So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

I. the origin of species by means of natural selection

It is clear that the majority of fl owering plants are pollinated by insects and other animals, with a minority utilising abiotic pollen vectors, mainly wind. However there is no accurate published calculation of the proportion of the ca 352 000 species of angiosperms that interact with pollinators. Widely cited fi gures range from 67% to 96% but these have not been based on fi rm data. We estimated the number and proportion of fl owering plants that are pollinated by animals using published and unpublished community-level surveys of plant pollination systems that recorded whether each species present was pollinated by animals or wind. Th e proportion of animal-pollinated species rises from a mean of 78% in temperate-zone communities to 94% in tropical communities. By correcting for the latitudinal diversity trend in fl owering plants, we estimate the global number and proportion of animal pollinated angiosperms as 308 006, which is 87.5% of the estimated species-level diversity of fl owering plants. Given current concerns about the decline in pollinators and the possible resulting impacts on both natural communities and agricultural crops, such estimates are vital to both ecologists and policy makers. Further research is required to assess in detail the absolute dependency of these plants on their pollinators, and how this varies with latitude and community type, but there is no doubt that plant – pollinator interactions play a signifi cant role in maintaining the functional integrity of most terrestrial ecosystems. Plant – pollinator relationships may be one of the most ecologically important classes of animal – plant interaction: without pollinators, many plants could not set seed and reproduce; and without plants to provide pollen, nectar and other rewards, many animal populations would decline, with consequent knock-on eff ects for other species (Kearns et al.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1600-0706.2010.18644.x

How many flowering plants are pollinated by animals

MUCKE aims to mine a large volume of images, to structure them conceptually and to use this conceptual structuring in order to improve large-scale image retrieval. The last decade witnessed important progress concerning low-level image representations. However, there are a number problems which need to be solved in order to unleash the full potential of image mining in applications. The central problem with low-level representations is the mismatch between them and the human interpretation of image content. This problem can be instantiated, for instance, by the incapability of existing descriptors to capture spatial relationships between the concepts represented or by their incapability to convey an explanation of why two images are similar in a content-based image retrieval framework. We start by assessing existing local descriptors for image classification and by proposing to use co-occurrence matrices to better capture spatial relationships in images. The main focus in MUCKE is on cleaning large scale Web image corpora and on proposing image representations which are closer to the human interpretation of images. Consequently, we introduce methods which tackle these two problems and compare results to state of the art methods. Note: some aspects of this deliverable are withheld at this time as they are pending review. Please contact the authors for a preview.

http://ieeexplore.ieee.org/iel2/4524/12820/00592460.pdf

Image Processing

Plants and their arbuscular mycorrhizal fungal symbionts interact in complex underground networks involving multiple partners. This increases the potential for exploitation and defection by individuals, raising the question of how partners maintain a fair, two-way transfer of resources. We manipulated cooperation in plants and fungal partners to show that plants can detect, discriminate, and reward the best fungal partners with more carbohydrates. In turn, their fungal partners enforce cooperation by increasing nutrient transfer only to those roots providing more carbohydrates. On the basis of these observations we conclude that, unlike many other mutualisms, the symbiont cannot be "enslaved." Rather, the mutualism is evolutionarily stable because control is bidirectional, and partners offering the best rate of exchange are rewarded.

https://science.sciencemag.org/content/sci/333/6044/880.full.pdf

Reciprocal Rewards Stabilize Cooperation in the Mycorrhizal Symbiosis

Highly coevolved pollination mutualism accompanied by reciprocal diversification has been known in only two plant genera, Ficus (Moraceae) and Yucca (Agavaceae), which are pollinated exclusively by obligate seed-parasitic wasps and moths, respectively. An additional, highly diversified, species-specific pollination mutualism between a monoecious tree genus, Glochidion (Euphorbiaceae), and a moth genus, Epicephala (Gracillariidae), is presented here. At night, the small female moth actively deposits pollen on the cryptic stigma of the female flower by using its proboscis, then oviposits into the style. The moth larva infests only a portion of the developing seeds within fruit. We confirmed that at least three Glochidion species are pollinated only by their respective seed-parasitic moth species, which could be distinguished by genitalic morphology and mitochondrial DNA sequences. These results and widespread evidence of limited seed infestation by the moths associated with Glochidion species suggest that speciation based on the highly specialized Glochidion stylar structure and moth oviposition behavior have promoted species diversification in Glochidion and its pollinators.

https://www.pnas.org/content/pnas/100/9/5264.full.pdf

An obligate pollination mutualism and reciprocal diversification in the tree genus Glochidion (Euphorbiaceae)

Highly coevolved pollination mutualism accompanied by reciprocal diversification has been known in only two plant genera, Ficus (Moraceae) and Yucca (Agavaceae), which are pollinated exclusively by obligate seed-parasitic wasps and moths, respectively. An additional, highly diversified, species-specific pollination mutualism between a monoecious tree genus, Glochidion (Euphorbiaceae), and a moth genus, Epicephala (Gracillariidae), is presented here. At night, the small female moth actively deposits pollen on the cryptic stigma of the female flower by using its proboscis, then oviposits into the style. The moth larva infests only a portion of the developing seeds within fruit. We confirmed that at least three Glochidion species are pollinated only by their respective seedparasitic moth species, which could be distinguished by genitalic morphology and mitochondrial DNA sequences. These results and widespread evidence of limited seed infestation by the moths associated with Glochidion species suggest that speciation based on the highly specialized Glochidion stylar structure and moth oviposition behavior have promoted species diversification in Glochidion and its pollinators.

An obligate pollination mutualism and reciprocal diversification in the tree genus Glochidion

Interspecific hybridization is one of the major factors leading to phylogenetic incongruence among loci, but the knowledge is still limited about the potential of each locus to introgress between species. By directly sequencing three DNA regions: chloroplast DNAs (matK gene and trnL-F noncoding region), the nuclear ribosomal external transcribed spacer (ETS) region, and internal transcribed spacer (ITS) regions, we construct three phylogenetic trees of Asian species of Mitella (Saxifragaceae), a genus of perennials in which natural hybrids are commonly observed. Within this genus, there is a significant topological conflict between chloroplast and nuclear phylogenies and also between the ETS and the ITS, which can be attributed to frequent hybridization within the lineage. Chloroplast DNAs show the most extensive introgression pattern, ITS regions show a moderate pattern, and the ETS region shows no evidence of introgression. Nonuniform concerted evolution best explains the difference in the introgression patterns between the ETS region and ITS regions, as the sequence heterogeneity of the ITS region within an individual genome is estimated to be twice that of an ETS in this lineage. Significant gene conversion patterns between two hybridizing taxa were observed in contiguous arrays of cloned ETS-ITS sequences, further confirming that only ITS regions have introgressed bidirectionally. The relatively slow concerted evolution in the ITS regions probably allows the coexistence of multiple alleles within a genome, whereas the strong concerted evolution in the ETS region rapidly eliminates heterogeneous alleles derived from other species, resulting in species delimitations highly concordant with those based on morphology. This finding indicates that the use of multiple molecular tools has the potential to reveal detailed organismal evolution processes involving interspecific hybridization, as an individual locus varies greatly in its potential to introgress between species.

/pdf/nonuniform-concerted-evolution-and-chloroplast-capture-1adixmzufv.pdf

Nonuniform Concerted Evolution and Chloroplast Capture: Heterogeneity of Observed Introgression Patterns in Three Molecular Data Partition Phylogenies of Asian Mitella (Saxifragaceae)

To test whether gaps resulting from sequence alignment contain phylogenetic signal concordant with those of base substitutions, we analyzed the occurrence of indel mutations upon a well-resolved, substitution-based tree for three nuclear genes in bumble bees (Bombus, Apidae: Bombini). The regions analyzed were exon and intron sequences of long-wavelength rhodopsin (LW Rh), arginine kinase (ArgK), and elongation factor-1alpha (EF-1alpha) F2 copy genes. LW Rh intron had only a few uninformative gaps, ArgK intron had relatively long gaps that were easily aligned, and EF-1alpha intron had many short gaps, resulting in multiple optimal alignments. The unambiguously aligned gaps within ArgK intron sequences showed no homoplasy upon the substitution-based tree, and phylogenetic signals within ambiguously aligned regions of EF-1alpha intron were highly congruent with those of base substitutions. We further analyzed the contribution of gap characters to phylogenetic reconstruction by incorporating them in parsimony analysis. Inclusion of gap characters consistently improved support for nodes recovered by substitutions, and inclusion of ambiguously aligned regions of EF-1alpha intron resolved several additional nodes, most of which were apical on the phylogeny. We conclude that gaps are an exceptionally reliable source of phylogenetic information that can be used to corroborate and refine phylogenies hypothesized by base substitutions, at least at lower taxonomic levels. At present, full use of gaps in phylogenetic reconstruction is best achieved in parsimony analysis, pending development of well-justified and generally applicable methods for incorporating indels in explicitly model-based methods.

/pdf/evolution-and-phylogenetic-utility-of-alignment-gaps-within-1jrh9dlsd6.pdf

Evolution and Phylogenetic Utility of Alignment Gaps Within Intron Sequences of Three Nuclear Genes in Bumble Bees (Bombus)

The well-known figfig wasp and yuccayucca moth mutualisms are classic examples of obligate mutualisms that have been shaped by millions of years of coevolution. Pollination systems involving obliga...

Atsushi Kawakita

Papers

An obligate pollination mutualism and reciprocal diversification in the tree genus Glochidion (Euphorbiaceae)

An obligate pollination mutualism and reciprocal diversification in the tree genus Glochidion

Nonuniform Concerted Evolution and Chloroplast Capture: Heterogeneity of Observed Introgression Patterns in Three Molecular Data Partition Phylogenies of Asian Mitella (Saxifragaceae)

Evolution and Phylogenetic Utility of Alignment Gaps Within Intron Sequences of Three Nuclear Genes in Bumble Bees (Bombus)

Repeated independent evolution of obligate pollination mutualism in the Phyllantheae-Epicephala association.