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FIGURE 8 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 8. Cetacean stem and Neoceti taxa diversity through time. "Archaeoceti" includes all stem taxa that are not included in the two extant groups. Dashed vertical lines: black, epoch boundaries; gray, age boundaries.

FIGURE 16 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 16. Ancestral state reconstruction of prey capture strategies and tooth pattern and cusp shape in Odobenidae. Topology follows Berta et al. (2018). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch lengths can be found in the Supplementary Information uploaded to Dryad repository (https:// doi.org/10.6086/d14671).

FIGURE 17 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 17. Ancestral state reconstruction of prey type preference in stem and crown Pinnipedimorpha. Topology follows Rybczynski et al. (2009), Dewaele et al. (2017), and Berta et al. (2018). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch can be found in the Supplementary Information (https:// doi.org/10.6086/d14671).

FIGURE 19 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 19. Ancestral state reconstruction of prey capture strategies and tooth pattern and cusp shape in stem Odontoceti. Topology follows Gatesy et al. (2013) and Boessenecker et al. (2017). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch lengths can be found in the Supplementary Information (https://doi.org/10.6086/d14671).

FIGURE 20 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 20. Ancestral state reconstruction of prey capture strategies and tooth pattern and cusp shape in crown Odontoceti. Topology follows McGowen et al. (2009) and Gatesy et al. (2013). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch lengths can be found in the Supplementary Information (https://doi.org/10.6086/d14671).

FIGURE 1 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 1. Feeding strategies of extant marine mammal predators (from Kienle et al., 2017) with the addition of grazing (sirenians, authors' work).

opencc-by-4.0Feb 2018View details →

Supporting data for Guzzo et al. 2018, Methods in Ecology and Evolution, DOI: 10.1111/2041-210X.12993

Supporting data for Guzzo et al. MEE, Field testing a novel high residence positioning system for monitoring the fine‐scale movements of aquatic organisms (DOI: 10.1111/2041-210X.12993)

opencc-by-4.0Apr 2018View details →

Complete numerical solutions for "Inference of ecological and social drivers of human brain-size evolution" by Mauricio González-Forero and Andy Gardner

This zip file contains the complete numerical solutions across the parameter sweep over the P parameters for the six cases considered. /1RatioForm/ -> solutions for power competence. /2DiffForm/ -> solutions for exponential competence. /1RatioForm/1BenchmarkFromSimpleInitialGuess -> solution for the step 1 of initialization (section 5 of the SI). /1RatioForm/2Benchmark/ -> solution for the step 2 of the initialization (section 5 of the SI). /1RatioForm/3AdditiveCoop/ -> solutions across the P parameter combinations for additive cooperation. /1RatioForm/4MultCoop/ -> solutions across the P parameter combinations for multiplicative cooperation. /1RatioForm/5SubMultCoop/ -> solutions across the P parameter combinations for submultiplicative cooperation. The contents of /2DiffForm/ are analogous. The P vector is written in these files in the order (etas,etac,etaC,etag), where etas -> P1 etac -> P3 etaC -> P2 etag -> P4 The files 1runNotesACMC.pdf and 2runNotesSC.pdf contain the tree structure of the parameter sweep, specifying which parameter combination was used as the resident and which combinations converged to an uninvadable strategy (those with a checkmark). The file 3runNotesMaternalCareOptimization.pdf contains the 10 parameter combinations that yielded the best adult fit, which then were subject to variation in the parameter phi to find the combination that yielded the best ontogenetic fit. The file 4runNotesDuplicates.pdf gives the parameter combinations that were not run because they are equivalent to other parameter combinations. Running [T,N1,run,Tshort,N1short,runShort]=etaCombinations in Matlab and typing run.seed{i}.parallel{:} gives the "next" parameter combinations from parameter combination i (where i is a number 1,2,...) for PC-AC, EC-MC, PC-SC, and EC-SC. The meaning of "next" is explained in step 4 of the parameter sweep (section 5 of the SI). Typing runShort.seed{i}.parallel{:} gives the "next" parameter combinations from parameter combination i for PC-MC and EC-AC. The terminal folders contain the solutions and have the following files: brainNashDeep.m -> the master file launching the iteration of best responses. brainMainDeep.m -> the file launching one iteration solving the optimal control problem to find best response. brainMainTestRunDeep.m -> runs a test to check if there are infeasibility warnings. brainContinuous.m -> specifies the dynamic constraints. brainEndpoint.m -> specifies the terminal constraints. parameters.m -> specifies the parameter values and rescales them to rescale units as specified in section 5 of the SI. getSolution.m -> extracts solution. plots.m -> plots solutions over best response iterations. brainPlot.m -> plots solution of a given best response iteration. guessDeep.mat -> initial guess and resident used. solutionNashDeep.mat -> solutions over best response iterations. solutionDeep.mat -> solution of last best response iteration.

Fig. 5. Parsimony splits network constructed from a per and ITS2 concatenated sequence data set. Heterozygous specimens are indicated with A and B in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism

Fig. 5. Parsimony splits network constructed from a per and ITS2 concatenated sequence data set. Heterozygous specimens are indicated with A and B. 'bufonivora_EUROPE_A' represents a consistent haplotype present in all 12 samples from Europe (Table 1), of which just two were heterozygous ('bufonivora_frog' and 'bufonivora_NLWi'). 'bufonivora_CAN' and 'elongata_CAN' are represented by two samples each, none of which were heterozygous. Scale bar represents expected changes per site.

Fig. 2. Bayesian Inference tree constructed from Internal transcribed Spacer 2 in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism

Fig. 2. Bayesian Inference tree constructed from Internal transcribed Spacer 2 (non-coding) sequence data. Each specimen is labelled with the species name and location abbreviation as indicated in Table 1. Green text corresponds to European samples of Lucilia bufonivora; red represents Lucilia elongata; purple represents Canadian L. bufonivora; orange represents Lucilia silvarum. Scale bar represents expected changes per site. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6. Divergence times estimated from a in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism

Fig. 6. Divergence times estimated from a concatenated data set of per, COX1 and ITS2 sequences for the Lucilia bufornivora species group. Substitution model and relaxed clock models were unlinked for each gene. The tree was calibrated by setting the root to the node age corresponding to the split between Luciilinae and Calliphorinae subfamilies (~19 mya) as estimated by Wallman et al. (2005). Blue bars represent 95% highest posterior density (HPD) of each node age. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism

Fig. 1. Location of samples for which the COX1 gene was sequenced in this study. Boxes represent the locations of individual samples: red, Lucilia elongata; orange, Lucilia silvarum; green, Lucilia bufonivora.

opencc-by-4.0Dec 2010View details →

Figure 2 in Fly parasitism in Papuan frogs, with a discussion of ecological factors influencing evolution of life-history differences

Figure 2. Regressions of weight versus snout–vent length (SV) for male Rana supragrisea. Larger frogs infested with fly larvae (closed squares, dashed line) exhibit lower weights compared to uninfested frogs (open circles, solid line), but this difference in regressions is determined solely by the largest infested specimen.

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The opportunity for selection: an important but slippery concept in ecology and evolution.

1. The concept of the opportunity for selection (I), measured as the variance in relative fitness, is over 60 years old, yet remains poorly understood by, or even unknown to, many ecologists and evolutionary biologists. This essay aims to clarify key conceptual and practical issues concerning use and estimation of I, which represents a theoretical upper limit on the rate of evolutionary adaptation. 2. The component of I caused by linear selection on a single trait is equal to the square of its standardised selection differential i. Even if no phenotypic selection occurs (i=0), however, realised I will typically be nonzero, owing to environmental or stochastic variation in fitness. 3. The opportunity for viability selection depends only on the mean survival rate, but selective mortality will typically account for only a small fraction of total mortality. 4. Fecundity selection is accompanied by expected overdispersion in reproductive success (variance > mean), but overdispersion can also occur for reasons unrelated to phenotype, or by chance. The estimated opportunity for fecundity selection can also vary independently of i if estimated mean reproductive success is affected by study design, e.g. offspring are counted at different life stages or a variable fraction are missed. 5. For these reasons, I alone should not be used to make inferences about selection in progress and its drivers. Nevertheless, some empirical studies have documented weak to moderate correlations between I and phenotypic selection, so variation in I or related metrics across ecological contexts might provide clues that unmeasured traits are under variable selection. 20-Oct-2022 --

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Appendices B to E for the Thesis: Investigating the Evolution and Ecology of Obscure Bacterial Symbioses found in Invertebrates, Ciliates and Algae

Appendix B1 contains all metadata for genomes assembled and genomes used, including accession numbers, CheckM scores and Gtdbtk taxonomy. You will also find supporting data for Chapter 2. Yellow tabs contain: <ul> <li>accessions and species information for all whole genomes used</li> <li>brief details on hosts and environment for new genomes described in this study</li> <li>metadata such as N50s and genome lengths for all new genomes</li> <li>completeness scores and assembly levels for all genomes</li> <li>information on where all the published genomes were used in this study</li> <li>taxonomy calculations from GTDBtk</li> </ul> Red tabs contain: <ul> <li>Phi scores from reticulate analysis for all core genome clusters extracted from the pangenome aswell as their associated COG and KEGG functions</li> <li>Functional enrichment tables exploring the association of different metabolic functions with different groups of bacteria</li> </ul> ---------------------------------------------------------------------------------------------------- Appendix C1 contains all metadata for genomes assembled and genomes used, including accession numbers and CheckM scores. You will also find raw data used to produce the figures in Chapter 3. Yellow tabs contain:                                                                                                  S1 - Meta data tables for draft genomes examined in this study                              S2 - Accessions for additional genomes used Red tabs contain:                                                                                                       S3 - AAI % similarity across Ca. Megaira used in figure 3a S4 - ANIb % Similarity across Ca. Megaira used in figure 3b S5 - KEGG ko hits                                                                                             S6 - KEGG module completeness used in figure 5 and 6        S7 - 16S rRNA accessions used in phylogeny Figure 2 S8 - Gene cluster presence absence matrix used in figure 3.4 and Appendix figure 1          S9 - GTDBtk results for SRA and GenBank Environmental MAGs                              S10 - top 10 blastp results for RiPP, NRPS and CDPS regions identified by antiSMASH ---------------------------------------------------------------------------------------------------- Appendix D1 contains all metadata for genomes assembled and genomes used, including accession numbers, CheckM scores and Gtdbtk taxonomy. You will also find raw data used to produce the figures in Chapter 4. Yellow tabs contain: S1 - Metadata for genomes assembled in this study S2 - Metadata for environmental MAGs recovered from NCBI non redundant sequence database S3 - Metadata for additional Chlamydiota genomes used Red tabs contain: S4 - AAI percentage similarity scores used to produce genera similarity networks S5 - ANIb percentage similarity scores used to produce species similarity networks S6 - CRISPRcas finder results S7 - KEGG pathway hits S8 - KEGG pathway completeness S9 - Gene cluster presence absence matrix used in figure 4.3a for Rhabdochlamydiaceae S10 - Gene cluster presence absence matrix used in figure 4.3b for Simkaniaceae ---------------------------------------------------------------------------------------------------- Appendix E1 contains screening results, environmental data extracted from climate databases and additional genome information. Yellow tabs contain: S1 - 'Ca. Tisiphia' in Anopheles plumbeus across Germany. PCR screening and geographic data S2 - additional genome accessions and metadata Red tabs contain: S3 - KEGG completeness S4 - KEGG ko_hits presence

Fig. 3 in Phylogeny of Maculinea blues (Lepidoptera: Lycaenidae) based on morphological and ecological characters: evolution of parasitic myrmecophily

Fig. 3. One of the four equally most parsimonious trees (length 306, CI 0.33, RI 0.63; chosen at random: individual source trees differ only in position of terminals within Phengaris, M. teleius and M. alcon group: see Fig. 2), with character states that support individual clades. Nonhomoplastic autapomorphies are black, homoplastic apomorphies white. Numbers above branches refer to characters, numbers below branches to character states (see Appendix 1 for character descriptions).

Fig. 4 in Phylogeny of Maculinea blues (Lepidoptera: Lycaenidae) based on morphological and ecological characters: evolution of parasitic myrmecophily

Fig. 4. Evolution of the life history traits of Maculinea butterflies and their relatives. Only the species for which states of all relevant characters are reliably well-known are included (see Table 1), but the overall topology of the tree including all terminals (Figs 2 & 3) is preserved. (A) Myrmecophily. M. nausithous is optimized as a modified predatory species (see ''Evolution of life histories''). (B) Host plants and habitat associations. Rosids and asterids are two well-supported clades of eudicot angiosperm plants (see Angiosperm Phylogeny Group, 2003): Fabaceae and Rosaceae are included in the former, Lamiaceae, Gentianaceae, and Campanulaceae in the latter. In some cases, character-state optimization is derived from the all-species tree (Fig. 3).

Fig. 1 in Phylogeny of Maculinea blues (Lepidoptera: Lycaenidae) based on morphological and ecological characters: evolution of parasitic myrmecophily

Fig. 1. System of coding of wing pattern traits used in the phylogenetic study of Maculinea and their relatives.

Fig. 2 in Phylogeny of Maculinea blues (Lepidoptera: Lycaenidae) based on morphological and ecological characters: evolution of parasitic myrmecophily

Fig. 2. Strict consensus of the four equally most parsimonious trees (length 306, CI 0.33, RI 0.63) showing proposed phylogenetic relationships within the ''Glaucopsyche-section'' of Lycaenidae: Polyommatini. Bootstrap and Bremer support are shown above and below the nodes, respectively.