Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

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

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

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Modern Applied Statistics With S

I. the origin of species by means of natural selection

 Premise of the study : The use of continuous morphological characters in taxonomy is traditionally contingent on the existence of discrete diagnostic characters. When plant species are the result of recent divergence and gene fl ow and/or hybridization occur, the use of continuous morphological characters may help in species identifi cation and delimitation. Between nine and 15 species have been recognized in the last treatments of Hedera . The recent divergence of the species and the involvement of allopolyploidization as the main force in this process may have greatly impeded the establishment of clear limits and contributed to multiple taxonomic proposals.  Methods : A multivariate statistical decision-making procedure was applied to 56 quantitative morphological characters and 602 specimens to identify and delimit Hedera species under the general lineage concept. Species ’ exclusive genetic ancestry was evaluated with the genealogical sorting index from the Bayesian inference trees of 30 Hedera ITS sequences.  Key results : The decision-making procedure allowed recognizing 12 species and two groups (stellate and scale-like trichome groups) in Hedera and provided statistical support for making decisions about long-standing taxonomic controversies. Common ancestry was detected for the populations of three species even in the absence of the species monophyly.  Conclusions : Quantitative variation supports discrete variation and provides statistical support for the taxa recognized in some recent proposals of Hedera . The need of explicit analysis of quantitative data are claimed to reduce taxonomic subjectivity and ease decision-making when qualitative data fail.

https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.3732/ajb.1000115

Quantitative morphology and species delimitation under the general lineage concept: Optimization for Hedera (Araliaceae)

Phylogenetic reconstructions in the Mediterranean genus Erodium are for the first time performed using two matrices: one with 96 trnL-trnF sequences from Erodium (90 accessions plus four outgroups) and the other with 72 trnL-trnF sequences plus 23 morphological characters (66 species of a total of 74), using Maximum Parsimony (MP) and Bayesian Inference (BI). An association between reproductive properties (high selfing rates, flower asymmetry, insect-attraction structures), life form, and breeding system distributed in different lineages suggests multiple shifts from allogamy to autogamy in the course of evolution, whereas dioecy has occurred only once. The phylogenetic analyses revealed a remarkable capability for dispersal in Erodium because closely related species occur in different continents. Major lineages containing sublineages of species also from several continents lead us to interpret ancient dispersal activity. Establishment of Mediterranean-like climates in most continents may have been crucial in the evolution of Erodium, as manifested by occurrence of species of the Mediterranean floristic region in the four major lineages. The body of knowledge accumulated from molecular phylogenetics and morphology lead us to conclude that the Mediterranean region harbors the major center of diversity of Erodium, where active radiation in dry, disturbed environments, is still operating.

Phylogenetic Relationships and Evolution in Erodium (Geraniaceae) based on trnL-trnF Sequences

Fundamentals of microoptics

The subgenus Xiphium is one of the six infrageneric divisions of the genus Iris. Chromosome numbers of six of the seven Xiphium species are known. Here the aim was to infer genetic and phylogenetic relationships based on chromosome numbers, chromosome markers and plastid sequences. Chromosomal locations of 5S and 45S rDNA loci were determined in 19 populations of the 7 species by fluorescence in situ hybridization (FISH). Additionally, the trnL–trnF plastid spacer was sequenced and a phylogenetic analysis performed. Based on chromosome markers, subgenus Xiphium species were classified into four groups that differed in the number and locations of both types of nrDNA: (1) I. tingitana (2n = 28), I. filifolia (2n = 30, 34) and I. xiphium (2n = 34), (2) I. juncea (2n = 32) and I. boissieri (2n = 36), (3) I. serotina (2n = 34) and (4) I. latifolia (2n = 42). Although the trnL–trnF phylogeny was not fully resolved, the sequence analysis showed a well-supported subgroup of I. filifolia, I. tingitana and I. xiphium, as well as I. juncea. FISH physical maps of the Iris subgenus Xiphium taxa are species dependent. I. filifolia, I. tingitana and I. xiphium are very closely related species and share cytogenetic characteristics. Disploidy appears to have been central in the evolution of this subgenus, given a series of chromosome numbers (2n = 28, 30, 32, 34, 36, 42) and our phylogenetic results. Clear differences were found among European and African populations of I. filifolia. A different taxonomic treatment of I. filifolia is supported for populations on both sides of the Strait of Gibraltar.

Evolution of Iris subgenus Xiphium based on chromosome numbers, FISH of nrDNA (5S, 45S) and trnL-trnF sequence analysis

A review of 27 angiosperm clades (26 genera) of species-rich and species-poor plant groups of the Mediterranean floristic region was performed with phylogenetic and biological trait data. The emergent pattern is that a majority of Mediterranean plant clades split from their sister groups between the Miocene (23-5 Ma) and the Oligocene (34-23 Ma), far earlier than the onset of the Mediterranean climate (ca. 3.2 Ma). In addition, 12 of 14 clades of the species-poor group have stem ages inferred for each clade in the Miocene or older, and six of 13 clades within the species-rich group show divergence of each stem clade within the Oligocene and/or Miocene. High levels of species diversity are related to an ancient (Paleocene-Miocene) origin and also to recent origin (Pliocene-Pleistocene) followed by active speciation and even explosive radiations: some species and lineages diversified over a short period (Aquilegia, Cistus, Dianthus, Linaria sect. Supinae, Reseda). In the species-rich group, key reproductive characters were found to be significantly more important for species recognition than key vegetative characters in eight clades, but no difference was found in four clades, and vegetative characters were predominant in one clade (Saxifraga). Geographical differentiation is proposed as predominant over divergence driven by pollination ecology. We hypothesise an evolutionary process in which lineages adapted to pre-Mediterranean (pre-Pliocene) conditions in relatively small, xeric areas became strongly competitive and expanded as the Mediterranean climate became dominant (Pliocene-Quaternary) across the Mediterranean Basin.

/pdf/phylogenetic-evidence-for-a-miocene-origin-of-mediterranean-4a5nt741xm.pdf

Pablo Vargas

Papers

Quantitative morphology and species delimitation under the general lineage concept: Optimization for Hedera (Araliaceae)

Phylogenetic Relationships and Evolution in Erodium (Geraniaceae) based on trnL-trnF Sequences

Fundamentals of microoptics

Evolution of Iris subgenus Xiphium based on chromosome numbers, FISH of nrDNA (5S, 45S) and trnL-trnF sequence analysis

Phylogenetic evidence for a Miocene origin of Mediterranean lineages: species diversity, reproductive traits and geographical isolation.