Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The past few years have seen the publication of numerous books and articles on the origins of agriculture, but this work by MacNeish surely ranks as the most idiosyncratic of the bunch. In The Origins of Agriculture and Settled Life, MacNeish carries on in the style of his The Science of Archaeology? These two books are largely autobiographical, the former documenting the evolution of his research, this one attempting to fit global agricultural origins into the developmental rubric he began to develop in Tehuacan. Both recount his lifelong personal quest to reconstruct the texture of the past from the shreds of prehistory, but his indomitable will and seemingly boundless energy and endless excavations have not sufficed to finally lay to rest the question of how and why agriculture started. As he says at the end, \"we have reached no final conclusions.\

The Origins of Agriculture and Settled Life

Transgressive segregation describes the occurrence of novel phenotypes in hybrids with extreme trait values not observed in either parental species A previously experimentally untested prediction is that the amount of transgression increases with the genetic distance between hybridizing species This follows from QTL studies suggesting that transgression is most commonly due to complementary gene action or epistasis, which become more frequent at larger genetic distances This is because the number of QTLs fixed for alleles with opposing signs in different species should increase with time since speciation provided that speciation is not driven by disruptive selection We measured the amount of transgression occurring in hybrids of cichlid fish bred from species pairs with gradually increasing genetic distances and varying phenotypic similarity Transgression in multi-trait shape phenotypes was quantified using landmark-based geometric morphometric methods We found that genetic distance explained 52% and 78% of the variation in transgression frequency in F1 and F2 hybrids, respectively Confirming theoretical predictions, transgression when measured in F2 hybrids, increased linearly with genetic distance between hybridizing species Phenotypic similarity of species on the other hand was not related to the amount of transgression The commonness and ease with which novel phenotypes are produced in cichlid hybrids between unrelated species has important implications for the interaction of hybridization with adaptation and speciation Hybridization may generate new genotypes with adaptive potential that did not reside as standing genetic variation in either parental population, potentially enhancing a population's responsiveness to selection Our results make it conceivable that hybridization contributed to the rapid rates of phenotypic evolution in the large and rapid adaptive radiations of haplochromine cichlids

https://www.dora.lib4ri.ch/eawag/islandora/object/eawag%3A8772/datastream/PDF/Stelkens-2009-Phenotypic_novelty_in_experimental_hybrids-%28published_version%29.pdf

Phenotypic novelty in experimental hybrids is predicted by the genetic distance between species of cichlid fish.

Adaptive radiation plays a fundamental role in our understanding of the evolutionary process. However, the concept has provoked strong and differing opinions concerning its definition and nature among researchers studying a wide diversity of systems. Here, we take a broad view of what constitutes an adaptive radiation, and seek to find commonalities among disparate examples, ranging from plants to invertebrate and vertebrate animals, and remote islands to lakes and continents, to better understand processes shared across adaptive radiations. We surveyed many groups to evaluate factors considered important in a large variety of species radiations. In each of these studies, ecological opportunity of some form is identified as a prerequisite for adaptive radiation. However, evolvability, which can be enhanced by hybridization between distantly related species, may play a role in seeding entire radiations. Within radiations, the processes that lead to speciation depend largely on (1) whether the primary drivers of ecological shifts are (a) external to the membership of the radiation itself (mostly divergent or disruptive ecological selection) or (b) due to competition within the radiation membership (interactions among members) subsequent to reproductive isolation in similar environments, and (2) the extent and timing of admixture. These differences translate into different patterns of species accumulation and subsequent patterns of diversity across an adaptive radiation. Adaptive radiations occur in an extraordinary diversity of different ways, and continue to provide rich data for a better understanding of the diversification of life.

/pdf/comparing-adaptive-radiations-across-space-time-and-taxa-30gqnbujkv.pdf

Comparing Adaptive Radiations Across Space, Time, and Taxa

Intraspecific variation in stomatal traits, leaf traits and physiology reflects adaptation along aridity gradients in a South African shrub

Microsatellite markers (N = 5) were developed for analysis of genetic variation in 15 populations of the columnar cactus Stenocereus stellatus, managed under traditional agriculture practices in central Mexico. Microsatellite diversity was analyzed within and among populations, between geographic regions, and among population management types to provide detailed insight into historical gene flow rates and population dynamics associated with domestication. Our results corroborate a greater diversity in populations managed by farmers compared with wild ones (HE = 0.64 vs. 0.55), but with regional variation between populations among regions. Although farmers propagated S. stellatus vegetatively in home gardens to diversify their stock, asexual recruitment also occurred naturally in populations where more marginal conditions have limited sexual recruitment, resulting in lower genetic diversity. Therefore, a clear-cut relationship between the occurrence of asexual recruitment and genetic diversity was not evident. Two managed populations adjacent to towns were identified as major sources of gene movement in each sampled region, with significant migration to distant as well as nearby populations. Coupled with the absence of significant bottlenecks, this suggests a mechanism for promoting genetic diversity in managed populations through long distance gene exchange. Cultivation of S. stellatus in close proximity to wild populations has led to complex patterns of genetic variation across the landscape that reflects the interaction of natural and cultural processes. As molecular markers become available for nontraditional crops and novel analysis techniques allow us to detect and evaluate patterns of genetic diversity, genetic studies provide valuable insights into managing crop genetic resources into the future against a backdrop of global change. Traditional agriculture systems play an important role in maintaining genetic diversity for plant species.

Managing diversity: Domestication and gene flow in Stenocereus stellatus Riccob. (Cactaceae) in Mexico

Calathea, with an estimated 285 species, is the largest genus of Marantaceae and an important component of Neotropical herbaceous diversity. The genus is also of high importance for horticulture as species are cultivated for their showy, patterned leaves. Previous molecular phylogenetic studies indicated that the genus is polyphyletic, but have not provided a basis for redefining generic limits due to incomplete taxon sampling. To address this problem we analyzed DNA sequence data from three plastid markers (matK with flanking 30 trnK intron, trnL intron and trnL-trnF intergenic spacer) and one nuclear marker (ITS) under a maximum parsimony criterion for a large and representative taxon sample covering all previously proposed infrageneric entities, and representing the full range of morphological variation known in the genus. Our results confirm that Calathea is polyphyletic. One clade, including subgenus Calathea ,t heC. lanicaulis group, and the genus Sanblasia, is sister to a clade formed by Ischnosiphon and Pleiostachya .T he genusMonotagma is placed as sister to this clade. The remaining species form a second strongly supported clade as sister to a clade containing these other genera. Based on these findings Calathea is recircumscribed in a narrow sense and Sanblasia is placed in synonymy. The genus Goeppertia is resurrected and redefined to include all members of the second Calathea clade. Morphological characters defining each genus are provided. A total of 246 new combinations are made. Keywords—Goeppertia, ITS, matK, maximum parsimony, Sanblasia, trnL-F region. Marantaceae, with approximately 550 species, is the sec- ond largest family in the Zingiberales. The family is particu- larly diverse in the Neotropics where it is represented by an estimated 450 species. Phylogenetic studies at the family level (Andersson and Chase 2001; Prince and Kress 2006a) have shown Neotropical diversity to primarily involve two large groups: the Maranta clade with nine genera and ca. 70 species is concentrated in southeastern Brazil; and the Calathea clade with five genera and ca. 370 species is distrib- uted throughout the Neotropics but with highest diversity in northwestern South America. Within the Calathea clade, Calathea G. Mey. is by far the largest genus with an esti- mated 300 species (Andersson 1998). Govaerts and Kennedy (2012) list 285 accepted names. These numbers clearly make Calathea the largest genus in the family. The genus is also important for horticulture as indoor plants and in tropical garden landscaping due to their variegated leaves with spots or bands of white, orange, or red, and often bright purple underside. Several species have been used as model organisms for studies of reproductive ecology, plant phys- iology, and demography (e.g. Kennedy 1978; Horvitz and Schemske 2002; Clasen-Bockhoff and Heller 2008; Matlaga and Sternberg, 2009; Swenson 2009; Maron et al. 2010). Other

https://bioone.org/journals/systematic-botany/volume-37/issue-3/036364412X648571/Molecular-Phylogeny-and-Redefined-Generic-Limits-of-Calathea-Marantaceae/10.1600/036364412X648571.pdf

Molecular Phylogeny and Redefined Generic Limits of Calathea (Marantaceae)

Adaptive diversification can be viewed as a balance between the conservative force of interpopulation gene flow and selection for differential environments. In this paper, we examine ecological, morphological, and genetic differentiation in a small clade consisting of four East Maui-endemic species of Dubautia: D. menziesii, D. platyphylla, D. reticulata, and D. waianapanapaensis, in the Hawaiian silversword alliance (Asteraceae). The East Maui clade is apparently recently derived (less than 1 million years ago) and is geographically restricted yet displays significant ecological and morphological differences. We used geographic data from historical herbarium specimens, measure- ments of plant architecture and leaf morphometrics, and measures of genetic differentiation in both microsatellite and nuclear coding loci to examine the correlation of different forms of divergence in this small species flock. We found overlap in large-scale geographic distributions, significant differentiation in most habitat factors, significant micro- satellite differentiation, and many shared alleles at nuclear coding loci suggesting on-going lineage sorting. Despite the presence of apparent hybrids in some populations, microsatellite variation is consistent with isolation among species. Using Mantel tests, we compared the direction and extent of diversification among different datasets, to determine whether ecological/morphological divergence was correlated with genetic divergence. Correlations among different datasets showed that habitat was strongly correlated with plant architecture but not leaf morphology. Taken together, these results indicate that ecological and morphological diversification has driven genetic divergence at rapidly evolving microsatellite loci, whereas there is continuing lineage sorting at neutral sites in nuclear coding loci.

https://bioone.org/journals/Evolution/volume-60/issue-9/05-345.1/ECOLOGICAL-SPECIATION-IN-THE-EAST-MAUIENDEMIC-DUBAUTIA-ASTERACEAE-SPECIES/10.1554/05-345.1.pdf

Ecological speciation in the east maui–endemic dubautia (asteraceae) species

Incongruence among different estimates of species relationships in plants, from different molecules, cytogenetic data, biogeographic data, morphological/anatomical data or other sources, has been used frequently as an indication of introgression, hybrid species origin, or chloroplast (cp) capture. In plants, these incongruences are most often seen between data derived from the nuclear vs. the cp genomes and the nuclear markers used for comparison usually have been from the nuclear ribosomal (nr) internal transcribed spacer region (ITS). The amount of genomic material shared between introgressing species can be highly variable. In some of these cases, other nuclear genomic regions have moved between species without leaving a signature on the nrITS. An example of well-supported phylogenetic incongruence is the placement of Dubautia scabra (DC.) D. D. Keck in the Hawaiian silversword alliance (HSA); evolutionary hypotheses for D. scabra based on molecular as opposed to cytogenetic data are strongly ...

Linda M. Prince

Papers

Managing diversity: Domestication and gene flow in Stenocereus stellatus Riccob. (Cactaceae) in Mexico

Molecular Phylogeny and Redefined Generic Limits of Calathea (Marantaceae)

Ecological speciation in the east maui–endemic dubautia (asteraceae) species

Hybrid Origin and Genomic Mosaicism of Dubautia scabra (Hawaiian Silversword Alliance; Asteraceae, Madiinae)