• The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and ...divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny.
• We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny of the world’s oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.
• Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity.
• The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.
The 196 parties to the Convention on Biological Diversity (CBD) will soon agree to a post-2020 global framework for conserving the three elements of biodiversity (genetic, species, and ecosystem ...diversity) while ensuring sustainable development and benefit sharing. As the most significant global conservation policy mechanism, the new CBD framework has far-reaching consequences- it will guide conservation actions and reporting for each member country until 2050. In previous CBD strategies, as well as other major conservation policy mechanisms, targets and indicators for genetic diversity (variation at the DNA level within species, which facilitates species adaptation and ecosystem function) were undeveloped and focused on species of agricultural relevance. We assert that, to meet global conservation goals, genetic diversity within all species, not just domesticated species and their wild relatives, must be conserved and monitored using appropriate metrics. Building on suggestions in a recent Letter in Science (Laikre et al., 2020) we expand argumentation for three new, pragmatic genetic indicators and modifications to two current indicators for maintaining genetic diversity and adaptive capacity of all species, and provide guidance on their practical use. The indicators are: 1) the number of populations with effective population size above versus below 500, 2) the proportion of populations maintained within species, 3) the number of species and populations in which genetic diversity is monitored using DNA-based methods. We also present and discuss Goals and Action Targets for post-2020 biodiversity conservation which are connected to these indicators and underlying data. These pragmatic indicators and goals have utility beyond the CBD; they should benefit conservation and monitoring of genetic diversity via national and global policy for decades to come.
Local adaptation is a critical evolutionary process that allows plants to grow better in their local compared to non‐native habitat and results in species‐wide geographic patterns of adaptive genetic ...variation. For forest tree species with a long generation time, this spatial genetic heterogeneity can shape the ability of trees to respond to rapid climate change. Here, we identify genomic variation that may confer local environmental adaptations and then predict the extent of adaptive mismatch under future climate as a tool for forest restoration or management of the widely distributed high‐elevation oak species Quercus rugosa in Mexico. Using genotyping by sequencing, we identified 5,354 single nucleotide polymorphisms (SNPs) genotyped from 103 individuals across 17 sites in the Trans‐Mexican Volcanic Belt, and, after controlling for neutral genetic structure, we detected 74 FST outlier SNPs and 97 SNPs associated with climate variation. Then, we deployed a nonlinear multivariate model, Gradient Forests, to map turnover in allele frequencies along environmental gradients and predict areas most sensitive to climate change. We found that spatial patterns of genetic variation were most strongly associated with precipitation seasonality and geographic distance. We identified regions of contemporary genetic and climatic similarities and predicted regions where future populations of Q. rugosa might be at risk due to high expected rate of climate change. Our findings provide preliminary details for future management strategies of Q. rugosa in Mexico and also illustrate how a landscape genomic approach can provide a useful tool for conservation and resource management strategies.
Poleward Pleistocene plant migration has been an important process structuring modern temperate and boreal plant communities, but the contribution of equator-ward migration remains poorly understood. ...Paleobotanical evidence suggests Miocene or Pleistocene origin for temperate 'sky island' plant taxa in Mexico. These 'rear edge' populations situated in a biodiversity hotspot may be an important reserve of genetic diversity in changing climates. We used mtDNA sequences, cpDNA sequences and chloroplast microsatellites to test hypotheses of Miocene vs Pleistocene colonization of temperate Douglas-fir in Mexico, explore geographic patterns of molecular variation in relation to Pleistocene climate history using ecological niche models, and assess the taxonomic and conservation implications. We found strong evidence for Pleistocene divergence of Douglas-fir in Mexico (958 thousand yr before present (ka) with the 90% highest posterior density interval ranging from 1.6 million yr before present (Ma) to 491 ka), consistent with the southward Pleistocene migration hypothesis. Genetic diversity was high and strongly partitioned among populations. Spatial patterns of molecular variation and ecological niche models suggest a complex late Pleistocene history involving periods of isolation and expansion along mountain corridors. These results highlight the importance of southward Pleistocene migration in establishing modern high-diversity plant communities and provide critical insights into proposals to conserve the unique biodiversity of Mexican Douglas-fir and associated taxa.
Post-2020 goals overlook genetic diversity Laikre, Linda; Hoban, Sean; Bruford, Michael W ...
Science (American Association for the Advancement of Science),
03/2020, Letnik:
367, Številka:
6482
Journal Article
Premise
Phylogeographical studies are fundamental for understanding factors that influence the spatial distribution of genetic lineages within species. Population expansions and contractions, ...distribution shifts, and climate changes are among the most important factors shaping the genetic compositions of populations.
Methods
We investigated the phylogeography of an endemic oak, Quercus mexicana (Fagaceae), which has a restricted distribution in northeastern Mexico along the Sierra Madre Oriental and adjacent areas. Nuclear and chloroplast DNA microsatellite markers were used to describe the genetic diversity and structure of 39 populations of Q. mexicana along its entire distribution area. We tested whether population expansion or contraction events influenced the genetic diversity and structure of the species. We also modeled the historical distributional range of Q. mexicana (for the Mid Holocene, the Last Glacial Maximum, and the Last Interglacial) to estimate the extent to which climate fluctuations have impacted the distribution of this oak species.
Results
Our results revealed high genetic diversity and low genetic structure in Q. mexicana populations. Ecological niche models suggested historical fluctuations in the distributional range of Q. mexicana. Historical range changes, gene flow, and physical barriers seem to have played an important role in shaping the phylogeographic structure of Q. mexicana.
Conclusions
Our study indicates that the genetic structure of Q. mexicana may have been the result of responses of oak trees not only to heterogeneous environments present in the Sierra Madre Oriental and adjacent areas, but also to elevational and latitudinal shifts in response to climate changes in the past.
The climatic and geological changes that occurred during the Quaternary, particularly the fluctuations during the glacial and interglacial periods of the Pleistocene, shaped the population demography ...and geographic distribution of many species. These processes have been studied in several groups of organisms in the Northern Hemisphere, but their influence on the evolution of Neotropical montane species and ecosystems remains unclear. This study contributes to the understanding of the effect of climatic fluctuations during the late Pleistocene on the evolution of Andean mountain forests. First, we describe the nuclear and plastidic DNA patterns of genetic diversity, structure, historical demography, and landscape connectivity of Quercus humboldtii, which is a typical species in northern Andean montane forests. Then, these patterns were compared with the palynological and evolutionary hypotheses postulated for montane forests of the Colombian Andes under climatic fluctuation scenarios during the Quaternary. Our results indicated that populations of Q. humboldtii have high genetic diversity and a lack of genetic structure and that they have experienced a historical increase in connectivity from the last glacial maximum (LGM) to the present. Furthermore, our results showed a dramatic reduction in the effective population size followed by an expansion before the LGM, which is consistent with the results found by palynological studies, suggesting a change in dominance in Andean forests that may be related to ecological factors rather than climate change.
This study describes the nuclear and plastidic DNA patterns of genetic diversity, structure, historical demography, and landscape connectivity of Quercus humboldtii. We found a high population genetic diversity, lack of genetic structure, and evidence of a demographic expansion predating the LGM
Key message
Oak species displayed high interspecific functional trait variation. The resource use strategy among oaks both at the above and belowground organs was guided by the fast-slow continuum.
...Plant functional ecology has focused on the study of functional strategies and general patterns of trait covariation. Mostly, studies intend to elucidate how plants cope with resource capture both at the above and belowground organs and to understand how the capacity for resource gain relates with the species distribution. American oaks are an interesting and important tree clade, they radiated into diverse environments outside temperate regions implying the development of adaptations to persist under different environmental regimes. Therefore, we explored patterns of differentiation in functional traits related with the capacity for resource use in 3-month seedlings of ten Mexican oak species representative from semiarid, temperate and subtropical montane regions. We examined the fast–slow trade-off and its importance in species differentiation on both above and belowground organs. Additionally, we investigated how resource acquisition strategy of the species was related with the environmental conditions experienced in their habitats. We found a significant differentiation in both above and belowground traits, and in both cases oak species segregated along the fast–slow continuum. We found only a few significant trait-by-trait relationships, implying a weak coordination among aerial and subterranean organs. Additionally, species from sites with higher precipitation seasonality had a higher root growth, and species from humid sites had larger leaves. These findings highlight important functional variation among oak seedlings which was related with the climatic conditions encompassed along their native geographic range.
In this study, the effect of hybridization on the interspecific differentiation of two species of red oaks,
Quercus acutifolia
and
Q. grahamii,
was evaluated. It is thought that hybridization is ...possible between these two species since they can inhabit adjacently and have periods of synchronous flowering. In addition, individuals with intermediate morphological attributes have been detected within their populations. To resolve this question, samples were collected from 280 adult individuals from 28 sampling locations: 17 of
Q. acutifolia
and 11 of
Q. grahamii
. To identify the individuals belonging to the parental species and those with the presence of hybridization, the individuals were genotyped with 10 nuclear microsatellite loci. To determine the patterns of leaf variation, two sets of morphological traits were considered: the first was 22 foliar morphological measurements, and the second was a geometric morphometry analysis using 40 two-dimensional pseudolandmarks. The results of the analysis of genetic allocation revealed that a large proportion of individuals from all populations showed evidence of introgression in their genomes. The morphological comparison showed that there was a clear differentiation between individuals classified as purebred members of the species
Q. acutifolia
and
Q. grahamii
. Individuals with evidence of primary hybridization (F1) were scarce and had morphologies similar to those of the
Q. grahamii
species. On the other hand, introgressed individuals (F2) seemed to be very similar to their genetically closest parents. The results show that the patterns of foliar morphological variation are not very useful for detecting hybridization events between species with continuous genetic exchange.
In this response, we address comments and clarify the rationale behind the choice of hypotheses aimed to describe the Quercus humboldtii phylogeography in the Colombian Andes. Finally, we explain our ...disagreement with the conclusions of a previous critique, since these are not necessarily adequate under the implemented population genetics approach.
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