Nuclear Microsatellite Markers Research Articles

Genetic Diversity and Population Structural Analysis Reveal the Unique Genetic Composition of Populus tomentosa Elite Trees

Genetic diversity analysis provides the scientific basis for the preservation, evaluation, and utilization of the germplasm resources of tree species. We explored the genetic diversity and structure of Populus tomentosa elite trees in North China using 13 nuclear microsatellite markers. We compared nine groups of accessions including 20 originating from Beijing (BJ), 122 from Hebei (HB), 20 from Shandong (SD), 113 from Henan (HN), 270 from Shanxi (SX), 54 from Shaanxi (SAX), 8 from Gansu (GS), 10 from Anhui (AH), and 6 from Jiangsu (JS). All of the studied primer pairs were polymorphic and generated 125 alleles. Analyses of molecular variance revealed that 79%, 14%, and 8% of the total variation was due to variations within the individual, among individuals, and among populations, respectively. Based on principal coordinate and STRUCTURE cluster analyses, individuals distributed in the southern region (HN, SAX, AH, and JS) were roughly classified into one group, while those distributed in the northeastern region (BJ, HB, and SD) and northwestern regions (SX) were separately divided into one group each. Moreover, the northwestern region included two-thirds of the SX trees, and the remainder were in the northeast region. By analyzing genetic diversity and structure within populations, individuals with different genetic backgrounds were screened for constituent training populations (TRS), including broad allelic variation for related traits. This ensures that the genomic prediction model can accurately capture genetic effects and provide reliable predictions across a broad spectrum of genetic backgrounds. Therefore, our results will benefit genome breeding technology.

Comparison of population genetic structure of Pinus mugo Turra forest stands in the Giant Mountains by analysis of nSSR molecular marker data

Abstract Pinus mugo (dwarf mountain pine) communities in the protected area of Krkonoše National Park are extremely valuable. After extensive deforestation during the sixteenth to nineteenth centuries, P. mugo recovered naturally in some parts of the Giant Mountains, and in some places imported seeds were likely used for reforestation. To distinguish between native and possibly introduced local P. mugo populations, genetic variations between 12 populations from the Czech Sudeten part of the Giant Mountains and between the two populations from the Tatra Mountains were analysed using 12 nuclear microsatellite markers (nuclear simple sequence repeats). Based on the simple sequence repeat data, 146 alleles were found, and Shannon’s information index, number of private alleles, and expected heterozygosity (HE) of populations averaged 1.12, 0.16, and 0.53, respectively. Analysis of molecular variance indicated that most of the variation was detected within populations. Low levels of genetic differentiation were also observed (average FST = 0.023). The population structure was examined by Bayesian clustering. The results of STRUCTURE analysis confirmed that the introduced populations were different from the autochthonous populations. Some of the introduced Czech Sudeten populations had similar genetic structure as the more distant native populations from the Tatra Mountains. Our results provide important genetic information for the reconstruction of natural communities in the Giant Mountains.

Differentiation and Taxonomic Identification of Roburoid Oaks in the Caucasian and Crimean Regions Using Nuclear Microsatellite Markers

Differentiation and Taxonomic Identification of Roburoid Oaks in the Caucasian and Crimean Regions Using Nuclear Microsatellite Markers

Genetic diversity and shallow genetic differentiation of the endangered scaly-sided merganser Mergus squamatus.

Examining patterns of genetic diversity are crucial for conservation planning on endangered species, while inferring the underlying process of recent anthropogenic habitat modifications in the context potential long-term demographic changes remains challenging. The globally endangered scaly-sided merganser (SSME), Mergus squamatus, is endemic to a narrow range in Northeast Asia, and its population has recently been contracted into two main breeding areas. Although low genetic diversity has been suggested in the Russian population, the genetic status and demographic history of these individuals have not been fully elucidated. We therefore examined the genetic diversity and structure of the breeding populations of the SSME and investigated the relative importance of historical and recent demographic changes to the present-day pattern of genetic diversity. Using 10 nuclear microsatellite (SSR) markers and mitochondrial DNA (mtDNA) control region sequences, we found limited female-inherited genetic diversity and a high level of nuclear genetic diversity. In addition, analysis of both markers consistently revealed significant but weak divergence between the breeding populations. Inconsistent demographic history parameters calculated from mtDNA and bottleneck analysis results based on SSR suggested a stable historical effective population size. By applying approximate Bayesian computation, it was estimated that populations started to genetically diverge from each other due to recent fragmentation events caused by anthropogenic effects rather than isolation during Last Glacial Maximum (LGM) and post-LGM recolonization. These results suggest that limited historical population size and shallow evolutionary history may be potential factors contributing to the contemporary genetic diversity pattern of breeding SSME populations. Conservation efforts should focus on protecting the current breeding habitats from further destruction, with priority given to both the Russian and Chinese population, as well as restoring the connected suitable breeding grounds.

Pleistocene climate oscillations have shaped the expansion and contraction speciation model of the globose Eriosyce sect. Neoporteria cacti in Central Chile.

Pleistocene climatic oscillations, characterized by arid (interglacial) and pluvial (glacial) phases, have profoundly impacted the floras of Mediterranean climates. Our study investigates the hypothesis that these climatic extremes have promoted phases of range expansion and contraction in the Eriosyce sect. Neoporteria, resulting in pronounced genetic structuring and restricted gene flow. Utilizing nuclear microsatellite markers, we genotyped 251 individuals across 18 populations, encompassing all 14 species and one subspecies within the Eriosyce sect. Neoporteria. Additionally, Species Distribution Models (SDMs) were employed to reconstruct past (Last Interglacial, Last Glacial Maximum, Mid-Holocene) and current potential distribution patterns, aiming to delineate the climatic influences on species' range dynamics. The gene flow analysis disclosed disparate levels of genetic interchange among species, with marked restrictions observed between entities that are geographically or ecologically separated. Notably, E. subgibbosa from Hualpen emerged as genetically distinct, warranting its exclusion for clearer genetic clustering into north, central, and south clusters. The SDMs corroborated these findings, showing marked range expansions during warmer periods and contractions during colder times, indicating significant shifts in distribution patterns in response to climatic changes. Our findings emphasize the critical role of Pleistocene climatic fluctuations in driving the dynamic patterns of range expansions and contractions that have led to geographic isolation and speciation within the Eriosyce sect. Neoporteria. Even in the face of ongoing gene flow, these climate-driven processes have played a pivotal role in sculpting the species' genetic architecture and diversity. This study elucidates the complex interplay between climatic variability and evolutionary dynamics among Mediterranean cacti in central Chile, highlighting the necessity of considering historical climatic millenial oscillations in conservation and evolutionary biology studies.

Genetic Differentiation and Relationship among Castanopsis chinensis, C. qiongbeiensis, and C. glabrifolia (Fagaceae) as Revealed by Nuclear SSR Markers.

Castanopsis chinensis (Spreng.) Hance is widespread in the subtropical forests of China. Castanopsis qiongbeiensis G.A. Fu and Castanopsis glabrifolia J. Q. Li & Li Chen are limited to the coastal beaches of Wenchang county in the northeast of Hainan Island, and have similar morphological characteristics to C. chinensis. It is supposed that C. qiongbeiensis and C. glabrifolia are closely related to C. chinensis. In the present study, the genetic differentiation, gene flow, and genetic relationship of C. chinensis, C. qiongbeiensis, and C. glabrifolia were investigated by using 15 nuclear microsatellite markers; a total of 308 individuals from 17 populations were sampled in the three species. The allelic variation of nuclear microsatellites revealed moderate but significant genetic differentiation (FCT = 0.076) among C. chinensis, C. qiongbeiensis, and C. glabrifolia, and genetic differentiation between C. chinensis and C. glabrifolia was larger than that between C. chinensis and C. qiongbeiensis. Demographic simulations revealed unidirectional gene flow from C. chinensis to C. glabrifolia and C. qiongbeiensis, which highlight dispersal from mainland to island. The isolation effect of Qiongzhou Strait increased the genetic differentiation of species on both sides of the strait; however, the differentiation was diminished by gene flow that occurred during the historical period when Hainan Island was connected to mainland China. Our results supported the argument that C. glabrifolia should be considered an independent species and argued that C. qiongbeiensis should be regarded as an incipient species and independent conservation unit.

Population genetic structure of bottlenose and whitespotted wedgefishes from the Southwest Indian Ocean using a dual marker approach

Wedgefishes (Rhinidae) are threatened by unsustainable fishing globally, and especially in the Southwest Indian Ocean (SWIO), due to their high-value fins in the shark trade. The whitespotted wedgefish Rhynchobatus djiddensis and the bottlenose wedgefish R. australiae are both classified as Critically Endangered on the IUCN Red List of Threatened Species, yet a lack of species-specific knowledge and taxonomic uncertainty still exists within this genus. Genetic approaches aid in taxonomic classification and identifying distinct populations for targeted conservation. Morphological specimen identification of samples (n = 189) collected across the SWIO was confirmed based on the cytochrome oxidase c subunit I (COI) and/or nicotinamide adenine dehydrogenase subunit 2 (ND2) gene regions. The genetic diversity and population structure within and between species and sampling locations were investigated using a dual marker approach: (1) 2 concatenated mitochondrial gene regions, namely COI and the control region (n = 117), and (2) 9 nuclear microsatellite markers (n = 146). The overall genetic diversity was moderate, with an indication that different evolutionary forces are at play on a mitochondrial versus nuclear level. The 2 species were delineated based on both marker types, and for R. djiddensis, the sampling locations of South Africa and Mozambique were genetically homogeneous. For R. australiae, significant differentiation was found between sampling locations, with Madagascar and Tanzania being genetically the most similar. This information provides critical insights into the distribution range and population structure of the whitespotted wedgefish species complex that can support the sustainable management of wedgefishes.

Development and characterization of nuclear microsatellite markers for the African walnut Coula edulis Baill (Coulaceae).

Coula edulis Baill (Coulaceae) is a common tree species in the Guineo-Congolian forests producing an edible fruit known as African walnut, which is an important food and income resource for rural populations. However, the species suffers from a deficit of natural regeneration. We developed here nuclear microsatellite markers for C. edulis to be able to study the genetic structure of its natural populations and gene flow. A genomic library was obtained using the Illumina platform, and 21 polymorphic microsatellite loci were developed. The polymorphic microsatellites displayed eight to 22 alleles per locus (average: 14.2), with a mean expected heterozygosity ranging from 0.33 to 0.72 in five populations from Central and West Africa. The high polymorphism of the nuclear microsatellite markers developed makes them useful to investigate gene flow and the organization of genetic diversity in C. edulis, and to assess whether particular genetic resources require conservation efforts.

The Poultry Red Mite, Dermanyssus gallinae, travels far but not frequently, and takes up permanent residence on farms

Management of Dermanyssus gallinae, a cosmopolitan hematophagous mite responsible for damage in layer poultry farming, is hampered by a lack of knowledge of its spatio-temporal population dynamics. Previous studies have shown that the circulation of this pest between farms is of strictly anthropogenic origin, that a mitochondrial haplogroup has been expanding on European farms since the beginning of the 21st century and that its local population growth may be particularly rapid. To refine our understanding of how D. gallinae spreads within and among farms, we characterized the genetic structure of mite populations at different spatial scales and sought to identify the main factors interrupting gene flow between poultry houses and between mitochondrial haplogroups. To this end, we selected and validated the first set of nuclear microsatellite markers for D. gallinae and sequenced a region of the CO1-encoding mitochondrial gene in a subsample of microsatellite-genotyped mites. We also tested certain conditions required for effective contamination of a poultry house through field experimentation, and conducted a survey of practices during poultry transfers. Our results confirm the role of poultry transport in the dissemination of mite populations, but the frequency of effective contamination after the introduction of contaminated material into poultry houses seems lower than expected. The high persistence of mites on farms, even during periods when poultry houses are empty and cleaned, and the very large number of nodes in the logistic network (large number of companies supplying pullets or transporting animals) undoubtedly explain the very high prevalence on farms. Substantial genetic diversity was measured in farm populations, probably as a result of the mite's known haplodiploid mode of sexual reproduction, coupled with the dense logistic network. The possibility of the occasional occurrence of asexual reproduction in this sexually reproducing mite was also revealed in our analyses, which could explain the extreme aggressiveness of its demographic dynamics under certain conditions.

Genetic diversity and population structure in Quercus suber L. revealed by nuclear microsatellite markers and generation of a core collection

Genetic diversity and population structure in Quercus suber L. revealed by nuclear microsatellite markers and generation of a core collection

Human‐associated genetic landscape of walnuts in the Himalaya: implications for conservation and utilization

AbstractAimsA comprehensive understanding of the genetic variation of walnuts (Juglans regia and J. sigillata) in the Himalaya and its potential drivers are essential for the conservation and sustainable utilization of these plant genetic resources. In this study, we aimed to uncover the genetic landscape of walnuts and potential drivers in the Himalaya for better utilization, awareness, sustainable management and conservation of the extant genetic resources of walnuts in the vast Himalayan landscape.LocationThe Himalaya biodiversity hotspot.MethodsA total of 1410 wild or feral walnut trees from 65 populations of J. regia and J. sigillata across four countries in the Himalaya were collected. The genetic diversity, population structure, hybridization and gene flow were thoroughly investigated based on the chloroplast genome and 31 nuclear microsatellite markers. The patterns and drivers of the walnut genetic landscape were further explored.ResultsWe detected three genetic groups of J. regia (JR1, JR2, JR3), one of J. sigillata (JS) and two hybrid types (JR1 × JS and JR3 × JS) of walnut in the Himalaya, with the western Himalaya identified as the genetic diversity hotspot of J. regia. The spatial genetic pattern of the J. regia was significantly influenced by geographic and climatic factors. Human‐mediated dispersal probably promoted the hybridization and gene introgression between J. regia and J. sigillata, which reshaped the genetic landscape of walnut populations in the Himalaya.Main ConclusionsThe extant genetic landscape of walnuts in the Himalaya was driven by natural and anthropogenic forces. Regarding conservation, the western and eastern Himalaya are the genetic reservoir of J. regia and J. sigillata, and hence, pure individuals should be urgently protected from frequent hybridization and introgression. In addition, we propose the utilization of natural hybrid resources coupled with new breeding techniques that combine genomic and phenotypic data.

Anthropogenic and natural disturbances increase local genetic diversity in an early spring geophyte (Ficaria verna Huds)

AbstractThe tetraploid Ficaria verna is a common spring geophyte in central Europe and is considered invasive in the USA and Canada. It is considered an almost seed‐sterile taxon, relying on vegetative reproduction by underground tubers and aerial bulbils. Recent studies have revealed high levels of population genetic diversity in F. verna, raising the question of how genetic diversity is maintained and which factors may be responsible for the observed patterns. Polymorphic nuclear microsatellite markers were established to define multi‐locus genotypes (MLGs), to analyze fine‐scale spatial genetic structure (SGS) using grid and cross‐sampling schemes, and to quantify genetic diversity within and between nine populations with different disturbance regimes in central Germany. In total, 115 MLGs were identified among a total of 347 samples. The G/N ratio varied between 0.16 and 0.70 among populations, and in each population several unique MLGs occurred. Genotypes were highly intermingled within populations, suggesting a “guerrilla” dispersal strategy. Significant SGS (negative regression slope of kinship coefficients against inter‐individual distances) was found in four out of nine populations in fine‐scale cross‐sampling (up to 4 m) and in only one population in grid sampling (up to 14.6 m). No single MLG was found in more than one population, while many alleles were shared between populations. Within‐population clonal and allelic diversity increased with greater exposure to both anthropogenic and natural disturbances. Regular gap openings, facilitated propagule establishment, and propagule dispersal by water and mowing machines are likely important factors explaining the positive effects of disturbance on local genetic diversity of F. verna.

Apomixis goes a long way: Genetic evidence of persistence and long‐distance seed dispersal in an ancient landscape

AbstractAimApomixis is a widespread trait in extreme environments worldwide, yet phylogeographical studies for species exhibiting these complex reproductive systems are still limited to temperate zones in the Northern Hemisphere. Through analyses of a combination of adult plants and seedlings, and nuclear and chloroplast DNA, we assessed the contemporary genetic outcomes of apomixis and phylogeographical patterns in an arid unglaciated landscape to understand the evolutionary trajectory of apomictic species.LocationPilbara bioregion, north‐western Australia.TaxonSenna glutinosa subsp. glutinosa.Materials and MethodsSpatial patterns of genetic diversity and differentiation in three chloroplast regions and 17 nuclear microsatellite markers were evaluated in 480 plants from 20 populations of S. glutinosa subsp. glutinosa across the Pilbara bioregion. We also germinated and genotyped seed for a progeny analysis to quantify polyembryony and the relative frequency of asexual versus sexual reproduction.ResultsWe found frequent polyembryony and a high proportion of asexual offspring (84.56%), resulting in low within‐population genotypic diversity. The nuclear dataset identified 72 multilocus lineages (MLLs) with moderate pairwise population genetic fixation and low differentiation among populations with no geographically structured genetic clustering. Chloroplast DNA showed high haplotype diversity and a widespread distribution of haplotypes. Only one peripheral population presented a single unique haplotype and MLL.Main ConclusionsAnalysis of this woody perennial in an arid landscape shows the influence of apomixis on genetic patterns and species persistence. Haplotype diversity was indicative of long‐term persistence within the ancient Pilbara region. Widespread distribution of haplotypes and sharing of several nuclear MLLs among distant populations indicated extensive seed dispersal throughout the study area. The combination of polyploidy, facultative apomixis and extensive seed dispersal maintains genetic variability within local populations and promotes the spread of advantageous genotypes across wide geographical distances. Therefore, apomixis, rather than an evolutionary ‘dead‐end’, can be regarded as a mechanism facilitating evolutionary success of apomictic species in extreme and complex environments.

Nuclear and chloroplast DNA phylogeography reveals high genetic diversity and postglacial range expansion in Quercus mexicana.

Phylogeographical studies are fundamental for understanding factors that influence the spatial distribution of genetic lineages within species. Population expansions and contractions, distribution shifts, and climate changes are among the most important factors shaping the genetic compositions of populations. We investigated the phylogeography of an endemic oak, Quercus mexicana (Fagaceae), which has a restricted distribution in northeastern Mexico along the Sierra Madre Oriental and adjacent areas. Nuclear and chloroplast DNA microsatellite markers were used to describe the genetic diversity and structure of 39 populations of Q. mexicana along its entire distribution area. We tested whether population expansion or contraction events influenced the genetic diversity and structure of the species. We also modeled the historical distributional range of Q. mexicana (for the Mid Holocene, the Last Glacial Maximum, and the Last Interglacial) to estimate the extent to which climate fluctuations have impacted the distribution of this oak species. Our results revealed high genetic diversity and low genetic structure in Q. mexicana populations. Ecological niche models suggested historical fluctuations in the distributional range of Q. mexicana. Historical range changes, gene flow, and physical barriers seem to have played an important role in shaping the phylogeographic structure of Q. mexicana. Our study indicates that the genetic structure of Q. mexicana may have been the result of responses of oak trees not only to heterogeneous environments present in the Sierra Madre Oriental and adjacent areas, but also to elevational and latitudinal shifts in response to climate changes in the past.

Can a Forest Tree Species Progeny Trial Serve as an Ex Situ Collection? A Case Study on Alnus glutinosa

Scientifically informed decisions for the long-term conservation of extant genetic diversity should combine in situ and ex situ conservation methods. The aim of the present study was to assess if a progeny plantation consisting of several open pollinated (OP) families and established for breeding purposes can also serve as an ex situ conservation plantation, using the case study of a Lithuanian progeny trial of Alnus glutinosa, a keystone species of riparian ecosystems that warrants priority conservation actions. We employed 17 nuclear microsatellite (Simple Sequence Repeat) markers and compared the genetic diversity and copy number of the captured alleles of 22 OP progeny families from this plantation, with 10 wild A. glutinosa populations, originating from the two provenance regions of the species in Lithuania. We conclude that the progeny plantation could be used as an ex situ plantation for the A. glutinosa populations from the first provenance region (represented by eight genetic conservation units (GCU)). Based on the present study’s results, we can expect that the A. glutinosa progeny plantation harbors enough genetic diversity of wild A. glutinosa populations from the first provenance region. This progeny plantation can serve as a robust ex situ collection containing local alleles present in at least one wild population with at least 0.05 frequency with 25 replications.

Patterns of genetic diversity and structure of Eucalyptus grandis breeding population in Kenya: Implication for genetic improvement

Eucalyptus grandis is an important commercial plantation tree species providing raw materials for many industrial products. The species is widely cultivated in the tropics because of its wood quality and adaptability to wider climatic conditions, and is currently undergoing genetic improvement in Kenya for first growth and superior wood quality. Generally, tree breeding operations involve recurrent selection of genetically superior individuals, which potentially alters genetic diversity in the breeding populations. It is therefore essential to determine the genetic diversity of breeding populations to support improvement programmes. We evaluated the genetic diversity and structure of 250 individuals from five first generation breeding populations of E. grandis in Kenya using seventeen nuclear microsatellite markers. The microsatellite markers revealed an average polymorphic information content (PIC) of 0.826, confirming their suitability for discriminating the genotypes and populations. High genetic diversity was found within all the breeding populations. The number of alleles per population (Na), observed heterozygosity (Ho), expected heterozygosity (He), and Shannon’s information index (I) averaged at 6.9, 0.801, 0.821, and 1.662, respectively. The findings indicate that the breeding population has high levels of genetic variability offering possibilities to develop advanced generation breeding programmes for the species. Furthermore, lower fixation index (F) was detected in the seed trees (-0.101) than their offspring (0.121), suggesting selection against inbred individuals between seedling and adult stages. The genetic differentiation among the breeding populations was low and non-significant (Rst = 0.017; P = 0.117), indicating close genetic relationship among the germplasm used to establish the breeding populations. The studied breeding populations are viable for genetic improvement; however, new genetic infusions are recommended to expand the gene pool in the subsequent breeding generations.

Relict stands of Central European oaks: Unravelling autochthony and genetic structure based on a multi-population study

Central European white oaks expanded rapidly after the last glacial period and reached their current distribution range during the early Holocene. They have been an important resource of timber, fuelwood and animal feed for humans, who actively promoted their presence in forests and other landscape types at least since the early historical times. Besides stands with intensive management, putatively relict populations of three native oak species can be found on unproductive sites with restricted accessibility. Here, we apply chloroplast and nuclear microsatellite markers in order to address the autochthony of relict and managed stands and compare the spatial distribution of genetic variation between them. Based on data from more than 150 populations, we demonstrate that oak autochthony was preserved throughout historical times which is likely the result of traditional silvicultural treatment. This is supported by the fact that the spatial pattern of chloroplast haplotype distribution still reflects the post-glacial recolonization in both relict and old managed stands. We observed significant admixture of haplotypes only in stands established after the Second World War, which is attributable to the transfer of reproductive material used for afforestation. In terms of nuclear genetic variation, we observed marked differences among species. Quercus pubescens exhibited a pronounced genetic structure. Genetic drift and limited gene flow among its small and isolated populations in our study area might have contributed to this pattern. Varying extent of genetic introgression with other sympatric oak species could offer an additional explanation. On the contrary, the gene pools of Q. petraea and Q. robur are highly homogenous, displaying only weak isolation-by-distance. We found no significant differences of genetic diversity and differentiation between relict and managed stands. This suggests that seed transfer mostly occurred within our study area, even in those stands established in post-war times, verifying previous findings which point out limited human interference. We recommend consideration of population genetic structure for gene conservation, with a finer resolution of gene conservation units needed for Q. pubescens due to its spatial genetic structure. Both relict and old managed stands, species-pure or mixed, are suitable for conservation, as they host autochthonous gene pools. Coppice-with-standard management could contribute to preservation of autochthony. In the face of climate change, it is also important to maintain the evolutionary potential of the stands, by facilitating generative reproduction and allowing for hybridization in mixed stands.

Species Delimitation and Genetic Relationship of Castanopsis hainanensis and Castanopsis wenchangensis (Fagaceae).

Castanopsis is one of the most common genus of trees in subtropical evergreen broad-leaved forests and tropical monsoon rainforests in China. Castanopsis hainanensis and Castanopsis wenchangensis are endemic to Hainan Island, but they were once confused as the same species due to very similar morphologies. In this study, nuclear microsatellite markers and chloroplast genomes were used to delimit C. hainanensis and C. wenchangensis. The allelic variations of nuclear microsatellites revealed that C. hainanensis and C. wenchangensis were highly genetically differentiated with very limited gene admixture. Both showed higher genetic diversity within populations and lower genetic diversity among populations, and neither had further population genetic structure. Furthermore, C. wenchangensis and C. hainanensis had very different chloroplast genomes. The independent genetic units, very limited gene admixture, different distribution ranges, and distinct habitats all suggest that C. wenchangensis and C. hainanensis are independent species, thus they should be treated as distinct conservation units.

Introgressive hybridization levels of Tilapiine species in Lake Victoria basin, Kenya inferred from microsatellite and mitochondrial DNA genotyping based on next-generation sequencing

Despite their high abundance and species richness, tilapiines have been compromised by various factors especially overfishing, climate change, and uncontrolled fish transfers and introductions. Fish introductions have negatively impacted native tilapiine populations through competition, predation, hybridization, and introgression compromising their genetic integrity. The hybridization levels of different tilapiines in the Lake Victoria basin remain relatively understudied. The study utilized nuclear microsatellite and mitochondrial DNA (mtDNA) genetic markers to investigate hybridization signals and compare the genetic diversity of different tilapiines in Lake Victoria, Kenya, using next-generation sequencing. Low levels of hybridization from Oreochromis niloticus into other Oreochromis species were detected by Bayesian clustering analysis and principal coordinate analysis (PCoA). The results contribute to the need for conservation measures for these fish species.

Genetic and morphological diversity in populations of Annona senegalensis Pers. occurring in Western (Benin) and Southern (Mozambique) Africa.

Understanding morpho-genetic diversity and differentiation of species with relatively large distributions is crucial for the conservation and sustainable management of their genetic resources. The present study focused on Annona senegalensis Pers., an important multipurpose wild plant, distributed exclusively in natural ecosystems but facing several threats. The study assessed the genetic and morphological diversity, structure, and differentiation of the species in populations from Western (Benin) and Southern (Mozambique) Africa. The material was evaluated to ascertain the environmental (climatic) determinants of the variation within this species. Four sub-populations comprised of 154 individuals were phenotyped based on nineteen plant, fruit, and leaf morphological traits and further genotyped using ten polymorphic nuclear microsatellite (nSSR) markers. The results indicated strong differences in plant, fruit, and leaf morphological traits between Western and Southern populations. Furthermore, the studied populations were characterized by high genetic diversity, with an average genetic diversity index of 1.02. Western populations showed higher heterozygosity values (0.61-0.71) than Southern populations (0.41-0.49). Western and Southern populations were clearly differentiated into two different genetic groups, with further genetic subdivisions reflecting four sub-populations. Genetic variation between regions (populations) was higher (69.1%) than among (21.3%) and within (9.6%) sub-populations. Four distinct morphological clusters were obtained, which were strongly associated with the four genetic groups representing each sub-population. Climate, mainly precipitation and temperature indexes, explained the relatively higher variation found in morphological traits from Western (40.47%) in relation to Southern (27.98%) populations. Our study suggests that both environmental and genetic dynamics play an important role in the development of morphological variation in A. senegalensis.