Genetic differentiation and phylogeography of partially sympatric species complex Rhizophora mucronata Lam. and R. stylosa Griff. using SSR markers
Alison K. S. WeeKōji TakayamaJasher L ChuaTakeshi AsakawaSankararamasubramanian Halasya MeenakshisundaramOnrizal OnrizalBayu AdjieErwin Riyanto ArdliSarawood SungkaewNorhaslinda Binti MalekalNguyen Xuan TungSeverino G. SalmoOrlex B. YllanoMohd Nazre SalehKhin Khin SoeYoichi TateishiYasuyuki WatanoShigeyuki BabaEdward L. WebbTadashi Kajita
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Mangrove forests are ecologically important but globally threatened intertidal plant communities. Effective mangrove conservation requires the determination of species identity, management units, and genetic structure. Here, we investigate the genetic distinctiveness and genetic structure of an iconic but yet taxonomically confusing species complex Rhizophora mucronata and R. stylosa across their distributional range, by employing a suite of 20 informative nuclear SSR markers. Our results demonstrated the general genetic distinctiveness of R. mucronata and R. stylosa, and potential hybridization or introgression between them. We investigated the population genetics of each species without the putative hybrids, and found strong genetic structure between oceanic regions in both R. mucronata and R. stylosa. In R. mucronata, a strong divergence was detected between populations from the Indian Ocean region (Indian Ocean and Andaman Sea) and the Pacific Ocean region (Malacca Strait, South China Sea and Northwest Pacific Ocean). In R. stylosa, the genetic break was located more eastward, between populations from South and East China Sea and populations from the Southwest Pacific Ocean. The location of these genetic breaks coincided with the boundaries of oceanic currents, thus suggesting that oceanic circulation patterns might have acted as a cryptic barrier to gene flow. Our findings have important implications on the conservation of mangroves, especially relating to replanting efforts and the definition of evolutionary significant units in Rhizophora species. We outlined the genetic structure and identified geographical areas that require further investigations for both R. mucronata and R. stylosa. These results serve as the foundation for the conservation genetics of R. mucronata and R. stylosa and highlighted the need to recognize the genetic distinctiveness of closely-related species, determine their respective genetic structure, and avoid artificially promoting hybridization in mangrove restoration programmes.Keywords:
Rhizophora mucronata
Conservation Genetics
Abstract Aim Mangroves are intertidal plants with sea‐dispersed propagules, hence their population structure can offer valuable insights into the biogeographical processes driving population subdivision in coastal species. In this study, we used molecular markers and ocean circulation simulations to examine the effects of ocean currents and land masses on the genetic structure of the major mangrove species Rhizophora mucronata . Location Southeast Asia. Methods We assessed the genetic structure of 13 R. mucronata populations from continental Southeast Asia and Sumatra using 10 microsatellite loci. We first examined the relative effects of geographical distance and land mass (the Malay Peninsula) in shaping the genetic structure of R. mucronata in Southeast Asia. We then characterized the genetic structure of R. mucronata and compared it to the simulated ocean circulation patterns within our study region. Results Despite the low genetic diversity, significant genetic structuring was detected across R. mucronata populations. Contrary to observations on other mangrove species, genetic differentiation in R. mucronata was not found across the coasts of the Malay Peninsula, nor was it correlated with geographical distance. Instead, the most distinct genetic discontinuity was found at the boundary between the Andaman Sea and the Malacca Strait, and this can be explained by the prevailing ocean currents in this region. Main conclusions Our study presents novel evidence that the genetic structure of R. mucronata is maintained by ocean current‐facilitated propagule dispersal.
Rhizophora mucronata
Rhizophoraceae
Propagule
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We examined the phylogeography of the South American subterranean rodent Ctenomys talarum (Talas tuco-tuco) using mitochondrial DNA control region (D-loop) sequences. This species is an herbivorous rodent endemic to the province of Buenos Aires, Argentina, that lives in natural grasslands in coastal sand dune habitats and in some fragmented inland populations. In this study we assessed the genetic relationship among populations of C. talarum across its entire distributional range and analyzed how the geological history of the habitat has affected the genetic structure and demographic history of these populations. A complex network of haplotypes in conjunction with analysis of molecular variance results showed high genetic subdivision and a strong phylogeographic pattern among populations of C. talarum. Pairwise FST-values showed significant differentiation among all populations studied. The overall pattern was similar to that expected under the isolation-by-distance model, suggesting equilibrium between gene flow and local genetic drift. Major geographical barriers (e.g., rivers and unsuitable habitat) in the area, in conjunction with population isolation, appeared to be associated with strong genetic differentiation among the different geographical groups. Local mismatch distributions and tests of neutrality suggest contrasting histories for different groups of populations; although some populations appeared to be characterized by demographic stability and no significant departures from neutrality, others showed departures from strict neutrality consistent with a recent demographic expansion. Finally, a close association seems to exist between the major climatic changes that occurred during the late Pleistocene and Holocene in the central region of Argentina and the main historical demographic changes inferred from C. talarum. Current populations of C. talarum appear to be relicts of a more extended historical distribution along the Argentinean Pampas. These historical extinctions, however, have not erased the signature of long-term stability and geographical structure in this species along the coastal and inland distribution ranges.
Demographic history
Isolation by distance
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Understanding the phylogeography of a species requires not only elucidating patterns of genetic structure among populations, but also identifying the possible evolutionary events creating that structure. The use of a single phylogeographic test or analysis, however, usually provides a picture of genetic structure without revealing the possible underlying evolutionary causes. We used current analytical techniques in a sequential approach to examine genetic structure and its underlying causes in the bogus yucca moth Prodoxus decipiens (Lepidoptera: Prodoxidae). Both historical biogeography and recent human transplantations of the moth's host plants provided a priori expectations of the pattern of genetic structure and its underlying causes. We evaluated these expectations by using a progression of phylogenetic, demographic, and population genetic analyses of mtDNA sequence data from 476 individuals distributed across 25 populations that encompassed the range of P. decipiens. The combination of these analyses revealed that much of the genetic structure has evolved more recently than suggested by historical biogeography, has been influenced by changes in demography, and can be best explained by long distance dispersal and isolation by distance. We suggest that performing a suite of analyses that focus on different temporal scales may be an effective approach to investigating the patterns and causes of genetic structure within species.
Isolation by distance
Population Genetics
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Population Genetics
Local adaptation
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Summary Phylogeographic studies provide insights about complex systems at different evolutionary scales. In addition to providing evidence about ecological processes at the organismal level, a synthesis of studies across taxa can illuminate broad phylogeographic patterns at the landscape scale. We compared the phylogeographic patterns of two codistributed species of aquatic insects, Pteronarcella badia ( P lecoptera: P teronarcyidae) and D runella grandis ( E phemeroptera: E phemerellidae), across much of their range in western N orth A merica. We conducted population genetic analyses of P . badia and D . grandis individuals that co‐occurred in 22 western N orth A merican localities. Patterns of genetic structure and gene flow were compared to test for differential dispersal ability and to determine whether broad‐scale phylogeographic trends are consistent with patterns seen in terrestrial taxa across a similar geographic area. We also evaluated whether patterns observed in these species fit previously proposed models of genetic structure in aquatic organisms. P teronarcella badia showed greater genetic structure and lower rates of dispersal than D . grandis . Both taxa showed several shared geographic regions of genetic isolation, including the B itterroot V alley in M ontana, the P acific N orthwest, the southern R ocky M ountains and the C olorado P lateau. These broad‐scale phylogeographic patterns are largely consistent with trends observed in several terrestrial taxa across the sample area. D . grandis showed patterns of gene flow consistent with an isolation‐by‐distance model of genetic structure. Patterns observed in P . badia reflect elements of multiple models and may highlight the value of the dendritic network approach to understanding genetic patterns of aquatic taxa at broad geographic scales.
Isolation by distance
Vicariance
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Nutrient-poor, dry calcareous grasslands in Central Europe are characterized by their immense regional biodiversity and are of high conservation value. Human beings have transformed these regions for centuries by clearing woods, grazing livestock and cutting grass. Today dry grasslands and many of their related species are greatly endangered by intensification of agricultural practice or abandonment. The establishment of adequate conservation management techniques to preserve the unique floristic composition of dry grasslands demands new scientific investigations on biology, ecology and genetics of endangered species. Therefore, the present study focused on several different aspects in life history of steppe plants and demonstrated the importance of consolidated knowledge on taxonomic, phylogeographic, biological and population genetic conditions to develop new conservation strategies and to set adequate conservation priorities.
Chapter 2 dealt with the early colonization history of Scorzonera purpurea during the glacial and postglacial period. We reconstructed the postglacial expansion processes of the steppe plant into Central Europe by using molecular markers (AFLP). A survey of genetic variation among and within populations across the whole distribution range provided insights into potential refugial areas and immigration pathways. The phylogeographic analysis revealed that S. purpurea might have survived times of glaciations within at least two separated refugial areas, one located in the southern part of France and one located in the south-eastern part of Europe near the Hungarian Plains. After the retreat of glaciers and the following climate warming, S. purpurea immigrated via two main migration routes into Germany, both coming from the eastern part of Europe. One route may have lead along the river Danube into Bavaria and up to Central Germany. The other one have lead via Moravia, Silesia into the river valleys of Oder and Elbe. In Central Germany both genetic lineages have met and formed contact zones. The French populations, which were strongly isolated and genetically differentiated from all other populations, did not contribute any genetic material to the colonization of Central Germany. The detection of a potential contact zone in Germany, where different genetic lineages have met, highlights this region for conservation efforts.
Chapter 3 focused on the same species compiling a copious monograph on plant’s life history, habitat requirements, population dynamics and conservation status. We prepared basic information by literature survey as well as own measurements including field work, laboratory experiments and greenhouse studies to enable the detection of potential life cycle risk factors and to improve existing conservation programs for S. purpurea. Furthermore, in chapter 7 we used all gained information on S. purpurea to compile a population viability analysis and to elaborate detailed recommendations for future managements.
Chapter 4 dealt with the genetic affiliation of Stipa bavarica, an endemic steppe species of Bavaria, to its closely related taxa. We investigated wether molecular analyses support its taxonomic status as a distinct species and its importance as management unit of high conservation value. The analysis comprised individuals from populations of S. bavarica, S. pulcherrima and S. pennata. Genetic differentiation between species was high for S. pulcherrima and S. pennata as well as S. pennata and S. bavarica. In contrast, there was no genetic differentiation among populations of S. bavarica and S. pulcherrima indicating strong effects of still existing or recently interrupted gene flow. From this point of view the taxonomic separation of S. bavarica as a distinct species seemed not to be very reasonable. However, genetic variation within population and the content of rare bands emphasized the genetic importance of S. bavarica as valuable management unit for the preservation of genetic biodiversity in ex situ conservation programs.
In chapter 5 we elucidated the doubtful taxonomic position of Tephroseris integrifolia in Bavaria. High morphological variation within and among populations of T. integrifolia complicated the exact taxonomic positioning of individual populations for long time. Especially one population in the north of Bavaria is supposed to be a local endemic subspecies, which would grant stronger legal protection. Using a population genetic approach we analysed individuals of three Bavarian and one Austrian population by AFLP. All studied populations differentiated on a very low level, in which the strongest genetic differentiation could be revealed for the grouping of all Bavarian populations against the Austrian population. Within the Bavarian populations no genetic differentiation could be detected and therefore, the taxonomic separation of the population in the north of Bavaria as a distinct subspecies seemed not to be very reasonable in the view of population genetics.
In chapter 6 we focused on the population dynamics of the strongly endangered perennial grassland herb Tephroseris integrifolia subsp. vindelicorum by using demographic, site-specific and climatic approaches. Long-term demographic investigations over five years in permanent plots gave valuable insights into magnitude and consequences of spatio-temporal fluctuations as well as demographic sensitivities associated with environmental conditions. Annual finite rates of increase strongly varied among years and sites, but on average both studied populations showed positive population developments (λ > 1). Recruitment was usually high and positively correlated with site-specific parameters such as percentage of bare ground, moss layer and Ellenberg indicator value for light. However, mean annual transition probabilities among different age stage categories revealed high mortality rates for recruits and determined this age stage category to be the most critical for population dynamic. Furthermore, individuals of Tephroseris integrifolia subsp. vindelicorum showed high sensitivities against climatic fluctuations. Reduced flowering rates seemed to result from lacking vernalization processes by low winter and early spring temperatures. Therefore, we concluded that long-term survival of Tephroseris integrifolia subsp. vindelicorum is well supported by grazing as management regime, which enables the creation of safe sites for germination, but due to its strong climatic sensitivity Tephroseris integrifolia subsp. vindelicorum is permanently facing the unpredictable threats by environmental stochasticity.
Finally, in chapter 7 we concluded with a comparison of population viability analyses for two steppe species, which demonstrated the importance of different and comprehensive scientific approaches in plant conservation to define best management recommendations. The chapter dealt also with perspectives for future scientific research. Especially the extension of genetic analyses on threatened species is required to increase the understanding of past processes and actual patterns of genetic variation. Large-scale genetic screenings of indigenous plant species are essential to localize hotspots of genetic biodiversity and ecologically important genetic regions. From obtained information, a network of best sites for genetic plant conservation throughout Europe could be identified by molecular markers and used for conserving genetic biodiversity. This may force the improvement of conservation priority settings and the selection of taxa which we focus our conservation activities on.
Conservation Genetics
Steppe
Population Genetics
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On the basis of allozyme and mtDNA sequence variation, we elucidated genetic relationships between two sympatric genetic types of Onychodactylus japonicus in Kinki and adjacent districts, and investigated their phylogeography. Allozymic analysis revealed the presence of two distinct genetic types (the SW-Honshu and Kinki groups) in this area, and their sympatric occurrence in three of 10 sampling sites. Fixed or nearly fixed allele differences in several loci strongly suggested reproductive isolation between the two types, although one hybrid specimen was found in a locality. Analyses of mtDNA using 194 specimens from 22 localities also demonstrated two genetic types. From phylogeographic and population genetic analyses, it was surmised that these two types diverged allopatrically, and secondarily contacted to become sympatric by the Pleistocene uplift of mountains. Our results indicate different specific status for these two types and separation of the Kinki group from O. japonicus, to which the SW-Honshu group belongs.
Type locality
Reproductive isolation
Population Genetics
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Abstract Understanding the phylogeography of a species requires not only elucidating patterns of genetic structure among populations, but also identifying the possible evolutionary events creating that structure. The use of a single phylogeographic test or analysis, however, usually provides a picture of genetic structure without revealing the possible underlying evolutionary causes. We used current analytical techniques in a sequential approach to examine genetic structure and its underlying causes in the bogus yucca moth Prodoxus decipiens (Lepidoptera: Prodoxidae). Both historical biogeography and recent human transplantations of the moth's host plants provided a priori expectations of the pattern of genetic structure and its underlying causes. We evaluated these expectations by using a progression of phylogenetic, demographic, and population genetic analyses of mtDNA sequence data from 476 individuals distributed across 25 populations that encompassed the range of P. decipiens. The combination of these analyses revealed that much of the genetic structure has evolved more recently than suggested by historical biogeography, has been influenced by changes in demography, and can be best explained by long distance dispersal and isolation by distance. We suggest that performing a suite of analyses that focus on different temporal scales may be an effective approach to investigating the patterns and causes of genetic structure within species.
Isolation by distance
Population Genetics
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Isolation by distance
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Conservation Genetics
Mediterranean Basin
Endemism
Biodiversity hotspot
Conservation Biology
Population Genetics
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