Exploring how species diverge is vital for understanding the drivers of speciation. Factors such as geographical separation and ecological selection, hybridization, polyploidization and shifts in ...mating system are all major mechanisms of plant speciation, but their contributions to divergence are rarely well understood. Here we test these mechanisms in two plant species, Gentiana lhassica and G. hoae, with the goal of understanding recent allopatric species divergence on the Qinghai-Tibet Plateau (QTP).
We performed Bayesian clustering, phylogenetic analysis and estimates of hybridization using 561 302 nuclear genomic single nucleotide polymorphisms (SNPs). We performed redundancy analysis, and identified and annotated species-specific SNPs (ssSNPs) to explore the association between climatic preference and genetic divergence. We also estimated genome sizes using flow cytometry to test for overlooked polyploidy.
Genomic evidence confirms that G. lhassica and G. hoae are closely related but distinct species, while genome size estimates show divergence occurred without polyploidy. Gentiana hoae has significantly higher average FIS values than G. lhassica. Population clustering based on genomic SNPs shows no signature of recent hybridization, but each species is characterized by a distinct history of hybridization with congeners that has shaped genome-wide variation. Gentiana lhassica has captured the chloroplast and experienced introgression with a divergent gentian species, while G. hoae has experienced recurrent hybridization with related taxa. Species distribution modelling suggested range overlap in the Last Interglacial Period, while redundancy analysis showed that precipitation and temperature are the major climatic differences explaining the separation of the species. The species differ by 2993 ssSNPs, with genome annotation showing missense variants in genes involved in stress resistance.
This study suggests that the distinctiveness of these species on the QTP is driven by a combination of hybridization, geographical isolation, mating system differences and evolution of divergent climatic preferences.
Understanding the evolutionary and ecological processes driving population differentiation and speciation can provide critical insights into the formation of biodiversity. Here, we examine the link ...between population genetic processes and biogeographic history underlying the generation of diversity in the Hengduan Mountains (HM), a region harboring a rich and dynamic flora. We used restriction site-associated DNA sequencing to generate 1,907 single-nucleotide polymorphisms (SNPs) and four-kb of plastid sequence in species of the
Gentiana hexaphylla
complex (Gentianaceae). We performed genetic clustering with spatial and non-spatial models, phylogenetic reconstructions, and ancestral range estimation, with the aim of addressing the processes influencing diversification of
G. hexaphylla
in the HM. We find the
G. hexaphylla
complex is characterized by geographic genetic structure with clusters corresponding to the South, North and the central HM. Phylogenetic reconstruction and pairwise
F
ST
analyses showed deep differentiation between Southern and Northern populations in the HM. The population in Mount Taibai exhibited the highest genetic similarity to the North HM. Ancestral range estimation indicated that the
G. hexaphylla
complex originated in the central HM and then diverged in the Pliocene and the Early Pleistocene, before dispersing widely, resulting in the current distinct lineages. Overall, we found deep genomic differentiation in the
G. hexaphylla
complex corresponds to geographic barriers to dispersal in the HM and highlights a critical role of the uplift of the Daxue Mountains and subsequent climatic fluctuations underlying diversification. The colonization of
G. hexaphylla
in the Mount Taibai region suggests directional dispersal between the alpine flora of the Qinling Mountains and the HM.
A major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In Begonia, one of the largest plant genera (1900+ species), it has been postulated that the high number ...of endemic species is a by‐product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by homogenizing gene flow in zones of secondary contact. Here, we test the outcomes of secondary contact in Begonia by genotyping multiple sympatric sites with 12 nuclear and seven plastid loci. We show that three sites of secondary contact between B. heracleifolia and B. nelumbiifolia are highly structured, mostly containing parental genotypes, with few F1 hybrids. A sympatric site between B. heracleifolia and B. sericoneura contains a higher proportion of F1s, but little evidence of introgression. The lack of later‐generation hybrids contrasts with that documented in many other plant taxa, where introgression is extensive. Our results, in conjunction with previous genetic work, show that Begonia demonstrate properties making them exceptionally prone to speciation, at multiple stages along the divergence continuum. Not only are populations weakly connected by gene flow, promoting allopatric speciation, but species often show strong reproductive barriers in secondary contact. Whether similar mechanisms contribute to diversification in other large genera remains to be tested.
Disentangling the phylogenetic relationships of taxonomically complex plant groups is often mired by challenges associated with recent speciation, hybridization, complex mating systems, and ...polyploidy. Here, we perform a phylogenomic analysis of eyebrights (
Euphrasia
), a group renowned for taxonomic complexity, with the aim of documenting the extent of phylogenetic discordance at both deep and at shallow phylogenetic scales. We generate whole-genome sequencing data and integrate this with prior genomic data to perform a comprehensive analysis of nuclear genomic, nuclear ribosomal (nrDNA), and complete plastid genomes from 57 individuals representing 36
Euphrasia
species. The species tree analysis of 3,454 conserved nuclear scaffolds (46 Mb) reveals that at shallow phylogenetic scales postglacial colonization of North Western Europe occurred in multiple waves from discrete source populations, with most species not being monophyletic, and instead combining genomic variants from across clades. At a deeper phylogenetic scale, the
Euphrasia
phylogeny is structured by geography and ploidy, and partially by taxonomy. Comparative analyses show Southern Hemisphere tetraploids include a distinct subgenome indicative of independent polyploidy events from Northern Hemisphere taxa. In contrast to the nuclear genome analyses, the plastid genome phylogeny reveals limited geographic structure, while the nrDNA phylogeny is informative of some geographic and taxonomic affinities but more thorough phylogenetic inference is impeded by the retention of ancestral polymorphisms in the polyploids. Overall our results reveal extensive phylogenetic discordance at both deeper and shallower nodes, with broad-scale geographic structure of genomic variation but a lack of definitive taxonomic signal. This suggests that
Euphrasia
species either have polytopic origins or are maintained by narrow genomic regions in the face of extensive homogenizing gene flow. Moreover, these results suggest genome skimming will not be an effective extended barcode to identify species in groups such as
Euphrasia
, or many other postglacial species groups.
Premise
Species delimitation in parasitic organisms is challenging because traits used to identify species are often plastic and vary depending on the host. Here, we use species from a recent ...radiation of generalist hemiparasitic Euphrasia to investigate trait variation and trait plasticity. We tested whether Euphrasia species show reliable trait differences, investigated whether these differences correspond to life history trade‐offs between growth and reproduction, and quantified plasticity in response to host species.
Methods
Common garden experiments were used to evaluate trait differences between 11 Euphrasia taxa grown on a common host, document phenotypic plasticity when a single Euphrasia species is grown on eight different hosts, and relate observations to trait differences recorded in the wild.
Results
Euphrasia exhibited variation in life history strategies; some individuals transitioned rapidly to flowering at the expense of early season growth, while others invested in vegetative growth and delayed flowering. Life history differences were present between some species, though many related taxa lacked clear trait differences. Species differences were further blurred by phenotypic plasticity—many traits were plastic and changed with host type or between environments.
Conclusions
Phenotypic plasticity in response to host and environment confounds species delimitation in Euphrasia. When grown in a common garden environment, some morphologically distinct taxa can be identified, though others represent morphologically similar shallow segregates. Trait differences present between some species and populations demonstrate the rapid evolution of distinct life history strategies in response to local ecological conditions.
Digest Joffard, Nina; Silva, Willian T.A.F.; Twyford, Alex D.
Evolution,
March 2021, Letnik:
75, Številka:
3
Journal Article
Recenzirano
Odprti dostop
Recently diverged species often show incomplete reproductive isolation and subsequently experience hybridization and introgression. The plant genus Mimulus includes many such examples of closely ...related taxa that prove useful for studying incipient speciation. However, Sandstedt et al. show that in contrast to other Mimulus species, species of the M. tilingii complex are characterized by strong postzygotic isolation mediated by multiple barriers. This finding highlights the diverse speciation histories of related plant groups.
Color polymorphisms have long been of evolutionary interest for their diverse roles, including mate choice, predator avoidance, and pollinator attraction. While color variation is often under strong ...selection, some taxa demonstrate unexpectedly high frequencies of presumed deleterious color forms. Here we show that a genetic variant underlying complete loss of anthocyanin pigmentation has risen to an unexpectedly high frequency of >0.2 in a natural population of the plant Mimulus guttatus. Decreased expression of MYB5 transcription factor is associated with unpigmented morphs. While the allele was found only in heterozygote adults in the wild, suggesting negative selection, experiments were unable to demonstrate a fitness cost for unpigmented plants, suggesting a cryptic selection pressure in the wild. However, life-history differences among morphs suggests that unpigmented individuals benefit from later flowering and clonal growth. Overall, our study highlights the complex interplay of factors maintaining variation in nature, even for genes of major effect.
Planting of native trees for habitat restoration is a widespread practice, but the consequences for the retention and transmission of genetic diversity in planted and natural populations are unclear. ...Using Inga vera subsp. affinis as a model species, we genotyped five natural and five planted populations in the Atlantic forest of northeastern Brazil at polymorphic microsatellite loci. We studied the breeding system and population structure to test how much genetic diversity is retained in planted relative to natural populations. We then genotyped seedlings from these populations to test whether genetic diversity in planted populations is restored by outcrossing to natural populations of I. vera. The breeding system of natural I. vera populations was confirmed to be highly outcrossing (t = 0.92; FIS = -0.061, P = 0.04), with populations showing weak population substructure (FST = 0.028). Genetic diversity in planted populations was 50% less than that of natural populations (planted: AR = 14.9, HO = 0.865 and natural: AR = 30.8, HO = 0.655). However, seedlings from planted populations showed a 30% higher allelic richness relative to their parents (seedlings AR = 10.5, parents AR = 7.6). Understanding the processes and interactions that shape this system are necessary to provide ecologically sensible goals and successfully restore hyper-fragmented habitats. Future restoration plans for I. vera must consider the genetic diversity of planted populations and the potential for gene flow between natural populations in the landscape, in order to preserve ecological interactions (i.e. pollination), and promote opportunities for outcrossing.
In intimate ecological interactions, the interdependency of species may result in correlated demographic histories. For species of conservation concern, understanding the long-term dynamics of such ...interactions may shed light on the drivers of population decline. Here, we address the demographic history of the monarch butterfly, Danaus plexippus, and its dominant host plant, the common milkweed Asclepias syriaca (A. syriaca), using broad-scale sampling and genomic inference. Because genetic resources for milkweed have lagged behind those for monarchs, we first release a chromosome-level genome assembly and annotation for common milkweed. Next, we show that despite its enormous geographic range across eastern North America, A. syriaca is best characterized as a single, roughly panmictic population. Using approximate Bayesian computation with random forests (ABC-RF), a machine learning method for reconstructing demographic histories, we show that both monarchs and milkweed experienced population expansion during the most recent recession of North American glaciers 10,000–20,000 years ago. Our data also identify concurrent population expansions in both species during the large-scale clearing of eastern forests (∼200 years ago). Finally, we find no evidence that either species experienced a reduction in effective population size over the past 75 years. Thus, the well-documented decline of monarch abundance over the past 40 years is not visible in our genomic dataset, reflecting a possible mismatch of the overwintering census population to effective population size in this species.
•A new, chromosome-level assembly and annotation is provided for common milkweed•Milkweed forms an enormous, panmictic population across its North American range•Monarchs and milkweeds both had two concurrent population expansions in the past•Neither species shows signs of recent declines in effective population size
Boyle et al. find correlated population histories for the monarch butterfly and its common milkweed food plant over the past 25,000 years. Using genomic data and a new, chromosome-level milkweed assembly, they find expansions in both species corresponding to the recession of glaciers and to the more recent clearing of North American forests.
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