Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs

Studies investigating the evolution of flowering plants have long focused on isolating mechanisms such as pollinator specificity. Some recent studies have proposed a role for introgressive hybridization between species, recognizing that isolating processes such as pollinator specialization may not be complete barriers to hybridization. Occasional hybridization may therefore lead to distinct yet reproductively connected lineages. We investigate the balance between introgression and reproductive isolation in a diverse clade using a densely sampled phylogenomic study of fig trees (Ficus, Moraceae). Codiversification with specialized pollinating wasps (Agaonidae) is recognized as a major engine of fig diversity, leading to about 850 species. Nevertheless, some studies have focused on the importance of hybridization in Ficus, highlighting the consequences of pollinator sharing. Here, we employ dense taxon sampling (520 species) throughout Moraceae and 1,751 loci to investigate phylogenetic relationships and the prevalence of introgression among species throughout the history of Ficus. We present a well-resolved phylogenomic backbone for Ficus, providing a solid foundation for an updated classification. Our results paint a picture of phylogenetically stable evolution within lineages punctuated by occasional local introgression events likely mediated by local pollinator sharing, illustrated by clear cases of cytoplasmic introgression that have been nearly drowned out of the nuclear genome through subsequent lineage fidelity. The phylogenetic history of figs thus highlights that while hybridization is an important process in plant evolution, the mere ability of species to hybridize locally does not necessarily translate into ongoing introgression between distant lineages, particularly in the presence of obligate plant-pollinator relationships.

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. St. Vincent was the first significant point of Caribbean introduction and played a vital role in subsequent breadfruit distribution throughout the region. Hundreds of cultivars are documented in breadfruit's native Oceania. It remains a mystery, however, which ones were introduced to the Caribbean 230 years ago-still comprising the vast diversity found there today. Integrating local knowledge, historical documents and specimens, morphological data, and DNA, we identify eight major global breadfruit lineages-five of which are found in the Caribbean and likely represent the original 1793 introduction. Genetic data were able to match two Caribbean cultivar names confidently to their Oceania counterparts. Genetics and morphology together enabled additional possible matches. Many other named cultivars within lineages are too genetically similar to differentiate, highlighting difficulties of defining and identifying variation among clonally propagated triploid crops. Breadfruit is important in resilient agroforestry in tropical islands predicted to be especially affected by climate change. Findings reveal global links, building upon collective knowledge that can be used to inform breadfruit management. Results are also summarized in a brochure about breadfruit history and diversity in St. Vincent, and the Caribbean more broadly.

Rapid improvement in soil health following the conversion of abandoned farm fields to annual or perennial agroecosystems

Incorporating perennial crops into agroecosystems has been shown to mitigate soil degradation and improve soil health by enhancing soil aggregation and soil organic carbon (SOC) accrual. However, our understanding of the ability and timeframe for perennial crop systems to build soil health within the context of conversion from abandoned crop land remains limited. Here, we examined changes in soil health in the first year following the conversion of an abandoned crop field into an agroecosystem planted with various treatments, including: novel perennial grain (intermediate wheatgrass, IWG; Thinopyrum intermedium), IWG/ alfalfa biculture, forage grass, tallgrass prairie, or annual wheat. We analyzed factors considered central to the concept of mitigating soil degradation to improve soil health (soil aggregation, aggregate organic carbon (OC), bulk SOC) and their soil biological and physicochemical correlates throughout the first growing season. Comparisons between treatments showed that both annual and perennial treatments rapidly and significantly improved soil health metrics including aggregation, aggregate stability, and OC levels compared to pre-conversion conditions. Such increases were positively correlated with the abundance of arbuscular mycorrhizal fungi (AMF hyphae, root colonization), labile SOC and microbial activity. Notably, IWG/ alfalfa biculture resulted in significantly higher levels of macroaggregate OC in comparison to other treatments, including tallgrass prairie, supporting the potential of perennial grasses to contribute to soil carbon gains. Overall, the conversion of this abandoned land to an agroecosystem produced rapid and substantial increases in soil health in the first year after planting.

Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes

Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species' establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.

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. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the inclusion of flanking non-coding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of datasets increased convergence between analysis methods but did not reduce gene tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. While the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of datasets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution.

Genetic diversity and structure of the critically endangered Artocarpus annulatus, a crop wild relative of jackfruit (A. heterophyllus)

Limestone karsts of Southeast Asia can harbor high levels of endemism, but are highly fragmented, increasingly threatened, and their biodiversity is often poorly studied. This is true of the Padawan Limestone Area of Sarawak, Malaysia, home to the endemic Artocarpus annulatus, the closest known wild relative of two important and underutilized fruit tree crops, jackfruit (A. heterophyllus) and cempedak (A. integer). Identifying and conserving crop wild relatives is critical for the conservation of crop genetic diversity and breeding. In 2016 and 2017, five A. annulatus populations were located, and leaf material, locality information, and demographic data were collected. Microsatellite markers were used to assess genetic diversity and structure among populations, and to compare levels of genetic diversity to closely related congeneric species. Results indicate no evidence of inbreeding in A. annulatus, and there is no genetic structure among the five populations. However, diversity measures trended lower in seedlings compared to mature trees, suggesting allelic diversity may be under threat in the youngest generation of plants. Also, genetic diversity is lower in A. annulatus compared to closely related congeners. The present study provides a baseline estimate of A. annulatus genetic diversity that can be used for comparison in future studies and to other species in the unique limestone karst ecosystems. Considerations for in situ and ex situ conservation approaches are discussed.

A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.)

PREMISE OF THE STUDY

Underutilized crops, such as breadfruit (Artocarpus altilis, Moraceae) have the potential to improve global food security. Humans have artificially selected many cultivars of breadfruit since its domestication began approximately 3500 years ago. The goal of this research was to identify transcriptomic signals of positive selection and to develop genomic resources that may facilitate the development of improved breadfruit cultivars in the future.

METHODS

A reference transcriptome of breadfruit was assembled de novo and annotated. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that may have resulted from local adaptation or natural selection. Emphasis was placed on MADS-box genes, which are important because they often regulate fruiting timing and structures, and on carotenoid biosynthesis genes, which can impact the nutritional quality of the fruit.

KEY RESULTS

Over 1000 genes showed signals of positive selection, and these genes were enriched for localization to plastids. Nucleotide sites and individuals under positive selection were discovered in MADS-box genes and carotenoid biosynthesis genes, with several sites located in cofactor or DNA-binding domains. A McDonald-Kreitman test comparing wild to cultivated samples revealed selection in one of the carotenoid biosynthesis genes, abscisic acid 8'-hydroxylase 3.

CONCLUSIONS

This research highlights some of the many genes that may have been intentionally or unintentionally selected for during the human-mediated dispersal of breadfruit and stresses the importance of conserving a varied germplasm collection. It has revealed candidate genes for further study and produced new genomic resources for breadfruit.

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.] is a significant crop in Malaysia but underutilized elsewhere. Here we performed molecular characterization of cempedak and its putative wild relative bangkong (Artocarpus integer (Thunb). Merr. var. silvestris Corner) to address questions regarding the origin and diversity of cempedak.

METHODS

Using data from 12 microsatellite loci, we assessed the genetic diversity and genetic/geographic structure for 353 cempedak and 175 bangkong accessions from Malaysia and neighboring countries and employed clonal analysis to characterize cempedak cultivars. We conducted haplotype network analyses on the trnH-psbA region in a subset of these samples. We also analyzed key vegetative characters that reportedly differentiate cempedak and bangkong.

KEY RESULTS

We show that cempedak and bangkong are sister taxa and distinct genetically and morphologically, but the directionality of domestication origin is unclear. Genetic diversity was generally higher in bangkong than in cempedak. We found a distinct genetic cluster for cempedak from Borneo as compared to cempedak from Peninsular Malaysia. Finally, cempedak cultivars with the same names did not always share the same genetic fingerprint.

CONCLUSIONS

Cempedak origins are complex, with likely admixture and hybridization with bangkong, warranting further investigation. We provide a baseline of genetic diversity of cempedak and bangkong in Malaysia and found that germplasm collections in Malaysia represent diverse coverage of the four cempedak genetic clusters detected.

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. Many phylogenetic reconstructions ignore heterozygosity because it is difficult to assemble allele sequences and combine allele data across unlinked loci, and it is unclear how reconstruction methods accommodate variable sequences. We review the common methods of including heterozygosity in phylogenetic studies and present a novel method for assembling allele sequences from target-enriched Illumina sequencing libraries.

METHODS

We performed supermatrix phylogeny reconstruction and species tree estimation of Artocarpus based on three methods of accounting for heterozygous sequences: a consensus method based on de novo sequence assembly, the use of ambiguity characters, and a novel method for incorporating read information to phase alleles. We characterize the extent to which highly heterozygous sequences impeded phylogeny reconstruction and determine whether the use of allele sequences improves phylogenetic resolution or decreases topological uncertainty.

KEY RESULTS

We show here that it is possible to infer phased alleles from target-enriched Illumina libraries. We find that highly heterozygous sequences do not contribute disproportionately to poor phylogenetic resolution and that the use of allele sequences for phylogeny reconstruction does not have a clear effect on phylogenetic resolution or topological consistency.

CONCLUSIONS

We provide a framework for inferring phased alleles from target enrichment data and for assessing the contribution of allelic diversity to phylogenetic reconstruction. In our data set, the impact of allele phasing on phylogeny is minimal compared to the impact of using phylogenetic reconstruction methods that account for gene tree incongruence.

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. Maclura pomifera, the Osage orange, is considered a classic example of an anachronistic fruit. Native to the central USA, the grapefruit-sized Osage oranges are unpalatable and have no known extant native dispersers, leading to speculation that the fruits were adapted to extinct megafauna. Our aim was to reconstruct the phylogeny, estimate divergence dates, and infer ancestral ranges of Maclura in order to test the monophyly of subgeneric classifications and to understand evolution and dispersal patterns in this globally distributed group.

METHODS

Employing Bayesian and maximum-likelihood methods, we reconstructed the Maclura phylogeny using two nuclear and five chloroplast loci from all Maclura species and outgroups representing all Moraceae tribes. We reconstructed ancestral ranges and syncarp sizes using a family level dated tree, and used Ornstein-Uhlenbeck models to test for significant changes in syncarp size in the Osage orange lineage.

KEY RESULTS

Our analyses support a monophyletic Maclura with a Paleocene crown. Subgeneric sections were monophyletic except for the geographically-disjunct Cardiogyne. There was strong support for current species delineations except in the widespread M. cochinchinensis. South America was reconstructed as the ancestral range for Maclura with subsequent colonization of Africa and the northern hemisphere. The clade containing M. pomifera likely diverged in the Oligocene, closely coinciding with crown divergence dates of the mammoth/mastodon and sloth clades that contain possible extinct dispersers. The best fitting model for syncarp size evolution indicated an increase in both syncarp size and the rate of syncarp size evolution in the Osage orange lineage.

CONCLUSIONS

We conclude that our findings are consistent with the hypothesis that M. pomifera was adapted to dispersal by extinct megafauna. In addition, we consider dispersal rather than vicariance to be most likely responsible for the present distribution of Maclura, as crown divergence post-dated the separation of Africa and South America. We propose revised sectional delimitations based on the phylogeny. This study represents a complete phylogenetic and biogeographic analysis of this globally distributed genus and provides a basis for future work, including a taxonomic revision.

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.

METHODS

To investigate the phylogeny and biogeography of Artocarpeae, this study used Bayesian and maximum likelihood approaches to analyze DNA sequences from six plastid and two nuclear regions from 75% of Artocarpus species, both neotropical Artocarpeae genera, and members of all other Moraceae tribes. Six fossil-based calibrations within the Moraceae family were used to infer divergence times. Ancestral areas and estimated dispersal events were also inferred.

KEY RESULTS

Artocarpeae, Artocarpus and four monophyletic Artocarpus subgenera were well supported. A late Cretaceous origin of the Artocarpeae tribe in the Americas is inferred, followed by Eocene radiation of Artocarpus in Asia, with the greatest diversification occurring during the Miocene. Borneo is reconstructed as the ancestral range of Artocarpus , with dozens of independent in situ diversification events inferred there, as well as dispersal events to other regions of Southeast Asia. Dispersal pathways of Artocarpus and its ancestors are proposed.

CONCLUSIONS

Borneo was central in the diversification of the genus Artocarpus and probably served as the centre from which species dispersed and diversified in several directions. The greatest amount of diversification is inferred to have occurred during the Miocene, when sea levels fluctuated and land connections frequently existed between Borneo, mainland Asia, Sumatra and Java. Many species found in these areas have extant overlapping ranges, suggesting that sympatric speciation may have occurred. By contrast, Artocarpus diversity east of Borneo (where many of the islands have no historical connections to the landmasses of the Sunda and Sahul shelves) is unique and probably the product of over water long-distance dispersal events and subsequent diversification in allopatry. This work represents the most comprehensive Artocarpus phylogeny and biogeography study to date and supports Borneo as an evolutionary biodiversity hotspot.

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. Phylogenetic markers for Moraceae were developed from 333 inferred single-copy exons. Ninety-eight putative MADS-box genes were identified. Analysis of all predicted coding regions resulted in preliminary annotation of 49,089 genes. An analysis of synonymous substitutions for pairs of orthologs (Ks analysis) in M. notabilis and A. camansi strongly suggested a lineage-specific whole-genome duplication in Artocarpus.

CONCLUSIONS

This study substantially increases the genomic resources available for Artocarpus and Moraceae and demonstrates the value of low-coverage de novo assemblies for nonmodel organisms with moderately large genomes.

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).

METHODS AND RESULTS

HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus.

CONCLUSIONS

HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper.

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. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners.

METHODS AND RESULTS

Fifteen simple sequence repeats (SSRs) were identified in chloroplast sequences from four Artocarpus transcriptome assemblies. The markers were evaluated using capillary electrophoresis in A. odoratissimus (105 accessions) and A. altilis (73). They were also evaluated in silico in A. altilis (10), A. camansi (6), and A. altilis × A. mariannensis (7) transcriptomes. All loci were polymorphic in at least one species, with all 15 polymorphic in A. camansi. Per species, average alleles per locus ranged between 2.2 and 2.5. Three loci had evidence of fragment-length homoplasy.

CONCLUSIONS

These markers will complement existing nuclear markers by enabling confident identification of maternal and clone lines, which are often important in vegetatively propagated crops such as breadfruit.

Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species

PREMISE OF THE STUDY

Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. •

METHODS AND RESULTS

A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. •

CONCLUSIONS

These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit.

Biogeography and divergence times in the mulberry family (Moraceae)

The biogeographical history of the mulberry family (Moraceae) was investigated using phylogenetic inferences from nuclear and chloroplast DNA, molecular dating with multiple fossil calibrations, and independent geological evidence. The Moraceae are centered in the tropics which has invited the hypothesis that the family has Gondwanan origins and extant distribution is the result of vicariance due to the break-up of Gondwana. However, the cosmopolitan distribution of Moraceae suggests a more complicated biogeographical history. The timing and location of Moraceae diversification also bears on the origin of the fig pollination mutualism, a model for the study of coevolution and specialization. Recent molecular dating of pollinating fig wasps suggested that an ancient Gondwanan origin coupled with vicariance and dispersal could account for the present day distribution of the mutualism. Here, we provide the first assessment of this hypothesis based on dating of figs and their relatives. Minimum age estimates suggest that the Moraceae had diversified by at least the mid-Cretaceous and major clades including the figs may have radiated during the Tertiary after the break-up of Gondwanaland. Molecular evidence together with Eurasian fossils suggest that the early diversification of Moraceae in Eurasia and subsequent migration into the southern hemisphere is at least as plausible as the Gondwanan hypothesis. These findings invite a reevaluation of the biogeography of fig pollination and highlight the need for incorporating multiple sources of evidence in biogeographical reconstructions.

Complex origins of breadfruit (Artocarpus altilis, Moraceae): implications for human migrations in Oceania

Breadfruit (Artocarpus altilis, Moraceae), a traditional starch crop in Oceania, has enjoyed legendary status ever since its role in the infamous mutiny aboard the H.M.S. Bounty in 1789, yet its origins remain unclear. Breadfruit's closest relatives are A. camansi and A. mariannensis. DNA fingerprinting data (AFLP, amplified fragment length polymorphisms) from over 200 breadfruit cultivars, 30 A. camansi, and 24 A. mariannensis individuals were used to investigate the relationships among these species. Multivariate analyses and the identification of species-specific AFLP markers indicate at least two origins of breadfruit. Most Melanesian and Polynesian cultivars appear to have arisen over generations of vegetative propagation and selection from A. camansi. In contrast, most Micronesian breadfruit cultivars appear to be the result of hybridization between A. camansi-derived breadfruit and A. mariannensis. Because breadfruit depends on humans for dispersal, the data were compared to theories on the human colonization of Oceania. The results agree with the well-supported theory that humans settled Polynesia via Melanesia. Additionally, a long-distance migration from eastern Melanesia into Micronesia is supported.