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opencc-zeroSep 2020View details →

The origins of coca: museum genomics reveals multiple independent domestications from progenitor Erythroxylum gracilipes

Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within E. novogranatense (D.Morris) Hieron.) but our understanding of their wild progenitor(s) and origins remains rudimentary. In this study we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species E. gracilipes; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant.

opencc-zeroDec 2021View details →

Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species

The repeated transition from outcrossing to selfing is a key topic in evolutionary biology. However, the molecular basis of such shifts has been rarely examined due to lack of knowledge of the genes controlling these transitions. A classic example of mating system transition is the repeated shift from heterostyly to homostyly. Occurring in 28 angiosperm families, heterostyly is characterized by the reciprocal position of male and female sexual organs in two (or three) distinct, usually self-incompatible floral morphs. Conversely, homostyly is characterized by a single, self-compatible floral morph with reduced separation of male and female organs, facilitating selfing. Here, we investigate the origins of homostyly in Primula vulgaris and its microevolutionary consequences by integrating surveys of the frequency of homostyles in natural populations, DNA sequence analyses of the gene controlling the position of female sexual organs (CYPᵀ), and microsatellite genotyping of both progeny arrays and natural populations characterized by varying frequencies of homostyles. As expected, we found that homostyles displace short-styled individuals, but long-style morphs are maintained at low frequencies within populations. We also demonstrated that homostyles repeatedly evolved from short-styled individuals in association with different types of loss-of-function mutations in CYPᵀ. Additionally, homostyly triggers a shift to selfing, promoting increased inbreeding within and genetic differentiation among populations. Our results elucidate the causes and consequences of repeated transitions to homostyly within species, and the putative mechanisms precluding its fixation in P. vulgaris. This study represents a benchmark for future analyses of losses of heterostyly in other angiosperms.

publicOct 2020View details →

The origins of coca: museum genomics reveals multiple independent domestications from progenitor Erythroxylum gracilipes

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publicDec 2021View details →

Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species

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opencc-zeroDec 2011View details →

Data from: Genetic analysis of the peatmoss Sphagnum cribrosum (Sphagnaceae) indicates independent origins of an extreme infra-specific morphology shift

Within Sphagnum cribrosum, a dioicous aquatic peatmoss, a unique morphological variant (the "waveform"), found at only two lakes in North Carolina, has a branching architecture that is extremely differentiated from anything otherwise known in Sphagnum, though the plants are microscopically indistinguishable from S. cribrosum. At one site where the two morphologies co-occur, sixty years of field observations demonstrate the persistence of each morphology, even where the two forms grow intermixed. We conducted a reciprocal transplant experiment in which waveform and normal plants maintained their divergent morphologies for eight months. We sampled populations throughout the range and conducted genetic and phylogenetic analyses with microsatellite markers and DNA sequences to investigate the genetic context of the waveform morphology within S. cribrosum. Haplotype networks from DNA sequences showed the two waveform populations are separated by 11 substitutions across three loci. Microsatellite analyses using non-parametric clustering and admixture models also indicated genetic dissimilarity between genotypes with waveform morphology at the two lakes. Both molecular datasets suggest that the waveform morphology had at least two independent origins despite proximity of the two lakes where it uniquely occurs. Given the clonal nature of the waveform, it is unlikely to form a cohesive evolutionary lineage deserving of taxonomic status. The analysis also revealed a genetically diverse population in Georgia as the potential source of variation found in all other populations of S. cribrosum.

opencc-zeroDec 2015View details →

Data from: Genetic structure reveals a history of multiple independent origins followed by admixture in the allopolyploid weed Salsola ryanii

It has recently become clear that many invasive species have evolved in situ via hybridization or polyploidy from progenitors which themselves are introduced species. For species formed by hybridization or polyploidy, genetic diversity within the newly formed species is influenced by the number of independent evolutionary origins of the species. For recently formed species, an analysis of genetic structure can provide insight into the number of independent origin events involved in the formation of the species. For a putative invasive allopolyploid species, the number of origins involved in the species formation, the genetic diversity present within these origins, and the level of gene flow between independent origins determines the genetic composition of the neospecies. Here we analyze the genetic structure of the newly formed allopolyploid species, Salsola ryanii, a tumbleweed which evolved within the last 20–100 years in California. We utilize the genetic structure analysis to determine that this new species is the result of at least three independent allopolyplodization events followed by gene flow between the descendants of independent origins.

opencc-zeroOct 2019View details →

Data from: Unraveling independent origins of two tetraploid Achillea species by amplicon sequencing

Allopolyploidy is a significant mechanism of plant speciation, and many allopolyploid species have arisen recurrently. However, the probability that allopolyploidization between the same two parental species may lead to the origin of different taxa has received little attention. Here we used a new progenitor-specific amplicon sequencing method to demonstrate the independent origins of two yarrow species, Achillea alpina and A. wilsoniana, via allotetraploidy from the same diploid progenitor species pair, A. acuminata and A. asiatica. Based on the sequences of 17 nuclear genes from 21 wild populations of the four Achillea species investigated, a clear view of genetic structure and demographic history was obtained with each species. Significant genetic differentiation was evident between the two tetraploid species. Two genetically distinguishable groups were detected within one of the progenitor, A. acuminata, and ancestors belonging to those two groups contributed to the two tetraploid species, respectively. Excluding fixed heterozygosity, we detected extremely low genetic diversity in many populations of both tetraploid species. Approximate Bayesian computation indicated that both tetraploid species originated before the Last Glacial Maximum, and nearly all diploid lineages went through population declines after the allopolyploidization events. Our study demonstrates that independent allopolyploidization events between the same Achillea parental species have generated two genetically and ecologically distinct taxa.

opencc-zeroDec 2016View details →

Data from: Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards

Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics. Here we ask whether convergent evolution of pad-bearing lizards have followed similar evolutionary dynamics, or whether independent origins are accompanied by unique constraints and selective pressures over macroevolutionary time. We hypothesized that geckos and anoles each have unique evolutionary tempos and modes. Using performance data from 59 species, we modified Brownian Motion (BM) and Ornstein-Uhlenbeck (OU) models to account for repeated origins estimated using Bayesian ancestral state reconstructions. We discovered that adhesive performance in geckos evolved in a fashion consistent with Brownian Motion with a trend, whereas anoles evolved in bounded performance space consistent with more constrained evolution (an Ornstein-Uhlenbeck model). Our results suggest that convergent phenotypes can have quite distinctive evolutionary patterns, likely as a result of idiosyncratic constraints or ecological opportunities.

opennotspecifiedDec 2014View details →

Fig. 3 in Phylogenetic evidence for multiple independent origins of functional kleptoplasty in Sacoglossa (Heterobranchia, Gastropoda)

Fig. 3 Phylogeny of the Sacoglossa based on Bayesian analysis (50 % majority rule consensus tree). Numbers at nodes indicate Posterior Probability (PP), black circles indicate PP=100, and black asterisks indicate PP=95–99. The inner dark gray circle borders functional-retention information of taxa, the outer food sources (displayed are only three major food sources per species). The scale bar displays substitutions per site. Yellow highlighted is the "outgroup", pink the Oxynoacea, purple the Platyhedylidae, green the " Limapontioidea ", and blue the

opennotspecifiedDec 2014View details →

Fig. 2 in Phylogenetic evidence for multiple independent origins of functional kleptoplasty in Sacoglossa (Heterobranchia, Gastropoda)

Fig. 2 Maximum quantum yield measurements (Fv/Fm) of Elysia clarki. Specimens of E. clarki were either starved under 40 μmol quanta m−2 s−1 (diamonds) or in complete darkness (rectangles) over a period of 49 days. Error bars indicate standard deviation between different specimens for each measuring point. Because specimens were fixed at certain intervals, finally only one individual was left at day 49

opencc-zeroDec 2020View details →

Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae

The volvocine algae, which include the single-celled species Chlamydomonas reinhardtii and the colonial species Volvox carteri, serve as a model in which to study the evolution of multicellularity and cellular differentiation. Studies reconstructing the history of this group have by and large relied on datasets of one to a few genes for phylogenetic inference and ancestral character state reconstruction. As a result, volvocine phylogenies lack concordance depending on the number and/or type of genes (i.e., chloroplast vs nuclear) chosen for phylogenetic inference. While multiple studies suggest that multicellularity evolved only once in the volvocine algae, that each of its three colonial families is monophyletic, and that there have been at least three independent origins of cellular differentiation in the group, other studies call into question one or more of these conclusions. An accurate assessment of the evolutionary history of the volvocine algae requires inference of a more robust phylogeny. We performed RNA sequencing (RNA-seq) on 55 strains representing 47 volvocine algal species and obtained similar data from curated databases on 13 additional strains. We then compiled a dataset consisting of transcripts for 40 single-copy, protein-coding, nuclear genes, and subjected the predicted amino acid sequences of these genes to maximum likelihood, Bayesian inference, and coalescent-based analyses. These analyses show that multicellularity independently evolved at least twice in the volvocine algae and that the colonial family Goniaceae is not monophyletic. Our data further indicate that cellular differentiation arose independently at least four, and possibly as many as six times, within the volvocine algae. Altogether, our results demonstrate that multicellularity and cellular differentiation are evolutionarily labile in the volvocine algae, affirming the importance of this group as a model system for the study of major transitions in the history of life.

FIGURES 46–51. Notophlebia jobi. 46–49 in New Oriental tribe Iscini, new non-dilatognathan species of Notophlebia Peters & Edmunds 1970 and independent origin of Dilatognathus-type mouth apparatus in Atalophlebiinae (Ephemeroptera: Leptophlebiidae)

FIGURES 46–51. Notophlebia jobi. 46–49, third segment of maxillary palp (46 and 48, ventral side; 47 and 49, dorsal side); 50–51, base of third segment of labial palp, dorsal side).

FIGURES 31–45. 31–38 in New Oriental tribe Iscini, new non-dilatognathan species of Notophlebia Peters & Edmunds 1970 and independent origin of Dilatognathus-type mouth apparatus in Atalophlebiinae (Ephemeroptera: Leptophlebiidae)

FIGURES 31–45. 31–38, Notophlebia ganeshi sp. n.; 39–45, Notophlebia jobi. 31–34 and 40–43, tergalii of I, II, V and VI pairs (ventral lamella turned back); 35, claw; 36 and 44, pronotum and mesonotum of last instar larva; 37 and 45, posterior margin of abdominal sternum IX of mature male larva and protopenis, dorsal view (gonoducts lined by cuticle shown by interrupted lines); 38 and 39, posterior margin of larval abdominal tergum VI (37, 38, holotype).

FIGURES 52–54. Notophlebia jobi. 52 in New Oriental tribe Iscini, new non-dilatognathan species of Notophlebia Peters & Edmunds 1970 and independent origin of Dilatognathus-type mouth apparatus in Atalophlebiinae (Ephemeroptera: Leptophlebiidae)

FIGURES 52–54. Notophlebia jobi. 52, distal part of larval fore tibia, posterior side; 53, the same, anterior side; 54, distal part of larval middle tibia, anterior side. Abbreviations: a, row of stout setae on anterior side; h, hair-like setae on outer side; p, row of stout setae on posterior side.

FIGURES 11–20 in New Oriental tribe Iscini, new non-dilatognathan species of Notophlebia Peters & Edmunds 1970 and independent origin of Dilatognathus-type mouth apparatus in Atalophlebiinae (Ephemeroptera: Leptophlebiidae)

FIGURES 11–20. Notophlebia ganeshi sp. n. 11, male imaginal mesonotum; 12, male subimaginal exuviae of right half of mesonotum. 13–19, legs at the same magnification (arrows show ontogenesis): 13, fore leg of male imago; 14, fore leg of male larva (long hair-like setae not shown); 15–17, fore, middle and hind legs of male subimago; 18, hind leg of male imago; 19, fore leg of female imago. 20, tarsus of larval hind leg before molt to subimago (larval cuticle shown as optic section by black; subimaginal cuticle shown by integral lines; imaginal claw developing under subimaginal cuticle shown by interrupted lines). 21, posterior margin of abdominal sternum IX of mature female larva; 22, the same, of female imago (12–18, holotype). Abbreviations: LPs, lateroparapsidal suture; MNS, mesonotal suture; MPs, medioparapsidal suture.

FIGURES 4–10 in New Oriental tribe Iscini, new non-dilatognathan species of Notophlebia Peters & Edmunds 1970 and independent origin of Dilatognathus-type mouth apparatus in Atalophlebiinae (Ephemeroptera: Leptophlebiidae)

FIGURES 4–10. Notophlebia ganeshi sp. n. Larval mouthparts (at the same magnification, except 6). 4, hypopharynx and superlinguae; 5, labrum (setae of distal transverse row not shown, their bases shown as dots and levels of their apices shown by dotted line); 6, apex of maxilla, ventral view; 7, maxilla, ventral view (apical and median setae not shown, their apices shown by dotted lines); 8, labium (dorsal view at left, ventral view at right); 9, apex of labial palp, dorsal view; 10, left mandible (5, 10, holotype).