Phylogenomic analyses of the Neotropical Artocarpeae (Moraceae) reveal a history of introgression and support the reinstatement of Acanthinophyllum.

This molecular study of the Neotropical Artocarpeae, the closest living allies of the Asia-Pacific breadfruit genus, uses phylogenomic and network analyses to untangle the evolutionary history of this difficult group. Results paint a picture of a rapid radiation, with introgression, incomplete lineage sorting, and lack of gene tree resolution confounding attempts to reconstruct a well-supported bifurcating tree. While coalescent-based species trees were markedly at odds with morphology, multifurcating phylogenetic network analyses recovered multiple histories, with clearer traces of morphological alliances.

Corrigendum: Phylogenomics of the Andean tetraploid clade of the American Amaryllidaceae (subfamily Amaryllidoideae): Unlocking a polyploid generic radiation abetted by continental geodynamics.

[This corrects the article DOI: 10.3389/fpls.2020.

Linking breadfruit cultivar names across the globe connects histories after 230 years of separation.

Every crop has a story. The story of breadfruit (Artocarpus altilis), an increasingly valued staple crop in tropical agroforestry systems, is filled with intrigue, oppression, and remains incomplete. The Caribbean is a major producer and consumer of breadfruit, yet most breadfruit there came from a single 1793 introduction aimed at providing a cheap food source for slaves forced to work on British plantations.

Amis Pacilo and Yami Cipoho are not the same as the Pacific breadfruit starch crop-Target enrichment phylogenomics of a long-misidentified Artocarpus species sheds light on the northward Austronesian migration from the Philippines to Taiwan.

'Breadfruit' is a common tree species in Taiwan. In the indigenous Austronesian Amis culture of eastern Taiwan, 'breadfruit' is known as Pacilo, and its fruits are consumed as food. On Lanyu (Botel Tobago) where the indigenous Yami people live, 'breadfruit' is called Cipoho and used for constructing houses and plank-boats.

Engagement with indigenous people preserves local knowledge and biodiversity alike.

Indigenous peoples are important stewards of biodiversity, often living near and possessing intimate knowledge of ecosystems. As a result, species new to science may be long known to indigenous people. While the scientific endeavor has long benefitted from indigenous knowledge, it has usually not engaged with it on equal footing.

(Plantaginaceae), a rare new species from southern Brazil, supported by phylogenomic and morphological evidence.

High-throughput sequencing, when combined with taxonomic expertise, is a powerful tool to refine and advance taxonomic classification, including at the species level. In the present work, a new species, , is described out of the species complex, based on phylogenomic and morphological evidence. The main morphological characters that distinguish the new species from are the glabrous posterior sepals and the slightly broader leaves.

Phylogenomics of the Andean Tetraploid Clade of the American Amaryllidaceae (Subfamily Amaryllidoideae): Unlocking a Polyploid Generic Radiation Abetted by Continental Geodynamics.

One of the two major clades of the endemic American Amaryllidaceae subfam. Amaryllidoideae constitutes the tetraploid-derived ( = 23) Andean-centered tribes, most of which have 46 chromosomes. Despite progress in resolving phylogenetic relationships of the group with plastid and nrDNA, certain subclades were poorly resolved or weakly supported in those previous studies.

Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).

We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling.

Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants.

The reduced cost of high-throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per-sample cost, which can be inflated when using off-the-shelf kits or reagents not purchased in bulk. Here, we discuss methods to reduce per-sample costs in high-throughput targeted sequencing projects.

Land bridges in the Pleistocene contributed to flora assembly on the continental islands of South China: Insights from the evolutionary history of Quercus championii.

The South China Mainland (SCM) and its adjacent continental islands are a global biodiversity hotspot. However, how and when plants dispersed between SCM and Hainan/Taiwan Islands remains largely unknown. In this study, we used restriction site-associated DNA sequencing (RAD-seq) to identify the demographic dynamics and local adaptation of Quercus championii, a dominant forests tree distributed in SCM and Hainan/Taiwan Islands.

Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above.

Reconstructing phylogenetic relationships at the micro- and macroevoutionary levels within the same tree is problematic because of the need to use different data types and analytical frameworks. We test the power of target enrichment to provide phylogenetic resolution based on DNA sequences from above species to within populations, using a large herbarium sampling and Euphorbia balsamifera (Euphorbiaceae) as a case study. Target enrichment with custom probes was combined with genome skimming (Hyb-Seq) to sequence 431 low-copy nuclear genes and partial plastome DNA.

Origin and diversity of an underutilized fruit tree crop, cempedak (Artocarpus integer, Moraceae).

Premise Of The Study: Underutilized crops and their wild relatives are important resources for crop improvement and food security. Cempedak [Artocarpus integer (Thunb). Merr.

Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus.

Premise Of The Study: Untapped information about allele diversity within populations and individuals (i.e., heterozygosity) could improve phylogenetic resolution and accuracy.

Phylogeny and biogeography of Maclura (Moraceae) and the origin of an anachronistic fruit.

Background And Aims: Maclura (ca. 12spp., Moraceae) is a widespread genus of trees and woody climbers found on five continents.

Out of Borneo: biogeography, phylogeny and divergence date estimates of Artocarpus (Moraceae).

Background And Aims: The breadfruit genus ( Artocarpus , Moraceae) includes valuable underutilized fruit tree crops with a centre of diversity in Southeast Asia. It belongs to the monophyletic tribe Artocarpeae, whose only other members include two small neotropical genera. This study aimed to reconstruct the phylogeny, estimate divergence dates and infer ancestral ranges of Artocarpeae, especially Artocarpus , to better understand spatial and temporal evolutionary relationships and dispersal patterns in a geologically complex region.

HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment.

Premise Of The Study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae).

Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery.

Premise Of The Study: We used moderately low-coverage (17×) whole-genome sequencing of Artocarpus camansi (Moraceae) to develop genomic resources for Artocarpus and Moraceae.

Methods And Results: A de novo assembly of Illumina short reads (251,378,536 pairs, 2 × 100 bp) accounted for 93% of the predicted genome size. Predicted coding regions were used in a three-way orthology search with published genomes of Morus notabilis and Cannabis sativa.

Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences.

Premise Of The Study: Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus altilis (breadfruit) and A. camansi (breadnut). They were tested in A.