Strong Genetic Differentiation Research Articles

Gene Flow Between Populations With Highly Divergent Mitogenomes in the Australian Stingless Bee, Tetragonula hockingsi.

Coadaptation of mitochondrial and nuclear genes is essential for proper cellular function. When populations become isolated, theory predicts that they should maintain mito-nuclear coadaptation in each population, even as they diverge in genotype. Mito-nuclear incompatibilities may therefore arise when individuals from populations with divergent co-evolved mito-nuclear gene sets are re-united and hybridise, contributing to selection against inter-population hybrids and, potentially, to speciation. Here, we explored genetic divergence and gene flow between populations of a stingless bee (Tetragonula hockingsi) that have highly divergent mitogenomes. We identified three distinct populations across the species' 2500 km range on the east coast of Queensland (Australia): 'Cape York', 'Northern', and 'Southern'. The mitogenomes of each population showed > 12% pairwise nucleotide divergence from each other, and > 7% pairwise amino acid divergence. Based on nuclear SNPs from reduced representation sequencing, we identified at least two zones of gene flow between populations: a narrow natural zone between Northern and Southern populations (coinciding with a biogeographic barrier, the Burdekin Gap), and an artificial zone at the southern edge of the species' distribution, where Cape York, Northern, and Southern mito-lineages have been brought together in recent decades due to beekeeping. In the artificial hybrid zone, we also confirmed that males of all three mito-lineages were attracted to the mating aggregations of Southern queens, consistent with inter-population hybridisation. Populations of T. hockingsi thus appear to be in the 'grey zone' of the speciation continuum, having strong genetic differentiation but incomplete reproductive isolation. Among the nuclear SNPs most differentiated between Northern and Southern populations, several were associated with genes involved in mitochondrial function, consistent with populations having co-diverged mito-nuclear gene sets. Our observations suggest that coadapted sets of mitochondrial and nuclear genes unique to each population of T. hockingsi may play a role in maintaining population boundaries, though more study is needed to confirm the fitness costs of mito-nuclear incompatibilities in hybrid individuals.

The rise and transformation of Bronze Age pastoralists in the Caucasus.

The Caucasus and surrounding areas, with their rich metal resources, became a crucible of the Bronze Age1 and the birthplace of the earliest steppe pastoralist societies2. Yet, despite this region having a large influence on the subsequent development of Europe and Asia, questions remain regarding its hunter-gatherer past and its formation of expansionist mobile steppe societies3-5. Here we present new genome-wide data for 131 individuals from 38 archaeological sites spanning 6,000 years. We find a strong genetic differentiation between populations north and south of the Caucasus mountains during the Mesolithic, with Eastern hunter-gatherer ancestry4,6 in the north, and a distinct Caucasus hunter-gatherer ancestry7 with increasing East Anatolian farmer admixture in the south. During the subsequent Eneolithic period, we observe the formation of the characteristic West Eurasian steppe ancestry and heightened interaction between the mountain and steppe regions, facilitated by technological developments of the Maykop cultural complex8. By contrast, the peak of pastoralist activities and territorial expansions during the Early and Middle Bronze Age is characterized by long-term genetic stability. The Late Bronze Age marks another period of gene flow from multiple distinct sources that coincides with a decline of steppe cultures, followed by a transformation and absorption of the steppe ancestry into highland populations.

Habitat fragmentation strongly restricts gene flow in endangered ectomycorrhizal fungal populations: Evidence from Rhizopogon togasawarius, specific to Pseudotsuga japonica, across the entire distribution range.

Habitat fragmentation reduces gene flow, causing genetic differentiation and diversity loss in endangered species through genetic drift and inbreeding. However, the impact of habitat fragmentation on ectomycorrhizal (ECM) fungi remains unexplored, despite their critical roles in forest ecosystems. Here, we investigated the population genetic structure and the demographic history of Rhizopogon togasawarius, the ECM fungus specifically colonizing the host tree Pseudotsuga japonica, across its entire distribution range (>200 km). These two species are designated as endangered species on the IUCN Red List since they are found only in small, fragmented forests in Japan. We analysed 236 R. togasawarius individuals from five remaining populations across the Kii Peninsula and the Shikoku Island, separated by a sea channel. Simple sequence repeat analyses using 20 loci revealed strong genetic differentiation among populations (FST = 0.255), even significant in the nearest population pair separated by a distance of only 8 km (FST = 0.075), indicating extremely limited gene flow between populations. DIYABC-RF analyses implied that population divergence occurred approximately 6000 generations ago between the two regions, and nearly 1500 generations ago between the nearest populations within Shikoku Island, related to past climate events. Because of prolonged genetic isolation, significant inbreeding was confirmed in four of five populations, where effective population sizes became very small (Ne = 9.0-58.0). Although evaluation of extinction risks for microorganisms is challenging, our conservation genetic results indicated that habitat fragmentation increases extinction risk through population genetic mechanisms, and therefore should not be overlooked in biodiversity conservation efforts.

Genetic diversity and incidence of cassava bacterial blight (CBB) caused by Xanthomonas phaseoli pv. manihotis in Burkina Faso

AbstractCassava bacterial blight (CBB), caused by Xanthomonas phaseoli pv. manihotis (Xpm), poses a significant threat to cassava production in Burkina Faso. Prior to this study, the geographical distribution, incidence and origin of CBB introductions were poorly understood. In this investigation, we assessed the incidence of CBB in major cassava‐cropping regions and analysed the genetic diversity of 344 Xpm strains collected from 19 fields between 2015 and 2016, using a multilocus variable number of tandem repeat analysis (MLVA) scheme targeting 14 microsatellite markers. Our results reveal the presence of CBB in three out of four cropping regions, with incidences ranging from 0% to 100% at locality and variety scale. Burkina Faso's Xpm strains exhibited high genetic diversity at multiple levels, including country scale (He = 0.6), cropping region (0.43 to 0.57), locality (0.25 to 0.50) and field (0.25 to 0.52). Pairwise comparisons among populations from different cropping areas indicated a strong genetic differentiation. The categorical minimum spanning tree reveals that the Cascades region has the higher diversity indices and consequently could be the origin site of dispersion of Xpm in the other cropping regions of cassava. Human activities play a major role in the dissemination of Xpm through cassava cuttings. The importance of the sanitary state of cuttings must be emphasized in order to avoid CBB and ensure good cassava production.

Cytochrome b Mitochondrial Gene Revealed a Strong Genetic Differentiation between Two Populations of the Endemic Freshwater Fish Moroccan Loach Cobitis maroccana Pellegrin, 1929

Cobitis maroccana, also known as the Moroccan loach, is an endemic freshwater fish found in the rivers of the Loukkos and Sebou basins in Morocco. In order to gain a better understanding of the genetic differentiation within C. maroccana from the Loukkos and Sebou populations, a comprehensive study was conducted, focusing on the mitochondrial cytochrome b gene. A total of 30 sequences of the complete cytochrome b (1140 bp) were obtained from C. maroccana specimens. Through a combination of phylogenetic analysis, phylogeographic assessments, as well as the estimation of the Fst index, the research outcomes revealed significant genetic differentiation between the two juxtaposed basin populations. Notably, each of these basins displayed unique and distinct haplotype groups within the C. maroccana specimens. These intriguing findings strongly suppose that the populations in the Loukkos and Sebou basins have become reproductively isolated from each other over time, indicating limited or no interbreeding between them.

Genetic monitoring uncovers long-distance marine feeding coupled with strong spatial segregation in sea trout (Salmo trutta L.) consistent at annual and decadal time scales

Abstract Genetic data have greatly increased means to understand fish marine migration behaviours at large spatial scale within a quantitative framework. The anadromous sea trout is a prized target of recreational fishery and an important ecosystem component in freshwater and marine coastal habitats in large parts of temperate northern Europe. Nonetheless, little is known about population distributions while feeding at sea. To reconcile notions about feeding migrations being predominantly locally restricted or not, we used SNP data for 3465 trout representing >100 rivers to identify population origins of 903 coastally feeding fish captured throughout the North Sea-Baltic Sea transition area. Across areas, coastal collections generally showed marked stock-mixing and overall 70:30% native:non-native fish with seasonal variation corresponding with spawning run timing. Data revealed strong spatial feeding segregation between trout from the Scandinavian Peninsula and the European continent. This is surprising given the short distances between areas, but is in alignment with strong genetic differentiation between populations in these areas. Estimation of stock complexity of coastal feeding aggregations showed no spatial trend through the North Sea-Baltic Sea transition area otherwise characterized by strong environmental clines. Analyses of scale samples collected in the 1950s indicate that stock-mixing was consistent over almost 70 years.

Population genetic diversity and structure of Tephritis angustipennis and Campiglossa loewiana (Diptera: Tephritidae) based on COI DNA barcodes in the three-river source region, China.

Tephritis angustipennis (Diptera: Tephritidae)and Campiglossa loewiana (Diptera: Tephritidae) are phytophagous pests in China. Their damage has significantly impacted the collection and cultivation of germplasm resources of native Asteraceae plants. However, the genetic characteristics and structure of their population are unclear. This study focused on the highly damaging species of T. angustipennis and C. loewiana collected from the three-river source region (TRSR). We amplified the mitochondrial cytochrome C oxidase subunit I (mtCOI) gene sequences of these pests collected from this area and compared them with COI sequences from GenBank. We also analyzed their genetic diversity and structure. In T. angustipennis, 5 haplotypes were identified from 5 geographic locations; the genetic differentiation between France population FRPY (from Nylandia, Uusimaa) and China populations GLJZ (from Dehe Longwa Village, Maqin County), GLDR (from Zhique Village, Dari County), and GLMQ (from Rijin Village, Maqin County) was the strongest. GLJZ exhibited strong genetic differentiation from GLDR and GLMQ, with relatively low gene flow. For C. loewiana, 11 haplotypes were identified from 5 geographic locations; the genetic differentiation between the Chinese population GLMQ-YY (from Yangyu Forest Farm, Maqin County) and Finnish population FDNL (from Nylandia, Uusimaa) was the strongest, with relatively low gene flow, possibly due to geographical barriers in the Qinghai-Tibet plateau. Only 1 haplotype was identified across GLDR, GLMQ, and GLBM. High gene flow between distant locations indicates that human activities or wind dispersal may facilitate the dispersal of fruit flies and across different geographic. Geostatistical analysis suggested a recent population expansion of these 2 species in TRSR. Our findings provide technical references for identifying pests in the TRSR region and theoretical support for managing resistance, monitoring pest occurrences, analyzing environmental adaptability, and formulating biological control strategies for Tephritidae pests on Asteraceae plants.

Limited variation in microbial communities across populations of Macrosteles leafhoppers (Hemiptera: Cicadellidae).

Microbial symbionts play crucial roles in insect biology, yet their diversity, distribution, and temporal dynamics across host populations remain poorly understood. In this study, we investigated the spatio-temporal distribution of bacterial symbionts within the widely distributed and economically significant leafhopper genus Macrosteles, with a focus on Macrosteles laevis. Using host and symbiont marker gene amplicon sequencing, we explored the intricate relationships between these insects and their microbial partners. Our analysis of the cytochrome oxidase subunit I (COI) gene data revealed several intriguing findings. First, there was no strong genetic differentiation across M. laevis populations, suggesting gene flow among them. Second, we observed significant levels of heteroplasmy, indicating the presence of multiple mitochondrial haplotypes within individuals. Third, parasitoid infections were prevalent, highlighting the complex ecological interactions involving leafhoppers. The 16S rRNA data confirmed the universal presence of ancient nutritional endosymbionts-Sulcia and Nasuia-in M. laevis. Additionally, we found a high prevalence of Arsenophonus, another common symbiont. Interestingly, unlike most previously studied species, M. laevis exhibited only occasional cases of infection with known facultative endosymbionts and other bacteria. Notably, there was no significant variation in symbiont prevalence across different populations or among sampling years within the same population. Comparatively, facultative endosymbionts such as Rickettsia, Wolbachia, Cardinium and Lariskella were more common in other Macrosteles species. These findings underscore the importance of considering both host and symbiont dynamics when studying microbial associations. By simultaneously characterizing host and symbiont marker gene amplicons in large insect collections, we gain valuable insights into the intricate interplay between insects and their microbial partners. Understanding these dynamics contributes to our broader comprehension of host-microbe interactions in natural ecosystems.

A new species of Vallisneria L. for Western Australia and recircumscription of V. triptera S.W.L.Jacobs & K.Frank

Vallisneria kristinae R.W.Jobson & Dunning (Hydrocharitaceae) is described as a new species endemic to North Kimberley, Western Australia. It was previously included within the Northern Territory species V. triptera S.W.L.Jacobs & K.A.Frank. Here it is distinguished from that species based on its overall smaller size and weakly-winged fruit capsules. We also find strong genetic differentiation with accessions sampled from across the entire distribution of both taxa. We present a phylogeny based on nuclear ITS and plastid trnK 5′ intron data that also includes all Australian species of Vallisneria. Along with a redescription of V. triptera s. str., diagnostic features are illustrated, a taxonomic key containing all Australian species is provided, and distribution, habitat, and conservation status are discussed.

The Anopheles coluzzii range extends into Kenya: detection, insecticide resistance profiles and population genetic structure in relation to conspecific populations in West and Central Africa

BackgroundAnopheles coluzzii is a primary vector of malaria found in West and Central Africa, but its presence has hitherto never been documented in Kenya. A thorough understanding of vector bionomics is important as it enables the implementation of targeted and effective vector control interventions. Malaria vector surveillance efforts in the country have tended to focus on historically known primary vectors. The current study sought to determine the taxonomic status of samples collected from five different malaria epidemiological zones in Kenya as well as describe the population genetic structure and insecticide resistance profiles in relation to other An. coluzzii populations.MethodsMosquitoes were sampled as larvae from Busia, Kwale, Turkana, Kirinyaga and Kiambu counties, representing the range of malaria endemicities in Kenya, in 2019 and 2021 and emergent adults analysed using Whole Genome Sequencing (WGS) data processed in accordance with the Anopheles gambiae 1000 Genomes Project phase 3. Where available, historical samples from the same sites were included for WGS. Comparisons were made with An. coluzzii cohorts from West and Central Africa.ResultsThis study reports the detection of An. coluzzii for the first time in Kenya. The species was detected in Turkana County across all three time points from which samples were analyzed and its presence confirmed through taxonomic analysis. Additionally, there was a lack of strong population genetic differentiation between An. coluzzii from Kenya and those from the more northerly regions of West and Central Africa, suggesting they represent a connected extension to the known species range. Mutations associated with target-site resistance to DDT and pyrethroids and metabolic resistance to DDT were found at high frequencies up to 64%. The profile and frequencies of the variants observed were similar to An. coluzzii from West and Central Africa but the ace-1 mutation linked to organophosphate and carbamate resistance present in An. coluzzii from coastal West Africa was absent in Kenya.ConclusionsThese findings emphasize the need for the incorporation of genomics in comprehensive and routine vector surveillance to inform on the range of malaria vector species, and their insecticide resistance status to inform the choice of effective vector control approaches.

Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences

Nemipterus randalli, commonly known as Randall’s threadfin bream, is a commercially important marine finfish. Understanding its genetic structure is critical to effective management and conservation efforts. Previous investigations on population structure in this species were limited by geographic coverage. In this study, we utilized the mitochondrial Cytochrome b gene and nuclear Ribosomal protein gene intron Rp S7 sequences to investigate the population genetic structure, demography and genetic diversity of N. randalli along Indian waters. Our results revealed high haplotype diversity but low nucleotide diversity. AMOVA revealed that the variation among the population was highly significant. Hierarchical AMOVA provided further evidence of significant genetic differentiation between the west and east coasts, which was corroborated by the Bayesian tree and the median-joining network diagram. The mtDNA sequences revealed significant genetic structure between populations based on fixation index analysis following the isolation-by-distance model. Furthermore, the neutrality test and mismatch analysis suggest that N. randalli populations may have experienced a population expansion. However, nuclear marker RpS7, showed a high level of polymorphism, which obscured the population structuring observed with the mitochondrial marker. Consequently, concordant results were not obtained when comparing the mitochondrial and nuclear DNA sequences. The strong genetic differentiation between the east and west coast observed using mitochondrial marker could be attributed to a combination of geographic and environmental factors. These findings lay the groundwork for developing effective conservation and management strategies for N. randalli, considering its genetic structure.

2bRAD reveals fine-scale genetic structuring among populations within the Mediterranean zoanthid Parazoanthus axinellae (Schmidt, 1862)

The zoanthid Parazoanthus axinellae (Schmidt, 1862) is a widespread coral species in the Mediterranean coralligenous assemblages where two morphotypes are found: Slender and Stocky, differing in size, color, and preferred substrate. Due to these marked differences, Slender and Stocky morphotypes were hypothesized to be two species. Here, we used 2bRAD to obtain genome‐wide genotyped single nucleotide polymorphisms (SNPs) to investigate the genetic differentiation between Slender and Stocky morphs, as well as their population structure. A total of 101 specimens of P. axinellae were sampled and genotyped from eight locations along the Italian coastline. In four locations, samples of the two morphotypes were collected in sympatry. 2bRAD genome-wide SNPs were used to assess the genetic divergence between the two morphotypes (1319 SNPs), and population connectivity patterns within Slender (1926 SNPs) and Stocky (1871 SNPs) morphotypes. Marked and consistent differentiation was detected between Slender and Stocky morphotypes. The widely distributed Slender morphotype showed higher population mixing patterns, while populations of the Stocky morphotype exhibited a stronger genetic structure at a regional scale. The strong genetic differentiation observed between P. axinellae Slender and Stocky morphotypes provides additional evidence that these morphs could be attributed to different species, although further morphological and ecological studies are required to validate this hypothesis. Our study highlights the importance of resolving phylogenetic and taxonomic disparities within taxonomically problematic groups, such as the P. axinellae species complex, when performing genetic connectivity studies for management and conservation purposes.Graphical Schematic overview of the main genetic structuring patterns observed in this study. Coral polyps were colored to intuitively associate the reader to Parazoanthus axinellae morphotypes, with orange tones being attributed to the Stocky morphotype, and yellow tones to the Slender morphotype. Bidirectional arrows represent gene flow between coral individuals, with the number and thickness of arrows corresponding to the intensity of gene flow rates. The red dashed line represents the potential reproductive isolation between Slender and Stocky morphs

Stronger genetic differentiation among within-population genetic groups than among populations in Scots pine provides new insights into within-population genetic structuring

We investigated the presence of spatial genetic groups within forest tree populations and determined if the genetic divergence among these groups is greater than that between populations using Scots pine (Pinus sylvestris) as a model species. We genotyped 890 adult trees of Scots pine in six natural populations in Lithuania at 11 nuclear microsatellite loci. We used a Bayesian clustering approach to identify the within-population genetic groups within each of the six populations. We calculated the differentiation indexes among the genetic groups within each population and among the six populations by ignoring the genetic groups. The Bayesian clustering revealed 2 to 6 distinct genetic groups of varying size as the most likely genetic structures within populations. The genetic differentiation indexes among the genetic groups within populations were nearly tenfold greater (FST = 0.012–0.070) than those between the populations (FST = 0.003). We conclude on the existence of markedly stronger structuring of genetic variation within populations than between populations of Scots pine in large forest tracts of northern Europe. Such genetic structures serve as a contributing factor to large within population genetic diversity in northern conifers. We assume that within population mating in Scots pine is not completely random but rather is stratified into genetic clusters. Our study provides pioneering novel key insights into structuring of genetic variation within populations. Our findings have implications for examining within-population genetic diversity and genetic structure, conservation, and management of genetic resources.

Conservation Genetics of the Endangered Lompoc Yerba Santa (Eriodictyon capitatum Eastw., Namaceae), including Phylogenomic Insights into the Evolution of Eriodictyon.

Eriodictyon capitatum (Namaceae) is a narrowly distributed shrub endemic to western Santa Barbara County, where it is known from only 10 extant California Natural Diversity Database element occurrences (EOs). Owing to low numbers of plants in nature, a limited overall extent, and multiple current threats, E. capitatum is listed as Endangered under the Federal Endangered Species Act and as Rare under the California Native Plant Protection Act. In the present study, high-throughput DNA sequence data were analyzed to investigate genetic diversity within and among all accessible EOs; to determine the extent of genetic isolation among EOs; to examine clonality within EOs; and to examine the taxonomic circumscriptions of E. capitatum, E. altissimum, E. angustifolium, and E. californicum through phylogenomic analysis. Population genetic analyses of E. capitatum reveal a pattern of strong genetic differentiation by location/EO. The clonality assessment shows that certain small EOs may support relatively few multilocus genotypes. The phylogenomic analyses strongly support the present-day taxonomic circumscriptions of both E. altissimum and E. capitatum, showing them to be reciprocally monophyletic and sister with strong support. Taken together, these results paint a picture of an evolutionarily and morphologically distinct species known from relatively few, genetically isolated stations.

Gorges partition diversity within New Zealand flathead Galaxias populations.

Understanding the landscape factors governing population connectivity in riverine ecosystems represents an ongoing challenge for freshwater biologists. We used DNA sequence analysis to test the hypothesis that major geomorphological features underpin freshwater-limited fish diversity in a tectonically dynamic region of New Zealand. Phylogeographic analysis of 101 Galaxias depressiceps cytochrome b sequences, incorporating 55 localities from southern New Zealand, revealed 26 haplotypes, with only one shared among rivers. We detect strong hierarchical genetic differentiation both among and within river systems. Genetic structuring is particularly pronounced across the Taieri River system (63 individuals from 35 sites, 18 haplotypes), with 92% of variation partitioned among locations. Distinctive within-river genetic clusters are invariably associated with major subcatchment units, typically isolated by substantial gorges. The anomalous distribution of a single lineage across a major drainage divide is consistent with local, tectonically driven headwater capture. We conclude that major landscape features such as gorges can strongly partition riverine fish diversity and constrain freshwater biodiversity.

Unravelling the genetic pattern of seagrass (Posidonia oceanica) meadows in the Eastern Mediterranean Sea

AbstractThe genetic traits of seagrass populations are a crucial aspect of their ecology and evolution, influencing their adaptability and resilience. Here, we studied the genetic diversity, population structure, and connectivity of eighteen Posidonia oceanica meadows extending in the Eastern Mediterranean Sea (Aegean, Ionian and Cretan Seas, Greece), combining twelve microsatellite markers and Lagrangian particle drift modelling. Our findings revealed a strong genetic differentiation between the Ionian Sea and the Aegean and Cretan Seas, suggesting limited genetic exchange between these two groups. High gene flow was observed within the meadows of the Aegean and Cretan Seas, indicating a well-connected group of populations. Notably, populations of the North Aegean Sea displayed the lowest genetic diversity and the highest clonality compared to the rest of the populations. The lack of substantial oceanographic connectivity between Ionian and Aegean/Cretan Sea populations supported their genetic differentiation. However, the Lagrangian simulations did not fully support gene flow patterns in the Aegean Sea, suggesting that in addition to contemporary processes, historical events may have contributed to the formation of the observed genetic pattern. The genetic information provided here can be incorporated into management strategies aimed at identifying suitable areas as management units in conservation efforts and determining meadows that may serve as donor sites in transplantation initiatives.

Genetic diversity and population structure analysis of Philippine native pigs highlight five priority populations for conservation.

The Philippine native pig (PhNP) is a unique genetic resource composed of multiple domesticated Sus scrofa lineages and interspecific hybrids. No prior study has determined the population structure and genetic diversity of PhNPs on multiple islands and provinces, which is essential for establishing conservation priorities. In this study, we explore the population structure and genetic diversity of various PhNP populations in Luzon and the Visayas, Philippines, to identify conservation priorities. We analyzed seven PhNP populations (n = 20-27 samples each; Benguet [B], Kalinga [K], Nueva Vizcaya [N], Isabela [I], Quezon [Q], Marinduque [M], and Samar [S]) and four transboundary breeds present in the Philippines (n = 9-11 samples each; Duroc, Large White, Landrace, and Berkshire). The pigs were compared against a panel of 20 microsatellite markers recommended by the ISAG-FAO. We tested for population structure at the island, region, and province levels. Strong genetic differentiation between native and transboundary breeds was confirmed by Bayesian clustering (k = 2) and Nei's D A genetic distance (100% bootstrap support for the PhNP cluster). PhNP exhibited high heterozygosity (Ho: 0.737), a high allele count (Na: 7.771), and a low inbreeding coefficient (Fis: -0.040-0.125). Bayesian clustering supported genetic differentiation at the island (k = 2; North Luzon and South Luzon-Visayas cluster), region (k = 3), and population (k = 8) levels. The pairwise F'st between PhNP populations ranged from 0.084 (N and I) to 0.397 (Q and K), confirming that some PhNP populations exhibited sufficient genetic distance to be considered separate populations. This study shows that native pigs from B, K, I, Q, M, and S are unique genetic units for conservation. Furthermore, the small effective population sizes of B, I, Q, M, and S (Ne: 3.9, 19.1, 14.2, 44.7, and 22.5, respectively) necessitate immediate conservation actions, such as incentivizing PhNP farming.

Combining genetic and environmental data to map and model regions of provenance for silver fir (Abies alba Mill.) in Italy

Regions of provenance for forest reproductive materials are the basis for wise use of forest resources in a changing climate. In this work a modelling framework is proposed for silver fir (Abies alba Mill.) in Italy where genetic clusters described by nuclear microsatellites were combined with high-resolution climatic data. When the genetic clusters were too large or had an uncertain ecological niche expression, an additional subregion division-was evaluated according to a climatic assessment. Subsequently each genecological group (Region of Provenance, RoP) was projected in geographic space separately using species distribution modelling (SDM) procedure under current (1991–2020) and a future climate scenario derived from the 6th assessment report for the period 2041–2070. The final division into nine RoPs was able to explain 77.41% of the total climatic variance, a good trade-off between statistical significance and practical usability. The modelling steps then showed a large degree of ecological overlap between RoPs with some of them occurring in similar ecological environments but characterized by a different genetic structure. When projected at the continental scale, the Italian RoPs were found to be suitable for almost all the current European range of silver fir, with potential expansion in Nordic countries in the future, beyond the current distribution range. The study showed that the combination of genetic and ecological data can be a robust way to proceed in areas where a strong genetic differentiation between populations occurs, such as in Italy. New markers such as SNPs can then be used to detect adaptive traits and drive the selection of provenances for common garden experiments in areas where the SDM modelscurrently extrapolate potential sites outside the current natural range.

Geographical Variation Reveals Strong Genetic Differentiation in Cryptomeria japonica var. sinensis

The adaptive capacity of tree species is crucial for their survival under environmental change. Liushan (Cryptomeria japonica var. sinensis), an allogamous conifer species, is widely distributed across southern China. However, despite its broad distribution, there have been few investigations on the geographical variation and environmental adaptability of this species. Here, we combined the phenotypic (eight needle traits) and genetic data (14 nSSR loci) to fill this gap by assessing the genetic variation of geographical populations and exploring environmental adaptations of this species. Both phenotypic and molecular genetic analyses indicated a strong genetic differentiation among geographic populations. All populations could be clustered into three groups that were consistent with their geography. Most of the needle traits showed significantly correlated with geography and environmental factors. Geographical isolation and environmental differences are the main factors that have shaped current morphological traits and patterns of genetic variation. We suggest conservation measures to be implemented on a population level with existing populations, especially those with rare phenotypes as the main goal. Our findings shed light on the geographic variation in Liushan and expanded the knowledge of its putative adaptive mechanisms, ultimately benefiting the conservation of this species.

Population genetic differentiation of the ubiquitous brooding coral Pocillopora acuta along Phuket Island reefs in the Andaman Sea, Thailand

BackgroundThe widespread Indo-Pacific coral species Pocillopora acuta Lamarck, 1816 displays varying levels of asexual versus sexual reproduction, with strong repercussions on genetic diversity, connectivity and genetic structuring within and among populations. For many geographic regions, baseline information on genetic diversity is still lacking, particularly in the Andaman Sea. The region suffered a massive heat-induced bleaching event in 2010 with high coral cover loss of branching coral species such as P. acuta. A subsequent bleaching in 2016, however, revealed a mild bleaching response in pocilloporids compared to other coral taxa in the region, suggesting that rare, heat tolerant genotypes had been selected by the 2010 bleaching event. In order to test whether this potential ‘evolutionary rescue’ event has led to a low genetic diversity, we conducted a population genetic survey covering a total of nine different P. acuta populations (336 individuals) along a 50 km coastal stretch around Phuket Island, Thailand. We used six microsatellite markers to assess genotypic diversity and to determine the prevalent mode of reproduction (i.e. sexual or asexual recruitment).ResultsIn contrast to other Indian Ocean P. acuta populations, the majority of corals in this study adopted a sexual reproduction mode (75% across all populations). At the same time, substantial regional gene flow was observed around Phuket Island with strong genetic differentiation as indicated by three genetic clusters that were separated by only a few kilometers. Patterns of isolation by distance over 0.7 – 40 km suggest small-scale genetic barriers, such as changing currents throughout each monsoonal season, potentially contributing to locally restricted dispersal of P. acuta larvae.ConclusionsThe occurrence of distinct genetic clusters within short coastal stretches suggests that the 2010 bleaching event has not led to extreme genetic impoverishment. While more in-depth genomic analyses are necessary to investigate changes in genetic diversity following extreme bleaching events, our results will help guide conservation efforts to maintain genetic diversity of a coral species that likely will be dominant in future, warmer Andaman Sea reefs.