North Andean origin and diversification of the largest ithomiine butterfly genus

Deciphering the patterns and timing of diversification of the genus Melanastera (Hemiptera: Psylloidea: Liviidae) in the Neotropics

Even after decades of research on diversification in the Neotropics, our understanding of the evolutionary processes that shaped Neotropical clades is still incomplete. In the present study, we used different divergence times and likelihood-based methods to investigate the influence of biogeography and host plant associations on the diversification of the most species-rich psyllid genus Melanastera (Liviidae) from the Neotropics as a model group of herbivorous insects. We used molecular phylogenetic data from seven gene fragments (four mitochondrial and three nuclear). The putatively monophyletic group of Neotropical Melanastera species has an estimated crown node age of 20.2 Ma (ML, CI 20.2-30.6) or 23.2 Ma (BI, 95 % HPD 16.6-32.6), with diversification occurring mainly in the Upper Miocene, although some species groups diversified in the Pliocene or Pleistocene. Biogeographic analysis suggests that the Neotropical Melanastera originated from the Pacific region of South and Central America. We detected a shift in diversification rates that likely occurred either at the time of origin of Melanastera or during the main colonisation of the Atlantic and Amazon Forests, followed by a subsequent slowdown in speciation rates. State-dependent speciation and extinction models revealed a significant relationship between this diversification shift and the shift of Melanastera to the plant families Melastomataceae and Annonaceae, reflecting the impact of host switching on speciation rates in this group. This period also coincides with several independent dispersal events from the Atlantic and Amazon Forests to other parts of the Neotropics. Taken together, the results of the current study suggest that diversification of Melanastera was facilitated by shifts to new host families, which may have promoted the dispersal of Melanastera into new adaptive zones with subsequent processes of local speciation.

Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae)

Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies suggest that hybridization is frequent, the extent of reticulation within Petunia and its closely related genera has never been examined from a phylogenetic perspective. In this study, we used transcriptomic data from 11 Petunia, 16 Calibrachoa, and 10 Fabiana species to illuminate the relationships between these species and investigate whether hybridization played a significant role in the diversification of the clade. We inferred that gene tree discordance within genera is linked to hybridization events along with high levels of ILS due to their rapid diversification. Moreover, network analyses estimated deeper hybridization events between Petunia and Calibrachoa, genera that have different chromosome numbers. Although these genera cannot hybridize at the present time, ancestral hybridization could have played a role in their parallel radiations, as they share the same habitat and life history.

Viviparity imparts a macroevolutionary signature of ecological opportunity in the body size of female Liolaemus lizards

Viviparity evolved ~115 times across squamate reptiles, facilitating the colonization of cold habitats, where oviparous species are scarce or absent. Whether the ecological opportunity furnished by such colonization reconfigures phenotypic diversity and accelerates evolution is unclear. We investigated the association between viviparity and patterns and rates of body size evolution in female Liolaemus lizards, the most species-rich tetrapod genus from temperate regions. Here, we discover that viviparous species evolve ~20% larger optimal body sizes than their oviparous relatives, but exhibit similar rates of body size evolution. Through a causal modeling approach, we find that viviparity indirectly influences body size evolution through shifts in thermal environment. Accordingly, the colonization of cold habitats favors larger body sizes in viviparous species, reconfiguring body size diversity in Liolaemus. The catalyzing influence of viviparity on phenotypic evolution arises because it unlocks access to otherwise inaccessible sources of ecological opportunity, an outcome potentially repeated across the tree of life.

The Andes as a semi-permeable geographical barrier: Genetic connectivity between structured populations in a widespread spider

Geographical barriers like mountain ranges impede genetic exchange among populations, promoting diversification. The effectiveness of these barriers in limiting gene flow varies between lineages due to each species' dispersal modes and capacities. Our understanding of how the Andes orogeny contributes to species diversification comes from well-studied vertebrates and a few arthropods and plants, neglecting organisms unable to fly or walk long distances. Some arachnids, such as Gasteracantha cancriformis, have been hypothesized to disperse long distances via ballooning (i.e. using their silk to interact with the wind). Yet, we do not know how the environment and geography shape its genetic diversity. Therefore, we tested whether the Andes contributed to the diversification of G. cancriformis acting as an absolute or semi-permeable barrier to genetic connectivity between populations of this spider at opposite sides of the mountain range. We sampled thousands of loci across the distribution of the species and implemented population genetics, phylogenetic, and landscape genetic analyses. We identified two genetically distinct groups structured by the Central Andes, and a third less structured group in the Northern Andes that shares ancestry with the previous two. This structure is largely explained by the altitude along the Andes, which decreases in some regions, possibly facilitating cross-Andean dispersal and gene flow. Our findings support that altitude in the Andes plays a major role in structuring populations in South America, but the strength of this barrier can be overcome by organisms with long-distance dispersal modes together with altitudinal depressions.

The rapid radiation of Bomarea (Alstroemeriaceae: Liliales), driven by the rise of the Andes

Geological events such as mountain uplift affect how, when, and where species diversify, but measuring those effects is a longstanding challenge. Andean orogeny impacted the evolution of regional biota by creating barriers to gene flow, opening new habitats, and changing local climate. B⁢o⁢m⁢a⁢r⁢e⁢a (Alstroemeriaceae) are tropical plants with (often) small, isolated ranges; in total, B⁢o⁢m⁢a⁢r⁢e⁢a species occur from central Mexico to central Chile. This genus appears to have evolved rapidly and quite recently, and rapid radiations are often challenging to resolve with traditional phylogenetic inference. In this study, we apply phylogenomics-with hundreds of loci, gene-tree-based data curation, and a multispecies-coalescent approach-to infer the phylogeny of B⁢o⁢m⁢a⁢r⁢e⁢a. We use this phylogeny to untangle the potential drivers of diversification and biogeographic history. In particular, we test if Andean orogeny contributed to the diversification of B⁢o⁢m⁢a⁢r⁢e⁢a. We find that B⁢o⁢m⁢a⁢r⁢e⁢a originated in the central Andes during the mid-Miocene, then spread north, following the trajectory of mountain uplift. Furthermore, Andean lineages diversified faster than non-Andean relatives. B⁢o⁢m⁢a⁢r⁢e⁢a thus demonstrates that-at least in some cases-geological change rather than environmental stability has driven high species diversity in a tropical biodiversity hotspot. These results also demonstrate the utility (and danger) of genome-scale data for making macroevolutionary inferences.

Fossil berries reveal global radiation of the nightshade family by the early Cenozoic

Fossil discoveries can transform our understanding of plant diversification over time and space. Recently described fossils in many plant families have pushed their known records farther back in time, pointing to alternative scenarios for their origin and spread. Here, we describe two new Eocene fossil berries of the nightshade family (Solanaceae) from the Esmeraldas Formation in Colombia and the Green River Formation in Colorado (USA). The placement of the fossils was assessed using clustering and parsimony analyses based on 10 discrete and five continuous characters, which were also scored in 291 extant taxa. The Colombian fossil grouped with members of the tomatillo subtribe, and the Coloradan fossil aligned with the chili pepper tribe. Along with two previously reported early Eocene fossils from the tomatillo genus, these findings indicate that Solanaceae were distributed at least from southern South America to northwestern North America by the early Eocene. Together with two other recently discovered Eocene berries, these fossils demonstrate that the diverse berry clade and, in turn, the entire nightshade family, is much older and was much more widespread in the past than previously thought.

Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding

Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.

Is Psathyromyia shannoni (Diptera: Psychodidae: Phlebotominae) a species complex? Retrospective study of genetic diversity of COI gene, pathogens and geographic distribution

The sand fly Psathyromyia shannoni is a broadly distributed species that is relevant for the transmission of pathogens such as Leishmania, Bartonella and viruses in several countries of America. This species belongs to the Shannoni complex. Yet its identification is difficult due to morphologic intraspecific polymorphisms that make it difficult to distinguish between species, and could therefore lead to misidentification and overestimation of its distribution. The aim of this study was to perform a retrospective study on the genetic diversity of Pa. shannoni based on the Cytochrome Oxidase subunit 1 gene and considering its geographic distribution to achieve a better identification and differentiation from other species of the Shannoni complex. According to the Maximum Likelihood analysis and the data on the genetic structure, we propose a modified delimitation of Pa. shannoni species by classifying it into at least three genetic lineages, based on genetic variability and distribution. However, more genetic information on the COI gene, mainly from countries where this species has been reported, is needed to strengthen this proposal.

Landscape genetics across the Andes mountains: Environmental variation drives genetic divergence in the leaf-cutting ant Atta cephalotes

Distinguishing among the mechanisms underlying the spatial distribution of genetic variation resulting from the environmental or physical barriers from those arising due to simple geographic distance is challenging in complex landscapes. The Andean uplift represents one of the most heterogeneous habitats where multiple mechanisms may interact, confounding their relative roles. We explore this broad question in the leaf-cutting ant Atta cephalotes, a species that is distributed across the Andes mountains, using nuclear microsatellite markers and mtCOI gene sequences. We investigate spatial genetic divergence across the western range of the northern Andes in Colombia by testing the relative role of alternative scenarios of population divergence, including isolation by geographic distance (IBD), climatic conditions (IBE), and the physical barriers presented by the Andes mountains (IBB). Our results reveal substantial genetic differentiation among A. cephalotes populations for both types of markers, but only nuclear divergence followed a hierarchical pattern with multiple models of genetic divergence imposed by the western range. Model selection showed that the IBD, IBE (temperature and precipitation), and IBB (Andes mountains) models, often proposed as individual drivers of genetic divergence, interact, and explain up to 33% of the genetic divergence in A. cephalotes. The IBE model remained significant after accounting for IBD, suggesting that environmental factors play a more prominent role than IBB. These factors, in combination with the idiosyncratic dispersal patterns of ants, appear to determine the hierarchical patterns of gene flow. This study enriches our understanding of the forces shaping population divergence in complex habitat landscapes.

Diversification of chiles (Capsicum, Solanaceae) through time and space: New insights from genome-wide RAD-seq data

Capsicum L. encompasses 43 American species, including the five domesticated worldwide consumed sweet and hot chiles. This study presents new, updated and age-calibrated phylogenetic hypothesis on the genus evolution incorporating nearly all currently accepted Capsicum species. A new model of spatial diversification of Capsicum is proposed based on analyses of several thousands of genome-wide RAD-seq derived SNPs. Maximum likelihood approaches were used to reconstruct phylogenies and to estimate dates of all major splits. Ancestral ranges were inferred and diversification events were modeled in a time frame using a Bayesian approach. Nine clades corresponding to genetically and (mostly) geographically well-defined lineages, which diversified starting around mid-upper Miocene, were recovered with strong support. The Northern and Central Andes were inferred to represent the most likely ancestral range of the genus Capsicum. A few early vicariant and dispersal events were estimated to have driven the geographic divergence of the main Capsicum clades. Each lineage was inferred to have diversified within a distinct region of South America and expanded geographically to different extent. Extant species diversification was inferred to have begun at the beginning of Pliocene and continued through the Pleistocene. The Central Andes, represented mainly by the territory of present-day Bolivia, were proposed to play a central role in the diversification of lineages comprising domesticated capsicums and their wild allies. The genome-wide approach allowed for high resolution and support of deep phylogenetic nodes providing novel insights into the affinities of major lineages and clades as well as on the geographic expansion of Capsicum. This study provides the first dated evolutionary history of the genus encompassing most of the chile species diversity.

Genomic analyses of the scorpion mud turtle (Kinosternon scorpioides) (Linnaeus, 1766) in insular and continental Colombia: Evidence for multiple conservation and taxonomic units

The turtle genus Kinosternon is widespread with at least 25 species distributed from Mexico to northern Argentina. The taxonomy of this genus is controversial and requires a full revision using both morphological and molecular approaches. In this study, we did a genomic analysis on the species Kinosternon scorpioides distributed in insular and continental Colombia in order to define conservation units. Total DNA was extracted from 24 tissue samples and RADseq genotyping analysis was done. In addition, the intron R35 was amplified and sequenced for a subset of samples. A total of 35,507 SNPs combined with 1,047 bp of the intron were used for spatiotemporal colonization pattern reconstruction and phylogenetic analyses. In addition, SNPs were used for population structure inferences and allele frequency-based analyses. Reciprocal monophyly, significant differences in allele frequencies (Fst = 0.32 - 0.78), and evidence of reproductive isolation (no admixture/geneflow), indicate long-term divergence between groups (2-8 MYA), possibly due to geographical barriers. Four Evolutionarily Significant Units (ESUs) were defined within our samples. One ESU was represented by the insular subspecies K. scorpioides albogulare, found on San Andrés island, and three ESUs were defined for the subspecies K. s. scorpioides in continental Colombia: one trans-Andean, found in northwestern Colombia (Caribbean region) and two cis-Andean, found in eastern and southeastern Colombia in the Orinoco and Amazon regions, respectively. Colonization of this species occurred from an ancestral area on South of Central America region (~ 8.43 MYA), followed by an establishing of current populations on San Andrés Island and then, in the continent. First, in the Colombian Caribbean, next, in the Orinoco, and more recently, in the Amazon. We hypothesize that the emergence of the Panamá Isthmus, as well as the final uplift of the North Eastern Andes and Vaupes Arch, were key event leading to the differentiation of these ESUs. For management and conservation purposes, each of these ESUs should be considered as a separate management unit. A full revision of the taxonomy of the genus Kinosternon is warranted.

A multidisciplinary framework for biodiversity prediction in the Brazilian Atlantic Forest hotspot

Abstract: We briefly describe selected results from our thematic project focused on the biodiversity of the Atlantic Forest (“AF BIOTA”), which was jointly funded by FAPESP’s BIOTA Program, the U.S. National Science Foundation Dimensions of Biodiversity Program, and the National Aeronautics and Space Administration (NASA). As one of the five most important hotspots of biodiversity in the world, the Atlantic Forest (AF) holds less than 16% of its vegetation cover, yet, amongst the hotspots, it still harbors one of the highest numbers of species, including endemics. By gathering specialists across multiple disciplines (biology, geology, engineering), we aimed to understand how this megabiodiversity was built through time, informing biodiversity science and conservation. Among the results, we trained 18 Master’s and 26 Ph.D. students, published more than 400 peer-reviewed papers that improved our knowledge about the forest’s biologic and climatic diversity and dynamics through time, developed new analytical methods, produced outreach videos and articles, and provided data to help define biodiversity conservation policies.

Comparative transcriptome analysis at the onset of speciation in a mimetic butterfly-The Ithomiini Melinaea marsaeus

Ecological speciation entails divergent selection on specific traits and ultimately on the developmental pathways responsible for these traits. Selection can act on gene sequences but also on regulatory regions responsible for gene expression. Mimetic butterflies are a relevant system for speciation studies because wing colour pattern (WCP) often diverges between closely related taxa and is thought to drive speciation through assortative mating and increased predation on hybrids. Here, we generate the first transcriptomic resources for a mimetic butterfly of the tribe Ithomiini, Melinaea marsaeus, to examine patterns of differential expression between two subspecies and between tissues that express traits that likely drive reproductive isolation; WCP and chemosensory genes. We sequenced whole transcriptomes of three life stages to cover a large catalogue of transcripts, and we investigated differential expression between subspecies in pupal wing discs and antennae. Eighteen known WCP genes were expressed in wing discs and 115 chemosensory genes were expressed in antennae, with a remarkable diversity of chemosensory protein genes. Many transcripts were differentially expressed between subspecies, including two WCP genes and one odorant receptor. Our results suggest that in M. marsaeus the same genes as in other mimetic butterflies are involved in traits causing reproductive isolation, and point at possible candidates for the differences in those traits between subspecies. Differential expression analyses of other developmental stages and body organs and functional studies are needed to confirm and expand these results. Our work provides key resources for comparative genomics in mimetic butterflies, and more generally in Lepidoptera.

Punctuational ecological changes rather than global factors drive species diversification and the evolution of wing phenotypes in Morpho butterflies

Assessing the relative importance of geographical and ecological drivers of evolution is paramount to understand the diversification of species and traits at the macroevolutionary scale. Here, we use an integrative approach, combining phylogenetics, biogeography, ecology and quantified phenotypes to investigate the drivers of both species and phenotypic diversification of the iconic Neotropical butterfly genus Morpho. We generated a time-calibrated phylogeny for all known species and inferred historical biogeography. We fitted models of time-dependent (accounting for rate heterogeneity across the phylogeny) and paleoenvironment-dependent diversification (accounting for global effect on the phylogeny). We used geometric morphometrics to assess variation of wing size and shape across the tree and investigated their dynamics of evolution. We found that the diversification of Morpho is best explained when considering variable diversification rates across the tree, possibly associated with lineages occupying different microhabitat conditions. First, a shift from understory to canopy was characterized by an increased speciation rate partially coupled with an increasing rate of wing shape evolution. Second, the occupation of dense bamboo thickets accompanying a major host-plant shift from dicotyledons towards monocotyledons was associated with a simultaneous diversification rate shift and an evolutionary 'jump' of wing size. Our study points to a diversification pattern driven by punctuational ecological changes instead of a global driver or biogeographic history.

Mesoamerica is a cradle and the Atlantic Forest is a museum of Neotropical butterfly diversity: insights from the evolution and biogeography of Brassolini (Lepidoptera: Nymphalidae)

Regional species diversity is explained ultimately by speciation, extinction and dispersal. Here, we estimate dispersal and speciation rates of Neotropical butterflies to propose an explanation for the distribution and diversity of extant species. We focused on the tribe Brassolini (owl butterflies and allies), a Neotropical group that comprises 17 genera and 108 species, most of them endemic to rainforest biomes. We inferred a robust species tree using the multispecies coalescent framework and a dataset including molecular and morphological characters. This formed the basis for three changes in Brassolini classification: (1) Naropina syn. nov. is subsumed within Brassolina; (2) Aponarope syn. nov. is subsumed within Narope; and (3) Selenophanes orgetorix comb. nov. is reassigned from Catoblepia to Selenophanes. By applying biogeographical stochastic mapping, we found contrasting species diversification and dispersal dynamics across rainforest biomes, which might be explained, in part, by the geological and environmental history of each bioregion. Our results revealed a mosaic of biome-specific evolutionary histories within the Neotropics, where butterfly species have diversified rapidly (cradles: Mesoamerica), have accumulated gradually (museums: Atlantic Forest) or have diversified and accumulated alternately (Amazonia). Our study contributes evidence from a major butterfly lineage that the Neotropics are a museum and a cradle of species diversity.

Extraordinary diversification of the “bristle flies” (Diptera: Tachinidae) and its underlying causes

The family Tachinidae (“bristle flies”) is the most diverse and ecologically important group of insect parasitoids outside the parasitic wasps. It is among the most species rich families of flies (Diptera) and has experienced a recent adaptive radiation across the globe. We make use of a molecular phylogeny of the family to examine its rapid radiation and explore the traits of tachinid lineages that may have contributed to variation in their diversification. We apply a range of diversification analyses to assess the consistency and robustness of effects. We find that the Tachinidae are among the most rapidly diversifying families of animals. Six to eight clades of bristle flies, distributed across the phylogeny, exhibit strong evidence of accelerated diversification. Our results suggest that the use of holometabolous insect larvae, and specifically caterpillars (Lepidoptera), as hosts, is associated with increased diversification rates. However, these effects were inconsistent across analyses. We detected little influence of oviposition strategy (egg type) or host feeding habit, and we recovered evidence that unmeasured “hidden” traits may explain greater variance in diversification. We evaluated the strengths and weaknesses of different Maximum Likelihood and Bayesian approaches for analysing diversification and the potential for extrinsic factors, such as geography, to influence patterns of richness and diversification. In general, we conclude that although certain traits may provide opportunities for diversification, whether this is capitalized on may depend on additional traits and/or historical contingency.

Use of species delimitation approaches to tackle the cryptic diversity of an assemblage of high Andean butterflies (Lepidoptera: Papilionoidea)

Cryptic biological diversity has generated ambiguity in taxonomic and evolutionary studies. Single-locus methods and other approaches for species delimitation are useful for addressing this challenge, enabling the practical processing of large numbers of samples for identification and inventory purposes. This study analyzed an assemblage of high Andean butterflies using DNA barcoding and compared the identifications based on the current morphological taxonomy with three methods of species delimitation (automatic barcode gap discovery, generalized mixed Yule coalescent model, and Poisson tree processes). Sixteen potential cryptic species were recognized using these three methods, representing a net richness increase of 11.3% in the assemblage. A well-studied taxon of the genus Vanessa, which has a wide geographical distribution, appeared with the potential cryptic species that had a higher genetic differentiation at the local level than at the continental level. The analyses were useful for identifying the potential cryptic species in Pedaliodes and Forsterinaria complexes, which also show differentiation along altitudinal and latitudinal gradients. This genetic assessment of an entire assemblage of high Andean butterflies (Papilionoidea) provides baseline information for future research in a region characterized by high rates of endemism and population isolation.

The roles of wing color pattern and geography in the evolution of Neotropical Preponini butterflies

Diversification rates and evolutionary trajectories are known to be influenced by phenotypic traits and the geographic history of the landscapes that organisms inhabit. One of the most conspicuous traits in butterflies is their wing color pattern, which has been shown to be important in speciation. The evolution of many taxa in the Neotropics has also been influenced by major geological events. Using a dated, species-level molecular phylogenetic hypothesis for Preponini, a colorful Neotropical butterfly tribe, we evaluated whether diversification rates were constant or varied through time, and how they were influenced by color pattern evolution and biogeographical events. We found that Preponini originated approximately 28 million years ago and that diversification has increased through time consistent with major periods of Andean uplift. Even though some clades show evolutionarily rapid transitions in coloration, contrary to our expectations, these shifts were not correlated with shifts in diversification. Involvement in mimicry with other butterfly groups might explain the rapid changes in dorsal color patterns in this tribe, but such changes have not increased species diversification in this group. However, we found evidence for an influence of major Miocene and Pliocene geological events on the tribe's evolution. Preponini apparently originated within South America, and range evolution has since been dynamic, congruent with Andean geologic activity, closure of the Panama Isthmus, and Miocene climate variability.

New physaloid fruit-fossil species from early Eocene South America

PREMISE

Solanaceae is a scientifically and economically important angiosperm family with a minimal fossil record and an intriguing early evolutionary history. Here, we report a newly discovered fossil lantern fruit with a suite of features characteristic of Physalideae within Solanaceae. The fossil comes from the early Eocene Laguna del Hunco site (ca. 52 Ma) in Chubut, Argentina, which previously yielded the only other physaloid fruit fossil, Physalis infinemundi.

METHODS

The fruit morphology and calyx venation pattern of the new fossil were compared with P. infinemundi and extant species of Solanaceae.

RESULTS

Physalis hunickenii sp. nov. is clearly distinct from P. infinemundi in its fruiting calyx with wider primary veins, longer and thinner lobes, and especially in its venation pattern with high density, transverse tertiary veins; these features support its placement in a new species. In comparison with extant physaloid genera, the calyx venation pattern and other diagnostic traits reinforce placement of the new fossil, like P. infinemundi, within the tribe Physalideae of Solanaceae.

CONCLUSIONS

Both species of fossil nightshades from Laguna del Hunco represent crown-group Solanaceae but are older than all prior age estimates of the family. Although at least 20 transoceanic dispersals have been proposed as the driver of range expansion of Solanaceae, the Patagonian fossils push back the diversification of the family to Gondwanan times. Thus, overland dispersal across Gondwana is now a likely scenario for at least some biogeographic patterns, in light of the ancient trans-Antarctic land connections between South America and Australia.

An exploration of the complex biogeographical history of the Neotropical banner-wing damselflies (Odonata: Polythoridae)

BACKGROUND

The New World Tropics has experienced a dynamic landscape across evolutionary history and harbors a high diversity of flora and fauna. While there are some studies addressing diversification in Neotropical vertebrates and plants, there is still a lack of knowledge in arthropods. Here we examine temporal and spatial diversification patterns in the damselfly family Polythoridae, which comprises seven genera with a total of 58 species distributed across much of Central and South America.

RESULTS

Our time-calibrated phylogeny for 48 species suggests that this family radiated during the late Eocene (~ 33 Ma), diversifying during the Miocene. As with other neotropical groups, the Most Recent Common Ancestor (MRCA) of most of the Polythoridae genera has a primary origin in the Northern Andes though the MRCA of at least one genus may have appeared in the Amazon Basin. Our molecular clock suggests correlations with some major geographical events, and our biogeographical modeling (with BioGeoBEARS and RASP) found a significant influence of the formation of the Pebas and Acre systems on the early diversification of these damselflies, though evidence for the influence of the rise of the different Andean ranges was mixed. Diversification rates have been uniform in all genera except one-Polythore-where a significant increase in the late Pliocene (~ 3 mya) may have been influenced by recent Andean uplift.

CONCLUSION

The biogeographical models implemented here suggest that the Pebas and Acre Systems were significant geological events associated with the diversification of this damselfly family; while diversification in the tree shows some correlation with mountain building events, it is possible that other abiotic and biotic changes during our study period have influenced diversification as well. The high diversification rate observed in Polythore could be explained by the late uplift of the Northern Andes. However, it is possible that other intrinsic factors like sexual and natural selection acting on color patterns could be involved in the diversification of this genus.

Revisional Notes on the Cloud Forest Butterfly Genus Oxeoschistus Butler in Central America (Lepidoptera: Nymphalidae: Satyrinae)

So far, six species of Oxeoschistus Butler, including its junior synonym Dioriste Thieme, were listed from Central America, with five of them from Costa Rica alone, which appears to represent the highest regional diversity of this Neotropical montane butterfly genus. Our research based on field work, morphological studies and barcode analysis proved that one record is a misunderstanding perpetuated in scientific literature for over a century: Oxeoschistus cothonides Grose-Smith is identified here as an individual form of the female of O. cothon Salvin. The presence of Oxeoschistus tauropolis (Westwood) in Costa Rica, subject to some controversy, is confirmed, and a new local subspecies is described from Costa Rica, O. tauropolis mitsuko Pyrcz & Nakamura n. ssp. Specific status of O. euriphyle Butler is reinstated based on morphological and molecular data. A new subspecies O. hilara lempira Pyrcz n. ssp. is described from Honduras. O. puerta submaculatus Butler is reported for the first time from the Darién region on the Panama-Colombia border. Species relationships are preliminarily evaluated based on COI data concluding, among others, that O. hilara and O. euriphyle are less closely related than previously assumed. Altitudinal and distributional data are revised, and ecological and behavioural information of all the species of Central American Oxeoschistus is provided.

Genetic diversification of Panstrongylus geniculatus (Reduviidae: Triatominae) in northern South America

Triatomines are the vectors of Trypanosoma cruzi, the etiological agent of Chagas disease. Although Triatoma and Rhodnius are the most-studied vector genera, other triatomines, such as Panstrongylus, also transmit T. cruzi, creating new epidemiological scenarios. Panstrongylus has at least 13 reported species but there is limited information about its intraspecific genetic variation and patterns of diversification. Here, we begin to fill this gap by studying populations of P. geniculatus from Colombia and Venezuela and including other epidemiologically important species from the region. We examined the pattern of diversification of P. geniculatus in Colombia using mitochondrial and nuclear ribosomal data. Genetic diversity and differentiation were calculated within and among populations of P. geniculatus. Moreover, we constructed maximum likelihood and Bayesian inference phylogenies and haplotype networks using P. geniculatus and other species from the genus (P. megistus, P. lignarius, P. lutzi, P. tupynambai, P. chinai, P. rufotuberculatus and P. howardi). Using a coalescence framework, we also dated the P. geniculatus lineages. The total evidence tree showed that P. geniculatus is a monophyletic species, with four clades that are concordant with its geographic distribution and are partly explained by the Andes orogeny. However, other factors, including anthropogenic and eco-epidemiological effects must be investigated to explain the existence of recent geographic P. geniculatus lineages. The epidemiological dynamics in structured vector populations, such as those found here, warrant further investigation. Extending our knowledge of P. geniculatus is necessary for the accurate development of effective strategies for the control of Chagas disease vectors.

Flight over the Proto-Caribbean seaway: Phylogeny and macroevolution of Neotropical Anaeini leafwing butterflies

Our understanding of the origin and evolution of the astonishing Neotropical biodiversity remains somewhat limited. In particular, decoupling the respective impacts of biotic and abiotic factors on the macroevolution of clades is paramount to understand biodiversity assemblage in this region. We present the first comprehensive molecular phylogeny for the Neotropical Anaeini leafwing butterflies (Nymphalidae, Charaxinae) and, applying likelihood-based methods, we test the impact of major abiotic (Andean orogeny, Central American highland orogeny, Proto-Caribbean seaway closure, Quaternary glaciations) and biotic (host plant association) factors on their macroevolution. We infer a robust phylogenetic hypothesis for the tribe despite moderate support in some derived clades. Our phylogenetic inference recovers the genus Polygrapha Staudinger, [1887] as polyphyletic, rendering the genera FountaineaRydon, 1971 and Memphis Hübner, [1819] paraphyletic. Consequently, we transfer Polygrapha tyrianthina (Salvin & Godman, 1868) comb. nov. to Fountainea and Polygrapha xenocrates (Westwood, 1850) comb. nov. to Memphis. We infer an origin of the group in the late Eocene ca. 40 million years ago in Central American lowlands which at the time were separated from South America by the Proto-Caribbean seaway. The biogeographical history of the group is very dynamic, with several oversea colonization events from Central America into the Chocó and Andean regions during intense stages of Andean orogeny. These events coincide with the emergence of an archipelagic setting between Central America and northern South America in the mid-Miocene that likely facilitated dispersal across the now-vanished Proto-Caribbean seaway. The Amazonian region also played a central role in the diversification of the Anaeini, acting both as a museum and a cradle of diversity. We recover a diversification rate shift in the Miocene within the species-rich genus Memphis. State speciation and extinction models recover a significant relationship between this rate shift and host plant association, indicating a positive role on speciation rates of a switch between Malpighiales and new plant orders. We find less support for a role of abiotic factors including the progressive Andean orogeny, Proto-Caribbean seaway closure and Quaternary glaciations. Miocene host plant shifts possibly acted in concert with abiotic and/or biotic factors to shape the diversification of Anaeini butterflies.

DNA barcodes and evidence of cryptic diversity of anthropophagous mosquitoes in Quintana Roo, Mexico

Culicidae mosquitoes are potential vectors of pathogens that affect human health. The correct species identification, as well as the discovery and description of cryptic species, is important in public health for the control and management of specific vectors. In the present study, the diversity of anthropophagous mosquitoes in Quintana Roo, at the border between Mexico and Belize, was evaluated using morphological and molecular data (COI-DNA Barcoding). A total of 1,413 adult female specimens were collected, belonging to eight genera and 31 morphospecies. Most species formed well-supported clades. Intraspecific Kimura 2 parameters (K2P) distance average was 0.75%, and a maximum distance of 4.40% was observed for Anopheles crucianss.l. ABGD method identified 28 entities, while 32 entities were identified with the BIN system. In Culex interrogator and Culex nigripalpus a low interspecific genetic distance of 0.1% was observed. One undescribed species belonging to the genus Aedes (Aedesn. sp.) was discovered, but no clear genetic divergence was found between this species and the closely related species Aedes angustivittatus. An intraspecific K2P distance greater than 2.7% was observed in Aedes serratus(3.9%), Anopheles crucianss.l. (4.4%), Culex taeniopus (3.7%), Haemagogus equinus (3.9%), Culex erraticus (5.0%), Psorophora ferox (4.5%), and in Anopheles apicimacula(8.10%); therefore, evidences of cryptic diversity are shown in these species. This study showed that DNA barcodes offer a reliable framework for mosquito species identification in Quintana Roo, except for some closely related species for which it is recommended to use additional nuclear genetic markers such as ITS2, in order to resolve these small discrepancies.

Repeated evolution of a morphological novelty: a phylogenetic analysis of the inflated fruiting calyx in the Physalideae tribe (Solanaceae)

PREMISE OF THE STUDY

The evolution of novel fruit morphologies has been integral to the success of angiosperms. The inflated fruiting calyx, in which the balloon-like calyx swells to completely surround the fruit, has evolved repeatedly across angiosperms and is postulated to aid in protection and dispersal. We investigated the evolution of this trait in the tomatillos and their allies (Physalideae, Solanaceae).

METHODS

The Physalideae phylogeny was estimated using four regions (ITS, LEAFY, trnL-F, waxy) with maximum likelihood (ML) and Bayesian inference. Under the best-fitting ML model of trait evolution, we estimated ancestral states along with the numbers of gains and losses of fruiting calyx accrescence and inflation with Bayesian stochastic mapping. Also, phylogenetic signal in calyx morphology was examined with two metrics (parsimony score and Fritz and Purvis's D).

KEY RESULTS

Based on our well-resolved and densely sampled phylogeny, we infer that calyx evolution has proceeded in a stepwise and directional fashion, from non-accrescent to accrescent to inflated. In total, we inferred 24 gains of accrescence, 24 subsequent transitions to a fully inflated calyx, and only two reversals. Despite this lability, fruiting calyx accrescence and inflation showed strong phylogenetic signal.

CONCLUSIONS

Our phylogeny greatly improves the resolution of Physalideae and highlights the need for taxonomic work. The comparative analyses reveal that the inflated fruiting calyx has evolved many times and that the trajectory toward this phenotype is generally stepwise and irreversible. These results provide a strong foundation for studying the genetic and developmental mechanisms responsible for the repeated origins of this charismatic fruit trait.

Why are red flowers so rare? Testing the macroevolutionary causes of tippiness

Traits that have arisen multiple times yet still remain rare present a curious paradox. A number of these rare traits show a distinct tippy pattern, where they appear widely dispersed across a phylogeny, are associated with short branches and differ between recently diverged sister species. This phylogenetic pattern has classically been attributed to the trait being an evolutionary dead end, where the trait arises due to some short-term evolutionary advantage, but it ultimately leads species to extinction. While the higher extinction rate associated with a dead end trait could produce such a tippy pattern, a similar pattern could appear if lineages with the trait speciated slower than other lineages, or if the trait was lost more often that it was gained. In this study, we quantify the degree of tippiness of red flowers in the tomato family, Solanaceae, and investigate the macroevolutionary processes that could explain the sparse phylogenetic distribution of this trait. Using a suite of metrics, we confirm that red-flowered lineages are significantly overdispersed across the tree and form smaller clades than expected under a null model. Next, we fit 22 alternative models using HiSSE (Hidden State Speciation and Extinction), which accommodates asymmetries in speciation, extinction and transition rates that depend on observed and unobserved (hidden) character states. Results of the model fitting indicated significant variation in diversification rates across the family, which is best explained by the inclusion of hidden states. Our best fitting model differs between the maximum clade credibility tree and when incorporating phylogenetic uncertainty, suggesting that the extreme tippiness and rarity of red Solanaceae flowers makes it difficult to distinguish among different underlying processes. However, both of the best models strongly support a bias towards the loss of red flowers. The best fitting HiSSE model when incorporating phylogenetic uncertainty lends some support to the hypothesis that lineages with red flowers exhibit reduced diversification rates due to elevated extinction rates. Future studies employing simulations or targeting population-level processes may allow us to determine whether red flowers in Solanaceae or other angiosperms clades are rare and tippy due to a combination of processes, or asymmetrical transitions alone.

Gene flow and Andean uplift shape the diversification of Gasteracantha cancriformis (Araneae: Araneidae) in Northern South America

The Andean uplift has played a major role in shaping the current Neotropical biodiversity. However, in arthropods other than butterflies, little is known about how this geographic barrier has impacted species historical diversification. Here, we examined the phylogeography of the widespread color polymorphic spider Gasteracantha cancriformis to evaluate the effect of the northern Andean uplift on its divergence and assess whether its diversification occurred in the presence of gene flow. We inferred phylogenetic relationships and divergence times in G. cancriformis using mitochondrial and nuclear data from 105 individuals in northern South America. Genetic diversity, divergence, and population structure were quantified. We also compared multiple demographic scenarios for this species using a model-based approach (phrapl) to determine divergence with or without gene flow. At last, we evaluated the association between genetic variation and color polymorphism. Both nuclear and mitochondrial data supported two well-differentiated clades, which correspond to populations occurring on opposite sides of the Eastern cordillera of the Colombian Andes. The final uplift of this cordillera was identified as the most likely force that shaped the diversification of G. cancriformis in northern South America, resulting in a cis- and trans-Andean phylogeographic structure for the species. We also found shared genetic variation between the cis- and trans-Andean clades, which is better explained by a scenario of historical divergence in the face of gene flow. This has been likely facilitated by the presence of low-elevation passes across the Eastern Colombian cordillera. Our work constitutes the first example in which the Andean uplift coupled with gene flow influenced the evolutionary history of an arachnid lineage.

Contrasting patterns of Andean diversification among three diverse clades of Neotropical clearwing butterflies

The Neotropical region is the most biodiverse on Earth, in a large part due to the highly diverse tropical Andean biota. The Andes are a potentially important driver of diversification within the mountains and for neighboring regions. We compared the role of the Andes in diversification among three subtribes of Ithomiini butterflies endemic to the Neotropics, Dircennina, Oleriina, and Godyridina. The diversification patterns of Godyridina have been studied previously. Here, we generate the first time‐calibrated phylogeny for the largest ithomiine subtribe, Dircennina, and we reanalyze a published phylogeny of Oleriina to test different biogeographic scenarios involving the Andes within an identical framework. We found common diversification patterns across the three subtribes, as well as major differences. In Dircennina and Oleriina, our results reveal a congruent pattern of diversification related to the Andes with an Andean origin, which contrasts with the Amazonian origin and multiple Andean colonizations of Godyridina. In each of the three subtribes, a clade diversified in the Northern Andes at a faster rate. Diversification within Amazonia occurred in Oleriina and Godyridina, while virtually no speciation occurred in Dircennina in this region. Dircennina was therefore characterized by higher diversification rates within the Andes compared to non‐Andean regions, while in Oleriina and Godyridina, we found no difference between these regions. Our results and discussion highlight the importance of comparative approaches in biogeographic studies.

The evolution of floral sonication, a pollen foraging behavior used by bees (Anthophila)

Over 22,000 species of biotically pollinated flowering plants, including some major agricultural crops, depend primarily on bees capable of floral sonication for pollination services. The ability to sonicate ("buzz") flowers is widespread in bees but not ubiquitous. Despite the prevalence of this pollinator behavior and its importance to natural and agricultural systems, the evolutionary history of floral sonication in bees has not been previously studied. Here, we reconstruct the evolutionary history of floral sonication in bees by generating a time-calibrated phylogeny and reconstructing ancestral states for this pollen extraction behavior. We also test the hypothesis that the ability to sonicate flowers and thereby efficiently access pollen from a diverse assemblage of plant species, led to increased diversification among sonicating bee taxa. We find that floral sonication evolved on average 45 times within bees, possibly first during the Early Cretaceous (100-145 million years ago) in the common ancestor of bees. We find that sonicating lineages are significantly more species rich than nonsonicating sister lineages when comparing sister clades, but a probabilistic structured rate permutation on phylogenies approach failed to support the hypothesis that floral sonication is a key driver of bee diversification. This study provides the evolutionary framework needed to further study how floral sonication by bees may have facilitated the spread and common evolution of angiosperm species with poricidal floral morphology.

A novel R3 MYB transcriptional repressor associated with the loss of floral pigmentation in Iochroma

Losses of floral pigmentation represent one of the most common evolutionary transitions in flower color, yet the genetic basis for these changes has been elucidated in only a handful of cases. Here we used crossing studies, bulk-segregant RNA sequencing, phylogenetic analyses and functional tests to identify the gene(s) responsible for the transition to white flowers in Iochroma loxense. Crosses between I. loxense and its blue-flowered sister species, I. cyaneum, suggested that a single locus controls the flower color difference and that the white allele causes a nearly complete loss of pigmentation. Examining sequence variation across phenotypic pools from the crosses, we found that alleles at a novel R3 MYB transcription factor were tightly associated with flower color variation. This gene, which we term MYBL1, falls into a class of MYB transcriptional repressors and, accordingly, higher expression of this gene is associated with downregulation of multiple anthocyanin pigment pathway genes. We confirmed the repressive function of MYBL1 through stable transformation of Nicotiana. The mechanism underlying the evolution of white flowers in I. loxense differs from that uncovered in previous studies, pointing to multiple mechanisms for achieving fixed transitions in flower color intensity.

Diversification rates, host plant shifts and an updated molecular phylogeny of Andean Eois moths (Lepidoptera: Geometridae)

Eois is one of the best-investigated genera of tropical moths. Its close association with Piper plants has inspired numerous studies on life histories, phylogeny and evolutionary biology. This study provides an updated view on phylogeny, host plant use and temporal patterns of speciation in Eois. Using sequence data (2776 bp) from one mitochondrial (COI) and one nuclear gene (Ef1-alpha) for 221 Eois species, we confirm and reinforce previous findings regarding temporal patterns of diversification. Deep diversification within Andean Eois took place in the Miocene followed by a sustained high rate of diversification until the Pleistocene when a pronounced slowdown of speciation is evident. In South America, Eois diversification is very likely to be primarily driven by the Andean uplift which occurred concurrently with the entire evolutionary history of Eois. A massively expanded dataset enabled an in-depth look into the phylogenetic signal contained in host plant usage. This revealed several independent shifts from Piper to other host plant genera and families. Seven shifts to Peperomia, the sister genus of Piper were detected, indicating that the shift to Peperomia was an easy one compared to the singular shifts to the Chloranthaceae, Siparunaceae and the Piperacean genus Manekia. The potential for close co-evolution of Eois with Piper host plants is therefore bound to be limited to smaller subsets within Neotropical Eois instead of a frequently proposed genus-wide co-evolutionary scenario. In regards to Eois systematics we confirm the monophyly of Neotropical Eois in relation to their Old World counterparts. A tentative biogeographical hypothesis is presented suggesting that Eois originated in tropical Asia and subsequently colonized the Neotropics and Africa. Within Neotropical Eois we were able to identify the existence of six clades not recognized in previous studies and confirm and reinforce the monophyly of all 9 previously delimited infrageneric clades.

Phylogenetic relationships of Deprea: New insights into the evolutionary history of physaloid groups

Deprea is the genus with the second highest species richness in tribe Physalideae (Solanaceae) and comprises 50 species that are mainly distributed in the Andes of South America. The taxonomy of Deprea has been unstable after controversial hypotheses about its position and circumscription. Additionally, biogeographical inferences are only based on observations of the restricted area of distribution of some species and no ancestral area estimation have been performed. Here, we present a phylogenetic analysis and an ancestral area reconstruction of Deprea in order to establish its circumscription, resolve its position within Physalideae, and reconstruct its biogeographical history. Phylogenetic analyses were conducted using Maximum Likelihood and Bayesian approaches. Forty-three Deprea species and 26 related taxa were sampled for three DNA markers (psbA-trnH, ITS, and waxy). A Bayesian binary MCMC model was applied in order to infer ancestral areas. Deprea is resolved as a strongly supported monophyletic group according to its current circumscription and is placed within subtribe Withaninae of Physalideae. The phylogenetic relationships enabled us to solve taxonomic problems including the rejection and acceptance of previous synonyms. The most probable ancestral area for Deprea is the Northern Andes of South America and the Amotape-Huancabamba zone. Our phylogeny provides increased resolution and support for the current position and circumscription of Deprea. Better resolution of interspecific relationships was also obtained, although some affinities remain unclear. The phylogenetic and ancestral area reconstructions provide a framework for addressing taxonomic problems and investigating new evolutionary questions.