Beyond FST: Analysis of population genetic data for conservation

Prickly Problems: Cylindropuntia's Low Genetic Diversity Despite Inbreeding Avoidance

Dioecy, the separation of sexes, is found in 6% of flowering plants. One widely known hypothesis suggests that it is an adaptation to mitigate inbreeding. A contrary hypothesis suggests that dioecy is an evolutionary dead end. However, contrasting patterns emerged from population genetic studies that compared the genetic diversity between dioecy versus hermaphroditic species. Specifically, in Silene, it was shown that dioecious species possess higher genetic diversity than hermaphroditic species, challenging the dead end hypothesis. To evaluate whether dioecy is indeed advantageous, further studies are needed in systems with diverse sexual systems such as the genus Cylindropuntia (Cactaceae). It encompasses species with sexual separation observed solely in polyploids. Notably, these polyploids (C. wolfii and C. chuckwallensis) share similar ploidy, flower colors, and geographic proximity, raising speculation about their shared ancestry. Moreover, C. wolfii has been reported to have a low seed production, highlighting the need to assess the reproductive strategies of the species. Our first goal was to compare the genetic diversity patterns among species with different sexual systems within the genus Cylindropuntia (Cactaceae). Our second goal was to investigate genetic shared ancestry among the polyploid species. As C. wolfii is struggling to sexually reproduce, our third objective was to investigate whether it is dominated by clonal reproduction, diversity parameters, and population structure. The clonality of C. wolfii was assessed using a combination of field survey and genetic analysis. The pattern of genetic diversity in species with diverse sexual systems did not support the dead end hypothesis. The field survey of C. wolfii revealed no seed recruitment, but the genetic analysis on the current adult plants showed low signs of clonality, suggesting that this species has recently shifted to clonal reproduction. Results showed that overall, this genus had low genetic diversity and high differentiation, implying that it is vulnerable to environmental threats.

Incorporating microbiome analyses can enhance conservation of threatened species and ecosystem functions

Conservation genomics is a rapidly growing subdiscipline of conservation biology that uses genome-wide information to inform management of biodiversity at all levels. Such efforts typically focus on species or systems of conservation interest, but rarely consider associated microbes. At least three major approaches have been used to study how microorganisms broadly contribute to conservation areas: (1) diversity surveys map out microbial species distribution patterns in a variety of hosts, natural environments or regions; (2) functional surveys associate microbial communities with factors of interest, such as host health, symbiotic interactions, environmental characteristics, ecosystem processes, and biological invasions; and (3) manipulative experiments examine the response of changes to microbial communities or determine the functional roles of specific microbes within hosts or communities by adding, removing, or genetically modifying microbes. In practice, multiple approaches are often applied simultaneously. The results from all three conservation genomics approaches can be used to help design practical interventions and improve management actions, some of which we highlight below. However, experimental manipulations allow for more robust causal inferences and should be the ultimate goal of future work. Here we discuss how further integration of microbial research of a host's microbiome and of free living microbes into conservation biology will be an essential advancement for conservation of charismatic organisms and ecosystem functions in light of ongoing global environmental change.

Genetic Diversity Analysis and Core Collection Construction of Ancient Sophora japonica L. Using SSR Markers

Sophora japonica is an important native tree species in northern China, with high ornamental, medicinal, and ecological value. In order to elucidate the genetic resources of ancient S. japonica, 16 simple sequence repeat (SSR) markers were used to evaluate its genetic diversity and population structure and build a core collection of 416 germplasms from the Shandong, Shanxi, and Hebei provinces. A total of 160 alleles were detected, the mean major allele frequency (MAF)was 0.39, and the mean effective number of alleles (Ne) was 4.08. Shannon's information index (I), the observed heterozygosity (Ho), the expected heterozygosity (He), and the polymorphism information content (PIC) were 1.58, 0.64, 0.74, and 0.70, respectively, indicating relatively high genetic diversity in ancient S. japonica germplasms. Low genetic differentiation coefficient (Fst = 0.04) and frequent gene flow (Nm = 9.74) were found in the tested S. japonica populations, and an analysis of molecular variance (AMOVA) indicated that the genetic variation mainly came from within individuals (84%). A genetic structure and cluster analysis indicated that 416 ancient S. japonica germplasms could be divided into five subgroups, and there were obvious genetic exchanges among different subgroups. A core collection consisting of 104 (25% of the original collection) germplasms was constructed using the R language package Genetic Subsetter version 0.8 based on the stepwise regression method. The retention rates of the number of alleles (Na), Ne, I, He, and PIC were 87.50%, 106.24%, 103.02%, 102.50%, and 102.74%, respectively. The t-test analysis suggested that there were no significant differences between the core collection and the original collection. The principal coordinate analysis (PCoA) showed that the core collection was uniformly distributed within the initial collection and was able to fully represent the genetic diversity of the original collection. These results provide a scientific basis for the conservation and utilization of ancient S. japonica germplasms.

Genetic Diversity and Population Structure Analysis of Pinus elliottii Germplasm Resources in Jiangxi Province

This study aimed to compare and assess the genetic diversity and trends among the introduced family provenance, first-cycle superior trees breeding provenance, and improved-generation superior trees breeding provenance of Pinus elliottii using EST-SSR markers. The goal was to provide a foundation for advanced genetic improvement and sustainable utilization of P. elliottii in Jiangxi Province. A total of 417 individuals were analyzed for their genetic diversity and population structure using 19 pairs of SSR markers. The analysis identified 103 alleles across all the samples, with an average of 5.421 alleles per locus. Compared to other coniferous species, P. elliottii exhibited a moderate to high level of genetic diversity (I = 0.862, He = 0.457). Analysis of the molecular variance (AMOVA) revealed that 97.90% of the genetic variation occurred within provenances, consistent with a low genetic differentiation coefficient (Fst = 0.016 < 0.05) and high gene flow (Nm = 15.715) among provenances. In addition, analysis using STRUCTURE v. 2.3.4 software divided the 417 germplasm samples into two distinct groups, corroborating the results of the principal coordinates analysis (PCoA) and the unweighted pair group method with arithmetic (UPGMA) clustering analysis. Overall, the germplasm resources of P. elliottii exhibited rich genetic diversity, with the majority of the genetic variation occurring within provenances. For the genetic improvement of high-resin-yielding slash pines, breeding programs should prioritize populations with high genetic diversity while carefully selecting superior individuals from within those populations. These findings provide a solid foundation for breeding high-resin-yielding varieties and for future research on the sustainable utilization of these valuable resources.

Genetic Diversity and Association Analysis of Traits Related to Water-Use Efficiency and Nitrogen-Use Efficiency of Populus deltoides Based on SSR Markers

Populus deltoides is one of the primary tree species for bioenergy production in temperate regions. In arid/semi-arid northern China, the scarcity of water and nitrogen significantly limits the productivity of poplar plantations. The identification of relevant molecular markers can promote the breeding of resource-efficient varieties. In this study, 188 genotypes of P. deltoides from six provenances served as experimental material. Genetic differentiation analysis, analysis of molecular variance (AMOVA), principal coordinate analysis (PCoA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and genetic structure analysis were performed using selected simple sequence repeat (SSR) markers. Based on these analyses, the association analysis of water-use efficiency (WUE) and nitrogen-use efficiency (NUE) were conducted using general linear model (GLM) and mixed linear model (MLM) approaches. The results showed that 15 pairs of SSR primers successfully amplified across all 188 individuals, with an average of 7.33 alleles (Na) observed per primer pair. The polymorphism information content (PIC) ranged from 0.060 to 0.897, with an average of 0.544, indicating high genetic diversity in the selected markers. The average inbreeding coefficient intra-population (Fis), inbreeding coefficient inter-population (Fit), and inter-population genetic fraction coefficient (Fst) values were 0.005, 0.135, and 0.132, respectively, indicating high heterozygosity, substantial inbreeding within populations, and moderate genetic differentiation, with an average gene flow (Nm) of 1.964, suggesting substantial gene flow between populations. Additionally, molecular variance was primarily within individuals (84.12%). Genetic structure analysis revealed four subgroups, with some degree of genetic admixture among the provenances. In the GLM model, 11 markers were significantly associated with five traits (p < 0.05), with an average contribution rate of 15.82%. Notably, SSR132 and SSR143 were significantly associated with multiple traits (p < 0.05). The MLM model identified two markers (SSR47 and SSR85) significantly associated with ground diameter (p < 0.05) and one marker (SSR80) significantly associated with NUE (p < 0.05). This study identifies loci associated with WUE and NUE, laying a foundation for future genetic improvement and marker-assisted breeding strategies in poplar.

A spatial approach to jointly estimate Wright's neighborhood size and long-term effective population size

Spatially continuous patterns of genetic differentiation, which are common in nature, are often poorly described by existing population genetic theory or methods that assume panmixia or discrete, clearly definable populations. There is therefore a need for statistical approaches in population genetics that can accommodate continuous geographic structure, and that ideally use georeferenced individuals as the unit of analysis, rather than populations or subpopulations. In addition, researchers are often interested describing the diversity of a population distributed continuously in space, and this diversity is intimately linked to the dispersal potential of the organism. A statistical model that leverages information from patterns of isolation-by-distance to jointly infer parameters that control local demography (such as Wright's neighborhood size), and the long-term effective size (Ne) of a population would be useful. Here, we introduce such a model that uses individual-level pairwise genetic and geographic distances to infer Wright's neighborhood size and long-term Ne. We demonstrate the utility of our model by applying it to complex, forward-time demographic simulations as well as an empirical dataset of the Red Sea clownfish (Amphiprion bicinctus). The model performed well on simulated data relative to alternative approaches and produced reasonable empirical results given the natural history of clownfish. The resulting inferences provide important insights into the population genetic dynamics of spatially structure populations.

Assessing the current genetic structure of 21 remnant populations and predicting the impacts of climate change on the geographic distribution of Phoebe sheareri in southern China

Phoebe sheareri is a valuable tree species known as "Golden Nanmu" and is one of the most important protected tree species in China. However, natural populations are decreasing because of climate change and anthropogenic factors. To evaluate the genetic diversity and structure of remnant populations and the impacts of climate change on the distribution of potential suitable habitats, we conducted a field investigation and sampled 21 P. sheareri natural populations to evaluate their genetic diversity and structure using simple sequence repeat (SSR) molecular markers. Then, we predicted the distribution of suitable P. sheareri habitats across China under future scenarios (RCP 2.6 and RCP 8.5) and periods (2050 and 2070) using multivariate modeling methods-the MaxEnt model. The results showed a medium level of genetic diversity and low inbreeding in the 21 P. sheareri natural populations, and genetic differentiation among populations was significant, with 21.2 % genetic variation among populations. The remnant populations of P. sheareri were grouped into four genetic clusters based on genetic structure; five environmental variables involving four temperature variables and precipitation seasonality (Bio12) might determine the distribution of P. sheareri populations. In the future, the suitable habitats of P. sheareri are manifested as northward migration, and the highly suitable habitats are expected to increase. Our results highlight the importance of conservation units in situ, giving priority to populations with higher genetic diversity (e.g., TMS, FJS, and THY populations); sampling strategies for ex situ conservation, breeding and reforestation should consider climate change, especially Bio1 (annual mean temperature) and Bio12 (annual precipitation). Overall, this study may provide useful genetic information for strategies for the protection, management, and utilization of P. sheareri.

Phylogenetic and phenotypic characterization of Fusarium oxysporum f. sp. niveum isolates from Florida-grown watermelon

Fusarium wilt of watermelon (Citrullus lanatus) caused by Fusarium oxysporum f. sp. niveum (Fon), has become an increasing concern of farmers in the southeastern USA, especially in Florida. Management of this disease, most often through the use of resistant cultivars and crop rotation, requires an accurate understanding of an area’s pathogen population structure and phenotypic characteristics. This study improved the understanding of the state’s pathogen population by completing multilocus sequence analysis (MLSA) of two housekeeping genes (BT and TEF) and two loci (ITS and IGS), aggressiveness and race-determining bioassays on 72 isolates collected between 2011 and 2015 from major watermelon production areas in North, Central, and South Florida. Multilocus sequence analysis (MLSA) failed to group race 3 isolates into a single large clade; moreover, clade membership was not apparently correlated with aggressiveness (which varied both within and between clades), and only slightly with sampling location. The failure of multilocus sequence analysis using four highly conserved housekeeping genes and loci to clearly group and delineate known Fon races provides justification for future whole genome sequencing efforts whose more robust genomic comparisons will provide higher resolution of intra-species genetic distinctions. Consequently, these results suggest that identification of Fon isolates by race determination alone may fail to detect economically important phenotypic characteristics such as aggressiveness leading to inaccurate risk assessment.

Phylogeographic analyses of a migratory freshwater fish (Megalobrama terminalis) reveal a shallow genetic structure and pronounced effects of sea-level changes

Different types of fish taxa generally seem to present diverse phylogeographic structures and show different responses to environmental changes. In southern China, however, a large number of phylogeographic studies have been employed for small and/or benthic fish species, while phylogeographic patterns of larger and migratory species are not well understood. In this study, we chose Megalobrama terminalis, an endemic cyprinid from Southern China with a median size and relatively high migratory potential as a candidate to explore the phylogeographic structure and to seek the relevant driving forces using a multilocus approach (two mitochondrial markers and three nuclear markers). Our results show that M. terminalis exhibits three mtDNA genetic groups, each presenting genetic structure to the local geography, but the differentiation level was much weaker than that of small and/or benthic fish species reported in earlier studies. Nuclear loci did not observe pronounced genetic group subdivision, but did examine noteworthy genetic differentiation between the Hainan Island population and the mainland populations. Divergence time estimation and demographic analyses suggest that sea-level changes associated with the Late Pleistocene glacial cycles have exerted pronounced effects on the divergence of the three groups and the expansion of M. terminalis populations. Above all, our study provides important knowledge that can be used to improve monitoring programs and develop a conservation strategy for this endemic organism.

The geography of evolutionary divergence in the highly endemic avifauna from the Sierra Madre del Sur, Mexico

Background

Mesoamerica is a remarkable region with a high geological and ecological complexity. Within northern Mesoamerica, the biotic province of the Sierra Madre del Sur (SMS) in southwestern Mexico harbors exceptionally high avian endemism and diversity. Herein, we searched for spatially and temporally concordant phylogeographic patterns, in four bird genera from three distinct avian orders co-distributed across Mesoamerica and investigated their causes through hypothesis testing regarding historical processes. Selected species include endemic and differentiated populations across the montane forests of Mesoamerica, and particularly within the SMS.

Results

We gathered mitochondrial DNA sequences for at least one locus from 177 individuals across all species. We assessed genetic structure, demographic history, and defined a framework for the coalescent simulations used in biogeographic hypothesis testing temporal and spatial co-variance. Our analyses suggested shared phylogeographic breaks in areas corresponding to the SMS populations, and between the main montane systems in Mesoamerica, with the Central Valley of Oaxaca and the Nicaragua Depression being the most frequently shared breaks among analyzed taxa. Nevertheless, dating analyses and divergence patterns observed were consistent with the hypothesis of broad vicariance across Mesoamerica derived from mechanisms operating at distinct times across taxa in the SMS.

Conclusions

Our study provides a framework for understanding the evolutionary origins and historical factors enhancing speciation in well-defined regions within Mesoamerica, indicating that the evolutionary history of extant biota inhabiting montane forests is complex and often idiosyncratic.

Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus): a dietary-specialist species distributed across heterogeneous environments

The Australian koala is an iconic marsupial with highly specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions. Genetic clustering analysis and phylogenetic reconstruction reveals a lack of support for current taxonomic classification of three koala subspecies, with only a single evolutionary significant unit supported. Furthermore, ~70% of genetic variance is accounted for at the individual level. The Sydney Basin region is highlighted as a unique reservoir of genetic diversity, having higher diversity levels (i.e., Blue Mountains region; AvHecorr=0.20, PL% = 68.6). Broad-scale population differentiation is primarily driven by an isolation by distance genetic structure model (49% of genetic variance), with clinal local adaptation corresponding to habitat bioregions. Signatures of selection were detected between bioregions, with no single region returning evidence of strong selection. The results of this study show that although the koala is widely considered to be a dietary-specialist species, this apparent specialisation has not limited the koala's ability to maintain gene flow and adapt across divergent environments as long as the required food source is available.

Anadromy Redux? Genetic Analysis to Inform Development of an Indigenous American River Steelhead Broodstock

The construction of dams and water diversions has severely limited access to spawning habitat for anadromous fishes. To mitigate for these impacts, hatchery programs rear and release millions of juvenile salmonids, including steelhead, the anadromous ecotype of the species Oncorhynchus mykiss. These programs sometimes use nonindigenous broodstock sources that may have negative effects on wild populations. In California, however, only one anadromous fish hatchery program currently uses nonnative broodstock: the steelhead program at Nimbus Fish Hatchery on the American River, a tributary of the Sacramento River in the California Central Valley. The goal of this study was to determine if potentially appropriate sources to replace the broodstock for the Nimbus Hatchery steelhead program exist in the Upper American River, above Nimbus and Folsom dams. We show that all Upper American River O. mykiss sampled share ancestry with other populations in the Central Valley steelhead distinct population segment, with limited introgression from out-of-basin sources in some areas. Furthermore, some Upper American River populations retain adaptive genomic variation associated with a migratory life history, supporting the hypothesis that these populations display adfluvial migratory behavior. Together, these results provide insights into the evolution of trout populations above barrier dams. We conclude that some Upper American River O. mykiss populations represent genetically appropriate sources from which fisheries managers could potentially develop a new broodstock for the Nimbus Hatchery steelhead program to reestablish a native anadromous population in the Lower American River and contribute to recovery of the threatened Central Valley steelhead distinct population segment.