2 PREMISE OF THE STUDY: The Last Glacial Maximum (LGM) was a period of massive range contraction. Post-LGM, water-dispersed coastal species, including the red mangrove ( Rhizophora mangle ), expanded poleward as propagules were transported by ocean currents. We assessed postglacial marine expan- sion pathways for R. mangle within the Caribbean Basin and Florida. METHODS: Six microsatellite loci were used to genotype 237 individuals from nine R. mangle populations in the Caribbean, Florida, and Northwest Africa. We evaluated genetic variation, population structure, gene fl ow along alternative post-LGM expansion pathways to Florida, and potential long-distance dispersal (LDD) from West Africa to Caribbean islands. KEY RESULTS: These R. mangle populations had substantial genetic structure ( F ST = 0.37, P < 0.0001) with three discrete population clusters (Caribbean mainland, Caribbean islands, and Florida). Genetic connectivity along the mainland pathway (Caribbean mainland to Florida) vs. limited gene dispersal along the Antilles Island pathway (Caribbean islands to Florida) supported Florida recolonization from Caribbean mainland sources. Genetic similarity of North- west Africa and two Caribbean islands provided evidence for trans-Atlantic LDD. We did not fi nd a pattern of decreasing genetic diversity with latitude. CONCLUSIONS: We outline a complex expansion history for R. mangle , with discrete pathways of recolonization for Florida and Caribbean islands. Contrary to expectation, connectivity to putative Caribbean mainland refugial populations via ocean currents, and not latitude, appears to dictate genetic diversity within Caribbean island and Florida R. mangle . These fi ndings provide a framework for further investigation of additional water-dispersed neotropical species, and insights for management initiatives.

/pdf/postglacial-expansion-pathways-of-red-mangrove-rhizophora-29a3vigczw.pdf

Postglacial expansion pathways of red mangrove, Rhizophora mangle, in the Caribbean Basin and Florida

Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP) region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, R. mucronata, and R. stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa, suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the effects of their life history traits. Recent population fragmentation and disturbances arising from human activities could further endanger genetic diversity in mangrove trees.

/pdf/comparative-analysis-of-the-pattern-of-population-genetic-2anljyghi9.pdf

Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species.

Mangrove plants comprise plants with similar ecological features that have enabled them to adapt to life between the sea and the land. Within a geographic region, different mangrove species share not only similar adaptations but also similar genetic structure patterns. Along the eastern coast of South America, there is a subdivision between the populations north and south of the continent's northeastern extremity. Here, we aimed to test for this north-south genetic structure in Rhizophora mangle, a dominant mangrove plant in the Western Hemisphere. Additionally, we aimed to study the relationships between R. mangle, R. racemosa, and R. × harrisonii and to test for evidence of hybridization and introgression. Our results confirmed the north-south genetic structure pattern in R. mangle and revealed a less abrupt genetic break in the northern population than those observed in Avicennia species, another dominant and widespread mangrove genus in the Western Hemisphere. These results are consistent with the role of oceanic currents influencing sea-dispersed plants and differences between Avicennia and Rhizophora propagules in longevity and establishment time. We also observed that introgression and hybridization are relevant biological processes in the northeastern coast of South America and that they are likely asymmetric toward R. mangle, suggesting that adaptation might be a process maintaining this hybrid zone.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.3900

Population genetic structure, introgression, and hybridization in the genus Rhizophora along the Brazilian coast.

Members of the mangrove genus Rhizophora represent the most commonly occurring and highly valued species in the Indo-West Pacific region. However, to date, few studies have been directed towards the understanding of their genetic variation. The levels and patterns of genetic variation at chloroplast and nuclear gene regions were studied in R. apiculata, R. mucronata, and R. stylosa sampled from Southeast Asia and Japan. All three species were characterized by low intraspecific genetic variation and a deficiency of heterozygotes in populations within the region, consistent with findings in studies on other mangrove species. Rhizophora mucronata and R. stylosa were also found to be more closely related than any of them with R. apiculata. During the Last Glacial Maximum, sea levels dropped to 120 m below the current levels, exposing part of the Sunda Shelf that became a barrier that limited gene flow between marine species living in the Pacific and Indian Oceans. Today, the Malay Peninsula is thought to still serve as a barrier to gene flow between populations occurring on its coasts. The pattern of genetic differentiation of R. apiculata supports the hypothesis of the land barrier effect of the Malay Peninsula, but such patterns were not found in R. mucronata and R. stylosa. Our findings suggest that R. apiculata, R. mucronata, and R. stylosa have different demographic histories despite being closely related and having sympatric distributions today. Furthermore, all three species appear to have high levels of inbreeding due to limited pollen and propagule dispersal, and that both these factors contributed to population differentiation.

Closely related and sympatric but not all the same: genetic variation of Indo-West Pacific Rhizophora mangroves across the Malay Peninsula

Aim: Population genomics data were used to determine the genetic diversity, genetic divergence and genetic structure of the mangrove, Rhizophora apiculata, across its distributional range and to re-assess the evolutionary processes that shaped its current distribution.

Location: The Indo-Malesian region section of the Indo-West Pacific region.

Methods: Next-generation sequencing technology was used to sequence 81 nuclear loci from a pooled DNA sample of 31–44 individuals of Rhizophora apiculata from 11 populations. Five nuclear loci from six to eight individuals from 18 populations were sequenced using conventional Sanger sequencing technology to validate the results.

Results: Genetic diversity at the population level was low (π and θ were < 1.0 × 10−3 in most of the populations), but relatively high at the species level (π = 2.419 × 10−3 and θ = 1.362 × 10−3). The populations of R. apiculata in the Indo-Malesian region were genetically differentiated and grouped into three clusters: east Indian Ocean (EIO), South China Sea (SCS) and Australasia (AUA). Based on the genetic distance matrices, two genetic discontinuities were observed, and they correspond to the Malay Peninsula land barrier and the Wallacea zone. The admixture observed in populations from the Malacca Strait was attributed to asymmetric gene flow through the strait, which was simulated by the isolation-with-migration (IM) model.

Main conclusion: Both the Sunda shelf barrier and ocean currents in Wallacea contributed to the observed genetic discontinuity, which separated R. apiculata into three clusters (SCS, EIO and AUA). The cycle between extinction and recolonization in the SCS in response to Pleistocene sea level fluctuations reduced the genetic diversity within populations. The repeated opening and closing of the gene flow corridors, such as the Malacca Strait, may have blurred the genetic discontinuities to an extent and introduced an admixture into populations in boundary areas.

Genetic discontinuities in a dominant mangrove Rhizophora apiculata (Rhizophoraceae) in the Indo‐Malesian region

Genetic variations within and among Rhizophora apiculata populations in the Greater Sunda Islands of Indonesia were studied using microsatellite markers. The study found 38 alleles on five loci in 15 populations. The observed (H
 o) and expected (H
 e) heterozygosity values are 0.338 and 0.378, respectively. Inbreeding effect from self-pollination might explain its heterozygote deficiency. Population genetic differentiation (F
 ST = 0.381) was similar to other mangrove species. The genetic diversity of R. apiculata populations along the coastline inside the archipelago (e.g., Buleleng, Donggala, Mamuju, and Takalar) was higher than those of population along the coastline outside the archipelago, especially northern Sumatra populations (i.e., Langkat, Tapanuli Tengah, Dumai, and Padang). The isolation by distances and sea currents directions as well as their connectivity might affect the gene flow and genetic exchange. The more isolated with fewer connections by sea currents, the smaller gene flow and genetic exchange observed between populations. The higher genetic exchange, on the contrary, occurred when population location was closer to the meeting point of the sea currents. The study also showed that the patterns of sea current movement seemed to have influence genetic clustering of populations which fell into three main groups (Sunda Shelf Mangroves) and one isolated population (New Guinea Mangroves).

Genetic variation and population genetic structure of Rhizophora apiculata (Rhizophoraceae) in the Greater Sunda Islands, Indonesia using microsatellite markers.

The Korean plum yew (Cephalotaxus koreana Nakai) is a shade-tolerant, coniferous shrub. The seeds have been used as a folk medicine in Korea, and an alkaloid extract (HTT) is known to have anticancer properties. We estimated the genetic diversity of 429 trees in 16 populations in South Korea using 194 polymorphic amplicons from seven combinations of AFLP primer-restriction enzymes. The average number of effective alleles and the percentage of polymorphic loci were 1.37 and 79.4%, respectively. Shannon’s diversity index and the expected heterozygosity were 0.344 and 0.244, respectively. We divided 16 populations into four groups on the UPGMA dendrogram and the PCA biplot. The first two principal components explained 84% of the total genetic variation. Genetic differentiation between populations explained 14% of total genetic variation, and the remaining 86% came from difference between individuals within populations, as determined by an analysis of molecular variance (AMOVA). However, the genetic differentiation did not correlate with the geographic distance between populations from the Mantel test. The Bayesian statistics, which are comparable to Wright’s FST and Nei’s GST, were θ I = 0.406 and θ II = 0.172, respectively. The population genetic diversity was slightly lower, and the strength of genetic differentiation was much weaker, than the average of those plants having similar life histories, as assessed using arbitrary marker systems. We discuss strategies for the genetic conservation of the plum yew in Korea.

Genetic Diversity and Population Genetic Structure of Cephalotaxus koreana in South Korea

Torreya nucifera (L.) Siebold & Zucc. (Taxaceae) is a tertiary relict tree species with a distribution that is limited to South Korea and Japan. In the present study, the complete chloroplast (cp) ...

The complete chloroplast genome of Torreya nucifera (Taxaceae) and phylogenetic analysis.

Genetic Diversity and Population Genetic Structure of Exochorda serratifolia in South Korea

=0.101)에서 유의할 만한 차이를 보이는 집단은 없었다. 군집분석과 주성분분석에서 7개의 집단들을 3개 군집으로 나눌 수 있었으나, 두 방법의 군집 양상은일치하지 않았다. 또한 베이즈 군집분석에서 집단간 유연관계와 지리적 분포의 상관성을 확인할 수 없었다. Abstract: Population genetic structure and diversity of Ulmus davidiana var. japonica in South Korea werestudied using ISSR markers. A total of 45 polymorphic ISSR amplicons were cropped from 7 ISSR primers and171 individuals of 7 populations. The average of effective alleles and the proportion of polymorphic loci were1.5 and 89% respectively. The Shannon’s diversity index (I) was 0.435 and the expected heterozygosity fromthe frequentist’s method (H

Kyung Nak Hong

Papers

Genetic variation and population genetic structure of Rhizophora apiculata (Rhizophoraceae) in the Greater Sunda Islands, Indonesia using microsatellite markers.

Genetic Diversity and Population Genetic Structure of Cephalotaxus koreana in South Korea

The complete chloroplast genome of Torreya nucifera (Taxaceae) and phylogenetic analysis.

Genetic Diversity and Population Genetic Structure of Exochorda serratifolia in South Korea

Population Genetic Variation of Ulmus davidiana var. japonica in South Korea Based on ISSR Markers