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•Myrcia s.l. biogeography was influenced by Neotropical geology and past climate.•Diversification of Myrcia s.l. subgroups took place during the Miocene.•Montane Atlantic Forest had a ...central role in the origin of most subgroups.•Guayana Region and Caribbean were also important for some lineages.•The importance of these regions highlights the montane preference of Myrcia s.l.
Many recent studies discuss the influence of climatic and geological events in the evolution of Neotropical biota by correlating these events with dated phylogenetic hypotheses. Myrtaceae is one of the most diverse Neotropical groups and it therefore a good proxy of plant diversity in the region. However, biogeographic studies on Neotropical Myrtaceae are still very limited. Myrcia s.l. is an informal group comprising three accepted genera (Calyptranthes, Marlierea and Myrcia) making up the second largest Neotropical group of Myrtaceae, totalling about 700 species distributed in nine subgroups. Exclusively Neotropical, the group occurs along the whole of the Neotropics with diversity centres in the Caribbean, the Guiana Highlands and the central-eastern Brazil. This study aims to identify the time and place of divergence of Myrcia s.l. lineages, to examine the correlation in light of geological and climatic events in the Neotropics, and to explore relationships among Neotropical biogeographic areas. A dated phylogenetic hypothesis was produced using BEAST and calibrated by placing Paleomyrtinaea princetonensis (56Ma) at the root of the tree; biogeographic analysis used the DEC model with dispersal probabilities between areas based on distance and floristic affinities. Myrcia s.l. originated in the Montane Atlantic Forest between the end of Eocene and early Miocene and this region acted as a secondary cradle for several lineages during the evolution of this group. The Caribbean region was important in the diversification of the Calyptranthes clade while the Guayana shield appears as ancestral area for an older subgroup of Myrcia s.l. The Amazon Forest has relatively low diversity of Myrcia s.l. species but appears to have been important in the initial biogeographic history of old lineages. Lowland Atlantic Forest has high species diversity but species rich lineages did not originate in the area. Diversification of most subgroups of Myrcia s.l. occurred throughout the Miocene, as reported for other Neotropical taxa. During the Miocene, geological events may have influenced the evolution of the Caribbean and Amazon forest lineages, but other regions were geological stable and climate changes were the most likely drivers of diversification. The evolution of many lineages in montane areas suggests that Myrcia s.l. may be particularly adapted to such environments.
Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods ...for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number of studies have shown that recently dried specimens can be used to yield ploidy data. Recent studies have started to explore whether high-throughput sequencing (HTS) data can be used to assess ploidy levels by analyzing allelic frequencies from single copy nuclear genes. Here, we compare different approaches using a range of yam (
) tissues of varying ages, drying methods and quality, including herbarium tissue. Our aims were to: (1) explore the limits of flow cytometry in estimating ploidy level from dried samples, including herbarium vouchers collected between 1831 and 2011, and (2) optimize a HTS-based method to estimate ploidy by considering allelic frequencies from nuclear genes obtained using a target-capture method. We show that, although flow cytometry can be used to estimate ploidy levels from herbarium specimens collected up to fifteen years ago, success rate is low (5.9%). We validated our HTS-based estimates of ploidy using 260 genes by benchmarking with dried samples of species of known ploidy (
,
, and
). Subsequently, we successfully applied the method to the 85 herbarium samples analyzed with flow cytometry, and successfully provided results for 91.7% of them, comprising species across the phylogenetic tree of
. We also explored the limits of using this HTS-based approach for identifying high ploidy levels in herbarium material and the effects of heterozygosity and sequence coverage. Overall, we demonstrated that ploidy diversity within and between species may be ascertained from historical collections, allowing the determination of polyploidization events from samples collected up to two centuries ago. This approach has the potential to provide insights into the drivers and dynamics of ploidy level changes during plant evolution and crop domestication.
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•Our results highlight the importance of the number of locules in Myrcia classification.•The widespread and taxonomically complex Myrcia guianensis is non-monophyletic.•Myrcia sect. ...Aguava appears to have originated in the Cerrado.•Transitions from Cerrado to humid forests occurred in the evolution of M. sect. Aguava.•Combination of NGS and Sanger data is possible and generates robust phylogenetic trees.
Myrcia is one of the largest exclusively Neotropical angiosperm genera, including ca. 800 species divided into nine sections. Myrcia sect. Aguava is one of most complex sections of Myrcia due to high morphological variation and wide distribution range of some species, including M. guianensis, with distribution throughout South America and a complex taxonomic history. We used complete plastid DNA sequences data generated using next-generation sequencing of 45 terminals, mostly from Myrcia sect. Aguava. These data were combined with five target DNA regions (ITS, psbA-trnH, trnL-trnF, trnQ-rps16, ndhF) of additional terminals to increase taxonomic coverage. Phylogenetic analyses were conducted using a maximum likelihood approach, and divergence times and ancestral range distributions were estimated. Myrcia sect. Aguava is monophyletic and exclusively comprises species with trilocular ovaries but has no relationship with other groups within Myrcia that possess trilocular ovaries. Three main lineages that correspond to geographical distribution are recognized within Myrcia sect. Aguava. Multiple accessions reveal a non-monophyletic Myrcia guianensis and stress the biogeographical structure inside the group. Myrcia sect. Aguava had a probable mid-Miocene origin in the Cerrado, but lineages that persisted there diversified only more recently, when the present-day vegetation started to stabilize. Posterior migrations to Atlantic Forest, Amazon and Caribbean occurred at the end of Miocene, evidencing transitions from open and dry to forested and more humid areas that are less frequent in the Neotropics. Overall, it is observed that related lineages remained in ecologically similar environments. Future perspectives on Myrcia and Myrteae in the phylogenomic era are also discussed.
Premise
Both universal and family‐specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, ...we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships.
Methods
We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit and a family‐specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies‐coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support.
Results
For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae‐specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae‐specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. Merging of data obtained with the two kits resulted in a well‐supported phylogenetic tree.
Conclusions
The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.
Hybridization and polyploidy are now hypothesized to have regularly stimulated speciation in angiosperms, but individual or combined involvement of these two processes seems to involve significant ...differences in pathways of formation, establishment and evolutionary consequences of resulting lineages. We evaluate here the classical cytological hypothesis that ploidy in hybrid speciation is governed by the extent of chromosomal rearrangements among parental species. Within a phylogenetic framework, we calculate genetic divergence indices for 50 parental species pairs and use these indices as surrogates for the overall degree of genomic divergence (that is, as proxy for assessments of dissimilarity of the parental chromosomes). The results confirm that genomic differentiation between progenitor taxa influences the likelihood of diploid (homoploid) versus polyploid hybrid speciation because genetic divergence between parents of polyploids is found to be significantly greater than in the case of homoploid hybrid species. We argue that this asymmetric relationship may be reinforced immediately after hybrid formation, during stabilization and establishment. Underlying mechanisms potentially producing this pattern are discussed.
The use of phylogenetic tools and studies has strongly increased in the last two decades especially in conservation biology and community ecology. Phylogenetic trees are essential to understand the ...processes of community or network assembly, to identify centers of diversification, and to help protect Earth’s evolutionary heritage. Despite two decades of research and syntheses, there are still many discussions on how phylogenetic diversity (PD) methods should be effectively applied to those fields. In particular, conservation approaches based on PD have become similar to these used in community ecology. Thus, the main benefit of using PD calculations in conservation biology may have been ignored or misinterpreted. Our goal is to discuss and provide guidelines to the use of PD in biodiversity conservation so that its benefits are not hidden or lost in the approaches employed. We also aim that benefits and uses are better recognized and more easily understood by researchers or practitioners who would like to include PD in their studies and conservation planning.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We reviewed the status of orthodox seed collections of globally threatened plants conserved in − 20 °C long-term storage at the Millennium Seed Bank, Royal Botanic Gardens, Kew, UK in terms of their ...geographic and bioclimatic representativeness, taxonomic and genetic diversity, quality and physiological status. The comprehensive dataset used spans over 45 years of worldwide conservation effort across various organisations. The data provides evidence-based results and future directions for the represented globally threatened flora that are of relevance to all plant conservation and seed banking organisations across the globe. The reviewed sample includes 523 collections and represents a wide geographic range, originating from 67 countries, from all nine bio-geographic continents. The majority of collections originated from temperate climates and from habitats with no dry seasons but experiencing warm summer periods. The taxonomic composition of the collections highlighted a substantial diversity, with 303 taxa (four extinct in the wild; 56 critically endangered; 105 endangered; and 138 vulnerable) represented by 297 species, 199 genera and 74 families. Almost four fifths of the collections were harvested from wild habitats. Whilst wild-origin collections can harbour useful genes not available in the cultivated gene pool, for threatened plants both collections and taxa are likely to suffer from low genetic diversity as a low number of individual plants, populations and/or potentially viable or usable seeds were sampled at the original harvest. Large numbers of empty and infested seeds in the original harvest have significantly affected the quality of collections in terms of availability of potentially viable or usable seeds in collections. As a result, just over one third of taxa and one fifth of collections consisted of ≥ 5000 potentially viable or usable seeds. Viable seeds exhibited a sound physiological status in terms of germinability and viability at the initial round of germination tests after storage, but on average, relative germination and viability achieved were below 85%. A decline in germinability during their variable time of storage was evident for 16% of the 78 collections analysed for longevity. According to a set of criteria, suitable germination protocols for propagation of plants from seeds were identified for 165 taxa. Given the apparent differences between wild species, especially those that are rare and threatened, and domesticated crops, the quality and physiological status of reviewed collections are reasonably sound. The characteristics we observed for collections, the challenges we identified for conserving them and the germination protocols we suggested for propagation of plants from seeds have the scope to be noted, integrated and used globally across various conservation activities and policies.
AIM: Dioscorea (Dioscoreaceae) is a predominantly pantropical genus (< 600 species) that includes the third most important tropical tuber crop and species of pharmacological value. Fossil records ...from both the Northern and Southern Hemispheres were used to test hypotheses about the origin of the genus Dioscorea, and to examine potential macroevolutionary processes that led to its current distribution. LOCATION: Pantropical distribution. METHODS: Divergence times were estimated using the most comprehensive phylogeny of the group published to date based on plastid sequences and fossil calibrations, applying a relaxed‐clock model approach. Ancestral areas and range shifts were reconstructed using time‐stratified likelihood‐based models, reflecting past continental connectivity and biogeographical models incorporating the spatial range of fossils. RESULTS: Fossil‐informed biogeographical analysis supported colonization of the Nearctic by ancient yam lineages from the western Palaearctic and subsequent migration to the South. Most of the pantropical South American, African and Southeast Asian lineages experienced a relatively recent diversification in the Oligocene–Miocene. Long‐distance dispersals were inferred for the colonizations of the New World, Africa and Madagascar. MAIN CONCLUSIONS: Dioscorea likely originated between the Late Cretaceous and the Early Eocene in the Laurasian Palaearctic, followed by possible dispersal to South America via the Eocene North Atlantic Land Bridge.
Myrcia section Aulomyrcia includes ∼120 species that are endemic to the Neotropics and disjunctly distributed in the moist Amazon and Atlantic coastal forests of Brazil. This paper presents the first ...comprehensive phylogenetic study of this group and this phylogeny is used as a basis to evaluate recent classification systems and to test alternative hypotheses associated with the history of this clade.
Fifty-three taxa were sampled out of the 120 species currently recognized, plus 40 outgroup taxa, for one nuclear marker (ribosomal internal transcribed spacer) and four plastid markers (psbA-trnH, trnL-trnF, trnQ-rpS16 and ndhF). The relationships were reconstructed based on Bayesian and maximum likelihood analyses. Additionally, a likelihood approach, 'geographic state speciation and extinction', was used to estimate region- dependent rates of speciation, extinction and dispersal, comparing historically climatic stable areas (refugia) and unstable areas.
Maximum likelihood and Bayesian inferences indicate that Myrcia and Marlierea are polyphyletic, and the internal groupings recovered are characterized by combinations of morphological characters. Phylogenetic relationships support a link between Amazonian and north-eastern species and between north-eastern and south-eastern species. Lower extinction rates within glacial refugia suggest that these areas were important in maintaining diversity in the Atlantic forest biodiversity hotspot.
This study provides a robust phylogenetic framework to address important ecological questions for Myrcia s.l. within an evolutionary context, and supports the need to unite taxonomically the two traditional genera Myrcia and Marlierea in an expanded Myrcia s.l. Furthermore, this study offers valuable insights into the diversification of plant species in the highly impacted Atlantic forest of South America; evidence is presented that the lowest extinction rates are found inside refugia and that range expansion from unstable areas contributes to the highest levels of plant diversity in the Bahian refugium.
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