Low Levels Of Genetic Diversity Research Articles

History of Diversification and Adaptation from North to South Revealed by Genomic Data: Guanacos from the Desert to Sub-Antarctica.

The increased availability of quality genomic data has greatly improved the scope and resolution of our understanding of the recent evolutionary history of wild species adapted to extreme environments and their susceptibility to anthropogenic impacts. The guanaco (Lama guanicoe), the largest wild ungulate in South America, is a good example. The guanaco is well adapted to a wide range of habitats, including the Sechura Desert, the high Andes Mountains to the north, and the extreme temperatures and conditions of Navarino Island to the south. Guanacos also have a long history of overexploitation by humans. To assess the evolutionary impact of these challenging habitats on the genomic diversity, we analyzed 38 genomes (∼10 to 16×) throughout their extensive latitudinal distribution from the Sechura and Atacama Desert to southward into Tierra del Fuego Island. These included analyses of patterns of unique differentiation in the north and geographic region further south with admixture among L. g. cacsilensis and L. g. guanicoe. Our findings provide new insights on the divergence of the subspecies ∼800,000 yr BP and document two divergent demographic trajectories and to the initial expansion of guanaco into the more southern portions of the Atacama Desert. Patagonian guanacos have experienced contemporary reductions in effective population sizes, likely the consequence of anthropogenic impacts. The lowest levels of genetic diversity corresponded to their northern and western limits of distribution and some varying degrees of genetic differentiation. Adaptive genomic diversity was strongly linked with environmental variables and was linked with colonization toward the south followed by adaptation.

Tests of evolutionary and genetic rescue using flour beetles, Tribolium castaneum, experimentally evolved to thermal conditions.

Small, isolated populations are often characterised by low levels of genetic diversity. This can result in inbreeding depression and reduced capacity to adapt to changes in the environment, and therefore higher risk of extinction. However, sometimes these populations can be rescued if allowed to increase in size or if migrants enter, bringing in new allelic variation and thus increasing genetic diversity. This study uses experimental manipulation of population size and migration to quantify their effects on fitness in a challenging environment to better understand genetic rescue. Using small, replicated populations of Tribolium castaneum experimentally evolved to different temperature regimes we tested genetic and demographic rescue, by performing large-scale manipulations of population size and migration and examining fitness consequences over multiple generations. We measured fitness in high temperature (38°C) thermal lines maintained at their usual 'small' population size of N = 100 individuals, and with 'large' scaled up duplicates containing N≈10,000 individuals. We compared these large lines with and without migration (m = 0.1) for 10 generations. Additionally, we assessed the effects of outcrossing at an individual level, by comparing fitness of hybrid (thermal line × stock) offspring with within-line crosses. We found that, at the population level, a rapid increase in the number of individuals in the population resulted in reduced fitness (represented by reproductive output and survival through heatwave conditions), regardless of migration. However, at an individual level, the hybrid offspring of migrants with native individuals generally demonstrated increased longevity in high temperature conditions compared with individuals from thermal selection lines. Overall, these populations showed no evidence that demographic manipulations led to genetic or evolutionary rescue. Following the effects of migration in individuals over several generations may be the next step in unravelling these conflicting results. We discuss these findings in the context of conservation intervention.

Exploring the genetic diversity pattern of PvEBP/DBP2: A promising candidate for an effective Plasmodium vivax vaccine

Malaria remains a public health challenge. Since many control strategies have proven ineffective in eradicating this disease, new strategies are required, among which the design of a multivalent vaccine stands out. However, the effectiveness of this strategy has been hindered, among other reasons, by the genetic diversity observed in parasite antigens. In Plasmodium vivax, the Erythrocyte Binding Protein (PvEBP, also known as DBP2) is an alternate ligand to Duffy Binding Protein (DBP); given its structural resemblance to DBP, EBP/DBP2 is proposed as a promising antigen for inclusion in vaccine design. However, the extent of genetic diversity within the locus encoding this protein has not been comprehensively assessed. Thus, this study aimed to characterize the genetic diversity of the locus encoding the P. vivax EBP/DBP2 protein and to determine the evolutionary mechanisms modulating this diversity. Several intrapopulation genetic variation parameters were estimated using 36 gene sequences of PvEBP/DBP2 from Colombian P. vivax clinical isolates and 186 sequences available in databases. The study then evaluated the worldwide genetic structure and the evolutionary forces that may influence the observed patterns of genetic variation. It was found that the PvEBP/DBP2 gene exhibits one of the lowest levels of genetic diversity compared to other vaccine-candidate antigens. Four major haplotypes were shared worldwide. Analysis of the protein's 3D structure and epitope prediction identified five regions with potential antigenic properties. The results suggest that the PvEBP/DBP2 protein possesses ideal characteristics to be considered when designing a multivalent effective antimalarial vaccine against P. vivax.

Determining evolutionary origin and phylogenetic relationships of mallard-like ducks of Oceania, greater Indonesia, and the Philippines with ddRAD-seq data

AimWe aim to determine the evolutionary origins and population genetics of mallard-like ducks of Oceania, greater Indonesia, and the Philippines. LocationOceania, greater Indonesia, and the Philippines. TaxonMallard (Anas platyrhynchos), Pacific black duck (A. superciliosa spp.), and Philippine duck (A. luzonica) MethodsThousands of nuclear ddRAD-seq loci and the mitochondrial DNA control region were assayed across individuals representative of each species’ range. We assessed population structure and phylogenetic relationships, as well as estimated demographic histories to reconstruct the biogeographical history of each species. ResultsPhilippine and Pacific black ducks represent unique genetic lineages that diverged from the mallard 1–2 million years ago. We find no support for the Philippine duck representing a hybrid species as once posited; however, their low levels of genetic diversity requires further attention. We find a lack of substructure among Philippine ducks. However, we found pronounced differentiation between subspecies of Pacific black ducks, especially between A. s. superciliosa from New Zealand and A. s. rogersi from Australia, Tasmania, Papua New Guinea, and Timor-Leste. Anas superciliosa pelewensis gave mixed results; individuals from the Solomon Islands were differentiated from the other subspecies, but those from the island of Aunu’u, American Samoa, were genetically more similar to A. s. rogersi than A. s. pelewensis samples from the Solomon Islands. Finally, we find limited evidence of interspecific gene flow at evolutionary scales, and mallard introgression among contemporary samples. Main conclusionsMallard-like ducks radiated across Oceania, greater Indonesia, and the Philippines within the last 2 million years. Only the Pacific black duck showed unique sub-structuring that largely followed known sub-species ranges, except for A. s. pelewensis. We posit that the high interrelatedness among Solomon Island samples suggests that their genetic distinctiveness may simply be the result of high levels of genetic drift. In contrast, we conclude that mainland Australian Pacific black ducks were the most likely source for the recent colonization of American Samoa. As a result, our findings suggest that either the A. s. pelewensis subspecies designations and/or its geographical range may require re-evaluation. Continued re-evaluation of evolutionary and taxonomic relationships is necessary when attempting to reconstruct and understand biogeographical histories, with important implications towards any attempts to implement conservation strategies.

Population structure, genetic diversity and evolutionary history of the narrow endemic squirrel Sciurus meridionalis

Endemic species and their genetic diversity are critical components of global biodiversity, yet they usually face a higher risk of decline and extinction than species with broader distributions. Loss of genetic diversity within geographically restricted and fragmented ranges plays a significant role in driving endemic species to extinction, threatening their ability to adapt to environmental challenges. Hence, considering genetic diversity and its spatial distribution within populations is mandatory in planning conservation actions for narrow endemic species. Here, we investigated the population genetic diversity, structure and evolutionary history of the Calabrian black squirrel Sciurus meridionalis, a species endemic to the Calabrian region in the south of the Italian peninsula. A fine-scale sampling procedure was carried out throughout the whole species range, and genetic variation was assessed from multiple mitochondrial and nuclear markers. Phylogeographic and population structure analyses showed three evolutionary significant units within the current species range, each characterised by extremely low levels of genetic diversity. Bayesian phylogeographic analyses suggested that Calabrian black squirrel populations experienced a range fragmentation during the Last Glacial Maximum (∼20 ka), which geographically mirrors the three main mountain massifs within the species range. Historical demographic reconstructions revealed a recent and still ongoing demographic expansion for Calabrian black squirrel populations, likely promoted by a concurrent expansion of the Calabrian black pine in this area. Overall, our findings clarify the designation of the evolutionary significant units for a narrow endemic squirrel and underscore the importance of analysing range-wide population genetic data and considering species interactions when defining management strategies for narrow endemic species’ conservation.

De novo assembly and analysis of Sonneratia ovata genome and population analysis

Mangroves are an important part of coastal and estuarine ecosystems where they serve as nurseries for marine species and prevent coastal erosion. Here we report the genome of Sonneratia ovata, which is a true mangrove that grows in estuarine environments and can tolerate moderate salt exposure. We sequenced the S. ovata genome and assembled it into chromosome-level scaffolds through the use of Hi-C. The genome is 212.3 Mb and contains 12 chromosomes that range in size from 12.2 to 23.2 Mb. Annotation identified 29,829 genes with a BUSCO completeness of 95.9%. We identified salt genes and found copy number expansion of salt genes such as ADP-ribosylation factor 1, and elongation factor 1-alpha. Population analysis identified a low level of genetic variation and a lack of population structure within S. ovata.

Exploring mtDNA Databases to Evaluate the Population Structure and Genetic Diversity of Tursiops truncatus in the Atlantic Ocean: Implications for the Conservation of a Small, Offshore Population

Inshore and offshore bottlenose dolphin, Tursiops truncatus, ecotypes were distinguished through genetics, distribution, diet, morphology, diversity, and social behaviors. Although T. truncatus is a widely studied species, few studies have focused on offshore populations. Offshore biodiversity is frequently neglected due to the difficulty of data collection, and therefore, it is challenging to assess how threatened these populations are. A small, offshore population of dolphins residing around the Saint Peter Saint Paul Archipelago (SPSPA) in the middle of the Atlantic Ocean has been monitored for several years, and a decrease in the number of dolphin sightings has recently been noticed. We analyzed a comprehensive mtDNA control-region sequence dataset for this species to infer the conservation status and better understand the relationships between the SPSPA population and other offshore populations. We assessed the genetic diversity and population structure of the bottlenose dolphin from inshore and offshore populations of the Atlantic Ocean. Offshore populations are more genetically diverse and have less variation between populations than inshore populations. The offshore populations share haplotypes, indicating potential gene flow. However, the SPSPA population presented the lowest levels of genetic diversity between populations. The conservation status of the SPSPA population is concerning, and it is necessary to apply effective management strategies to guarantee its protection.

Emerging patterns of genetic diversity in the critically endangered Malayan tiger (Panthera tigris jacksoni)

Southeast Asia experiences some of the highest deforestation in the world. Loss of tropical forest typically leads to widespread habitat fragmentation, with detrimental effects on dispersal ability and gene flow—particularly for large carnivores. We conducted mtDNA and microsatellite analysis to assess—for the first time—contemporary patterns of genetic diversity in the Malayan tiger. We collected 295 suspected carnivore samples in Peninsular Malaysia, from which we identified 26 as originating from tiger using 16 polymorphic microsatellite loci, comprising 22 individual tigers. Despite limitations of the study, our findings suggest tiger subpopulations in the north of the peninsula maintain some genetic connectivity and migration between two putative geographic subpopulations in the Main Range and Greater Taman Negara, with negligible population segregation due to dispersal barriers such as road infrastructure. We identified consistently lower levels of genetic diversity in tigers in the Greater Taman Negara region compared to tigers in the Main Range and small but emerging differences in nuclear and mitochondrial genetic diversity. Our mtDNA haplotype and nuclear DNA analyses suggest the levels of genetic diversity in Malayan tigers may be amongst some of the lowest of the surviving tiger subspecies, though the study is limited both in scale and genomic loci. Our findings are consistent with an expected lag between the rapid decline of tigers in Peninsular Malaysia by over 95% in the last 70 years and observed differences in their levels of genetic diversity.

Forest fragmentation causes an isolated population of the golden takin (Budorcas taxicolor bedfordi Thomas, 1911) (Artiodactyla: Bovidae) in the Qinling Mountains (China)

Budorcas taxicolor bedfordi is a rare animal uniquely distributed in the Qinling Mountains (China). Human disturbance and habitat fragmentation have directly affected the survival of B. t. bedfordi. It is urgent to clarify the genetic diversity and genetic structure of the B. t. bedfordi population and implement effective conservation measures. In this study, 20 new polymorphic microsatellite loci were isolated by Illumina sequencing. The genetic diversity and population structure of 124 B. t. bedfordi individuals from three populations (Niubeliang population, Zhouzhi population, and Foping population) were analysed according to these 20 microsatellite loci. Our results indicated that B. t. bedfordi had a low level of genetic variability and that there was inbreeding in the three populations. The population genetic structure analyses showed that the Niubeliang population had a trend of differentiation from other populations. National roads can affect population dispersal, while ecological corridors can promote population gene exchange. None of the three B. t. bedfordi populations experienced bottleneck effects. For conservation management plans, the Zhouzhi population and Foping population should be considered one management unit, and the Niubeliang population should be considered another management unit. We suggest building an ecological corridor to keep the habitat connected and formulating tourism management measures to reduce the influence of human disturbance on B. t. bedfordi.

A reduced SNP panel optimised for non-invasive genetic assessment of a genetically impoverished conservation icon, the European bison.

The European bison was saved from the brink of extinction due to considerable conservation efforts since the early twentieth century. The current global population of > 9500 individuals is the result of successful ex situ breeding based on a stock of only 12 founders, resulting in an extremely low level of genetic variability. Due to the low allelic diversity, traditional molecular tools, such as microsatellites, fail to provide sufficient resolution for accurate genetic assessments in European bison, let alone from non-invasive samples. Here, we present a SNP panel for accurate high-resolution genotyping of European bison, which is suitable for a wide variety of sample types. The panel accommodates 96markers allowing for individual and parental assignment, sex determination, breeding line discrimination, and cross-species detection. Two applications were shown to be utilisable in further Bos species with potential conservation significance. The new SNP panel will allow to tackle crucial tasks in European bison conservation, including the genetic monitoring of reintroduced populations, and a molecular assessment of pedigree data documented in the world's first studbook of a threatened species.

Population structure and demographic history for year cohort dynamics of landlocked ayu Plecoglossus altivelis altivelis in dam reservoir of Japan.

Ayu Plecoglossus altivelis altivelis is a valuable osmeroid species for inland fishery in Japan. It is classified into two ecological forms of amphidromous migrating between rivers and sea and landlocked migrating between rivers and lakes or dam reservoirs. The number of dams and their reservoirs has remarkably increased in the twenty-first century under climate change, because of their respective roles in hydropower generation with negligible carbon emissions and in flood control. Dam reservoirs therefore become increasingly important as inland nursery grounds of ayu. In this study, we investigated the reproduction status of landlocked ayu migrating in the Haidzuka Dam reservoir and the Tabusa River in western Japan by molecular phylogenetic analysis based on population structure and demographic history for year cohort dynamics. A total of 849 individuals were collected monthly from October 2018 to September 2021 according to an annual life cycle of ayu. Nucleotide sequences of the partial mitochondrial DNA control region yielded 31 haplotypes, consisting of 4 shared haplotypes among the 2019, 2020 and 2021 cohorts and 27 unique haplotypes. The overall haplotype diversity and nucleotide diversity were calculated to be relatively low at 0.3503 ± 0.0206 and 0.0077 ± 0.0045, respectively, suggesting a founder event by dominant haplotypes. Star-shaped radiational haplotypes from dominant shared haplotypes on the median-joining network likely support a founder event. Although pairwise ФST values were determined to be very low among the year cohorts, only the 2019 cohort was found to have a significant difference from the 2020 and 2021 cohorts, for both of which Tajima's D values were also statistically significant. For the overall population, multimodal mismatch distribution and negative Tajima's D and Fu's Fs values in the neutrality test suggested population expansion or population subdivision. The native riverine population in the Tabusa River suffered habitat fragmentation and population bottleneck from dam construction, and therefore severe founder effect remained behind the artificially landlocked population with a low level of genetic diversity in the Haidzuka Dam reservoir.

The demographic history and adaptation of Canarian goat breeds to environmental conditions through the use of genome-wide SNP data

BackgroundThe presence of goats in the Canary Islands dates back to the late 1st millennium BC, which coincides with the colonization by the Amazigh settlers. However, the exact geographic origin of Canarian goats is uncertain since the Amazigh peoples were distributed over a wide spatial range. Nowadays, three Canarian breeds (Palmera, Majorera and Tinerfeña) are officially recognized, along with two distinct South and North Tinerfeña ecotypes, with the South Tinerfeña and Majorera goats thriving in arid and dry semi-desertic environments and the Palmera and North Tinerfeña goats are adapted to humid and temperate areas that are influenced by trade winds. Genotypes for 224 Canarian goats were generated using the Illumina Goat single nucleotide polymorphism (SNP)50 BeadChip. By merging these data with the genotypes from 1007 individuals of African and Southern European ancestry, our aim was to ascertain the geographic origin of the Canarian goats and identify genes associated with adaptation to diverse environmental conditions.ResultsThe diversity indices of the Canarian breeds align with most of those of the analyzed local breeds from Africa and Europe, except for the Palmera goats that showed lower levels of genetic variation. The Canarian breeds demonstrate a significant genetic differentiation compared to other populations, which indicates a history of prolonged geographic isolation. Moreover, the phylogenetic reconstruction indicated that the ancestry of the Canarian goats is fundamentally North African rather than West African. The ADMIXTURE and the TreeMix analyses showed no evidence of gene flow between Canarian goats and other continental breeds. The analysis of runs of homozygosity (ROH) identified 13 ROH islands while the window-based FST method detected 25 genomic regions under selection. Major signals of selection were found on Capra hircus (CHI) chromosomes 6, 7, and 10 using various comparisons and methods.ConclusionsThis genome-wide analysis sheds new light on the evolutionary history of the four breeds that inhabit the Canary Islands. Our findings suggest a North African origin of the Canarian goats. In addition, within the genomic regions highlighted by the ROH and FST approaches, several genes related to body size and heat tolerance were identified.

Low genetic diversity of Treponema pallidum ssp. pertenue (TPE) isolated from patients' ulcers in Namatanai District of Papua New Guinea: Local human population is infected by three TPE genotypes.

Yaws is an endemic disease caused by Treponema pallidum subsp. pertenue (TPE) that primarily affects children in rural regions of the tropics. The endemic character of yaws infections and the expected exclusive reservoir of TPE in humans opened a new opportunity to start a yaws eradication campaign. We have developed a multi-locus sequence typing (MLST) scheme for TPE isolates combining the previously published (TP0548, TP0488) and new (TP0858) chromosomal loci, and we compared this typing scheme to the two previously published MLST schemes. We applied this scheme to TPE-containing clinical isolates obtained during a mass drug administration study performed in the Namatanai District of Papua New Guinea between June 2018 and December 2019. Of 1081 samples collected, 302 (28.5%) tested positive for TPE DNA, from which 255 (84.4%) were fully typed. The TPE PCR-positivity in swab samples was higher in younger patients, patients with single ulcers, first ulcer episodes, and with ulcer duration less than six months. Non-treponemal serological test positivity correlated better with PCR positivity compared to treponema-specific serological tests. The MLST revealed a low level of genetic diversity among infecting TPE isolates, represented by just three distinct genotypes (JE11, SE22, and TE13). Two previously used typing schemes revealed similar typing resolutions. Two new alleles (one in TP0858 and one in TP0136) were shown to arise by intragenomic recombination/deletion events. Compared to samples genotyped as JE11, the minor genotypes (TE13 and SE22) were more frequently detected in samples from patients with two or more ulcers and patients with higher values of specific TP serological tests. Moreover, the A2058G mutation in the 23S rRNA genes of three JE11 isolates was found, resulting in azithromycin resistance.

A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years.

The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950s, opossum shrimp (Mysis diluviana) individuals from Clearwater Lake in Minnesota, USA were transported and introduced to Twin Lakes in Colorado, USA by fisheries managers to supplement food sources for trout. Mysis were subsequently introduced from Twin Lakes into numerous lakes throughout Colorado. Because managers kept detailed records of the timing of the introductions, we had the opportunity to test for evolutionary divergence within a known time interval. Here, we used reduced representation genomic data to investigate patterns of genetic diversity, test for genetic divergence between populations, and for evidence of adaptive evolution within the introduced populations in Colorado. We found very low levels of genetic diversity across all populations, with evidence for some genetic divergence between the Minnesota source population and the introduced populations in Colorado. There was little differentiation among the Colorado populations, consistent with the known provenance of a single founding population, with the exception of the population from Gross Reservoir, Colorado. Demographic modeling suggests that at least one undocumented introduction from an unknown source population hybridized with the population in Gross Reservoir. Despite the overall low genetic diversity we observed, F ST outlier and environmental association analyses identified multiple loci exhibiting signatures of selection and adaptive variation related to elevation and lake depth. The success of introduced species is thought to be limited by genetic variation, but our results imply that populations with limited genetic variation can become established in a wide range of novel environments. From an applied perspective, the observed patterns of divergence between populations suggest that genetic analysis can be a useful forensic tool to determine likely sources of invasive species.

Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird.

Combating the current biodiversity crisis requires the accurate documentation of population responses to human-induced ecological change. However, our ability to pinpoint population responses to human activities is often limited to the analysis of populations studied well after the fact. Museum collections preserve a record of population responses to anthropogenic change that can provide critical baseline data on patterns of genetic diversity, connectivity, and population structure prior to the onset of human perturbation. Here, we leverage a spatially replicated time series of specimens to document population genomic responses to the destruction of nearly 90% of coastal habitats occupied by the Savannah sparrow (Passerculus sandwichensis) in California. We sequenced 219 sparrows collected from 1889 to 2017 across the state of California using an exome capture approach. Spatial-temporal analyses of genetic diversity found that the amount of habitat lost was not predictive of genetic diversity loss. Sparrow populations from southern California historically exhibited lower levels of genetic diversity and experienced the most significant temporal declines in genetic diversity. Despite experiencing the greatest levels of habitat loss, we found that genetic diversity in the San Francisco Bay area remained relatively high. This was potentially related to an observed increase in gene flow into the Bay Area from other populations. While gene flow may have minimized genetic diversity declines, we also found that immigration from inland freshwater-adapted populations into tidal marsh populations led to the erosion of divergence at loci associated with tidal marsh adaptation. Shifting patterns of gene flow through time in response to habitat loss may thus contribute to negative fitness consequences and outbreeding depression. Together, our results underscore the importance of tracing the genomic trajectories of multiple populations over time to address issues of fundamental conservation concern.

Genetic diversity and population structure of a rare and endangered freshwater macrophyte <i>Potamogeton rutilus</i> Wolfg.

Comprehending genetic variation and population structure is paramount for devising optimal management strategies and conservation efforts. In this study, we employed amplified fragment length polymorphism (AFLP) analysis to assess the distribution of genetic variation within and among populations of the rare macrophyte <i>Potamogeton rutilus</i> Wolfg. This species has experienced habitat alterations leading to its disappearance from numerous previously known European locations. Our analysis encompassed eight populations collected from Poland, Lithuania, and Estonia, situated within the central region of <i>P. rutilus</i> distribution. The results of our study indicate that the analyzed populations are characterized by relatively low levels of genetic diversity (the mean of Nei’s gene diversity was 0.031±0.003 and the Shannon’s information index 0.049± 0.004), and intermediate gene flow (Nm = 0.289). Analysis of molecular variance (AMOVA) revealed higher levels of variation among populations (63%) than within populations (37%); PhiPT = 0.634, <i>p</i> < 0.001, which might be attributed to the founder effect, frequent vegetative propagation, and limited seedling recruitment. The results of STRUCTURE, PCoA and NeighbourNet analyses suggest that the genetic structure of the studied populations falls into three main clusters not fully corresponding to geographical regions. The Mantel test did not show a significant correlation between genetic distance and geographical distance among populations. The most geographically isolated population sampled in Poland (ROT) is genetically close to the Estonian population VAL and VIT, although it is located far closer to the stations in Lithuania. Implications of acquired data for the genetic management of the species are discussed.

Microsatellite (SSR) Analysis of Dolichos Lablab (Lablab purpureus (L.) Sweet) Germplasm in Namibia

Dolichos lablab (Lablab purpureus (L.) Sweet)) is a multipurpose drought tolerant protein-rich legume crop native to Africa and grown in warm temperate to tropical climates for its edible seeds and manure. Literature informs that Lablab purpureus holds significant benefits to subsistence farmers and offers a great promise for sustainable crop productivity, especially in marginalised areas. Its uses range from human consumption as a vegetable to improving soil fertility, and as forage. Not with standing Lablab purpureus crucial potential functions in Namibia, there is currently limited information regarding the plant’s genetic diversity. This study followed a descriptive quantitative research approach where the data collected was used to describe the samples collected. The study aimed at evaluating the genetic diversity among 26 accessions of Lablab purpureus. The plant’s genetic diversity was determined by PCR amplification of three SSR markers namely VM38, AGB8 and GATS911. The SSR markers had PIC values of 0.452663 for marker VM38, 0.473373 for marker AGB8 and 0.260355 for marker GATS911. The Shannon Index of diversity gave a value of 1.25 meaning low levels of genetic diversity among the accessions. The study was the first report of Lablab purpureus’s genetic diversity in Namibia.

Population Structure and Genetic Diversity Analyses Provide New Insight into the Endemic Species Aster spathulifolius Maxim. and Its Evolutionary History.

Aster spathulifolius, an ecologically significant plant species native to the coastal regions of Korea and Japan, remains understudied in terms of its genetic structure and evolutionary history. In this study, we employed four chloroplast markers and the nuclear ITS region from 15 populations of A. spathulifolius from both Korea and Japan, including their islands, to unravel the spatial genetic structure, differentiation, gene flow, phylogenetic, and biogeographical relationships. Analysis based on multiple methods identified a low level of genetic diversity, genetic differentiation and gene flow among A. spathulifolius populations. Network analysis and principal coordinates analysis showed that 15 populations could be divided into two groups: mainland and island. Furthermore, UPGMA, neighbor-net, maximum-likelihood and Bayesian inference-based phylogenetic tree confirmed that these populations formed two distinct clades. Therefore, the island populations might be treated as A. spathulifolius populations rather than A. oharai populations. Divergence time analysis estimated the divergence of A. spathulifolius lineages approximately 23.09 million years ago, while ancestral area reconstruction analysis suggested Korea as the potential origin, conflicting with alternative scenarios. These findings contribute to a comprehensive understanding of the evolutionary history, genetic structure, and adaptive strategies of A. spathulifolius in coastal environments. Our study challenges previous assumptions and underscores the necessity for further population studies to elucidate the intricate dynamics of this distinctive plant species.

Genetic footprints of Quaternary climatic fluctuations on the endangered Tuco-tuco-das-dunas (Ctenomys flamarioni)

Abstract The biogeographic history of a species results from responses to past and current processes, and understanding those responses at both temporal scales is essential. We explored phylogeographic and current genetic variation structure in Ctenomys flamarioni—a subterranean rodent that inhabits a small region of the coastal plain of Brazil—and contrasted the roles of “present-day niche suitability” versus “historical climate stability” to understand current and past intraspecific genetic diversity. We used both mitochondrial DNA sequences (concatenated Cytb and D-loop, n = 78) and nuclear DNA (9 microsatellites loci, n = 154) molecular markers for individuals across the entire distribution of the species. We used phylogeographic trees, Bayesian clustering, and haplotype networks to explore genetic variation and diversity. We correlated genetic diversity with measures of current niche suitability and potential areas of Late Quaternary paleostability. Phylogeographic patterns confirmed low levels of genetic diversity structured at different hierarchical levels. We also found a weak but significant pattern of isolation by distance, indicating that geographical distance partially modulates genetic differences among populations. We also observed a positive correlation between genetic diversity and climate paleostability for microsatellites at local and regional scales. However, we found no significant association between genetic diversity and niche suitability for microsatellites at local or regional scales. We observed several signatures of bottleneck and population expansion at different geographic scales. Our results suggest that Quaternary climatic fluctuations—acting together with habitat suitability and other contemporary factors—played a fundamental role in elucidating the evolutionary history of the species—including patterns of historical dispersal, and current patterns of habitat occupation and genetic structure. In addition, based on our molecular and environmental data sets from the across the range of the species and considering the restricted endemism of C. flamarioni, we emphasize the urgency of conservation actions to protect this endangered species.

What happens in ice age, does not stay in ice age: Phylogeography of Bombus terrestris revealed a low genetic diversity amongst the Eurasian populations

The objective of this research was to assess the genetic diversity and phylogeography of Bombus terrestris and examine the historical events that shaped its contemporary genetic structures using the COI mitochondrial marker. Specimens of the species were collected from its distribution range alongside the Alborz Mountain range, and GenBank sequences from the Eurasian distribution range were incorporated into the dataset. The COI sequences were employed in Bayesian and Maximum Likelihood analyses to generate phylogenetic trees for the species populations and to investigate the evolutionary history of the species. Additionally, species occurrence points and climate data were utilized in Species Distribution Modeling (SDM) analyses to reconstruct the species range under past, present, and future climate conditions. The ML and BI trees yielded similar topologies, indicating extremely low genetic diversity and a homogeneous structure in the species population distribution range in Eurasia. Demographic analyses suggested that the species may have experienced a bottleneck during the last glacial maximum in Eurasia, followed by a recent expansion. The SDM analyses revealed significant fluctuations in the species range in the past and expansion under present conditions. Given the high dispersal ability of the species, the population expansion rate has surpassed the rate of developing new genetic diversity, and the estimated polymorphic sites for the species are likely relatively recent. This low level of genetic variation can also be attributed to the absence of geographical barriers and the excellent flying ability of the queen bee, leading to sustained gene flow throughout the entire continent. Despite the general correlation between larger populations and higher genetic diversity, bumblebees can expand their population size without increasing genetic diversity when residing in resourceful habitats.