High‐throughput DNA sequencing facilitates the analysis of large portions of the genome in nonmodel organisms, ensuring high accuracy of population genetic parameters. However, empirical studies ...evaluating the appropriate sample size for these kinds of studies are still scarce. In this study, we use double‐digest restriction‐associated DNA sequencing (ddRADseq) to recover thousands of single nucleotide polymorphisms (SNPs) for two physically isolated populations of Amphirrhox longifolia (Violaceae), a nonmodel plant species for which no reference genome is available. We used resampling techniques to construct simulated populations with a random subset of individuals and SNPs to determine how many individuals and biallelic markers should be sampled for accurate estimates of intra‐ and interpopulation genetic diversity. We identified 3646 and 4900 polymorphic SNPs for the two populations of A. longifolia, respectively. Our simulations show that, overall, a sample size greater than eight individuals has little impact on estimates of genetic diversity within A. longifolia populations, when 1000 SNPs or higher are used. Our results also show that even at a very small sample size (i.e. two individuals), accurate estimates of FST can be obtained with a large number of SNPs (≥1500). These results highlight the potential of high‐throughput genomic sequencing approaches to address questions related to evolutionary biology in nonmodel organisms. Furthermore, our findings also provide insights into the optimization of sampling strategies in the era of population genomics.
The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of ...the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.
Chloroplast (cp) genome organization, gene order, and content have long been considered conserved among land plants. Despite that, the generation of thousands of complete plastomes through ...next-generation sequencing (NGS) has challenged their conserved nature. In this study, we analyze 11 new complete plastomes of
(Bignonieae, Bignoniaceae), a diverse genus of Neotropical lianas, and that of
. We explored the structure and content of the assembled plastomes and performed comparative analyses within
and among other plastomes available for Bignoniaceae. The overall gene content and orientation of plastomes is similar in all species studied. Plastomes are not conserved among
, showing significant differences in length (155,262-164,786 bp), number of genes duplicated in the IRs (eight, 18, or 19), and location of the SC/IR boundaries (i.e., LSC/IRa junction between
and
genes, within
, or within
). Length differences reflect expansions of the IRs and contractions of the LSC regions. The plastome of
is 168,172 bp, includes 19 duplicated genes, and has the LSC/IRa boundary located within the
gene.
plastomes show high nucleotide diversity, with many hypervariable regions, and 16 genes with signatures of positive selection. Multiple SSRs and repeat regions were identified for
and
. The differences in structure detected within
plastomes in terms of LSC/IR and IR/SSC boundaries, number of duplicated genes, and genome sizes are mostly shared between taxa that belong to the same clade. Our results bring new insights into the evolution of plastomes at low taxonomic levels.
The tribe Bignonieae (Bignoniaceae) is a large and morphologically diverse clade of neotropical lianas. Despite being a conspicuous component of the neotropical flora, the systematics of the tribe ...has remained uncertain due to confusing patterns of morphological variation within the group. Chloroplast (ndhF) and nuclear (PepC) DNA sequences were used here to reconstruct the phylogeny of Bignonieae. Individual analyses of ndhF and PepC were highly similar to one another, yet localized differences in the placement of six species suggests some conflict between data sets. Combined analyses result in trees that are consistent with those from the individual analyses and provide greater support for the suggested relationships. This phylogeny provides important new insights into the systematics of the tribe. It identifies 21 strongly supported species groups, eight of which broadly correspond to currently recognized genera. In addition, each of these 21 species groups is supported by morphological synapomorphies. The consistency between morphological and molecular data suggests that the current phylogeny provides a solid framework for a formal revision of the generic-level classification and for addressing other aspects of the biology of Bignonieae.
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•We assembled new plastomes for 34 species of Adenocalymma, and Neojobertia.•Phylogenetic relationships were inferred with high throughput and Sanger sequencing.•Adenocalymma emerged ...as non monophyletic.•The evolution of 19 characters was investigated and six were synapomorphies.•Some characters did not shown phylogenetic signal and state transitions occured multiple times. Those are habit and several flower morphology characters.
Combining high-throughput sequencing data with amplicon sequences allows the reconstruction of robust phylogenies based on comprehensive sampling of characters and taxa. Here, we combine Next Generation Sequencing (NGS) and Sanger sequencing data to infer the phylogeny of the “Adenocalymma-Neojobertia” clade (Bignonieae, Bignoniaceae), a diverse lineage of Neotropical plants, using Maximum Likelihood and Bayesian approaches. We used NGS to obtain complete or nearly-complete plastomes of members of this clade, leading to a final dataset with 54 individuals, representing 44 members of ingroup and 10 outgroups. In addition, we obtained Sanger sequences of two plastid markers (ndhF and rpl32-trnL) for 44 individuals (43 ingroup and 1 outgroup) and the nuclear PepC for 64 individuals (63 ingroup and 1 outgroup). Our final dataset includes 87 individuals of members of the “Adenocalymma-Neojobertia” clade, representing 66 species (ca. 90% of the diversity), plus 11 outgroups. Plastid and nuclear datasets recovered congruent topologies and were combined. The combined analysis recovered a monophyletic “Adenocalymma-Neojobertia” clade and a paraphyletic Adenocalymma that also contained a monophyletic Neojobertia plus Pleonotoma albiflora. Relationships are strongly supported in all analyses, with most lineages within the “Adenocalymma-Neojobertia” clade receiving maximum posterior probabilities. Ancestral character state reconstructions using Bayesian approaches identified six morphological synapomorphies of clades namely, prophyll type, petiole and petiolule articulation, tendril ramification, inflorescence ramification, calyx shape, and fruit wings. Other characters such as habit, calyx cupular trichomes, corolla color, and corolla shape evolved multiple times. These characters are putatively related with the clade diversification and can be further explored in diversification studies.
The Amazon hosts one of the largest and richest rainforests in the world, but its origins remain debated. Growing evidence suggests that geodiversity and geological history played essential roles in ...shaping the Amazonian flora. Here we summarize the geo-climatic history of the Amazon and review paleopalynological records and time-calibrated phylogenies to evaluate the response of plants to environmental change. The Neogene fossil record suggests major sequential changes in plant composition and an overall decline in diversity. Phylogenies of eight Amazonian plant clades paint a mixed picture, with the diversification of most groups best explained by constant speciation rates through time, while others indicate clade-specific increases or decreases correlated with climatic cooling or increasing Andean elevation. Overall, the Amazon forest seems to represent a museum of diversity with a high potential for biological diversification through time. To fully understand how the Amazon got its modern biodiversity, further multidisciplinary studies conducted within a multimillion-year perspective are needed.
The history of the Amazon rainforest goes back to the beginning of the Cenozoic (66 Ma) and was driven by climate and geological forces.
In the early Neogene (23-13.8 Ma), a large wetland developed with episodic estuarine conditions and vegetation ranging from mangroves to terra firme forest.
In the late Neogene (13.8-2.6 Ma), the Amazon changed into a fluvial landscape with a less diverse and more open forest, although the details of this transition remain to be resolved.
These geo-climatic changes have left imprints on the modern Amazonian diversity that can be recovered with dated phylogenetic trees.
Amazonian plant groups show distinct responses to environmental changes, suggesting that Amazonia is both a refuge and a cradle of biodiversity.
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