More Like this

1. Polyploidy in creosote bush ( Larrea tridentata ) shapes the biogeography of specialist herbivores

   https://doi.org/10.1111/jbi.13490  

   O'Connor, Timothy K. ; Laport, Robert G. ; Whiteman, Noah K. ( January 2019 , Journal of Biogeography)

   Whole‐genome duplication (polyploidy) can influence the biogeography and ecology of plants that differ in ploidy level (cytotype). Here, we address how two consequences of plant polyploidy (parapatry of cytotypes and altered species interactions) shape the biogeography of herbivorous insects.

   Warm deserts of North America.

   Gall midges (Asphondylia auripilagroup, Diptera: Cecidomyiidae) that attack three parapatric cytotypes of creosote bush (Larrea tridentata, Zygophyllaceae).

   We surveyedAsphondyliaspecies diversity at 177 sites across a 2300‐km extent. After noting a correspondence between the distributions of eightAsphondyliaspecies andL. tridentatacytotypes, we fine‐mappedAsphondyliaspecies range limits with transects spanning cytotype contact zones. We then tested whether plant–insect interactions and/or abiotic factors explain this coincidence by (a) comparing attack rates and gall midge communities on alternative cytotypes in a narrow zone of sympatry and (b) using species distribution models (SDMs) to determine if climatically suitable habitat for each midge species extended beyond cytotype contact zones.

   The range limits of 6/17Asphondyliaspecies (including two novel putative species confirmed withCOIsequencing) perfectly coincided with the contact zone of diploid and tetraploidL. tridentata. One midge species was restricted to diploid host plants while five were restricted to tetraploid and hexaploid host plants. Where diploid and tetraploidL. tridentataare sympatric, cytotype‐restricted midge species more frequently attacked their typical host andAsphondyliacommunity structure differed markedly between cytotypes.SDMs predicted that distributions of cytotype‐restricted midge species were not constrained by climatic conditions near cytotype contact zones.

   Contact zones between plant cytotypes are dispersal barriers for manyAsphondyliaspecies due to plant–insect interactions. The distribution ofL. tridentatacytotypes therefore shapes herbivore species ranges and herbivore community structure across North American deserts. Our results demonstrate that polyploidy in plants can affect the biogeography of ecological communities.

    

   more » « less
2. A basic dd RAD seq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera

   https://doi.org/10.1002/aps3.11344  

   Jordon‐Thaden, Ingrid E. ; Beck, James B. ; Rushworth, Catherine A. ; Windham, Michael D. ; Diaz, Nicolas ; Cantley, Jason T. ; Martine, Christopher T. ; Rothfels, Carl J. ( April 2020 , Applications in Plant Sciences)

   The ability to sequence genome‐scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double‐digest restriction site–associatedDNAsequencing (ddRADseq) protocol usingDNAs from four genera extracted from both silica‐dried and herbarium tissue.

   DNAs fromDraba,Boechera,Solidago, andIlexwere processed with a ddRADseq protocol. The effects ofDNAdegradation, taxon, and specimen age were assessed.

   Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were obtained from the majority of samples.

   These results suggest that herbarium samples can be incorporated into ddRADseq project designs, and that specimen age can be used as a rapid on‐site guide for sample choice. The detailed protocol we provide will allow users to pursue herbarium‐based ddRADseq projects that minimize the expenses associated with fieldwork and sample evaluation.

    

   more » « less
3. Population genomics and geographical parthenogenesis in Japanese harvestmen (Opiliones, Sclerosomatidae, Leiobunum )

   https://doi.org/10.1002/ece3.3605  

   Burns, Mercedes ; Hedin, Marshal ; Tsurusaki, Nobuo ( November 2017 , Ecology and Evolution)

   Naturally occurring population variation in reproductive mode presents an opportunity for researchers to test hypotheses regarding the evolution of sex. Asexual reproduction frequently assumes a geographical pattern, in which parthenogenesis‐dominated populations are more broadly dispersed than their sexual conspecifics. We evaluate the geographical distribution of genomic signatures associated with parthenogenesis using nuclear and mitochondrialDNAsequence data from two Japanese harvestman sister taxa,Leiobunum manubriatumandLeiobunum globosum. Asexual reproduction is putatively facultative in these species, and female‐biased localities are common in habitat margins. Past karyotypic and current cytometric work indicatesL. globosumis entirely tetraploid, whileL. manubriatummay be either diploid or tetraploid. We estimated species phylogeny, genetic differentiation, diversity, and mitonuclear discordance in females collected across the species range in order to identify range expansion toward marginal habitat, potential for hybrid origin, and persistence of asexual lineages. Our results point to northward expansion of a tetraploid ancestor ofL. manubriatumandL. globosum, coupled with support for greater male gene flow in southernL. manubriatumlocalities. Specimens from localities in the Tohoku and Hokkaido regions were indistinct, particularly those ofL. globosum, potentially due to little mitochondrial differentiation or haplotypic variation. AlthoughL. manubriatumoverlaps withL. globosumacross its entire range,L. globosumwas reconstructed as monophyletic with strong support using mtDNA, and marginal support with nuclear loci. Ultimately, we find evidence for continued sexual reproduction in both species and describe opportunities to clarify the rate and mechanism of parthenogenesis.

    

   more » « less
4. A new null model approach to quantify performance and significance for ecological niche models of species distributions

   https://doi.org/10.1111/jbi.13573  

   Bohl, Corentin L. ; Kass, Jamie M. ; Anderson, Robert P. ( May 2019 , Journal of Biogeography)

   Ecological niche modelling requires robust estimation of model performance and significance, but common evaluation approaches often yield biased estimates. Null models provide a solution but are rarely used in this field. We implemented an important modification to existing null model tests, evaluating null models with the same withheld records that were used to evaluate the real model. We built and evaluated models across a range of modelling scenarios and for various performance measures using the algorithmMaxentand the monk parakeet (Myiopsitta monachus).

   Native range in Southern America and global invasions predominantly in North/Central America and Europe.

   We tested the ability of models built under 15 scenarios (five sets of calibration records and three settings that varied the level of model complexity) to predict spatially independent evaluation data in the invaded range (in effect, testing the models under spatial transfer). We quantified performance with measures of discriminatory ability and overfitting based on area under the receiver operating characteristic curve (AUC) and the omission error rate. We estimated null distributions of these measures and calculated effect size and significance. We determined how these estimates varied across modelling scenarios, comparing with two tests existing in the literature.

   Performance varied starkly across modelling scenarios. As expected, the measures of overfitting agreed with each other and provided different information than that of discriminatory ability. However, high performance per se did not show strong association with high effect size and significance.

   Ecological niche models should be assessed with measures of effect size and significance based on appropriate null distributions, in contrast to several approaches existing in the literature. The proposed approach using independent evaluation data, implemented with our accompanying code and R package, allows such estimates for either the same or a different region/time period, and it merits use and continued development.

    

   more » « less
5. Identification and characterization of a natural polymorphism in FT-A2 associated with increased number of grains per spike in wheat

   https://doi.org/10.1007/s00122-021-03992-y  

   Glenn, Priscilla ; Zhang, Junli ; Brown-Guedira, Gina ; DeWitt, Noah ; Cook, Jason P. ; Li, Kun ; Akhunov, Eduard ; Dubcovsky, Jorge ( November 2021 , Theoretical and Applied Genetics)

   We discovered a naturalFT-A2allele that increases grain number per spike in both pasta and bread wheat with limited effect on heading time.

   Increases in wheat grain yield are necessary to meet future global food demands. A previous study showed that loss-of-function mutations inFLOWERING LOCUS T2(FT2) increase spikelet number per spike (SNS), an important grain yield component. However, these mutations were also associated with reduced fertility, offsetting the beneficial effect of the increases in SNS on grain number. Here, we report a natural mutation resulting in an aspartic acid to alanine change at position 10 (D10A) associated with significant increases in SNS and no negative effects on fertility. Using a high-density genetic map, we delimited the SNS candidate region to a 5.2-Mb region on chromosome 3AS including 28 genes. Among them, onlyFT-A2showed a non-synonymous polymorphism (D10A) present in two different populations segregating for the SNS QTL on chromosome arm 3AS. These results, together with the known effect of theft-A2mutations on SNS, suggest that variation inFT-A2is the most likely cause of the observed differences in SNS. We validated the positive effects of the A10 allele on SNS, grain number, and grain yield per spike in near-isogenic tetraploid wheat lines and in an hexaploid winter wheat population. The A10 allele is present at very low frequency in durum wheat and at much higher frequency in hexaploid wheat, particularly in winter and fall-planted spring varieties. These results suggest that theFT-A2A10 allele may be particularly useful for improving grain yield in durum wheat and fall-planted common wheat varieties.

    

   more » « less