restriction-site associated DNA (ddRAD) sequencing to analyze 16,285 genome-wide single-nucleotide polymorphisms (SNPs) from 401 broadly sampled pumas. Our analyses indicated support for 4–10 geographically nested, broad- to fine-scale genetic clusters. At the broadest scale, the 4 genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating pumas have retained statewide genomic diversity. However, multiple lines of evidence indicated substructure, including 10 fine-scale genetic clusters, some of which exhibited allelic fixation and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at-risk populations are typically nested within a broader-scale group of interconnected populations that collectively retains high genetic diversity and heterogeneous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state- and genome-wide results are critically important for science-based conservation and management practices. Our broad- and fine-scale population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for fragmented population conservation management.

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Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?

10.1101/016493 ◽

2015 ◽

Author(s):

Emiliano Trucchi ◽

Benoit Facon ◽

Paolo Gratton ◽

Emiliano Mori ◽

Nils Chr. Stenseth ◽

...

Keyword(s):

Genetic Diversity ◽

Evolutionary Dynamics ◽

Leading Edge ◽

High Genetic Diversity ◽

Hystrix Cristata ◽

The North ◽

Fundamental Information ◽

Genome Wide ◽

Crested Porcupine ◽

Species Specific

AbstractStudying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of the genetic diversity and the demographic dynamics of the H. cristata invasive populations and compare their genetic diversity with that of native African populations of both H. cristata and its sister species, H. africaeaustralis. First, we demonstrate that genetic diversity is lower in both the invasive Italian and the North Africa source range relative to other native populations from Sub-Saharan and South Africa. Second, we find evidence of multiple introduction events in the invasive range followed by very limited gene flow. Through coalescence-based demographic reconstructions, we also show that the bottleneck at introduction was mild and did not affect the introduced genetic diversity. Finally, we reveal that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. We conclude that the level of genome-wide diversity of H. cristata invasive populations is less important in explaining its successful invasion than species-specific life-history traits or the phylogeographic history in the native source range.

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Insights into reproductive isolation within the pelagic copepod Pleuromamma abdominalis with high genetic diversity using genome-wide SNP data

Marine Biology ◽

10.1007/s00227-019-3618-x ◽

2019 ◽

Vol 167 (1) ◽

Cited By ~ 2

Author(s):

Junya Hirai

Keyword(s):

Genetic Diversity ◽

Reproductive Isolation ◽

High Genetic Diversity ◽

Pelagic Copepod ◽

Snp Data ◽

Genome Wide

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Genome-wide assessment of genetic diversity and population structure in Magnolia odoratissima based on SLAF-Seq

10.21203/rs.3.rs-747821/v1 ◽

2021 ◽

Author(s):

Tao Zhang ◽

Xue Li ◽

Shuilian He

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Flow ◽

Natural Populations ◽

Environmental Parameters ◽

Candidate Snps ◽

Small Populations ◽

Nucleotide Polymorphisms ◽

High Genetic Diversity ◽

Genome Wide

Abstract Magnolia odoratissima is a highly threatened species with small populations and scattered distribution due to habitat fragmentation and human activity. The species is recognized as a Plant Species with Extremely Small Populations (PSESP) and is endemic to China. In the current study, the population structure and levels of genetic diversity of M. odoratissima in the five remaining natural populations and three cultivated populations were evaluated using single nucleotide polymorphisms (SNPs) derived from Specific-Locus Amplified Fragment Sequencing (SLAF-seq). A total of 180,650 SNP loci were found in seventy M. odoratissima individuals. The genome-wide Nei’s and Shannon’s nucleotide diversity indexes of the total M. odoratissima population were 0.3035 and 0.4695, respectively. The observed heterozygosity (Ho) and expected heterozygosity (He) were 0.1122 and 0.3011. Our results suggest that M. odoratissima has relatively high genetic diversity at the genomic level. FST and AMOVA indicated that high genetic differentiation existed among populations. A phylogenetic neighbor-joining tree, Bayesian model–based clustering and principal components analysis (PCA) all divided the studied M. odoratissima individuals into three distinct clusters. The Treemix analysis showed that there was low gene flow among the natural populations and a certain gene flow from the wild populations to the cultivated population (LS to KIB, and GN to JD). In addition, a total of 36 unique SNPs were detected as being significantly associated with environmental parameters (altitude, temperature and precipitation). These candidate SNPs were found to be involved in multiple pathways including several molecular functions and biological process, suggesting they may play key roles in environmental adaptation. Our results suggested that three distinct evolutionary significant units (ESUs) should be set up to conserve this critically endangered species.

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Genetic diversity and mating system of an endangered tree Eucalyptus morrisbyi

Australian Journal of Botany ◽

10.1071/bt04182 ◽

2005 ◽

Vol 53 (4) ◽

pp. 367 ◽

Cited By ~ 22

Author(s):

R. C. Jones ◽

G. E. McKinnon ◽

B. M. Potts ◽

R. E. Vaillancourt

Keyword(s):

Genetic Diversity ◽

Small Population ◽

Ex Situ ◽

Endangered Tree ◽

High Genetic Diversity ◽

Vegetative Regeneration ◽

Adult Trees ◽

Outcrossing Rates ◽

Chloroplast Haplotypes ◽

The 19Th Century

Eucalyptus morrisbyi is an endangered eucalypt, restricted to four populations on the island of Tasmania. The two main populations are separated by 20 km, occurring in the Risdon Hills and on Calverts Hill, and differ markedly in size and health. Although they are both in reserves, the small population at Risdon Hills has experienced a marked decline in the last two decades. The other two populations (Lumeah Point and Honeywood Drive) are very small and under threat because of urbanisation. They are close to the large Calverts Hill population and may be remnants of a once larger population in this area prior to clearing for agriculture in the 19th century. A hypervariable chloroplast marker and six nuclear microsatellites, used to quantify genetic diversity among and within populations, indicated marked genetic differences between the two main populations (Risdon and Calverts Hills), with virtually no sharing of chloroplast haplotypes and little sharing of microsatellite alleles among populations. Both of the main populations are clearly required to adequately conserve the genetic diversity in this species, whereas the Lumeah Point and Honeywood Drive populations are similar to the proximal Calverts Hill population. The two main populations showed equally high levels of genetic diversity (average HE = 0.69) in the adult trees, using microsatellites, and little difference in inbreeding levels despite the large difference in population size. Analyses of 366 offspring from 9–11 trees from each main population revealed high outcrossing rates, little bi-parental inbreeding and high genetic diversity (average HE = 0.65) in both seedling populations. This indicates that open-pollinated seed collections from these populations capture sufficient genetic diversity for ex situ conservation plantings. It is argued that the high genetic diversity maintained in the small Risdon Hills population is due to a combination of the longevity of its genotypes (possibly up to 1155–1523 years) through a well developed mechanism of vegetative regeneration from lignotubers, coupled with high outcrossing rates maintained by a strong self-incompatibility mechanism.

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