Rethinking pathways to the dioecy-polyploidy association: Genera with many dioecious species have fewer polyploids

PREMISE

Numerous studies have found a positive association between dioecy and polyploidy; however, this association presents a theoretical conflict: While polyploids are predicted to benefit from self-reproduction for successful establishment, dioecious species cannot self-reproduce. We propose a theoretical framework to resolve this apparent conflict. We hypothesize that the inability of dioecious species to self-reproduce hinders their establishment as polyploids. We therefore expect that genera with many dioecious species have fewer polyploids, leading to a negative association between polyploidy and dioecy across genera.

METHODS

We used three publicly available databases to determine ploidy and sexual systems for 131 genera and 546 species. We quantified (1) the relationship between the frequency of polyploid species and the frequency of dioecious species across genera, and (2) the proportion of polyploids with hermaphroditism and dioecy across species, adjusting for phylogenetic history.

RESULTS

Across genera, we found a negative relationship between the proportion of polyploids and the proportion of dioecious species, a consistent trend across clades. Across all species, we found that sexual system (dioecious or not) was not associated with polyploidy.

CONCLUSIONS

Polyploids are rare in genera in which the majority of species are dioecious, consistent with the theory that self-reproduction favors polyploid establishment. The low frequency of polyploidy among dioecious species indicates the association is not as widespread as previously suggested. Our findings are consistent with previous studies identifying a positive relationship between the two traits, but only if polyploidy promotes a transition to dioecy, and not the reverse.

Madagascar’s extraordinary biodiversity: Evolution, distribution, and use

Madagascar’s biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar’s past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique “living laboratory” for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth’s biodiversity.

Madagascar’s extraordinary biodiversity: Threats and opportunities

Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.

The origin of modern patterns of continental diversity in Mauritiinae palms: the Neotropical museum and the Afrotropical graveyard

While the latitudinal diversity gradient has received much attention, biodiversity and species richness also vary between continents across similar latitudes. Fossil information can be used to understand the evolutionary mechanisms that generated such variation between continents of similar latitudes. We integrated fossil data into a phylogenetic analysis of the Mauritiinae palms, whose extant diversity is restricted to the Neotropics, but extended across Africa and India during most of the Cenozoic. Mauritiinae diverged from its sister lineage Raphiinae ca 106 Ma. Using ancestral state estimation and a lineage through time analysis, we found that diversity arose globally during the late Cretaceous and Palaeocene across South America, Africa and India. The Palaeocene-Eocene transition (ca 56 Ma) marked the end of global Mauritiinae expansion, and the beginning of their decline in both Africa and India. Mauritiinae disappeared from the Indian subcontinent and Africa at the end of the Eocene and the Miocene, respectively. By contrast, Neotropical diversity steadily increased over the last 80 Myr. Taken together, our results suggest that the Neotropics functioned as a continental-scale refuge for Mauritiinae palms, where lineages survived and diversified while global climatic changes that drastically reduced rainforests led to their demise on other continents.

Limited decadal growth of mountain birch saplings has minor impact on surrounding tundra vegetation

Temperatures over the Arctic region are increasing at three times the rate of the global average. Consequently, Arctic vegetation is changing and trees are encroaching into the tundra. In this study, we examine the establishment and growth of mountain birch (Betula pubescens ssp. tortuosa), which forms the treeline in subarctic Europe, and its impact on community composition across the treeline ecotone nearby Abisko, Sweden. Birch advancement along elevational gradients was studied by comparing data collected in 2016 with data collected 10 and 15 years previously. Species identity, cover, and phylogenetic relatedness were used to assess the impact of birch encroachment on community composition. Our results show that birch occurrence above the treeline did not affect plant community composition, probably owing to the observed lack of significant growth due to herbivore browsing, nitrogen limitation, or a reduction in snow cover. Independent of birch performance, the tundra community structure shifted toward a novel community dissimilar from the forest plant community found below the treeline. Taken together, our findings are explained by species‐specific responses to climate change, rather than by a linear forest advance. Future treeline advancements are likely more restricted than previously expected.

A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics

The increasing availability of short‐read whole genome sequencing (WGS) provides unprecedented opportunities to study ecological and evolutionary processes. Although loci of interest can be extracted from WGS data and combined with target sequence data, this requires suitable bioinformatic workflows. Here, we test different assembly and locus extraction strategies and implement them into secapr, a pipeline that processes short‐read data into multilocus alignments for phylogenetics and molecular ecology analyses. We integrate the processing of data from low‐coverage WGS (<30×) and target sequence capture into a flexible framework, while optimizing de novo contig assembly and loci extraction. Specifically, we test different assembly strategies by contrasting their ability to recover loci from targeted butterfly protein‐coding genes, using four data sets: a WGS data set across different average coverages (10×, 5× and 2×) and a data set for which these loci were enriched prior to sequencing via target sequence capture. Using the resulting de novo contigs, we account for potential errors within contigs and infer phylogenetic trees to evaluate the ability of each assembly strategy to recover species relationships. We demonstrate that choosing multiple sizes of kmer simultaneously for assembly results in the highest yield of extracted loci from de novo assembled contigs, while data sets derived from sequencing read depths as low as 5× recovers the expected species relationships in phylogenetic trees. By making the tested assembly approaches available in the secapr pipeline, we hope to inspire future studies to incorporate complementary data and make an informed choice on the optimal assembly strategy.

In situ radiation explains the frequency of dioecious palms on islands

BACKGROUND AND AIMS

Dioecy has evolved up to 5000 times in angiosperms, despite the potentially high intrinsic costs to unisexuality. Dioecy prevents inbreeding, which is especially relevant on isolated islands when gene pools are small. Dioecy is also associated with certain dispersal traits, such as fruit size and type. However, the influence of dioecy on other life history traits and island distribution remains poorly understood. Here, we test the effect of dioecy on palm (Arecaceae) speciation rates, fruit size and frequency on islands.

METHODS

We used phylogenetic comparative methods to estimate the ancestral state of the sexual system and its impact on speciation rates and fruit size. Frequency of sexual systems, effect of insularity on the probability of being dioecious, and phylogenetic clustering of island dioecious vs. mainland species were inferred. Lastly, we determined the interplay of insularity and sexual system on speciation rates.

KEY RESULTS

Palms repeatedly evolved different sexual systems (dioecy, monoecy and polygamy) from a hermaphrodite origin. Differences in speciation rates and fruit size among the different sexual systems were not identified. An effect of islands on the probability of the palms being dioecious was also not found. However, we found a high frequency and phylogenetic clustering of dioecious palms on islands, which were not correlated with higher speciation rates.

CONCLUSIONS

The high frequency and phylogenetic clustering may be the result of in situ radiation and suggest an 'island effect' for dioecious palms, which was not explained by differential speciation rates. This island effect also cannot be attributed to long-distance dispersal due to the lack of fruit size difference among sexual systems, and particularly because palm dispersal to islands is highly constrained by the interaction between the sizes of fruit and frugivores. Taken together, we suggest that trait flexibility in sexual system evolution and the in situ radiation of dioecious lineages are the underlying causes of the outstanding distribution of palms on islands.

Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)

Background

The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events.

Results

Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in > 54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus.

Conclusions

Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

Biogeographic origins of southern African Silene (Caryophyllaceae)

Silene (Caryophyllaceae) is distributed predominantly in the northern Hemisphere, where it is most diverse around the Mediterranean Basin. The genus is also well represented in North Africa, extending into tropical, sub-Saharan and southern Africa. Eight native species are recognized in southern Africa, taxonomically placed in two sections: Elisanthe and Silene s.l. Although the taxonomy of the southern African taxa has recently been revised, their phylogenetic relationships and biogeographic history remain unclear. This study aims to infer the phylogenetic position and geographic origins of the southern African taxa. We generated DNA sequences of nuclear and plastid loci from several individuals belonging to all eight species of Silene recognized from southern Africa, and combined our DNA sequences with existing data representing species from major clades (i.e. sections) based on the recently revised Silene infrageneric taxonomy. We used a Bayesian coalescent species tree continuous diffusion approach to co-estimate the species tree and the ancestral areas of representative members of the genus. Our results show that the perennial southern African members of section Elisanthe form a strongly-supported clade with the Eurasian annual S. noctiflora and the Central Asian perennial S. turkestanica. The rest of the perennial species form a strongly-supported clade together with the annual S. aethiopica, which is nested in a larger Mediterranean clade comprising mostly annual species classified in section Silene s.l. Estimates of ancestral areas indicate a late Pleistocene dispersal to southern Africa from central and East Africa for the sub-Saharan members of section Silene s.l. The Elisanthe clade is inferred to have colonized southern Africa through long-distance dispersal from Eurasia during the late Pleistocene. Our findings support the hypothesis of a relatively recent colonization into southern Africa resulting from two independent dispersal events during the Pleistocene.

Fossil data support a pre-Cretaceous origin of flowering plants

Flowering plants (angiosperms) are the most diverse of all land plants, becoming abundant in the Cretaceous and achieving dominance in the Cenozoic. However, the exact timing of their origin remains a controversial topic, with molecular clocks generally placing their origin much further back in time than the oldest unequivocal fossils. To resolve this discrepancy, we developed a Bayesian method to estimate the ages of angiosperm families on the basis of the fossil record (a newly compiled dataset of ~15,000 occurrences in 198 families) and their living diversity. Our results indicate that several families originated in the Jurassic, strongly rejecting a Cretaceous origin for the group. We report a marked increase in lineage accumulation from 125 to 72 million years ago, supporting Darwin's hypothesis of a rapid Cretaceous angiosperm diversification. Our results demonstrate that a pre-Cretaceous origin of angiosperms is supported not only by molecular clock approaches but also by analyses of the fossil record that explicitly correct for incomplete sampling.

Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm

Despite the global importance of tropical ecosystems, few studies have identified how natural selection has shaped their megadiversity. Here, we test for the role of adaptation in the evolutionary success of the widespread, highly abundant Neotropical palm Mauritia flexuosa. We used a genome scan framework, sampling 16,262 single-nucleotide polymorphisms (SNPs) with target sequence capture in 264 individuals from 22 populations in rainforest and savanna ecosystems. We identified outlier loci as well as signal of adaptation using Bayesian correlations of allele frequency with environmental variables and detected both selective sweeps and genetic hitchhiking events. Functional annotation of SNPs with selection footprints identified loci affecting genes related to adaptation to environmental stress, plant development, and primary metabolic processes. The strong differences in climatic and soil variables between ecosystems matched the high differentiation and low admixture in population Bayesian clustering. Further, we found only small differences in allele frequency distribution in loci putatively under selection among widespread populations from different ecosystems, with fixation of a single allele in most populations. Taken together, our results indicate that adaptive selective sweeps related to environmental stress shaped the spatial pattern of genetic diversity in M. flexuosa, leading to high similarity in allele frequency among populations from different ecosystems.

Higher evolutionary rates in life-history traits in insular than in mainland palms

Isolated islands, due to the reduced interspecific competition compared to mainland habitats, present ecological opportunities for colonizing lineages. As a consequence, island lineages may be expected to experience higher rates of trait evolution than mainland lineages. However, island effects on key life-history traits of vascular plants remain underexplored at broad spatiotemporal scales, even for emblematic island clades such as palms. Here, we used phylogenetic comparative methods to evaluate potential differences in size and macroevolutionary patterns of height and fruit diameter among mainland, continental, and volcanic island palms. Further, phylogenetic beta-diversity was used to determine if lineage turnover supported an adaptive radiation scenario on volcanic islands. Volcanic island palms were taller than their continental island and mainland counterparts, whereas continental island palms exhibited smaller fruit size. Height and fruit size of palms evolved under evolutionary constraints towards an optimal value. However, scenarios of adaptive radiation and niche conservatism were not supported for the height and fruit size of volcanic and mainland palm clades, respectively, as expected. Instead, continental island palms exhibited higher evolutionary rates for height and fruit size. Insular palm assemblages (continental and volcanic) are composed of unique lineages. Beyond representing evolutionary sources of new palm lineages, our results demonstrate that insular habitats are important in shaping palm trait diversity. Also, the higher phenotypic evolutionary rates of continental island palms suggest disparate selection pressures on this habitat type, which can be an important driver of trait diversification over time. Taken together, these results stress the importance of insular habitats for conservation of functional, phylogenetic, and taxonomic diversity of palms.

Pollinators drive floral evolution in an Atlantic Forest genus

Pollinators are important drivers of angiosperm diversification at both micro- and macroevolutionary scales. Both hummingbirds and bats pollinate the species-rich and morphologically diverse genus Vriesea across its distribution in the Brazilian Atlantic Forest. Here, we (i) determine if floral traits predict functional groups of pollinators as documented, confirming the pollination syndromes in Vriesea and (ii) test if genetic structure in Vriesea is driven by geography (latitudinal and altitudinal heterogeneity) or ecology (pollination syndromes). We analysed 11 floral traits of 58 Vriesea species and performed a literature survey of Vriesea pollination biology. The genealogy of haplotypes was inferred and phylogenetic analyses were performed using chloroplast (rps16-trnk and matK) and nuclear (PHYC) molecular markers. Floral traits accurately predict functional groups of pollinators in Vriesea. Genetic groupings match the different pollination syndromes. Species with intermediate position were found between the groups, which share haplotypes and differ morphologically from the typical hummingbird- and bat-pollinated flowers of Vriesea. The phylogeny revealed moderately to well-supported clades which may be interpreted as species complexes. Our results suggest a role of pollinators driving ecological isolation in Vriesea clades. Incipient speciation and incomplete lineage sorting may explain the overall low genetic divergence within and among morphologically defined species, precluding the identification of clear species boundaries. The intermediate species with mixed floral types likely represent a window into shifts between pollinator syndromes. This study reports the morphological-genetic continuum that may be typical of ongoing pollinator-driven speciation in biodiversity hotspots.

Selective extinction against redundant species buffers functional diversity

The extinction of species can destabilize ecological processes. A way to assess the ecological consequences of species loss is by examining changes in functional diversity. The preservation of functional diversity depends on the range of ecological roles performed by species, or functional richness, and the number of species per role, or functional redundancy. However, current knowledge is based on short timescales and an understanding of how functional diversity responds to long-term biodiversity dynamics has been limited by the availability of deep-time, trait-based data. Here, we compile an exceptional trait dataset of fossil molluscs from a 23-million-year interval in the Caribbean Sea (34 011 records, 4422 species) and develop a novel Bayesian model of multi-trait-dependent diversification to reconstruct mollusc (i) diversity dynamics, (ii) changes in functional diversity, and (iii) extinction selectivity over the last 23 Myr. Our results identify high diversification between 23–5 Mya, leading to increases in both functional richness and redundancy. Conversely, over the last three million years, a period of high extinction rates resulted in the loss of 49% of species but only 3% of functional richness. Extinction rates were significantly higher in small, functionally redundant species suggesting that competition mediated the response of species to environmental change. Taken together, our results identify long-term diversification and selective extinction against redundant species that allowed functional diversity to grow over time, ultimately buffering the ecological functions of biological communities against extinction.

Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae)

Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material. Raphia is divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy of Raphia is problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology. R. regalis is strongly supported as sister to all other Raphia species and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical species R. taedigera is supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that the Raphia individuals from Madagascar are potentially a distinct species different from the widely distributed R. farinifera. In conclusion, our results support the infra generic classification of Raphia based on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling, and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution, and other eco-evolutionary aspects of this charismatic, socially, and economically important palm genus.

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies.

Drivers of bromeliad leaf and floral bract variation across a latitudinal gradient in the Atlantic Forest

AIM

Understanding the complex interaction and relative contributions of factors involved in species and trait diversification is crucial to gain insights into the evolution of Neotropical biodiversity. Here, we investigated the drivers of morphological variation in bromeliads along a latitudinal gradient in a biodiversity hotspot.

LOCATION

Atlantic Forest, Brazil.

TAXON

A species complex in the genus Vriesea (Bromeliaceae).

METHODS

We measured shape and size variation for 208 floral bracts and 176 leaves in individuals from 14 localities using geometric morphometrics. We compiled data for two chloroplast regions (matK and trnL-F) from 89 individuals to assess genetic diversity, population structure and phylogenetic relationships. We tested the influence of climate, altitude and genetic distance on morphological traits using linear statistical models.

RESULTS

Temperature seasonality is a main driver of floral bract shape. Together with precipitation, it also explains changes in leaf size across the latitudinal gradient. Shifts in morphological traits are correlated with genetic structure and partly support the recent taxonomic delimitation proposed for the species complex. The species started to diversify in the Pliocene ca. 5 Mya. We detected a phylogeographical break in species distribution into northern and southern clades between the Bocaina region and the southern portion of the Atlantic Forest.

MAIN CONCLUSIONS

We identify how geography and environmental changes through time shape floral bracts and leaves in similar ways. At highly seasonal sites with lower annual precipitation (in the southern subtropical portion of the Atlantic Forest), leaves are larger and floral bracts are wide-elliptic, making them better suited for increased water accumulation. In contrast, at less seasonal sites (in the tropical north, where rainfall is more abundant and temperatures are higher), leaves are narrower and floral bracts are lanceolate-shaped, facilitating water drainage. The biogeographical break we identified suggests a role of tectonic activity and climatic oscillations in promoting species divergence and diversification.

Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae

The tribe Geonomateae is a widely distributed group of 103 species of Neotropical palms which contains six ecologically important understory or subcanopy genera. Although it has been the focus of many studies, our understanding of the evolutionary history of this group, and in particular of the taxonomically complex genus Geonoma, is far from complete due to a lack of molecular data. Specifically, the previous Sanger sequencing-based studies used a few informative characters and partial sampling. To overcome these limitations, we used a recently developed Arecaceae-specific target capture bait set to undertake a phylogenomic analysis of the tribe Geonomateae. We sequenced 3,988 genomic regions for 85% of the species of the tribe, including 84% of the species of the largest genus, Geonoma. Phylogenetic relationships were inferred using both concatenation and coalescent methods. Overall, our phylogenetic tree is highly supported and congruent with taxonomic delimitations although several morphological taxa were revealed to be non-monophyletic. It is the first time that such a large genomic dataset is provided for an entire tribe within the Arecaceae. Our study lays the groundwork not only for detailed macro- and micro-evolutionary studies within the group, but also sets a workflow for understanding other species complexes across the tree of life.

Ancient Polyploidy and Genome Evolution in Palms

Mechanisms of genome evolution are fundamental to our understanding of adaptation and the generation and maintenance of biodiversity, yet genome dynamics are still poorly characterized in many clades. Strong correlations between variation in genomic attributes and species diversity across the plant tree of life suggest that polyploidy or other mechanisms of genome size change confer selective advantages due to the introduction of genomic novelty. Palms (order Arecales, family Arecaceae) are diverse, widespread, and dominant in tropical ecosystems, yet little is known about genome evolution in this ecologically and economically important clade. Here, we take a phylogenetic comparative approach to investigate palm genome dynamics using genomic and transcriptomic data in combination with a recent, densely sampled, phylogenetic tree. We find conclusive evidence of a paleopolyploid event shared by the ancestor of palms but not with the sister clade, Dasypogonales. We find evidence of incremental chromosome number change in the palms as opposed to one of recurrent polyploidy. We find strong phylogenetic signal in chromosome number, but no signal in genome size, and further no correlation between the two when correcting for phylogenetic relationships. Palms thus add to a growing number of diverse, ecologically successful clades with evidence of whole-genome duplication, sister to a species-poor clade with no evidence of such an event. Disentangling the causes of genome size variation in palms moves us closer to understanding the genomic conditions facilitating adaptive radiation and ecological dominance in an evolutionarily successful, emblematic tropical clade.

Soil fertility and flood regime are correlated with phylogenetic structure of Amazonian palm communities

BACKGROUND AND AIMS

Identifying the processes that generate and maintain biodiversity requires understanding of how evolutionary processes interact with abiotic conditions to structure communities. Edaphic gradients are strongly associated with floristic patterns but, compared with climatic gradients, have received relatively little attention. We asked (1) How does the phylogenetic composition of palm communities vary along edaphic gradients within major habitat types? and (2) To what extent are phylogenetic patterns determined by (a) habitat specialists, (b) small versus large palms, and (c) hyperdiverse genera?

METHODS

We paired data on palm community composition from 501 transects of 0.25 ha located in two main habitat types (non-inundated uplands and seasonally inundated floodplains) in western Amazonian rain forests with information on soil chemistry, climate, phylogeny and metrics of plant size. We focused on exchangeable base concentration (cmol+ kg-1) as a metric of soil fertility and a floristic index of inundation intensity. We used a null model approach to quantify the standard effect size of mean phylogenetic distance for each transect (a metric of phylogenetic community composition) and related this value to edaphic variables using generalized linear mixed models, including a term for spatial autocorrelation.

KEY RESULTS

Overall, we recorded 112 008 individuals belonging to 110 species. Palm communities in non-inundated upland transects (but not floodplain transects) were more phylogenetically clustered in areas of low soil fertility, measured as exchangeable base concentration. In contrast, floodplain transects with more severe flood regimes (as inferred from floristic structure) tended to be phylogenetically clustered. Nearly half of the species recorded (44 %) were upland specialists while 18 % were floodplain specialists. In both habitat types, phylogenetic clustering was largely due to the co-occurrence of small-sized habitat specialists belonging to two hyperdiverse genera (Bactris and Geonoma).

CONCLUSIONS

Edaphic conditions are associated with the phylogenetic community structure of palms across western Amazonia, and different factors (specifically, soil fertility and inundation intensity) appear to underlie diversity patterns in non-inundated upland versus floodplain habitats. By linking edaphic gradients with palm community phylogenetic structure, our study reinforces the need to integrate edaphic conditions in eco-evolutionary studies in order to better understand the processes that generate and maintain tropical forest diversity. Our results suggest a role for edaphic niche conservatism in the evolution and distribution of Amazonian palms, a finding with potential relevance for other clades.

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.

Adjacency and Area Explain Species Bioregional Shifts in Neotropical Palms

Environmental and geographical variables are known drivers of community assembly, however their influence on phylogenetic structure and phylogenetic beta diversity of lineages within different bioregions is not well-understood. Using Neotropical palms as a model, we investigate how environmental and geographical variables affect the assembly of lineages into bioregions across an evolutionary time scale. We also determine lineage shifts between tropical (TRF) and non-tropical (non-TRF) forests. Our results identify that distance and area explain phylogenetic dissimilarity among bioregions. Lineages in smaller bioregions are a subset of larger bioregions and contribute significantly to the nestedness component of phylogenetic dissimilarity, here interpreted as evidence for a bioregional shift. We found a significant tendency of habitat shifts occurring preferentially between TRF and non-TRF bioregions (31 shifts) than from non-TRF to TRF (24) or from TRF to TRF (11) and non-TRF to non-TRF (9). Our results also present cases where low dissimilarity is found between TRF and non-TRF bioregions. Most bioregions showed phylogenetic clustering and larger bioregions tended to be more clustered than smaller ones, with a higher species turnover component of phylogenetic dissimilarity. However, phylogenetic structure did not differ between TRF and non-TRF bioregions and diversification rates were higher in only two lineages, Attaleinae and Bactridinae, which are widespread and overabundant in both TRF and non-TRF bioregions. Area and distance significantly affected Neotropical palm community assembly and contributed more than environmental variables. Despite palms being emblematic humid forest elements, we found multiple shifts from humid to dry bioregions, showing that palms are also important components of these environments.

The road to evolutionary success: insights from the demographic history of an Amazonian palm

Evolutionary success, as demonstrated by high abundance and a wide geographical range, is related to genetic variation and historical demography. Here we assess how climatic change during the Quaternary influenced the demography and distribution of the Neotropical swamp palm Mauritia flexuosa. Using microsatellite loci and coalescent analyses we examined how demographical dynamics affected genetic diversity, effective population size and connectivity through time and space. Mauritia flexuosa presents significant genetic differentiation between the Amazonian and Cerrado biomes and among different river basins. Amazonian lineages are ancient compared to lineages from the Cerrado, a pattern corroborated using the fossil pollen record, where the species was absent from the Cerrado during the cold and dry periods of the last glacial cycles, then returned during the wet, interglacial phases. Coalescent simulations show that the pattern of observed genetic diversity for M. flexuosa is most likely due to a range retraction during the Last Glacial Maximum, leading to multiple refugia and resulting in high differentiation between Amazonian and Cerrado biomes. Isolation-by-distance and by-environment also shaped the distribution and evolutionary success of M. flexuosa. Our study provides new insights into the historical factors that affected geographical distribution and structure genetic diversity, contributing to long-term evolutionary success.

Rivers shape population genetic structure in Mauritia flexuosa (Arecaceae)

The Mauritia flexuosa L.f. palm is known as the "tree of life" given its importance as fundamental food and construction resources for humans. The species is broadly distributed in wet habitats of Amazonia and dry habitats of the Amazon and Orinoco river basins and in the Cerrado savanna. We collected 179 individuals from eight different localities throughout these habitats and used microsatellites to characterize their population structure and patterns of gene flow. Overall, we found high genetic variation, except in one savanna locality. Gene flow between populations is largely congruent with river basins and the direction of water flow within and among them, suggesting their importance for seed dispersal. Further, rivers have had a higher frequency of human settlements than forested sites, contributing to population diversity and structure through increased human use and consumption of M. flexuosa along rivers. Gene flow patterns revealed that migrants are sourced primarily from within the same river basin, such as those from Madeira and Tapajós basins. Our work suggests that rivers and their inhabitants are a critical element of the landscape in Amazonia and have impacted the dispersal and subsequent distribution of tropical palm species, as shown by the patterns of genetic variation in M. flexuosa.

phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R

The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness. A key issue in this domain is the high frequency of sequence mislabeling encountered when searching for suitable sequences for phylogenetic analysis. These issues include, among others, the incorrect identification of sequenced species, non-standardized and ambiguous sequence annotation, and the inadvertent addition of paralogous sequences by users. Taken together, these issues likely add considerable noise, error or bias to phylogenetic inference, a risk that is likely to increase with the size of phylogenies or the molecular datasets used to generate them. Here we present a software package, phylotaR that bypasses the above issues by using instead an alignment search tool to identify orthologous sequences. Our package builds on the framework of its predecessor, PhyLoTa, by providing a modular pipeline for identifying overlapping sequence clusters using up-to-date GenBank data and providing new features, improvements and tools. We demonstrate and test our pipeline’s effectiveness by presenting trees generated from phylotaR clusters for two large taxonomic clades: Palms and primates. Given the versatility of this package, we hope that it will become a standard tool for any research aiming to use GenBank data for phylogenetic analysis.

Evolutionary persistence in Gunnera and the contribution of southern plant groups to the tropical Andes biodiversity hotspot

Several studies have demonstrated the contribution of northern immigrants to the flora of the tropical Andes—the world’s richest and most diverse biodiversity hotspot. However, much less is known about the biogeographic history and diversification of Andean groups with southern origins, although it has been suggested that northern and southern groups have contributed roughly equally to the high Andean (i.e., páramo) flora. Here we infer the evolutionary history of the southern hemisphere plant genus Gunnera, a lineage with a rich fossil history and an important ecological role as an early colonising species characteristic of wet, montane environments. Our results show striking contrasts in species diversification, where some species may have persisted for some 90 million years, and whereas others date to less than 2 Ma since origination. The outstanding longevity of the group is likely linked to a high degree of niche conservatism across its highly disjunct range, whereby Gunnera tracks damp and boggy soils in cool habitats. Colonisation of the northern Andes is related to Quaternary climate change, with subsequent rapid diversification appearing to be driven by their ability to take advantage of environmental opportunities. This study demonstrates the composite origin of a mega-diverse biota.

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa

Rapidly growing biological data—including molecular sequences and fossils—hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable.

Comment (1) on "Formation of the Isthmus of Panama" by O'Dea et al

A review and reanalysis of geological, molecular, and paleontological data led O'Dea et al. (1) to propose (i) that reports by Montes et al. (2) and Bacon et al. (3) regarding a middle Miocene closure of the Central American Seaway (CAS) are unsupported, and (ii) a new age of the formation of the Isthmus at 2.8 million years ago (Ma). Here, we reject both of these conclusions.

Endemic palm species shed light on habitat shifts and the assembly of the Cerrado and Restinga floras

Species expansions into new habitats are often associated with physiological adaptations, for instance when rain forest lineages colonize dry habitats. Although such shifts have been documented for the Brazilian savanna (Cerrado), little is known about the biogeographic origin of species occupying an extreme South American habitat type, the coastal dunes (Restinga). We examined the formation of this poorly known, endangered habitat by reconstructing the evolutionary history of two endemic species. Due to the proposed recency and uniqueness of this habitat, we hypothesized that Restinga species of the palm genus Allagoptera to be recently evolved and to present derived morphological characters. To detect habit shifts in absolute time, we used one plastid and nine nuclear genes to reconstruct the phylogenetic and biogeographic history of Allagoptera. We used light microscopy and stable isotope analysis to explore whether morphological adaptations occurred concomitantly with habitat shifts. Phylogenetic relationships were well supported and we found ancestral lineages of Allagoptera to be widely distributed throughout habitats that are currently occupied by extant species. Over the last ca. 7Ma Allagoptera has shifted its preference to increasingly dry habitats. Coincident with the colonization of the Cerrado and Restinga, morphological adaptations also evolved, including subterranean stems that are fire-resistant and long underground stem and root systems that facilitate water access. We did not find differences in metabolic pathway or modifications to pollen morphology when compared to other palm lineages. Assuming that the evolutionary history of Allagoptera is indicative of the habitat in which it occurs, our results infer a recent origin for Cerrado species. Although little is known about the formation of the Restinga habitat, our results also suggest a longer history than currently proposed; with an origin of Restinga habitats dating back to the Late Pliocene.

Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record

Plants have a long evolutionary history, during which mass extinction events dramatically affected Earth's ecosystems and its biodiversity. The fossil record can shed light on the diversification dynamics of plant life and reveal how changes in the origination-extinction balance have contributed to shaping the current flora. We use a novel Bayesian approach to estimate origination and extinction rates in plants throughout their history. We focus on the effect of the 'Big Five' mass extinctions and on estimating the timing of origin of vascular plants, seed plants and angiosperms. Our analyses show that plant diversification is characterized by several shifts in origination and extinction rates, often matching the most important geological boundaries. The estimated origin of major plant clades predates the oldest macrofossils when considering the uncertainties associated with the fossil record and the preservation process. Our findings show that the commonly recognized mass extinctions have affected each plant group differently and that phases of high extinction often coincided with major floral turnovers. For instance, after the Cretaceous-Paleogene boundary we infer negligible shifts in diversification of nonflowering seed plants, but find significantly decreased extinction in spore-bearing plants and increased origination rates in angiosperms, contributing to their current ecological and evolutionary dominance.

An engine for global plant diversity: highest evolutionary turnover and emigration in the American tropics

Understanding the processes that have generated the latitudinal biodiversity gradient and the continental differences in tropical biodiversity remains a major goal of evolutionary biology. Here we estimate the timing and direction of range shifts of extant flowering plants (angiosperms) between tropical and non-tropical zones, and into and out of the major tropical regions of the world. We then calculate rates of speciation and extinction taking into account incomplete taxonomic sampling. We use a recently published fossil calibrated phylogeny and apply novel bioinformatic tools to code species into user-defined polygons. We reconstruct biogeographic history using stochastic character mapping to compute relative numbers of range shifts in proportion to the number of available lineages through time. Our results, based on the analysis of c. 22,600 species and c. 20 million geo-referenced occurrence records, show no significant differences between the speciation and extinction of tropical and non-tropical angiosperms. This suggests that at least in plants, the latitudinal biodiversity gradient primarily derives from other factors than differential rates of diversification. In contrast, the outstanding species richness found today in the American tropics (the Neotropics), as compared to tropical Africa and tropical Asia, is associated with significantly higher speciation and extinction rates. This suggests an exceedingly rapid evolutionary turnover, i.e., Neotropical species being formed and replaced by one another at unparalleled rates. In addition, tropical America stands out from other continents by having “pumped out” more species than it received through most of the last 66 million years. These results imply that the Neotropics have acted as an engine for global plant diversity.

Geographic and taxonomic disparities in species diversity: dispersal and diversification rates across Wallace's line

Broad-scale patterns of species diversity have received much attention in the literature, yet the mechanisms behind their formation may not explain species richness disparities across small spatial scales. Few taxa display high species diversity on either side of Wallace's Line and our understanding of the processes causing this biogeographical pattern remains limited, particularly in plant lineages. To understand the evolution of this biogeographical pattern, a time-calibrated molecular phylogeny of Livistoninae palms (Arecaceae) was used to infer the colonization history of the Sahul tectonic plate region and to test for disparities in diversification rates across taxa and across each side of Wallace's Line. Our analyses allowed us to examine how timing, migration history, and shifts in diversification rates have contributed to shape the biogeographical pattern observed in Livistoninae. We inferred that each of the three genera found in Sahul crossed Wallace's Line only once and relatively recently. In addition, at least two of the three dispersing genera underwent an elevation in their diversification rate leading to high species richness on each side of Wallacea. The correspondence of our results with Southeast Asian geologic and climatic history show how palms emerge as excellent models for understanding the historical formation of fine-scale biogeographic patterns in a phylogenetic framework.

Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia)

BACKGROUND

Robust species delimitations are fundamental for conservation, evolutionary, and systematic studies, but they can be difficult to estimate, particularly in rapid and recent radiations. The consensus that species concepts aim to identify evolutionarily distinct lineages is clear, but the criteria used to distinguish evolutionary lineages differ based on the perceived importance of the various characteristics of evolving populations. We examined three different species-delimitation criteria (monophyly, absence of genetic intermediates, and diagnosability) to determine whether currently recognized species of Hawaiian Pritchardia are distinct lineages.

RESULTS

Data from plastid and nuclear genes, microsatellite loci, and morphological characters resulted in various levels of lineage subdivision that were likely caused by differing evolutionary rates between data sources. Additionally, taxonomic entities may be confounded because of the effects of incomplete lineage sorting and/or gene flow. A coalescent species tree was largely congruent with the simultaneous analysis, consistent with the idea that incomplete lineage sorting did not mislead our results. Furthermore, gene flow among populations of sympatric lineages likely explains the admixture and lack of resolution between those groups.

CONCLUSIONS

Delimiting Hawaiian Pritchardia species remains difficult but the ability to understand the influence of the evolutionary processes of incomplete lineage sorting and hybridization allow for mechanisms driving species diversity to be inferred. These processes likely extend to speciation in other Hawaiian angiosperm groups and the biota in general and must be explicitly accounted for in species delimitation.

Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae)

The study of three island groups of the palm tribe Trachycarpeae (Arecaceae/Palmae) permits both the analysis of each independent radiation and comparisons across the tribe to address general processes that drive island diversification. Phylogenetic relationships of Trachycarpeae were inferred from three plastid and three low-copy nuclear genes. The incongruent topological position of Brahea in CISP5 was hypothesized to be caused by a gene duplication event and was addressed using uninode coding. The resulting phylogenetic trees were well-resolved and the genera were all highly supported except for Johannesteijsmannia and Serenoa. Divergence time analysis estimated the stem of the tribe to be approximately 86 Ma and the crown to be 38 Ma, indicating that significant extinction may have occurred along this branch. Historical biogeographic analysis suggested that Trachycarpeae are of southern North American, Central American, or Caribbean origin and supports previous hypotheses of a Laurasian origin. The biogeography and disjunctions within the tribe were interpreted with respect to divergence times, the fossil record, and geological factors such as the formation of the Greater Antilles--Aves Ridge, the Bering and the North Atlantic land bridges, tectonic movement in Southeast Asia, climatic shifts between the Eocene and Pliocene, and volcanism in the Pacific basin. In considering the three major island radiations within Trachycarpeae, Miocene dispersal appears to have been the driving force in allopatric speciation and is highlighted here as an emerging pattern across the tree of life.

Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes

The phylogeny of Celastraceae tribe Euonymeae (≈ 230 species in eight genera in both the Old and New Worlds) was inferred using morphological characters together with plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) genes. Tribe Euonymeae has been defined as those genera of Celastraceae with generally opposite leaves, isomerous carpels, loculicidally dehiscent capsules, and arillate seeds (except Microtropis). Euonymus is the most diverse (129 species) and widely cultivated genus in the tribe. We infer that tribe Euonymeae consists of at least six separate lineages within Celastraceae and that a revised natural classification of the family is needed. Microtropis and Quetzalia are inferred to be distinct sister groups that together are sister to Zinowiewia. The endangered Monimopetalum chinense is an isolated and early derived lineage of Celastraceae that represents an important component of phylogenetic diversity within the family. Hedraianthera is sister to Brassiantha, and we describe a second species (Brassiantha hedraiantheroides A.J. Ford) that represents the first reported occurrence of this genus in Australia. Euonymus globularis, from eastern Australia, is sister to Menepetalum, which is endemic to New Caledonia, and we erect a new genus (Dinghoua R.H. Archer) for it. The Madagascan species of Euonymus are sister to Pleurostylia and recognized as a distinct genus (Astrocassine ined.). Glyptopetalum, Torralbasia, and Xylonymus are all closely related to Euonymus sensu stricto and are questionably distinct from it. Current intrageneric classifications of Euonymus are not completely natural and require revision.

Development of microsatellites in the Hawaiian endemic palm Pritchardia martii (Arecaceae) and their utility in congeners

PREMISE OF THE STUDY

Pritchardia (loulu palm) is the seventh largest flowering plant genus in the Hawaiian archipelago, and many species are of high conservation concern. The island radiation has produced many cryptic species complexes across fine ecological gradients. Microsatellite primers were optimized to investigate genetic diversity of Pritchardia martii (Gaudich.) H. Wendl. and species boundaries among the Hawaiian Pritchardia.

METHODS AND RESULTS

Six new loci and three previously described loci for a closely related genus, Phoenix, were optimized and tested. Five loci were polymorphic, and 72 alleles were detected across loci within P. martii. The five loci were also polymorphic across the other 27 currently recognized Pritchardia species. •

CONCLUSIONS

These results indicate the utility of these microsatellite markers for understanding the conservation genetics of P. martii and species delimitation and hybridization across the genus.

Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation

Background

Developing a greater understanding of population genetic structure in lowland tropical plant species is highly relevant to our knowledge of increasingly fragmented forests and to the conservation of threatened species. Specific studies are particularly needed for taxa whose population dynamics are further impacted by human harvesting practices. One such case is the fishtail or xaté palm (Chamaedorea ernesti-augusti) of Central America, whose wild-collected leaves are becoming progressively more important to the global ornamental industry. We use microsatellite markers to describe the population genetics of this species in Belize and test the effects of climate change and deforestation on its recent and historical effective population size.

Results

We found high levels of inbreeding coupled with moderate or high allelic diversity within populations. Overall high gene flow was observed, with a north and south gradient and ongoing differentiation at smaller spatial scales. Immigration rates among populations were more difficult to discern, with minimal evidence for isolation by distance. We infer a tenfold reduction in effective population size ca. 10,000 years ago, but fail to detect changes attributable to Mayan or contemporary deforestation.

Conclusion

Populations of C. ernesti-augusti are genetically heterogeneous demes at a local spatial scale, but are widely connected at a regional level in Belize. We suggest that the inferred patterns in population genetic structure are the result of the colonization of this species into Belize following expansion of humid forests in combination with demographic and mating patterns. Within populations, we hypothesize that low aggregated population density over large areas, short distance pollen dispersal via thrips, low adult survival, and low fruiting combined with early flowering may contribute towards local inbreeding via genetic drift. Relatively high levels of regional connectivity are likely the result of animal-mediated long-distance seed dispersal. The greatest present threat to the species is the potential onset of inbreeding depression as the result of increased human harvesting activities. Future genetic studies in understory palms should focus on both fine-scale and landscape-level genetic structure.

Leveraging the rice genome sequence for monocot comparative and translational genomics

Common genome anchor points across many taxa greatly facilitate translational and comparative genomics and will improve our understanding of the Tree of Life. To add to the repertoire of genomic tools applicable to the study of monocotyledonous plants in general, we aligned Allium and Musa ESTs to Oryza BAC sequences and identified candidate Allium-Oryza and Musa-Oryza conserved intron-scanning primers (CISPs). A random sampling of 96 CISP primer pairs, representing loci from 11 of the 12 chromosomes in rice, were tested on seven members of the order Poales and on representatives of the Arecales, Asparagales, and Zingiberales monocot orders. The single-copy amplification success rates of Allium (31.3%), Cynodon (31.4%), Hordeum (30.2%), Musa (37.5%), Oryza (61.5%), Pennisetum (33.3%), Sorghum (47.9%), Zea (33.3%), Triticum (30.2%), and representatives of the palm family (32.3%) suggest that subsets of these primers will provide DNA markers suitable for comparative and translational genomics in orphan crops, as well as for applications in conservation biology, ecology, invasion biology, population biology, systematic biology, and related fields.

Taxonomy and conservation: A case study from Chamaedorea alternans

BACKGROUND AND AIMS

The establishment of justified recommendations in conservation biology requires robust taxonomic treatments for the group(s) being considered. Controversial or poorly developed taxonomies can have a negative impact on conservation assessments. One example of a taxonomically difficult and controversial species complex that is important in conservation involves two species of Mexican palms, Chamaedorea tepejilote and C. alternans. The goal of this study was to investigate whether C. alternans and C. tepejilote are genetically distinct within the Los Tuxtlas region of Veracruz.

METHODS

Individuals corresponding to the morphology of C. alternans and C. tepejilote were collected from sympatric and allopatric regions within the Los Tuxtlas Biological Station. Eighty-eight samples were genotyped using amplified fragment length polymorphism (AFLP) markers. Cluster and ordination analyses were used to investigate patterns of differentiation.

KEY RESULTS

UPGMA and PCO analyses of AFLP profiles recovered two divergent clusters corresponding to morphologically defined C. tepejilote and C. alternans. No intermediate genotypes were observed and five of the 45 loci were fixed for either the presence or absence between the species. The patterns of divergence observed do not identify a role for sympatric speciation.

CONCLUSIONS

The observed patterns of differentiation support the recognition of C. alternans as distinct from C. tepejilote. A suite of vegetative and reproductive morphological features can be used to help distinguish these taxa in the field, but they can be difficult to differentiate from preserved material. Previous treatments of the variation found within the complex (C. alternans and C. tepejilote) as intraspecific variance is unjustified. Given that the Los Tuxtlas region has suffered from historical and ongoing deforestation and that Chamaedorea includes numerous endangered taxa, retaining conservation status for C. alternans serves to help safeguard individuals of the species as well as a region and larger taxonomic group all under considerable threat from human activities.